diff --git a/gramene/conf/MartDefs.pm b/gramene/conf/MartDefs.pm deleted file mode 100755 index af7afa34..00000000 --- a/gramene/conf/MartDefs.pm +++ /dev/null @@ -1,523 +0,0 @@ - -#!/usr/local/bin/perl -w -#====================================================================== -# -# Name: MartDefs.pm -# -# Description: module to create/store/retrieve martview config data -# using the EnsemblMart::MartInfo module -# -#====================================================================== - -package MartDefs; -use strict; -use Storable qw( freeze thaw ); - -use Data::Dumper; - -use EnsemblMart::MartInfo; -use EnsemblMart::LocationAdaptor; -use SiteDefs; -use SpeciesDefs; - -use vars qw( @ISA @EXPORT ); -use Exporter; -@ISA = qw(Exporter); -@EXPORT = qw( is_filter_available - all_species - all_foci - species_by_focus - foci_by_species - assembly_info - strains_available - traits_available - encode_available); - -#---------------------------------------------------------------------- -# Some class variables -my $CONFFILE = "${SiteDefs::ENSEMBL_SERVERROOT}/conf/martconf.packed"; -my $CONF = undef(); - -#---------------------------------------------------------------------- -# Prepare the config - -=head2 new - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub new{ - - # If config is stored, just deserialise - if( -e $CONFFILE ){ - open FH, $CONFFILE || die ("Can't open $CONFFILE: $!" ); - local $/ = undef; - $CONF = thaw(); - - warn( ( '-' x 78 ) ."\n" ); - warn("[MARTCONF][INFO] Retrieving conf from $CONFFILE\n" ); - warn( ( '-' x 78 ) ."\n" ); - #warn Dumper( $CONF ); - return 1; - } - - # No config found; create new - - # Get database handle - my $dbh = SpeciesDefs::db_connect_multi_species( 'ENSEMBL_MART' ) || - warn( "[MARTCONF][WARN] Could not connect to mart database \n" ) && return 0; - - # Get MartInfo instance, and use to get all species+foci - my $mart_info = EnsemblMart::MartInfo->new( $dbh ); - my $mart_location = EnsemblMart::LocationAdaptor->new( $dbh ); - my @species = @{$mart_info->species_available()}; - my @foci = @{$mart_info->foci_available() }; - - $CONF->{all_species} = \@species; - $CONF->{all_foci} = \@foci; - $CONF->{all_filters} = []; - $CONF->{all_attributes} = []; - $CONF->{foci_by_species} = {}; - $CONF->{species_by_focus} = {}; - $CONF->{chromosomes_by_species} = {}; - $CONF->{bands_by_species} = {}; - $CONF->{filters} = {}; - $CONF->{attributes} = {}; - $CONF->{strains} = {}; - $CONF->{traits} = {}; - $CONF->{trait_regions_by_species} = {}; - $CONF->{encode} = {}; - $CONF->{encode_regions_by_species} = {}; - - # Loop for each species - foreach my $sp( @species ){ - - # Update mart_info with the species - $mart_info->species($sp); - $mart_location->species($sp); - - my $assembly = $mart_info->retrieve_assembly($sp); - $CONF->{assembly} ->{$sp} = $assembly; - - #my @strains = $mart_info->strains_available($sp); - $CONF->{strains} ->{$sp} = $mart_info->strains_available($sp); - - $CONF->{traits} ->{$sp} = $mart_info->traits_available($sp); - $CONF->{encode} ->{$sp} = $mart_info->encode_available($sp); - - # Loop for each focus - foreach my $fo( @{$mart_info->foci_available} ){ - - # Get a list of all available filters for the species+focus - my $filters = $mart_info->filters_available($fo); - my $attribs = $mart_info->attributes_available($fo); - - # Add each filter to the master config - if( @$filters or @$attribs ){ - $CONF->{foci_by_species} ->{$sp} ||= {}; - $CONF->{species_by_focus}->{$fo} ||= {}; - $CONF->{foci_by_species} ->{$sp}->{$fo} = 1; - $CONF->{species_by_focus}->{$fo}->{$sp} = 1; - } - - # Save typing! - my $fconf = $CONF->{filters}; - foreach( @$filters ){ - $fconf->{$_} ||= {}; - $fconf->{$_}->{$sp} ||= {}; - $fconf->{$_}->{$sp}->{$fo} = 1; - } - my $aconf = $CONF->{attributes}; - foreach( @$attribs ){ - $aconf->{$_} ||= {}; - $aconf->{$_}->{$sp} ||= {}; - $aconf->{$_}->{$sp}->{$fo} = 1; - } - } - - # Update chromosomes by species - $CONF->{chromosomes_by_species}->{$sp} = $mart_info->chrs_available; - $CONF->{bands_by_species}->{$sp} = {$mart_location->gen_chr_band_hash}; - $CONF->{trait_regions_by_species}->{$sp} = {$mart_location->gen_trait_regions_hash}; - $CONF->{encode_regions_by_species}->{$sp} = {$mart_location->gen_encode_regions_hash}; - } - # Get a sorted list of all filters - $CONF->{all_filters} = [ sort keys %{$CONF->{filters}} ]; - $CONF->{all_attributes} = [ sort keys %{$CONF->{attributes}} ]; - - warn("[MARTCONF][INFO] Writing Configuration to $CONFFILE"); - warn( ( '-' x 78 ) ."\n" ); - - # Save away the conf - open( FH, "> $CONFFILE" ) || die ("Can't open $CONFFILE for writing: $!" ); - print FH ( freeze($CONF) ); -} - -#---------------------------------------------------------------------- - -=head2 all_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub all_species { - if( ! $CONF ){ new() }; - return @{$CONF->{all_species}}; -} -#---------------------------------------------------------------------- - -=head2 assembly_info - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub assembly_info { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{assembly}->{$species} || return (); - return $CONF->{assembly}->{$species}; -} -#---------------------------------------------------------------------- - -=head2 strains_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub strains_available { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{strains}->{$species} || return []; - return @{$CONF->{strains}->{$species}}; -} -#---------------------------------------------------------------------- - -=head2 traits_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub traits_available { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{traits}->{$species} || return []; - return @{$CONF->{traits}->{$species}}; -} -#---------------------------------------------------------------------- - -=head2 encode_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub encode_available { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{encode}->{$species} || return []; - return @{$CONF->{encode}->{$species}}; -} -#--------------------------------------------------------------------- -=head2 all_foci - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub all_foci { - if( ! $CONF ){ new() }; - return @{$CONF->{all_foci}}; -} - -#---------------------------------------------------------------------- - -=head2 all_filters - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub all_filters { - if( ! $CONF ){ new() }; - return @{$CONF->{all_filters}}; -} - -#---------------------------------------------------------------------- - -=head2 all_attributes - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub all_attributes { - if( ! $CONF ){ new() }; - return @{$CONF->{all_attributes}}; -} - -#---------------------------------------------------------------------- - -=head2 all_names - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub all_names { - if( ! $CONF ){ new() }; - return( @{$CONF->{all_filters}}, @{$CONF->{all_attributes}} ); -} - - - - -#---------------------------------------------------------------------- - -=head2 species_by_focus - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub species_by_focus { - my $focus = shift; - if( ! $CONF ){ new() }; - $CONF->{species_by_focus}->{$focus} || return (); - return sort keys %{$CONF->{species_by_focus}->{$focus}}; -} - -#---------------------------------------------------------------------- - -=head2 foci_by_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub foci_by_species { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{foci_by_species}->{$species} || return (); - return sort keys %{$CONF->{foci_by_species}->{$species}}; -} - -#---------------------------------------------------------------------- - -=head2 chromosomes_by_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub chromosomes_by_species { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{chromosomes_by_species}->{$species} || return (); - return @{$CONF->{chromosomes_by_species}->{$species}}; -} - -#---------------------------------------------------------------------- - - -=head2 bands_by_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub bands_by_species { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{bands_by_species}->{$species} || return (); - return %{$CONF->{bands_by_species}->{$species}}; -} - -#---------------------------------------------------------------------- - - -=head2 trait_regions_by_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub trait_regions_by_species { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{trait_regions_by_species}->{$species} || return (); - return %{$CONF->{trait_regions_by_species}->{$species}}; -} - -#---------------------------------------------------------------------- - - -=head2 encode_regions_by_species - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub encode_regions_by_species { - my $species = shift; - if( ! $CONF ){ new() }; - $CONF->{encode_regions_by_species}->{$species} || return (); - return %{$CONF->{encode_regions_by_species}->{$species}}; -} -#---------------------------------------------------------------------- - -=head2 is_focus_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub is_focus_available { - if( ! $CONF ){ new }; - my $species = shift; - my $focus = shift; - my $species_conf = $CONF->{foci_by_species}->{$species} || return 0; - return $species_conf->{$focus} ? 1 : 0; -} - -#---------------------------------------------------------------------- - -=head2 is_filter_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub is_filter_available { - if( ! $CONF ){ new } - my $name = shift; - my $species = shift; - my $focus = shift; - my $name_conf = $CONF->{filters}->{$name} || return 0; - my $species_conf = $name_conf->{$species} || return 0; - return $species_conf->{$focus} ? 1 : 0; -} - -#---------------------------------------------------------------------- - -=head2 is_attribute_available - - Arg [1] : - Function : - Returntype: - Exceptions: - Caller : - Example : - -=cut - -sub is_attribute_available { - if( ! $CONF ){ new } - my $name = shift; - my $species = shift; - my $focus = shift; - my $name_conf = $CONF->{attributes}->{$name} || return 0; - my $species_conf = $name_conf->{$species} || return 0; - return $species_conf->{$focus} ? 1 : 0; -} - - - - - -#---------------------------------------------------------------------- -1; diff --git a/gramene/conf/Plugins.pm b/gramene/conf/Plugins.pm deleted file mode 100644 index 23d4b44a..00000000 --- a/gramene/conf/Plugins.pm +++ /dev/null @@ -1,22 +0,0 @@ -## If you wish to use the EnsEMBL web-code from the command line, you will -## need to hardcode the server root here - -## $SiteDefs::ENSEMBL_SERVERROOT = '/path to root of ensembl tree'; -my $ENSROOT = $SiteDefs::ENSEMBL_SERVERROOT; -my $GRMROOT = $SiteDefs::ENSEMBL_SERVERROOT.'/gramene-live'; -$SiteDefs::ENSEMBL_PLUGINS = [ - 'EnsEMBL::Gramene' => $GRMROOT.'/gramene', - 'EnsEMBL::Mart' => $ENSROOT.'/public-plugins/mart', - 'EG::EBEyeSearch' => $ENSROOT.'/eg-web-search/', - 'EnsEMBL::Genoverse' => $ENSROOT.'/public-plugins/genoverse', - 'EG::Plants' => $ENSROOT.'/eg-web-plants/', - 'EG::Common' => $ENSROOT.'/eg-web-common/', - 'EnsEMBL::Widgets' => $ENSROOT.'/public-plugins/widgets', - 'EnsEMBL::Tools_hive' => $ENSROOT.'/public-plugins/tools_hive', - 'EnsEMBL::Tools' => $ENSROOT.'/public-plugins/tools', - 'EnsEMBL::Users' => $ENSROOT.'/public-plugins/users', - 'EnsEMBL::Memcached' => $ENSROOT.'/public-plugins/memcached', - 'EnsEMBL::Doc' => $ENSROOT.'/public-plugins/docs', -]; - -1; diff --git a/gramene/conf/Plugins.pm.eg b/gramene/conf/Plugins.pm.eg deleted file mode 100644 index 6961d34f..00000000 --- a/gramene/conf/Plugins.pm.eg +++ /dev/null @@ -1,20 +0,0 @@ -## If you wish to use the EnsEMBL web-code from the command line, you will -## need to hardcode the server root here - -## $SiteDefs::ENSEMBL_SERVERROOT = '/path to root of ensembl tree'; -my $ENSROOT = $SiteDefs::ENSEMBL_SERVERROOT; -my $GRMROOT = $SiteDefs::ENSEMBL_SERVERROOT.'/gramene-live'; -$SiteDefs::ENSEMBL_PLUGINS = [ - 'EnsEMBL::Gramene' => $GRMROOT.'/gramene', - 'EnsEMBL::Mart' => $ENSROOT.'/public-plugins/mart', - 'EG::EBEyeSearch' => $ENSROOT.'/eg-web-search/', - 'EnsEMBL::Genoverse' => $ENSROOT.'/public-plugins/genoverse', - 'EG::Plants' => $ENSROOT.'/eg-web-plants/', - 'EG::Common' => $ENSROOT.'/eg-web-common/', - 'EnsEMBL::Tools' => $ENSROOT.'/public-plugins/tools', - 'EnsEMBL::Users' => $ENSROOT.'/public-plugins/users', - 'EnsEMBL::Memcached' => $ENSROOT.'/public-plugins/memcached', - 'EnsEMBL::Doc' => $ENSROOT.'/public-plugins/docs', -]; - -1; diff --git a/gramene/conf/SiteDefs.pm b/gramene/conf/SiteDefs.pm index 700cb8c1..546557da 100644 --- a/gramene/conf/SiteDefs.pm +++ b/gramene/conf/SiteDefs.pm @@ -1,133 +1,137 @@ + package EnsEMBL::Gramene::SiteDefs; use strict; -# These are the gramene-specific edits to the main Ensembl SiteDefs.pm file sub update_conf { + $SiteDefs::ENSEMBL_PORT = 8888; + #$SiteDefs::ENSEMBL_PROXY_PORT = 80; + $SiteDefs::ENSEMBL_SERVERNAME = 'oryza-ensembl.gramene.org'; + #$SiteDefs::ENSEMBL_PROTOCOL = 'https'; + $SiteDefs::ENSEMBL_BASE_URL = 'https://oryza-ensembl.gramene.org/'; + $SiteDefs::SITE_RELEASE_VERSION = 7; + $SiteDefs::SITE_RELEASE_DATE = 'Jul 2023'; + #'May 2022'; - #$SiteDefs::ENSEMBL_SERVERNAME = 'ensembl.gramene.org'; - $SiteDefs::ENSEMBL_SERVERNAME = 'ensembl-dev.gramene.org'; - $SiteDefs::ENSEMBL_MAX_PROCESS_SIZE = 2000000; - $SiteDefs::ENSEMBL_BASE_URL = $SiteDefs::ENSEMBL_SERVERNAME; - $SiteDefs::SITE_RELEASE_VERSION = 58; -# $SiteDefs::SITE_RELEASE_VERSION_EG = 40; - $SiteDefs::SITE_RELEASE_DATE = 'July 2018'; - $SiteDefs::SITE_NAME = 'Gramene'; - $SiteDefs::ENSEMBL_SITETYPE = 'Gramene-Ensembl Plants'; - $SiteDefs::SITE_FTP = 'ftp://ftp.gramene.org/pub'; - $SiteDefs::PE_URL = 'http://plants.ensembl.org'; - $SiteDefs::ENSEMBL_PORT = 80; - $SiteDefs::ENSEMBL_PROXY_PORT = 80; # Port used for self-referential URLs - $SiteDefs::ENSEMBL_USER = 'nobody';#getpwuid($>); - $SiteDefs::ENSEMBL_GROUP = 'nobody';#getgrgid($)); +$SiteDefs::DIVISION = 'plants'; + $SiteDefs::EG_DIVISION = 'plants'; +$SiteDefs::SUBDOMAIN_DIR = 'plants'; + $SiteDefs::ENSEMBL_SITETYPE = 'Ensembl Plants'; + $SiteDefs::SITE_NAME = 'GrameneOryza'; + $SiteDefs::SITE_FTP = 'http://ftp.gramene.org/oryza'; + $SiteDefs::PE_URL = 'http://plants.ensembl.org'; - $SiteDefs::ENSEMBL_SERVERADMIN = 'weix@cshl.edu'; - $SiteDefs::ENSEMBL_MAIL_SERVER = 'localhost'; + $SiteDefs::ENSEMBL_USER = 'nobody';#getpwuid($>); + $SiteDefs::ENSEMBL_GROUP = 'nobody';#getgrgid($)); + $SiteDefs::ENSEMBL_SERVERADMIN = 'weix@cshl.edu'; + $SiteDefs::ENSEMBL_MAIL_SERVER = 'localhost'; - $SiteDefs::MAX_PROCESS_SIZE = 2000000; - $SiteDefs::GRAPHIC_TTF_PATH = "/usr/share/fonts/msttcorefonts/"; + $SiteDefs::MAX_PROCESS_SIZE = 2000000; + # this is defined in default.ini + #$SiteDefs::GRAPHIC_TTF_PATH = "/usr/share/fonts/msttcorefonts/"; - $SiteDefs::SAMTOOLS_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/samtools'; + $SiteDefs::SAMTOOLS_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/samtools'; $SiteDefs::ENSEMBL_DEBUG_FLAGS = 0; # 24; $SiteDefs::ENSEMBL_LONGPROCESS_MINTIME = 10; - $SiteDefs::EBEYE_REST_ENDPOINT = 'http://data.gramene.org/ebeye' . $SiteDefs::SITE_RELEASE_VERSION; - - $SiteDefs::ENSEMBL_TOOLS_PERL_BIN = '/usr/local/bin/perl'; - $SiteDefs::ENSEMBL_TMP_DIR_BLAST = $SiteDefs::ENSEMBL_SERVERROOT."/blastqueue"; - $SiteDefs::ENSEMBL_BLASTSCRIPT = $SiteDefs::ENSEMBL_WEBROOT."/utils/runblast.pl"; - -# $SiteDefs::ENSEMBL_BLAT_BIN_PATH = '/usr/local/ucscblat/blat'; -# $SiteDefs::ENSEMBL_BLAT_TWOBIT_DIR = '/usr/local/ucscblat/'; - $SiteDefs::ENSEMBL_NCBIBLAST_BIN_PATH = '/usr/local/ncbi-blast-2.2.30+/bin'; # path to blast executables -# $SiteDefs::ENSEMBL_NCBIBLAST_MATRIX = '/path/to/ncbi-blast/data'; # path to blast matrix files - $SiteDefs::ENSEMBL_NCBIBLAST_DATA_PATH_DNA = "/usr/local/blastdb/ncbi_blast/genomic"; # path for the blast DNA index files - $SiteDefs::ENSEMBL_NCBIBLAST_DATA_PATH = "/usr/local/blastdb/ncbi_blast/genes"; # path for the blast index files (other than DNA) - $SiteDefs::ENSEMBL_REPEATMASK_BIN_PATH = '/usr/local/RepeatMasker'; # path to RepeatMasker executable - $SiteDefs::ASSEMBLY_CONVERTER_BIN_PATH = '/usr/local/bin/CrossMap.py'; - $SiteDefs::ENSEMBL_CHAIN_FILE_DIR = '/usr/local/ensembl-live/tools_data/assembly_chain'; - -$SiteDefs::ENSEMBL_VEP_CACHE_DIR = "/usr/local/ensembl-live/tools_data/vep/"; -$SiteDefs::ENSEMBL_VEP_PLUGIN_DATA_DIR = "/usr/local/ensembl-live/tools_data/vep/Plugins"; # path to vep plugin data files on the LSF host (or local machine if job running locally) - + + $SiteDefs::DATAFILE_ROOT = '/usr/local'; ## Base path for ro data files + $SiteDefs::DATAFILE_BASE_PATH = '/usr/local/vcf'; + +#$SiteDefs::EBEYE_REST_ENDPOINT = 'https://data.gramene.org/oryza-ebeye4'; +$SiteDefs::EBEYE_REST_ENDPOINT = 'http://squam:21007'; + +# This should be set by the plugin, but not working. Need to hard code! + #@SiteDefs::ENSEMBL_PERL_DIRS = + # ( $SiteDefs::ENSEMBL_WEBROOT.'/perl', + # $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-common/perl', + # $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-plants/perl', + # ); + +$SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Oryza_sativa'; +$SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Arabidopsis_thaliana'; + +# $SiteDefs::ENSEMBL_DATASETS + +#$SiteDefs::PRODUCTION_NAMES = ['Oryza_sativa']; + +$SiteDefs::ENSEMBL_DATASETS = [sort qw( + Oryza_aus + Oryza_barthii + Oryza_brachyantha + Oryza_carolina + Oryza_glaberrima + Oryza_glumaepatula + Oryza_indica + Oryza_indicair8 + Oryza_meridionalis + Oryza_nivara + Oryza_punctata + Oryza_rufipogon + Oryza_sativa + Oryza_sativa117425 + Oryza_sativa125619 + Oryza_sativa125827 + Oryza_sativa127518 + Oryza_sativa127564 + Oryza_sativa127652 + Oryza_sativa127742 + Oryza_sativa128077 + Oryza_sativa132278 + Oryza_sativa132424 + Oryza_sativaazucena + Oryza_sativair64 + Oryza_sativakitaake + Oryza_sativamh63 + Oryza_sativazs97 + Leersia_perrieri + Arabidopsis_thaliana + Chlamydomonas_reinhardtii + Drosophila_melanogaster + Selaginella_moellendorffii + Sorghum_bicolor + Vitis_vinifera + Zea_maysb73 + Zea_maysb73v4 + ), qw( + )]; + push @$SiteDefs::ENSEMBL_EXTRA_INC, '/usr/local/ensembl-live/htslib', '/usr/local/BioPerl-1.6.922', '/usr/local/ensembl-live/ensembl-io/modules', '/usr/local/ensembl-live/ensembl-funcgen/modules', '/usr/local/ensembl-live/ensembl-variation/modules'; - -$SiteDefs::ENSEMBL_VEP_SCRIPT_DEFAULT_OPTIONS = { # Default options for command line vep script (keys with value undef get ignored) - 'host' => 'colden', # Database host (defaults to ensembldb.ensembl.org) - 'user' => 'weix', # Defaults to 'anonymous' - 'password' => 'warelab', # Not used by default - 'port' => 3306, # Defaults to 5306 - 'fork' => 4, # Enable forking, using 4 forks - }; - - #---------- - # User database - $SiteDefs::ENSEMBL_USERDB_NAME = 'ensembl_accounts'; #changed to ensembl_accounts lately - $SiteDefs::ENSEMBL_USERDB_USER = 'gramene_web'; - $SiteDefs::ENSEMBL_USERDB_HOST = 'colden.cshl.edu'; - $SiteDefs::ENSEMBL_USERDB_PORT = 3306; - $SiteDefs::ENSEMBL_USERDB_PASS = 'gram3n3'; - - #---------- - # Logging - $SiteDefs::ENSEMBL_LOGDIR = $SiteDefs::ENSEMBL_SERVERROOT."/logs"; - $SiteDefs::ENSEMBL_PIDFILE = "$SiteDefs::ENSEMBL_LOGDIR/httpd.pid"; - $SiteDefs::ENSEMBL_ERRORLOG = "$SiteDefs::ENSEMBL_LOGDIR/error.log"; - $SiteDefs::ENSEMBL_CUSTOMLOG = "$SiteDefs::ENSEMBL_LOGDIR/access.log combined"; -#our $ENSEMBL_LOGDIR = defer { "$ENSEMBL_SYS_DIR/logs/$ENSEMBL_SERVER_SIGNATURE" }; # Path for log files -#our $ENSEMBL_PIDFILE = defer { "$ENSEMBL_LOGDIR/httpd.pid" }; # httpd process id -#our $ENSEMBL_ERRORLOG = defer { "$ENSEMBL_LOGDIR/error_log" }; # Error log file -#our $ENSEMBL_CUSTOMLOG = defer { "$ENSEMBL_LOGDIR/access_log ensembl_extended" }; - - - #---------- - # Mart/Blast - $SiteDefs::ENSEMBL_BLAST_ENABLED = 1; # Creates header link for blast - $SiteDefs::ENSEMBL_BLAST_BY_SEQID = 1; # blast on gene page sequence - $SiteDefs::ENSEMBL_MART_ENABLED = 1; # And mart - - $SiteDefs::ENSEMBL_VEP_ENABLED = 1; - $SiteDefs::ENSEMBL_AC_ENABLED = 1; - $SiteDefs::ENSEMBL_IDM_ENABLED = 0; - $SiteDefs::ENSEMBL_FC_ENABLED = 0; - $SiteDefs::ENSEMBL_LD_ENABLED = 0; - $SiteDefs::ENSEMBL_VP_ENABLED = 0; - $SiteDefs::ENSEMBL_DS_ENABLED = 0; - - push @SiteDefs::ENSEMBL_HTDOCS_DIRS, # Needed due to EG plugin - $SiteDefs::ENSEMBL_SERVERROOT.'/biomart-perl/htdocs'; - - #---------- - # Temp files - #$SiteDefs::ENSEMBL_TMP_URL = "/ens-tmp"; - - #---------- - #GeoLiteCity database file - $SiteDefs::GEOCITY_DAT = $SiteDefs::ENSEMBL_SERVERROOT.'/geocity/GeoLiteCity.dat'; - - #---------- - # Paths and so on - # This should be set by the plugin, but not working. Need to hard code! -# push @SiteDefs::ENSEMBL_PERL_DIRS, $SiteDefs::ENSEMBL_SERVERROOT -# .'/gramene-live/ensembl-plugins/gramene/perl'; - - #---------- - # Species stuff - - $SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Oryza_sativa'; # Default - $SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Arabidopsis_thaliana'; - #%SiteDefs::__species_aliases = - # ( - # These are supplimental species to EnsemblGenomes - # %SiteDefs::__species_aliases, - # 'Zea_mays' => [('zea_mays', 'zm','maize')], - # 'Physcomitrella_patens' => [('physcomitrella_patens', 'pp','physcomitrella')], - # 'Arabidopsis_thaliana' => [('arabidopsis_thaliana')], - # ); -# push(@{$SiteDefs::__species_aliases{'Populus_trichocarpa'}},'poplar'); + #push @SiteDefs::ENSEMBL_HTDOCS_DIRS, $SiteDefs::ENSEMBL_SERVERROOT. '/../biomarts/plants/biomart-perl/htdocs'; + + #$SiteDefs::DOCSEARCH_INDEX_DIR = $SiteDefs::ENSEMBL_SERVERROOT.'/eg-web-plants/data/docsearch'; + + #$SiteDefs::ENA_COLLECTION_ID = 224; + + #$SiteDefs::ENA_SAMPLE_SEQ = "MDDCRFETSELQASVMISTPLFTDSWSSCNTANCNGSIKIHDIAGITYVAIPAVSMIQLGNLVGLPVTGDVLFPGLSSDEPLPMVDAAILKLFLQLKIKEGLELELLGKKLVVITGHSTGGALAAFTALWLLSQSSPPSFRVFCITFGSPLLGNQSLSTSISRSRLAHNFCHVVSIHDLVPRSSNEQFWPFGTYLFCSDKGGVCLDNAGSVRLMFNILNTTATQNTEEHQRYGHYVFTLSHMFLKSRSFLGGSIPDNSYQAGVALAVEALGFSNDDTSGVLVKECIETATRIVRAPILRSAELANELASVLPARLEIQWYKDRCDASEEQLGYYDFFKRYSLKRDFKVNMSRIRLAKFWDTVIKMVETNELPFDFHLGKKWIYASQFYQLLAEPLDIANFYKNRDIKTGGHYLEGNRPKRYEVIDKWQKGVKVPEECVRSRYASTTQDTCFWAKLEQAKEWLDEARKESSDPQRRSLLREKIVPFESYANTLVTKKEVSLDVKAKNSSYSVWEANLKEFKCKMGYENEIEMVVDESDAMET"; + + #$SiteDefs::GXA = 1; + + #$SiteDefs::ENSEMBL_HMMER_ENABLED = 1; + + $SiteDefs::ENSEMBL_BLAST_ENABLED = 1; # Creates header link for blast + $SiteDefs::ENSEMBL_BLAST_BY_SEQID = 1; # blast on gene page sequence + + $SiteDefs::NCBIBLAST_REST_ENDPOINT = 'http://squam:2502'; #brie:5202'; + + $SiteDefs::ENSEMBL_TOOLS_LIST = [ + 'Blast' => 'BLAST/BLAT', + # 'VEP' => 'Variant Effect Predictor', + #'FileChameleon' => 'File Chameleon', + # 'AssemblyConverter' => 'Assembly Converter', + #'IDMapper' => 'ID History Converter', + #'AlleleFrequency' => 'Allele Frequency Calculator', + #'VcftoPed' => 'VCF to PED Converter', + #'DataSlicer' => 'Data Slicer', + #'VariationPattern' => 'Variation Pattern Finder', + #'LD' => 'Linkage Disequilibrium Calculator', + ]; + +# our $VCF_LIB = $SiteDefs::ENSEMBL_SERVERROOT.'/vcftools/perl'; +# push @SiteDefs::ENSEMBL_LIB_DIRS, $VCF_LIB; } diff --git a/gramene/conf/ini-files.bad/Aegilops_tauschii.ini b/gramene/conf/ini-files.bad/Aegilops_tauschii.ini new file mode 100755 index 00000000..3dc73b8b --- /dev/null +++ b/gramene/conf/ini-files.bad/Aegilops_tauschii.ini @@ -0,0 +1,67 @@ +[general] +SPECIES_RELEASE_VERSION=1 + +[databases] +DATABASE_CORE=%_core_%_% +DATABASE_OTHERFEATURES=%_otherfeatures_%_% +DATABASE_USERDATA=aegilops_tauschii_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_INTERNAL_BAM_SOURCES] +Lastz_Wheat_D_subsequences_alignments = wheat_assembly +Lastz_Wheat_cap3_subsequences_alignments = wheat_assembly + +[Lastz_Wheat_D_subsequences_alignments] +source_name = Brenchley et al. T. urartu D sequences +description = Lastz Alignments of the T. aestivum D sequences from Brenchley et al. against T. urartu +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/atauschii/LastZ_Wheat_Genome_D.atauschii.bam +source_type = bam +display = off + +[Lastz_Wheat_cap3_subsequences_alignments] +source_name = Brenchley et al. A. tauschii cap3 sequences +description = Lastz Alignments of the T. aestivum cap3 sequences from Brenchley et al. against A. tauschii +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/atauschii/LastZ_Wheat_Genome_cap3.atauschii.bam +source_type = bam +display = off + +[ENSEMBL_INTERNAL_BIGWIG_SOURCES] +DRS001323 = wheat_transcriptomics +DRS001324 = wheat_transcriptomics +SRS072843 = wheat_transcriptomics + +[DRS001323] +source_name = Aegilops tauschii IG47182 +description = RNASeq from seedling leaves of Aegilops tauschii (Study DRP000562), aligned using Star software +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/DRS001323.bw +source_type = bigWig +display = off + +[DRS001324] +source_name = Aegilops tauschii PI476874 +description = RNASeq from seedling leaves of Aegilops tauschii (Study DRP000562), aligned using Star software +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/DRS001324.bw +source_type = bigWig +display = off + +[SRS072843] +source_name = Aegilops tauschii +description = Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors (Study SRP002455), aligned using Star software +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/atauschii/SRS072843.bw +source_type = bigWig +display = off diff --git a/gramene/conf/ini-files.bad/Amborella_trichopoda.ini b/gramene/conf/ini-files.bad/Amborella_trichopoda.ini new file mode 100755 index 00000000..75974e5a --- /dev/null +++ b/gramene/conf/ini-files.bad/Amborella_trichopoda.ini @@ -0,0 +1,29 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = amborella_trichopoda_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + diff --git a/gramene/conf/ini-files.bad/Arabidopsis_lyrata.ini b/gramene/conf/ini-files.bad/Arabidopsis_lyrata.ini new file mode 100755 index 00000000..42283e2e --- /dev/null +++ b/gramene/conf/ini-files.bad/Arabidopsis_lyrata.ini @@ -0,0 +1,40 @@ +[general] +ENSEMBL_GENOME_SIZE = 0.2 +SPECIES_RELEASE_VERSION = 10 +DB_BUILDER = NASC + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = arabidopsis_lyrata_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/lyrata/?name=scaffold_###CHR###%3A###START###..###END### +#EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/lyrata/?name=scaffold_1:8156101..8226101 + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + + diff --git a/gramene/conf/ini-files.bad/Beta_vulgaris.ini b/gramene/conf/ini-files.bad/Beta_vulgaris.ini new file mode 100755 index 00000000..f0cfb2da --- /dev/null +++ b/gramene/conf/ini-files.bad/Beta_vulgaris.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 2 + +[databases] +#DATABASE_USERDATA = beta_vulgaris_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Brassica_napus.ini b/gramene/conf/ini-files.bad/Brassica_napus.ini new file mode 100755 index 00000000..d529b2c6 --- /dev/null +++ b/gramene/conf/ini-files.bad/Brassica_napus.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +#DATABASE_USERDATA = brassica_napus_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Brassica_oleracea.ini b/gramene/conf/ini-files.bad/Brassica_oleracea.ini new file mode 100755 index 00000000..56f03d75 --- /dev/null +++ b/gramene/conf/ini-files.bad/Brassica_oleracea.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_USERDATA = brassica_oleracea_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Brassica_rapa.ini b/gramene/conf/ini-files.bad/Brassica_rapa.ini new file mode 100755 index 00000000..45658fc8 --- /dev/null +++ b/gramene/conf/ini-files.bad/Brassica_rapa.ini @@ -0,0 +1,29 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = brassica_rapa_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + diff --git a/gramene/conf/ini-files.bad/Chlamydomonas_reinhardtii.ini b/gramene/conf/ini-files.bad/Chlamydomonas_reinhardtii.ini new file mode 100755 index 00000000..de3ff80f --- /dev/null +++ b/gramene/conf/ini-files.bad/Chlamydomonas_reinhardtii.ini @@ -0,0 +1,38 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = chlamydomonas_reinhardtii_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files.bad/Cyanidioschyzon_merolae.ini b/gramene/conf/ini-files.bad/Cyanidioschyzon_merolae.ini new file mode 100755 index 00000000..028ea2c4 --- /dev/null +++ b/gramene/conf/ini-files.bad/Cyanidioschyzon_merolae.ini @@ -0,0 +1,27 @@ +[general] +SPECIES_RELEASE_VERSION = 1 +ENSEMBL_GENOME_SIZE = 0.2 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = cyanidioschyzon_merolae_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files.bad/DEFAULTS.ini b/gramene/conf/ini-files.bad/DEFAULTS.ini new file mode 100755 index 00000000..fbd6783b --- /dev/null +++ b/gramene/conf/ini-files.bad/DEFAULTS.ini @@ -0,0 +1,71 @@ +[general] +DISPLAY_ONTOLOGIES = [ GO PO TO GRO GR_TAX EFO EO ] +ONTOLOGY_SUBSETS = [ goslim_generic goslim_plant ] +ENSEMBL_GENOME_SIZE = 2 +SPECIES_RELEASE_VERSION = 3 +DEFAULT_FAVOURITES = [ Oryza_sativa Oryza_indica Oryza_glaberrima Oryza_barthii Oryza_nivara ] +TAXON_ORDER = [ Oryzeae Liliopsida eudicotyledons Lycopodiophyta Bryophyta Chlorophyta Rhodophyta Eukaryota Amborellales] +DATA_SOURCE = EMBL Nucleotide Sequence Database +COMPARA_DB_NAME = Plant Compara +GENOMIC_UNIT = +#plants +ENSEMBL_SITENAME = GrameneOryza +ENSEMBL_FTP_URL = http://ftp.gramene.org/oge +SPECIES_FTP_URL = http://ftp.gramene.org/oge/release-###VERSION###/###FORMAT###/###SPECIES### +SITE_VERSION = 4 + +DATABASE_HOST = cabot.cshl.edu +DATABASE_DBUSER = gramene_web +DATABASE_DBPASS = gram3n3 +DATABASE_HOST_PORT = 3306 +DATABASE_WRITE_USER = gramene_web +DATABASE_WRITE_PASS = gram3n3 + +SITE_ICON = favicon.ico +ACKNOWLEDGEMENT = I-OMAP genome browser is produced in collaboration with Gramene +ACKNOWLEDGEMENT_URL = http://www.gramene.org + +ENSEMBL_REST_URL = https://data.gramene.org/pansite-ensembl/ + +; +; Species lists on the home page +; + +# Each taxon in TAXON_ORDER can have a colour defined here (use 0 otherwise). +TAXON_GENETREE_BGCOLOUR = [f0f0ff fff0e0 d0fafa 0 0 d0fad0 lemonchiffon 0 lightblue1 ffe0f0 0 0] +TAXON_GENETREE_FGCOLOUR = [000050 403000 005050 0 0 005000 yellow4 0 royalblue4 tomato3 0 0] + + +[ENSEMBL_STYLE] + +MH_BG = 7EB693 +TAB_TEXT = E5EFE7 +MH_TEXT = ffffff +MH_LINK = ffffff +MH_VISITED = ffffff +MH_HOVER = cc0000 +TINT_BG = E5EFE7 + + +SITE_LOGO = oryza_logo_small.png +SITE_LOGO_WIDTH = 100 +SITE_LOGO_HEIGHT = 40 +SITE_LOGO_ALT = Gramene Home +SITE_LOGO_HREF = https://oryza.gramene.org + +GRAPHIC_TTF_PATH = /usr/share/fonts/msttcorefonts/ +GRAPHIC_FONT_FIXED = cour +GRAPHIC_FONT = cour +GRAPHIC_FONTSIZE = 8 + + +[ENSEMBL_EXTERNAL_URLS] +GENOMICUSSYNTENY = http://www.genomicus.biologie.ens.fr/genomicus-plants/cgi-bin/search.pl?view=default&query=###ID### +TAIR = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +TAIR_LOCUS = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +TAIR_LOCUS_MODEL = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +NASC_GENE_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/geneview?db=core;gene=###ID### +NASC_TRANSCRIPT_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/transview?db=core;transcript=###ID### +NASC_TRANSLATION_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/transview?db=core;peptide=###ID### +TIGRGENEINDEX = http://compbio.dfci.harvard.edu/cgi-bin/tgi/tc_report.pl?gudb=arab&tc=###ID### +MTGD = http://medicago.jcvi.org/MTGD/?q=feature/###ID### diff --git a/gramene/conf/ini-files.bad/Glycine_max.ini b/gramene/conf/ini-files.bad/Glycine_max.ini new file mode 100755 index 00000000..1535245d --- /dev/null +++ b/gramene/conf/ini-files.bad/Glycine_max.ini @@ -0,0 +1,42 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = glycine_max_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome +EGB_SOY = Soybase + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/soybean/?name=chr###CHR###%3A###START###..###END### +EGB_SOY = http://soybase.org/gb2/gbrowse/gmax1.01/?###CHR###%3A###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files.bad/Hordeum_vulgare.ini b/gramene/conf/ini-files.bad/Hordeum_vulgare.ini new file mode 100755 index 00000000..64c71b75 --- /dev/null +++ b/gramene/conf/ini-files.bad/Hordeum_vulgare.ini @@ -0,0 +1,623 @@ +[general] +SPECIES_RELEASE_VERSION = 2 + +ASSEMBLY_CONVERTER_FILES = [030312v2_to_ASM32608v1 ASM32608v1_to_030312v2] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_VARIATION = %_variation_%_% +DATABASE_FUNCGEN = %_funcgen_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = hordeum_vulgare_userdata + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +Lastz_Wheat_A_subsequences_alignments = wheat_assembly +Lastz_Wheat_B_subsequences_alignments = wheat_assembly +Lastz_Wheat_D_subsequences_alignments = wheat_assembly +Lastz_Wheat_X_subsequences_alignments = wheat_assembly +Lastz_Wheat_cap3_subsequences_alignments = wheat_assembly +Gmap_Wheat_ERR125556 = wheat_transcriptomics +Gmap_Wheat_ERR125557 = wheat_transcriptomics +Gmap_Wheat_ERR125558 = wheat_transcriptomics +Gmap_Wheat_ERR125559 = wheat_transcriptomics +Gmap_Wheat_ERR125560 = wheat_transcriptomics +Gmap_Wheat_ERR125561 = wheat_transcriptomics +Gmap_Wheat_ERR125562 = wheat_transcriptomics +Gmap_Wheat_ERR125563 = wheat_transcriptomics +Gmap_Wheat_ERR125564 = wheat_transcriptomics +Gmap_Wheat_ERR125565 = wheat_transcriptomics +Gmap_Wheat_ERR125566 = wheat_transcriptomics +Gmap_Wheat_ERR125567 = wheat_transcriptomics +Gmap_Wheat_ERR125568 = wheat_transcriptomics +Gmap_Wheat_ERR125569 = wheat_transcriptomics +Gmap_Wheat_ERR125570 = wheat_transcriptomics +Gmap_Wheat_ERR125571 = wheat_transcriptomics +Gmap_Wheat_ERR125572 = wheat_transcriptomics +Gmap_Wheat_ERR125573 = wheat_transcriptomics +Gmap_Wheat_ERR125574 = wheat_transcriptomics +Gmap_Wheat_ERR125575 = wheat_transcriptomics +Gmap_Wheat_ERR125576 = wheat_transcriptomics +Gmap_Wheat_ERR125577 = wheat_transcriptomics +Gmap_Wheat_ERR125578 = wheat_transcriptomics +Gmap_Wheat_ERR125579 = wheat_transcriptomics +Gmap_Wheat_ERR125580 = wheat_transcriptomics +Gmap_Wheat_ERR125581 = wheat_transcriptomics +Gmap_Wheat_ERR169814 = wheat_transcriptomics +Gmap_Wheat_ERR169815 = wheat_transcriptomics +Gmap_Wheat_ERR169816 = wheat_transcriptomics +Gmap_Wheat_ERR169817 = wheat_transcriptomics + +[Gmap_Wheat_ERR125556] +source_name = ERR125556: Triticum aestivum; non-normalised cDNA from roots, young flowers, young leaves +description = ERR125556: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125556.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125557] +source_name = ERR125557: Triticum aestivum; normalised cDNA from roots, young flowers, young leaves +description = ERR125557: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125557.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125558] +source_name = ERR125558: Triticum aestivum; normalised cDNA from roots, young flowers, young leaves +description = ERR125558: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125558.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125559] +source_name = ERR125559: Triticum aestivum; normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125559: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125559.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125560] +source_name = ERR125560: Triticum aestivum; normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125560: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125560.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125561] +source_name = ERR125561: Triticum aestivum; normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125561: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125561.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125562] +source_name = ERR125562: Triticum aestivum; normalised cDNA from 6- and 11-day drought leaves and 3 DAA and 5 DAA senescent leaves +description = ERR125562: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125562.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125563] +source_name = ERR125563: Triticum aestivum; normalised cDNA from 6- and 11-day drought leaves and 3 DAA and 5 DAA senescent leaves +description = ERR125563: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125563.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125564] +source_name = ERR125564: Triticum aestivum; normalised cDNA from 6- and 11-day drought leaves and 3 DAA and 5 DAA senescent leaves +description = ERR125564: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125564.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125565] +source_name = ERR125565: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125565: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125565.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125566] +source_name = ERR125566: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125566: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125566.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125567] +source_name = ERR125567: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125567: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125567.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125568] +source_name = ERR125568: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125568: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125568.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125569] +source_name = ERR125569: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125569: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125569.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125570] +source_name = ERR125570: non-normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125570: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125570.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125571] +source_name = ERR125571: non-normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125571: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125571.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125572] +source_name = ERR125572: non-normalised cDNA from roots, young flowers, young leaves, immature seeds +description = ERR125572: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125572.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125573] +source_name = ERR125573: non-normalised cDNA from various tissues, drought-stressed and senescent leaves, and leaves over a circadian time-course +description = ERR125573: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125573.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125574] +source_name = ERR125574: non-normalised cDNA from various tissues, drought-stressed and senescent leaves, and leaves over a circadian time-course +description = ERR125574: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125574.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125575] +source_name = ERR125575: normalised cDNA from various tissues, drought-stressed and senescent leaves, and leaves over a circadian time-course +description = ERR125575: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125575.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125576] +source_name = ERR125576: normalised cDNA from various tissues, drought-stressed and senescent leaves, and leaves over a circadian time-course +description = ERR125576: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125576.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125577] +source_name = ERR125577: normalised cDNA from various tissues, drought-stressed and senescent leaves, and leaves over a circadian time-course +description = ERR125577: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125577.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125578] +source_name = ERR125578: normalised cDNA from various tissues, drought- and salt-stressed samples, and leaves over a circadian time-course +description = ERR125578: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125578.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125579] +source_name = ERR125579: normalised cDNA from roots, young flowers, young leaves, young shoots and immature seeds +description = ERR125579: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125579.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125580] +source_name = ERR125580: normalised cDNA from salt-stressed roots and shoots and 6-day drought leaves +description = ERR125580: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125580.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR125581] +source_name = ERR125581: normalised cDNA from seedling leaves in a circadian time-course +description = ERR125581: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR125581.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR169814] +source_name = ERR169814: normalised cDNA from seedling leaves in a circadian time-course +description = ERR169814: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR169814.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR169815] +source_name = ERR169815: normalised cDNA from seedling leaves in a circadian time-course +description = ERR169815: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR169815.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR169816] +source_name = ERR169816: normalised cDNA from seedling leaves in a circadian time-course +description = ERR169816: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR169816.gmap.exons.bam +source_type = rnaseq +display = off + +[Gmap_Wheat_ERR169817] +source_name = ERR169817: normalised cDNA from seedling leaves in a circadian time-course +description = ERR169817: 454 sequencing of the Triticum aestivum cv. Chinese spring transcriptome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/hv.ERR169817.gmap.exons.bam +source_type = rnaseq +display = off + + +[Lastz_Wheat_A_subsequences_alignments] +source_name = Brenchley et al. T. aestivum A sequences +description = Lastz Alignments of the T. aestivum A sequences from Brenchley et al. against the Hordeum vulgare genome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/LastZ_Wheat_Genome_A.hvulgare.bam +source_type = bam +display = off + +[Lastz_Wheat_B_subsequences_alignments] +source_name = Brenchley et al. T. aestivum B sequences +description = Lastz Alignments of the T. aestivum B sequences from Brenchley et al. against the Hordeum vulgare genome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/LastZ_Wheat_Genome_B.hvulgare.bam +source_type = bam +display = off + +[Lastz_Wheat_D_subsequences_alignments] +source_name = Brenchley et al. T. aestivum D sequences +description = Lastz Alignments of the T. aestivum D sequences from Brenchley et al. against the Hordeum vulgare genome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/LastZ_Wheat_Genome_D.hvulgare.bam +source_type = bam +display = off + +[Lastz_Wheat_X_subsequences_alignments] +source_name = Brenchley et al. T. aestivum unassigned sequences +description = Lastz Alignments of the T. aestivum unassigned sequences from Brenchley et al. against the Hordeum vulgare genome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/LastZ_Wheat_Genome_X.hvulgare.bam +source_type = bam +display = off + +[Lastz_Wheat_cap3_subsequences_alignments] +source_name = Brenchley et al. T. aestivum cap3 sequences +description = Lastz Alignments of the T. aestivum cap3 sequences from Brenchley et al. against the Hordeum vulgare genome +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/hvulgare/LastZ_Wheat_Genome_cap3.hvulgare.bam +source_type = bam +display = off + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +;EGB_PHY = Phytozome +;EGB_SOY = Soybase + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +;EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/soybean/?name=chr###CHR###%3A###START###..###END### +;EGB_SOY = http://soybase.org/gb2/gbrowse/gmax1.01/?###CHR###%3A###START###..###END### +IBSC = http://mips.helmholtz-muenchen.de/plant/barley/ga/reportsjsp/geneticElement.jsp?gene=###ID### + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +ERS154249 = rnaseq_cultivar +ERS154256 = rnaseq_cultivar +ERS154253 = rnaseq_cultivar +ERS154254 = rnaseq_cultivar +ERS154250 = rnaseq_cultivar +ERS154255 = rnaseq_cultivar +ERS157253 = rnaseq_cultivar +ERS154252 = rnaseq_cultivar +ERS154257 = rnaseq_cultivar +ERS154251 = rnaseq_cultivar + +[ERS154249] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Barke' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154249.bam +source_type = bam +display = off +[ERS154256] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Sergeant' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154256.bam +source_type = bam +display = off +[ERS154253] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Intro' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154253.bam +source_type = bam +display = off +[ERS154254] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Optic' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154254.bam +source_type = bam +display = off +[ERS154250] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Betzes' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154250.bam +source_type = bam +display = off +[ERS154255] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Quench' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154255.bam +source_type = bam +display = off +[ERS157253] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Morex' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS157253.bam +source_type = bam +display = off +[ERS154252] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Derkado' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154252.bam +source_type = bam +display = off +[ERS154257] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Tocada' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154257.bam +source_type = bam +display = off +[ERS154251] +source_name = Hordeum vulgare subsp. vulgare; RNASeq of cultivar 'Bowman' +description = SNP Discovery in Nine Lines of Cultivated Barley (Study ERP001573) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERS154251.bam +source_type = bam +display = off + +[ENSEMBL_INTERNAL_BAM_SOURCES] +RNASEQ_ROO_A = rnaseq_tissue +RNASEQ_ROO_B = rnaseq_tissue +RNASEQ_ROO_C = rnaseq_tissue + +RNASEQ_CAR15_1 = rnaseq_tissue +RNASEQ_CAR15_2 = rnaseq_tissue +RNASEQ_CAR15_3 = rnaseq_tissue + +RNASEQ_INF1_A = rnaseq_tissue +RNASEQ_INF1_B = rnaseq_tissue +RNASEQ_INF1_C = rnaseq_tissue + +RNASEQ_INF2_F = rnaseq_tissue +RNASEQ_INF2_G = rnaseq_tissue +RNASEQ_INF2_H = rnaseq_tissue + +RNASEQ_LEA_A = rnaseq_tissue +RNASEQ_LEA_B = rnaseq_tissue +RNASEQ_LEA_C = rnaseq_tissue + +RNASEQ_EMB_A = rnaseq_tissue +RNASEQ_EMB_B = rnaseq_tissue +RNASEQ_EMB_C = rnaseq_tissue + +RNASEQ_NOD_A = rnaseq_tissue +RNASEQ_NOD_B = rnaseq_tissue +RNASEQ_NOD_C = rnaseq_tissue + +RNASEQ_CAR5_2 = rnaseq_tissue +RNASEQ_CAR5_3 = rnaseq_tissue +RNASEQ_CAR5_4 = rnaseq_tissue + +[RNASEQ_ROO_A] +source_name = ROO-A, BBSRC_Waugh_BarleyRNAseq +description = Roots from the seedlings (10cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155523.bam +source_type = bam +display = off +[RNASEQ_ROO_B] +source_name = ROO-B, BBSRC_Waugh_BarleyRNAseq +description = Roots from the seedlings (10cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155521.bam +source_type = bam +display = off +[RNASEQ_ROO_C] +source_name = ROO-C, BBSRC_Waugh_BarleyRNAseq +description = Roots from the seedlings (10cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155522.bam +source_type = bam +display = off + +[RNASEQ_CAR15_1] +source_name = CAR15-1, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (15 days post-anthesis) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155524.bam +source_type = bam +display = off +[RNASEQ_CAR15_2] +source_name = CAR15-2, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (15 days post-anthesis) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155527.bam +source_type = bam +display = off +[RNASEQ_CAR15_3] +source_name = CAR15-4, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (15 days post-anthesis) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155526.bam +source_type = bam +display = off + +[RNASEQ_INF1_A] +source_name = INF1-A, BBSRC_Waugh_BarleyRNAseq +description = Young developing inflorescences (5mm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155506.bam +source_type = bam +display = off +[RNASEQ_INF1_B] +source_name = INF1-B, BBSRC_Waugh_BarleyRNAseq +description = Young developing inflorescences (5mm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155505.bam +source_type = bam +display = off +[RNASEQ_INF1_C] +source_name = INF1-C, BBSRC_Waugh_BarleyRNAseq +description = Young developing inflorescences (5mm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155504.bam +source_type = bam +display = off + +[RNASEQ_INF2_F] +source_name = INF2-F, BBSRC_Waugh_BarleyRNAseq +description = Developing inflorescences (1-1.5 cm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155518.bam +source_type = bam +display = off +[RNASEQ_INF2_G] +source_name = INF2-G, BBSRC_Waugh_BarleyRNAseq +description = Developing inflorescences (1-1.5 cm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155515.bam +source_type = bam +display = off +[RNASEQ_INF2_H] +source_name = INF2-H, BBSRC_Waugh_BarleyRNAseq +description = Developing inflorescences (1-1.5 cm) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155516.bam +source_type = bam +display = off + +[RNASEQ_LEA_A] +source_name = LEA-A, BBSRC_Waugh_BarleyRNAseq +description = Shoots from the seedlings (10 cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155512.bam +source_type = bam +display = off +[RNASEQ_LEA_B] +source_name = LEA-B, BBSRC_Waugh_BarleyRNAseq +description = Shoots from the seedlings (10 cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155511.bam +source_type = bam +display = off +[RNASEQ_LEA_C] +source_name = LEA-C, BBSRC_Waugh_BarleyRNAseq +description = Shoots from the seedlings (10 cm shoot stage) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155510.bam +source_type = bam +display = off + +[RNASEQ_EMB_A] +source_name = EMB-A, BBSRC_Waugh_BarleyRNAseq +description = 4-day embyros dissected from germinating grains (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155509.bam +source_type = bam +display = off +[RNASEQ_EMB_B] +source_name = EMB-B, BBSRC_Waugh_BarleyRNAseq +description = 4-day embyros dissected from germinating grains +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155508.bam +source_type = bam +display = off +[RNASEQ_EMB_C] +source_name = EMB-C, BBSRC_Waugh_BarleyRNAseq +description = 4-day embyros dissected from germinating grains (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155507.bam +source_type = bam +display = off + +[RNASEQ_NOD_A] +source_name = NOD-A, BBSRC_Waugh_BarleyRNAseq +description = Developing tillers at six - leaf stage, 3rd internode(Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155519.bam +source_type = bam +display = off +[RNASEQ_NOD_B] +source_name = NOD-B, BBSRC_Waugh_BarleyRNAseq +description = Developing tillers at six - leaf stage, 3rd internode (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155520.bam +source_type = bam +display = off +[RNASEQ_NOD_C] +source_name = NOD-C, BBSRC_Waugh_BarleyRNAseq +description = Developing tillers at six - leaf stage, 3rd internode +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155517.bam +source_type = bam +display = off + +[RNASEQ_CAR5_2] +source_name = CAR5-2, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (5 days post-anthesis) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155513.bam +source_type = bam +display = off +[RNASEQ_CAR5_3] +source_name = CAR5-3, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (5 days post-anthesis) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155514.bam +source_type = bam +display = off +[RNASEQ_CAR5_4] +source_name = CAR5-4, BBSRC_Waugh_BarleyRNAseq +description = Developing grain, bracts removed (5 days post-anthesis) (Study ERP001600) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/ERP001600/ERS155525.bam +source_type = bam +display = off + +[ENSEMBL_INTERNAL_BAM_SOURCES] +RNASEQ_SAL_A = dna_align_cdna +RNASEQ_SAL_B = dna_align_cdna + +[RNASEQ_SAL_A] +source_name = Transcript - RNA-Seq - Hordeum vulgare cv. Hindmarsh; control sample (SRS380124) - Ziemann (2013) +description = (Study SRP017703) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/SRP017703/SRS380124.bam +source_type = bam +display = off +[RNASEQ_SAL_B] +source_name = Transcript - RNA-Seq - Hordeum vulgare cv. Hindmarsh; salinity stress (SRS380125) - Ziemann (2013) +description = (Study SRP017703) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/SRP017703/SRS380125.bam +source_type = bam +display = off + +[ENSEMBL_INTERNAL_BAM_SOURCES] +RNASEQ_HULLESS_A = dna_align_cdna +RNASEQ_HULLESS_B = dna_align_cdna + +[RNASEQ_HULLESS_A] +source_name = Transcript - RNA-Seq - Hordeum vulgare cv Nimubai (SRS503432) - Chen (2014) +description = (Study SRP032924) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/SRP032924/SRS503432.bam +source_type = bam +display = off +[RNASEQ_HULLESS_B] +source_name = Transcript - RNA-Seq - Hordeum vulgare cv. XQ754 (SRS501331) - Chen (2014) +description = (Study SRP032924) +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/barley/SRP032924/SRS501331.bam +source_type = bam +display = off diff --git a/gramene/conf/ini-files.bad/Medicago_truncatula.ini b/gramene/conf/ini-files.bad/Medicago_truncatula.ini new file mode 100755 index 00000000..990b178d --- /dev/null +++ b/gramene/conf/ini-files.bad/Medicago_truncatula.ini @@ -0,0 +1,31 @@ +[general] +SPECIES_RELEASE_VERSION = 2 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = medicago_truncatula_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] +GRAMENE_PATHWAY = http://pathway.gramene.org/MEDIC/NEW-IMAGE?type=REACTION&object=###ID### + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + diff --git a/gramene/conf/ini-files.bad/Musa_acuminata.ini b/gramene/conf/ini-files.bad/Musa_acuminata.ini new file mode 100755 index 00000000..db00916c --- /dev/null +++ b/gramene/conf/ini-files.bad/Musa_acuminata.ini @@ -0,0 +1,52 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = musa_acuminata_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +musa_acuminata_SRS373715 = resequencing + +[musa_acuminata_SRS373715] +source_name = Ensete ventricosum WGS +description = SRS373715: Whole genome shotgun sequencing of Ensete ventricosum with Illumina HiSeq +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/macuminata/SRS373715.bam +source_type = bam +display = off + + +[ENSEMBL_INTERNAL_VCF_SOURCES] +musa_acuminata_SRS373715_variation = variation + +[musa_acuminata_SRS373715_variation] +source_name = Variations based on Ensete ventricosum WGS +description = SNPs and InDels derived from SRS373715, the whole genome shotgun sequencing of Ensete ventricosum with Illumina HiSeq. SNPs were called using BWA (0.6.1) and SAMtools (0.1.18) with default parameters for alignment, calling and filtering steps. +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/vcf/macuminata/SRS373715.vcf.gz +source_type = vcf +display = off + + + diff --git a/gramene/conf/ini-files.bad/Ostreococcus_lucimarinus.ini b/gramene/conf/ini-files.bad/Ostreococcus_lucimarinus.ini new file mode 100755 index 00000000..4cc9c7d1 --- /dev/null +++ b/gramene/conf/ini-files.bad/Ostreococcus_lucimarinus.ini @@ -0,0 +1,26 @@ +[general] +SPECIES_RELEASE_VERSION = 1 +ENSEMBL_GENOME_SIZE = 0.2 + +[databases] +DATABASE_USERDATA = ostreococcus_lucimarinus_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Physcomitrella_patens.ini b/gramene/conf/ini-files.bad/Physcomitrella_patens.ini new file mode 100755 index 00000000..7ba131c7 --- /dev/null +++ b/gramene/conf/ini-files.bad/Physcomitrella_patens.ini @@ -0,0 +1,40 @@ +[general] +SPECIES_RELEASE_VERSION = 11 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = physcomitrella_patens_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/physcomitrella/?name=chr###CHR###%3A###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files.bad/Plants_rhodophyta1.ini b/gramene/conf/ini-files.bad/Plants_rhodophyta1.ini new file mode 100644 index 00000000..e3afec07 --- /dev/null +++ b/gramene/conf/ini-files.bad/Plants_rhodophyta1.ini @@ -0,0 +1,25 @@ +[general] +COLLECTION_DEFAULT_FAVOURITES = +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_collection_core_%_% +#DATABASE_USERDATA = plants_rhodophyta1_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini +; +; [ENSEMBL_EXTERNAL_INDEXERS] +; ; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files.bad/Populus_trichocarpa.ini b/gramene/conf/ini-files.bad/Populus_trichocarpa.ini new file mode 100755 index 00000000..91c25916 --- /dev/null +++ b/gramene/conf/ini-files.bad/Populus_trichocarpa.ini @@ -0,0 +1,38 @@ +[general] +SPECIES_RELEASE_VERSION = 20 + +ASSEMBLY_CONVERTER_FILES = [JGI2.0_to_jgi2004 jgi2004_to_JGI2.0] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_FUNCGEN = %_funcgen_%_% +DATABASE_USERDATA = populus_trichocarpa_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/poplar/?name=scaffold_###CHR###%3A###START###..###END### +GRAMENE_PATHWAY = http://pathway.gramene.org/POPLAR/NEW-IMAGE?type=REACTION&object=###ID### + + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Prunus_persica.ini b/gramene/conf/ini-files.bad/Prunus_persica.ini new file mode 100755 index 00000000..9d6bbf82 --- /dev/null +++ b/gramene/conf/ini-files.bad/Prunus_persica.ini @@ -0,0 +1,30 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = prunus_persica_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + diff --git a/gramene/conf/ini-files.bad/Selaginella_moellendorffii.ini b/gramene/conf/ini-files.bad/Selaginella_moellendorffii.ini new file mode 100755 index 00000000..aad52860 --- /dev/null +++ b/gramene/conf/ini-files.bad/Selaginella_moellendorffii.ini @@ -0,0 +1,37 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_USERDATA = selaginella_moellendorffii_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files.bad/Setaria_italica.ini b/gramene/conf/ini-files.bad/Setaria_italica.ini new file mode 100755 index 00000000..ef548668 --- /dev/null +++ b/gramene/conf/ini-files.bad/Setaria_italica.ini @@ -0,0 +1,31 @@ +[general] +SPECIES_RELEASE_VERSION = 21 +HIDDEN_COORDSYS = [ chunk ] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = Setaria_italica_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/brachy/?name=chr###CHR###%3A###START###..###END### + + diff --git a/gramene/conf/ini-files.bad/Solanum_lycopersicum.ini b/gramene/conf/ini-files.bad/Solanum_lycopersicum.ini new file mode 100755 index 00000000..0c127685 --- /dev/null +++ b/gramene/conf/ini-files.bad/Solanum_lycopersicum.ini @@ -0,0 +1,34 @@ +[general] +SPECIES_RELEASE_VERSION = 250 + +ASSEMBLY_CONVERTER_FILES = [SL2.40_to_SL2.50 SL2.50_to_SL2.40] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_VARIATION = %_variation_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = solanum_lycopersicum_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] +GRAMENE_PATHWAY = http://pathway.gramene.org/LYCO/NEW-IMAGE?type=REACTION&object=###ID### +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/brachy/?name=chr###CHR###%3A###START###..###END### + + diff --git a/gramene/conf/ini-files.bad/Solanum_tuberosum.ini b/gramene/conf/ini-files.bad/Solanum_tuberosum.ini new file mode 100755 index 00000000..e20c13f8 --- /dev/null +++ b/gramene/conf/ini-files.bad/Solanum_tuberosum.ini @@ -0,0 +1,164 @@ +[general] +SPECIES_RELEASE_VERSION = 4 +HIDDEN_COORDSYS = [ split ] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% +DATABASE_USERDATA = solanum_tuberosum_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] +GRAMENE_PATHWAY = http://pathway.gramene.org/POTATO/NEW-IMAGE?type=REACTION&object=###ID### + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + + +[ENSEMBL_INTERNAL_BAM_SOURCES] + +solanum_tuberosum_ERS023593 = functional +solanum_tuberosum_ERS023594 = functional +solanum_tuberosum_ERS023595 = functional +solanum_tuberosum_ERS023596 = functional +solanum_tuberosum_ERS023597 = functional +solanum_tuberosum_ERS023598 = functional +solanum_tuberosum_ERS023599 = functional +solanum_tuberosum_ERS023600 = functional +solanum_tuberosum_ERS023601 = functional +solanum_tuberosum_ERS023602 = functional +solanum_tuberosum_ERS023603 = functional +solanum_tuberosum_ERS023604 = functional +solanum_tuberosum_ERS023605 = functional +solanum_tuberosum_ERS023606 = functional +solanum_tuberosum_ERS023607 = functional +solanum_tuberosum_ERS023608 = functional + +[solanum_tuberosum_ERS023593] +source_name = ERS023593: Solanum tuberosum; Mature Tuber +description = ERS023593: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023593.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023594] +source_name = ERS023594: Solanum tuberosum; Tuber sprout +description = ERS023594: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer II sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023594.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023595] +source_name = ERS023595: Solanum tuberosum; Young Tuber +description = ERS023595: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023595.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023596] +source_name = ERS023596: Solanum tuberosum; Mature Tuber +description = ERS023596: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023596.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023597] +source_name = ERS023597: Solanum tuberosum; Leaf +description = ERS023597: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023597.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023598] +source_name = ERS023598: Solanum tuberosum; Stamen +description = ERS023598: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023598.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023599] +source_name = ERS023599: Solanum tuberosum; Flower +description = ERS023599: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023599.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023600] +source_name = ERS023600: Solanum tuberosum; Stolon +description = ERS023600: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023600.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023601] +source_name = ERS023601: Solanum tuberosum; Petiole +description = ERS023601: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023601.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023602] +source_name = ERS023602: Solanum tuberosum; Tuber cortex +description = ERS023602: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023602.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023603] +source_name = ERS023603: Solanum tuberosum; Root +description = ERS023603: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023603.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023604] +source_name = ERS023604: Solanum tuberosum; Water stressed leaf +description = ERS023604: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023604.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023605] +source_name = ERS023605: Solanum tuberosum; Tuber peel +description = ERS023605: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023605.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023606] +source_name = ERS023606: Solanum tuberosum; Shoot apex +description = ERS023606: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023606.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023607] +source_name = ERS023607: Solanum tuberosum; Stem +description = ERS023607: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023607.bam +source_type = rnaseq +display = off + +[solanum_tuberosum_ERS023608] +source_name = ERS023608: Solanum tuberosum; Whole in vitro plant +description = ERS023608: Transcriptome Analysis of the potato (genotype RH89-039-16) with Illumina Genome Analyzer sequencing +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/potato/ERS023608.bam +source_type = rnaseq +display = off + diff --git a/gramene/conf/ini-files.bad/Theobroma_cacao.ini b/gramene/conf/ini-files.bad/Theobroma_cacao.ini new file mode 100755 index 00000000..3f52f150 --- /dev/null +++ b/gramene/conf/ini-files.bad/Theobroma_cacao.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_USERDATA = theobroma_cacao_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Trifolium_pratense.ini b/gramene/conf/ini-files.bad/Trifolium_pratense.ini new file mode 100755 index 00000000..3ef569da --- /dev/null +++ b/gramene/conf/ini-files.bad/Trifolium_pratense.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +#DATABASE_USERDATA = trifolium_pratense_userdata +DATABASE_CORE = %_core_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files.bad/Triticum_aestivum.ini b/gramene/conf/ini-files.bad/Triticum_aestivum.ini new file mode 100755 index 00000000..92fc142b --- /dev/null +++ b/gramene/conf/ini-files.bad/Triticum_aestivum.ini @@ -0,0 +1,224 @@ +[general] +SPECIES_RELEASE_VERSION = 3 +; HIDDEN_COORDSYS = [ wheat_ena chromosome ] +BIGWIG_HEIGHT = 0.5 + +ASSEMBLY_CONVERTER_FILES = [IWGSC1_to_TGACv1 TGACv1_to_IWGSC1 IWGSC_3B_to_TGACv1 TGACv1_to_IWGSC_3B] + +HAS_INTRASPECIES_ALIGNMENTS = 1 + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_VARIATION = %_variation_%_% +DATABASE_OTHERFEATURES = %_otherfeatures_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] +;EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/brachy/?name=chr###CHR###%3A###START###..###END### + + +[SAMPLE_DATA] +; +;[ENSEMBL_INTERNAL_BAM_SOURCES] +;ERP004505_WE_10DPA = functional +;ERP004505_WE_20DPA = functional +;ERP004505_AL_20DPA = functional +;ERP004505_SE_20DPA = functional +;ERP004505_SE_30DPA = functional +;ERP004505_AL_SE_30DPA = functional +;ERP004505_TC_20DPA = functional +; +;ERP004714_Grain = functional +;ERP004714_Leaf = functional +;ERP004714_Root = functional +;ERP004714_Spike = functional +;ERP004714_Stem = functional +; +;TGAC_Leaf = functional +;TGAC_Root = functional +;TGAC_Seed = functional +;TGAC_Seedling = functional +;TGAC_Spike = functional +;TGAC_Stem = functional +; +; +; +[ENSEMBL_INTERNAL_BED_SOURCES] +S12_METH = functional +S27_METH = functional +PROBE_COORDS = functional + +[S27_METH] +source_name = Methylation sites at 27 degrees +description = Methylation sites at 27 degrees +source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bed/S27_Methylation.bed +source_type = bed +display = labels +;colour = +; +[S12_METH] +source_name = Methylation sites at 12 degrees +description = Methylation sites at 12 degrees +source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bed/S12_Methylation.bed +source_type = bed +display = labels +colour = +; +[PROBE_COORDS] +source_name = Pre-methylation probe coordinates for TGACv1 +description = Potential methylation capture sites +source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bed/Probe_coordinates_on_TGAC.bed +source_type = bed +display = labels +colour = blue +; +; +; +; +;[ERP004505_WE_10DPA] +;source_name = Whole endosperm 10 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/WE_10DPA/Aligned.canonical-rename1.bam +;source_type = bam +;display = off +;external = +; +;[ERP004505_WE_20DPA] +;source_name = Whole endosperm 20 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/WE_20DPA/Aligned.canonical-rename4.bam +;source_type = bam +;display = off +;external = +; +;[ERP004505_AL_20DPA] +;source_name = Aleuron layer 20 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/AL_20DPA/Aligned.canonical-rename2.bam +;source_type = bam +;display = off +; +;[ERP004505_SE_20DPA] +;source_name = Starchy endosperm 20 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/SE_20DPA/Aligned.canonical-rename5.bam +;source_type = bam +;display = off +; +;[ERP004505_SE_30DPA] +;source_name = Starchy endosperm 30 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/SE_30DPA/Aligned.canonical-rename6.bam +;source_type = bam +;display = off +; +;[ERP004505_AL_SE_30DPA] +;source_name = Aleuron layer and starchy endosperm 30 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/AL_SE_30DPA/Aligned.canonical-rename3.bam +;source_type = bam +;display = off +; +;[ERP004505_TC_20DPA] +;source_name = Transfer cells 20 days post anthesis +;description = Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal. Study ERP004505. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004505/TC_20DPA/Aligned.canonical-rename7.bam +;source_type = bam +;display = off +; +; +; +;[ERP004714_Grain] +;source_name = 3B Grain +;description = Whole transcriptome sequencing of wheat 3B chromosome. Study ERP004714. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004714/Grain/Aligned.canonical-rename-Grain.bam +;source_type = bam +;display = off +; +;[ERP004714_Leaf] +;source_name = 3B Leaf +;description = Whole transcriptome sequencing of wheat 3B chromosome. Study ERP004714. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004714/Leaf/Aligned.canonical-rename-Leaf.bam +;source_type = bam +;display = off +; +;[ERP004714_Root] +;source_name = 3B Root +;description = Whole transcriptome sequencing of wheat 3B chromosome. Study ERP004714. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004714/Root/Aligned.canonical-rename-Root.bam +;source_type = bam +;display = off +; +;[ERP004714_Spike] +;source_name = 3B Spike +;description = Whole transcriptome sequencing of wheat 3B chromosome. Study ERP004714. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004714/Spike/Aligned.canonical-rename-Spike.bam +;source_type = bam +;display = off +; +;[ERP004714_Stem] +;source_name = 3B Stem +;description = Whole transcriptome sequencing of wheat 3B chromosome. Study ERP004714. +;source_url = ftp://ftp.ensemblgenomes.org/pub/plants/pre/bam/triticum_aestivum/ERP004714/Stem/Aligned.canonical-rename-Stem.bam +;source_type = bam +;display = off +; +;[TGAC_Leaf] +;source_name = Leaf +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Leaf/Aligned.canonical-rename-TGAC-Leaf.bam +;source_type = bam +;display = on +; +;[TGAC_Root] +;source_name = Root +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Root/Aligned.canonical-rename-TGAC-Root.bam +;source_type = bam +;display = off +; +;[TGAC_Seed] +;source_name = Seed +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Seed/Aligned.canonical-rename-TGAC-Seed.bam +;source_type = bam +;display = off +; +;[TGAC_Seedling] +;source_name = Seedling +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Seedling/Aligned.canonical-rename-TGAC-Seedling.bam +;source_type = bam +;display = off +; +;[TGAC_Spike] +;source_name = Spike +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Spike/Aligned.canonical-rename-TGAC-Spike.bam +;source_type = bam +;display = off +; +;[TGAC_Stem] +;source_name = Stem +;description = Whole transcriptome sequencing. +;source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/Wheat/.ZkA4CA/TGAC/Stem/Aligned.canonical-rename-TGAC-Stem.bam +;source_type = bam +;display = off +; diff --git a/gramene/conf/ini-files.bad/Triticum_urartu.ini b/gramene/conf/ini-files.bad/Triticum_urartu.ini new file mode 100755 index 00000000..6c945a3c --- /dev/null +++ b/gramene/conf/ini-files.bad/Triticum_urartu.ini @@ -0,0 +1,52 @@ +[general] +SPECIES_RELEASE_VERSION=1 +BIGWIG_HEIGHT = 0.5 + +[databases] +DATABASE_CORE=%_core_%_% +DATABASE_OTHERFEATURES=%_otherfeatures_%_% +DATABASE_USERDATA=triticum_urartu_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_INTERNAL_BAM_SOURCES] +Lastz_Wheat_A_subsequences_alignments = wheat_assembly +Lastz_Wheat_cap3_subsequences_alignments = wheat_assembly + +[Lastz_Wheat_A_subsequences_alignments] +source_name = Brenchley et al. T. urartu A sequences +description = Lastz Alignments of the T. aestivum A sequences from Brenchley et al. against T. urartu +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/turartu/LastZ_Wheat_Genome_A.turartu.bam +source_type = bam +display = off + +[Lastz_Wheat_cap3_subsequences_alignments] +source_name = Brenchley et al. T. urartu cap3 sequences +description = Lastz Alignments of the T. aestivum cap3 sequences from Brenchley et al. against T. urartu +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bam/wheat/turartu/LastZ_Wheat_Genome_cap3.turartu.bam +source_type = bam +display = off + +[ENSEMBL_INTERNAL_BIGWIG_SOURCES] +SRS072842 = wheat_transcriptomics + +[SRS072842] +source_name = Triticum urartu +description = Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors (Study SRP002455), aligned using Star software +source_url = ftp://ftp.ensemblgenomes.org/pub/misc_data/bigwig/turartu/SRS072842.bw +source_type = bigWig +display = off diff --git a/gramene/conf/ini-files.bad/Vitis_vinifera.ini b/gramene/conf/ini-files.bad/Vitis_vinifera.ini new file mode 100755 index 00000000..1c7ae372 --- /dev/null +++ b/gramene/conf/ini-files.bad/Vitis_vinifera.ini @@ -0,0 +1,40 @@ +[general] +SPECIES_RELEASE_VERSION = 3 + +ASSEMBLY_CONVERTER_FILES = [8X_to_IGGP_12x IGGP_12x_to_8X] + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_VARIATION = %_variation_%_% +DATABASE_FUNCGEN = %_funcgen_%_% +DATABASE_USERDATA = vitis_vinifera_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/grape/?name=chr###CHR###%3A###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files/Zea_mays.ini.v3 b/gramene/conf/ini-files.bad/Zea_mays.ini old mode 100644 new mode 100755 similarity index 65% rename from gramene/conf/ini-files/Zea_mays.ini.v3 rename to gramene/conf/ini-files.bad/Zea_mays.ini index 36d1eba4..ea336f69 --- a/gramene/conf/ini-files/Zea_mays.ini.v3 +++ b/gramene/conf/ini-files.bad/Zea_mays.ini @@ -1,28 +1,61 @@ -#[general] -#DATABASE_HOST = cabot.cshl.edu -#SPECIES_RELEASE_VERSION = 6 +[general] +SPECIES_RELEASE_VERSION = 7 + +ASSEMBLY_CONVERTER_FILES = [AGPv2_to_AGPv4 AGPv3_to_AGPv4 AGPv4_to_AGPv2 AGPv4_to_AGPv3] -[ENSEMBL_INTERNAL_BAM_SOURCES] -rpd1_unique = mrna_prot -wt_unique = mrna_prot +THR_ASSEMBLY_PARAM = ASSEMBLY_VERSION + +[databases] +DATABASE_CORE = %_core_%_% +DATABASE_OTHERFEATURES=%_otherfeatures_%_% +DATABASE_VARIATION = %_variation_%_% +DATABASE_FUNCGEN = %_funcgen_%_% +DATABASE_USERDATA = zea_mays_userdata + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/maize/?name=chr###CHR###%3A###START###..###END### +GRAMENE_PATHWAY = http://pathway.gramene.org/MAIZE/NEW-IMAGE?type=REACTION&object=###ID### +MAIZEGDB_GENE = http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=###ID### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] -[rpd1_unique] -source_name = rpd1_nascent_RNA_unique -description = rpd1 nascent RNA unique hits -source_url = http://brie.cshl.edu/data/Zea_mays/RNAseq/Talbot/rpd1_unique.bam -source_type = bam -display = normal -[wt_unique] -source_name = wt_nascent_RNA_unique -description = wt nascent RNA unique hits -source_url = http://brie.cshl.edu/data/Zea_mays/RNAseq/Talbot/wt_unique.bam +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + + +[ENSEMBL_INTERNAL_BAM_SOURCES] + +[B73_1_RNAseq] +source_name = RNAseq +description = testing RNAseq BAM +source_url = http://brie.cshl.edu/data/Zea_mays/RNAseq/B73_1_sequence.accepted_hits.bam source_type = bam -display = normal +display = off [ENSEMBL_INTERNAL_BIGBED_SOURCES] HClncRNAs = mrna_prot -MAKERP = gene_transcript [HClncRNAs] source_name = HC_lncRNAs @@ -30,12 +63,6 @@ description = High Confidence lncRNAs source_url = http://brie.cshl.edu/data/Zea_mays/HC-lncRNAs.bb source_type = bigbed -[MAKERP] -source_name = MAKER-P_genes -description = Gene annotations contributed by developers of the MAKER-P annotation system -source_url = http://brie.cshl.edu/data/Zea_mays/6a.bb -source_type = bigbed - [ENSEMBL_INTERNAL_BIGWIG_SOURCES] B73_CpG_ratio = functional B73_CpG_coverage = functional @@ -51,56 +78,56 @@ source_name = B73_CpG_ratio description = B73 CpG methylation ratio from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/B73_CpG_ratio.bw source_type = bigwig -display = wiggle +display = off [B73_CpG_coverage] source_name = B73_CpG_coverage description = B73 CpG methylation coverage from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/B73_CpG_coverage.bw source_type = bigwig -display = wiggle +display = off [B73_CHG_ratio] source_name = B73_CHG_ratio description = B73 CHG methylation ratio from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/B73_CHG_ratio.bw source_type = bigwig -display = wiggle +display = off [B73_CHG_coverage] source_name = B73_CHG_coverage description = B73 CHG methylation coverage from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/B73_CHG_coverage.bw source_type = bigwig -display = wiggle +display = off [MO17_CpG_ratio] source_name = MO17_CpG_ratio description = MO17 CpG methylation ratio from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/MO17_CpG_ratio.bw source_type = bigwig -display = wiggle +display = off [MO17_CpG_coverage] source_name = MO17_CpG_coverage description = MO17 CpG methylation coverage from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/MO17_CpG_coverage.bw source_type = bigwig -display = wiggle +display = off [MO17_CHG_ratio] source_name = MO17_CHG_ratio description = MO17 CHG methylation ratio from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/MO17_CHG_ratio.bw source_type = bigwig -display = wiggle +display = off [MO17_CHG_coverage] source_name = MO17_CHG_coverage description = MO17 CHG methylation coverage from bisulfite sequencing source_url = http://brie.cshl.edu/data/Zea_mays/methylome/MO17_CHG_coverage.bw source_type = bigwig -display = wiggle +display = off [ENSEMBL_INTERNAL_DAS_SOURCES] MAKERP = gene_transcript diff --git a/gramene/conf/ini-files/Arabidopsis_thaliana.ini b/gramene/conf/ini-files/Arabidopsis_thaliana.ini new file mode 100755 index 00000000..48a81c83 --- /dev/null +++ b/gramene/conf/ini-files/Arabidopsis_thaliana.ini @@ -0,0 +1,36 @@ +[general] +SPECIES_RELEASE_VERSION = 11 +ENSEMBL_GENOME_SIZE = 0.2 + + +[databases] +DATABASE_CORE = arabidopsis_thaliana_core_2_87_11 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome +EGB_GB = TAIR + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +ARAPORT_GENE = http://www.araport.org/locus/###ID### +GRAMENE_PATHWAY = http://pathway.gramene.org/ARA/NEW-IMAGE?type=REACTION&object=###ID### +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/arabi/?name=Chr###CHR###%3A###START###..###END### +EGB_GB = http://gbrowse.arabidopsis.org/cgi-bin/gb2/gbrowse/arabidopsis/?name=Chr###CHR###%3A###START###..###END### + +DGVA = +#http://gbrowse.arabidopsis.org/cgi-bin/gbrowse/arabidopsis/?name=chr1:316000..338000 +#http://www.phytozome.net/cgi-bin/gbrowse/arabi/?name=Chr3:5554317..5594317 + + +[ENSEMBL_SPECIES_SITE] + + diff --git a/gramene/conf/ini-files/BK/Oryza_sativa.ini.indeltracks b/gramene/conf/ini-files/BK/Oryza_sativa.ini.indeltracks new file mode 100755 index 00000000..c6b6558d --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa.ini.indeltracks @@ -0,0 +1,321 @@ +[general] +SPECIES_RELEASE_VERSION = 7 + +[databases] +DATABASE_CORE = oryza_sativa_core_7_87_7 +#oryza_sativa_core_5_105_7 +# oryza_sativa_core_2_87_7 is the irgsp genes, not cshl genes +DATABASE_VARIATION = oryza_sativa_variation_5_87_7 +# oryza_sativa_variation_5_87_7: this has Magic 16 IRGSP and MH63 variations 18M and 19M SNPs as well as EVA set with Rice 3K GATK3 +#oryza_sativa_variation_58_93_7 + +#oryza_sativa_variation_2_79_7 contains old variation +#we are using EVA file configed in json + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/rice/?name=Chr###CHR###%3A###START###..###END### +GRAMENE_PATHWAY = http://pathway.gramene.org/RICE/NEW-IMAGE?type=REACTION&object=###ID### +IRGSPV1_GENE = http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=###ID### +IRGSPV1_TRANSCRIPT = http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=###ID### +TIGR_LOCUS = http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=###ID### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +OsjapLeaf = dna_align_cdna +OsjapPanicle = dna_align_cdna +OsjapRoot = dna_align_cdna + +[OsjapLeaf] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; leaf tissue +description = Oryza sativa japonica leaf tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_leaf.tophat.bam +source_type = bam +display = off + +[OsjapPanicle] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; panicle tissue +description = Oryza sativa japonica panicle tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_panicle.tophat.bam +source_type = bam +display = off + +[OsjapRoot] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; root tissue +description = Oryza sativa japonica root tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_root.tophat.bam +source_type = bam +display = off + + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Azucena_INS = variation +Azucena_DEL = variation +MH63RS2_INS = variation +MH63RS2_DEL = variation +Os117425RS1_INS = variation +Os117425RS1_DEL = variation +Os125619RS1_INS = variation +Os125619RS1_DEL = variation +Os125827RS1_INS = variation +Os125827RS1_DEL = variation +Os127518RS1_INS = variation +Os127518RS1_DEL = variation +Os127564RS1_INS = variation +Os127564RS1_DEL = variation +Os127652RS1_INS = variation +Os127652RS1_DEL = variation +Os127742RS1_INS = variation +Os127742RS1_DEL = variation +Os128077RS1_INS = variation +Os128077RS1_DEL = variation +Os132278RS1_INS = variation +Os132278RS1_DEL = variation +Os132424RS1_INS = variation +Os132424RS1_DEL = variation +OsIR64RS1_INS = variation +OsIR64RS1_DEL = variation +OsN22RS2_INS = variation +OsN22RS2_DEL = variation +ZS97RS2_INS = variation +ZS97RS2_DEL = variation + +[Azucena_INS] +source_name = insertionMagic16AzucenaSV +description = structure variation of Azucena against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/AzucenaRS1_SV_ABS.bed +source_type = bed +display = labels + +[Azucena_DEL] +source_name = deletionMagic16AzucenaSV +description = structure variation of Azucena against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/AzucenaRS1_SV_PRE.bed +source_type = bed +display = label +colour = blue + +[MH63RS2_INS] +source_name = insertionMagic16MH63RS2SV +description = structure variation of MH63RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/MH63RS2_SV_ABS.bed +source_type = bed +display = labels + +[MH63RS2_DEL] +source_name = deletionMagic16MH63RS2SV +description = structure variation of MH63RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/MH63RS2_SV_PRE.bed +source_type = bed +display = labels +colour = blue + +[Os117425RS1_INS] +source_name = insertionMagic16Os117425RS1SV +description = structure variation of Os117425RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os117425RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = deletionMagic16Os117425RS1SV +description = structure variation of Os117425RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os117425RS1_SV_PRE.bed +source_type = bed +display = labels +colour = blue + +[Os125619RS1_INS] +source_name = insertionMagic16Os125619RS1SV +description = structure variation of Os125619RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os125619RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = deletionMagic16Os125619RS1SV +description = structure variation of Os125619RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os125619RS1_SV_PRE.bed +source_type = bed +display = labels +colour = blue + +[Os125827RS1_INS] +source_name = insertionMagic16Os125827RS1SV +description = structure variation of Os125827RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os125827RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = deletionMagic16Os125827RS1SV +description = structure variation of Os125827RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os125827RS1_SV_PRE.bed +source_type = bed +display = labels +colour = blue + +[Os127518RS1_INS] +source_name = insertionMagic16Os127518RS1SV +description = structure variation of Os127518RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127518RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = deletionMagic16Os127518RS1SV +description = structure variation of Os127518RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127518RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = insertionMagic16Os127564RS1SV +description = structure variation of Os127564RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127564RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = deletionMagic16Os127564RS1SV +description = structure variation of Os127564RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127564RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = insertionMagic16Os127652RS1SV +description = structure variation of Os127652RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127652RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = deletionMagic16Os127652RS1SV +description = structure variation of Os127652RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127652RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = insertionMagic16Os127742RS1SV +description = structure variation of Os127742RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127742RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = deletionMagic16Os127742RS1SV +description = structure variation of Os127742RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os127742RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = insertionMagic16Os128077RS1SV +description = structure variation of Os128077RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os128077RS1_SV_ABS.bed +source_type = bed +display = labels +colour = blue + +[Os128077RS1_DEL] +source_name = deletionMagic16Os128077RS1SV +description = structure variation of Os128077RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os128077RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = insertionMagic16Os132278RS1SV +description = structure variation of Os132278RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os132278RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = deletionMagic16Os132278RS1SV +description = structure variation of Os132278RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os132278RS1_SV_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = insertionMagic16Os132424RS1SV +description = structure variation of Os132424RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os132424RS1_SV_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = deletionMagic16Os132424RS1SV +description = structure variation of Os132424RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/Os132424RS1_SV_PRE.bed +source_type = bed +display = labels + +[OsIR64RS1_INS] +source_name = insertionMagic16OsIR64RS1SV +description = structure variation of OsIR64RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/OsIR64RS1_SV_ABS.bed +source_type = bed +display = labels + +[OsIR64RS1_DEL] +source_name = deletionMagic16OsIR64RS1SV +description = structure variation of OsIR64RS1 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/OsIR64RS1_SV_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = insertionMagic16OsN22RS2SV +description = structure variation of OsN22RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/OsN22RS2_SV_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = deletionMagic16OsN22RS2SV +description = structure variation of OsN22RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/OsN22RS2_SV_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = insertionMagic16ZS97RS2SV +description = structure variation of ZS97RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/ZS97RS2_SV_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = deletionMagic16ZS97RS2SV +description = structure variation of ZS97RS2 against Nipponbare reference +source_url = http://squam.cshl.edu/data/Magic16_Nip_SV/ZS97RS2_SV_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/BK/Oryza_sativa117425.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa117425.ini.bk new file mode 100755 index 00000000..98bbddea --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa117425.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa117425_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa125619.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa125619.ini.bk new file mode 100755 index 00000000..abc3dcf6 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa125619.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa125619_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa125827.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa125827.ini.bk new file mode 100755 index 00000000..b20ac0ab --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa125827.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa125827_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa127518.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa127518.ini.bk new file mode 100755 index 00000000..44341e05 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa127518.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127518_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa127564.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa127564.ini.bk new file mode 100755 index 00000000..1054f166 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa127564.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127564_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa127652.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa127652.ini.bk new file mode 100755 index 00000000..b18ef077 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa127652.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127652_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa127742.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa127742.ini.bk new file mode 100755 index 00000000..c010cee2 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa127742.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127742_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa128077.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa128077.ini.bk new file mode 100755 index 00000000..1699611c --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa128077.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa128077_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa132278.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa132278.ini.bk new file mode 100755 index 00000000..865e0a2c --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa132278.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa132278_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativa132424.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativa132424.ini.bk new file mode 100755 index 00000000..844bdc96 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativa132424.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa132424_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/BK/Oryza_sativaazucena.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativaazucena.ini.bk new file mode 100755 index 00000000..dbdefebf --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativaazucena.ini.bk @@ -0,0 +1,268 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativaazucena_core_4_87_1 +DATABASE_VARIATION = oryza_sativaazucena_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +MH63RS2_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsIR64RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +MH63RS2_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsIR64RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[MH63RS2_INS] +source_name = MH63RS2_INS +description = structure variation of MH63RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/MH63RS2_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsIR64RS1_INS] +source_name = OsIR64RS1_INS +description = structure variation of OsIR64RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsIR64RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[MH63RS2_DEL] +source_name = MH63RS2_DEL +description = structure variation of MH63RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/MH63RS2_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsIR64RS1_DEL] +source_name = OsIR64RS1_DEL +description = structure variation of OsIR64RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsIR64RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/BK/Oryza_sativair64.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativair64.ini.bk new file mode 100755 index 00000000..f0867d0b --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativair64.ini.bk @@ -0,0 +1,267 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativair64_core_4_87_1 +DATABASE_VARIATION = oryza_sativair64_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +AzucenaRS1_INS = variation +MH63RS2_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +AzucenaRS1_DEL = variation +MH63RS2_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[AzucenaRS1_INS] +source_name = AzucenaRS1_INS +description = structure variation of AzucenaRS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/AzucenaRS1_ABS.bed +source_type = bed +display = labels + +[MH63RS2_INS] +source_name = MH63RS2_INS +description = structure variation of MH63RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/MH63RS2_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[AzucenaRS1_DEL] +source_name = AzucenaRS1_DEL +description = structure variation of AzucenaRS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/AzucenaRS1_PRE.bed +source_type = bed +display = labels + +[MH63RS2_DEL] +source_name = MH63RS2_DEL +description = structure variation of MH63RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/MH63RS2_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/BK/Oryza_sativamh63.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativamh63.ini.bk new file mode 100755 index 00000000..fc06fb06 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativamh63.ini.bk @@ -0,0 +1,269 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativamh63_core_4_87_1 +DATABASE_VARIATION = oryza_sativamh63_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +AzucenaRS1_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsIR64RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +AzucenaRS1_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsIR64RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[AzucenaRS1_INS] +source_name = AzucenaRS1_INS +description = structure variation of AzucenaRS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/AzucenaRS1_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsIR64RS1_INS] +source_name = OsIR64RS1_INS +description = structure variation of OsIR64RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsIR64RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[AzucenaRS1_DEL] +source_name = AzucenaRS1_DEL +description = structure variation of AzucenaRS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/AzucenaRS1_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsIR64RS1_DEL] +source_name = OsIR64RS1_DEL +description = structure variation of OsIR64RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsIR64RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/BK/Oryza_sativazs97.ini.bk b/gramene/conf/ini-files/BK/Oryza_sativazs97.ini.bk new file mode 100755 index 00000000..e5496db3 --- /dev/null +++ b/gramene/conf/ini-files/BK/Oryza_sativazs97.ini.bk @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativazs97_core_4_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Chlamydomonas_reinhardtii.ini b/gramene/conf/ini-files/Chlamydomonas_reinhardtii.ini new file mode 100755 index 00000000..56be73da --- /dev/null +++ b/gramene/conf/ini-files/Chlamydomonas_reinhardtii.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 3 + +[databases] +DATABASE_CORE = chlamydomonas_reinhardtii_core_2_87_3 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Creinhardtii&loc=chromosome_###CHR###:###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/DEFAULTS.ini b/gramene/conf/ini-files/DEFAULTS.ini old mode 100644 new mode 100755 index 84c26c19..300261a1 --- a/gramene/conf/ini-files/DEFAULTS.ini +++ b/gramene/conf/ini-files/DEFAULTS.ini @@ -1,19 +1,21 @@ -###################################################################### -# -# Name: DEFAULTS.ini -# -# Description: This is the Gramene plugin that is layered over -# the following; -# conf/ini-files/DEFAULTS.ini -# eg-plugins/common/conf/ini-files/DEFAULTS.ini -# eg-plugins/plants/conf/ini-files/DEFAULTS.ini -# conf and eg-plugins are both available from Ensembl CVS. -# -###################################################################### - [general] -DATABASE_HOST = colden.cshl.edu; -#colden.cshl.edu +DISPLAY_ONTOLOGIES = [ GO PO TO GRO GR_TAX EFO EO ] +ONTOLOGY_SUBSETS = [ goslim_generic goslim_plant ] +ENSEMBL_GENOME_SIZE = 2 +SPECIES_RELEASE_VERSION = 3 +DEFAULT_FAVOURITES = [ Oryza_sativa Oryza_indica Oryza_indicair8 Oryza_carolina Oryza_glaberrima Oryza_barthii ] +TAXON_ORDER = [ Oryzeae Liliopsida eudicotyledons Lycopodiophyta Bryophyta Chlorophyta Rhodophyta Eukaryota Amborellales] +DATA_SOURCE = EMBL Nucleotide Sequence Database +COMPARA_DB_NAME = Plant Compara +GENOMIC_UNIT = +#plants +ENSEMBL_SITENAME = GrameneOryza +ENSEMBL_FTP_URL = https://ftp.gramene.org/oryza +ENSEMBL_FTP_URL_EG = https://ftp.gramene.org/oryza +#SPECIES_FTP_URL = https://ftp.gramene.org/oryza/release-###VERSION###/###FORMAT###/###SPECIES### +SITE_VERSION = 6 + +DATABASE_HOST = cabot.cshl.edu DATABASE_DBUSER = gramene_web DATABASE_DBPASS = gram3n3 DATABASE_HOST_PORT = 3306 @@ -21,231 +23,50 @@ DATABASE_WRITE_USER = gramene_web DATABASE_WRITE_PASS = gram3n3 SITE_ICON = favicon.ico +#ACKNOWLEDGEMENT = OryzaGramene genome browser is produced in collaboration with Gramene +#ACKNOWLEDGEMENT_URL = http://www.gramene.org -ENSEMBL_SITENAME = Gramene -SITE_VERSION = 58 -ACKNOWLEDGEMENT = Gramene is produced in collaboration with Ensembl Plants - -ENSEMBL_GENOME_SIZE = 2 -#ENSEMBL_BLAST_DATA_PATH = /scratch/ensembl/fasta_55 - -ENSEMBL_FTP_URL = ftp://ftp.gramene.org/pub/gramene -#ftp://ftp.ensemblgenomes.org/pub/plants -TRACKHUB_REGISTRY_URL = http://www.trackhubregistry.org - -# Which search type to use by default -ENSEMBL_DEFAULT_SEARCHCODE = gramene_ensembl - -; -; Web services (Used for DAS etc) -; -ENSEMBL_DAS_SERVERS = [das.sanger.ac.uk] - - +ENSEMBL_REST_URL = https://data.gramene.org/pansite-ensembl/ +TRACKHUB_REGISTRY_URL = https://www.trackhubregistry.org ; ; Species lists on the home page ; -DEFAULT_FAVOURITES = [ Arabidopsis_thaliana Oryza_sativa Triticum_aestivum Hordeum_vulgare Zea_mays Physcomitrella_patens ] -TAXON_ORDER = [ Liliopsida eudicotyledons Lycopodiophyta Bryophyta Chlorophyta Rhodophyta Eukaryota Amborellales] - -#[TAXON_LABEL] -#Oryzeae = Rice -#Liliopsida = Other Monocots -#eudicotyledons = Dicots +# Each taxon in TAXON_ORDER can have a colour defined here (use 0 otherwise). +TAXON_GENETREE_BGCOLOUR = [f0f0ff fff0e0 d0fafa 0 0 d0fad0 lemonchiffon 0 lightblue1 ffe0f0 0 0] +TAXON_GENETREE_FGCOLOUR = [000050 403000 005050 0 0 005000 yellow4 0 royalblue4 tomato3 0 0] [ENSEMBL_STYLE] -#MH_BG = 000000 -#MH_HOVER = ea8e75 -#MH_TAB = dde5e3 -#MH_TAB_ACTIVE = 9abe6c -#MH_LINK = 547b74 -#MH_BG = 9abe6c #cae8a0 +MH_BG = 7EB693 +TAB_TEXT = E5EFE7 +MH_TEXT = ffffff +MH_LINK = ffffff +MH_VISITED = ffffff +MH_HOVER = cc0000 +TINT_BG = E5EFE7 -#MAIN_V_DARK = ece8e8 -#ffffff -#00fa9a -#MAIN_DARK = 6cac84 -#MAIN_MEDIUM = add1ba -#MAIN_LIGHT = deede4 -#MAIN_V_LIGHT = eff6f1 - -#CONTRAST_DARK = ffcc66 -#CONTRAST_MEDIUM = ffeecc -#CONTRAST_LIGHT = fff7e6 - -SITE_LOGO_ALT = Gramene Home -#SITE_LOGO_HREF = http://www.gramene.org -SITE_LOGO_HREF = http://dev.gramene.org -#SITE_LOGO = gramene_logo_med.png -#SITE_LOGO_WIDTH = 150 -#SITE_LOGO_HEIGHT = 55 - -SITE_LOGO = gramene_logo_small.png +SITE_LOGO = oryza_logo_small.png SITE_LOGO_WIDTH = 100 SITE_LOGO_HEIGHT = 40 +SITE_LOGO_ALT = Gramene Home +SITE_LOGO_HREF = https://oryza.gramene.org GRAPHIC_TTF_PATH = /usr/share/fonts/msttcorefonts/ GRAPHIC_FONT_FIXED = cour GRAPHIC_FONT = cour -GRAPHIC_FONTSIZE = 8 +GRAPHIC_FONTSIZE = 8 -[ENSEMBL_EXTERNAL_DATABASES] -EMBL = WEBSRS -EMBLNEW = WEBSRS -SPTREMBL = WEBSRS -TREMBLNEW = WEBSRS -SWIR = WEBSRS -SWISSPROT = WEBSRS -TREMBL = WEBSRS -UNIPROT/SPTREMBL = WEBSRS -UNIPROT/SWISSPROT = WEBSRS -UNIPROT/VARSPLIC = WEBSRS -UNIGENE = WEBSRS -PFAM = WEBSRS -PUBLIC = WEBSRS -REFSEQ = WEBSRS -DEFAULT = WEBSRS [ENSEMBL_EXTERNAL_URLS] -# Gramene-override -SPECIES_FTP_URL = ftp://ftp.gramene.org/pub/gramene/release-###VERSION###/###FORMAT###/###SPECIES### -GO = /db/ontology/search_term?id=###ID### -GOTERMNAME = /db/ontology/search?query=###ID###&ontology_type=GO -GOEVIDENCECODE = /plant_ontology/evidence_codes.html####ID### -SRS_FALLBACK = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val='###ID###' - -REFSEQ_DNA = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=###ID### -REFSEQ = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=###ID### -REFSEQ_PEPTIDE = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=###ID### -REFSEQPROTEIN = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=###ID### -#UNIPROT/SPTREMBL = /db/protein/protein_search?acc=###ID### -#UNIPROT/SWISSPROT = http://www.ebi.uniprot.org/entry/###ID### - - -# Gramene-specific -PO = /db/ontology/search_term?id=###ID### -GRAMENE_MARKER = /db/markers/marker_view?marker_name=###ID### -GRAMENE_MARKERSDB = /db/markers/marker_view?marker_name=###ID### -GRAMENE_SPECIES_MARKER = /db/markers/marker_view?marker_name=###ID###&species=###SP### -GRAMENE_MARKERSDB_EST = /db/markers/marker_view?marker_name=###ID### -GRAMENE_MARKERSDB_MRNA = /db/markers/marker_view?marker_name=###ID### -PLANTGDB_PUT = /db/markers/marker_view?marker_name=###ID### -KOME = /db/markers/marker_view?marker_name=###ID### -BGI_EST_CLUSTER = /db/markers/marker_view?marker_name=###ID### -LGBPRATT_EST_CLUSTER = /db/markers/marker_view?marker_name=###ID### -ENTREZ_NUCLEOTIDE = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=###ID### -ENTREZ_NUC_QUERY = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&term=###ID### -#PLANTGDB = http://www.plantgdb.org/data.php?Seq_ID=###ID### -PLANTGDB = http://www.plantgdb.org/search/display/data.php?Seq_ID=###ID### -TIGR_GENEINDEX = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?tc=###ID###&species=Rice -TIGR_GI_RICE = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?species=Rice&tc=###ID### -TIGR_GI_BARLEY = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?species=Barley&tc=###ID### -TIGR_GI_MAIZE = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?species=Maize&tc=###ID### -TIGR_GI_SORGHUM = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?species=Sorghum&tc=###ID### -TIGR_GI_WHEAT = http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?species=Wheat&tc=###ID### -TIGR_AZM_MAIZE = http://www.tigr.org/tigr-scripts/tgi/asm_report.pl?seqid=###ID###&species=zmg -ORION_CREDIT = http://www.gramene.org/Orion_link.html -PRATT_ESTCLUSTER = http://www.fungen.org:8080/externalDataLink/entry.jsp?contigIDctgMagicSeqID=###ID###&submit_button=Submit -PRATT_EST = http://www.fungen.org:8080/externalDataLink/entry.jsp?GBAccessNum=###ID### -BGI_HOME = http://btn.genomics.org.cn:8080/rice/ -KOME_CDNA = http://cdna01.dna.affrc.go.jp/cgi-bin/cDNA/Annotate_clone_list.cgi?select_cluster=DDBJ+accession&text1=###ID###&seni_flg=1 -BARLEYBASE = http://www.barleybase.org/barley1contig.php?exemplar=###ID### -MAIZEGDB_OVERGO = http://www.maizegdb.org/cgi-bin/displayovergoresults.cgi?term=###ID### -MAIZEGDB_EST = http://www.maizegdb.org/cgi-bin/displayestseqresults.cgi?term=###ID### -MAIZEGDB_MARKER = http://www.maizegdb.org/cgi-bin/anythingsearch.cgi?term=###ID### -GRAINGENES_EST = http://www.graingenes.org/cgi-bin/WebAce/webace?db=graingenes&class=Sequence&object=###ID###&display=text&.submit=show+object%28s%29&Condition= -AFFYMETRIX_FINDER = https://www.affymetrix.com/products/arrays/array_finder/array_finder_wait.jsp?keyword=###ID### -AFFYMETRIX_SUPPORT = http://www.affymetrix.com/support/technical/byproduct.affx?product=###ID### - -#PLEXDB links -WHEATPLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Wheat&exemplar=###ID### -#old link http://www.plexdb.org/modules.php?name=PD_probeset&page=annotation.php&genechip=Wheat&exemplar=###ID### -RICEPLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Rice57k&exemplar=###ID### -# old link http://www.plexdb.org/modules.php?name=PD_probeset&page=contig_rice57k.php&exemplar=###ID### -BARLEYPLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Barley1&exemplar=###ID### -# old link http://www.plexdb.org/modules.php?name=PD_probeset&page=barley1contig.php&exemplar=###ID### -MAIZEPLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize18k&exemplar=###ID### -# old link http://www.plexdb.org/modules.php?name=PD_probeset&page=contig_maize18k.php&exemplar=###ID### -SUGARCANEPLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=sugarcane8k&exemplar=###ID### -# old link http://www.plexdb.org/modules//PD_probeset/probealign_sugarcane8k.php?exemplar=Choose%20one&exemplartext=###ID###&ProbeImageWidth=1000 -MAIZECORNCHIP0PLEX = http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize8k&exemplar=###ID### -# old link http://www.plexdb.org/modules//PD_probeset/probealign_maize8k.php?exemplar=Choose%20one&exemplartext=###ID###&ProbeImageWidth=1000 - -BARLEYPLEXEXPR = http://www.plexdb.org/modules/PD_probeset/expressionplot.php?Probeset_name=###ID###&chipdesign=Barley1 -MAIZECORNCHIP0PLEXEXPR = http://www.plexdb.org/modules/PD_probeset/expressionplot.php?Probeset_name=###ID###&chipdesign=Cornchip0 -WHEATPLEXEXPR = http://www.plexdb.org/modules/PD_probeset/expressionplot.php?Probeset_name=###ID###&chipdesign=Wheat - -RICEARRAY = http://www.ricearray.org/tigr-scripts/ricearray/search/search_basic.pl?result_type=result_html&search_type=search_match&search_section=search_tigr_id&search_term=###ID### -RICEMPSS = http://mpss.udel.edu/rice/Signature.php?tagName=###ID### -IRGSP_GENE = http://rapdb.dna.affrc.go.jp/cgi-bin/gbrowse_details/IRGSP40?name=###ID###;class=locus_id -TIGR_LOCUS = http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=###ID### -TIGR_LOCUS_MODEL = http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=###ID### -ENTREZPRO = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=###ID### -#UNIPROT = http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=###ID### -UNIPROT = http://us.expasy.org/cgi-bin/niceprot.pl?###ID### -SPTREMBL = /db/protein/protein_search?acc=###ID### -GRAMENE_PROT = /db/protein/protein_search?acc=###ID### -GENBANK = http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=###ID### -CMAP = /db/markers/marker_view?marker_name=###ID### -MARKER = /db/markers/marker_view?marker_name=###ID### -CMAP_FEATURE = /db/cmap/feature_search?features=###ID### -#MAIZE_TIGR_ARRAY = http://www.maizearray.org/tigr-scripts/maizearray/virtual_northern/search_result.pl?search_type=search_contains&search_term=###ID###&search_section=oligo_id&submit=Submit -MAIZE_TIGR_ARRAY = http://www.maizearray.org/tigr-scripts/maizearray/search/search_basic.pl?search_type=search_match&search_term=###ID###&search_section=search_tigr_id&show_design=on&show_db=on&result_type=result_html -RICESAGE = http://www.mgosdb.org/cgi-bin/sage/advTagSearchResult.cgi?tag=###ID###&submit=Search -QTL = /db/qtl/qtl_display?qtl_accession_id=###ID### -FEATUREVIEW_DNA = /###SPECIES###/featureview?type=DnaAlignFeature;db=core;id=###ID### -MARKERVIEW = /###SPECIES###/markerview?marker=###ID### -QTL = /db/qtl/qtl_display?qtl_accession_id=###ID### -PANZEA_LOCUS = http://www.panzea.org/db/gateway?page=gene_locus&key=gene_locus&query=###ID### -GRAMENE_PATHWAY = http://pathway.gramene.org/RICE/NEW-IMAGE?type=REACTION&object=###ID### -EC_NUMBER = http://www.genome.ad.jp/dbget-bin/www_bget?ec:###ID### -GRAMENE_GENESDB = /db/genes/search_gene?acc=###ID### -MIRNA_ACCESSION = http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=###ID### -#MIRNA_REGISTRY = http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=###ID### this is in the ensembl defaults.ini - -# Arabidopsis-specific -NASC_GENE_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/geneview?db=core;gene=###ID### -NASC_TRANSCRIPT_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/transview?db=core;transcript=###ID### -TAIR = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene -TAIR_LOCUS = https://apps.araport.org/thalemine/portal.do?externalids=###ID### -TAIR_LOCUS_MODEL = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene - - - -# Fix the GoSearch link. Broken in Ens40, may be fixed in recent versions -GOSEARCH = http://www.ebi.ac.uk/ego/GSearch?query=###ID###&mode=name_syno&ontology=all_ont - -# For use with ENSEMBL_SPECIES_SITE -GRAMENE = /###SPECIES### -MAIZE = http://beta.maizesequence.org/###SPECIES### - -[ENSEMBL_SPECIES_SITE] -Arabidopsis_lyrata = GRAMENE -Arabidopsis_thaliana = GRAMENE -Brachypodium_distachyon = GRAMENE -Oryza_barthii = GRAMENE -Oryza_brachyantha = GRAMENE -Oryza_glaberrima = GRAMENE -Oryza_indica = GRAMENE -Oryza_nivara = GRAMENE -Oryza_punctata = GRAMENE -Oryza_rufipogon = GRAMENE -Oryza_rufipogon3s = GRAMENE -Oryza_sativa = GRAMENE -Oryza_minutabb = GRAMENE -Oryza_minutacc = GRAMENE -Oryza_officinalis = GRAMENE -Oryza_glumaepatula = GRAMENE -Oryza_meridionalis = GRAMENE -Oryza_granulata = GRAMENE -Oryza_longistaminata = GRAMENE -Leersia_perrieri = GRAMENE -Populus_trichocarpa = GRAMENE -Sorghum_bicolor = GRAMENE -Vitis_vinifera = GRAMENE -Zea_mays = MAIZE -Physcomitrella_patens = GRAMENE +GENOMICUSSYNTENY = http://www.genomicus.biologie.ens.fr/genomicus-plants/cgi-bin/search.pl?view=default&query=###ID### +TAIR = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +TAIR_LOCUS = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +TAIR_LOCUS_MODEL = http://arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&name=###ID###&sub_type=gene +NASC_GENE_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/geneview?db=core;gene=###ID### +NASC_TRANSCRIPT_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/transview?db=core;transcript=###ID### +NASC_TRANSLATION_ID = http://atensembl.arabidopsis.info/Arabidopsis_thaliana_TAIR/transview?db=core;peptide=###ID### +TIGRGENEINDEX = http://compbio.dfci.harvard.edu/cgi-bin/tgi/tc_report.pl?gudb=arab&tc=###ID### +MTGD = http://medicago.jcvi.org/MTGD/?q=feature/###ID### diff --git a/gramene/conf/ini-files/Drosophila_melanogaster.ini b/gramene/conf/ini-files/Drosophila_melanogaster.ini new file mode 100755 index 00000000..b475b65b --- /dev/null +++ b/gramene/conf/ini-files/Drosophila_melanogaster.ini @@ -0,0 +1,35 @@ +[general] +SPECIES_RELEASE_VERSION = 6 + + +[databases] +DATABASE_CORE = drosophila_melanogaster_core_2_87_6 +#brachypodium_distachyon_core_52_86_12 +DATABASE_OTHERFEATURES = +#%_otherfeatures_%_% +DATABASE_VARIATION = +#%_variation_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] +GRAMENE_PATHWAY = http://pathway.gramene.org/BRACHY/NEW-IMAGE?type=REACTION&object=###ID### +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/brachy/?name=chr###CHR###%3A###START###..###END### + + diff --git a/gramene/conf/ini-files/Leersia_perrieri.ini b/gramene/conf/ini-files/Leersia_perrieri.ini new file mode 100755 index 00000000..d3d55f3e --- /dev/null +++ b/gramene/conf/ini-files/Leersia_perrieri.ini @@ -0,0 +1,50 @@ +[general] +SPECIES_RELEASE_VERSION = 14 + +[databases] +DATABASE_CORE = leersia_perrieri_core_3_87_14 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +LeerLeaf = dna_align_cdna +LeerPanicle = dna_align_cdna +LeerRoot = dna_align_cdna + +[LeerLeaf] +source_name = Transcript - RNA-Seq - Leersia perrieri; leaf tissue +description = Leersia perrieri leaf tissue RNA reads mapped to the Leersia perrieri assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Leer_leaf.tophat.bam +source_type = bam +display = off + +[LeerPanicle] +source_name = Transcript - RNA-Seq - Leersia perrieri; panicle tissue +description = Leersia perrieri panicle tissue RNA reads mapped to the Leersia perrieri assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Leer_panicle.tophat.bam +source_type = bam +display = off + +[LeerRoot] +source_name = Transcript - RNA-Seq - Leersia perrieri; root tissue +description = Leersia perrieri root tissue RNA reads mapped to the Leersia perrieri assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Leer_root.tophat.bam +source_type = bam +display = off diff --git a/gramene/conf/ini-files/MULTI.ini b/gramene/conf/ini-files/MULTI.ini old mode 100644 new mode 100755 index fa299c28..9170c514 --- a/gramene/conf/ini-files/MULTI.ini +++ b/gramene/conf/ini-files/MULTI.ini @@ -1,93 +1,48 @@ [general] - -[DATABASE_BLAST] -HOST = colden -PORT = 3306 -USER = gramene_web -PASS = gram3n3 +[databases] +DATABASE_WEBSITE = ensembl_website_88 +DATABASE_COMPARA = ensembl_compara_7_87_rice0523 +#RAP-DB gene 2022-09-01 +#ensembl_compara_4_87_rice0222 +#ensembl_compara_4_87_rice1021 #restored o.glaberrima chr8 genes +#ensembl_compara_4_87_rice0921 #missing o.glaberrima chr8 genes +DATABASE_GO = ensemblgenomes_ontology_34_87 +DATABASE_METADATA = ensemblgenomes_info_49 +#use to be ensemblgenomes_info_34, but ensemblgenomes_info_49 is the same and it is used by Sorghumbase config + +DATABASE_COMPARA_PAN_ENSEMBL = +#ensembl_compara_pan_homology_2_% +DATABASE_WEB_TOOLS = ensembl_web_tools_oge +DATABASE_WEB_HIVE = ensembl_web_hive_oge +#DATABASE_PRODUCTION = weix_ensembl_production_% +#DATABASE_ARCHIVE = ensembl_archive_% +DATABASE_SESSION = ensembl_accounts_oge3 +DATABASE_ACCOUNTS = ensembl_accounts_oge3 [DATABASE_SESSION] -HOST = colden -PORT = 3306 -USER = gramene_web -PASS = gram3n3 +HOST = cabot +PORT = 3306 +USER = weix +PASS = warelab [DATABASE_ACCOUNTS] -HOST = colden -PORT = 3306 -USER = gramene_web -PASS = gram3n3 - +HOST = cabot +PORT = 3306 +USER = weix +PASS = warelab -[databases] -DATABASE_WEBSITE = ensembl_website_93 -DATABASE_COMPARA = ensembl_compara_plants_58_% -DATABASE_GO = ensembl_ontology_93 -DATABASE_COMPARA_PAN_ENSEMBL = ensembl_compara_pan_homology_58_% -DATABASE_WEB_TOOLS = ensembl_web_tools_% -DATABASE_WEB_HIVE = ensembl_web_hive_% -DATABASE_PRODUCTION = -#ensembl_production_% -DATABASE_ARCHIVE = ensembl_archive_93 -#DATABASE_METADATA = ensemblgenomes_info_57 -DATABASE_ACCOUNTS = ensembl_accounts_93 -DATABASE_SESSION = ensembl_accounts_93 [DATABASE_WEB_TOOLS] -HOST = colden +HOST = cabot PORT = 3306 -USER = gramene_web -PASS = gram3n3 +USER = weix +PASS = warelab [DATABASE_WEB_HIVE] -HOST = colden +HOST = cabot PORT = 3306 USER = weix PASS = warelab -[ENSEMBL_BLAST_TYPES] -# Key to label pair -# To add another blast, simply add an entry eg. "XYZBLAST = XYZ's blast" in ENSEMBL_BLAST_TYPE -# and then add ENSEMBL_BLAST_METHODS_XYZBLAST and XYZBLAST_DATASOURCES values -ORDER = [NCBIBLAST] -NCBIBLAST = NCBI Blast - -[ENSEMBL_BLAST_QUERY_TYPES] -dna = DNA -peptide = Protein - -[ENSEMBL_BLAST_DB_TYPES] -dna = DNA database -peptide = Protein database - -[ENSEMBL_BLAST_METHODS_NCBIBLAST] -# METHOD = [query_type query_type search_type min_length] -ORDER = [BLASTN BLASTX BLASTP TBLASTN TBLASTX] -BLASTN = [dna dna blastn] -BLASTX = [dna peptide blastx] -BLASTP = [peptide peptide blastp] -TBLASTN = [peptide dna tblastn] -TBLASTX = [dna dna tblastx] - - - -[ENSEMBL_BLAST_DATASOURCES_ALL] -ORDER = [LATESTGP LATESTGP_MASKED LATESTGP_SOFT CDNA_ALL CDNA_ABINITIO PEP_ALL PEP_ABINITIO] ; order preserved -LATESTGP = dna Genomic sequence -LATESTGP_MASKED = dna Genomic sequence (hard masked) -LATESTGP_SOFT = dna Genomic sequence (soft masked) -CDNA_ALL = dna cDNAs (transcripts/splice variants) -CDNA_ABINITIO = dna Ab-initio cDNAs -PEP_ALL = peptide Proteins -PEP_ABINITIO = peptide Ab-initio Peptides - -[ENSEMBL_BLAST_DATASOURCES_BY_TYPE] ; datasources that are valid for all species (modify this in species.ini to remove any invalid datasource) -NCBIBLAST = [LATESTGP LATESTGP_MASKED LATESTGP_SOFT CDNA_ALL CDNA_ABINITIO PEP_ALL PEP_ABINITIO] ; order not preserved - - - - - - diff --git a/gramene/conf/ini-files/Oryza_aus.ini b/gramene/conf/ini-files/Oryza_aus.ini new file mode 100755 index 00000000..c2ed3e76 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_aus.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 2 + + +[databases] +DATABASE_CORE = oryza_aus_core_7_87_2 +#oryza_aus_core_7_87_2 + +DATABASE_VARIATION = oryza_aus_variation_5_87_2 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_barthii.ini b/gramene/conf/ini-files/Oryza_barthii.ini new file mode 100755 index 00000000..47a21f2b --- /dev/null +++ b/gramene/conf/ini-files/Oryza_barthii.ini @@ -0,0 +1,53 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_barthii_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +ObartLeaf = dna_align_cdna +ObartPanicle = dna_align_cdna +ObartRoot = dna_align_cdna + +[ObartLeaf] +source_name = Transcript - RNA-Seq - Oryza barthii; leaf tissue +description = Oryza barthii leaf tissue RNA reads mapped to the Oryza barthii assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Obart_leaf.tophat.bam +source_type = bam +display = off + +[ObartPanicle] +source_name = Transcript - RNA-Seq - Oryza barthii; panicle tissue +description = Oryza barthii panicle tissue RNA reads mapped to the Oryza barthii assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Obart_panicle.tophat.bam +source_type = bam +display = off + +[ObartRoot] +source_name = Transcript - RNA-Seq - Oryza barthii; root tissue +description = Oryza barthii root tissue RNA reads mapped to the Oryza barthii assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Obart_root.tophat.bam +source_type = bam +display = off diff --git a/gramene/conf/ini-files/Oryza_brachyantha.ini b/gramene/conf/ini-files/Oryza_brachyantha.ini new file mode 100755 index 00000000..3a6b5b41 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_brachyantha.ini @@ -0,0 +1,28 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_brachyantha_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/brachy/?name=chr###CHR###%3A###START###..###END### + + diff --git a/gramene/conf/ini-files/Oryza_carolina.ini b/gramene/conf/ini-files/Oryza_carolina.ini new file mode 100755 index 00000000..7bccb784 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_carolina.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_carolina_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_glaberrima.ini b/gramene/conf/ini-files/Oryza_glaberrima.ini new file mode 100755 index 00000000..83eba673 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_glaberrima.ini @@ -0,0 +1,25 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + + +[databases] +DATABASE_CORE = oryza_glaberrima_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files/Oryza_glumaepatula.ini b/gramene/conf/ini-files/Oryza_glumaepatula.ini new file mode 100755 index 00000000..fda8bedb --- /dev/null +++ b/gramene/conf/ini-files/Oryza_glumaepatula.ini @@ -0,0 +1,27 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_glumaepatula_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + diff --git a/gramene/conf/ini-files/Oryza_granulata3s.ini b/gramene/conf/ini-files/Oryza_granulata3s.ini deleted file mode 100644 index 68d079ba..00000000 --- a/gramene/conf/ini-files/Oryza_granulata3s.ini +++ /dev/null @@ -1,62 +0,0 @@ -############################################################################### -# -# Name: Oryza_barthii.ini -# -# Description: Configuration file for Gramene-ensembl -# -############################################################################### - -################# -# GENERAL CONFIG -################# -[general] - -# Assembly info -#ENSEMBL_CHROMOSOMES = [ granulata_3s ] -SPECIES_RELEASE_VERSION = 03 -DB_BUILDER = GRAMENE -AUTHORITY = MAKER-P -SCAFFOLDS = toplevel seqs: - -OGE_FTP_URL = ftp://ftp.gramene.org/pub/gramene/oge/release-current - -################## -# DATABASE CONFIG -# Change the values to the local names of these databases -################## -[databases] - -DATABASE_CORE = %_core_%_% - -#################### -# Configure search example links -#################### - -[SAMPLE_DATA] - -LOCATION_PARAM = -LOCATION_TEXT = - -GENE_PARAM = -GENE_TEXT = - -TRANSCRIPT_PARAM = -TRANSCRIPT_TEXT = - -VARIATION_PARAM = -VARIATION_TEXT = - -#SEARCH_TEXT = Carboxypeptidase - -#################### -# Accept section defaults -#################### - -[ENSEMBL_STYLE] -[ENSEMBL_EXTERNAL_URLS] -[ENSEMBL_SPECIES_SITE] -[ENSEMBL_INTERNAL_DAS_SOURCES] -[SPECIES_DISPLAY_NAME] -[ENSEMBL_EXTERNAL_DATABASES] -[ENSEMBL_EXTERNAL_INDEXERS] - diff --git a/gramene/conf/ini-files/Oryza_indica.ini b/gramene/conf/ini-files/Oryza_indica.ini new file mode 100755 index 00000000..61ef20d5 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_indica.ini @@ -0,0 +1,27 @@ +[general] +SPECIES_RELEASE_VERSION = 3 + + +[databases] +DATABASE_CORE = oryza_indica_core_7_87_3 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files/Oryza_indicair8.ini b/gramene/conf/ini-files/Oryza_indicair8.ini new file mode 100755 index 00000000..e2d7e8a3 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_indicair8.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_indicair8_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_meridionalis.ini b/gramene/conf/ini-files/Oryza_meridionalis.ini new file mode 100755 index 00000000..200ac255 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_meridionalis.ini @@ -0,0 +1,26 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_meridionalis_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + diff --git a/gramene/conf/ini-files/Oryza_minutabb3s.ini b/gramene/conf/ini-files/Oryza_minutabb3s.ini deleted file mode 100644 index d59f7b5d..00000000 --- a/gramene/conf/ini-files/Oryza_minutabb3s.ini +++ /dev/null @@ -1,50 +0,0 @@ -############################################################################### -# -# Name: Oryza_minutaBB.ini -# -# Description: Configuration file for Gramene-ensembl -# -############################################################################### - -################# -# GENERAL CONFIG -################# -[general] - -# Assembly info -#ENSEMBL_CHROMOSOMES = [ minutaBB_3s ] -AUTHORITY = MAKER-P -SPECIES_RELEASE_VERSION = 03 - -OGE_FTP_URL = ftp://ftp.gramene.org/pub/gramene/oge/release-current - -################## -# DATABASE CONFIG -# Change the values to the local names of these databases -################## -[databases] - -DATABASE_CORE = %_core_%_% - - -#################### -# Configure search example links -#################### - -[SAMPLE_DATA] - - -#SEARCH_TEXT = Carboxypeptidase - -#################### -# Accept section defaults -#################### - -[ENSEMBL_STYLE] -[TAXON_LABEL] -[ENSEMBL_EXTERNAL_DATABASES] -[ENSEMBL_EXTERNAL_INDEXERS] -[ENSEMBL_EXTERNAL_URLS] -[ENSEMBL_SPECIES_SITE] -[ENSEMBL_INTERNAL_DAS_SOURCES] - diff --git a/gramene/conf/ini-files/Oryza_minutacc3s.ini b/gramene/conf/ini-files/Oryza_minutacc3s.ini deleted file mode 100644 index c664e955..00000000 --- a/gramene/conf/ini-files/Oryza_minutacc3s.ini +++ /dev/null @@ -1,50 +0,0 @@ -############################################################################### -# -# Name: Oryza_minutaCC.ini -# -# Description: Configuration file for Gramene-ensembl -# -############################################################################### - -################# -# GENERAL CONFIG -################# -[general] - -# Assembly info -#ENSEMBL_CHROMOSOMES = [ minutaCC_3s ] -AUTHORITY = MAKER-P -SPECIES_RELEASE_VERSION = 03 - -OGE_FTP_URL = ftp://ftp.gramene.org/pub/gramene/oge/release-current - -################## -# DATABASE CONFIG -# Change the values to the local names of these databases -################## -[databases] - -DATABASE_CORE = %_core_%_% - - -#################### -# Configure search example links -#################### - -[SAMPLE_DATA] - - -#SEARCH_TEXT = Carboxypeptidase - -#################### -# Accept section defaults -#################### - -[ENSEMBL_STYLE] -[TAXON_LABEL] -[ENSEMBL_EXTERNAL_DATABASES] -[ENSEMBL_EXTERNAL_INDEXERS] -[ENSEMBL_EXTERNAL_URLS] -[ENSEMBL_SPECIES_SITE] -[ENSEMBL_INTERNAL_DAS_SOURCES] - diff --git a/gramene/conf/ini-files/Oryza_nivara.ini b/gramene/conf/ini-files/Oryza_nivara.ini new file mode 100755 index 00000000..c23ec8b7 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_nivara.ini @@ -0,0 +1,26 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_nivara_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + diff --git a/gramene/conf/ini-files/Oryza_officinalis3s.ini b/gramene/conf/ini-files/Oryza_officinalis3s.ini deleted file mode 100644 index 921f482a..00000000 --- a/gramene/conf/ini-files/Oryza_officinalis3s.ini +++ /dev/null @@ -1,51 +0,0 @@ -############################################################################### -# -# Name: Oryza_officinalis.ini -# -# Description: Configuration file for Gramene-ensembl -# -############################################################################### - -################# -# GENERAL CONFIG -################# -[general] - -# Assembly info -#ENSEMBL_CHROMOSOMES = [ officinalis_3s ] -SPECIES_RELEASE_VERSION = 03 -#DB_BUILDER = GRAMENE -AUTHORITY = MAKER-P - -OGE_FTP_URL = ftp://ftp.gramene.org/pub/gramene/oge/release-current - -################## -# DATABASE CONFIG -# Change the values to the local names of these databases -################## -[databases] - -DATABASE_CORE = %_core_%_% - - -#################### -# Configure search example links -#################### - -[SAMPLE_DATA] - - -#SEARCH_TEXT = Carboxypeptidase - -#################### -# Accept section defaults -#################### - -[ENSEMBL_STYLE] -[ENSEMBL_EXTERNAL_URLS] -[ENSEMBL_SPECIES_SITE] -[ENSEMBL_INTERNAL_DAS_SOURCES] -[SPECIES_DISPLAY_NAME] -[ENSEMBL_EXTERNAL_DATABASES] -[ENSEMBL_EXTERNAL_INDEXERS] - diff --git a/gramene/conf/ini-files/Oryza_punctata.ini b/gramene/conf/ini-files/Oryza_punctata.ini new file mode 100755 index 00000000..5b8b3fd6 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_punctata.ini @@ -0,0 +1,28 @@ +[general] +SPECIES_RELEASE_VERSION = 4 + +[databases] +DATABASE_CORE = oryza_punctata_core_7_87_4 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_URLS] + + + diff --git a/gramene/conf/ini-files/Oryza_rufipogon.ini b/gramene/conf/ini-files/Oryza_rufipogon.ini new file mode 100755 index 00000000..57005787 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_rufipogon.ini @@ -0,0 +1,51 @@ +[general] +SPECIES_RELEASE_VERSION = 11 + +[databases] +DATABASE_CORE = oryza_rufipogon_core_7_87_11 + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +OrufiLeaf = dna_align_cdna +OrufiPanicle = dna_align_cdna +OrufiRoot = dna_align_cdna + +[OrufiLeaf] +source_name = Transcript - RNA-Seq - Oryza rufipogon; leaf tissue +description = Oryza rufipogon leaf tissue RNA reads mapped to the Oryza rufipogon assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Orufi_leaf.tophat.bam +source_type = bam +display = off + +[OrufiPanicle] +source_name = Transcript - RNA-Seq - Oryza rufipogon; panicle tissue +description = Oryza rufipogon panicle tissue RNA reads mapped to the Oryza rufipogon assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Orufi_panicle.tophat.bam +source_type = bam +display = off + +[OrufiRoot] +source_name = Transcript - RNA-Seq - Oryza rufipogon; root tissue +description = Oryza rufipogon root tissue RNA reads mapped to the Oryza rufipogon assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Orufi_root.tophat.bam +source_type = bam +display = off + diff --git a/gramene/conf/ini-files/Oryza_sativa.ini b/gramene/conf/ini-files/Oryza_sativa.ini new file mode 100755 index 00000000..16c64a22 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa.ini @@ -0,0 +1,71 @@ +[general] +SPECIES_RELEASE_VERSION = 7 + +[databases] +DATABASE_CORE = oryza_sativa_core_7_87_7 +#oryza_sativa_core_5_105_7 +# oryza_sativa_core_2_87_7 is the irgsp genes, not cshl genes +DATABASE_VARIATION = oryza_sativa_variation_5_87_7 +# oryza_sativa_variation_5_87_7: this has Magic 16 IRGSP and MH63 variations 18M and 19M SNPs as well as EVA set with Rice 3K GATK3 +#oryza_sativa_variation_58_93_7 + +#oryza_sativa_variation_2_79_7 contains old variation +#we are using EVA file configed in json + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/rice/?name=Chr###CHR###%3A###START###..###END### +GRAMENE_PATHWAY = http://pathway.gramene.org/RICE/NEW-IMAGE?type=REACTION&object=###ID### +IRGSPV1_GENE = http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=###ID### +IRGSPV1_TRANSCRIPT = http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=###ID### +TIGR_LOCUS = http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=###ID### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + +[ENSEMBL_INTERNAL_BAM_SOURCES] +OsjapLeaf = dna_align_cdna +OsjapPanicle = dna_align_cdna +OsjapRoot = dna_align_cdna + +[OsjapLeaf] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; leaf tissue +description = Oryza sativa japonica leaf tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_leaf.tophat.bam +source_type = bam +display = off + +[OsjapPanicle] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; panicle tissue +description = Oryza sativa japonica panicle tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_panicle.tophat.bam +source_type = bam +display = off + +[OsjapRoot] +source_name = Transcript - RNA-Seq - Oryza sativa japonica; root tissue +description = Oryza sativa japonica root tissue RNA reads mapped to the Oryza sativa japonica assembly with tophat alignement tool. +source_url = http://brie.cshl.edu/data/OGE_RNA_seq/Osjap_root.tophat.bam +source_type = bam +display = off + diff --git a/gramene/conf/ini-files/Oryza_sativa117425.ini b/gramene/conf/ini-files/Oryza_sativa117425.ini new file mode 100755 index 00000000..3644639e --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa117425.ini @@ -0,0 +1,24 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa117425_core_7_87_1 + +DATABASE_VARIATION = oryza_sativa117425_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa125619.ini b/gramene/conf/ini-files/Oryza_sativa125619.ini new file mode 100755 index 00000000..96fb6947 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa125619.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa125619_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa125827.ini b/gramene/conf/ini-files/Oryza_sativa125827.ini new file mode 100755 index 00000000..6a0b9ab0 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa125827.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa125827_core_7_87_1 +DATABASE_VARIATION = oryza_sativa125827_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa127518.ini b/gramene/conf/ini-files/Oryza_sativa127518.ini new file mode 100755 index 00000000..68ea9df9 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa127518.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127518_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa127564.ini b/gramene/conf/ini-files/Oryza_sativa127564.ini new file mode 100755 index 00000000..6b8cbf30 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa127564.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127564_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa127652.ini b/gramene/conf/ini-files/Oryza_sativa127652.ini new file mode 100755 index 00000000..a691be33 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa127652.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127652_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa127742.ini b/gramene/conf/ini-files/Oryza_sativa127742.ini new file mode 100755 index 00000000..4eb912c2 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa127742.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa127742_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa128077.ini b/gramene/conf/ini-files/Oryza_sativa128077.ini new file mode 100755 index 00000000..64de6d86 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa128077.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa128077_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa132278.ini b/gramene/conf/ini-files/Oryza_sativa132278.ini new file mode 100755 index 00000000..b827c75d --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa132278.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa132278_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativa132424.ini b/gramene/conf/ini-files/Oryza_sativa132424.ini new file mode 100755 index 00000000..a93c16fa --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativa132424.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativa132424_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativaazucena.ini b/gramene/conf/ini-files/Oryza_sativaazucena.ini new file mode 100755 index 00000000..c43adbf3 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativaazucena.ini @@ -0,0 +1,268 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativaazucena_core_7_87_1 +DATABASE_VARIATION = oryza_sativaazucena_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +MH63RS2_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsIR64RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +MH63RS2_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsIR64RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[MH63RS2_INS] +source_name = MH63RS2_INS +description = structure variation of MH63RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/MH63RS2_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsIR64RS1_INS] +source_name = OsIR64RS1_INS +description = structure variation of OsIR64RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsIR64RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[MH63RS2_DEL] +source_name = MH63RS2_DEL +description = structure variation of MH63RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/MH63RS2_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsIR64RS1_DEL] +source_name = OsIR64RS1_DEL +description = structure variation of OsIR64RS1 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsIR64RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against AzucenaRS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_AzucenaRS1_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/Oryza_sativair64.ini b/gramene/conf/ini-files/Oryza_sativair64.ini new file mode 100755 index 00000000..def42ee2 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativair64.ini @@ -0,0 +1,267 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativair64_core_7_87_1 +DATABASE_VARIATION = oryza_sativair64_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +AzucenaRS1_INS = variation +MH63RS2_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +AzucenaRS1_DEL = variation +MH63RS2_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[AzucenaRS1_INS] +source_name = AzucenaRS1_INS +description = structure variation of AzucenaRS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/AzucenaRS1_ABS.bed +source_type = bed +display = labels + +[MH63RS2_INS] +source_name = MH63RS2_INS +description = structure variation of MH63RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/MH63RS2_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[AzucenaRS1_DEL] +source_name = AzucenaRS1_DEL +description = structure variation of AzucenaRS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/AzucenaRS1_PRE.bed +source_type = bed +display = labels + +[MH63RS2_DEL] +source_name = MH63RS2_DEL +description = structure variation of MH63RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/MH63RS2_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against OsIR64RS1 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_OsIR64RS1_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/Oryza_sativakitaake.ini b/gramene/conf/ini-files/Oryza_sativakitaake.ini new file mode 100755 index 00000000..e0b56359 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativakitaake.ini @@ -0,0 +1,22 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativakitaake_core_7_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Oryza_sativamh63.ini b/gramene/conf/ini-files/Oryza_sativamh63.ini new file mode 100755 index 00000000..f184bb66 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativamh63.ini @@ -0,0 +1,269 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativamh63_core_7_87_1 +DATABASE_VARIATION = oryza_sativamh63_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + + +[ENSEMBL_INTERNAL_BED_SOURCES] + +Nipponbare_INS = variation +AzucenaRS1_INS = variation +Os117425RS1_INS = variation +Os125619RS1_INS = variation +Os125827RS1_INS = variation +Os127518RS1_INS = variation +Os127564RS1_INS = variation +Os127652RS1_INS = variation +Os127742RS1_INS = variation +Os128077RS1_INS = variation +Os132278RS1_INS = variation +Os132424RS1_INS = variation +OsIR64RS1_INS = variation +OsN22RS2_INS = variation +ZS97RS2_INS = variation +Nipponbare_DEL = variation +AzucenaRS1_DEL = variation +Os117425RS1_DEL = variation +Os125619RS1_DEL = variation +Os125827RS1_DEL = variation +Os127518RS1_DEL = variation +Os127564RS1_DEL = variation +Os127652RS1_DEL = variation +Os127742RS1_DEL = variation +Os128077RS1_DEL = variation +Os132278RS1_DEL = variation +Os132424RS1_DEL = variation +OsIR64RS1_DEL = variation +OsN22RS2_DEL = variation +ZS97RS2_DEL = variation + +[Nipponbare_INS] +source_name = Nipponbare_INS +description = structure variation of Nipponbare against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Nipponbare_ABS.bed +source_type = bed +display = labels + +[AzucenaRS1_INS] +source_name = AzucenaRS1_INS +description = structure variation of AzucenaRS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/AzucenaRS1_ABS.bed +source_type = bed +display = labels + +[Os117425RS1_INS] +source_name = Os117425RS1_INS +description = structure variation of Os117425RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os117425RS1_ABS.bed +source_type = bed +display = labels + +[Os125619RS1_INS] +source_name = Os125619RS1_INS +description = structure variation of Os125619RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125619RS1_ABS.bed +source_type = bed +display = labels + +[Os125827RS1_INS] +source_name = Os125827RS1_INS +description = structure variation of Os125827RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125827RS1_ABS.bed +source_type = bed +display = labels + +[Os127518RS1_INS] +source_name = Os127518RS1_INS +description = structure variation of Os127518RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127518RS1_ABS.bed +source_type = bed +display = labels + +[Os127564RS1_INS] +source_name = Os127564RS1_INS +description = structure variation of Os127564RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127564RS1_ABS.bed +source_type = bed +display = labels + +[Os127652RS1_INS] +source_name = Os127652RS1_INS +description = structure variation of Os127652RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127652RS1_ABS.bed +source_type = bed +display = labels + +[Os127742RS1_INS] +source_name = Os127742RS1_INS +description = structure variation of Os127742RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127742RS1_ABS.bed +source_type = bed +display = labels + +[Os128077RS1_INS] +source_name = Os128077RS1_INS +description = structure variation of Os128077RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os128077RS1_ABS.bed +source_type = bed +display = labels + +[Os132278RS1_INS] +source_name = Os132278RS1_INS +description = structure variation of Os132278RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132278RS1_ABS.bed +source_type = bed +display = labels + +[Os132424RS1_INS] +source_name = Os132424RS1_INS +description = structure variation of Os132424RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132424RS1_ABS.bed +source_type = bed +display = labels + +[OsIR64RS1_INS] +source_name = OsIR64RS1_INS +description = structure variation of OsIR64RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsIR64RS1_ABS.bed +source_type = bed +display = labels + +[OsN22RS2_INS] +source_name = OsN22RS2_INS +description = structure variation of OsN22RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsN22RS2_ABS.bed +source_type = bed +display = labels + +[ZS97RS2_INS] +source_name = ZS97RS2_INS +description = structure variation of ZS97RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/ZS97RS2_ABS.bed +source_type = bed +display = labels + +[Nipponbare_DEL] +source_name = Nipponbare_DEL +description = structure variation of Nipponbare against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Nipponbare_PRE.bed +source_type = bed +display = labels + +[AzucenaRS1_DEL] +source_name = AzucenaRS1_DEL +description = structure variation of AzucenaRS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/AzucenaRS1_PRE.bed +source_type = bed +display = labels + +[Os117425RS1_DEL] +source_name = Os117425RS1_DEL +description = structure variation of Os117425RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os117425RS1_PRE.bed +source_type = bed +display = labels + +[Os125619RS1_DEL] +source_name = Os125619RS1_DEL +description = structure variation of Os125619RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125619RS1_PRE.bed +source_type = bed +display = labels + +[Os125827RS1_DEL] +source_name = Os125827RS1_DEL +description = structure variation of Os125827RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os125827RS1_PRE.bed +source_type = bed +display = labels + +[Os127518RS1_DEL] +source_name = Os127518RS1_DEL +description = structure variation of Os127518RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127518RS1_PRE.bed +source_type = bed +display = labels + +[Os127564RS1_DEL] +source_name = Os127564RS1_DEL +description = structure variation of Os127564RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127564RS1_PRE.bed +source_type = bed +display = labels + +[Os127652RS1_DEL] +source_name = Os127652RS1_DEL +description = structure variation of Os127652RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127652RS1_PRE.bed +source_type = bed +display = labels + +[Os127742RS1_DEL] +source_name = Os127742RS1_DEL +description = structure variation of Os127742RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os127742RS1_PRE.bed +source_type = bed +display = labels + +[Os128077RS1_DEL] +source_name = Os128077RS1_DEL +description = structure variation of Os128077RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os128077RS1_PRE.bed +source_type = bed +display = labels + +[Os132278RS1_DEL] +source_name = Os132278RS1_DEL +description = structure variation of Os132278RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132278RS1_PRE.bed +source_type = bed +display = labels + +[Os132424RS1_DEL] +source_name = Os132424RS1_DEL +description = structure variation of Os132424RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/Os132424RS1_PRE.bed +source_type = bed +display = labels + +[OsIR64RS1_DEL] +source_name = OsIR64RS1_DEL +description = structure variation of OsIR64RS1 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsIR64RS1_PRE.bed +source_type = bed +display = labels + +[OsN22RS2_DEL] +source_name = OsN22RS2_DEL +description = structure variation of OsN22RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/OsN22RS2_PRE.bed +source_type = bed +display = labels + +[ZS97RS2_DEL] +source_name = ZS97RS2_DEL +description = structure variation of ZS97RS2 against MH63RS2 reference (1K and bigger) +source_url = http://squam.cshl.edu/data/Magic16_MH63RS2_SV/ZS97RS2_PRE.bed +source_type = bed +display = labels + diff --git a/gramene/conf/ini-files/Oryza_sativazs97.ini b/gramene/conf/ini-files/Oryza_sativazs97.ini new file mode 100755 index 00000000..5bf9a1b5 --- /dev/null +++ b/gramene/conf/ini-files/Oryza_sativazs97.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + + +[databases] +DATABASE_CORE = oryza_sativazs97_core_7_87_1 +DATABASE_VARIATION = oryza_sativazs97_variation_5_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Selaginella_moellendorffii.ini b/gramene/conf/ini-files/Selaginella_moellendorffii.ini new file mode 100755 index 00000000..493f2f55 --- /dev/null +++ b/gramene/conf/ini-files/Selaginella_moellendorffii.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = selaginella_moellendorffii_core_2_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +[ENSEMBL_EXTERNAL_URLS] +https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Smoellendorffii&loc=###CHR###:###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Sorghum_bicolor.ini b/gramene/conf/ini-files/Sorghum_bicolor.ini new file mode 100755 index 00000000..12339694 --- /dev/null +++ b/gramene/conf/ini-files/Sorghum_bicolor.ini @@ -0,0 +1,41 @@ +[general] +SPECIES_RELEASE_VERSION = 30 + +[databases] +DATABASE_CORE = sorghum_bicolor_core_2_87_30 +#sorghum_bicolor_core_34_87_20 +DATABASE_VARIATION = +DATABASE_USERDATA = + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +GRAMENE_PATHWAY = http://pathway.gramene.org/SORGHUM/NEW-IMAGE?type=REACTION&object=###ID### +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/sorghum/?name=chromosome_###CHR###%3A###START###..###END### +http://pathway.gramene.org/SORGHUM/NEW-IMAGE?type=REACTION&object=###ID### + + +[ENSEMBL_SPECIES_SITE] + +[ENSEMBL_INTERNAL_DAS_SOURCES] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + + diff --git a/gramene/conf/ini-files/Sorghum_bicolor.ini.v1.4EpiGmap b/gramene/conf/ini-files/Sorghum_bicolor.ini.v1.4EpiGmap deleted file mode 100644 index a1147c4b..00000000 --- a/gramene/conf/ini-files/Sorghum_bicolor.ini.v1.4EpiGmap +++ /dev/null @@ -1,147 +0,0 @@ -[ENSEMBL_INTERNAL_BIGWIG_SOURCES] -CpG_ratio = functional -CpG_coverage = functional -CHG_ratio = functional -CHG_coverage = functional -CHH_ratio = functional -CHH_coverage = functional -ABA_Root = mrna_prot -ABA_Shoot = mrna_prot -H2O_Root = mrna_prot -H2O_Shoot = mrna_prot -NaOH_Root = mrna_prot -NaOH_Shoot = mrna_prot -PEG_Root = mrna_prot -PEG_Shoot = mrna_prot -Embryos = mrna_prot -FloralMer = mrna_prot -Flowers = mrna_prot -VegMer = mrna_prot - -[CpG_ratio] -source_name = CpG_ratio -description = CpG methylation ratio from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CpG_ratio.bw -source_type = bigwig -display = wiggle - -[CHG_ratio] -source_name = CHG_ratio -description = CHG methylation ratio from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CHG_ratio.bw -source_type = bigwig -display = wiggle - -[CHH_ratio] -source_name = CHH_ratio -description = CHH methylation ratio from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CHH_ratio.bw -source_type = bigwig -display = wiggle - -[CpG_coverage] -source_name = CpG_coverage -description = CpG methylation coverage from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CpG_coverage.bw -source_type = bigwig -display = wiggle - -[CHG_coverage] -source_name = CHG_coverage -description = CHG methylation coverage from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CHG_coverage.bw -source_type = bigwig -display = wiggle - -[CHH_coverage] -source_name = CHH_coverage -description = CHH methylation coverage from bisulfite sequencing -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/methylome/CHH_coverage.bw -source_type = bigwig -display = wiggle - -[ABA_Root] -source_name = ABA_root -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/ABA_Root.bw -source_type = bigwig -display = wiggle - -[H2O_Root] -source_name = H2O_root -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/H2O_Root.bw -source_type = bigwig -display = wiggle - -[NaOH_Root] -source_name = NaOH_root -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/NaOH_Root.bw -source_type = bigwig -display = wiggle - -[PEG_Root] -source_name = PEG_root -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/PEG_Root.bw -source_type = bigwig -display = wiggle - -[ABA_Shoot] -source_name = ABA_shoot -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/ABA_Shoot.bw -source_type = bigwig -display = wiggle - -[H2O_Shoot] -source_name = H2O_shoot -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/H2O_Shoot.bw -source_type = bigwig -display = wiggle - -[NaOH_Shoot] -source_name = NaOH_shoot -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/NaOH_Shoot.bw -source_type = bigwig -display = wiggle - -[PEG_Shoot] -source_name = PEG_shoot -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/PEG_Shoot.bw -source_type = bigwig -display = wiggle - -[Embryos] -source_name = Embryos -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/Embryos.bw -source_type = bigwig -display = wiggle - -[FloralMer] -source_name = FloralMer -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/FloralMer.bw -source_type = bigwig -display = wiggle - -[Flowers] -source_name = Flowers -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/Flowers.bw -source_type = bigwig -display = wiggle - -[VegMer] -source_name = VegMer -description = RNAseq depth of coverage -source_url = http://brie.cshl.edu/data/Sorghum_bicolor/RNAseq/VegMer.bw -source_type = bigwig -display = wiggle - - diff --git a/gramene/conf/ini-files/Vitis_vinifera.ini b/gramene/conf/ini-files/Vitis_vinifera.ini new file mode 100755 index 00000000..c73cc9b1 --- /dev/null +++ b/gramene/conf/ini-files/Vitis_vinifera.ini @@ -0,0 +1,39 @@ +[general] +SPECIES_RELEASE_VERSION = 3 + + +[databases] +DATABASE_CORE = vitis_vinifera_core_2_87_3 +#vitis_vinifera_core_52_86_3 +#%_variation_%_% +#%_funcgen_%_% + +[DATABASE_USERDATA] + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +#################### +# Configure External URLs +# These are mainly for (1) External Genome Browse {EGB_ } +# (2) DAS tracks {DAS_ } +#################### + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/grape/?name=chr###CHR###%3A###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[SPECIES_DISPLAY_NAME] + + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + diff --git a/gramene/conf/ini-files/Zea_maysb73.ini b/gramene/conf/ini-files/Zea_maysb73.ini new file mode 100755 index 00000000..1f0795d8 --- /dev/null +++ b/gramene/conf/ini-files/Zea_maysb73.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 1 + +[databases] +DATABASE_CORE = zea_maysb73_core_3_87_1 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Creinhardtii&loc=chromosome_###CHR###:###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/Zea_maysb73v4.ini b/gramene/conf/ini-files/Zea_maysb73v4.ini new file mode 100755 index 00000000..c9098ade --- /dev/null +++ b/gramene/conf/ini-files/Zea_maysb73v4.ini @@ -0,0 +1,23 @@ +[general] +SPECIES_RELEASE_VERSION = 7 + +[databases] +DATABASE_CORE = zea_maysb73v4_core_2_87_7 + +[ENSEMBL_STYLE] + +[EXTERNAL_GENOME_BROWSERS] +EGB_PHY = Phytozome + +[ENSEMBL_EXTERNAL_URLS] +EGB_PHY = https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Creinhardtii&loc=chromosome_###CHR###:###START###..###END### + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + +[ENSEMBL_EXTERNAL_DATABASES] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini + +[ENSEMBL_EXTERNAL_INDEXERS] +; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/sorghum_bicolor.ini b/gramene/conf/ini-files/sorghum_bicolor.ini deleted file mode 100755 index c9118f58..00000000 --- a/gramene/conf/ini-files/sorghum_bicolor.ini +++ /dev/null @@ -1,26 +0,0 @@ -[general] -SPECIES_RELEASE_VERSION = 30 -ASSEMBLY_CONVERTER_FILES = [Sorbi1_to_Sorghum_bicolor_NCBIv3 Sorghum_bicolor_NCBIv3_to_Sorbi1 Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3 Sorghum_bicolor_NCBIv3_to_Sorghum_bicolor_v2] - -[databases] -DATABASE_CORE = %_core_%_% -DATABASE_VARIATION = %_variation_%_% - -[ENSEMBL_STYLE] - -[EXTERNAL_GENOME_BROWSERS] -EGB_PHY = Phytozome - -[ENSEMBL_EXTERNAL_URLS] -EGB_PHY = https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/SbicolorRio_er&loc=chromosome_###CHR###:###START###..###END### -;GRAMENE_PATHWAY = http://pathway.gramene.org/SORGHUM/NEW-IMAGE?type=REACTION&object=###ID### - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - -[ENSEMBL_EXTERNAL_DATABASES] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini - -[ENSEMBL_EXTERNAL_INDEXERS] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini diff --git a/gramene/conf/ini-files/zea_mays.ini b/gramene/conf/ini-files/zea_mays.ini deleted file mode 100644 index 923a5238..00000000 --- a/gramene/conf/ini-files/zea_mays.ini +++ /dev/null @@ -1,111 +0,0 @@ -[general] -SPECIES_RELEASE_VERSION = 7 - -ASSEMBLY_CONVERTER_FILES = [AGPv2_to_AGPv3 AGPv2_to_AGPv4 AGPv3_to_AGPv2 AGPv3_to_AGPv4 AGPv4_to_AGPv2 AGPv4_to_AGPv3] - -THR_ASSEMBLY_PARAM = ASSEMBLY_VERSION - -[databases] -DATABASE_CORE = %_core_%_% -DATABASE_OTHERFEATURES=%_otherfeatures_%_% -DATABASE_VARIATION = %_variation_%_% -DATABASE_FUNCGEN = %_funcgen_%_% - - -[ENSEMBL_STYLE] - -[EXTERNAL_GENOME_BROWSERS] -EGB_PHY = Phytozome - -#################### -# Configure External URLs -# These are mainly for (1) External Genome Browse {EGB_ } -# (2) DAS tracks {DAS_ } -#################### - -[ENSEMBL_EXTERNAL_URLS] -EGB_PHY = http://www.phytozome.net/cgi-bin/gbrowse/maize/?name=chr###CHR###%3A###START###..###END### -GRAMENE_PATHWAY = http://pathway.gramene.org/MAIZE/NEW-IMAGE?type=REACTION&object=###ID### -MAIZEGDB_GENE = http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=###ID### - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - -[SPECIES_DISPLAY_NAME] - - -[ENSEMBL_EXTERNAL_DATABASES] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini - -[ENSEMBL_EXTERNAL_INDEXERS] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini - - - -[ENSEMBL_INTERNAL_BIGWIG_SOURCES] -B73_CpG_ratio = functional -B73_CpG_coverage = functional -B73_CHG_ratio = functional -B73_CHG_coverage = functional -MO17_CpG_ratio = functional -MO17_CpG_coverage = functional -MO17_CHG_ratio = functional -MO17_CHG_coverage = functional - -[B73_CpG_ratio] -source_name = B73_CpG_ratio -description = B73 CpG methylation ratio from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/B73_CpG_ratio.bw -source_type = bigwig -display = off - -[B73_CpG_coverage] -source_name = B73_CpG_coverage -description = B73 CpG methylation coverage from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/B73_CpG_coverage.bw -source_type = bigwig -display = off - -[B73_CHG_ratio] -source_name = B73_CHG_ratio -description = B73 CHG methylation ratio from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/B73_CHG_ratio.bw -source_type = bigwig -display = off - -[B73_CHG_coverage] -source_name = B73_CHG_coverage -description = B73 CHG methylation coverage from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/B73_CHG_coverage.bw -source_type = bigwig -display = off - -[MO17_CpG_ratio] -source_name = MO17_CpG_ratio -description = MO17 CpG methylation ratio from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/MO17_CpG_ratio.bw -source_type = bigwig -display = off - -[MO17_CpG_coverage] -source_name = MO17_CpG_coverage -description = MO17 CpG methylation coverage from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/MO17_CpG_coverage.bw -source_type = bigwig -display = off - -[MO17_CHG_ratio] -source_name = MO17_CHG_ratio -description = MO17 CHG methylation ratio from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/MO17_CHG_ratio.bw -source_type = bigwig -display = off - -[MO17_CHG_coverage] -source_name = MO17_CHG_coverage -description = MO17 CHG methylation coverage from bisulfite sequencing -source_url = ftp://ftp.gramene.org/pub/gramene/Zea_mays/methylome/MO17_CHG_coverage.bw -source_type = bigwig -display = off - diff --git a/gramene/conf/json-bk/Oryza_sativa_vcf.json.old b/gramene/conf/json-bk/Oryza_sativa_vcf.json.old new file mode 100644 index 00000000..d647ef36 --- /dev/null +++ b/gramene/conf/json-bk/Oryza_sativa_vcf.json.old @@ -0,0 +1,97 @@ +{ + + "collections": [ + + { + "id": "BGI 2004", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/bgi_snps_2004.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Duitama et al. 2015", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/duitama_et_al_2015.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "McNally et al. 2009", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/mcnally_et_al_2009.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "OMAP 2007 DIV", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/omap_snps_2007_div.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "OMAP 2007 SNV", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/omap_snps_2007_snv.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Rice 3k", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/rice_3k.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Zhao et al. 2010", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-31/vcf/plants/oryza_sativa/zhao_et_al_2010.vcf.gz", + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + } + + ] + +} diff --git a/gramene/conf/json-bk/oryza_sativa_vcf.json b/gramene/conf/json-bk/oryza_sativa_vcf.json new file mode 100644 index 00000000..7f3a9d9e --- /dev/null +++ b/gramene/conf/json-bk/oryza_sativa_vcf.json @@ -0,0 +1,97 @@ +{ + + "collections": [ + + { + "id": "BGI 2004", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/bgi_snps_2004.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Duitama et al. 2015", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/duitama_et_al_2015.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "McNally et al. 2009", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/mcnally_et_al_2009.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "OMAP 2007 DIV", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/omap_snps_2007_div.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "OMAP 2007 SNV", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/omap_snps_2007_snv.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Rice 3k", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/rice_3k.vcf.gz", + "use_seq_region_synonyms": 1, + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + }, + + { + "id": "Zhao et al. 2010", + "species": "oryza_sativa", + "assembly": "IRGSP-1.0", + "type": "local", + "filename_template": "/oryza_sativa/IRGSP-1.0/variation_genotype/zhao_et_al_2010.vcf.gz", + "chromosomes": [ + "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" + ], + "strict_name_match": 0 + } + + ] + +} diff --git a/gramene/conf/json/oryza_sativa_vcf.json b/gramene/conf/json-bk/oryza_sativa_vcf.json.old similarity index 100% rename from gramene/conf/json/oryza_sativa_vcf.json rename to gramene/conf/json-bk/oryza_sativa_vcf.json.old diff --git a/gramene/conf/martRegistry.xml b/gramene/conf/martRegistry.xml deleted file mode 100644 index a3558b02..00000000 --- a/gramene/conf/martRegistry.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - - - - - - diff --git a/gramene/htdocs/genome_browser/index.html b/gramene/htdocs/genome_browser/index.html deleted file mode 100755 index 92db7be1..00000000 --- a/gramene/htdocs/genome_browser/index.html +++ /dev/null @@ -1,34 +0,0 @@ - - -[[SPECIESDEFS::SITE_NAME]] - -
-
-
-
-[[SCRIPT::EnsEMBL::Web::Document::HTML::HomeSearch]] -
-
-
- -[[SCRIPT::EnsEMBL::Web::Document::HTML::GenomeList]] -
-
-[[INCLUDE::/ssi/outline.inc]] -[[INCLUDE::/ssi/left_1.inc]] -[[INCLUDE::/ssi/left_2.inc]] -
-
-
-[[INCLUDE::/ssi/right_2.inc]] -[[INCLUDE::/ssi/collaborators.inc]] -
-
-

Organelle Annotation

-

For annotations relating to Organelles, see the - organelles page

-
- -
- - diff --git a/gramene/htdocs/i/48/grmsearch.png b/gramene/htdocs/i/48/grmsearch.png new file mode 100644 index 00000000..f277c3e1 Binary files /dev/null and b/gramene/htdocs/i/48/grmsearch.png differ diff --git a/gramene/htdocs/i/gramene_logo_small.png b/gramene/htdocs/i/gramene_logo_small.png.bk similarity index 100% rename from gramene/htdocs/i/gramene_logo_small.png rename to gramene/htdocs/i/gramene_logo_small.png.bk diff --git a/gramene/htdocs/i/oryza_logo_small.png b/gramene/htdocs/i/oryza_logo_small.png new file mode 100644 index 00000000..c469eca6 Binary files /dev/null and b/gramene/htdocs/i/oryza_logo_small.png differ diff --git a/gramene/htdocs/i/species/48/Drosophila_melanogaster.png b/gramene/htdocs/i/species/48/Drosophila_melanogaster.png new file mode 100644 index 00000000..2d881577 Binary files /dev/null and b/gramene/htdocs/i/species/48/Drosophila_melanogaster.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_aus.png b/gramene/htdocs/i/species/48/Oryza_aus.png new file mode 100644 index 00000000..52a83b9d Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_aus.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_carolina.png b/gramene/htdocs/i/species/48/Oryza_carolina.png new file mode 100644 index 00000000..ae967089 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_carolina.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_indicair8.png b/gramene/htdocs/i/species/48/Oryza_indicair8.png new file mode 120000 index 00000000..c30062d8 --- /dev/null +++ b/gramene/htdocs/i/species/48/Oryza_indicair8.png @@ -0,0 +1 @@ +Oryza_sativa_Indica_Group.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/48/Oryza_sativa.png b/gramene/htdocs/i/species/48/Oryza_sativa.png new file mode 100644 index 00000000..6b280bf2 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa117425.png b/gramene/htdocs/i/species/48/Oryza_sativa117425.png new file mode 100644 index 00000000..03a9cd70 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa117425.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa125619.png b/gramene/htdocs/i/species/48/Oryza_sativa125619.png new file mode 100644 index 00000000..d6038660 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa125619.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa125827.png b/gramene/htdocs/i/species/48/Oryza_sativa125827.png new file mode 100644 index 00000000..b39d931a Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa125827.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa127518.png b/gramene/htdocs/i/species/48/Oryza_sativa127518.png new file mode 100644 index 00000000..c09950b7 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa127518.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa127564.png b/gramene/htdocs/i/species/48/Oryza_sativa127564.png new file mode 100644 index 00000000..fc954a43 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa127564.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa127652.png b/gramene/htdocs/i/species/48/Oryza_sativa127652.png new file mode 100644 index 00000000..c8008fc0 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa127652.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa127742.png b/gramene/htdocs/i/species/48/Oryza_sativa127742.png new file mode 100644 index 00000000..f7dbbe78 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa127742.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa128077.png b/gramene/htdocs/i/species/48/Oryza_sativa128077.png new file mode 120000 index 00000000..916bdb4d --- /dev/null +++ b/gramene/htdocs/i/species/48/Oryza_sativa128077.png @@ -0,0 +1 @@ +Oryza_sativa.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/48/Oryza_sativa132278.png b/gramene/htdocs/i/species/48/Oryza_sativa132278.png new file mode 100644 index 00000000..c48f5200 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa132278.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativa132424.png b/gramene/htdocs/i/species/48/Oryza_sativa132424.png new file mode 100644 index 00000000..83162a12 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativa132424.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativaazucena.png b/gramene/htdocs/i/species/48/Oryza_sativaazucena.png new file mode 100644 index 00000000..c3efe664 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativaazucena.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativair64.png b/gramene/htdocs/i/species/48/Oryza_sativair64.png new file mode 100644 index 00000000..90bf7685 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativair64.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativakitaake.png b/gramene/htdocs/i/species/48/Oryza_sativakitaake.png new file mode 100644 index 00000000..065cd85f Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativakitaake.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativamh63.png b/gramene/htdocs/i/species/48/Oryza_sativamh63.png new file mode 100644 index 00000000..ed6a8c14 Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativamh63.png differ diff --git a/gramene/htdocs/i/species/48/Oryza_sativazs97.png b/gramene/htdocs/i/species/48/Oryza_sativazs97.png new file mode 100644 index 00000000..22504f2a Binary files /dev/null and b/gramene/htdocs/i/species/48/Oryza_sativazs97.png differ diff --git a/gramene/htdocs/i/species/48/RIGW.png b/gramene/htdocs/i/species/48/RIGW.png new file mode 100644 index 00000000..cc64f55e Binary files /dev/null and b/gramene/htdocs/i/species/48/RIGW.png differ diff --git a/gramene/htdocs/i/species/48/Zea_mays.png b/gramene/htdocs/i/species/48/Zea_mays.png new file mode 100644 index 00000000..a045610f Binary files /dev/null and b/gramene/htdocs/i/species/48/Zea_mays.png differ diff --git a/gramene/htdocs/i/species/48/Zea_maysb73.png b/gramene/htdocs/i/species/48/Zea_maysb73.png new file mode 120000 index 00000000..e694d140 --- /dev/null +++ b/gramene/htdocs/i/species/48/Zea_maysb73.png @@ -0,0 +1 @@ +Zea_mays.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/48/Zea_maysb73v4.png b/gramene/htdocs/i/species/48/Zea_maysb73v4.png new file mode 120000 index 00000000..e694d140 --- /dev/null +++ b/gramene/htdocs/i/species/48/Zea_maysb73v4.png @@ -0,0 +1 @@ +Zea_mays.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Drosophila_melanogaster.png b/gramene/htdocs/i/species/64/Drosophila_melanogaster.png new file mode 120000 index 00000000..5b2ef15f --- /dev/null +++ b/gramene/htdocs/i/species/64/Drosophila_melanogaster.png @@ -0,0 +1 @@ +../48/Drosophila_melanogaster.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_aus.png b/gramene/htdocs/i/species/64/Oryza_aus.png new file mode 120000 index 00000000..cee648b5 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_aus.png @@ -0,0 +1 @@ +../48/Oryza_aus.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_carolina.png b/gramene/htdocs/i/species/64/Oryza_carolina.png new file mode 120000 index 00000000..5d136206 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_carolina.png @@ -0,0 +1 @@ +../48/Oryza_carolina.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_indicair8.png b/gramene/htdocs/i/species/64/Oryza_indicair8.png new file mode 120000 index 00000000..c30062d8 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_indicair8.png @@ -0,0 +1 @@ +Oryza_sativa_Indica_Group.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa117425.png b/gramene/htdocs/i/species/64/Oryza_sativa117425.png new file mode 120000 index 00000000..8ff60dba --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa117425.png @@ -0,0 +1 @@ +../48/Oryza_sativa117425.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa125619.png b/gramene/htdocs/i/species/64/Oryza_sativa125619.png new file mode 120000 index 00000000..64373f64 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa125619.png @@ -0,0 +1 @@ +../48/Oryza_sativa125619.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa125827.png b/gramene/htdocs/i/species/64/Oryza_sativa125827.png new file mode 120000 index 00000000..45d3b0c9 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa125827.png @@ -0,0 +1 @@ +../48/Oryza_sativa125827.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa127518.png b/gramene/htdocs/i/species/64/Oryza_sativa127518.png new file mode 120000 index 00000000..2646ca61 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa127518.png @@ -0,0 +1 @@ +../48/Oryza_sativa127518.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa127564.png b/gramene/htdocs/i/species/64/Oryza_sativa127564.png new file mode 120000 index 00000000..6404a786 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa127564.png @@ -0,0 +1 @@ +../48/Oryza_sativa127564.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa127652.png b/gramene/htdocs/i/species/64/Oryza_sativa127652.png new file mode 120000 index 00000000..f2eea46d --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa127652.png @@ -0,0 +1 @@ +../48/Oryza_sativa127652.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa127742.png b/gramene/htdocs/i/species/64/Oryza_sativa127742.png new file mode 120000 index 00000000..0509de91 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa127742.png @@ -0,0 +1 @@ +../48/Oryza_sativa127742.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa128077.png b/gramene/htdocs/i/species/64/Oryza_sativa128077.png new file mode 120000 index 00000000..a1d239ad --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa128077.png @@ -0,0 +1 @@ +../48/Oryza_sativa.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa132278.png b/gramene/htdocs/i/species/64/Oryza_sativa132278.png new file mode 120000 index 00000000..39e279b5 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa132278.png @@ -0,0 +1 @@ +../48/Oryza_sativa132278.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativa132424.png b/gramene/htdocs/i/species/64/Oryza_sativa132424.png new file mode 120000 index 00000000..465e10d2 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativa132424.png @@ -0,0 +1 @@ +../48/Oryza_sativa132424.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativaazucena.png b/gramene/htdocs/i/species/64/Oryza_sativaazucena.png new file mode 120000 index 00000000..707f0505 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativaazucena.png @@ -0,0 +1 @@ +../48/Oryza_sativaazucena.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativair64.png b/gramene/htdocs/i/species/64/Oryza_sativair64.png new file mode 120000 index 00000000..7e891269 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativair64.png @@ -0,0 +1 @@ +../48/Oryza_sativair64.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativakitaake.png b/gramene/htdocs/i/species/64/Oryza_sativakitaake.png new file mode 120000 index 00000000..9a2cd79f --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativakitaake.png @@ -0,0 +1 @@ +../48/Oryza_sativakitaake.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativamh63.png b/gramene/htdocs/i/species/64/Oryza_sativamh63.png new file mode 120000 index 00000000..ffd6c0df --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativamh63.png @@ -0,0 +1 @@ +../48/Oryza_sativamh63.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Oryza_sativazs97.png b/gramene/htdocs/i/species/64/Oryza_sativazs97.png new file mode 120000 index 00000000..3992d7c0 --- /dev/null +++ b/gramene/htdocs/i/species/64/Oryza_sativazs97.png @@ -0,0 +1 @@ +../48/Oryza_sativazs97.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Zea_maysb73.png b/gramene/htdocs/i/species/64/Zea_maysb73.png new file mode 120000 index 00000000..e694d140 --- /dev/null +++ b/gramene/htdocs/i/species/64/Zea_maysb73.png @@ -0,0 +1 @@ +Zea_mays.png \ No newline at end of file diff --git a/gramene/htdocs/i/species/64/Zea_maysb73v4.png b/gramene/htdocs/i/species/64/Zea_maysb73v4.png new file mode 120000 index 00000000..e694d140 --- /dev/null +++ b/gramene/htdocs/i/species/64/Zea_maysb73v4.png @@ -0,0 +1 @@ +Zea_mays.png \ No newline at end of file diff --git a/gramene/htdocs/index.html b/gramene/htdocs/index.html old mode 100644 new mode 100755 index 8e06d2c3..25f4943e --- a/gramene/htdocs/index.html +++ b/gramene/htdocs/index.html @@ -1,7 +1,30 @@ - - - - Redirecting [here] - - + +[[SPECIESDEFS::SITE_NAME]] + +
+
+
+
+[[SCRIPT::EnsEMBL::Web::Document::HTML::HomeSearch]] +
+
+
+ +[[SCRIPT::EnsEMBL::Web::Document::HTML::FavouriteSpecies]] +[[SCRIPT::EnsEMBL::Web::Document::HTML::SpeciesList]] +
+
+[[INCLUDE::/ssi/left_1.inc]] +[[INCLUDE::/ssi/left_2.inc]] +
+
+
+[[INCLUDE::/ssi/outline.inc]] +[[INCLUDE::/ssi/right_2.inc]] +[[INCLUDE::/ssi/collaborators.inc]] +
+ +
+ + diff --git a/gramene/htdocs/opensearch/Arabidopsis_thaliana.xml b/gramene/htdocs/opensearch/Arabidopsis_thaliana.xml index 01fa3efa..f9ffb916 100644 --- a/gramene/htdocs/opensearch/Arabidopsis_thaliana.xml +++ b/gramene/htdocs/opensearch/Arabidopsis_thaliana.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Arabidopsis thaliana Arabidopsis thaliana /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Arabidopsis_thaliana/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Brachypodium_distachyon.xml b/gramene/htdocs/opensearch/Brachypodium_distachyon.xml index 81cf576a..30ab3670 100644 --- a/gramene/htdocs/opensearch/Brachypodium_distachyon.xml +++ b/gramene/htdocs/opensearch/Brachypodium_distachyon.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Brachypodium distachyon Brachypodium distachyon /i/ensembl-favicon.png + template="http://oge-ensembl.gramene.org:8888/Brachypodium_distachyon/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Chlamydomonas_reinhardtii.xml b/gramene/htdocs/opensearch/Chlamydomonas_reinhardtii.xml index c948d755..c3634594 100644 --- a/gramene/htdocs/opensearch/Chlamydomonas_reinhardtii.xml +++ b/gramene/htdocs/opensearch/Chlamydomonas_reinhardtii.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Chlamydomonas reinhardtii Chlamydomonas reinhardtii /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Chlamydomonas_reinhardtii/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Drosophila_melanogaster.xml b/gramene/htdocs/opensearch/Drosophila_melanogaster.xml new file mode 100644 index 00000000..3aecbfc9 --- /dev/null +++ b/gramene/htdocs/opensearch/Drosophila_melanogaster.xml @@ -0,0 +1,11 @@ + + + Ensembl (Droso) + Search Ensembl Genomes - Drosophila melanogaster - Drosophila melanogaster + UTF-8 + Ensembl genome browser Ensembl Genomes Drosophila melanogaster Drosophila melanogaster + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Eukaryota_cellular organisms.xml b/gramene/htdocs/opensearch/Eukaryota_cellular organisms.xml deleted file mode 100644 index c439ab0a..00000000 --- a/gramene/htdocs/opensearch/Eukaryota_cellular organisms.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - - - UTF-8 - Ensembl genome browser Ensembl - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Homo_sapiens.xml b/gramene/htdocs/opensearch/Homo_sapiens.xml deleted file mode 100644 index 304dd55b..00000000 --- a/gramene/htdocs/opensearch/Homo_sapiens.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (H.sap) - Search Ensembl - Human - Homo sapiens - UTF-8 - Ensembl genome browser Ensembl Human Homo sapiens - http://www.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Leersia_perrieri.xml b/gramene/htdocs/opensearch/Leersia_perrieri.xml index 6b78d5e8..c459ff66 100644 --- a/gramene/htdocs/opensearch/Leersia_perrieri.xml +++ b/gramene/htdocs/opensearch/Leersia_perrieri.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Leersia perrieri Leersia perrieri /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Leersia_perrieri/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_officinalis.xml b/gramene/htdocs/opensearch/Oryza_aus.xml similarity index 53% rename from gramene/htdocs/opensearch/Oryza_officinalis.xml rename to gramene/htdocs/opensearch/Oryza_aus.xml index 8626fb67..8b24d896 100644 --- a/gramene/htdocs/opensearch/Oryza_officinalis.xml +++ b/gramene/htdocs/opensearch/Oryza_aus.xml @@ -2,10 +2,10 @@ Ensembl (Oryza) - Search Ensembl Genomes - Oryza officinalis - Oryza officinalis + Search Ensembl Genomes - Oryza sativa (circum-Aus1 var. N22) - Oryza sativa aus cA1 var. N22 UTF-8 - Ensembl genome browser Ensembl Genomes Oryza officinalis Oryza officinalis + Ensembl genome browser Ensembl Genomes Oryza sativa (circum-Aus1 var. N22) Oryza sativa aus cA1 var. N22 /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_aus/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_barthii.xml b/gramene/htdocs/opensearch/Oryza_barthii.xml index 5d591e63..a5cbc2e3 100644 --- a/gramene/htdocs/opensearch/Oryza_barthii.xml +++ b/gramene/htdocs/opensearch/Oryza_barthii.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza barthii Oryza barthii /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_barthii/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_brachyantha.xml b/gramene/htdocs/opensearch/Oryza_brachyantha.xml index df310acf..59ebb0f5 100644 --- a/gramene/htdocs/opensearch/Oryza_brachyantha.xml +++ b/gramene/htdocs/opensearch/Oryza_brachyantha.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza brachyantha Oryza brachyantha /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_brachyantha/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_carolina.xml b/gramene/htdocs/opensearch/Oryza_carolina.xml new file mode 100644 index 00000000..5e4aac3a --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_carolina.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa japonica var. Carolina - Oryza sativa japonica var. Carolina + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa japonica var. Carolina Oryza sativa japonica var. Carolina + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_glaberrima(chr3s).xml b/gramene/htdocs/opensearch/Oryza_glaberrima(chr3s).xml deleted file mode 100644 index abc10506..00000000 --- a/gramene/htdocs/opensearch/Oryza_glaberrima(chr3s).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza glaberrima(chr3s) - - UTF-8 - Ensembl genome browser Ensembl Oryza glaberrima(chr3s) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_glaberrima.xml b/gramene/htdocs/opensearch/Oryza_glaberrima.xml index e018a0d4..59f57d05 100644 --- a/gramene/htdocs/opensearch/Oryza_glaberrima.xml +++ b/gramene/htdocs/opensearch/Oryza_glaberrima.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza glaberrima Oryza glaberrima /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_glaberrima/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_glaberrima3s.xml b/gramene/htdocs/opensearch/Oryza_glaberrima3s.xml deleted file mode 100644 index bbb4b60b..00000000 --- a/gramene/htdocs/opensearch/Oryza_glaberrima3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl - - Oryza glaberrima3s - UTF-8 - Ensembl genome browser Ensembl Oryza glaberrima3s - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_glumaepatula.xml b/gramene/htdocs/opensearch/Oryza_glumaepatula.xml index f2bf081c..314306dd 100644 --- a/gramene/htdocs/opensearch/Oryza_glumaepatula.xml +++ b/gramene/htdocs/opensearch/Oryza_glumaepatula.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza glumaepatula Oryza glumaepatula /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_glumaepatula/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_granulata.xml b/gramene/htdocs/opensearch/Oryza_granulata.xml deleted file mode 100644 index 33bffc6d..00000000 --- a/gramene/htdocs/opensearch/Oryza_granulata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl Genomes - Oryza granulata - - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza granulata - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_granulata3s.xml b/gramene/htdocs/opensearch/Oryza_granulata3s.xml deleted file mode 100644 index 8b120b61..00000000 --- a/gramene/htdocs/opensearch/Oryza_granulata3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza granulata3s - Oryza granulata3s - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza granulata3s Oryza granulata3s - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_indica.xml b/gramene/htdocs/opensearch/Oryza_indica.xml index 733d01a7..df6b281a 100644 --- a/gramene/htdocs/opensearch/Oryza_indica.xml +++ b/gramene/htdocs/opensearch/Oryza_indica.xml @@ -2,10 +2,10 @@ Ensembl (Oryza) - Search Ensembl Genomes - Oryza sativa Indica - Oryza sativa Indica Group + Search Ensembl Genomes - Oryza sativa indica 93-11 - Oryza indica UTF-8 - Ensembl genome browser Ensembl Genomes Oryza sativa Indica Oryza sativa Indica Group + Ensembl genome browser Ensembl Genomes Oryza sativa indica 93-11 Oryza indica /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_indica/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_indicair8.xml b/gramene/htdocs/opensearch/Oryza_indicair8.xml new file mode 100644 index 00000000..d9dc3a6c --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_indicair8.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa indica var. IR8 - Oryza sativa indica var. IR8 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa indica var. IR8 Oryza sativa indica var. IR8 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_longistaminata.xml b/gramene/htdocs/opensearch/Oryza_longistaminata.xml index 7a38ad09..064066ea 100644 --- a/gramene/htdocs/opensearch/Oryza_longistaminata.xml +++ b/gramene/htdocs/opensearch/Oryza_longistaminata.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza longistaminata Oryza longistaminata /i/ensembl-favicon.png + template="http://oge-ensembl.gramene.org:8888/Oryza_longistaminata/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_meridionalis.xml b/gramene/htdocs/opensearch/Oryza_meridionalis.xml index 457b7c18..ab9c485a 100644 --- a/gramene/htdocs/opensearch/Oryza_meridionalis.xml +++ b/gramene/htdocs/opensearch/Oryza_meridionalis.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza meridionalis Oryza meridionalis /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_meridionalis/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_minuta.xml b/gramene/htdocs/opensearch/Oryza_minuta.xml deleted file mode 100644 index 49a8204c..00000000 --- a/gramene/htdocs/opensearch/Oryza_minuta.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (O.min) - Search Ensembl - Oryza minuta - Oryza minuta - UTF-8 - Ensembl genome browser Ensembl Oryza minuta Oryza minuta - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutaCC.xml b/gramene/htdocs/opensearch/Oryza_minutaCC.xml deleted file mode 100644 index 60d2cc2e..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutaCC.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (O.min) - Search Ensembl - Oryza minutaCC - Oryza minutaCC - UTF-8 - Ensembl genome browser Ensembl Oryza minutaCC Oryza minutaCC - http://www.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3).xml b/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3).xml deleted file mode 100644 index 1f28518c..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza minutaCC (chr3) - - UTF-8 - Ensembl genome browser Ensembl Oryza minutaCC (chr3) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3s).xml b/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3s).xml deleted file mode 100644 index d9a8a4b8..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutaCC_(chr3s).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza minutaCC (chr3s) - - UTF-8 - Ensembl genome browser Ensembl Oryza minutaCC (chr3s) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutaCC_chr3s.xml b/gramene/htdocs/opensearch/Oryza_minutaCC_chr3s.xml deleted file mode 100644 index 263bb0ee..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutaCC_chr3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza minutaCC chr3s - - UTF-8 - Ensembl genome browser Ensembl Oryza minutaCC chr3s - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minuta_(chr3s).xml b/gramene/htdocs/opensearch/Oryza_minuta_(chr3s).xml deleted file mode 100644 index 300eb660..00000000 --- a/gramene/htdocs/opensearch/Oryza_minuta_(chr3s).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza minuta (chr3s) - - UTF-8 - Ensembl genome browser Ensembl Oryza minuta (chr3s) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minuta_chr3s.xml b/gramene/htdocs/opensearch/Oryza_minuta_chr3s.xml deleted file mode 100644 index 03e0df14..00000000 --- a/gramene/htdocs/opensearch/Oryza_minuta_chr3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza minuta chr3s - - UTF-8 - Ensembl genome browser Ensembl Oryza minuta chr3s - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutabb.xml b/gramene/htdocs/opensearch/Oryza_minutabb.xml deleted file mode 100644 index 40741aa9..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutabb.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza minutabb - Oryza minutabb - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza minutabb Oryza minutabb - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutabb3s.xml b/gramene/htdocs/opensearch/Oryza_minutabb3s.xml deleted file mode 100644 index 15189a12..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutabb3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza minutabb3s - Oryza minutabb3s - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza minutabb3s Oryza minutabb3s - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutacc.xml b/gramene/htdocs/opensearch/Oryza_minutacc.xml deleted file mode 100644 index b4cdbf61..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutacc.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza minutacc - Oryza minutacc - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza minutacc Oryza minutacc - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_minutacc3s.xml b/gramene/htdocs/opensearch/Oryza_minutacc3s.xml deleted file mode 100644 index 205231a2..00000000 --- a/gramene/htdocs/opensearch/Oryza_minutacc3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza minutacc3s - Oryza minutacc3s - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza minutacc3s Oryza minutacc3s - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_nivara.xml b/gramene/htdocs/opensearch/Oryza_nivara.xml index 467b5924..60a3b4a4 100644 --- a/gramene/htdocs/opensearch/Oryza_nivara.xml +++ b/gramene/htdocs/opensearch/Oryza_nivara.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza nivara Oryza nivara /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_nivara/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_officinalis_(chr3s).xml b/gramene/htdocs/opensearch/Oryza_officinalis_(chr3s).xml deleted file mode 100644 index 31334e49..00000000 --- a/gramene/htdocs/opensearch/Oryza_officinalis_(chr3s).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza officinalis (chr3s) - - UTF-8 - Ensembl genome browser Ensembl Oryza officinalis (chr3s) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_punctata.xml b/gramene/htdocs/opensearch/Oryza_punctata.xml index 9f2cf8e2..9d6c38d0 100644 --- a/gramene/htdocs/opensearch/Oryza_punctata.xml +++ b/gramene/htdocs/opensearch/Oryza_punctata.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza punctata Oryza punctata /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_punctata/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_punctata_(chr3s).xml b/gramene/htdocs/opensearch/Oryza_punctata_(chr3s).xml deleted file mode 100644 index 1428168f..00000000 --- a/gramene/htdocs/opensearch/Oryza_punctata_(chr3s).xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza punctata (chr3s) - - UTF-8 - Ensembl genome browser Ensembl Oryza punctata (chr3s) - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_rufipogon.xml b/gramene/htdocs/opensearch/Oryza_rufipogon.xml index 2b92dfd2..e9ade61c 100644 --- a/gramene/htdocs/opensearch/Oryza_rufipogon.xml +++ b/gramene/htdocs/opensearch/Oryza_rufipogon.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Oryza rufipogon Oryza rufipogon /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_rufipogon/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_rufipogon3s.xml b/gramene/htdocs/opensearch/Oryza_rufipogon3s.xml deleted file mode 100644 index 8eb9abf0..00000000 --- a/gramene/htdocs/opensearch/Oryza_rufipogon3s.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl (Oryza) - Search Ensembl Genomes - Oryza rufipogon3s - Oryza rufipogon3s - UTF-8 - Ensembl genome browser Ensembl Genomes Oryza rufipogon3s Oryza rufipogon3s - /i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_rufipogon_physical_map.xml b/gramene/htdocs/opensearch/Oryza_rufipogon_physical_map.xml deleted file mode 100644 index 5d296138..00000000 --- a/gramene/htdocs/opensearch/Oryza_rufipogon_physical_map.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza rufipogon physical map - - UTF-8 - Ensembl genome browser Ensembl Oryza rufipogon physical map - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_sativa Indica Group.xml b/gramene/htdocs/opensearch/Oryza_sativa Indica Group.xml deleted file mode 100644 index 19e61eb8..00000000 --- a/gramene/htdocs/opensearch/Oryza_sativa Indica Group.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - - - UTF-8 - Ensembl genome browser Ensembl - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_sativa Japonica Group.xml b/gramene/htdocs/opensearch/Oryza_sativa Japonica Group.xml deleted file mode 100644 index e9c4ee41..00000000 --- a/gramene/htdocs/opensearch/Oryza_sativa Japonica Group.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - - - UTF-8 - Ensembl genome browser Ensembl - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_sativa.xml b/gramene/htdocs/opensearch/Oryza_sativa.xml index 62d565d4..7ae99304 100644 --- a/gramene/htdocs/opensearch/Oryza_sativa.xml +++ b/gramene/htdocs/opensearch/Oryza_sativa.xml @@ -2,10 +2,10 @@ Ensembl (Oryza) - Search Ensembl Genomes - Oryza sativa Japonica - Oryza sativa Japonica Group + Search Ensembl Genomes - Oryza sativa Japonica Nipponbare - Oryza sativa Japonica Nipponbare UTF-8 - Ensembl genome browser Ensembl Genomes Oryza sativa Japonica Oryza sativa Japonica Group + Ensembl genome browser Ensembl Genomes Oryza sativa Japonica Nipponbare Oryza sativa Japonica Nipponbare /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Oryza_sativa/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_sativa117425.xml b/gramene/htdocs/opensearch/Oryza_sativa117425.xml new file mode 100644 index 00000000..0c8073c9 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa117425.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (circum-Basmati var. ARC 10497) - Oryza sativa indica cB var. ARC 10497 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (circum-Basmati var. ARC 10497) Oryza sativa indica cB var. ARC 10497 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa125619.xml b/gramene/htdocs/opensearch/Oryza_sativa125619.xml new file mode 100644 index 00000000..f8b17da1 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa125619.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-2B var. Larha Mugad) - Oryza sativa indica XI-2B var. Os125619 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-2B var. Larha Mugad) Oryza sativa indica XI-2B var. Os125619 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa125827.xml b/gramene/htdocs/opensearch/Oryza_sativa125827.xml new file mode 100644 index 00000000..acf8a3dc --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa125827.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-3B2 var. Liu Xu) - Oryza sativa indica XI-3B2 var. Liu Xu + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-3B2 var. Liu Xu) Oryza sativa indica XI-3B2 var. Liu Xu + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa127518.xml b/gramene/htdocs/opensearch/Oryza_sativa127518.xml new file mode 100644 index 00000000..3531ae5e --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa127518.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang) - Oryza sativa indica XI-3B1 var. Os127518 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang) Oryza sativa indica XI-3B1 var. Os127518 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa127564.xml b/gramene/htdocs/opensearch/Oryza_sativa127564.xml new file mode 100644 index 00000000..fd0a059a --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa127564.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-3A var. Lima) - Oryza sativa indica XI-3A var. Os127564 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-3A var. Lima) Oryza sativa indica XI-3A var. Os127564 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa127652.xml b/gramene/htdocs/opensearch/Oryza_sativa127652.xml new file mode 100644 index 00000000..df298234 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa127652.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (circum-Aus2 var. Natel Boro) - Oryza sativa aus cA2 var. Os127652 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (circum-Aus2 var. Natel Boro) Oryza sativa aus cA2 var. Os127652 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa127742.xml b/gramene/htdocs/opensearch/Oryza_sativa127742.xml new file mode 100644 index 00000000..b8dc0995 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa127742.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-1B2 var. PR106) - Oryza sativa indica XI-1B2 var. Os127742 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-1B2 var. PR106) Oryza sativa indica XI-1B2 var. Os127742 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa128077.xml b/gramene/htdocs/opensearch/Oryza_sativa128077.xml new file mode 100644 index 00000000..8b15ccf4 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa128077.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) - Oryza sativa japonica GJ-trop2 var. Os128077 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) Oryza sativa japonica GJ-trop2 var. Os128077 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa132278.xml b/gramene/htdocs/opensearch/Oryza_sativa132278.xml new file mode 100644 index 00000000..7a122e46 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa132278.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo) - Oryza sativa japonica GJ-subtrp var. Os132278 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo) Oryza sativa japonica GJ-subtrp var. Os132278 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa132424.xml b/gramene/htdocs/opensearch/Oryza_sativa132424.xml new file mode 100644 index 00000000..5205a840 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativa132424.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-2A var. Gobol Sail) - Oryza sativa indica XI-2A var. Os132424 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-2A var. Gobol Sail) Oryza sativa indica XI-2A var. Os132424 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativa_Indica_Group.xml b/gramene/htdocs/opensearch/Oryza_sativa_Indica_Group.xml deleted file mode 100644 index 5cc8655b..00000000 --- a/gramene/htdocs/opensearch/Oryza_sativa_Indica_Group.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - Ensembl () - Search Ensembl - Oryza sativa Indica Group - - UTF-8 - Ensembl genome browser Ensembl Oryza sativa Indica Group - http://dev.gramene.org/i/ensembl-favicon.png - - diff --git a/gramene/htdocs/opensearch/Oryza_sativaazucena.xml b/gramene/htdocs/opensearch/Oryza_sativaazucena.xml new file mode 100644 index 00000000..84e357fe --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativaazucena.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Geng/Japonica-trop1 var. Azucena) - Oryza sativa japonica GJ-trop1 var. Azucena + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Geng/Japonica-trop1 var. Azucena) Oryza sativa japonica GJ-trop1 var. Azucena + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativair64.xml b/gramene/htdocs/opensearch/Oryza_sativair64.xml new file mode 100644 index 00000000..6de7a989 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativair64.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-1B1 var. IR64) - Oryza sativa indica XI-1B1 var. IR64 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-1B1 var. IR64) Oryza sativa indica XI-1B1 var. IR64 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativakitaake.xml b/gramene/htdocs/opensearch/Oryza_sativakitaake.xml new file mode 100644 index 00000000..2fd0a81d --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativakitaake.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa ssp. japonica var. KitaakeX - Oryza sativa ssp. japonica var. KitaakeX + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa ssp. japonica var. KitaakeX Oryza sativa ssp. japonica var. KitaakeX + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativamh63.xml b/gramene/htdocs/opensearch/Oryza_sativamh63.xml new file mode 100644 index 00000000..b0de2ff1 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativamh63.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-adm var. Minghui 63) - Oryza sativa indica XI-adm var MH63 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-adm var. Minghui 63) Oryza sativa indica XI-adm var MH63 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Oryza_sativazs97.xml b/gramene/htdocs/opensearch/Oryza_sativazs97.xml new file mode 100644 index 00000000..c6fbf6a7 --- /dev/null +++ b/gramene/htdocs/opensearch/Oryza_sativazs97.xml @@ -0,0 +1,11 @@ + + + Ensembl (Oryza) + Search Ensembl Genomes - Oryza sativa (Xian/Indica-1A var. Zhenshan 97) - Oryza sativa indica XI-1A var ZS97 + UTF-8 + Ensembl genome browser Ensembl Genomes Oryza sativa (Xian/Indica-1A var. Zhenshan 97) Oryza sativa indica XI-1A var ZS97 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/Selaginella_moellendorffii.xml b/gramene/htdocs/opensearch/Selaginella_moellendorffii.xml index 8e2a42bf..f1420d6b 100644 --- a/gramene/htdocs/opensearch/Selaginella_moellendorffii.xml +++ b/gramene/htdocs/opensearch/Selaginella_moellendorffii.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes Selaginella moellendorffii Selaginella moellendorffii /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Selaginella_moellendorffii/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Sorghum_bicolor.xml b/gramene/htdocs/opensearch/Sorghum_bicolor.xml index 7ba93443..5e4949d8 100644 --- a/gramene/htdocs/opensearch/Sorghum_bicolor.xml +++ b/gramene/htdocs/opensearch/Sorghum_bicolor.xml @@ -2,10 +2,10 @@ Ensembl (Sorgh) - Search Ensembl Genomes - Sorghum bicolor - Sorghum bicolor + Search Ensembl Genomes - Sorghum bicolor ssp. bicolor BTx623 - Sorghum bicolor UTF-8 - Ensembl genome browser Ensembl Genomes Sorghum bicolor Sorghum bicolor + Ensembl genome browser Ensembl Genomes Sorghum bicolor ssp. bicolor BTx623 Sorghum bicolor /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Sorghum_bicolor/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Vitis_vinifera.xml b/gramene/htdocs/opensearch/Vitis_vinifera.xml index 33c04f38..aeeca250 100644 --- a/gramene/htdocs/opensearch/Vitis_vinifera.xml +++ b/gramene/htdocs/opensearch/Vitis_vinifera.xml @@ -2,10 +2,10 @@ Ensembl (Vitis) - Search Ensembl Genomes - Vitis vinifera - Vitis vinifera + Search Ensembl Genomes - Vitis vinifera ssp. vinifera PN40024 v3 - Vitis vinifera UTF-8 - Ensembl genome browser Ensembl Genomes Vitis vinifera Vitis vinifera + Ensembl genome browser Ensembl Genomes Vitis vinifera ssp. vinifera PN40024 v3 Vitis vinifera /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Vitis_vinifera/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Oryza_officinalis3s.xml b/gramene/htdocs/opensearch/Zea_maysb73.xml similarity index 52% rename from gramene/htdocs/opensearch/Oryza_officinalis3s.xml rename to gramene/htdocs/opensearch/Zea_maysb73.xml index e73f15cf..046a98ca 100644 --- a/gramene/htdocs/opensearch/Oryza_officinalis3s.xml +++ b/gramene/htdocs/opensearch/Zea_maysb73.xml @@ -1,11 +1,11 @@ - Ensembl (Oryza) - Search Ensembl Genomes - Oryza officinalis3s - Oryza officinalis3s + Ensembl (Zea m) + Search Ensembl Genomes - Zea mays B73 v5 - Zea mays B73 v5 UTF-8 - Ensembl genome browser Ensembl Genomes Oryza officinalis3s Oryza officinalis3s + Ensembl genome browser Ensembl Genomes Zea mays B73 v5 Zea mays B73 v5 /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//Zea_maysb73/Psychic?q={searchTerms};site=ensembl"/> diff --git a/gramene/htdocs/opensearch/Zea_maysb73v4.xml b/gramene/htdocs/opensearch/Zea_maysb73v4.xml new file mode 100644 index 00000000..5dff9bcd --- /dev/null +++ b/gramene/htdocs/opensearch/Zea_maysb73v4.xml @@ -0,0 +1,11 @@ + + + Ensembl (Zea m) + Search Ensembl Genomes - Zea mays B73 v4 - Zea maysb73v4 + UTF-8 + Ensembl genome browser Ensembl Genomes Zea mays B73 v4 Zea maysb73v4 + /i/ensembl-favicon.png + + diff --git a/gramene/htdocs/opensearch/all.xml b/gramene/htdocs/opensearch/all.xml index 8c1a02d5..8cb15dd7 100644 --- a/gramene/htdocs/opensearch/all.xml +++ b/gramene/htdocs/opensearch/all.xml @@ -7,5 +7,5 @@ Ensembl genome browser Ensembl Genomes All species /i/ensembl-favicon.png + template="https://oryza-ensembl.gramene.org//common/Psychic?q={searchTerms};site=ensembl_all"/> diff --git a/gramene/htdocs/species.html b/gramene/htdocs/species.html new file mode 100644 index 00000000..ca7921f8 --- /dev/null +++ b/gramene/htdocs/species.html @@ -0,0 +1,14 @@ + + +Species List + + + + +

Find a Species

+ +[[SCRIPT::EnsEMBL::Web::Document::HTML::SpeciesPage]] + + + + diff --git a/gramene/htdocs/ssi.old/collaborators.inc b/gramene/htdocs/ssi.old/collaborators.inc new file mode 100644 index 00000000..f9eac332 --- /dev/null +++ b/gramene/htdocs/ssi.old/collaborators.inc @@ -0,0 +1,22 @@ + +

+ +
+
+ +
+ +

+This work is a joint project between EnsemblGenomes at the European Bioinformatics Institute and +the group of Doreen Ware at the +Cold Spring Harbor Laboratory, who +have developed the Gramene +database, a resource for plant comparative genomics based on Ensembl +technology. A common set of databases are available through +EnsemblGenomes and Gramene, and the two groups are collaborating on the +integration of content, quality control and the development of new +features. +

+
diff --git a/gramene/htdocs/ssi.old/outline.inc b/gramene/htdocs/ssi.old/outline.inc new file mode 100644 index 00000000..1f2dffe1 --- /dev/null +++ b/gramene/htdocs/ssi.old/outline.inc @@ -0,0 +1,11 @@ +

Gene Tree Statistics

+
+ +
+ + diff --git a/gramene/htdocs/ssi.old/outline.inc.bk b/gramene/htdocs/ssi.old/outline.inc.bk new file mode 100644 index 00000000..1a16f6d6 --- /dev/null +++ b/gramene/htdocs/ssi.old/outline.inc.bk @@ -0,0 +1,21 @@ +

What's New in Release 57

+

Did you know...?

The Track Hub Registry

+ +

You can search the Track Hub Registry to find more than 1,400 public RNA-Seq studies aligned to plants (read more)!

+
  • New features: +
    • Polyploid view for wheat has been enabled, allowing users to view alignments between all 3 wheat components simultaneously.
      • +
    • SIFT scores are now displayed on the Genes and regulation view of a gene variant. Here is a sorghum SNP.
    +
    • +
  • Updated data: +
    • Added gene name synonyms for O. sativa using from database sources such as CGSNL, Oryzabase and Rap-DB.
      • +
    • Updated protein features for all (nearly 2 million) plant proteins using InterProScan with version 67 of InterPro.
      • +
    • Updated BioMarts for all gene and variation data.
      • +
    • 26 new and updated functional genomic databases (example for Arabidopsis).
      • +
    • Tandem repeats annotated by the TRF program are no longer used to soft- and hardmask the genome sequences. This affects sequences retrieved via the API and the files on the FTP site.
    +
    • +
  • Updated software: + +
diff --git a/gramene/htdocs/ssi.old/right_2.inc b/gramene/htdocs/ssi.old/right_2.inc new file mode 100644 index 00000000..f51d207f --- /dev/null +++ b/gramene/htdocs/ssi.old/right_2.inc @@ -0,0 +1,39 @@ +

What's New in Release 4

+
+ + + diff --git a/gramene/htdocs/ssi/collaborators.inc b/gramene/htdocs/ssi/collaborators.inc index f9eac332..f14a33d1 100644 --- a/gramene/htdocs/ssi/collaborators.inc +++ b/gramene/htdocs/ssi/collaborators.inc @@ -1,22 +1,18 @@ +

Acknowledgements

-

- -
-
- -
+

Ensembl Plants is a joint project of the European Bioinformatics Institute and the group of Doreen Ware at the Cold Spring Harbor Laboratory, who have developed the Gramene database [1,2], a resource for plant comparative genomics based on Ensembl technology [3,4]. A common set of databases are available through Ensembl Plants and Gramene, and the two groups are collaborating on the integration of content, quality control and the development of new features.

+ +

+ +

References

+ +
  1. Tello-Ruiz MK, Jaiswal P, Ware D. (2022). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol. 2443:101-131. PMID: 35037202. doi: 10.1007/978-1-0716-2067-0_5. Free PDF
    2. + +
  2. Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J. Bolser DM, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49(D1):D1452-D1463. PMID: 33170273. doi: 10.1093/nar/gkaa979. Free PDF. +
    3. + +
  3. Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. (2018). Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46(D1):D1181-D1189. PMID: 29165610. doi: 10.1093/nar/gkx1111. Free PDF. +
    4. +
-

-This work is a joint project between EnsemblGenomes at the European Bioinformatics Institute and -the group of Doreen Ware at the -Cold Spring Harbor Laboratory, who -have developed the Gramene -database, a resource for plant comparative genomics based on Ensembl -technology. A common set of databases are available through -EnsemblGenomes and Gramene, and the two groups are collaborating on the -integration of content, quality control and the development of new -features. -

diff --git a/gramene/htdocs/ssi/outline.inc b/gramene/htdocs/ssi/outline.inc index cda4e9d0..e3a9b907 100644 --- a/gramene/htdocs/ssi/outline.inc +++ b/gramene/htdocs/ssi/outline.inc @@ -1,37 +1,52 @@ -

What's New in Release 58

-

Did you know...?

The Track Hub Registry

- -

You can search the Track Hub Registry to find more than 3,500 public RNA-Seq studies aligned to plants (read more)!

-
  • New genomes -
    • Release 58 of Gramene hosts the latest wheat assembly from the IWGSC (IWGSC RefSeq v1.0 and IWGSC RefSeq annotation v1.0). Current data includes: -
      • The Axiom 820K SNP Array from CerealsDB.
        • -
      • EMS-induced mutations from sequenced TILLING populations (Kronos and Cadensa).
        • -
      • Assembly to assembly mapping and gene ID mapping to the previous TGAC v1 assembly and annotation.
        • -
      • Whole genome alignments to rice, brachypodium and barley.
      -
      • -
    • This release will also bring in more sequenced plant genomes from INSDC using a 'direct import' method developed with ENA.
      - If a plant genome is submitted to INSDC along with AGP and gene models, it can be added it to Gramene! - -
    +

    What's New in Release 7

    + +

    New Functionality

    + +
    +
  • +

    Added new links to the Gene Tree Curation Tool in the Homology tab of Nipponbare genes. Example: Os05g0569300.

    +
    • +
  • +

    Added new links to the GrameneOryza search interface results, see for example: Os05g0113900.

    +
    • +
+ + +

New & Updated Data

+ +

Genes

+ +
    +
  • Updated gene names for the Magic16 genomes (except Nipponbare) with new prefixes: OsZS97, OsMH63, OsIR64, OsPr106, OsGoSa, OsLaMu, OsLima, OsKYG, OsLiXu, OsN22, OsNaBo, OsARC, OsKeNa, OsCMeo, and OsAzu. +
    • +
+ +

Genetic Variation

+ +

Approximately 19 million SNPs called per each of four Magic16 genomes from the 3000 rice genome project were called by Dr. Rod Wing's group from resequencing reads using GATK4 software:

+ + + +

Genetic variation for O. sativa Japonica Nipponbare IRGSP1 was imported from the Euorpean Variation Archive (EVA). It consists of the following data sets:

+ +
    +
  • 25.8 million SNPs from Duitama et al (2015)
    • +
  • 3 million SNPs from BGI (2004)
    • +
  • 1.6 million SNPs from OMAP (2007)
    • +
  • 366K SNPs from the 3K rice genome project
    • +
  • 157K SNPs from McNally et al (2009)
    • +
  • 1.3K SNPs from Zhao et al (2010)
    • +
+ + diff --git a/gramene/htdocs/ssi/outline.inc.R5 b/gramene/htdocs/ssi/outline.inc.R5 new file mode 100644 index 00000000..960e897a --- /dev/null +++ b/gramene/htdocs/ssi/outline.inc.R5 @@ -0,0 +1,12 @@ +

What's New in Release 5

+
  • Updates & highlights +
      +
    • Twenty-seven synteny maps between the IRGSP1 Nipponbare assembly and all rice accessions
      • +
    • New cross-species synteny maps between the Nipponbare assembly and Leersia, sorghum and maize
      • +
    • Whole-Genome Alignments between Nipponbare, sorghum and maize
      • +
    • Improved usability through direct links from the Ensembl Browser Gene pages to the Oryza Search pages
      • +
    • Updated nomenclature for naming of reference sequence assemblies based on standard recommendations from the NSF-DBI (#2029854): CIBR-BBSRC: PanOryza: Globally coordinated genomes, proteomes and pathways for rice
      • +
    +
    • +
+ diff --git a/gramene/htdocs/ssi/outline.inc.bk b/gramene/htdocs/ssi/outline.inc.bk index 1a16f6d6..d9ab779f 100644 --- a/gramene/htdocs/ssi/outline.inc.bk +++ b/gramene/htdocs/ssi/outline.inc.bk @@ -1,21 +1,20 @@ -

What's New in Release 57

-

Did you know...?

The Track Hub Registry

+

What's New in Release 6

+
-
+ + + + diff --git a/gramene/htdocs/ssi/right_2.inc b/gramene/htdocs/ssi/right_2.inc deleted file mode 100644 index 6110154e..00000000 --- a/gramene/htdocs/ssi/right_2.inc +++ /dev/null @@ -1,15 +0,0 @@ -

Polyploid View Enabled

- -

Polyploid view for wheat has been enabled, allowing users to view alignments between all 3 wheat components simultaneously.

- -

Functional Genomics

- -

26 new and updated functional genomic databases (example for Arabidopsis).

- -

Arabidopsis variation data from the 1001 Genomes Project

- -

The representation of genetic variation of Arabidopsis thaliana incorporates the full data set from the 1001 Genomes Project, covering more than 10 million variant loci across 1,135 samples (Cell 2016).

- -

Ensembl Plants Archive Site

- -

Alongside release 32, Ensembl Plants launched a new archive site, where selected previous releases of Ensembl Plants are being kept publicly available. The first release available on the archive site is release 31, and includes the previous assemblies for wheat and maize.

diff --git a/gramene/htdocs/ssi/right_2.inc.bk b/gramene/htdocs/ssi/right_2.inc.bk new file mode 100644 index 00000000..18d2c039 --- /dev/null +++ b/gramene/htdocs/ssi/right_2.inc.bk @@ -0,0 +1,9 @@ +

Updated assembly for wheat

+ +

The bread wheat assembly included in Ensembl Plants from release 25 onwards has been updated by ordering the existing Chromosome Survey Sequence (CSS) contigs into chromosomal pseudomolecules. This was done using anchoring data from high marker density population sequencing (POPSEQ) generated by Chapman et al.

+ +

The resulting set of chromosomes have been combined with the IWGSC's BAC by BAC assembly and annotation of chromosome 3B, generated by the GDEC group at INRA, which replaces the CSS-derived assembly and annotation of 3B.

+ +

The contig level gene models from the CSS assembly (version 2.2, provided by the PGSB group at the German Center for Environmental Health) were projected to the chromosome pseudomolecules using the Ensembl Assembly Converter Tool. For chromosome 3B, the GDEC-derived models have replaced the PGSB annotations are primary but where mappable, the PGSB genes are viewable as an additional track.

+ +

The anchoring process (with the exception of 3B) places 1,290,751 CSS contigs into chromosomal pseudomolecules for a total length of 4,237,502,413 bp. Ensembl Plants also incorporates 261,251 unanchored scaffolds, with cumulative length of 1,307,508,887 bp.

diff --git a/gramene/htdocs/ssi/right_3.inc.bk b/gramene/htdocs/ssi/right_3.inc.bk new file mode 100644 index 00000000..47b2a108 --- /dev/null +++ b/gramene/htdocs/ssi/right_3.inc.bk @@ -0,0 +1,11 @@ +

Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium. The transPLANT project is funded by the European Commission within its 7th Framework Programme, under the thematic area "Infrastructures", contract number 283496.

+ +

transPLANT logo The European flag

+ +

Wheat genomics resources are developed as part of our involvement in the consortium Triticeae Genomics For Sustainable Agriculture. Barley genomics resources are funded through the UK barley genome sequencing project. Both projects are funded by the BBSRC.

+ +

BBSRC logo

+ +

Databases are constructed in a direct collaboration with the Gramene resource, funded by the United States National Science Foundation award #1127112. Read more about our collaboration with Gramene.

+ +

Gramene logo

diff --git a/gramene/htdocs/ssi/right_4.incbk b/gramene/htdocs/ssi/right_4.incbk new file mode 100644 index 00000000..166a1c6d --- /dev/null +++ b/gramene/htdocs/ssi/right_4.incbk @@ -0,0 +1,3 @@ +

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. Click to see details of our funding.

+ +

EMBL-EBI logoEnsembl logo

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_aus.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_aus.html new file mode 100644 index 00000000..e9fc8455 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_aus.html @@ -0,0 +1,65 @@ +

About Oryza sativa aus (cA1) subgroup OsN22

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. N22 (collected from: India) is selected as the representative of cA1 subpopulation, in which the accessions are mostly collected from India, Bangladesh and Nepal.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. N22 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA1 subpopulation. The whole DNA was sequenced by 65 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ + +

OsN22RS2

+

Organism name: Oryza sativa aus subgroup (rice)

+

Infraspecific name: Cultivar: N 22::IRGC 19379-1 (IRGC 117534)

+

BioSample: SAMN04568482

+

BioProject: PRJNA315689

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_001952365.3 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: LWDA02

+

Assembly method: CANU v. v1.5; MECAT v. v1.3; FALCON v. 2017.06.28-18.01-py2.7-ucs4

+

Expected final version: no

+

Genome coverage: 65.0x

+

Sequencing technology: PacBio

+

IDs: 8130841 [UID] 22230838 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+

Stein, Joshua C., Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, et al. 2018. “Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation across the Genus Oryza.” Nature Genetics 50 (2): 285–96.

+ +

Wang, Wensheng, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, et al. 2018. “Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice.” Nature 557 (7703): 43–49.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/LWDA00000000.2/

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1010537

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=135816

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_barthii.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_barthii.html new file mode 100644 index 00000000..0b5989d1 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_barthii.html @@ -0,0 +1,29 @@ + + +

About Oryza barthii

+

Oryza barthii is the AA genome progenitor of the West African cultivated rice, O. glaberrima. It belongs to the AA genome group and has 12 chromosomes and a nuclear genome size of 411Mb (flow cytometry). It is found in mopane or savanna woodland, savanna or fadama. Grows in deep water, seasonally flooded land, stagnant water, and slowly flowing water or pools; prefers clay or black cotton soils. Found in open habitats. This work was part of the OGE project funded by NSF Award #1026200.

+ + +

Assembly

+

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using project accession ABRL03000000. The sequence data were generated by PacBio technology. The estimated coverage from the WGS was xxx. Total sequence length 344,913,874bp; Number of contigs 28; Contig N50 14,688,426bp.

+ + +

Annotation

+

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline at CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene and Ensembl Plants project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1) and other Oryza AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_brachyantha.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_brachyantha.html new file mode 100644 index 00000000..13a56a32 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_brachyantha.html @@ -0,0 +1,37 @@ + +

About Oryza brachyantha

+ +

Oryza brachyantha (wild rice) is a distant relative of cultivated rice (O. satia Japonica and O. sativa Indica). It is placed on the basal lineage of Oryza and is the only member of the genus assigned to the F-genome type. An annual or weekly perennial tufted grass, it is distributed in west and central Africa, and grows in open wetland habitats. It has potentially useful traits for rice breeding, including resistance/tolerance to yellow stem borer, leaffolder, whorl maggot and bacterial blight. The O. brachyantha genome provides an important resource for functional and evolutionary studies in the genus Oryza. Its nuclear genome is diploid (2n = 24) and ~362 Mbp.

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accessionAGAT0200000. The estimated coverage from the WGS was ?. Total sequence length 258,902,551 bp; Number of contigs 26; Contig N50 11,392,507 bp. +

+ + + +

Annotation

+ +

Protein-coding genes were annotated using an evidence-based MAKER-P pipeline in CSHL. +

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), Arabidopsis thaliana and a few other AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

+ +

Links

+ + + +

References

  1. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
    Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C et al. 2013. Nat Commun. 4:1595.
diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_carolina.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_carolina.html new file mode 100644 index 00000000..5900d24e --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_carolina.html @@ -0,0 +1,44 @@ +

About Oryza carolina rice

+ +

N/A

+ +

Assembly

+ +

Sequencing was performed using PacBio technology as deascribed in Vaughn et al (2021). Raw PacBio reads (n = 3,765,107; ~70x coverage) were assembled into 209 contigs, using Canu (v1.5)(Koren et al, 2017), and polished with Quiver (smrtlink v5.0.1 suite, now at github.com/PacificBiosciences/GenomicConsensus). PacBio raw reads were further polished with pilon v1.22 (Walker et al, 2017) using "10X Genomics" linked-reads aligned by Longranger v2.1.6 (github.com/10XGenomics/longranger). Repeat masking was performed as part of the MAKER-P pipeline (Campbell et al, 2014) using custom repeat libraries, PReDa_121015_short.fasta (DNA) and TE_protein_db_121015_short_header.fasta (protein)(Stein et al, 2018; Copetti et al, 2015). + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Copetti, Dario, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, et al. 2015. “RiTE Database: A Resource Database for Genus-Wide Rice Genomics and Evolutionary Biology.” BMC Genomics 16 (July): 538.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018;50:285–296.

+

Vaughn, Justin N., Walid Korani, Joshua C. Stein, Jeremy D. Edwards, Daniel G. Peterson, Sheron A. Simpson, Ramey C. Youngblood, et al. 2021. “Gene Disruption by Structural Mutations Drives Selection in US Rice Breeding over the Last Century.” PLoS Genetics 17 (3): e1009389.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank ?

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm?

+

- IRRI repo ?

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_glaberrima.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_glaberrima.html new file mode 100644 index 00000000..3f5b35b0 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_glaberrima.html @@ -0,0 +1,39 @@ + +

Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012).

+ + +

About Oryza glaberrima

+

Oryza glaberrima (African rice) is a cultivated grain distinct from its better known cousin Oryza sativa (Asian rice). African rice was independently domesticated ~3000 years ago in the Niger River Delta from its still extant progenitor, Oryza barthii. While lacking many of the agronomic and quality traits found in Asian rice, O. glaberrima is significant for its resistance to many pests and diseases and for its tolerance of drought and infertile soils. Interspecific crosses between African and Asian rice have produced cultivars with improved yield and quality traits, that have been adopted by many African countries to meet the growing need for rice as a staple food. From a scientific perspective the genome of O. glaberrima provides insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 Mbp.

+ + +

Assembly

+

The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000. The estimated coverage from the WGS was xxx. Total sequence length 344,456,705bp; Number of contigs 25; Contig N50 15,266,279bp.

+ + +

Annotation

+

Protein-coding genes were annotated with MAKER-P software in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1), and a few AA oryza genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +
  • Variation effect prediction with sequence ontology, for example.
    • +

Links

+ + +

References

  1. Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences.
    Li ZM, Zheng XM, Ge S. 2011. Theor. Appl. Genet.. 123:21-31.
    2. +
  2. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.
    Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. 2010. Plant J.. 63:990-1003.
    3. +
  3. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.
    Guyot R, Garavito A, Gavory F, Samain S, Tohme J, Ghesquire A, Lorieux M. 2011. PLoS ONE. 6:e17726.
    4. +
  4. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.
    Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA. 2011. BMC Genomics. 12:142.
    5. +
  5. Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
    Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M et al. 2011. Plant J.. 66:796-805.
    6. +
  6. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum.
    Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J et al. 2010. Mol. Biol. Evol.. 27:2487-2506.
    7. +
  7. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices.
    Roulin A, Chaparro C, Pigu B, Jackson S, Panaud O. 2010. Genome Biol Evol. 2:132-139.
diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_glumaepatula.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_glumaepatula.html new file mode 100644 index 00000000..2f020e01 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_glumaepatula.html @@ -0,0 +1,27 @@ + +

About Oryza glumaepatula

+

Oryza glumaepatula is a wild rice from South America, one of the rice species included in the OMAP project. It belongs to the AA genome group and has 12 chromosomes with a nuclear genome size of 464Mb (flow cytometry). It is found in deep and sometimes flowing water. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Antonio Oliveira (Brazil).

+ + +

Assembly

+

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession ALNU03000000. The estimated coverage from the WGS was ?. Total sequence length 386,178,655 bp; Number of contigs 33; Contig N50: 18,238,801bp.

+ + +

Annotation

+

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_indica.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_indica.html new file mode 100644 index 00000000..e8107b78 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_indica.html @@ -0,0 +1,31 @@ + +

About Oryza sativa Indica

+ +

Oryza sativa Indica is one of the two most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely grown in the hot climates of Southern Asia. The genome of Indica is very similar to that of Japonica, which is generally restricted to temperate climes such as Japan.

+ + + +

Assembly

+ +

The genome of Oryza sativa Indica Group cultivar 93-11 was sequenced by the Chinese Academy of Agricultural Sciences (CAAS) with PacBio technology and assembled using Canu v.1.5.

+ + + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + + + + + + + +

Links

+ + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_meridionalis.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_meridionalis.html new file mode 100644 index 00000000..badfdcff --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_meridionalis.html @@ -0,0 +1,37 @@ + + +

About Oryza meridionalis

+ +

Oryza meridionalis is a wild rice found in Australia, one of the wild rice species included in the OMAP project. It belongs to the AA genome group. It has 12 chromosomes with a nuclear genome size of 435Mb (flow cytometry). It is found at edges of freshwater lagoons, temporary pools, and swamps in 15-20 cm of water and grows in black, clay soil in open habitats. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Olivier Panaud (France) and Robert Henry (Australia).

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession ALNW03000000. The estimated coverage from the WGS was ?. Total sequence length 379,254,020 bp; Number of contigs 30; Contig N50: 16,096,529 bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1), see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_nivara.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_nivara.html new file mode 100644 index 00000000..0a36afc6 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_nivara.html @@ -0,0 +1,36 @@ + + +

About Oryza nivara

+ +

Oryza nivara is a wild rice from India; one of rice species being used in the OMAP project. It belongs to the AA genome group. Breeders are interested in this organism because it exhibits resistance to grassy stunt virus. It is found in swampy areas, at edges of ponds and tanks, beside streams, in ditches, in or around rice fields. It usually grows in shallow water up to 0.3 m. seasonally dry; in open habitats. It has 12 chromosomes and a nuclear genome size of 448Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Y. Hsing (Taiwan).

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession AWHD02000000. The estimated coverage from the WGS was ?. Total sequence length 393,961,846bp; Number of contigs 24; Contig N50: 18,986,252bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_punctata.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_punctata.html new file mode 100644 index 00000000..7cfd087e --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_punctata.html @@ -0,0 +1,36 @@ + + +

About Oryza punctata

+ +

Oryza punctata is a wild rice species native to Africa. Breeders are interested because of demonstrated resistance to bacterial blight and brown plant hoppers. O. punctata, a diploid, belongs to the O. officinalis complex within the Oryzeae genome groups, and belongs to the BB genome type. It can be found in open or semi-open habitats such as forest margins, grassland and thickets, scrub lands, open bush or shifting cultivation fields, and rice fields. It has 12 chromosomes and a nuclear genome size of 423Mb (flow cytometry). This work was part of the OGE project funded by NSF Award #1026200.

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession AVCL0200000. The estimated coverage from the WGS was ?. Total sequence length 419,076,415 bp; Number of contigs 28; Contig N50 18,594,736bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1) and other AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_rufipogon.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_rufipogon.html new file mode 100644 index 00000000..0e90264d --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_rufipogon.html @@ -0,0 +1,42 @@ + + +

About Oryza rufipogon

+ +

Oryza rufipogon (AA genome type) is a wild rice, perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-10 cm long; anthers >3 mm reaching 7.4 mm long.

+ +

Chromosome number: 2n=2x=24

+ +

Genome: AA

+Distribution: Australia, Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Sri Lanka, Thailand, and Vietnam.

+Habitat: Found in swamps and marshes, in open ditches, swampy grassland, ponds, along river banks, at the edges of lakes, and in or at the margins of rice fields, commonly found in deep water areas (0.2-4m). Grows in clay/loam soil and black soil, in full sun.

+ + + +

Assembly

+ +

The sequencing and assembly was done by Dr. Bin Han's group in Shanghai Institutes for Biological Sciences, CAS.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

+ + + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene and Ensembl Plants project include:

+ +
  • Gene phylogenetic trees with other other Gramene species, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa.html new file mode 100644 index 00000000..fb373c49 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa.html @@ -0,0 +1,70 @@ + +

About Oryza sativa Japonica

+ +

Oryza sativa Japonica (rice) is the staple food for 2.5 billion people. It is the grain with the second highest worldwide production after Zea mays. In addition to its agronomic importance, rice is an important model species for monocot plants and cereals such as maize, wheat, barley and sorghum. O. sativa has a compact diploid genome of approximately 500 Mbp (n=12) compared with the multi-gigabase genomes of maize, wheat and barley.

+ + + +

Assembly

+ +

Scientists from the MSU Rice Genome Annotation Project (MSU) and the International Rice Genome Sequencing Project (IRGSP) / Rice Annotation Project Database (RAP-DB) generated a unified assembly of the 12 rice pseudomolecules of Oryza sativa Japonica Group cv. Nipponbare [1,2].

+ +

The pseudomolecule for each chromosome was constructed by joining the nucleotide sequences of each PAC/BAC clone based on the order of the clones on the physical map. Overlapping sequences were removed and physical gaps were replaced with Ns. Updated pseudomolecules were constructed based on the original IRGSP sequence data [1] in combination with a BAC-optical map and error correction using 44-fold coverage next generation sequencing reads [2]. The nucleotide sequences of 7 new clones mapped on the euchromatin/telomere junctions were added in the new genome assembly. In addition, several clones in the centromere region of chromosome 5 were improved and one gap on chromosome 11 was closed [2].

+ +

Kawahara et al. (2013) describe the integrated Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules, also known as MSU7. Gene loci, gene models and associated annotations were independently created by each group, but can be easily compared using the common reference.

+ +

Read more about the assembly at MSU or on rap-db.

+ + +

Annotation

+ +

The IRGSP gene models were imported from rap-db [3]. The most recent update was from its's Aug 4, 2017 release. This version corrected numerous protein coding gene models with manual curation, also deprecated some bad models. In total, 35,667 protein-coding genes were included in this release. Compared with last release of 37,830 genes, 35,340 stayed the same, 2,173 got deprecated, 317 updated, 10 new genes added. Feature annotation and comparative analysis pipelines have been run and variations have been projected from the old annotation to the new one. In addition, 2,387 nonCoding genes and 8,115 predicted genes were added as seperate data sets.

+ +

The MSU-7 gene models [4] have been added into the rice genome browser for visual comparison to the IRGSP set. Gene models were generated, refined and updated for the estimated 40,000 to 60,000 rice genes, provided standardized automatic annotation pipeline described in detail here. Briefly, a number of ab initio methods have been combined with homology based evidence and refined with EST alignments.

+ +

Cross references between the two gene sets provided by rap-db allow searching and querying using either identifier space, but only the IRGSP gene models are used in our gene trees.

+ + +

Regulation

+ +
  • Probes from the Rice Genome Array for two rice cultivars were aligned to the genome [5].
    • +
+ + +

Variation

+ +

Variation data from six different large scale studies are available:

+ +
  1. The 3000 Rice Genome Project (2015, [6]), an international effort to sequence the genomes of 3,024 rice varieties from 89 countries providing 365,710 variant loci (SNPs and InDels).
    2. +
  2. Whole genome sequencing of 104 elite rice cultivars (Duitama et al. 2015, [7]), described as, "a comprehensive information resource for marker assisted selection" providing 25,769,548 variant loci.
    3. +
  3. Chip based analysis of 1,310 SNPs across 395 samples (Zhao et al. 2010, [8]), described as, "revealing the impact of domestication and breeding on the rice genome".
    4. +
  4. Chip based analysis of approximately 160k SNPs across 20 diversity rice accessions (OryzaSNP, McNally et al. 2009 [9]), described as, "revealing relationships among landraces and modern varieties of rice".
    5. +
  5. The Oryza Map Alignment Project (OMAP 2007): approximately 1.6M variant loci detected by comparing BAC End Sequences from four rice varieties to Japonica. [dbSNP]
    6. +
  6. Adaptive loss-of-function in domesticated rice (BGI 2004, [10]): A collection of approximately 3M variant loci from the comparison of the Indica (93-11) and Japonica (Nipponbare) genomes. [dbSNP]
    7. +

The following genetic markers were remapped to the IRGSP-1.0 assembly by industry collaborator KeyGene:

+ + + + +

Links

+ + + +

References

  1. The map-based sequence of the rice genome.
    2005. Nature. 436:793-800.
    2. +
  2. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
    Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S et al. 2013. Rice (N Y). 6:4.
    3. +
  3. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
    Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T et al. 2013. Plant Cell Physiol.. 54:e6.
    4. +
  4. The TIGR Rice Genome Annotation Resource: improvements and new features.
    Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L et al. 2007. Nucleic Acids Res.. 35:D883-7.
    5. +
  5. Global analysis of gene expression using GeneChip microarrays.
    Zhu T. 2003. Curr. Opin. Plant Biol.. 6:418-425.
    6. +
  6. The 3,000 rice genomes project.
    2014. Gigascience. 3:7.
    7. +
  7. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.
    Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E et al. 2015. PLoS ONE. 10:e0124617.
    8. +
  8. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.
    Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A et al. 2010. PLoS ONE. 5:e10780.
    9. +
  9. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
    McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE et al. 2009. Proc. Natl. Acad. Sci. U.S.A.. 106:12273-12278.
    10. +
  10. The Genomes of Oryza sativa: a history of duplications.
    Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al. 2005. PLoS Biol.. 3:e38.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa117425.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa117425.html new file mode 100644 index 00000000..24e3a73f --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa117425.html @@ -0,0 +1,72 @@ +

About Oryza sativa cB subgroup Os117425

+

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) (collected from: India) is selected as the representative of cB subpopulation, in which the accessions are mostly collected from India, Bangladesh, Nepal and Pakistan.

+ +

Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cB subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os117425RS1

+ +

Organism name: Oryza sativa aromatic subgroup (rice)

+

BioSample: SAMN12748569

+

BioProject: PRJNA565479

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831255.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYID01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 112.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433821 [UID] 15732448 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- [persephone page for the 16 PSRefSeqs: (https://web.persephonesoft.com/)

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125619.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125619.html new file mode 100644 index 00000000..3b074ee8 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125619.html @@ -0,0 +1,70 @@ +

About Oryza sativa XI-2B subgroup Os125619

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) (collected from India) is selected as the representative of XI-2B subpopulation, in which the accessions are mostly collected from India and Madagascar.

+ +

Notes for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-2B subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+ +

For more detailed information please see below:

+ +

Os125619RS1

+ +

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12748589

+

BioProject: PRJNA565480

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831355.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIE01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 113.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433761 [UID] 15732328 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC 125619):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYIE00000000

+

- [persephone page for the 16 PSRefSeqs: (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: N/A

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=125619

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125827.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125827.html new file mode 100644 index 00000000..ba87c18e --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa125827.html @@ -0,0 +1,69 @@ +

About Oryza sativa XI-3B2 subgroup Os125827

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 125827 (variety cv. LIU_XU::IRGC_109232-1) (collected from: China) is selected as the representative of XI-3B2 subpopulation, in which the accessions are mostly collected from China, and the Philippines.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 125827 (variety cv. LIU_XU::IRGC_109232-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3B2 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os125827RS1

+

Organism name: Oryza sativa (rice)

+

Infraspecific name: Cultivar: LIU XU::IRGC 109232-1

+

BioSample: SAMN13021815

+

BioProject: PRJNA577228

+

Submitter: University of ArizonaDate: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009829375.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: WGGU01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 138.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433841 [UID] 15732488 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127518.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127518.html new file mode 100644 index 00000000..d0c78e95 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127518.html @@ -0,0 +1,70 @@ +

About Oryza sativa XI-3B1 subgroup Os127518

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127518 (variety cv. KHAO_YAI_GUANG::IRGC_65972-1) (collected from: Thailand) is selected as the representative of XI-3B1 subpopulation, in which the accessions are mostly collected from Thailand, Lao_People_s_Democratic_Republic, and Cambodia.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Brief summary of the current assembly, please provide us with assembly accession, descriptions including data generator, sequencing technology, assembly strategy, quality, statistics and biosample

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127518 (variety cv. KHAO_YAI_GUANG::IRGC_65972-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3B1 subpopulation. The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os127518RS1

+

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12748590

+

BioProject: PRJNA565481

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831295.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIF01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 106.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433781 [UID] 15732368 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ + diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127564.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127564.html new file mode 100644 index 00000000..630c8162 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127564.html @@ -0,0 +1,73 @@ +

About Oryza sativa XI-3A subgroup Os127564

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127564 (variety cv. LIMA::IRGC_81487-1) (collected from: Indonesia) is selected as the representative of XI-3A subpopulation, in which the accessions are mostly collected from Indonesia, Thailand, and Malaysia.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Brief summary of the current assembly, please provide us with assembly accession, descriptions including data generator, sequencing technology, assembly strategy, quality, statistics and biosample

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127564 (variety cv. LIMA::IRGC_81487-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3A subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os127564RS1

+

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12715984

+

BioProject: PRJNA564572

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009829395.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VXJH01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 103.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433861 [UID] 15732528 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ +

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127652.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127652.html new file mode 100644 index 00000000..f5155494 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127652.html @@ -0,0 +1,42 @@ +

About Oryza sativa subgroup IR8

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations. Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa IRGC 127652 (aus variety cv. NATEL BORO::IRGC 34749-1) is selected as the representative of cA2 subpopulation.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127652 (aus variety cv. NATEL BORO::IRGC 34749-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA2 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank ?

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm?

+

- IRRI repo ?

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127742.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127742.html new file mode 100644 index 00000000..2f8c1def --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa127742.html @@ -0,0 +1,70 @@ +

About Oryza sativa XI-1B2 subgroup Os127742

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127742 (variety cv. PR_106::IRGC_53418-1) (collected from: India) is selected as the representative of XI-1B2 subpopulation, in which the accessions are mostly collected from India, and Philippines.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ + +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127742 (variety cv. PR_106::IRGC_53418-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1B2 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os127742RS1

+

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12672924

+

BioProject: PRJNA563359

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831045.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIB01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 105.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433811 [UID] 15732428 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa128077.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa128077.html new file mode 100644 index 00000000..79a900b5 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa128077.html @@ -0,0 +1,71 @@ +

About Oryza sativa GJ-trop2 subgroup Os128077

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 128077 (variety cv. KETAN_NANGKA::IRGC_19961-2) (collected from: Indonesia) is selected as the representative of GJ-trop2 subpopulation, in which the accessions are mostly collected from Indonesia.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 128077 (variety cv. KETAN_NANGKA::IRGC_19961-2) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-trop2 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

OS128077RS1

+

Organism name: Oryza sativa tropical japonica subgroup (rice)

+

BioSample: SAMN12718029

+

BioProject: PRJNA564615

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831275.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIC01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 125.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433801 [UID] 15732408 [GenBank]

+ + + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132278.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132278.html new file mode 100644 index 00000000..7797f32b --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132278.html @@ -0,0 +1,64 @@ +

About Oryza sativa GJ-subtrp subgroup Os132278

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 132278 (variety cv. CHAO_MEO::IRGC_80273-1) (collected from: Lao People's Democratic Republic) is selected as the representative of GJ-subtrp subpopulation, in which the accessions are mostly collected from India, Thailand, and Lao People’s Democratic Republic.

+ +

Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 132278 (variety cv. CHAO_MEO::IRGC_80273-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-subtrp subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os132278RS1

+

Organism name: Oryza sativa tropical japonica subgroup (rice)

+

BioSample: SAMN12748601

+

BioProject: PRJNA565484

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831315.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIH01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 123.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433791 [UID] 15732388 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC 132278):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYIH00000000

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: NA

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=132098

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132424.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132424.html new file mode 100644 index 00000000..17fac48c --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativa132424.html @@ -0,0 +1,64 @@ +

About Oryza sativa XI-2A subgroup Os132424

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 132424 (variety cv. GOBOL_SAIL_(BALAM)::IRGC_26624-2) (collected from: Bangladesh) is selected as the representative of XI-2A subpopulation, in which the accessions are mostly collected from India, and Bangladesh.

+ +

Notes for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 132424 (variety cv. GOBOL_SAIL_(BALAM)::IRGC_26624-2) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-2A subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os132424RS1

+

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12721963

+

BioProject: PRJNA564763

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831025.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VXJI01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 105.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433871 [UID] 15732538 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC 132424):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VXJI00000000

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: -NA

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=132244

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativaazucena.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativaazucena.html new file mode 100644 index 00000000..d5df4be4 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativaazucena.html @@ -0,0 +1,73 @@ +

About Oryza sativa GJ-trop1 subgroup OsAzucena

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 135833 (variety cv. Azucena) (collected from: Philippines) is selected as the representative of GJ-trop1 subpopulation, in which the accessions are mostly collected from Indonesia, Philippines, United_States_of_America, Cote_d_Ivoire, and Brazil.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 135833 (variety cv. Azucena) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-trop1 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

AzucenaRS1

+

Organism name: Oryza sativa Japonica Group (Japanese rice)

+

Infraspecific name: Cultivar: Azucena

+

BioSample: SAMN08217222

+

BioProject: PRJNA424001

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009830595.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: PKQC01

+

Assembly method: CANU v. 1.5; FALCON v. 1.8

+

Expected final version: no

+

Genome coverage: 130.0x

+

Sequencing technology: PacBio; Illumina

+

IDs: 5433851 [UID] 15732498 [GenBank]

+ + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to Azecena):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/PKQC00000000

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1180437

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1882787

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=125827

+ + +

Image

+ +

https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1882787

+ diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativair64.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativair64.html new file mode 100644 index 00000000..65559263 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativair64.html @@ -0,0 +1,77 @@ +

About Oryza sativa XI-1B1subgroup OsIR64

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 135929 (variety cv. IR64) (collected from: Philippines) is selected as the representative of XI-1B1 subpopulation, in which the accessions are mostly collected from the Philippines.

+ +

Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 135929 (variety cv. IR64) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1B1 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

OsIR64RS1

+

Organism name: Oryza sativa (rice)

+

Infraspecific name: Cultivar: IR64 (IRRI)

+

BioSample: SAMN10564385

+

BioProject: PRJNA509165

+

Submitter: University of Arizona

+

Date: 2020/01/22

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009914875.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: RWKJ01

+

Assembly method: MECAT v. 1.3; CANU v. 1.5; FALCON v. 2017.06.28-18.01-py2.7-ucs4

+

Expected final version: no

+

Genome coverage: 150.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5488871 [UID] 15884438 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ + +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IR64):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

+

Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

+

Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

+

Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

+

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/RWKJ00000000

+

- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1883010

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=135749

+ + +

Image

+ + + +

https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1883010

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativamh63.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativamh63.html new file mode 100644 index 00000000..92f3261e --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativamh63.html @@ -0,0 +1,68 @@ +

About Oryza sativa XI-adm subgroup MH63

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. Minghui 63 (collected from: China) is selected as the representative of XI-adm subpopulation, in which the accessions are mostly collected from China, India, Indonesia, Philippines, Bangladesh, Thailand, Lao_People_s_Democratic_Republic, Malaysia, Myanmar, Madagascar, abd Colombia.

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Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

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Assembly

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Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. Minghui 63 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-adm subpopulation.

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The whole DNA was sequenced by >100 X PacBio cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

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For more detailed information please refer to below:

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MH63RS2

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Organism name: Oryza sativa Indica Group (long-grained rice)

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Infraspecific name: Cultivar: Minghui 63

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BioSample: SAMN04274565

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BioProject: PRJNA302543

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Submitter: Huazhong Agricultural University

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Date: 2018/10/25

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Assembly level: Chromosome

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Genome representation: full

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GenBank assembly accession: GCA_001623365.2 (latest)

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RefSeq assembly accession: n/a

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RefSeq assembly and GenBank assembly identical: n/a

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WGS Project: LNNK02

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Assembly method: HGAP v. 3; FALCON v. 1.8; CANU v. 1.3; Miniasm v. 0.2

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Expected final version: no

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Genome coverage: 120.0x

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Sequencing technology: PacBio

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IDs: 2033571 [UID] 7637248 [GenBank]

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Annotation

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Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

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Variation

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Variation Data mapped to the assembly including SNP, SV, QTL, markers

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Large structural variation of 16 PSRefSeqs are available (including map to Minghui 63):

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  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
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  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
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  3. The syntenic region and variation could be identified between MH63 and ZS97 with the following link: https://rice.hzau.edu.cn/rice_rs2/
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References

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Zhang, Jianwei, Ling-Ling Chen, Shuai Sun, Dave Kudrna, Dario Copetti, Weiming Li, Ting Mu, et al. 2016. “Building Two Indica Rice Reference Genomes with PacBio Long-Read and Illumina Paired-End Sequencing Data.” Scientific Data.

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Zhang, Jianwei, Ling-Ling Chen, Feng Xing, David A. Kudrna, Wen Yao, Dario Copetti, Ting Mu, et al. 2016. “Extensive Sequence Divergence between the Reference Genomes of Two Elite Indica Rice Varieties Zhenshan 97 and Minghui 63.” Proceedings of the National Academy of Sciences of the United States of America 113 (35): E5163–71.

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Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

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Links

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- GenBank:https://www.ncbi.nlm.nih.gov/nuccore/LNNK00000000.2/

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- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

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- USDA repo for germplasm: NA

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- IRRI repo: NA

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Image

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http://rice.hzau.edu.cn/rice_rs2/

diff --git a/gramene/htdocs/ssi/species.incompl/about_Oryza_sativazs97.html b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativazs97.html new file mode 100644 index 00000000..b91b6167 --- /dev/null +++ b/gramene/htdocs/ssi/species.incompl/about_Oryza_sativazs97.html @@ -0,0 +1,69 @@ +

About Oryza sativa XI-1A subgroup OsZS97

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Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. Zhengshan 97 (collected from: China) is selected as the representative of XI-1A subpopulation, in which the accessions are mostly collected from China.

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Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

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Assembly

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Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. Zhengshan 97 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1A subpopulation.

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The whole DNA was sequenced by >100 X PacBio cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

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For more detailed information please refer to below:

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ZS97RS2

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Organism name: Oryza sativa Indica Group (long-grained rice)

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Infraspecific name: Cultivar: Zhenshan 97

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BioSample: SAMN04274564

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BioProject: PRJNA302542

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Submitter: Huazhong Agricultural University

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Date: 2018/10/23

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Assembly level: Chromosome

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Genome representation: full

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GenBank assembly accession: GCA_001623345.2 (latest)

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RefSeq assembly accession: n/a

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RefSeq assembly and GenBank assembly identical: n/a

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WGS Project: LNNJ02

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Assembly method: HGAP v. 3; FALCON v. 1.8; CANU v. 1.3; Miniasm v. 0.2

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Expected final version: no

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Genome coverage: 120.0x

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Sequencing technology: PacBio

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IDs: 2027271 [UID] 7620918 [GenBank]

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Annotation

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Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

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Variation

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Variation Data mapped to the assembly including SNP, SV, QTL, markers

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Large structural variation of 16 PSRefSeqs are available (including map to Zhengshan 97):

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  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020) (https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    3. +
  3. The syntenic region and variation could be identified between MH63 and ZS97 with the following link: https://rice.hzau.edu.cn/rice_rs2/
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References

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Zhang, Jianwei, Ling-Ling Chen, Shuai Sun, Dave Kudrna, Dario Copetti, Weiming Li, Ting Mu, et al. 2016. “Building Two Indica Rice Reference Genomes with PacBio Long-Read and Illumina Paired-End Sequencing Data.” Scientific Data.

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Zhang, Jianwei, Ling-Ling Chen, Feng Xing, David A. Kudrna, Wen Yao, Dario Copetti, Ting Mu, et al. 2016. “Extensive Sequence Divergence between the Reference Genomes of Two Elite Indica Rice Varieties Zhenshan 97 and Minghui 63.” Proceedings of the National Academy of Sciences of the United States of America 113 (35): E5163–71.

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Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

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Links

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Useful links to other resources

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- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/LNNJ00000000.2/

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- [persephone page for the 16 PSRefSeqs] (https://web.persephonesoft.com/)

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- USDA repo for germplasm: NA

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- IRRI repo: NA

+ + + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Aegilops_tauschii.html b/gramene/htdocs/ssi/species.weix/about_Aegilops_tauschii.html new file mode 100644 index 00000000..7a8a0487 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Aegilops_tauschii.html @@ -0,0 +1,72 @@ + +

Wheat genomics resources are developed as part of our involvement in the consortium Triticeae Genomics For Sustainable Agriculture, funded by the BBSRC, and led by TGAC.

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BBSRC logo

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About Aegilops tauschii

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Aegilops tauschii (goatgrass) is the diploid progenitor of the bread wheat D-genome, providing important evolutionary information for wheat. The bread wheat genome is a hexaploid, resulting from the hybridization of the wild A. tauschii with a cultivated tetraploid wheat, Triticum turgidum. This spontaneous event occured about 8,000 years ago in the Fertile Crescent.

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Assembly

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The genome of Aegilops tauschii accession AL8/78 was sequenced by the BGI using a whole-genome shotgum strategy, and assembled using SOAPdenovo software. The genome assembly achieved contigs with a N50 size of 4.51 kbp. Using paired-end information, and additional Roche/454 long-read sequences, the draft assembly was 4.23 Gbp, with a scaffold N50 length of 57.6 kbp.

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The chloroplast genome component and its gene annotation are also present. This was imported from ENA entry, JQ754651.

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Annotation

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34,498 protein-coding genes were predicted, using FGENESH and GeneID, supplemented with evidence-based information using RNA-Seq and ESTs sequences. For more details about genome sequencing and gene prediction see [1].

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Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

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Triticeae Repeats from TREP were aligned to the A. tauschii genome using RepeatMasker.

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Regulation and sequence alignments

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RNA-Seq data, ESTs and UniGene datasets have also been aligned to the Aegilops tauschii genome:

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Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. [5]

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The wheat genome assemblies previously generated by Brenchley et al. (PMID:23192148) have been aligned to the bread wheat survey sequence, Brachypodium, barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii). Homoeologous variants inferred between the three wheat genomes (A, B, and D) are displayed in the context of the gene models of these five genomes.

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Sequences of diploid progenitor and ancestral species permitted homoeologous variants to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

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The wheat gene alignments and the projected wheat SNPs are available on the Location view, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

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Links

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Links (Aegilops tauschii)

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  • GigaDB
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  • ENA study: SRP002455: Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors
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  • ENA study: DRP000562: RNASeq from seedling leaves of Aegilops tauschii
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  • TREP, the Triticeae Repeat Sequence Database
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Links (Triticum aestivum)

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  • MIPS Wheat Genome Database
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  • ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
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  • Triticum aestivum UniGene cluster sequences at NCBI
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  • Triticum aestivum ESTs at ENA
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References

  1. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.
    Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X et al. 2013. Nature. 496:91-95.
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  2. Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor.
    Iehisa JC, Shimizu A, Sato K, Nasuda S, Takumi S. 2012. DNA Res.. 19:487-497.
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  3. Image credit: Mark Nesbitt [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
    4. +
  4. Homoeolog-specific transcriptional bias in allopolyploid wheat.
    Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Amborella_trichopoda.html b/gramene/htdocs/ssi/species.weix/about_Amborella_trichopoda.html new file mode 100644 index 00000000..ceb98780 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Amborella_trichopoda.html @@ -0,0 +1,22 @@ + +

About Amborella trichopoda

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Amborella trichopoda is a small, tropical shrub endemic to New Caledonia. It is the only species in the genus Amborella, which is the only member of the family Amborellaceae. As the only living species on the sister lineage to all other flowering plants, it is an important reference for studying plant evolution. Individual Amborella trichopoda are usually sprawling understory shrubs, although occasionally they grow up to eight meters high. They have evergreen leaves and small, white to yellow flowers. The species is dioecious; female plants producing carpals and males producing stamens, and individual plants can change sex between flowerings. Unlike nearly all other flowering plants, they do not posses vessel elements for water conduction. Amborella's genome is a relatively compact 870Mb, arranged into 13 chromosome pairs.

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Assembly

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Amborella's draft genome sequence was published in December, 2013, by the Amborella Genome Project [1,2]. Initial sequencing and contig assembly was performed using a whole-genome shotgun (WGS) strategy. Contigs and scaffold assignments were refined, and superscaffolds constructed from them using evidence from end-sequenced BACs, single-molecule restriction digest (OpGen) experiments, and fluorescent in-situ hybridization (FISH) experiments.

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Annotation

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Ab initio annotation of genes and repetitive elements was performed using the DAWGPAWS [3] and EVidenceModeler [4] software packages. These annotations were refined through manual comparison with assembled Amborella cDNA transcripts, gene family analyses, and homology studies.

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References

  1. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
    Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC et al. 2013. Science. 342:1516-1517.
    2. +
  2. The Amborella genome and the evolution of flowering plants.
    2013. Science. 342:1241089.
    3. +
  3. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.
    Estill JC, Bennetzen JL. 2009. Plant Methods. 5:8.
    4. +
  4. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Genome Biol.. 9:R7.

Picture credit: Scott Zona via Wikimedia Commons: http://commons.wikimedia.org/wiki/File:Amborella_trichopoda_%283173820625%29.jpg

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About Arabidopsis lyrata

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Arabidopsis lyrata is a small perennial outcrossing brassica that is distributed within Eastern Asia, Europe and Northwestern America. A close relative of the dicot model, Arabidopsis thaliana, Arabidopsis lyrata has a genome size that is 1.5x larger with a haploid chromosome number of 8.

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Assembly

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The genome was assembled by the Stanford Human Genome Center with assistance from the A. lyrata community. Sequencing followed a whole genome shotgun strategy and achieved an average genome coverage of 8x. The 206.7 Mbp Araly1 assembly contains 695 nuclear scaffolds.

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Annotation

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The genome was annotated by the U.S. Department of Energy Joint Genome Institute (JGI) using collaborator-submitted data, custom JGI analyses, and the automated JGI Annotation Pipeline and is predicted to have approximately 32,670 genes.

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Links

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References

  1. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
    Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H et al. 2011. Nat. Genet.. 43:476-481.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Arabidopsis_thaliana.html b/gramene/htdocs/ssi/species.weix/about_Arabidopsis_thaliana.html new file mode 100644 index 00000000..c74f62a7 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Arabidopsis_thaliana.html @@ -0,0 +1,54 @@ + +

About Arabidopsis thaliana

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Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish. Arabidopsis is not of major agronomic significance, but it offers important advantages for basic research in genetics and molecular biology. Arabidopsis thaliana has a genome size of ~135 Mbp, and a haploid chromosome number of 5.

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Assembly

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The complete genome sequence of Arabidopsis thaliana was first published by the Arabidopsis Genome Initiative in 2000 [1] and was determined by a BAC-by-BAC sequencing strategy anchored to chromosomes using a variety of genetic and physical maps.

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Annotation

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This browser is based on data from Araport11 gene annotation, a comprehensive reannotation of the Col-0 genome released June, 2016. This annotation annotation was constructed using 113 public RNA-seq data sets along with annotation contributions from NCBI, UniProt, and laboratories conducting Arabidopsis thaliana research. Details of the structural and functional annotation steps to generate the Araport11 protein-coding gene set as well as consolidation and annotation of non-coding RNAs are described in this draft manuscript on bioRxiv

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Regulation

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Mappings for probes from the following expression arrays have been added:

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Variation

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The Arabidopsis variation database was updated in release 36 (June 2017) to the latest 1001 variation data set, covering more than 10 million variant loci across 1,135 samples (Cell 2016). The phenotypic data from a GWAS study of 107 phenotypes in 95 inbred lines carried out by Atwell et al. [5] has been retained.

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In this major update, the following arabidopsis variation datasets were obsoleted (but are still available in the Ensembl Plants Archive site):

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Links

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References

  1. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
    CHIA-YI Cheng, Vivek Krishnakumar, Agnes Chan, Seth Schobel, Christopher D. Town. 2016. bioRxiv.
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  2. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Arabidopsis Genome Initiative. 2000. Nature. 408:796-815.
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  3. The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
    Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L et al. 2008. Nucleic Acids Res.. 36:D1009-14.
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  4. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.
    Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjlmsson BJ et al. 2012. Nat. Genet.. 44:212-216.
    5. +
  5. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
    Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA et al. 2007. Science. 317:338-342.
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  6. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
    Atwell S, Huang YS, Vilhjlmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT et al. 2010. Nature. 465:627-631.

Picture credit: By Emmanuel Boutet (Own work) [GFDL, CC-BY-SA-3.0 or CC BY-SA 2.5-2.0-1.0], via Wikimedia Commons

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About Beta vulgaris

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Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates providing nearly 30% of the world's annual sugar production and a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n=18 chromosomes, has an estimated genome size of 714-758 Mbp and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops [1].

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Assembly

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The double haploid sugar beet line KWS2320 was sequenced using the Roche/454, Illumina and Sanger sequencing platforms. The initial assembly was integrated with genome-wide genetic and physical map information, resulting in 225 genetically anchored scaffolds (394.6 Mb), assigned to nine chromosomes. The final assembly comprised 566.6 Mbp in 2,171 scaffolds and 38,337 unscaffolded contigs. The N50 size was 2.01 Mb (the 72nd scaffold) and the chromosomally assigned fraction 84.7%. A total of 94% of the publicly available isogenic expressed sequence tags (ESTs) were located in the assembly, suggesting that gene-containing regions are comprehensively covered [1]

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Annotation

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A total of 27,421 protein-coding genes supported by mRNA evidence were predicted; 91% included start and stop codons [1].

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References

  1. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
    Dohm JC, Minoche AE, Holtgrwe D, Capella-Gutirrez S, Zakrzewski F, Tafer H, Rupp O, Srensen TR, Stracke R, Reinhardt R et al. 2014. Nature. 505:546-549.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Betula_pendula.html b/gramene/htdocs/ssi/species.weix/about_Betula_pendula.html new file mode 100644 index 00000000..e2d6783e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Betula_pendula.html @@ -0,0 +1,10 @@ + +

About Betula pendula

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About the assembly.

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About the annotation.

+ diff --git a/gramene/htdocs/ssi/species.weix/about_Brachypodium_distachyon.html b/gramene/htdocs/ssi/species.weix/about_Brachypodium_distachyon.html new file mode 100644 index 00000000..71076f9f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Brachypodium_distachyon.html @@ -0,0 +1,73 @@ + +

About Brachypodium distachyon

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Brachypodium distachyon, like Arabidopsis thaliana, has several features that recommend it as a model plant for functional genomic studies, especially in the grasses. It has a small, diploid genome (~355 Mbp), small physical size, a short life-cycle and few growth requirements. Brachypodium is related to the major cereal grain species but is understood to be more closely related to the Triticeae (wheat and barley) than to the other cereals.

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Assembly

+ +

This release represents the second improved Brachypodium distachyon (Bd21) genome including ~270 Mb of improved Brachypodium sequence. These regions were improved by dividing the gene space into ~2Mb overlapping pieces. Each region was manually inspected and then finished using a variety of technologies including Sanger (primer walks on subclones and fosmid templates, transposon sequencing on subclone templates), Illumina (small insert shatter libraries) and clone-based shotgun sequencing using both Sanger and Illumina libraries. 1,496 gaps were closed, and a total of 1.43 MB of base pairs was added to the assembly. Overall contiguity (contig N50) increased by a factor of 63 from 347.8Kb to 22 Mb.[1]

+ + + +

Annotation

+ +

74,756 transcript assemblies were constructed from 160M paired-end Illumina RNA-seq reads, 17,647 transcript assemblies from ~1.9M 454 reads. The transcript assemblies from RNA-seq reads were made using PERTRAN. 76,209 transcript assemblies were constructed using PASA from 314,866 sequences in total, consisting of the RNA-seq transcript assemblies above, as well as Sanger ESTs. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabidopsis (Arabidopsis thaliana), rice, sorghum, foxtail, grape, soybean and Swiss-Prot eukaryote proteins to soft-repeatmasked Brachypodium distachyon Bd21 genome using RepeatMasker with up to 2K BP extension on both ends unless extending into another locus on the same strand. Gene models were predicted by homology-based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan.

+ +

The end result was 34,310 loci containing protein-coding transcripts and 52,972 protein-coding transcripts

+ + + +

Sequence alignments

+ +

Brachypodium sylvaticum transcriptome

+ +

De novo gene models from the RNA-Seq analysis of three Brachypodium sylvaticum populations [2] were mapped to the B. distachyon reference genome. Click here for example. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC project PRJNA182761.

+ +

Triticum aestivum transcriptome

+ +

Wheat RNA-Seq, EST and UniGene datasets have been aligned to the Brachypodium distachyon genome:

+ + + + +

Variation

+ +

Brachypodium variation data

+ +

Approximately 394,000 genetic variations have been identified by the alignment of transcriptome assemblies from three slender false brome (Brachypodium sylvaticum) populations [2]. Two populations come from B. sylvaticum's native range (Greece and Spain) and one comes from its invasive range (Oregon). Both the transciptome alignments and variation data are available in Ensembl Plants. Click here for example.

+ +

Wheat inter-homoeologous variants

+ +

As part of the wheat genome analysis, we have aligned a set of Triticum aestivum (bread wheat) homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon genome. SNPs have been classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B [3].

+ +

The wheat sequence alignments and the projected homoeologous SNPs are available as tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

+ + + +

Links

+ +

Links (Brachypodium distachyon)

+ +

Links (Triticum aestivum)

+ +
  • MIPS Wheat Genome Database
    • +
  • ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
    • +
  • ENA study ERP001415: 454 sequencing of Triticum aestivum (bread wheat) cv. Chinese spring cDNA samples from a pool of tissues, from plants under drought stress and from circadian-sampled leaves
    • +
  • Triticum aestivum ESTs at ENA
    • +
  • Triticum aestivum UniGene cluster sequences at NCBI
    • +
+ +

References

  1. Genome sequencing and analysis of the model grass Brachypodium distachyon.
    The International Brachypodium Initiative. 2010. Nature. 463:763-768.
    2. +
  2. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae).
    Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, and Pankaj Jaiswal. 2013. Applications in Plant Sciences. 1(3):1200011.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Brassica_napus.html b/gramene/htdocs/ssi/species.weix/about_Brassica_napus.html new file mode 100644 index 00000000..2cb12e1c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Brassica_napus.html @@ -0,0 +1,19 @@ + +

About Brassica napus

+ +

Oilseed rape (Brassica napus) was formed ~7,500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72-fold genome multiplication since the origin of angiosperms and high gene content. Cultivation began in Europe during the Middle Ages and spread worldwide. Diversifying selection gave rise to oilseed rape (canola), rutabaga, fodder rape, and kale morphotypes grown for oil, fodder, and food.

+ + + +

Assembly

+ +

The homozygous B. napus genome of European winter oilseed cultivar ‘Darmor-bzh’ was assembled with long-read 454 GS-FLX+ Titanium and Sanger sequence. Correction and gap filling used 79 Gbp of Illumina HiSeq sequence. The final assembly of 849.7 Mbp was obtained using SOAP and Newbler, with 89% nongapped sequence. The assembly covers ~79% of the 1,130 Mbp genome and includes 95.6% of Brassica expressed sequence tags (ESTs) [1].

+ + + +

Annotation

+ +

A total of 101,040 gene models were estimated from 35.5 Gbp of RNA-Seq data in combination with ab initio gene prediction, protein and EST alignments, and transposon masking. Of these, 91,167 were confirmed by matches with B. rapa and/or B. oleracea predicted proteomes [1].

+ + +

References

  1. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B et al. 2014. Science. 345:950-953.
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About Brassica oleracea

+

Brassica oleracea L. (n=9, C genome) is a widely cultivated vegetable species integral to human diets, with a classification of cultivar groups based on the specialized morphology of their edible structures (kales, cabbages, Brussels sprouts, broccoli, kohl rabi and cauliflower).

+ + +

Assembly

+

The genomic sequence within this version of Ensembl includes 33,459 scaffolds (>200 bp) with an N50 of 850 kb that was assembled at NRC-Saskatoon using a hybrid approach from Illumina, Roche 454 and Sanger sequence data [1]. The assembly has been orientated and assigned to the nine pseudochromosomes using dense genotype-by-sequencing genetic maps.

+ + +

Annotation

+

Gene prediction of the assembled genomic scaffolds was conducted by JCVI and NRC-Saskatoon using MAKER and PASA [1]. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes.

+ + +

Links

+
  • http://brassica.info
    This site collates and exchanges open source information relating to Brassica genomics and genetics.
    • +
  • http://brassicadb.org
    The Brassica database (BRAD) is a web-based database of genetic data at the whole genome scale for important Brassica crops.
    • +
+ +

References

  1. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
    Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL et al. 2014. Genome Biol.. 15:R77.

Picture credit: "Fractal Broccoli" by Jon Sullivan. Licensed under Public domain via Wikimedia Commons.

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BrassicaInfoThe Brassica rapa genome browser has been developed through a joint effort by the Ensembl Genomes group and Rothamsted Research. From release 13 of Ensembl Genomes, the EBI will be maintaining the genome browser for B. rapa in the context of Ensembl Plants.

+ +

Rothamsted Research Acknowledges:

+ +
  • BBSRC for funding (grant number BB/E017797/1)
    • +
  • Ian Bancroft and Martin Trick at the John Innes Centre for providing the gene annotation.
    • +
  • Nick James and Sean May (NASC) for their assistance in establishing BrassEnsembl.
    • +
+ + +

About Brassica rapa

+ +

Brassica rapa (Chinese cabbage) is a widely cultivated leaf and root vegetable. The genome was sequenced as a contribution to the Multinational Brassica Genome Sequencing Project and was published in August 2011 (Wang X, et. al. Nature 2011).

+ + + +

Assembly

+ +

The genomic sequence within this version of Ensembl includes 193 large scaffolds assembled by CAAS-IVF, which have been orientated and assigned to pseudochromosomes using publicly available genetic markers.

+ + + +

Annotation

+ +

Gene prediction of the assembled genomic scaffolds has been conducted by CAAS-IVF using GLEAN and BLAT. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes (E=1E-5) and Gene Ontology terms are provided through significant similarity to UniProtKB proteins (E=1E-5).

+ + + +

Sequence alignments

+ +

Further annotations generated by RRes are displayed as additional tracks:

+ +
  • Arabidopsis coding sequences aligned using BLAT: +
    • Alignment parameters: minmatch(2), minscore(30), min identity(80), maxGap(2), evalue threshold(1e-5).
      • +
    • Dataset: 33,410 Arabidopsis TAIR v9 coding sequences.
      • +
    • External links: AtEnsembl transcripts.
      • +
    • +
  • A 95k Brassica UniGene set generated by JCVI aligned using BLAT: +
    • Alignment parameters: default BLAT (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
      • +
    • Dataset: 94,558 Brassica UniGenes.
      • +
    • +
  • A 135k Brassica UniGene set generated by RRes aligned using BLAT: +
    • Alignment parameters: default BLAT (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
      • +
    • Dataset: 135 201 Brassica UniGenes.
      • +
    • +
  • B. rapa BAC end sequences aligned using Decypher tera-blastn: +
    • Alignment parameters: match_score(1), mismatch_score(-3), open_penalty(-5), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-50), word_size (9), query_increment(3), extension_threshold(20), percent identity(95).
      • +
    • Dataset: 196,837 B. rapa BAC end sequences obtained from GenBank 5-Aug-2010.
      • +
    • External links: GenBank.
      • +
    • +
  • B. rapa ESTs aligned using Decypher tera-blastn: +
    • Alignment parameters: match_score(1), mismatch_score(-1), open_penalty(-1), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-20), word_size(9), query_increment(3), extension_threshold(20), percent identity(90).
      • +
    • Dataset: 902,700 Brassica ESTs obtained from GenBank 13-Aug-2010.
      • +
    • External links: GenBank.
      • +
    • +
+ +

References

  1. The genome of the mesopolyploid crop species Brassica rapa.
    Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F et al. 2011. Nat. Genet.. 43:1035-1039.

Picture credit: School Division, Houghton Mifflin Company

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About Cajunus cajan

+ +

Pigeonpea (Cajunus cajan) is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world[1]. Pigeonpea is grown on ∼5 million hectares, making it the sixth most important legume food crop globally. Domesticated >3,500 years ago in India, it is the main protein source for more than a billion people in the developing world and a cash crop that supports the livelihoods of millions of resource-poor farmers in Asia, Africa, South America, Central America and the Caribbean.

+ + + +

Assembly

+ +

Illumina GA and HiSeq 2000 Sequencing system were used to sequence 11 small-insert (180–800 bp) and 11 large-insert (2–20 kb) libraries [1]. This generated a total of 237.2 Gb of paired-end reads, ranging from 50–100 bp. Filtering and correction of the sequence data for very small and/or bad-quality sequences yielded 130.7 Gb of high-quality sequence, ∼163.4× coverage of the pigeonpea genome. Analysis of sequence data for GC content indicated a similar GC content distribution in the genomes of pigeonpea and soybean. Additionally, a set of 88,860 bacterial artificial chromosome (BAC) end sequences were generated using Sanger sequencing from two BAC libraries (69,120 clones) by using the HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes.

+ +

SOAPdenovo was used to assemble 605.78 Mb of the pigeonpea genome de novo, generating a sequence with a contig N50 of 21.95 kb, and longest contig length of 185.39 kb. This was then improved by using both the paired-BAC end sequences (41,302) that passed after filtering through RepeatMasker, and a genetic map comprising 833 marker loci. This increased N50 to 516.06 kb (longest scaffold in chromosome level of 48.97 Mb) . The draft genome assembly has <5.69% (∼34 Mb) unclosed gaps. These analyses showed that mapped genetic loci provide additional information for assembling superscaffolds, especially in regions in which scaffolds were not large enough to cross the repeat rich regions. The generated chromosome-scale scaffolds can be considered as 'pseudomolecules'. The estimated pigeonpea genome size, based on K-mer statistics, is 833.07 Mb, suggesting that the assembly captures 72.7% of the genome in the genome scaffolds. If only the 6,534 scaffolds >2 kb are considered, the assembly spans 578 Mb with an N50 of 0.58 Mb.

+ + + +

Annotation

+ +

A combination of de novo gene prediction programs and homology-based methods were used to predict gene models in the pigeonpea genome. These were combined using the GLEAN algorithm, resulting in the identification of 48,680 genes with an average transcript length of 2,348.70 bp, coding sequence size of 959.35 bp and 3.59 exons per gene. The majority of these predicted genes (99.6%) were supported either by de novo gene prediction, expressed sequence tags (EST)/unigenes or homology-based searching, or a combination of these approaches[1]. Of these genes Ensembl Plants display 2212 genes which were imported from ENA (European Nucleotide Archive).

+ + +

References

  1. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.
    Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena, Jessica A Schlueter, Mark T A Donoghue, Sarwar Azam, Guangyi Fan, Adam M Whaley et al. 2012. Nature Biotechnology. 30:83-89.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Chlamydomonas_reinhardtii.html b/gramene/htdocs/ssi/species.weix/about_Chlamydomonas_reinhardtii.html new file mode 100644 index 00000000..80b375f9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Chlamydomonas_reinhardtii.html @@ -0,0 +1,20 @@ + +

About Chlamydomonas reinhardtii

+ +

Chlamydomonas reinhardtii is a unicellular green alga from the phylum Chlorophyta, which diverged from land plants over a billion years ago. C. reinhardtii is a model species for studying a broad range of fundamental biological processes including the evolution of chloroplast-based photosynthesis and the structure of eukaryotic flagella. It is haploid, and has a nuclear genome comprising 17 chromosomes with a total size of ~120 Mbp.

+ + +

Assembly

+ +The 121 Mbp draft sequence of the Chlamydomonas nuclear genome was generated at 13x coverage by whole-genome, shotgun sequencing of plasmid and fosmid libraries, followed +by assembly into ~1500 contigs [1]. Assembly into chromosomes was done on the basis of genetic mapping. + + +

Annotation

+ +The set of gene predictions in version 5.5 incorporates new JGI gene expression data from 1M reads generated from nitrogen-starved cells on the 454 Titatnium platform as well as 239M 2x150 stranded Illumina reads and other smaller RNA-Seq datasets. The underlying gene prediction was performed by Mario Stanke using Augustus (annotation version u11.6) + +

The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).

+ + +

References

  1. The Chlamydomonas genome reveals the evolution of key animal and plant functions.
    Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marchal-Drouard L et al. 2007. Science. 318:245-250.

Picture credit: By Ninghui Shi [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0)], from Wikimedia Commons

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About Chondrus crispus

+ +

Wikipedia

+ +

Chondrus crispus - commonly called Irish moss or carrageen moss (Irish carraigín, "little rock") - is a species of red algae which grows abundantly along the rocky parts of the Atlantic coast of Europe and North America. In its fresh condition this protist is soft and cartilaginous, varying in color from a greenish-yellow, through red, to a dark purple or purplish-brown. The principal constituent is a mucilaginous body, made of the polysaccharide carrageenan, which constitutes 55% of its weight. The organism also consists of nearly 10% protein and about 15% mineral matter, and is rich in iodine and sulfur. When softened in water it has a sea-like odour and because of the abundant cell wall polysaccharides it will form a jelly when boiled, containing from 20 to 100 times its weight of water.

+ +

(Text and image from Wikipedia, the free encyclopaedia.)

+ + + +

Assembly

+ +

The assembly presented is the ASM35022v2 assembly submitted to INSDC with the assembly accession GCA_000350225.2.

+ + + +

Annotation

+ +

The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_000350225.2, with additional non-coding genes derived from Rfam. For more details, please visit INSDC annotation import.

+ +

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 59,047 Low complexity (Dust) features, covering 3 Mb (2.4% of the genome); 1,027 RepeatMasker features (annotated with the RepBase library), covering 0 Mb (0.1% of the genome); 19,602 RepeatMasker features (annotated with the PGSB-REdat library), covering 6 Mb (5.7% of the genome); 28,669 Tandem repeats (TRF) features, covering 3 Mb (2.7% of the genome).

+ + +

References

  1. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.
    Janoukovec J, Liu SL, Martone PT, Carr W, Leblanc C, Colln J, Keeling PJ. 2013. PLoS ONE. 8:e59001.

Picture credit: Wikipedia, the free encyclopedia

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About Corcorus capsularis

+ +

Corcorus capsularis (white jute) is one of the most important sources of natural fibre, along with Corcorus olitorius, covering ∼80% of global bast fibre production. The genome size is approximately 400 Mbp (n = 7). The assembly presented here is at the scaffold level, comprising 6,125 scaffolds with a scaffold N50 of 4.1 Mbp.

+ + + +

Assembly

+ +

Whole-genome shotgun sequencing was performed using Roche/454 GS FLX and was assembled using CABOG (version 7). A total of 13.69 Gbp of sequence data was generated (~30x), consisting of 7.87 Gbp of shotgun sequences (~20x), 2.04 Gbp of 3-kbp paired-end sequences (14x physical coverage), 2.26 Gbp of 8-kbp paired-end sequences (15x physical coverage), and 1.51 Gbp of 20-kbp paired-end sequences (11x physical coverage). The resulting assembly was 338 Mbp in 6,125 scaffolds with a scaffold N50 of 4.1 Mbp. Eighty per cent of the assembly was covered with 231 scaffolds (minimum length 120 kbp) and is estimated to cover about 82% of the genome [1].

+ +

More than 97% of the isotigs generated from transcriptome sequencing of seedlings aligned to the genome indicating comprehensive coverage of the gene-rich regions. In addition, more than 97% of the conserved core eukaryotic genes [2] were present in the genome.

+ + + +

Annotation

+ +

A total of 30,096 protein-coding genes were predicted by a combination of de novo, homology and transcriptome-based approaches [1].

+ + +

References

  1. Comparative genomics of two jute species and insight into fibre biogenesis.
    Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QM, Hossain MZ, Ahmed R, Hossain MS et al. 2017. Nature plants. 3:16223.
    2. +
  2. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
    Parra G, Bradnam K, Korf I. 2007. Bioinformatics. 23:1061.

Picture credit: By Luigi Chiesa (Scan by Luigi Chiesa) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.0 it (http://creativecommons.org/licenses/by-sa/2.0/it/deed.en)], via Wikimedia Commons

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About Cucumis sativus

+ +

Cucumber (Cucumis sativus) is a widely cultivated plant in the gourd family, Cucurbitaceae. It is a creeping vine that bears cucumiform fruits that are used as vegetables. There are three main varieties of cucumber: slicing, pickling, and seedless. Within these varieties, several cultivars have been created. In North America, the term "wild cucumber" refers to plants in the genera Echinocystis and Marah, but these are not closely related. The cucumber is originally from South Asia, but now grows on most continents. Many different types of cucumber are traded on the global market. [1]

+ + + +

Assembly

+ +

The 'Chinese long' inbred line 9930 was selected for the genome sequencing project. A total of 26.5 billion high-quality base pairs were generated, or 72.2-fold genome coverage, of which the Sanger reads provided 3.9-fold coverage and the Illumina GA reads provided 68.3-fold coverage The GA reads ranged in length from 42 to 53 bp. [2]

+ +

The final assembly is of length 195,669,205 bp consisting of 190 scaffolds (N50 = 29,076,228) and 11,366 contigs (N50 = 42,349) [3].

+ + + +

Annotation

+ +

Protein coding gene prediction was done using three methods (cDNA-EST, homology based and ab initio) and a consensus gene set was built by merging all of the results. A total of 26,682 genes were predicted, with a mean coding sequence size of 1,046 bp and an average of 4.39 exons per gene. Under an 80% sequence overlap threshold, 26.7% of the genes were supported by all three gene prediction methods, 25% had both ab initio prediction and homology-based evidence, and 7.4% had ab initio prediction and cDNA-EST expression evidence; the remaining genes were primarily derived from pure ab initio prediction, but the majority of these were supported by multiple gene finders. About 81% of the genes have homologs in the TrEMBL protein database, and 66% can be classified by InterPro. In total, 82% of the genes have either known homologs or can be functionally classified [2].

+ + +

References

  1. Cucumber.
    Wikipedia.
    2. +
  2. The genome of the cucumber, Cucumis sativus L.
    Sanwen Huang, Ruiqiang Li[]Songgang Li. 2009. Nature Genetics. 41:12751281.
    3. +
  3. NCBI page for Cucumis sativus (cucumber) assembly.
    NCBI.

Picture credit: By Francisco Manuel Blanco (O.S.A.) [Public domain], via Wikimedia Commons

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About Cyanidioschyzon merolae

+ +

Cyanidioschyzon merolae is a unicellular red alga from the phylum Rhodophyta and is one of the most primitive red algae. Rhodophyta is an evolutionarily interesting group that falls in Archaeplastida along with green plants but has also given rise to highly diverse groups of protists, including the photosynthetic and non-photosynthetic Chromalveolata. C. merolae can live in acidic hot springs, with pH below 2 and at 45°C.

+ + + +

Assembly

+ +

The nuclear genome is compact (16 Mbp), comprising 20 chromosomes with 5,331 predicted genes. Interestingly, only 26 of the predicted genes have introns.

+ + + +

Annotation

+ +

The genome annotation for Cyanidioschyzon merolae has been imported from Cyanidioschyzon merolae Genome project.

+ +

The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

+ + + +

Links

+ + + +

References

  1. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.
    Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K et al. 2004. Nature. 428:653-657.
    2. +
  2. Image credit: NEON (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons.
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About Daucus carota subsp. sativus

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Carrot is a globally important root crop whose production has quadrupled between 1976 and 2013, outpacing the overall rate of increase in vegetable production and world population growth through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions[1]

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Assembly

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An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. BAC end sequences was used and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions.

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The resulting v2.0 assembly spans 421.5 Mbp and contains 4,907 scaffolds (N50 of 12.7 Mbp), accounting for approximately 90% of the estimated genome size. The scaftig N50 of 31.2 kbp is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mbp) of the assembled genome is included in only 60 super-scaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4 [1].

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Annotation

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In assembly v1.0 gene annotation, 32,113 genes were predicted, of which 79% had substantial homology with known genes. The majority (98.7%) of gene predictions had supporting cDNA and/or EST evidence, demonstrating the high accuracy of gene prediction. Relative to five other closely related genomes, carrot was enriched for genes involved in a wide range of molecular functions. 564 tRNAs, 31 rRNA fragments, 532 small nuclear RNA (snRNA) genes, and 248 microRNAs (miRNAs) were also identified, distributed among 46 families.[1]

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References

  1. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.
    Massimo Iorizzo, Shelby Ellison, Douglas Senalik, Peng Zeng, Pimchanok Satapoomin, Jiaying Huang, Megan Bowman, Marina Iovene, Walter Sanseverino, Pablo Cavagnaro et al. 2016. Nature Genetics. 48:657666.
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About Dioscorea rotundata

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White Guinea yam (Dioscorea rotundata Poir.) is a common staple food that has contributed enormously to the subsistence and socio-cultural life of millions of people principally in West and Central Africa. Belonging to the monocotyledon the Dioscorea genus, under the family Dioscoreaceae, there are about 450 known species mainly distributed in tropical and subtropical regions of the world. The entire genus is characterised by the occurrence of separate male and female plants (dioecy), a rare trait in angiosperms that has limited efficient breeding. The reference for D. rotundata comes from a diploid individual with an assembled genome size of 594 Mb.

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Assembly

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The TDr96_F1 line used for whole genome sequencing was selected from F1 progeny obtained from an open-pollinated D. rotundata breeding line (TDr96/00629) grown under field conditions on the experimental fields of the International Institute of Tropical Agriculture (IITA) in Nigeria. Total DNA from leaf tissue was used for construction of paired-end and mate-pair libraries (2, 3, 4, 5, 6, 8, 20, and 40 Kb insert). These were sequenced using the Illumina MiSeq and HiSeq2500 platforms. In addition, 30,750 BAC clones corresponding to 3,072 Mb of sequence and 5.4× genome coverage were constructed. Of these, 9984 clones were used for BAC-end sequencing, with paired-end reads. A total of 85.14 Gb of sequence data was generated, representing ~149.4x coverage of the 570 Mb genome size estimated by flow cytometry [1].

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Reads were assembled following the ALLPATHS-LG pipeline, using paired-end and mate-pair data, with additional scaffolding carried out using SSPACE and the BAC-end reads. Scaffolds were anchored and ordered into 21 pseudo-chromosomes using a genetic map generated from 150 F1 individuals, obtained from a cross between TDr97/02627 (P1:Female) and TDr99/02627 (P2:Male) breeding lines using RAD-tags as linkage markers. The 21 pseudo-chromosomes represent 76.5 % of the total scaffolds, with a size of ~454 Mb [1].

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Annotation

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Gene models were generated using MAKER, with publicly available homologous EST and protein sequences from related species, and assembled transcripts generated using RNA-seq from 18 different D. rotundata tissues. An initial MAKER set of gene models was combined with a legacy AUGUSTUS annotation using JIGSAW to produce 26,198 gene models. These were functionally annotated using BLAST2GO and InterProSCAN [1].

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Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 8,371 RepeatMasker features (with the RepBase library), covering 1 Mb (0.2% of the genome); 918,128 Low complexity (Dust) features, covering 83 Mb (18.2% of the genome); 193,894 RepeatMasker features (with the reDAT library), covering 58 Mb (12.8% of the genome); 281,939 Tandem repeats (TRF) features, covering 22 Mb (4.9% of the genome).

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References

  1. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.
    Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A et al. 2017. BMC Biol.. 15:86.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Galdieria_sulphuraria.html b/gramene/htdocs/ssi/species.weix/about_Galdieria_sulphuraria.html new file mode 100644 index 00000000..9323bdde --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Galdieria_sulphuraria.html @@ -0,0 +1,21 @@ + +

About Galdieria sulphuraria

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Galdieria sulphuraria is an extremophilic unicellular species of red algae. It is the type species of the genus Galdieria. It is known for its broad metabolic capacities, including photosynthesis and heterotrophic growth on over 50 different extracellular carbon sources. The members of the Cyanidiophyceae family are among the most acidophilic known photosynthetic organisms, and the growth conditions of G. sulphuraria, pH between 0 and 4, and temperatures up to 56°C, are among the most extreme known for eukaryotes. Analysis of its genome suggests that its thermoacidophilic adaptations derive from horizontal gene transfer from archaea and bacteria, another rarity among eukaryotes.

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Assembly

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The assembly presented is the ASM34128v1 assembly submitted to INSDC with the assembly accession GCA_000341285.1.

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Annotation

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The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_000341285.1, with additional non-coding genes derived from Rfam. For more details, please visit INSDC annotation import.

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Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 9,272 Low complexity (Dust) features, covering 0 Mb (3.6% of the genome); 251 RepeatMasker features (annotated with the RepBase library), covering 0 Mb (0.3% of the genome); 1,654 RepeatMasker features (annotated with the PGSB-REdat library), covering 0 Mb (1.5% of the genome); 1,406 Tandem repeats (TRF) features, covering 0 Mb (1.0% of the genome).

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References

  1. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.
    Schnknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Brutigam A, Baker BJ, Banfield JF, Garavito RM et al. 2013. Science. 339:1207-1210.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Glycine_max.html b/gramene/htdocs/ssi/species.weix/about_Glycine_max.html new file mode 100644 index 00000000..d1c14bc8 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Glycine_max.html @@ -0,0 +1,27 @@ + +

About Glycine max

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Glycine max (soybean) is a crop legume that globally constitutes one of the most important sources of animal feed protein and cooking oil. Having originated in East Asia soy is now cultivated world-wide with greatest production in the U.S. Though only a minor proportion of the crop is eaten directly by humans, soybean is a valuable source of protein, containing all essential amino acids, and frequently used as a dietary substitute for meat. Like other legumes, soybean is able to fix atmospheric nitrogen by engaging in a symbiotic relationship with microbial organisms. The complete sequence of the soybean genome not only impacts research and breeding of this crop, but also serves as a reference for genomics research in other legumes. Representing the order Fabales within the eudicot taxonomy, the sequence will also advance research in comparative phylogenomics. As a paleopolyploid, the soybean genome shows evidence of two ancient whole genome duplications, one early in the legume lineage and a second more recent event specific to the soybean lineage. The soybean genome has 20 chromosomes and an estimated size of 1,115 Mbp.

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Assembly

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Glycine max var. Williams 82 was sequenced, assembled, and annotated by the U.S. Department of Energy Joint Genome Institute (JGI) in collaboration with a consortium of research labs and published in 2010. About 13 million shotgun Sanger reads were assembled into 20 chromosomes totalling 975 Mbp with an additional amount in unmapped scaffolds.

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Annotation

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The v1.1 gene set integrates ~1.6 M ESTs and 1.5 billion paired-end Illumina RNA-seq reads with homology- and ab initio-based gene predictions. A total of 54,175 protein-coding loci were predicted and classified into six levels of support (see JGI Phytozome for additional details).

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Links

+ + + +

References

  1. Genome sequence of the palaeopolyploid soybean.
    Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J et al. 2010. Nature. 463:178-183.
    2. +
  2. Image credit: USDA.
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About Gossypium raimondii

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Gossypium raimondii is a species of cotton plant endemic to northern Peru. The Gossypium genus is ideal for investigating emergent consequences of polyploidy. A-genome diploids native to Africa and Mexican D-genome diploids diverged ∼5–10 Myr ago. They were reunited ∼1–2 Myr ago by trans-oceanic dispersal of a maternal A-genome propagule resembling G. herbaceum to the New World, hybridization with a native D-genome species resembling G. raimondii, and chromosome doubling. The nascent AtDt allopolyploid spread throughout the American tropics and subtropics, diverging into at least five species; two of these species (G. hirsutum and G. barbadense) were independently domesticated to spawn one of the world’s largest industries (textiles) and become a major oilseed.[1]

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Assembly

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Assembly of 80,765,952 sequence reads used a modified version of Arachne, integrating linear (15x genome coverage) and paired (3.1x genome coverage) Roche 454 libraries corrected using 41.9 Gbp Illumina sequence, with 1.54x paired-end Sanger sequences from two subclone, six fosmid and two BAC libraries. Cotton genetic and physical maps, and Vitis vinifera and Theobroma cacao synteny were used to identify 51 joins across 64 scaffolds to form the 13 chromosomes. The remaining scaffolds were screened for contamination to produce a final assembly of 1,033 scaffolds (19,735 contigs) and 761.4 Mbp [1][2].

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Annotation

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85,746 transcript assemblies were made from about 1 billion pairs of D5 paired-end Illumina RNA-Seq reads, 55,294 transcript assemblies about 0.25B D5 single end Illumina RNAseq reads, 62,526 transcript assemblies from 0.15B TET single end Illumina RNAseq reads. All these transcript assemblies from RNAseq reads were made using PERTRAN. 120,929 transcript assemblies were constructed using PASA from 56,638 D5 Sanger ESTs, 2.5M D5 454 RNAseq reads and all RNA-Seq transcript assemblies above. 133,073 transcript assemblies were constructed using PASA from 296,214 TET Sanger ESTs and about 2.9M TET 454 reads. The larger number of transcript assemblies from fewer TET sequences is due to fragment nature of the assemblies. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabi (Arabidopsis thaliana), cacao, rice, soybean, grape and poplar proteins to repeat-soft-masked G. raimondii genome using RepeatMasker with up to 2 kbp extension on both ends unless extending into another locus on the same strand.

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Gene models were predicted by homology-based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan. The best scored predictions for each locus are selected using multiple positive factors including EST and protein support, and one negative factor: overlap with repeats. The selected gene predictions were improved by PASA. Improvement includes adding UTRs, splicing correction, and adding alternative transcripts. PASA-improved gene model proteins were subject to protein homology analysis to above mentioned proteomes to obtain Cscore and protein coverage. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score and protein coverage is highest percentage of protein aligned to the best of homologs. PASA-improved transcripts were selected based on Cscore, protein coverage, EST coverage, and its CDS overlapping with repeats. The transcripts were selected if its Cscore is larger than or equal to 0.5 and protein coverage larger than or equal to 0.5, or it has EST coverage, but its CDS overlapping with repeats is less than 20%. For gene models whose CDS overlaps with repeats for more that 20%, its Cscore must be at least 0.9 and homology coverage at least 70% to be selected. The selected gene models were subject to Pfam analysis and gene models whose protein is more than 30% in Pfam TE domains were removed. Final gene set has 37,505 protein coding genes and 77,267 protein coding transcripts[1][2].

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References

  1. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Andrew H. Paterson, Jonathan F. Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C. Showmaker, Shengqiang Shu, Joshua Udall et al. 2012. Nature. 492:423427.
    2. +
  2. Gossypium raimondii (D5) genome JGI assembly v2.0 (annot v2.1).
    COTTONGEN.
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About Helianthus annuus

+ +

The domesticated sunflower, Helianthus annuus, is a globally important oil crop that has promise for climate change adaptation, maintaining stable yields across a wide variety of environmental conditions, including drought. The large genome (3.6 gigabases) consists of long and highly similar repeats, making the assembly very challenging.

+ + + +

Assembly

+ +

The assembly of Helianthus annuus inbred line XRQ was performed using 102-fold coverage of single-molecule real-time (SMRT) cells on the PacBio RS II platform. In total 32.8 million subreads were generated with a read N50 of 13.7 kb and a mean read length of 10.3 kb. The 367 Gbp of raw sequence (340 Gbp of subread data) was assembled into 3 Gbp (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content [1].

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The assembly was performed using WGS 8.3. Reads were first corrected using the PBcR wgs8.3rc1 assembly pipeline and the assembly was polished with quiver after the construction of the pseudomolecules. To overcome challenges associated with the sunflower genome assembly, substantial parameter tuning, code modification and software development were required [1].

+ + + +

Annotation

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Gene models were predicted using EuGene 4.2. The plant early release of BUSCO (release July 2015) was run on the set of predicted transcripts, and it detected 92% of complete gene models (590 complete single copy and 291 duplicated, respectively) plus 10 additional fragmented gene models.

+ + +

References

  1. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.
    Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brire C, Owens GL, Carrre S, Mayjonade B et al. 2017. Nature. 546:148-152.

Picture credit: By i_am_jim (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

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About Hordeum vulgare

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Hordeum vulgare (barley) is the world's fourth most important cereal crop and an important model for ecological adaptation, having been cultivated in all temperate regions from the Arctic Circle to the tropics. It was one of the first domesticated cereal grains originating in the Fertile Crescent over 10,000 years ago. About two-thirds of the global barley crop is used for animal feed, while the remaining third underpins the malting, brewing, and distilling industries. Although the human diet is not a primary use, barley offers potential health benefits, and is still the major calorie source in several parts of the world. Barley is a diploid member of the grass family, making it a natural model for the genetics and genomics of the Triticeae tribe, including polyploid wheat and rye. With a haploid genome size of ~5.3 Gbp in 7 chromosomes, it is one of the largest diploid genomes sequenced to date.

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Assembly

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The barley genome assembly presented here was produced by the International Barley Genome Sequencing Consortium (IBSC) [1] using a hierarchical approach. Initially multiplexed short read BAC by BAC contig assemblies (N50: 79 kbp) were scaffolded using physical, genetic and optical maps (N50: 1.9 Mbp) and were assigned to chromosomes using a POPSEQ genetic map. Finally, the linear order and orientation of scaffold sequences was determined using chromosome-conformation capture sequencing (Hi-C) [2].

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The final chromosome-scale assembly consisted of 6,347 ordered super-scaffolds composed of merged assemblies of individual BACs, representing 4.79 Gbp (~95%) of the genomic sequence content, of which 4.54 Gbp have been assigned to precise chromosomal locations in the Hi-C map.

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The chloroplast genome component and its gene annotation are also present (KC912687).

+ + + +

Annotation

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Mapping of transcriptome data and reference protein sequences from other plant species identified 83,105 putative gene loci including protein coding genes, non-coding RNAs, pseudogenes and transcribed transposons. These loci were filtered and divided into 39,734 high-confidence and 41,949 low-confidence genes based on sequence homology. Additionally 19,908 long non-coding RNAs and 792 microRNA precursor loci were predicted. Using a set of conserved eukaryotic core genes (BUSCO), it was estimated that the predicted gene models represent 98% of the cv. Morex barley gene complement.

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Regulation

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Mappings for probes from the Barley1 GeneChip array, the Agilent barley full-length cDNA array, and the barley PGRC1 10k A and B array set can be viewed in the browser. For example, see the results for Contig2083_s_at.

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Variation

+ +

Five sources of barley variation data are shown:

+ +
  1. Variation data from WGS survey sequencing of four cultivars, Barke, Bowman, Igri, Haruna Nijo and a wild barley (H. spontaneum). The data was collected as described in [3].
    2. +
  2. SNPs discovered from RNA-Seq performed on the embryo tissues of 9 spring barley varieties (Barke, Betzes, Bowman, Derkado, Intro, Optic, Quench, Sergeant and Tocada) and Morex using Illumina HiSeq 2000 [3].
    3. +
  3. Approximately five million variations from population sequencing of 90 Morex x Barke individuals [4].
    4. +
  4. Approximately six million variations from population sequencing of 84 Oregon Wolfe barley individuals [4].
    5. +
  5. SNPs from the Illumina iSelect 9k barley SNP chip[6]. ~2,600 mapped genetic markers associated with these SNPs [5] are also displayed.
    6. +
+ +

References

  1. A chromosome conformation capture ordered sequence of the barley genome.
    Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J et al. 2017. Nature. 544:427-433.
    2. +
  2. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. 2009. Science. 326:289-93.
    3. +
  3. A physical, genetic and functional sequence assembly of the barley genome.
    International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K et al. 2012. Nature. 491:711-716.
    4. +
  4. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.
    Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S et al. 2014. Plant Physiol.. 164
    5. +
  5. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
    Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muoz-Amatrian M, Close TJ, Wise RP, Schulman AH et al. 2013. Plant J.. 76:718-727.

Picture credit: Lucash (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons

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These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the Leersia perrieri in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Leersia perrieri

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Leersia perrieri comes from Madagascar. It was the nearest outgroup of the genus Oryza included in the OMAP project. It has 12 chromosomes with a nuclear genome size of 323Mb (flow cytometry). The sequencing and assembly of this genome was carried out as part of the Oryza Genome Evolution project funded by NSF Award #1026200.

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Assembly

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The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession IRGC105164. Illumina reads of different library sizes were assembled with Allpaths-LG and gaps were closed with GapFiller. The estimated coverage from the WGS was 150x. Total sequence length is 266,687,832 bp; Number of contigs is 10,288; Contig N50: 48,151bp.

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Annotation

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Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

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Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene and Ensembl Plants project include:

+ +
  • Gene phylogenetic trees with other other Gramene species, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Lupinus_angustifolius.html b/gramene/htdocs/ssi/species.weix/about_Lupinus_angustifolius.html new file mode 100644 index 00000000..87af8f61 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Lupinus_angustifolius.html @@ -0,0 +1,19 @@ + +

About Lupinus angustifolius

+ +

Lupins are grain legumes that form an integral part of sustainable farming systems and have been an important part of the human diet for thousands of years. Planted in rotation with cereal crops, lupins reduce the need for nitrogenous fertilizer, provide valuable disease breaks and boost cereal yields. Lupins thrive on low-nutrient soils due to their ability to fix atmospheric nitrogen in symbiosis with beneficial bacteria and efficiently take up phosphorus from soils. Consequently, they are effective ecological pioneers and able to colonize extremely impoverished soils such as coastal sand dunes and new lava soils set down by recently erupted volcanoes. Narrow-leafed lupin (Lupinus angustifolius) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free [1].

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Assembly

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The haploid genome size for NLL was previously estimated by flow cytometry to be 924 Mbp. K-mer-based estimation of genome size predicted a similar value of 951 Mb. Initial assembly of the Tanjil genome using only paired-end Illumina data produced 191 701 scaffolds in 521 Mbp, with an N50 of 10,137 and N50 length of 13.8 kbp. The assembly was improved via scaffolding with additional paired-end, mate-pairs and BAC-end data totalling an average coverage of 162.8x. This resulted in a contig assembly with 1,068,669 contigs, totalling 810 Mbp or 85% of the k-mer-based estimated genome size. The final scaffold assembly after removing scaffolds less than 200 bp comprised 14,379 scaffolds totalling 609 Mbp with a contig N50 length of 45,646 bp and scaffold N50 of 232 and scaffold N50 length of 703 Kb [1].

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Annotation

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A total of 33,076 protein-coding genes were annotated after combining evidence from transcriptome alignments derived from five different tissue types (leaf, stem, root, flower and seed), protein homology, and in silico gene prediction. Additionally, peptide data from proteomics analysis of leaf, seed, stem and root samples were mapped to both the translated gene annotations and the 6-frame translation of the whole-genome assembly. Proteogenomic comparison of peptide-mapping versus gene annotation supported between 94 and 1134 annotations per tissue type, and provided valuable information on tissue localization for the products of these genes. InterPro terms were the most informative functional annotation assigned to NLL proteins with 26,580 (80.4%) proteins annotated [1].

+ + +

References

  1. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plantmicrobe interactions and legume evolution.
    James K. Hane, Yao Ming, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven Cannon et al. 2016. Plant Biotechnology Journal. 15:318-330.
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About Manihot esculenta

+ +

Cassava (Manihot esculenta Crantz) is grown throughout tropical Africa, Asia and the Americas for its starchy storage roots, and feeds an estimated 750 million people each day. Farmers choose it for its high productivity and its ability to withstand a variety of environmental conditions (including significant water stress) in which other crops fail. However, it has low protein content, and is susceptible to a range of biotic stresses. Despite these problems, the crop production potential for cassava is enormous, and its capacity to grow in a variety of environmental conditions makes it a plant of the future for emerging tropical nations. Cassava is also an excellent energy source - its roots contain 20-40% starch that costs 15-30% less to produce per hectare than starch from corn, making it an attractive and strategic source of renewable energy [2].

+ + + +

Assembly

+ +

This assembly was created by the DOE-Joint Genome Institute and was obtained by a whole genome shotgun (WGS) strategy, using 454 Life Sciences technology. The cassava genome assembled into 12,977 scaffolds span a total of 532.5 Mbp [1].

+ + + +

Annotation

+ +

To produce the current "Cassava V6.1" gene set, the homology-based gene prediction programs FgenesH and GenomeScan were used, along with the PASA program to integrate expression information from cassava ESTs and RNA-Seq.

+ +

Transcript data from three sources were integrated. First, RNA-Seq root and shoot tissues from Albert and Namikonga varieties, with and without challenge by CBSV 1x50 (1,055,722,008 initial reads, 895,271,180 reads after quality trimming) and 2x100 (340,899,946 initial reads; 282,586,400 reads after quality trimming) reads were aligned to the genome and assembled with phytozome in-house software Pertran. This yielded 51,588 and 62,488 transcript assemblies from PE and SE reads respectively. These were aligned to the genome with PASA (90 % identity and 60% coverage cutoffs) to make 69,624 aligned assemblies. In addition, ESTs from previous 454 sequencing were assembled with Pertran and added to 80,459 ESTs from GenBank and aligned to the genome with PASA (95% identity, 60% coverage) to generate 27,470 aligned assembles [2].

+ + +

References

  1. The Cassava Genome: Current Progress, Future Directions.
    Simon Prochnik, Pradeep Reddy Marri, Brian Desany, Pablo D. Rabinowicz, Chinnappa Kodira, Mohammed Mohiuddin, Fausto Rodriguez, Claude Fauquet, Joseph Tohme, Timothy Harkins et al. 2012. Tropical Plant Biology. 5:88-94.
    2. +
  2. Phytozome: a comparative platform for green plant genomics.
    David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam and Daniel S. Rokhsar. 2012. Nucleic Acids Research. 40
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Medicago_truncatula.html b/gramene/htdocs/ssi/species.weix/about_Medicago_truncatula.html new file mode 100644 index 00000000..fc840165 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Medicago_truncatula.html @@ -0,0 +1,43 @@ + +

About Medicago truncatula

+ +

Medicago truncatula (Barrel Medic) is a small annual legume native to the Mediterranean region. As other legumes, it forms symbioses with nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi.
+This species has been chosen as a model organism for legume biology because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production, and is amenable to genetic transformation.
M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox. The complete reference sequence displayed here is the 4.0 assembly update published in 2014 [2]. The nuclear genome has 8 chromosomes.

+ + + +

Assembly

+ +

Medicago truncatula cultivar A17 was sequenced and assembled by the Medicago truncatula Sequencing Consortium in 2011 [1]. The draft sequence is based on a BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes.

+ +

In 2014, the assembly was updated (Mt 4.0) [2] and replaces the previous assembly (Mt3.5). Whereas the Mt3.5 release consisted of ~250 Mb in pseudomolecules and ~100 Mb of unanchored sequence, the Mt4.0 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~330 Mb aligns accurately with the Optical Map. Most of the sequences and genes that were previously in the unanchored portion of Mt3.5 have now been incorporated into Mt4.0 pseudomolecules, with the exception of only ~20Mb of unplaced sequence.

+ + + +

Annotation

+ +

Genome annotation (Mt3.5) was carried out by the International Medicago Genome Annotation Group (IMGAG) [1]. JCVI has continued to curate and improve the M. truncatula genome sequence and annotation, and published in 2014 a new gene set (Mt4.0) [2]. Altogether, Pseudomolecules and unassigned BACs (Mt4.0) contain a total of 50,444 protein-coding gene loci (~31,500 high confidence genes and ~19,000 low confidence genes).

+ +

The new pseudomolecules were annotated by combining Mt3.5 gene models, with predictions from Augustus and FGENESH as well as expression data and protein matches primarily using Evidence Modeler (EVM). Whenever possible, gene identifiers have been preserved between Mt3.5 and Mt4.0.

+ +

Non coding RNA genes have also been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).

+ + + +

Regulation

+ +

269,501 EST sequences have been aligned to the genome with STAR.

+ + + +

Links

+ + + +

References

  1. The Medicago genome provides insight into the evolution of rhizobial symbioses.
    Young N,Debell F,Oldroyd GED,Geurts R, Cannon ED,Udvardi MK,Benedito VA,Mayer KFX,Gouzy J,Schoof H et al. 2011. Nature. 480:520-524.
    2. +
  2. An improved genome release (version Mt4.0) for the model legume Medicago truncatula.
    Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H et al. 2014. BMC Genomics. 15:312.
    3. +
  3. Image from WikiCommons.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Musa_acuminata.html b/gramene/htdocs/ssi/species.weix/about_Musa_acuminata.html new file mode 100644 index 00000000..3ffc20d0 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Musa_acuminata.html @@ -0,0 +1,22 @@ + +

About Musa acuminata

+ +

Musa acuminata (banana) is native to tropical South and Southeast Asia and is cultivated throughout the tropics. Grown primarily for its fruit, rich in starch, banana is the most popular fruit in industrialized countries. Cultivars mainly involve Musa acuminata (A-genome) and Musa balbisiana (B-genome) and are sometimes diploid but generally triploid. Banana is the first non-grass monocotyledon to be sequenced, making it an important genome for the comparative analysis of plants.

+ + + +

Assembly

+ +

The genome sequence, assembly and protein coding genes annotation of the Musa acuminata ssp. malaccensis doubled-haploid genome have been generated by the Global Musa Genomics Consortium, led jointly by the CIRAD and the Genoscope.

+ +

Its genome was released in July 2012 consisting of 24,425 contigs and 7,513 scaffolds with a total length of 472.2 Mbp, which represented 90% of the estimated DH-Pahang genome size. 70% of the assembly (332 Mbp) were anchored along the 11 Musa linkage groups of the Pahang genetic map.

+ + +

Annotation

+ +

About 36,500 protein-coding genes were identified, as well as 235 microRNAs from 37 families.

+ + +

References

  1. The Genetic Diversity of Banana in Figures.
    Lescot T.. 2011. FruiTrop..
    2. +
  2. Image credit: Telrnya (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
    3. +
  3. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
    D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M et al. 2012. Nature. 488:213-217.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Nicotiana_attenuata.html b/gramene/htdocs/ssi/species.weix/about_Nicotiana_attenuata.html new file mode 100644 index 00000000..e101a9ac --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Nicotiana_attenuata.html @@ -0,0 +1,19 @@ + +

About Nicotiana attenuata

+ +

The pyridine alkaloid nicotine, whose addictive properties are well known to humans, is the signature compound of the genus Nicotiana (Solanaceae). In nature, nicotine is arguably one of the most broadly effective plant defense metabolites, in that it poisons acetylcholine receptors and is thereby toxic to all heterotrophs with neuromuscular junctions. Field studies using genetically modified Nicotiana attenuata(coyote tobacco) plants, an annual wild diploid native to western North America, have revealed that this toxin fulfills multifaceted ecological functions that contribute to plant fitness [1].

+ + + +

Assembly

+ +

The sequencing of the genome of N. attenuata was done using 30× Illumina short reads, 4.5x 454 reads, and 10x PacBio single-molecule long reads. It was then assembled into 2.37 Gbp of sequences representing 92% of the expected genome size. From this was generated a 50x optical map and a high-density linkage map for super-scaffolding, which anchored 825.8 Mbp to 12 linkage groups and resulted in a final assembly with a N50 contig equal to 90.4 kbp and a scaffold size of 524.5 kb [1].

+ + + +

Annotation

+ +

Using approximately 50x Illumina short reads, the Nicotiana obtusifolia genome was assembled with a 59.5 kbp and 134.1 kbp N50 contig and scaffold N50 size, respectively. The combined annotation pipeline integrating both hint-guided AUGUSTUS and MAKER2 gene prediction pipelines predicted 33,449 gene models in the N. attenuata genome. More than 71% of these gene models were fully supported by RNA-sequencing (RNA-seq) reads and 12,617 and 18,176 of these genes are orthologous to Arabidopsis and tomato genes, respectively [1].

+ + +

References

  1. Wild tobacco genomes reveal the evolution of nicotine biosynthesis.
    Shuqing Xu, Thomas Brockmoller,a, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke et al. 2017. PNAS. 114(23):61336138.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_aus.html b/gramene/htdocs/ssi/species.weix/about_Oryza_aus.html new file mode 100644 index 00000000..cc762f88 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_aus.html @@ -0,0 +1,65 @@ +

About Oryza sativa aus (cA1) subgroup OsN22

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. N22 (collected from: India) is selected as the representative of cA1 subpopulation, in which the accessions are mostly collected from India, Bangladesh and Nepal.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. N22 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA1 subpopulation. The whole DNA was sequenced by 65 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ + +

OsN22RS2

+

Organism name: Oryza sativa aus subgroup (rice)

+

Infraspecific name: Cultivar: N 22::IRGC 19379-1 (IRGC 117534)

+

BioSample: SAMN04568482

+

BioProject: PRJNA315689

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_001952365.3 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: LWDA02

+

Assembly method: CANU v. v1.5; MECAT v. v1.3; FALCON v. 2017.06.28-18.01-py2.7-ucs4

+

Expected final version: no

+

Genome coverage: 65.0x

+

Sequencing technology: PacBio

+

IDs: 8130841 [UID] 22230838 [GenBank]

+ + +

Annotation

+ +

N/A

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

+

Stein, Joshua C., Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, et al. 2018. “Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation across the Genus Oryza.” Nature Genetics 50 (2): 285–96.

+ +

Wang, Wensheng, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, et al. 2018. “Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice.” Nature 557 (7703): 43–49.

+ + +

Links

+ +

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/LWDA00000000.2/

+

- Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

- USDA repo for germplasm: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1010537

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=135816

diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_barthii.html b/gramene/htdocs/ssi/species.weix/about_Oryza_barthii.html new file mode 100644 index 00000000..689cc3a1 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_barthii.html @@ -0,0 +1,31 @@ + +

Project funding: National Science Foundation Plant Genome Research Program (#1026200) for the Oryza Genome Evolution (OGE) Project. These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. barthii in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + +

About Oryza barthii

+

Oryza barthii is the AA genome progenitor of the West African cultivated rice, O. glaberrima. It belongs to the AA genome group and has 12 chromosomes and a nuclear genome size of 411Mb (flow cytometry). It is found in mopane or savanna woodland, savanna or fadama. Grows in deep water, seasonally flooded land, stagnant water, and slowly flowing water or pools; prefers clay or black cotton soils. Found in open habitats. This work was part of the OGE project funded by NSF Award #1026200.

+ + +

Assembly

+

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using project accession ABRL03000000. The sequence data were generated by PacBio technology. The estimated coverage from the WGS was xxx. Total sequence length 344,913,874bp; Number of contigs 28; Contig N50 14,688,426bp.

+ + +

Annotation

+

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline at CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene and Ensembl Plants project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1) and other Oryza AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_barthii3s.html b/gramene/htdocs/ssi/species.weix/about_Oryza_barthii3s.html new file mode 100644 index 00000000..05b3e18c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_barthii3s.html @@ -0,0 +1,27 @@ +

Current Release: OMAP Chromosome 3 Short Arm (AA genome type)

+ +

Oryza barthii + +A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of Oryza barthii using a heavily manually edited physical map. The BACs were divided into six 3Mb pools and Roche GSFLX sequenced (Titanium and paired-end reads) to a depth of 18X. Sequence reads were assembled with Newbler (454) and Bambus (Pop et al. 2004), followed by manual inspection of the assembly (Rounsley et al. 2009). The assembly resulted in a total of 119 scaffolds with a scaffold N50 of 370,878bp. + +

+ +
+

Additional annotations generated by the Gramene project include:

+ +
    + +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
  • + Ab initio gene prediction with program fgenesh +
    • + + +
diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_brachyantha.html b/gramene/htdocs/ssi/species.weix/about_Oryza_brachyantha.html new file mode 100644 index 00000000..13a56a32 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_brachyantha.html @@ -0,0 +1,37 @@ + +

About Oryza brachyantha

+ +

Oryza brachyantha (wild rice) is a distant relative of cultivated rice (O. satia Japonica and O. sativa Indica). It is placed on the basal lineage of Oryza and is the only member of the genus assigned to the F-genome type. An annual or weekly perennial tufted grass, it is distributed in west and central Africa, and grows in open wetland habitats. It has potentially useful traits for rice breeding, including resistance/tolerance to yellow stem borer, leaffolder, whorl maggot and bacterial blight. The O. brachyantha genome provides an important resource for functional and evolutionary studies in the genus Oryza. Its nuclear genome is diploid (2n = 24) and ~362 Mbp.

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accessionAGAT0200000. The estimated coverage from the WGS was ?. Total sequence length 258,902,551 bp; Number of contigs 26; Contig N50 11,392,507 bp. +

+ + + +

Annotation

+ +

Protein-coding genes were annotated using an evidence-based MAKER-P pipeline in CSHL. +

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), Arabidopsis thaliana and a few other AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

+ +

Links

+ + + +

References

  1. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
    Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C et al. 2013. Nat Commun. 4:1595.
diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_glaberrima.html b/gramene/htdocs/ssi/species.weix/about_Oryza_glaberrima.html new file mode 100644 index 00000000..3f5b35b0 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_glaberrima.html @@ -0,0 +1,39 @@ + +

Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012).

+ + +

About Oryza glaberrima

+

Oryza glaberrima (African rice) is a cultivated grain distinct from its better known cousin Oryza sativa (Asian rice). African rice was independently domesticated ~3000 years ago in the Niger River Delta from its still extant progenitor, Oryza barthii. While lacking many of the agronomic and quality traits found in Asian rice, O. glaberrima is significant for its resistance to many pests and diseases and for its tolerance of drought and infertile soils. Interspecific crosses between African and Asian rice have produced cultivars with improved yield and quality traits, that have been adopted by many African countries to meet the growing need for rice as a staple food. From a scientific perspective the genome of O. glaberrima provides insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 Mbp.

+ + +

Assembly

+

The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000. The estimated coverage from the WGS was xxx. Total sequence length 344,456,705bp; Number of contigs 25; Contig N50 15,266,279bp.

+ + +

Annotation

+

Protein-coding genes were annotated with MAKER-P software in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1), and a few AA oryza genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +
  • Variation effect prediction with sequence ontology, for example.
    • +

Links

+ + +

References

  1. Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences.
    Li ZM, Zheng XM, Ge S. 2011. Theor. Appl. Genet.. 123:21-31.
    2. +
  2. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.
    Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. 2010. Plant J.. 63:990-1003.
    3. +
  3. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.
    Guyot R, Garavito A, Gavory F, Samain S, Tohme J, Ghesquire A, Lorieux M. 2011. PLoS ONE. 6:e17726.
    4. +
  4. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.
    Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA. 2011. BMC Genomics. 12:142.
    5. +
  5. Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
    Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M et al. 2011. Plant J.. 66:796-805.
    6. +
  6. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum.
    Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J et al. 2010. Mol. Biol. Evol.. 27:2487-2506.
    7. +
  7. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices.
    Roulin A, Chaparro C, Pigu B, Jackson S, Panaud O. 2010. Genome Biol Evol. 2:132-139.
diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_glumaepatula.html b/gramene/htdocs/ssi/species.weix/about_Oryza_glumaepatula.html new file mode 100644 index 00000000..60768d96 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_glumaepatula.html @@ -0,0 +1,30 @@ + +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. glumaepatula in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + +

About Oryza glumaepatula

+

Oryza glumaepatula is a wild rice from South America, one of the rice species included in the OMAP project. It belongs to the AA genome group and has 12 chromosomes with a nuclear genome size of 464Mb (flow cytometry). It is found in deep and sometimes flowing water. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Antonio Oliveira (Brazil).

+ + +

Assembly

+

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession ALNU03000000. The estimated coverage from the WGS was ?. Total sequence length 386,178,655 bp; Number of contigs 33; Contig N50: 18,238,801bp.

+ + +

Annotation

+

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_granulata.html b/gramene/htdocs/ssi/species.weix/about_Oryza_granulata.html new file mode 100644 index 00000000..a91d27dc --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_granulata.html @@ -0,0 +1,71 @@ + +

+ About Oryza granulata +

+ +

Oryza granulata (GG genome type) is a wild rice, perennial and short (usually <1 m) with lanceolate and dark green leaves; compact panicles usually without secondary branching; spikelets 5.2-6.4 mm long and 2.4-2.7 mm wide, always awnless, with granulated texture to the lemma and palea; anthers 2.8-3.6 mm long. It natually distributed in south east Asia.

+ + + +

+ Assembly of Chromosome 3 short arm +

+ +

A minimum tiling path of 555 BAC clones was selected across the short arm of chromosome 3 of Oryza granulata using a heavily manually edited physical map< http://www.omap.org/fpc/WebAGCoL/OG_ABa/WebFPC/>. The BACs were divided into 19 3Mb pools and sequenced using Roche GSFLX+ chemistry (shotgun and paired-end reads) to a depth of 42X. Sequence reads were assembled with Newbler v2.6 (Roche 454) followed by order and orientation of the assembled scaffolds and contigs using Genome Puzzle Master (GPM) software (Zhang and Wing. unpublished). The assembly resulted in a single scaffold of 35,245,667 bp with 3,523 contigs.

+ +

The assembly was submitted into Genbank with accession ALNT00000000.

+ +

Data Usage

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + + +

+ Annotation +

+

Ab initio gene prediction with program fgenesh from Gramene

+ + + +

+ Gramene/Ensembl Genomes Annotation +

+

Additional annotations generated by the Gramene project include:

+ +
    +
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . +
    • +
  • + Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. +
    • +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
+ + + +

+ References and Links +

+

+

+ Links +

+ + + + + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_indica.html b/gramene/htdocs/ssi/species.weix/about_Oryza_indica.html new file mode 100644 index 00000000..ecab79a7 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_indica.html @@ -0,0 +1,43 @@ + +

About Oryza sativa Indica

+ +

Oryza sativa Indica is one of the two most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely grown in the hot climates of Southern Asia. The genome of Indica is very similar to that of Japonica, which is generally restricted to temperate climes such as Japan.

+ + + +

Assembly

+ +

The genome of Oryza sativa Indica Group cultivar 93-11 was sequenced by the Beijing Genome Institute (BGI) following a whole-genome shotgun strategy [1].

+ + + +

Annotation

+ +

Gene annotations were predicted by BGI using Glean as released on 10-28-2008. This browser presents data from the 2010 release of the BGI RISe Rice Information System[2].

+ + + +

Regulation

+ +
  • Probes from the Rice Genome Array for two rice cultivars were aligned to the genome.
    • +
+ + +

Variation

+ +

Two sources of variation data from NCBI dbSNP has been mapped onto the genome assembly:

+ +
  1. SNPs called from the comparison of Oryza sativa Indica and Oryza sativa Japonica, and
    2. +
  2. SNPs resulting from OMAP project alignments between O. glaberrima, O. punctata, O. nivara, and O. rufipogon agains O. sativa Japoinca mapped to O. sativa indica.
    3. +
+ + +

Links

+ + + +

References

  1. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al. 2002. Science. 296:79-92.
    2. +
  2. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
    Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X et al. 2004. Nucleic Acids Res.. 32:D377-82.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_longistaminata.html b/gramene/htdocs/ssi/species.weix/about_Oryza_longistaminata.html new file mode 100644 index 00000000..5ef7b690 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_longistaminata.html @@ -0,0 +1,32 @@ + +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. glumaepatula in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Oryza longistaminata

+ +

Oryza longistaminata (AA genome type) is a wild rice, Perennial, tall (2 m or more), erect, and rhizomatous grass; ligule of lower leaves >15 mm, acute or 2-cleft; panicles open to intermediately open; spikelets 4.5-11.4 mm long and 2-3 mm wide, awned (2-5 cm long); anther 1.5-8.2 mm long.

+ + + +

Assembly

+ +

A whole genome shotgun assembly (i.e. Illumina sequence, SOAP de novo assembly) of O. longistaminata was generated by Professor Wen Wang (Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China) in collaboration with BGI-Shenzhen, China. The genome assembly was composed of 135,973 scaffolds spanning 344.6Mb with a N50 scaffold size of 62.4kb. Using this assembly, the Arizona Genomics Institute (AGI) selected scaffolds and contigs that were syntenic to the short arm of chromosome 3 of O. sativa ssp.japonica, and the order and orientation of each scaffold/contig was confirmed using Genome Puzzle Mater software (GPM, unpublished) to produce a Chr3S pseudomoleclue. The final O. longistaminata chromosome 3 short arm resulted in a single scaffold of 14,404,039bp composed of 4,724 contigs.

+ + + +

Annotation

+ +

Protein-coding genes, annotation of repeats and transposable elements were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. MAKER-P was used as evidence-based genome annotation pipeline. RepeatMasker was used to annotate repeats and transposable elements using species-specific de novo repeat libraries. Non coding RNA genes were predicted by AGI with Infernal, tRNA genes with tRNAScan.

+ + + +

Links

+ + + +

References

  1. Hierarchical scaffolding with Bambus.
    Pop M, Kosack DS, Salzberg SL. 2004. Genome Res.. 14:149-159.

Picture credit: Paul Sanchez, Arizona Genomics Institute.

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_meridionalis.html b/gramene/htdocs/ssi/species.weix/about_Oryza_meridionalis.html new file mode 100644 index 00000000..0bf3f9bc --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_meridionalis.html @@ -0,0 +1,40 @@ + +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. meridionalis in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Oryza meridionalis

+ +

Oryza meridionalis is a wild rice found in Australia, one of the wild rice species included in the OMAP project. It belongs to the AA genome group. It has 12 chromosomes with a nuclear genome size of 435Mb (flow cytometry). It is found at edges of freshwater lagoons, temporary pools, and swamps in 15-20 cm of water and grows in black, clay soil in open habitats. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Olivier Panaud (France) and Robert Henry (Australia).

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession ALNW03000000. The estimated coverage from the WGS was ?. Total sequence length 379,254,020 bp; Number of contigs 30; Contig N50: 16,096,529 bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1), see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_minuta.html b/gramene/htdocs/ssi/species.weix/about_Oryza_minuta.html new file mode 100644 index 00000000..cc85a073 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_minuta.html @@ -0,0 +1,28 @@ +

Current Release: OMAP Chromosome 3 Short Arm (BB CC genome type)

+ +

Oryza minuta + +A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of each of the Oryza minuta BB and CC subgenomes using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually. + + +

+ +
+

Additional annotations generated by the Gramene project include:

+ +
    +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see more. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
  • + Ab initio gene prediction with program fgenesh +
    • +
  • + Pairwise Whole genome alignments (blastz-chain-net) with Oryza sativa Japonica +
    • + +
diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_minutabb.html b/gramene/htdocs/ssi/species.weix/about_Oryza_minutabb.html new file mode 100644 index 00000000..55533d29 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_minutabb.html @@ -0,0 +1,67 @@ + +

+ About Oryza minuta +

+ +

Oryza minuta (BBCC genome type) is a wild rice, perennial, scrambling, and stoloniferous grass, <1.5 m tall; panicles open, basal panicle branches usually not whorled; spikelets 4.1-5.6 mm long and 1.6-2.1 mm wide; anthers around 1.5-3 mm long.

+ + + + +

+ Assembly of BB subgenome Chromosome 3 short arm +

+ +

A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of each of the Oryza minuta BB subgenomes using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually.

+ +

Data Usage

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + + +

+ Annotation +

+

Ab initio gene prediction with program fgenesh from Gramene

+ + + +

+ Gramene/Ensembl Genomes Annotation +

+

Additional annotations generated by the Gramene project include:

+ +
    +
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . +
    • +
  • + Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. +
    • +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
+ + + +

+ References and Links +

+

+

+ Links +

+ + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_minutacc.html b/gramene/htdocs/ssi/species.weix/about_Oryza_minutacc.html new file mode 100644 index 00000000..19509868 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_minutacc.html @@ -0,0 +1,68 @@ + +

+ About Oryza minuta +

+ +

Oryza minuta (BBCC genome type) is a wild rice, perennial, scrambling, and stoloniferous grass, <1.5 m tall; panicles open, basal panicle branches usually not whorled; spikelets 4.1-5.6 mm long and 1.6-2.1 mm wide; anthers around 1.5-3 mm long.

+ + + + +

+ Assembly of CC subgenome Chromosome 3 short arm +

+ +

A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of each of the Oryza minuta CC subgenomes using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually.

+ +

Data Usage

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + + +

+ Annotation +

+

Ab initio gene prediction with program fgenesh from Gramene

+ + + +

+ Gramene/Ensembl Genomes Annotation +

+

Additional annotations generated by the Gramene project include:

+ +
    +
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . +
    • +
  • + Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. +
    • +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
+ + + +

+ References and Links +

+

+

+ Links +

+ + + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_nivara.html b/gramene/htdocs/ssi/species.weix/about_Oryza_nivara.html new file mode 100644 index 00000000..8af1280c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_nivara.html @@ -0,0 +1,39 @@ + +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. nivara in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Oryza nivara

+ +

Oryza nivara is a wild rice from India; one of rice species being used in the OMAP project. It belongs to the AA genome group. Breeders are interested in this organism because it exhibits resistance to grassy stunt virus. It is found in swampy areas, at edges of ponds and tanks, beside streams, in ditches, in or around rice fields. It usually grows in shallow water up to 0.3 m. seasonally dry; in open habitats. It has 12 chromosomes and a nuclear genome size of 448Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Y. Hsing (Taiwan).

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession AWHD02000000. The estimated coverage from the WGS was ?. Total sequence length 393,961,846bp; Number of contigs 24; Contig N50: 18,986,252bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_officinalis.html b/gramene/htdocs/ssi/species.weix/about_Oryza_officinalis.html new file mode 100644 index 00000000..ca9e1cd9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_officinalis.html @@ -0,0 +1,68 @@ + +

+ About Oryza officinalis +

+ +

Oryza officinalis (CC genome type) is a wild rice, Perennial, erect, and usually rhizomatous grass of variable height; panicles open, basal panicle branches whorled with spikelets inserted half way or more from base; spikelets 4.3-8.8 mm long and 2-3.3 mm wide; anthers around 1.5-4.5 mm long.

+ + + + + +

+ Assembly of Chromosome 3 short arm +

+ +

A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of Oryza officinalis using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually.

+ +

Data Usage

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + + +

+ Annotation +

+

Ab initio gene prediction with program fgenesh from Gramene

+ + + +

+ Gramene/Ensembl Genomes Annotation +

+

Additional annotations generated by the Gramene project include:

+ +
    +
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . +
    • +
  • + Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. +
    • +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
+ + + +

+ References and Links +

+

+

+ Links +

+ + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_punctata.html b/gramene/htdocs/ssi/species.weix/about_Oryza_punctata.html new file mode 100644 index 00000000..50737abd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_punctata.html @@ -0,0 +1,39 @@ + +

Project funding: National Science Foundation Plant Genome Research Program (#1026200) for the Oryza Genome Evolution (OGE) Project. These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. punctata in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Oryza punctata

+ +

Oryza punctata is a wild rice species native to Africa. Breeders are interested because of demonstrated resistance to bacterial blight and brown plant hoppers. O. punctata, a diploid, belongs to the O. officinalis complex within the Oryzeae genome groups, and belongs to the BB genome type. It can be found in open or semi-open habitats such as forest margins, grassland and thickets, scrub lands, open bush or shifting cultivation fields, and rice fields. It has 12 chromosomes and a nuclear genome size of 423Mb (flow cytometry). This work was part of the OGE project funded by NSF Award #1026200.

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession AVCL0200000. The estimated coverage from the WGS was ?. Total sequence length 419,076,415 bp; Number of contigs 28; Contig N50 18,594,736bp.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species: see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1) and other AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon.html b/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon.html new file mode 100644 index 00000000..854b00d9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon.html @@ -0,0 +1,45 @@ + +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. rufipogon in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Bin Han and Dr. Rod Wing.

+
+ + +

About Oryza rufipogon

+ +

Oryza rufipogon (AA genome type) is a wild rice, perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-10 cm long; anthers >3 mm reaching 7.4 mm long.

+ +

Chromosome number: 2n=2x=24

+ +

Genome: AA

+Distribution: Australia, Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Sri Lanka, Thailand, and Vietnam.

+Habitat: Found in swamps and marshes, in open ditches, swampy grassland, ponds, along river banks, at the edges of lakes, and in or at the margins of rice fields, commonly found in deep water areas (0.2-4m). Grows in clay/loam soil and black soil, in full sun.

+ + + +

Assembly

+ +

The sequencing and assembly was done by Dr. Bin Han's group in Shanghai Institutes for Biological Sciences, CAS.

+ + + +

Annotation

+ +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

+ + + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene and Ensembl Plants project include:

+ +
  • Gene phylogenetic trees with other other Gramene species, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon3s.html b/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon3s.html new file mode 100644 index 00000000..83547135 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_rufipogon3s.html @@ -0,0 +1,78 @@ + +

+ About Oryza rufipogon +

+ +

Oryza rufipogon (AA genome type) is a wild rice, perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-10 cm long; anthers >3 mm reaching 7.4 mm long. +

+ + + + +

+ Assembly of Chromosome 3 short arm +

+ +

A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of Oryza rufipogon using a heavily manually edited physical map. The BACs were divided into two 9Mb pools and Roche GSFLX sequenced (Titanium and paired-end reads) to a depth of 35X. Sequence reads were assembled with Newbler (454) and Bambus (Pop et al. 2004), followed by manual inspection of the assembly (Rounsley et al. 2009). The assembly resulted in a total of 532 scaffolds with a scaffold N50 of 45,715bp.

+ + + +

Data Usage

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+ + + +

+ Annotation +

+

Ab initio gene prediction with program fgenesh from Gramene

+ + + +

+ Gramene/Ensembl Genomes Annotation +

+

Additional annotations generated by the Gramene project include:

+ +
    +
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . +
    • +
  • + Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. +
    • +
  • + Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. +
    • +
  • + Identification of various repeat features from MIPS and AGI repeat libraries +
    • +
+ + + +

+ References and Links +

+

References

+
    + +
  • "Hierarchical scaffolding with Bambus." Pop M, Kosack DS, Salzberg SL, Genome Research, 2004. 14(1):149-59.
    • +
+ +

+ Links +

+ + + + + + + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_sativa.html b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa.html new file mode 100644 index 00000000..fb373c49 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa.html @@ -0,0 +1,70 @@ + +

About Oryza sativa Japonica

+ +

Oryza sativa Japonica (rice) is the staple food for 2.5 billion people. It is the grain with the second highest worldwide production after Zea mays. In addition to its agronomic importance, rice is an important model species for monocot plants and cereals such as maize, wheat, barley and sorghum. O. sativa has a compact diploid genome of approximately 500 Mbp (n=12) compared with the multi-gigabase genomes of maize, wheat and barley.

+ + + +

Assembly

+ +

Scientists from the MSU Rice Genome Annotation Project (MSU) and the International Rice Genome Sequencing Project (IRGSP) / Rice Annotation Project Database (RAP-DB) generated a unified assembly of the 12 rice pseudomolecules of Oryza sativa Japonica Group cv. Nipponbare [1,2].

+ +

The pseudomolecule for each chromosome was constructed by joining the nucleotide sequences of each PAC/BAC clone based on the order of the clones on the physical map. Overlapping sequences were removed and physical gaps were replaced with Ns. Updated pseudomolecules were constructed based on the original IRGSP sequence data [1] in combination with a BAC-optical map and error correction using 44-fold coverage next generation sequencing reads [2]. The nucleotide sequences of 7 new clones mapped on the euchromatin/telomere junctions were added in the new genome assembly. In addition, several clones in the centromere region of chromosome 5 were improved and one gap on chromosome 11 was closed [2].

+ +

Kawahara et al. (2013) describe the integrated Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules, also known as MSU7. Gene loci, gene models and associated annotations were independently created by each group, but can be easily compared using the common reference.

+ +

Read more about the assembly at MSU or on rap-db.

+ + +

Annotation

+ +

The IRGSP gene models were imported from rap-db [3]. The most recent update was from its's Aug 4, 2017 release. This version corrected numerous protein coding gene models with manual curation, also deprecated some bad models. In total, 35,667 protein-coding genes were included in this release. Compared with last release of 37,830 genes, 35,340 stayed the same, 2,173 got deprecated, 317 updated, 10 new genes added. Feature annotation and comparative analysis pipelines have been run and variations have been projected from the old annotation to the new one. In addition, 2,387 nonCoding genes and 8,115 predicted genes were added as seperate data sets.

+ +

The MSU-7 gene models [4] have been added into the rice genome browser for visual comparison to the IRGSP set. Gene models were generated, refined and updated for the estimated 40,000 to 60,000 rice genes, provided standardized automatic annotation pipeline described in detail here. Briefly, a number of ab initio methods have been combined with homology based evidence and refined with EST alignments.

+ +

Cross references between the two gene sets provided by rap-db allow searching and querying using either identifier space, but only the IRGSP gene models are used in our gene trees.

+ + +

Regulation

+ +
  • Probes from the Rice Genome Array for two rice cultivars were aligned to the genome [5].
    • +
+ + +

Variation

+ +

Variation data from six different large scale studies are available:

+ +
  1. The 3000 Rice Genome Project (2015, [6]), an international effort to sequence the genomes of 3,024 rice varieties from 89 countries providing 365,710 variant loci (SNPs and InDels).
    2. +
  2. Whole genome sequencing of 104 elite rice cultivars (Duitama et al. 2015, [7]), described as, "a comprehensive information resource for marker assisted selection" providing 25,769,548 variant loci.
    3. +
  3. Chip based analysis of 1,310 SNPs across 395 samples (Zhao et al. 2010, [8]), described as, "revealing the impact of domestication and breeding on the rice genome".
    4. +
  4. Chip based analysis of approximately 160k SNPs across 20 diversity rice accessions (OryzaSNP, McNally et al. 2009 [9]), described as, "revealing relationships among landraces and modern varieties of rice".
    5. +
  5. The Oryza Map Alignment Project (OMAP 2007): approximately 1.6M variant loci detected by comparing BAC End Sequences from four rice varieties to Japonica. [dbSNP]
    6. +
  6. Adaptive loss-of-function in domesticated rice (BGI 2004, [10]): A collection of approximately 3M variant loci from the comparison of the Indica (93-11) and Japonica (Nipponbare) genomes. [dbSNP]
    7. +

The following genetic markers were remapped to the IRGSP-1.0 assembly by industry collaborator KeyGene:

+ + + + +

Links

+ + + +

References

  1. The map-based sequence of the rice genome.
    2005. Nature. 436:793-800.
    2. +
  2. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
    Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S et al. 2013. Rice (N Y). 6:4.
    3. +
  3. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
    Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T et al. 2013. Plant Cell Physiol.. 54:e6.
    4. +
  4. The TIGR Rice Genome Annotation Resource: improvements and new features.
    Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L et al. 2007. Nucleic Acids Res.. 35:D883-7.
    5. +
  5. Global analysis of gene expression using GeneChip microarrays.
    Zhu T. 2003. Curr. Opin. Plant Biol.. 6:418-425.
    6. +
  6. The 3,000 rice genomes project.
    2014. Gigascience. 3:7.
    7. +
  7. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.
    Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E et al. 2015. PLoS ONE. 10:e0124617.
    8. +
  8. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.
    Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A et al. 2010. PLoS ONE. 5:e10780.
    9. +
  9. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
    McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE et al. 2009. Proc. Natl. Acad. Sci. U.S.A.. 106:12273-12278.
    10. +
  10. The Genomes of Oryza sativa: a history of duplications.
    Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al. 2005. PLoS Biol.. 3:e38.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_sativa117425.html b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa117425.html new file mode 100644 index 00000000..566cd577 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa117425.html @@ -0,0 +1,68 @@ +

About Oryza sativa cB subgroup Os117425

+

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) (collected from: India) is selected as the representative of cB subpopulation, in which the accessions are mostly collected from India, Bangladesh, Nepal and Pakistan.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cB subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ +

Os117425RS1

+ +

Organism name: Oryza sativa aromatic subgroup (rice)

+

BioSample: SAMN12748569

+

BioProject: PRJNA565479

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831255.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYID01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 112.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433821 [UID] 15732448 [GenBank]

+ + +

Annotation

+ +

N/A

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

A platinum standard pan-genome resource that represents the population structure of Asian rice. Yong Zhou, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, Noor Al-Bader, Chandler Sobel-Sorenson, Praveena Parakkal, Lady Johanna Arbelaez, Natalia Franco, Nickolai Alexandrov, N. Ruaraidh Sackville Hamilton, Hei Leung, Ramil Mauleon,

+

Mathias Lorieux, Andrea Zuccolo, Kenneth McNally, Jianwei Zhang, and Rod A. Wing (2020). Scientific data 7(1):1-11.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYID00000000

+

- [persephone page for the 16 PSRefSeqs: (https://web.persephonesoft.com/)

+

- USDA repo for germplasm:

+

https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1928762

+

- IRRI repo:

+

https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=117425

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Oryza_sativa125619.html b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa125619.html new file mode 100644 index 00000000..354fac8b --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Oryza_sativa125619.html @@ -0,0 +1,66 @@ +

About Oryza sativa XI-2B subgroup Os125619

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) (collected from: India) is selected as the representative of XI-2B subpopulation, in which the accessions are mostly collected from India and Madagascar.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-2B subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+ +

For more detailed information please see below:

+ +

Os125619RS1

+ +

Organism name: Oryza sativa Indica Group (long-grained rice)

+

BioSample: SAMN12748589

+

BioProject: PRJNA565480

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_009831355.1 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: VYIE01

+

Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

+

Expected final version: no

+

Genome coverage: 113.0x

+

Sequencing technology: PacBio Sequel; Illumina

+

IDs: 5433761 [UID] 15732328 [GenBank]

+ + +

Annotation

+ +

N/A

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

Large structural variation of 16 PSRefSeqs are available (including map to IRGC 125619):

+ +
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

A platinum standard pan-genome resource that represents the population structure of Asian rice. Yong Zhou, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, Noor Al-Bader, Chandler Sobel-Sorenson, Praveena Parakkal, Lady Johanna Arbelaez, Natalia Franco, Nickolai Alexandrov, N. Ruaraidh Sackville Hamilton, Hei Leung, Ramil Mauleon,

+

Mathias Lorieux, Andrea Zuccolo, Kenneth McNally, Jianwei Zhang, and Rod A. Wing (2020). Scientific data 7(1):1-11.

+ + +

Links

+ +

Useful links to other resources

+

- GenBank: https://www.ncbi.nlm.nih.gov/nuccore/VYIE00000000

+

- [persephone page for the 16 PSRefSeqs: (https://web.persephonesoft.com/)

+

- USDA repo for germplasm: N/A

+

- IRRI repo: https://gringlobal.irri.org/gringlobal/accessiondetail.aspx?id=125619

diff --git a/gramene/htdocs/ssi/species.weix/about_Ostreococcus_lucimarinus.html b/gramene/htdocs/ssi/species.weix/about_Ostreococcus_lucimarinus.html new file mode 100644 index 00000000..8850d5f7 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Ostreococcus_lucimarinus.html @@ -0,0 +1,42 @@ + +

This project is a collaborative effort involving:

+ +
+ + +

About Ostreococcus lucimarinus

+ +

Ostreococcus lucimarinus is a unicellular green alga and an important member of the picoplankton community, which plays a central role in the oceanic carbon cycle. It is one of the smallest known free-living eukaryotic species, with an average size of 0.8 µm. Its cellular structure is characterised by remarkable simplicity, lacking a cell wall and containing a single chloroplast, a single mitochondrion, and a single Golgi body as well as its nucleus.

+ + + +

Assembly

+ +

The genome of Ostreococcus lucimarinus CCE9901 was sequenced by JGI and finished at the Stanford Genome Center. The v2.0 release has 13.204,894 Mbp of finished sequence. The sequences have been deposited in GenBank under accession numbers CP000581-CP000601. Detailed information about the project is availabe at the JGI website.

+ +

The assembly release v.2.0 contains 13,204,894 bp of finished quality sequence in 21 chromosomes.

+ +

In detail [1], whole genome shotgun Sanger sequences were assembled using the Phred, Phrap, Consed pipeline. Manual inspection and finishing was performed by targeted resequencing. Because of the high GC content, primer walks failed to resolve a large number of the gaps; these were resolved by generating pooled small insert shatter libraries from 3-kb plasmid clones. Repeats were resolved by transposon-hopping 8-kb plasmid clones. Fosmid clones were shotgun-sequenced and finished to fill large gaps, resolve large repeats, or resolve chromosome duplications and extend into chromosome telomere regions. Finished chromosomes have no gaps, and the sequence has less than one error in 100,000 bp.

+ + + +

Annotation

+ +

This release includes a total of 7,651 predicted gene models produced through the collaboration of JGI, Ghent University (Belgium) and UCSD annotation teams.

+ +

In detail [1], gene prediction methods included ab initio Fgenesh, Fgenesh+, Genewise, MAGPIE, estExt, and EuGene. All predicted models were clustered and the best model per locus was selected based on homology to other proteins and EST support. The predicted set of gene models has been validated by using available experimental data and computational analysis.

+ + + +

Links

+ + + +

References

  1. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
    Palenik B, Grimwood J, Aerts A, Rouz P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S et al. 2007. Proc. Natl. Acad. Sci. U.S.A.. 104:7705-7710.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Phaseolus_vulgaris.html b/gramene/htdocs/ssi/species.weix/about_Phaseolus_vulgaris.html new file mode 100644 index 00000000..883f6edd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Phaseolus_vulgaris.html @@ -0,0 +1,22 @@ + +

About Phaseolus vulgaris

+ +

Legumes are the third largest family of angiosperms and include many populous species. The majority of legumes contain symbiotic bacteria within nodules in their roots that mediate nitrogen fixation and provide an advantage towards competing plants. Legume seeds are rich in protein content and thus many species have been used for human or animal consumption over the years. Legumes as a whole constitute the second largest class of crops, including peas, soybeans, peanuts, and beans. Common bean (Phaseolus vulgaris.), a major source of protein that complements carbohydrate-rich rice, maize, and cassava, is fundamental for the nutrition of more than 500 million people in developing countries [1].

+ + + +

Assembly

+ +

The P. vulgaris Mesoamerican common bean BAT93 genome was assembled using a hybrid sequencing strategy involving 454 single reads and 8, 10, and 20 kb mate pair libraries; 3 and 5 kb SOLiD mate pair libraries; and Sanger bacterial artificial chromosome (BAC)-end and genomic read pairs. Data free of redundancies were used as input for a Newbler assembly, and Illumina reads (45x coverage) were used to correct homopolymer errors and close or reduce gaps within scaffolds. Illumina genotyping-by-sequencing (GBS), data from a set of 60 F5 lines of a BAT93 x Jalo EEP558 advanced intercross (6.7x coverage per line on average), together with 827 public marker sequences, were used for assembly correction and scaffold anchoring. Discontinuous genotype profiles observed in 48 cases were manually corrected by breaking scaffolds at the mis-assembly points. Markers were aligned to the assembly and GBS profiles of these scaffolds were used as seeds to place other scaffolds with this or similar profiles onto chromosomes, followed by genetic map calculation. The final BAT93 genome sequence encompassed 549.6 Mbp, close to previous size estimates, with 81% of the assembly anchored to eleven linkage groups. The assembly included 97% of the conserved core eukaryotic genes, thus reflecting its completeness [1].

+ +

These assembly includes 68,335 scaffolds (N50=433,759 bp) and 111,805 contigs (N50=10,795 bp) [2].

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Annotation

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Transposable elements were identified by combining de novo and homology-based approaches, finding 35% of the P. vulgaris BAT93 genome assembly to be covered by repeats, mostly long terminal repeats. To aid in gene prediction and to obtain a global view of the transcriptome during development, sequencing was done with Illumina 61 RNA samples from 34 different organs and/or developmental stages from healthy plants. In addition, two normalized libraries derived from 162 RNA samples from plants grown under optimal and stress conditions were used for 454 pyrosequencing. Illumina and 454 RNA-Seq reads, as well as public expressed sequence tags (EST) and cDNA sequences, were combined with ab initio predictions to produce an initial gene set. This was filtered to remove genes lacking both similarity to other plant proteins and any evidence of expression, resulting in 30,491 protein coding genes (PCGs), whose 66,634 transcripts encode 53,904 unique proteins. Using protein signatures and phylogeny-based transference of functional annotations it was possible to associate functions with 94% of the bean transcripts, with 76 % of them specifically associated with Gene Ontology (GO) terms [2].

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References

  1. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
    Vlasova A, Capella-Gutirrez S, Rendn-Anaya M, Hernndez-Oate M, Minoche AE, Erb I, Cmara F, Prieto-Barja P, Corvelo A, Sanseverino W et al. 2016. Genome Biology. 17
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  2. Phaseolus vulgaris assembly in NCBI.
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About Physcomitrella patens

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The mosses (Bryophytes) are non-vascular plants that appeared very early in the fossil record, soon after the transition of plants to terrestrial environments. The Physcomitrella patens genome is therefore valuable in understanding early evolution and adaptation of land plants. Physcomitrella also serves as a model organism for studies of physiology and development. Unlike in higher plants, targeted gene-knockouts can be made efficiently in the laboratory, thereby facilitating reverse-genetics approaches to studying gene function. The annotated genome hosted here thereby represents an important resource to the plant research community.

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Assembly

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Information from JGI: The haploid genome of Physcomitrella patens ssp. patens ecotype Gransden 2004 is estimated to be ~480 Mbp contained in 27 pairs of chromosomes, and was sequenced to approximately 8.1x depth.

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The genome assembly has remained unchanged since release v.1.1 (March 2007). Approximately 5.5 million shotgun reads were initially assembled using JAZZ. There are a total of 2,106 scaffolds, composed of 19,136 contigs, with a total length of ~480 Mbp. Half of the assembly is contained in 111 scaffolds, all at least 1.3 Mbp in length. The length-weighted mean contig size is 72.5 kbp.

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Annotation

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Gene annotations are now updated to v1.6 from Cosmoss - The Physcomitrella patens resource. Annotations were originally made by JGI using a pipeline to predict and map gene models and associated transcripts/proteins using a variety of tools based on cDNA, protein homology and ab initio methods. The release v1.6 contains 32,272 gene models and 38,354 protein-coding transcripts. Scaffold and their associated gene models that were identified as contaminants in 2009 have been removed.

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Links

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References

  1. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
    Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y et al. 2008. Science. 319:64-69.
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  2. Image credit: Pirex at en.wikipedia [Public domain], from Wikimedia Commons.
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About Populus trichocarpa

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Populus trichocarpa (poplar) is a deciduous broadleaf tree that is native to Western North America. It is an economically important source of timber. Its rapid growth and compact genome size (~500 Mbp, n=18) has lead to its use as a model organism for tree species.[1]

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Assembly

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The v3 Populus genome assembly was constructed with Arachne version 20071016HA with an attempt to merge the outbred haplotypes and an extensive attempt to remove contaminating sequence. 81 Mb of finished clone sequence was also integrated, and the latest genetic map information to construct the 19 chromosome size scaffolds which contain 388 Mb of sequence, a majority of the assembled poplar sequence. Care was taken to minimize alternative haplotypes within the assembly. The first 19 scaffolds from the assembly correspond to the poplar chromosomes. The full release covers 423 Mb pairs of sequence with an average read depth of 9.44x assembled sequence. [3]

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Annotation

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75,566 RNAseq transcript assemblies were constructed from about 0.6B pairs of tremulas paired-end Illumina RNAseq reads using PERTRAN (Shu et. al., manuscript in preparation). Transcript assemblies (86,677 from Populus trichocarpa and 151,316 from related poplar ESTs/mRNA) were constructed using PASA from Populus trichocarpa RNAseq transcript assemblies, ESTs/mRNAs, and ESTs/mRNAs of other Poplar species including >2.6M 454-sequenced Populus deltoides EST reads generated at JGI. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabi ( Arabidopsis thaliana), rice, soybean or grape genomes to repeat-soft-masked P. trichocarpa genome using RepeatMasker . Gene models were predicated by homology-based predictors, mainly FGENESH+ , FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan . The best scored predictions for each locus are selected using multiple positive factors including EST and protein support, and one negative factor: overlap with repeats. The selected gene predictions were improved by PASA. Improvement includes adding UTRs, splicing correction, and adding alternative transcripts. PASA-improved gene model proteins were subject to protein homology analysis to above mentioned proteomes to obtain Cscore and protein coverage. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score and protein coverage is highest percentage of protein aligned to the best of homologs. PASA-improved transcripts were selected based on Cscore, protein coverage, EST coverage, and its CDS overlapping with repeats. The transcripts were selected if its Cscore is larger than or equal to 0.5 and protein coverage larger than or equal to 0.5, or it has EST coverage, but its CDS overlapping with repeats is less than 20%. For gene models whose CDS overlaps with repeats for more that 20%, its Cscore must be at least 0.9 and homology coverage at least 70% to be selected. The selected gene models were subject to Pfam analysis and gene models whose protein is more than 30% in Pfam TE domains were removed. The final result was 41,335 loci containing protein-coding transcripts and 73,013 protein-coding transcripts.[3]

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Regulation

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Links

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References

  1. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
    Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. Science. 313:1596-1604.
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  2. Image credit: Cherubino (Own work) [Public domain], via Wikimedia Commons.
    3. +
  3. Phytozome: a comparative platform for green plant genomics.
    David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam et al. 2012. Nucleic Acids Res. . 40 (D1) : D1178-D1186.
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About Prunus persica

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Prunus persica (peach) is an economically important deciduous tree in the Rosaceae family that produces 20 million tons of fruit per year. The rosaceae family contains herbs, shrubs and trees with a wide variety of fruit types and habits and includes several species grown for their fruits (peaches, apples and strawberries), lumber (black cherry) and ornamental value (roses).

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Peach was first domesticated and cultivated in North-West China and has a compact diploid genome (265 Mb, 2n =16).

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Assembly

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The initial assembly was performed using Sanger sequence reads representing 8.5-fold coverage of a double haploid genotype of cv. Lovell using Arachne. The resulting contigs and scaffolds were filtered to give 234 scaffolds covering 224.6 Mb of the peach genome (Peach v1.0) with scaffold and contig N50/L50 values of 4 Mb/26.8 Mb and 294 kb/214.2 kb, respectively with good QC statistics [1].

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Five DNA libraries were end-sequenced, giving a total of 8.47-fold sequence coverage: 536,032 reads from the 2.8 kb sized library, 606,680 reads from the 4.4 kb sized library, 2,106,103 reads from the 7.8 kb sized library, 419,424 reads from the 35.3 kb fosmid library, and 61,440 reads from the 69.5 kb BAC library.

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Annotation

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A total of 27,852 protein-coding genes and 28,689 protein-coding transcripts were predicted [1].

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Predictions began with PASA transcript assemblies based on ESTs from peach and related species. Transcript assemblies and a collection of plant peptide sequences were blasted against the assembly and gene models were predicted using by homology-based predictors FGENESH+ and GenomeScan. Predicted gene models were improved and refined by PASA.

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Sequence alignment

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Approximately 80,000 EST sequences have been aligned to the genome with STAR [View data]

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Links

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  • Prunus persica ESTs at ENA
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References

  1. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
    Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F et al. 2013. Nat. Genet.. 45:487-494.

Picture credit: Image created by skyseeker and released under a Creative Commons Attribution License.

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About Selaginella moellendorffii

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Selaginella moellendorffii is a spikemoss. They belong to the subdivsion of higher vascular plant called lycophytes, an ancient group of plants appeared around 410 million years ago. Selaginella moellendorffii is the first non-seeded plant genome reported, making it a key species for plant evolution studies.

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Assembly

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The nuclear genome size is ~100 Mbp, the smallest genome size of any plant yet reported.

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Annotation

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The genome annotation for Selaginella moellendorffii has been derived from annotation submitted to the EMBL/Genbank/DDBJ databases; and enhanced by importing data from additional sources, principally UniProtKB and GOA.

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References

  1. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
    Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA et al. 2011. Science. 332:960-963.

Picture credit: Emmanuel Boutet

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About Setaria italica

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Setaria italica (foxtail millet) is a grain crop widely grown in Asia with particular significance in semi-arid regions of Northern China. It is also grown on a moderate scale in other parts of the world as a forage crop. It is one of the oldest domesticated crops with archeological remains from 7,500 to 7,900 years BP in northern China. Motivation for sequencing foxtail millet includes its close relationship, both genetically and physiologically, to the biofuel crop switchgrass (Panicum virgatum). Direct study of switchgrass is complicated by its large genome size and polyploidy. Data from the foxtail millet genome assists in study and improvement of switchgrass and related biofuel crops. The nuclear genome (~490 Mbp) is diploid with 9 chromosomes (2n=18).

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Assembly

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Setaria italica cv. Yugu1 was sequenced and assembled by the Joint Genome Institute (JGI) in collaboration with community researchers. Sanger sequencing was performed on whole-genome shotgun clone libraries having different insert sizes. Reads totalling 8.29x coverage were assembled with Arachne giving scaffolds that were arranged predominantly into 9 pseudomolecules.

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Annotation

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Protein-coding genes were predicted using evidence-based approaches.

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References

  1. Reference genome sequence of the model plant Setaria.
    Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J et al. 2012. Nat. Biotechnol.. 30:555-561.
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  2. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.
    Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W et al. 2012. Nat. Biotechnol.. 30:549-554.
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  3. Image credit: Markus Hagenlocher, via WikiCommons.
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About Solanum lycopersicum

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Solanum lycopersicum (tomato) is a member of the nightshade family, Solanaceae, which includes a variety of agricultural crop plants (e.g. potato, pepper, eggplant, and tobacco). The tomato originated in the Andean region of South America, was grown by Aztecs in Mesoamerica, and spread to Europe by early Spanish explorers. Today, hundreds of varieties are grown throughout the world, with the largest producers being China and the United States. In addition to its value as a food, the tomato has served as an important model system for the study of fruit ripening, plant-pathogen interactions, and molecular genetic mapping. The nuclear genome contains 12 chromosomes and is ~950 Mbp in size.

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Assembly

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Solanum lycopersicum cv. Heinz 1706 was sequenced and assembled by the International Tomato Genome Sequencing Consortium. Assembly version SL2.40 combines a 22X whole genome shotgun sequence (Roche 454) with Sanger sequence data from BAC-ends, fosmid-ends and Selected BAC Mixture sequences, and additional data from Solexa and SOLiD technologies (total genome coverage 27X). The assembly is deposited into DDBJ/EMBL/GenBank under the accession AEKE00000000.2.

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Annotation

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Annotation was carried out by the International Tomato Annotation Group (ITAG) using a combination of evidence-based and ab initio methods.

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Variation

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The variation data for Solanum lycopersicum is from the study of genetic variation by whole-genome sequencing of 84 tomato accessions, including cultivated wild relatives representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group [2]. In detail, the study expored genetic variation in the tomato clade by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups. The variation data has been submitted to the ENA with accession ERP004618, and has been locus-level accessioned using the transPLANT variation archive.

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Links

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References

  1. The tomato genome sequence provides insights into fleshy fruit evolution.
    Tomato Genome Consortium. 2012. Nature. 485:635-641.
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  2. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
    Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L et al. 2014. Plant J.. 80:136-148.

Picture credit: David Besa from Sonoma, USA (Flickr) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons.

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About Solanum tuberosum

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Solanum tuberosum (potato) is the worlds fourth most important food crop after rice, wheat and maize. Potatoes were first introduced outside the Andes four centuries ago, and it is estimated that by the year 2020 over two billion people will depend on it for food, feed, or income. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 Mbp, making it a medium-sized plant genome. Potato is the first Solanaceae genome to be sequenced and as such, is the first asterid genome, representing a major clade of eudicots. The Solanaceae are a diverse family of agriculturally important plant species, including tomato, eggplant, pepper, tobacco, and petunia.

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Assembly

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Genome sequencing and gene prediction were performed as described in [2].

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Annotation

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Genome sequencing and gene prediction were performed as described in [2].

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Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

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Regulation

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  • Mapping using GSNAP of transcriptomics sequences from 16 samples from different tissues submitted to the ENA SRA as part of study ERP000527. [View data]
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  • ~194,000 EST sequences have been aligned to the genome with Exonerate [View data]
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References

  1. Genome sequence and analysis of the tuber crop potato.
    The Potato Genome Sequencing Consortium. 2011. Nature. 475:189-195.
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  2. Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the Worlds Third Most Important Food Crop.
    Visser RichardGF, Bachem ChristianWB, Boer JanMde, Bryan GlennJ, Chakrabati SwarupK, Feingold Sergio, Gromadka Robert, Ham RoelandCHJvan, Huang Sanwen, Jacobs JeanneME et al. 2009. Am. J. Potato Res.. 86:417-429.
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  3. Analyzing the potato abiotic stress transcriptome using expressed sequence tags.
    Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR. 2005. Genome. 48:598-605.
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  4. Gene expression profiling of potato responses to cold, heat, and salt stress.
    Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR. 2005. Funct. Integr. Genomics. 5:201-207.
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  5. Image credit: Scott Bauer, USDA ARS [Public domain], via Wikimedia Commons.
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About Sorghum bicolor

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Sorghum bicolor is a widely grown cereal crop, particularly in Africa, ranking 5th in global cereal production. It is also used as biofuel crop and potential cellulosic feedstock. The diploid genome (~730 Mbp) has a haploid chromosome number of 10. Although highly repetitive, the genome is more tractable for sequencing than its close relative, Zea mays.

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Assembly

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The first genome assembly of Sorghum bicolor cv. Moench was published in 2009 [1]. Sequencing by the US department of Energy Joint Genome Institute (JGI) Community Sequencing Program in collaboration with the Plant Genome Mapping Laboratory followed a whole genome shotgun strategy reaching 8x coverage with scaffolds, where possible, being assigned to the genetic map. Since then JGI made two rounds of improvements. The most recent update of release v3.0 includes ~351 Mb of finished sorghum sequence. A total of 349 clones were manually inspected, then finished and validated using a variety of technologies. They were integrated into chromosomes by aligning to v1.0 assembly. As a result, 4,426 gaps were closed, and a total of 4.96 MB of sequence was added to the assembly. Overall contiguity (contig N50) increased by a factor of 5.8x from 204.5 KB to 1.2 MB. For more details, see phytozome.

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Annotation

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This browser presents data from the v3.0.1 assembly and v3.1.1 gene set (March 2007). Gene prediction is an improved process based upon resources used in original v1.0 release (Sbi1 assembly and Sbi1.4 gene set) with new geneAtlas RNA-seq data. Read more at Phytozome.

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Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 6 repeats loaded from (ENA); 685,783 Low complexity (Dust) features, covering 29 Mb (4.0% of the genome); 455,749 RepeatMasker features (with the RepBase library), covering 451 Mb (62.1% of the genome); 392,778 RepeatMasker features (with the REdat library), covering 409 Mb (56.2% of the genome); and 245,654 Tandem repeats (TRF) features, covering 41 Mb (5.7% of the genome).

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Variation

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Morris et al. SNPs set [2]

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The Morris et al. set is from a 2013 study of agroclimatic traits in Sorghum [2]. In this study, approximately 265,000 single nucleotide polymorphisms (SNPs) were characterized from 971 worldwide accessions, combining three previously defined sorghum diversity panels. They are: the US sorghum association panel (SAP), the sorghum mini core collection (MCC) and the Generation Challenge Program sorghum reference set (RS). GWAS studies were subsequently performed on plant height components and inflorescence architecture using 336 SAP lines. The data presented here represents the genotype information of the 378 SAP lines provided by the author.

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Mace et al. SNPs set [3]

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This Sorghum variation data set corresponds to 6,578,420 SNPs (SNPs mapping to supercontigs were removed) genotyped in 45 Sorghum bicolor lines including the BTx623 reference genome plus 2 S. propinquum lines reported by Mace et al (2013). The data was obtained by resequencing the genomes of the 44 Sorghum bicolor lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group (i.e., major races of cultivated S. bicolor, landraces, improved inbreds, progenitors, wild and weedy), and the first resequenced genome of S. propinquum, all of which were mapped to the BTx623 S. bicolor reference genome.

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Jiao et al. EMS SNPs set [5]

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The Jiao EMS dataset includes ~1.8 millions ethyl methane sulfonate (EMS)-induced G/C to A/T transition mutations annotated from 252 M3 families selected from the 6,400 sorghum mutant library in BTx623 background [1]. Genomic DNA used for sequencing was pooled from 20 M3 plants per M2 family.

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Structural Variation

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Data for structural variation in sorghum has been imported from the Database of Genomic Variants archive (dGVA) from a single study containing around 32 thousand structural variations [4]. Click here for example.

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Links

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References

  1. The Sorghum bicolor genome and the diversification of grasses.
    Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. Nature. 457:551-556.
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  2. Population genomic and genome-wide association studies of agroclimatic traits in sorghum.
    Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE et al. 2013. Proc. Natl. Acad. Sci. U.S.A.. 110:453-458.
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  3. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum.
    Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X et al. 2013. Nat Commun. 4:2320.
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  4. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).
    Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM et al. 2011. Genome Biol.. 12:R114.
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  5. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses.
    Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. 2016. Plant Cell. 28:1551-1562.

Picture credit: By Sahaquiel9102 (Own work) [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

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This Cacao Genome Project is a collaboration among MARS, USDA-ARS, IBM, NCGR, Clemson University, HudsonAlpha Institute for Biotechnology, Indiana University and Washington State University with funding from MARS, USDA-ARS, and NSF, and contributions in effort from cacao breeders around the world.

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About Theobroma cacao

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Theobroma cacao (cacao or chocolate tree) is a neotropical plant native to Amazonian rainforests. It is now cultivated in over 50 countries. A member of Malvaceae family, its beans are harvested from pods for use as the food chocolate, in confections and cosmetics. This is the genome assembly and annotation of the Matina 1-6 cultivar, which belongs to the most cultivated cacao type worldwide.

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Assembly

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The 445 Mbp chromosome-level assembly of this cacao genome has scaffolds anchored and oriented to 10 chromosomes with BAC end sequencing and FISH karyotyping-based chromosome assignment, for 94.6% of total assembly, with 4.4% gap sequence, and the remainder in unlinked scaffolds. This assembly is primarily composed of Roche 454 Titanium STD reads, augmented by 6 recombination paired Titanium libraries, 3 fosmid packaged Sanger sequenced libraries, and 3 Sanger sequenced BAC Ends libraries. This genome assembly is produced by Jeremy Schmutz (Hudson Alpha, 2011-08-01).

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The genome sequence of the most widely cultivated cacao type and

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its use to identify candidate genes regulating pod color.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053823/

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http://www.ncbi.nlm.nih.gov/nuccore/CM001879.1

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Annotation

+ +

Illumina and 454 RNA-Seq reads totaling 62 Gigabases were collected from leaf, pistil and bean tissues, assembled with de-novo RNA assemblers Velvet/Oases [VELO], SOAPdenovo-Trans [SOAP], Roche Newbler, and genome-guided assembler Cufflinks [CUFF]. From this over-assembly of 1.2 million transcripts, the 48,404 most accurate cacao gene assemblies are selected with homology and genome map evidence scoring.

+ +

Proteins from 297,061 genes of 8 plants, arabidopsis, poplar, castorbean, grape, strawberry, potato, soybean, and sorhgum are used for homology evidence. Transposons are annotated as class I retrotransposon and II DNA transposon with subcategories, totaling 8,542 intact transposons with 122,552 copies, covering 137 Mbases or 42% of genome assembly.

+ +

Gene evidence from RNA mapped introns, plant species protein homology, expressed RNA alignments, transposons, is mapped to genome with GMAP/GSNAP [GMAP], tBLASTn, and exonerate [EXNR]. Several genome gene prediction sets were produced with AUGUSTUS [AUG], following HMM training of this predictor on cacao transcripts, by varying proportions of this gene evidence and parameters.

+ +

EvidentialGene software [EVG] is used to annotate, score and classify gene assemblies and models with weighted evidence scores. This includes hueristics to identify and reduce gene-joins and fragment models.

+ +

Highest evidence-scored models or assemblies are selected per locus for a primary transcript. Alternate transcripts are selected from remaining transcript assemblies (but not predictions) that vary from primary transcript in exon-intron structure. The resulting gene set is annotated with recripocal best blastp to several plant gene sets, clustered to gene families with OrthoMCL [OMCL], and annotated with family consensus function names, homology scores and references, and other gene quality scores.

+ +

This gene annotation includes 29,408 protein coding loci, with 14,806 alternate transcripts. Gene evidence recovered in this cacao gene set includes 91% of 161333 RNA-introns, 67% of 48404 RNA assemblies, and 76% of 36Mb of plant protein alignments. This gene set construction and annotation is produced by Don Gilbert (Indiana Univ., 2012-03-08) [EVG]

+ +

Annotation refs

+ +

[EVG] EvidentialGene: Perfect Genes Constructed from Gigabases of RNA http://arthropods.eugenes.org/EvidentialGene/

+ +

[AUG] Stanke M, Schoffmann O, Morgenstern B, Waack S: Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006, 7:62.

+ +

[OMCL] Li L, Stoeckert CJ, Jr., Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189.

+ +

[GMAP] Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.

+ +

[EXNR] Slater GSC, Birney E: Automated generation of heuristics for biological sequence comparison. Bmc Bioinformatics 2005, 6:31.

+ +

[VELO] Schulz, M.H., et al. (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels, Bioinformatics, 28, 1086-1092.

+ +

[SOAP] Y. Xie, et al. (2014) SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, Epub ahead of print.

+ +

[CUFF] Trapnell, C., et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, 28, 511-515.

+ + + +

Links

+ + + diff --git a/gramene/htdocs/ssi/species.weix/about_Trifolium_pratense.html b/gramene/htdocs/ssi/species.weix/about_Trifolium_pratense.html new file mode 100644 index 00000000..b5eb856c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Trifolium_pratense.html @@ -0,0 +1,31 @@ + +

The red clover genome is a joint effort of TGAC and IBERS. This work was funded by an Institute Programme Grant to IBERS (BB/J004405/1) from the Biotechnology and Biological Sciences Research Council (BBSRC), by the ERANET Plant Genomics programme (ERAPG038A-TRANSLEG) and by a Capacity, Capability Challenge Programme from TGAC.

+ +

+
+ + +

About Trifolium pratense

+ +

Red clover (Trifolium pratense) is one of the most important forage legume crops in temperate agriculture, and a key component of sustainable intensification of livestock farming systems. Red clover is a highly heterozygous diploid (2n = 2x = 14) species due to its gametophytic self-incompatibility system. This assembly provides a chromosome-scale reference draft genome for a red clover genotype of the variety Milvus (Milvus B). It was published in De Vega, J. J. et al. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement [1].

+ + + +

Assembly

+ +

This assembly provides a chromosome-scale reference draft genome for a red clover genotype of the variety Milvus (Milvus B) by integration of Whole Genome Sequencing (WGS) of short-length reads, Sanger-based bacterial artificial chromosome (BAC) end sequences, a physical and two genetic maps. WGS was assembled from paired-end and mate-pair libraries using the Platanus assembler. Three BAC libraries were created using high molecular weight DNA from a specific genotype of the Milvus variety (Milvus B). The mapping population used in this work consisted of 188 genotypes of F1 progeny from a cross between a genotype of the variety Milvus and a genotype of the variety Britta. We aligned 1,031 of the 1,388 markers from the two maps to place 532 of the longest scaffolds and used the BAC-end sequences as markers to further link unplaced scaffolds with already placed scaffolds from the same physical contig. The physical map contained 29,730 BACs, of which almost 23,000 were in contigs (77.3%).

+ + + +

Annotation

+ + + +

​Links

+ + + +

References

  1. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.
    De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon , Rognli OA, Jones C, Swain M, Geurts R et al. 2015. Sci Rep. 5:17394.

Picture credit: By Masaki Ikeda - Own work, CC BY-SA 3.0

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum.html b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum.html new file mode 100644 index 00000000..18c7b0bf --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum.html @@ -0,0 +1,68 @@ + +

For information about the assembly and annotation please view the IWGSC announcement.

+ +

The previous wheat assembly (TGACv1) and every other plant from release 31 is available in the new Ensembl Plants archive site.

+ +

+
+ + +

About Triticum aestivum

+ +

Triticum aestivum (bread wheat) is a major global cereal grain essential to human nutrition. Wheat was one of the first cereals to be domesticated, originating in the fertile crescent around 7000 years ago. Bread wheat is hexaploid, with a genome size estimated at ~17 Gbp, composed of three closely-related and independently maintained genomes that are the result of a series of naturally occurring hybridization events. The ancestral progenitor genomes are considered to be Triticum urartu (the A-genome donor) and an unknown grass thought to be related to Aegilops speltoides (the B-genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides) which hybridized again with Aegilops tauschii (the D-genome donor) to produce modern bread wheat.

+ + + +

Assembly

+ +

The IWGSC RefSeq v1.0 is an integration of the IWGSC WGA v0.4 (comprised of Illumina short sequence reads assembled with NRGene’s DeNovoMAGICTM software) with IWGSC chromosome-based and other resources (physical maps, MTP BAC WGPTM sequence tags; and for some chromosomes: sequenced BACs, BioNano optical maps, Alignment to RH maps & GBS map of the SynOp RIL population CsxRn genetic map) Scaffolds/superscaffold have been assigned to chromosomal locations using POPSEQ data and a HiC map. Chromosomal scaffold/ superscaffold N50 is 22.8 Mb.

+ + + +

Annotation

+ +

The IWGSC RefSeq v1.0 annotation includes gene models generated by integrating predictions made by INRA-GDEC using Triannot and PGSB using their customised pipeline (previously MIPS pipeline). The integration was undertaken by the Earlham institute (EI), who have also added UTRs to the gene models where supporting data are available. Gene models have been assigned to high confidence (HC) or low confidence (LC) classes based on completeness, similarity to genes represented in protein and DNA databases and repeat content. The automated assignment of functional annotation to genes has been generated by PGSB based on AHRD parameters.
+The annotation includes 110,790 high confidence genes, 158,793 low confidence genes and 13,044 long coding RNAs.
+98,270 high confidence genes from the TGACv1 annotation [3] were aligned to the assembly using Exonerate. For each gene up to 3 alignments are displayed, compromising 196,243 alignments of which 90,686 are protein coding.

+ +

+ + + +

+ +

+ + + +

Variation

+ +

Data from CerealsDB [1]

+ +

768664 markers from the 820K Axiom SNP array from CerealsDB were aligned to the assembly.
+This was done by CerealsDB[1] using Blast with a cutoff of 1e-05. The top three hits were parsed and compared to CerealsDB genetic map data. In cases where two or more of the top three hits had an identical score, the hit agreed with the genetic map was selected. In cases of no genetic map information for a particular SNP then the top hit was selected.

+ +

EMS Mutation data [2]

+ +

EMS-type variants from sequenced tetraploid (cv ‘Kronos’) and hexaploid (cv ‘Cadenza’) TILLING populations. Mutations were called on the IWGSC RefSeq V1.0 assembly using the Dragen system[4]

+ +
  • 4.4 million Kronos mutations
    • +
  • 9.0 million Cadenza mutations
    • +

Researchers and breeders can search this database online, identify mutations in the different copies of their target gene, and request seeds to study gene function or improve wheat varieties. Seeds can be requested from the UK SeedStor (https://www.seedstor.ac.uk/shopping-cart-tilling.php) or from the US based Dubcovsky lab (http://dubcovskylab.ucdavis.edu/wheat-tilling).

+ +

This resource was generated as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and the John Innes Centre.

+ +

+ +

+ + + +

+ +
+ +

References

  1. CerealsDB 3.0: expansion of resources and data integration.
    Wilkinson PA, Winfield MO, Barker GL,Tyrrell S, Bian X, Allen AM, Burridge A, Coghill JA, Waterfall C, Caccamo M et al. 2016. BMC Bioinformatics. 17:256.
    2. +
  2. Uncovering hidden variation in polyploid wheat.
    Ksenia V. Krasileva, Hans A. Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H. Ramirez-Gonzalez et al. . 2016. PNAS. 114:E913E921.
    3. +
  3. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
    Bernardo J. Clavijo, Luca Venturini,Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman et al. 2017. Genome Research.
    4. +
  4. Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGENTM Bio-IT Processor for Precision Medicine.
    Goyal, A., Kwon, H.J., Lee, K., Garg, R., Yun, S.Y. et al. 2017. Open Journal of Genetics. 7:9-19.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_a.html b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_a.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_a.html @@ -0,0 +1,40 @@ + +

Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

+

Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

+ + +

IWGSC Chromosome survey sequence

+

Assemblies

+

Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

+

The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

+ + +

Annotations

+

The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
The program findorf was used to predict the CDS within these transcripts as described in [2].

+ + +

Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

+

As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

+

The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

+

Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

+

These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

+

Wheat sequence search

+

The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

+

Search is performed via the ENA search service, and currently includes:

+

Links

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_b.html b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_b.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_b.html @@ -0,0 +1,40 @@ + +

Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

+

Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

+ + +

IWGSC Chromosome survey sequence

+

Assemblies

+

Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

+

The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

+ + +

Annotations

+

The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
The program findorf was used to predict the CDS within these transcripts as described in [2].

+ + +

Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

+

As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

+

The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

+

Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

+

These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

+

Wheat sequence search

+

The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

+

Search is performed via the ENA search service, and currently includes:

+

Links

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_d.html b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_d.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_d.html @@ -0,0 +1,40 @@ + +

Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

+

Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

+ + +

IWGSC Chromosome survey sequence

+

Assemblies

+

Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

+

The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

+ + +

Annotations

+

The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
The program findorf was used to predict the CDS within these transcripts as described in [2].

+ + +

Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

+

As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

+

The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

+

Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

+

These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

+

Wheat sequence search

+

The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

+

Search is performed via the ENA search service, and currently includes:

+

Links

+ + diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_pre.html b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_pre.html new file mode 100644 index 00000000..225225a2 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_aestivum_pre.html @@ -0,0 +1,45 @@ + +

This pre-site offers immediate public access to a new assembly of the wheat genome. For access to the main Ensembl Plants site, please click here.

+
+ + +

About Triticum aestivum

+ +

This Ensembl Plants pre-site contains the first release of the IWGSC RefSeq v1.0 genome assembly of Triticum aestivum cv. Chinese Spring, generated by IWGSC. The assembly has a chromosomal scaffold/ superscaffold N50 of 22.8 MBb.

+ +

Triticum aestivum (bread wheat) is a major global cereal grain essential to human nutrition. Wheat was one of the first cereals to be domesticated, originating in the fertile crescent around 7000 years ago. Bread wheat is hexaploid, with a genome size estimated at ~17 Gbp, composed of three closely-related and independently maintained genomes that are the result of a series of naturally occurring hybridization events. The ancestral progenitor genomes are considered to be Triticum urartu (the A-genome donor) and an unknown grass thought to be related to Aegilops speltoides (the B-genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides) which hybridized again with Aegilops tauschii (the D-genome donor) to produce modern bread wheat.

+ +

+ +

The main Ensembl Plants site (http://plants.ensembl.org/Triticum_aestivum/Info/Index) contains the TGACv1 assembly and will be replaced by IWGSCv1 in the next release (July).

+ +

The TGACv1 assembly will continue to be availble via the Ensmble Archive site.

+ + + +

Assembly

+ +

The IWGSC RefSeq v1.0, comprised of Illumina short sequence reads assembled with NRGene’s DeNovoMAGIC software, produced scaffolds totaling 14.5Gb with a chromosomal scaffold/superscaffold N50 of 22.8 Mb.
+Scaffolds have been assigned to chromosomal locations using POPSEQ data and a HiC map. Over 99% of chromosome survey contigs map to the new assembly.

+ + + +

Annotation

+ +

The IWGSC RefSeq v1.0 annotation includes gene models generated by integrating predictions made by INRA-GDEC using Triannot and PGSB using their customised pipeline (previously MIPS pipeline). The integration was undertaken by the Earlham institute (EI), who have also added UTRs to the gene models where supporting data are available. Gene models have been assigned to high confidence (HC) or low confidence (LC) classes based on completeness, similarity to genes represented in protein and DNA databases and repeat content. The automated assignment of functional annotation to genes has been generated by PGSB based on AHRD parameters.
+The annotation includes 110,790 high confidence genes, 158,793 low confidence genes and 13,044 long coding RNAs.
+98,270 high confidence genes from the TGACv1 annotation were aligned to the assembly using Exonerate. For each gene up to 3 alignments are displayed, compromising 196,243 alignments of which 90,686 are protein coding.

+ +

+ + + +

Variation

+ +

768664 markers from the 820K Axiom SNP array from CerealsDB were aligned to the assembly.
+This was done by CerealsDB[1] using Blast with a cutoff of 1e-05. The top three hits were parsed and compared to CerealsDB genetic map data. In cases where two or more of the top three hits had an identical score, the hit agreed with the genetic map was selected. In cases of no genetic map information for a particular SNP then the top hit was selected.

+ +

+ + +

References

  1. CerealsDB 3.0: expansion of resources and data integration.
    Paul A. Wilkinson, Mark O. Winfield, Gary L. A. Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Caccamo et al. 2016. BMC Bioinformatics. 17:256
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/about_Triticum_urartu.html b/gramene/htdocs/ssi/species.weix/about_Triticum_urartu.html new file mode 100644 index 00000000..58315baf --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/about_Triticum_urartu.html @@ -0,0 +1,73 @@ + +

Wheat genomics resources are developed as part of our involvement in the consortium Triticeae Genomics For Sustainable Agriculture, funded by the BBSRC, and led by TGAC.

+ +

BBSRC logo

+
+ + +

About Triticum urartu

+ +

Triticum urartu is the diploid progenitor of the bread wheat A-genome, providing important evolutionary information for bread and durum wheat. It is closely related to einkorn wheat, T. monococcum.

+ + + +

Assembly

+ +

The genome of Triticum urartu accession G1812 was sequenced by the BGI using a whole-genome shotgum strategy, and assembled using SOAPdenovo software. The genome assembly reached 3.92 Gbp with a N50 size of 3.42 kbp. After gap closure, the draft assembly was 4.66 Gbp, with a scaffold N50 length of 63.69 kbp.

+ +

The chloroplast genome component and its gene annotation are also present. This was imported from ENA entry, KC912693.

+ + + +

Annotation

+ +

34,879 protein-coding genes were predicted. For more details about genome sequencing and the protein_coding gene prediction protocol, see [1].

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Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

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Triticeae Repeats from TREP were aligned to the T. urartu genome using RepeatMasker.

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Regulation and sequence alignment

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RNA-Seq data, ESTs and UniGene datasets have also been aligned to the Triticum urartu genome:

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Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. [4]

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The wheat genome assemblies previously generated by Brenchley et al. (PMID:23192148) have been aligned to the bread wheat survey sequence, Brachypodium, barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii). Homoeologous variants inferred between the three wheat genomes (A, B, and D) are displayed in the context of the gene models of these five genomes.

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Sequences of diploid progenitor and ancestral species permitted homoeologous variants to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

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The wheat gene alignments and the projected wheat SNPs are available on the Location view, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

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Transcriptome assembly in diploid einkorn wheat Triticum monococcum - Fox et al. [5]

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Genome-wide transcriptomes of two Triticum monococcum subspecies were constructed, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC projects PRJNA203221 and PRJNA195398.

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The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. They were mapped to the bread wheat, barley and Triticum urartu genomes using STAR. Click here for a Triticum urartu example.

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Links

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Links (Triticum urartu)

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  • GigaDB
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  • ENA study: SRP002455: Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors
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  • TREP, the Triticeae Repeat Sequence Database
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Links (Triticum aestivum)

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References

  1. Draft genome of the wheat A-genome progenitor Triticum urartu.
    Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y et al. 2013. Nature. 496:87-90.
    2. +
  2. Image credit: Mark Nesbitt [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
    3. +
  3. Homoeolog-specific transcriptional bias in allopolyploid wheat.
    Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
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About Vigna angularis

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Vigna angularis (adzuki bean) is an annual legume crop, widely grown throughout East Asia and the Himalayas for food. It is widely used as an ingredient for traditional dessert cuisines due to its sweet taste, as well as its nutritious protein and starch contents. It is a diploid (2n = 2x = 22) with an estimated genome size of 538 Mbp.

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Assembly

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Paired-end (180 bp) and mate-pair (5 and 10 kbp) libraries were prepared using 100 bp short reads (Illumina HiSeq 2000) and were combined with a single unpaired library of average read length of 458 bp (Roche GS-FLX+) for a total physical coverage of 291x. The assembly produced 3,883 scaffolds with N50 length of 703 kbp, covering 75% of the estimated genome size. Scaffolds were assembled into pseudo-molecules using synteny and genetic mapping of a population of 133 F4 lines (814 SNPs in 11 linkage groups).

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Annotation

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Gene prediction using the MAKER pipeline revealed 26,857 high confidence protein-coding genes using RNA-Seq of flower, pod, leaf, and root tissues. In total, 86% of the 248 core eukaryotic genes in CEGMA pipeline were matched to the genome assembly.

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References

  1. Draft genome sequence of adzuki bean, Vigna angularis.
    Kang YJ, Satyawan D, Shim S, Lee T, Lee J, Hwang WJ, Kim SK, Lestari P, Laosatit K, Kim KH et al. 2015. Sci Rep. :8069.

Picture credit: By Sanjay Acharya [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], from Wikimedia Commons

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About Vitis vinifera

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Vitis vinifera (grape) is the most widely cultivated and economically important grape species. It has a diploid genome with haploid chromosome number of 19, and an estimated genome size of ~500 Mbp.

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Assembly

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This release is based on a 12x whole genome shotgun sequence assembly and the V1 annotation of the Vitis vinifera genome [1]. These data were prepared by a French-Italian Public Consortium for Grapevine Genome Characterization under the auspices of the International Grape Genome Program (IGGP). Further details of the sequencing and assembly are available from Genoscope.

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Annotation

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Protein-coding genes were predicted by combining ab initio models, V. vinifera complementary DNA alignments, and alignments of proteins and genomic DNA from other species. The integration of the data was performed with GAZE [2].

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Regulation

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Oligo probes from the GeneChip Vitis vinifera Genome Array have been aligned using the standard Ensembl mapping procedure. For example, see the the results for 1609916_s_at (a probe that comes up when browsing the sol1 gene (VIT_18s0157g00050).

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Variation

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Single nucleotide polymorphisms identified by re-sequencing a collection of grape cultivars and wild Vitis species from the USDA germplasm collection [3].

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Links

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References

  1. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al. 2007. Nature. 449:463-467.
    2. +
  2. GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
    Howe KL, Chothia T, Durbin R. 2002. Genome Res. 9:1418-27.
    3. +
  3. Rapid genomic characterization of the genus vitis.
    Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D. 2010. PLoS ONE. 5:e8219.
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About Zea mays

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Zea mays (maize) has the highest world-wide production of all grain crops, yielding 875 million tonnes in 2012 (http://faostat.fao.org/). Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. Maize was domesticated from wild teosinte in Central America and its cultivation spread throughout the Americas by Pre-Columbian civilizations. In addition to its economic value, maize is an important model organism for studies in plant genetics, physiology, and development. It has a large genome of of about 2.4 gigabases with a haploid chromosome number of 10 (Schnable et al., 2009; Zhang et al., 2009). Maize is distinguished from other grasses in that its genome arose from an ancient tetraploidy event unique to its lineage.

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Assembly

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This entirely new assembly of the maize genome (B73 RefGen_v4) is constructed from PacBio Single Molecule Real-Time (SMRT) sequencing at approximately 60-fold coverage and scaffolded with the aid of a high-resolution whole-genome restriction (optical) mapping. The pseudomolecules of maize B73 RefGen_v4 are assembled nearly end-to-end, representing a 52-fold improvement in average contig size relative to the previous reference (B73 RefGen_v3).

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Annotation

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Nomenclature of Maize RefGen_V4 gene models

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The gene models of Maize RefGen_V4 were named following the standard of Maize Genetics Nomenclature: www.maizegdb.org/nomenclature#GENEMODEL. Previous identifiers (e.g. GRMZM) are retained as synonyms and can be searched.

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Method

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Genes were annotated with Maker pipeline (Campbell et al. 2014) using 111,000 transcripts obtained by single-molecule sequencing. These long read Iso-Seq data (Wang et al. 2016) improved annotation of alternative splicing, more than doubling the number of alternative transcripts from 1.5 to 3.8 per gene, thereby improving our knowledge of gene structure and transcript variation, resulting in substantial improvements including resolved gaps and misassembles, corrections to strand, consolidation of gene models, and anchoring of unanchored genes.

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Gene annotation was performed in the laboratory of Doreen Ware (CSHL/USDA). Protein-coding genes were identified using MAKER-P software version 3.1 (Campbell et al 2014) with the following transcript evidence: 111,151 PacBio Iso-Seq long-reads from 6 tissues (Wang et al. 2016), 69,163 full-length cDNAs deposited in Genbank (Alexandrov et al. 2008; Soderlund et al. 2009), 1,574,442 Trinity-assembled transcripts from 94 B73 RNA-Seq experiments (Law et al 2015), and 112,963 transcripts assembled from deep sequencing of a B73 seedling (Martin et al 2014). Additional evidence included annotated proteins from Sorghum bicolor, Oryza sativa, Setaria italica, Brachypodium distachyon, and Arabidopsis thaliana downloaded from Ensembl Plants Release 29 (Oct-2015). Gene calling was assisted by Augustus (Keller et al. 2011) and FGENESH (Salamov & Solovyev, 2000) trained on maize and monocots, respectively. Low-confidence gene calls were filtered on the basis of AED score and other criteria and are viewable as a separate track. In the end, the higher confidence set (called filtered gene set) has 39,324 protein coding genes. Gene annotations from B73 RefGen_v3 were mapped to the new assembly and are also available as a separate track. In addition, 2,532 Long non-coding RNA (lncRNA) genes were mapped and annotated from prior studies (Li et al., 2014; Wang et al., 2016), while 2,290 tRNA genes were identified using tRNAscan-SE (Lowe & Eddy 1997), and 154 miRNA genes mapped from miRBase (Kozomara & Griffiths-Jones 2014).

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Repeats

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Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 1,335,693 Low complexity (Dust) features, covering 56 Mb (2.6% of the genome); 787,462 RepeatMasker features (with the reDAT library), covering 1,417 Mb (66.3% of the genome); 1,105,314 RepeatMasker features (with the RepBase library), covering 1,646 Mb (77.1% of the genome); 950,012 Tandem repeats (TRF) features, covering 103 Mb (4.8% of the genome).

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Regulation

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Gene expression probes

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Oligo probes from the GeneChip Maize Genome Array have been aligned using the standard Ensembl 2-step mapping procedure. For example, see the the results for Zm.155.1.A1_a_at.

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DNA methylation

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Genomewide patterns of DNA methylation for two maize inbred lines, B73 and Mo17, are now displayed on the maize genome browser. Cytosine methylation in symmetric (CG and CHG, where H is A, C, or T) context is associated with DNA replication and histone modification. CG (65%) and CHG (50%) methylation is also highest in transposons. Source: Maize methylome publication by Regulski et al. (2013).

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Variation

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HapMap2 dataset

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A variation set which comprises the maize HapMap2 data (Chia et al., 2012). This dataset incorporates approximately 55 million SNPs and InDels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass). Each line was sequenced to an average of 4.5-fold coverage using the Illumina GAIIx platform. The reads can be accessed from the SRA, with accession ID: SRA051245. Reads were initially mapped to the B73 RefGen_v3 reference genome using a combination of Bowtie, Novoalign and SOAP, then remapped to the most recent B73 RefGen_v4 reference genome. The variations were scored by taking into account identity-by-descent blocks that are shared among the lines.

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The Panzea 2.7 genotyped-by-sequencing (GBS) dataset

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This variation data set consists of 719,472 SNPs (excluding 332 SNPs that were removed for mapping to scaffolds) typed in 16,718 maize and teosinte lines, and grouped in 14 overlapping populations according to the germplasm set in the corresponding metadata table.

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Links

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References

  1. A genome-wide characterization of microRNA genes in maize.
    Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. 2009. PLoS Genet.. 5:e1000716.
    2. +
  2. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
    Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S et al. 2014. Sci Rep. 4:4519.
    3. +
  3. A novel hybrid gene prediction method employing protein multiple sequence alignments.
    Keller O, Kollmar M, Stanke M, Waack S. 2011. Bioinformatics. 27:757-763.
    4. +
  4. Ab initio gene finding in Drosophila genomic DNA.
    Salamov AA, Solovyev VV. 2000. Genome Res.. 10:516-522.
    5. +
  5. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.
    Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM et al. 2015. Plant Physiol.. 167:25-39.
    6. +
  6. Genome-wide discovery and characterization of maize long non-coding RNAs.
    Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE et al. 2014. Genome Biol.. 15:R40.
    7. +
  7. Insights into corn genes derived from large-scale cDNA sequencing.
    Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB et al. 2009. Plant Mol. Biol.. 69:179-194.
    8. +
  8. Maize HapMap2 identifies extant variation from a genome in flux.
    Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC et al. 2012. Nat. Genet.. 44:803-807.
    9. +
  9. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.
    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ et al. 2014. Plant Physiol.. 164:513-524.
    10. +
  10. miRBase: annotating high confidence microRNAs using deep sequencing data.
    Kozomara A, Griffiths-Jones S. 2014. Nucleic Acids Res.. 42:D68-73.
    11. +
  11. Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
    Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E et al. 2009. PLoS Genet.. 5:e1000740.
    12. +
  12. The B73 maize genome: complexity, diversity, and dynamics.
    Schnable PS, Ware D, et al.. 2009. Science. 326:1112-1115.
    13. +
  13. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
    Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D. 2016. Nat Commun. 7:11708.
    14. +
  14. FAOSTAT.
    15. +
  15. Comparative population genomics of maize domestication and improvement.
    Hufford MB, Xu X, van Heerwaarden J, Pyhjrvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM et al. 2012. Nat. Genet.. 44:808-811.
    16. +
  16. A first-generation haplotype map of maize.
    Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J et al. 2009. Science. 326:1115-1117.
    17. +
  17. Detailed analysis of a contiguous 22-Mb region of the maize genome.
    Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y et al. 2009. PLoS Genet.. 5:e1000728.
    18. +
  18. The physical and genetic framework of the maize B73 genome.
    Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W et al. 2009. PLoS Genet.. 5:e1000715.
    19. +
  19. A single molecule scaffold for the maize genome.
    Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S et al. 2009. PLoS Genet.. 5:e1000711.
    20. +
  20. Evidence-based gene predictions in plant genomes.
    Liang C, Mao L, Ware D, Stein L. 2009. Genome Res.. 19:1912-1923.

Picture credit: Nicolle Rager Fuller, National Science Foundation.

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Summary

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Assembly:ASM34733v1, Dec 2013
Database version:86.1
Base Pairs:2,691,777,557
Golden Path Length:3,313,764,331
Genebuild by: BGI
Genebuild method: Generated from ENA annotation
Genebuild started: May 2014
Genebuild released: Nov 2008
Genebuild last updated/patched: Dec 2013
Genebuild version: 2013-12-BGI
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Gene counts

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Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		33,929
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		66
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:37,035
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Coordinate Systems

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chromosome
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1 sequence
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SequenceLength (bp)
Pt114112
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supercontig429891 sequences
contig1107057 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Aegilops_tauschii_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Aegilops_tauschii_IPtop500.html new file mode 100644 index 00000000..6839ec2f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Aegilops_tauschii_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR032675
Leucine-rich repeat domain, L domain-like		19586141
2IPR011009
Protein kinase-like domain		17751973
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		17534545
4IPR000719
Protein kinase, catalytic domain		16844338
5IPR001810
F-box domain, cyclin-like		12902972
6IPR008271
Serine/threonine-protein kinase, active site		12841304
7IPR017441
Protein kinase, ATP binding site		10631078
8IPR013320
Concanavalin A-like lectin/glucanase, subgroup		9941272
9IPR002182
NB-ARC		697796
10IPR011990
Tetratricopeptide-like helical		5931813
11IPR001611
Leucine-rich repeat		5913412
12IPR013083
Zinc finger, RING/FYVE/PHD-type		528574
13IPR001128
Cytochrome P450		5253031
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		522695
15IPR002885
Pentatricopeptide repeat		49510949
16IPR016040
NAD(P)-binding domain		4531076
17IPR003591
Leucine-rich repeat, typical subtype		4133065
18IPR002401
Cytochrome P450, E-class, group I		3912273
19IPR017972
Cytochrome P450, conserved site		388390
20IPR029058
Alpha/Beta hydrolase fold		383958
21IPR009057
Homeodomain-like		382894
22IPR013210
Leucine-rich repeat-containing N-terminal, type 2		372376
23IPR008974
TRAF-like		353659
24IPR011333
BTB/POZ fold		351398
25IPR016024
Armadillo-type fold		347756
26IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		309824
27IPR020846
Major facilitator superfamily domain		307569
28IPR003593
AAA+ ATPase domain		305429
29IPR000210
BTB/POZ domain		303885
30IPR001841
Zinc finger, RING-type		288695
31IPR015943
WD40/YVTN repeat-like-containing domain		286448
32IPR005174
Protein of unknown function DUF295		286292
33IPR017853
Glycoside hydrolase, superfamily		270315
34IPR012677
Nucleotide-binding, alpha-beta plait		267798
35IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		266594
36IPR012336
Thioredoxin-like fold		262577
37IPR011989
Armadillo-like helical		252482
38IPR001005
SANT/Myb domain		252637
39IPR017986
WD40-repeat-containing domain		250601
40IPR002083
MATH/TRAF domain		243409
41IPR001680
WD40 repeat		2322131
42IPR000504
RNA recognition motif domain		2311005
43IPR013781
Glycoside hydrolase, catalytic domain		220284
44IPR010255
Haem peroxidase		218235
45IPR002016
Haem peroxidase, plant/fungal/bacterial		2161238
46IPR006566
FBD domain		208235
47IPR017930
Myb domain		205298
48IPR000823
Plant peroxidase		1981323
49IPR017451
F-box associated interaction domain		196200
50IPR020683
Ankyrin repeat-containing domain		187948
51IPR011991
Winged helix-turn-helix DNA-binding domain		186366
52IPR013830
SGNH hydrolase-type esterase domain		181476
53IPR025315
Domain of unknown function DUF4220		181194
54IPR023213
Chloramphenicol acetyltransferase-like domain		175303
55IPR002110
Ankyrin repeat		1711175
56IPR027443
Isopenicillin N synthase-like		169200
57IPR007658
Protein of unknown function DUF594		168168
58IPR012337
Ribonuclease H-like domain		166329
59IPR003959
ATPase, AAA-type, core		165214
60IPR025287
Wall-associated receptor kinase galacturonan-binding domain		164182
61IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		163630
62IPR011992
EF-hand-like domain		161394
63IPR003480
Transferase		158195
64IPR009072
Histone-fold		157315
65IPR005123
Oxoglutarate/iron-dependent dioxygenase		156292
66IPR021109
Aspartic peptidase		155440
67IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		155656
68IPR001480
Bulb-type lectin domain		154809
69IPR019793
Peroxidases heam-ligand binding site		152154
70IPR002048
EF-hand domain		151934
71IPR001461
Peptidase A1		149266
72IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		149352
73IPR011676
Domain of unknown function DUF1618		146147
74IPR008972
Cupredoxin		145493
75IPR015300
DNA-binding pseudobarrel domain		145466
76IPR003439
ABC transporter-like		144441
77IPR001650
Helicase, C-terminal		143414
78IPR023214
HAD-like domain		142415
79IPR012871
Protein of unknown function DUF1677, Oryza sativa		138164
80IPR003609
Apple-like		138368
81IPR014001
Helicase, superfamily 1/2, ATP-binding domain		137263
82IPR014710
RmlC-like jelly roll fold		136166
83IPR000858
S-locus glycoprotein		135136
84IPR009009
Barwin-related endoglucanase		135334
85IPR019775
WD40 repeat, conserved site		132212
86IPR018247
EF-Hand 1, calcium-binding site		132302
87IPR007087
Zinc finger, C2H2		130434
88IPR019794
Peroxidase, active site		129130
89IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		128160
90IPR032799
Xylanase inhibitor, C-terminal		126127
91IPR019734
Tetratricopeptide repeat		124768
92IPR000109
Proton-dependent oligopeptide transporter family		124272
93IPR029044
Nucleotide-diphospho-sugar transferases		123303
94IPR003340
B3 DNA binding domain		121569
95IPR013026
Tetratricopeptide repeat-containing domain		121157
96IPR001087
Lipase, GDSL		120120
97IPR003441
No apical meristem (NAM) protein		120362
98IPR033121
Peptidase family A1 domain		120126
99IPR010987
Glutathione S-transferase, C-terminal-like		120348
100IPR013785
Aldolase-type TIM barrel		115149
101IPR004045
Glutathione S-transferase, N-terminal		115229
102IPR015424
Pyridoxal phosphate-dependent transferase		115135
103IPR016177
DNA-binding, integrase-type		114140
104IPR012340
Nucleic acid-binding, OB-fold		114159
105IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		112127
106IPR015500
Peptidase S8, subtilisin-related		111314
107IPR026992
Non-haem dioxygenase N-terminal domain		110112
108IPR026961
PGG domain		109277
109IPR011051
RmlC-like cupin domain		107119
110IPR032861
Xylanase inhibitor, N-terminal		106111
111IPR001471
AP2/ERF domain		104597
112IPR002347
Glucose/ribitol dehydrogenase		103806
113IPR000209
Peptidase S8/S53 domain		103479
114IPR012334
Pectin lyase fold		101123
115IPR011050
Pectin lyase fold/virulence factor		100108
116IPR001220
Legume lectin domain		100111
117IPR003960
ATPase, AAA-type, conserved site		97111
118IPR003690
Mitochodrial transcription termination factor-related		96536
119IPR016039
Thiolase-like		95383
120IPR006501
Pectinesterase inhibitor		95377
121IPR001881
EGF-like calcium-binding		94143
122IPR005828
General substrate transporter		93126
123IPR003657
DNA-binding WRKY		93529
124IPR032867
DYW domain		9393
125IPR001623
DnaJ domain		92641
126IPR000742
Epidermal growth factor-like domain		92227
127IPR011011
Zinc finger, FYVE/PHD-type		92105
128IPR013128
Peptidase C1A, papain		91103
129IPR005225
Small GTP-binding protein domain		9193
130IPR000008
C2 calcium-dependent membrane targeting		90597
131IPR017871
ABC transporter, conserved site		88120
132IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		8791
133IPR002100
Transcription factor, MADS-box		86579
134IPR001932
Protein phosphatase 2C (PP2C)-like		86485
135IPR029071
Ubiquitin-related domain		8594
136IPR000668
Peptidase C1A, papain C-terminal		85295
137IPR007117
Expansin, cellulose-binding-like domain		84328
138IPR003245
Plastocyanin-like		83245
139IPR018097
EGF-like calcium-binding, conserved site		8383
140IPR013187
F-box associated domain, type 3		8283
141IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		8187
142IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		81174
143IPR006447
Myb domain, plants		7979
144IPR002902
Gnk2-homologous domain		79260
145IPR006045
Cupin 1		79173
146IPR008949
Terpenoid synthase		78165
147IPR001563
Peptidase S10, serine carboxypeptidase		78418
148IPR015655
Protein phosphatase 2C		78124
149IPR002528
Multi antimicrobial extrusion protein		77189
150IPR007125
Histone core		7777
151IPR017907
Zinc finger, RING-type, conserved site		7580
152IPR001356
Homeobox domain		75200
153IPR007118
Expansin/Lol pI		74330
154IPR011043
Galactose oxidase/kelch, beta-propeller		7481
155IPR006121
Heavy metal-associated domain, HMA		73204
156IPR022059
Protein of unknown function DUF3615		7373
157IPR003676
Auxin responsive SAUR protein		7378
158IPR020472
G-protein beta WD-40 repeat		72216
159IPR030184
WAT1-related protein		7281
160IPR024788
Malectin-like carbohydrate-binding domain		7278
161IPR016135
Ubiquitin-conjugating enzyme/RWD-like		71161
162IPR007112
Expansin/pollen allergen, DPBB domain		70123
163IPR001965
Zinc finger, PHD-type		7099
164IPR015880
Zinc finger, C2H2-like		70211
165IPR000073
Alpha/beta hydrolase fold-1		69130
166IPR011527
ABC transporter, transmembrane domain, type 1		69390
167IPR004265
Plant disease resistance response protein		6869
168IPR005829
Sugar transporter, conserved site		6896
169IPR013057
Amino acid transporter, transmembrane		6880
170IPR024171
S-receptor-like serine/threonine-protein kinase		6767
171IPR006553
Leucine-rich repeat, cysteine-containing subtype		67356
172IPR029052
Metallo-dependent phosphatase-like		67156
173IPR002035
von Willebrand factor, type A		66195
174IPR004158
Protein of unknown function DUF247, plant		6673
175IPR004827
Basic-leucine zipper domain		66217
176IPR001509
NAD-dependent epimerase/dehydratase		6571
177IPR023796
Serpin domain		65209
178IPR010259
Proteinase inhibitor I9		6484
179IPR000215
Serpin family		6480
180IPR000152
EGF-type aspartate/asparagine hydroxylation site		6464
181IPR004046
Glutathione S-transferase, C-terminal		6464
182IPR011032
GroES-like		62135
183IPR008978
HSP20-like chaperone		62123
184IPR009003
Trypsin-like cysteine/serine peptidase domain		6285
185IPR020568
Ribosomal protein S5 domain 2-type fold		6175
186IPR023828
Peptidase S8, subtilisin, Ser-active site		6162
187IPR001077
O-methyltransferase, family 2		6164
188IPR000620
Drug/metabolite transporter		6194
189IPR004843
Metallophosphoesterase domain		6060
190IPR011701
Major facilitator superfamily		6063
191IPR013201
Proteinase inhibitor I29, cathepsin propeptide		60119
192IPR000270
Phox/Bem1p		6093
193IPR001929
Germin		59171
194IPR016461
Caffeate O-methyltransferase (COMT) family		5993
195IPR005630
Terpene synthase, metal-binding domain		5859
196IPR016166
FAD-binding, type 2		58111
197IPR002085
Alcohol dehydrogenase superfamily, zinc-type		5877
198IPR000490
Glycoside hydrolase, family 17		5894
199IPR001878
Zinc finger, CCHC-type		58322
200IPR017877
Myb-like domain		5863
201IPR026057
PC-Esterase		5762
202IPR000873
AMP-dependent synthetase/ligase		5769
203IPR004320
Protein of unknown function DUF241, plant		5759
204IPR013763
Cyclin-like		57254
205IPR001906
Terpene synthase, N-terminal domain		57118
206IPR003613
U box domain		57164
207IPR011993
Pleckstrin homology-like domain		57114
208IPR001806
Small GTPase superfamily		5661
209IPR000608
Ubiquitin-conjugating enzyme, E2		55109
210IPR029962
Trichome birefringence-like family		5565
211IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		5594
212IPR000571
Zinc finger, CCCH-type		55412
213IPR008979
Galactose-binding domain-like		54125
214IPR013766
Thioredoxin domain		5396
215IPR019787
Zinc finger, PHD-finger		5393
216IPR031052
FHY3/FAR1 family		5361
217IPR008266
Tyrosine-protein kinase, active site		5354
218IPR018108
Mitochondrial substrate/solute carrier		53273
219IPR023395
Mitochondrial carrier domain		53127
220IPR011042
Six-bladed beta-propeller, TolB-like		5365
221IPR000757
Glycoside hydrolase, family 16		53108
222IPR003594
Histidine kinase-like ATPase, ATP-binding domain		52177
223IPR027640
Kinesin-like protein		52142
224IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5252
225IPR000626
Ubiquitin domain		51123
226IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		5184
227IPR004162
E3 ubiquitin-protein ligase SINA like		5154
228IPR001938
Thaumatin		51341
229IPR016159
Cullin repeat-like-containing domain		5160
230IPR004314
Domain of unknown function DUF239		5158
231IPR001752
Kinesin, motor domain		51396
232IPR011006
CheY-like superfamily		5051
233IPR008928
Six-hairpin glycosidase-like		5069
234IPR011706
Multicopper oxidase, type 2		5050
235IPR019780
Germin, manganese binding site		5050
236IPR001789
Signal transduction response regulator, receiver domain		50136
237IPR013601
FAE1/Type III polyketide synthase-like protein		4955
238IPR008962
PapD-like		49123
239IPR003663
Sugar/inositol transporter		49219
240IPR000743
Glycoside hydrolase, family 28		4974
241IPR013525
ABC-2 type transporter		4869
242IPR003137
Protease-associated domain, PA		4848
243IPR019786
Zinc finger, PHD-type, conserved site		4852
244IPR031107
Small heat shock protein HSP20		4849
245IPR000477
Reverse transcriptase		4862
246IPR024752
Myb/SANT-like domain		4849
247IPR025660
Cysteine peptidase, histidine active site		4848
248IPR000048
IQ motif, EF-hand binding site		48264
249IPR002403
Cytochrome P450, E-class, group IV		47240
250IPR001360
Glycoside hydrolase, family 1		47309
251IPR002068
Alpha crystallin/Hsp20 domain		4792
252IPR005202
Transcription factor GRAS		4798
253IPR001214
SET domain		47126
254IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4751
255IPR001117
Multicopper oxidase, type 1		4646
256IPR029055
Nucleophile aminohydrolases, N-terminal		4694
257IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4648
258IPR015915
Kelch-type beta propeller		4656
259IPR000863
Sulfotransferase domain		4548
260IPR000225
Armadillo		45346
261IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		4444
262IPR013323
SIAH-type domain		4444
263IPR011707
Multicopper oxidase, type 3		4444
264IPR000535
Major sperm protein		4396
265IPR000330
SNF2-related		4344
266IPR008250
P-type ATPase, A domain		4388
267IPR023393
START-like domain		4345
268IPR005135
Endonuclease/exonuclease/phosphatase		43131
269IPR002119
Histone H2A		43216
270IPR025659
Tubby C-terminal-like domain		4250
271IPR006912
Harbinger transposase-derived protein, plant		4247
272IPR023299
P-type ATPase, cytoplasmic domain N		4276
273IPR006094
FAD linked oxidase, N-terminal		4243
274IPR025661
Cysteine peptidase, asparagine active site		4242
275IPR007750
Protein of unknown function DUF674		4166
276IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		4143
277IPR004813
Oligopeptide transporter, OPT superfamily		4192
278IPR013126
Heat shock protein 70 family		41281
279IPR012967
Plant methyltransferase dimerisation		4141
280IPR000864
Proteinase inhibitor I13, potato inhibitor I		40195
281IPR013149
Alcohol dehydrogenase, C-terminal		4040
282IPR032454
Histone H2A, C-terminal domain		4040
283IPR013010
Zinc finger, SIAH-type		4040
284IPR002963
Expansin		40263
285IPR018303
P-type ATPase, phosphorylation site		4040
286IPR001757
Cation-transporting P-type ATPase		40139
287IPR000169
Cysteine peptidase, cysteine active site		4040
288IPR000070
Pectinesterase, catalytic		4043
289IPR004316
SWEET sugar transporter		3969
290IPR007657
Glycosyltransferase AER61, uncharacterised		3941
291IPR033124
Serine carboxypeptidases, histidine active site		3939
292IPR004140
Exocyst complex protein Exo70		3985
293IPR013154
Alcohol dehydrogenase GroES-like		3939
294IPR023296
Glycosyl hydrolase, five-bladed beta-propellor domain		3976
295IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		3940
296IPR004088
K Homology domain, type 1		39235
297IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3939
298IPR013189
Glycosyl hydrolase family 32, C-terminal		39105
299IPR031127
E3 ubiquitin ligase RBR family		3956
300IPR018202
Peptidase S10, serine carboxypeptidase, active site		3939
301IPR002921
Lipase, class 3		3838
302IPR025110
Domain of unknown function DUF4009		3838
303IPR006626
Parallel beta-helix repeat		38191
304IPR001969
Peptidase aspartic, active site		3857
305IPR023271
Aquaporin-like		3891
306IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		3873
307IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		3875
308IPR025875
Leucine rich repeat 4		3840
309IPR018253
DnaJ domain, conserved site		3838
310IPR020946
Flavin monooxygenase-like		3850
311IPR000425
Major intrinsic protein		38278
312IPR006671
Cyclin, N-terminal		3850
313IPR016181
Acyl-CoA N-acyltransferase		3779
314IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		3739
315IPR004263
Exostosin-like		3740
316IPR014014
RNA helicase, DEAD-box type, Q motif		3737
317IPR011013
Galactose mutarotase-like domain		3739
318IPR013771
Bifunctional trypsin/alpha-amylase inhibitor helical domain		3746
319IPR013094
Alpha/beta hydrolase fold-3		3737
320IPR002487
Transcription factor, K-box		3774
321IPR033389
AUX/IAA domain		3644
322IPR000558
Histone H2B		36260
323IPR026960
Reverse transcriptase zinc-binding domain		3636
324IPR012946
X8 domain		3682
325IPR016072
SKP1 component, dimerisation		3671
326IPR019378
GDP-fucose protein O-fucosyltransferase		3640
327IPR001232
SKP1 component		3637
328IPR000644
Cystathionine beta-synthase, core		36190
329IPR020843
Polyketide synthase, enoylreductase		3636
330IPR012341
Six-hairpin glycosidase		3647
331IPR003614
Knottin, scorpion toxin-like		3688
332IPR001251
CRAL-TRIO domain		35164
333IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3535
334IPR002109
Glutaredoxin		3567
335IPR014756
Immunoglobulin E-set		3538
336IPR023210
NADP-dependent oxidoreductase domain		35122
337IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		3537
338IPR015947
PUA-like domain		3543
339IPR013148
Glycosyl hydrolase family 32, N-terminal		3435
340IPR032710
NTF2-like domain		3462
341IPR007493
Protein of unknown function DUF538		34106
342IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		3449
343IPR005299
SAM dependent carboxyl methyltransferase		3441
344IPR025886
Phloem protein 2-like		3434
345IPR001362
Glycoside hydrolase, family 32		3434
346IPR004839
Aminotransferase, class I/classII		3437
347IPR025846
PMR5 N-terminal domain		3434
348IPR014720
Double-stranded RNA-binding domain		34119
349IPR006073
GTP binding domain		3491
350IPR001395
Aldo/keto reductase		3449
351IPR001229
Mannose-binding lectin		34188
352IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3434
353IPR008942
ENTH/VHS		3365
354IPR016073
SKP1 component, POZ		3334
355IPR002867
Zinc finger, C6HC-type		33106
356IPR004853
Domain of unknown function DUF250		3333
357IPR001296
Glycosyl transferase, family 1		3333
358IPR020904
Short-chain dehydrogenase/reductase, conserved site		3333
359IPR005150
Cellulose synthase		3353
360IPR002129
Pyridoxal phosphate-dependent decarboxylase		3340
361IPR001320
Ionotropic glutamate receptor		3362
362IPR001638
Extracellular solute-binding protein, family 3		3341
363IPR003855
K+ potassium transporter		3360
364IPR015916
Galactose oxidase, beta-propeller		3237
365IPR006016
UspA		3232
366IPR004864
Late embryogenesis abundant protein, LEA-14		3234
367IPR017970
Homeobox, conserved site		3232
368IPR016167
FAD-binding, type 2, subdomain 1		3233
369IPR029047
Heat shock protein 70kD, peptide-binding domain		3270
370IPR010402
CCT domain		3162
371IPR004141
Strictosidine synthase		3131
372IPR029021
Protein-tyrosine phosphatase-like		3170
373IPR013783
Immunoglobulin-like fold		3139
374IPR018181
Heat shock protein 70, conserved site		3170
375IPR003406
Glycosyl transferase, family 14		3135
376IPR011012
Longin-like domain		3132
377IPR027923
Hydrophobic seed protein		3131
378IPR029045
ClpP/crotonase-like domain		3188
379IPR020845
AMP-binding, conserved site		3131
380IPR002423
Chaperonin Cpn60/TCP-1		3036
381IPR000795
Elongation factor, GTP-binding domain		30159
382IPR023346
Lysozyme-like domain		3031
383IPR002562
3'-5' exonuclease domain		3038
384IPR002355
Multicopper oxidase, copper-binding site		3030
385IPR002293
Amino acid/polyamine transporter I		3083
386IPR019489
Clp ATPase, C-terminal		3058
387IPR022796
Chlorophyll A-B binding protein		3034
388IPR018121
Seven-in-absentia protein, TRAF-like domain		3030
389IPR029069
HotDog domain		3080
390IPR017938
Riboflavin synthase-like beta-barrel		2936
391IPR018490
Cyclic nucleotide-binding-like		2931
392IPR000726
Glycoside hydrolase, family 19, catalytic		2960
393IPR007612
LURP1-like domain		2932
394IPR016455
Xyloglucan endotransglucosylase/hydrolase		2929
395IPR001951
Histone H4		29178
396IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		2929
397IPR012328
Chalcone/stilbene synthase, C-terminal		2932
398IPR001701
Glycoside hydrolase, family 9		2931
399IPR000595
Cyclic nucleotide-binding domain		2975
400IPR032458
Histone H2A conserved site		2929
401IPR001270
Chaperonin ClpA/B		28101
402IPR000182
GNAT domain		2849
403IPR004041
NAF domain		2829
404IPR019821
Kinesin, motor region, conserved site		2828
405IPR001357
BRCT domain		28162
406IPR027806
Harbinger transposase-derived nuclease domain		2833
407IPR008991
Translation protein SH3-like domain		2830
408IPR004100
ATPase, F1 complex alpha/beta subunit, N-terminal domain		2853
409IPR007650
Protein of unknown function DUF581		2828
410IPR012675
Beta-grasp domain		2830
411IPR001763
Rhodanese-like domain		28128
412IPR027409
GroEL-like apical domain		2859
413IPR004087
K Homology domain		2852
414IPR028082
Periplasmic binding protein-like I		2842
415IPR023298
P-type ATPase, transmembrane domain		2863
416IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2866
417IPR005069
Nucleotide-diphospho-sugar transferase		2832
418IPR017927
Ferredoxin reductase-type FAD-binding domain		2727
419IPR000782
FAS1 domain		27116
420IPR029466
No apical meristem-associated, C-terminal domain		2729
421IPR013216
Methyltransferase type 11		2727
422IPR001279
Beta-lactamase-like		2792
423IPR033131
Pectinesterase, Asp active site		2727
424IPR011074
CRAL/TRIO, N-terminal domain		2763
425IPR031112
AP2-like ethylene-responsive transcription factor		2731
426IPR008263
Glycoside hydrolase, family 16, active site		2727
427IPR023631
Amidase signature domain		2795
428IPR008480
Protein of unknown function DUF761, plant		2727
429IPR002495
Glycosyl transferase, family 8		2728
430IPR020003
ATPase, alpha/beta subunit, nucleotide-binding domain, active site		2727
431IPR001574
Ribosome-inactivating protein		2754
432IPR003100
Argonaute/Dicer protein, PAZ		26103
433IPR005795
Major pollen allergen Lol pI		26162
434IPR006153
Cation/H+ exchanger		2628
435IPR033138
Multicopper oxidases, conserved site		2626
436IPR016164
FAD-linked oxidase-like, C-terminal		2631
437IPR009060
UBA-like		2630
438IPR018451
NAF/FISL domain		2627
439IPR010920
Like-Sm (LSM) domain		2626
440IPR002659
Glycosyl transferase, family 31		2647
441IPR019557
Aminotransferase-like, plant mobile domain		2627
442IPR001478
PDZ domain		2686
443IPR000408
Regulator of chromosome condensation, RCC1		26380
444IPR006694
Fatty acid hydroxylase		2626
445IPR006652
Kelch repeat type 1		2692
446IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2668
447IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2626
448IPR029039
Flavoprotein-like		2659
449IPR000793
ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal		2645
450IPR029062
Class I glutamine amidotransferase-like		2663
451IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2633
452IPR000120
Amidase		2630
453IPR001828
Extracellular ligand-binding receptor		2629
454IPR007770
Protein of unknown function DUF679		2629
455IPR023329
Chlorophyll a/b binding protein domain		2632
456IPR001099
Chalcone/stilbene synthase, N-terminal		2628
457IPR014718
Glycoside hydrolase-type carbohydrate-binding, subgroup		2534
458IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2531
459IPR009030
Insulin-like growth factor binding protein, N-terminal		2529
460IPR001353
Proteasome, subunit alpha/beta		2525
461IPR029056
Ribokinase-like		2557
462IPR004252
Transposase, Ptta/En/Spm, plant		2526
463IPR006461
Uncharacterised protein family Cys-rich		2552
464IPR022357
Major intrinsic protein, conserved site		2525
465IPR013780
Glycosyl hydrolase, family 13, all-beta		2526
466IPR024083
Fumarase/histidase, N-terminal		2527
467IPR018119
Strictosidine synthase, conserved region		2525
468IPR008948
L-Aspartase-like		2526
469IPR009606
Protein of unknown function DUF1218		2425
470IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2460
471IPR027214
Cystatin		2424
472IPR013581
Plant PDR ABC transporter associated		2424
473IPR000717
Proteasome component (PCI) domain		2446
474IPR011016
Zinc finger, RING-CH-type		2453
475IPR018368
Chaperonin ClpA/B, conserved site		2424
476IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		2424
477IPR001344
Chlorophyll A-B binding protein, plant		2426
478IPR008914
Phosphatidylethanolamine-binding protein PEBP		2473
479IPR027725
Heat shock transcription factor family		2430
480IPR004367
Cyclin, C-terminal domain		2443
481IPR022742
Alpha/beta hydrolase, N-terminal		2425
482IPR023313
Ubiquitin-conjugating enzyme, active site		2425
483IPR003165
Stem cell self-renewal protein Piwi		2482
484IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2429
485IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2442
486IPR016161
Aldehyde/histidinol dehydrogenase		2428
487IPR003311
AUX/IAA protein		2429
488IPR000010
Proteinase inhibitor I25, cystatin		2438
489IPR029048
Heat shock protein 70kD, C-terminal domain		2446
490IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2323
491IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2342
492IPR005821
Ion transport domain		2323
493IPR003689
Zinc/iron permease		2323
494IPR002067
Mitochondrial carrier protein		23106
495IPR028871
Blue (type 1) copper protein, binding site		2323
496IPR020635
Tyrosine-protein kinase, catalytic domain		2323
497IPR007728
Pre-SET domain		2266
498IPR000528
Plant lipid transfer protein/Par allergen		2286
499IPR010666
Zinc finger, GRF-type		2222
500IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2263
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda.html b/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda.html new file mode 100644 index 00000000..ac950ec4 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda.html @@ -0,0 +1,48 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AMTR1.0, Jan 2014
Database version:86.1
Base Pairs:668,218,890
Golden Path Length:706,332,640
Genebuild by: AGD
Genebuild method: Generated from ENA annotation
Genebuild started: Oct 2013
Genebuild released: Oct 2013
Genebuild last updated/patched: Jan 2014
Genebuild version: 2014-01-AGD
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		27,313
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		285
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:28,721
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Coordinate Systems

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supercontig5745 sequences
contig45301 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda_IPtop500.html new file mode 100644 index 00000000..2aa11e01 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Amborella_trichopoda_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		8902333
2IPR011009
Protein kinase-like domain		733801
3IPR000719
Protein kinase domain		6721614
4IPR002885
Pentatricopeptide repeat		65612794
5IPR011990
Tetratricopeptide-like helical		5641744
6IPR032675
Leucine-rich repeat domain, L domain-like		4861411
7IPR008271
Serine/threonine-protein kinase, active site		475475
8IPR013083
Zinc finger, RING/FYVE/PHD-type		401438
9IPR017441
Protein kinase, ATP binding site		390391
10IPR013320
Concanavalin A-like lectin/glucanase, subgroup		347474
11IPR016040
NAD(P)-binding domain		333726
12IPR016024
Armadillo-type fold		283663
13IPR001611
Leucine-rich repeat		2811423
14IPR001128
Cytochrome P450		2561261
15IPR029058
Alpha/Beta hydrolase fold		248600
16IPR015943
WD40/YVTN repeat-like-containing domain		238386
17IPR001841
Zinc finger, RING-type		235546
18IPR009057
Homeodomain-like		233527
19IPR017986
WD40-repeat-containing domain		224546
20IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		220327
21IPR003593
AAA+ ATPase domain		217280
22IPR011989
Armadillo-like helical		215460
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		214546
24IPR012677
Nucleotide-binding, alpha-beta plait		211629
25IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		206415
26IPR001680
WD40 repeat		2042061
27IPR017853
Glycoside hydrolase, superfamily		197232
28IPR001810
F-box domain		196500
29IPR000504
RNA recognition motif domain		188850
30IPR012336
Thioredoxin-like fold		181410
31IPR020846
Major facilitator superfamily domain		174335
32IPR007021
Domain of unknown function DUF659		163170
33IPR002401
Cytochrome P450, E-class, group I		159896
34IPR012337
Ribonuclease H-like domain		156236
35IPR003591
Leucine-rich repeat, typical subtype		1531020
36IPR013781
Glycoside hydrolase, catalytic domain		153173
37IPR001005
SANT/Myb domain		151364
38IPR013210
Leucine-rich repeat-containing N-terminal, type 2		137140
39IPR011991
Winged helix-turn-helix DNA-binding domain		135230
40IPR012334
Pectin lyase fold		128132
41IPR017972
Cytochrome P450, conserved site		128129
42IPR014001
Helicase, superfamily 1/2, ATP-binding domain		125246
43IPR002182
NB-ARC		124129
44IPR011050
Pectin lyase fold/virulence factor		124127
45IPR001650
Helicase, C-terminal		123364
46IPR027443
Isopenicillin N synthase-like		123128
47IPR019775
WD40 repeat, conserved site		116194
48IPR017930
Myb domain		116178
49IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		115449
50IPR023214
HAD-like domain		114331
51IPR003439
ABC transporter-like		112290
52IPR007087
Zinc finger, C2H2		110357
53IPR011992
EF-hand domain pair		108259
54IPR010255
Haem peroxidase		107108
55IPR002016
Haem peroxidase, plant/fungal/bacterial		105569
56IPR015500
Peptidase S8, subtilisin-related		103257
57IPR013785
Aldolase-type TIM barrel		101125
58IPR029044
Nucleotide-diphospho-sugar transferases		101240
59IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		101121
60IPR019557
Aminotransferase-like, plant mobile domain		100107
61IPR002048
EF-hand domain		98566
62IPR019734
Tetratricopeptide repeat		97677
63IPR003959
ATPase, AAA-type, core		97111
64IPR000823
Plant peroxidase		97633
65IPR005123
Oxoglutarate/iron-dependent dioxygenase		94160
66IPR013026
Tetratricopeptide repeat-containing domain		94123
67IPR012340
Nucleic acid-binding, OB-fold		92132
68IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		92387
69IPR021109
Aspartic peptidase domain		91249
70IPR000209
Peptidase S8/S53 domain		91378
71IPR015424
Pyridoxal phosphate-dependent transferase		9096
72IPR011011
Zinc finger, FYVE/PHD-type		88102
73IPR020683
Ankyrin repeat-containing domain		87378
74IPR023213
Chloramphenicol acetyltransferase-like domain		87129
75IPR018247
EF-Hand 1, calcium-binding site		86187
76IPR001623
DnaJ domain		85603
77IPR016177
DNA-binding domain		8197
78IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		8186
79IPR014710
RmlC-like jelly roll fold		7993
80IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		7880
81IPR003480
Transferase		7883
82IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		77170
83IPR026992
Non-haem dioxygenase N-terminal domain		7676
84IPR005225
Small GTP-binding protein domain		7677
85IPR013830
SGNH hydrolase-type esterase domain		76190
86IPR001471
AP2/ERF domain		75471
87IPR001878
Zinc finger, CCHC-type		74414
88IPR008972
Cupredoxin		72241
89IPR002110
Ankyrin repeat		71466
90IPR019793
Peroxidases heam-ligand binding site		7070
91IPR000008
C2 domain		69429
92IPR001461
Aspartic peptidase		68157
93IPR002085
Alcohol dehydrogenase superfamily, zinc-type		6880
94IPR020472
G-protein beta WD-40 repeat		66198
95IPR010987
Glutathione S-transferase, C-terminal-like		65171
96IPR002347
Glucose/ribitol dehydrogenase		64543
97IPR029055
Nucleophile aminohydrolases, N-terminal		64105
98IPR017871
ABC transporter, conserved site		6482
99IPR005828
General substrate transporter		6367
100IPR004265
Plant disease resistance response protein		6264
101IPR032799
Xylanase inhibitor, C-terminal		6262
102IPR011051
RmlC-like cupin domain		6269
103IPR032861
Xylanase inhibitor, N-terminal		6165
104IPR029071
Ubiquitin-related domain		6162
105IPR033121
Peptidase family A1 domain		6163
106IPR001965
Zinc finger, PHD-type		6188
107IPR011032
GroES (chaperonin 10)-like		60121
108IPR009072
Histone-fold		59117
109IPR000073
Alpha/beta hydrolase fold-1		58132
110IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		5866
111IPR000270
Phox/Bem1p		5893
112IPR001087
Lipase, GDSL		5758
113IPR000109
Proton-dependent oligopeptide transporter family		57110
114IPR001480
Bulb-type lectin domain		57312
115IPR000225
Armadillo		57437
116IPR008928
Six-hairpin glycosidase-like		5564
117IPR015880
Zinc finger, C2H2-like		55160
118IPR019787
Zinc finger, PHD-finger		5492
119IPR004045
Glutathione S-transferase, N-terminal		54105
120IPR011333
BTB/POZ fold		5462
121IPR030184
WAT1-related protein		5455
122IPR013766
Thioredoxin domain		5397
123IPR013057
Amino acid transporter, transmembrane		5355
124IPR002528
Multi antimicrobial extrusion protein		53116
125IPR017907
Zinc finger, RING-type, conserved site		5353
126IPR000571
Zinc finger, CCCH-type		53405
127IPR018108
Mitochondrial substrate/solute carrier		52283
128IPR019794
Peroxidase, active site		5252
129IPR023395
Mitochondrial carrier domain		52115
130IPR003690
Mitochodrial transcription termination factor-related		50400
131IPR020568
Ribosomal protein S5 domain 2-type fold		5063
132IPR001356
Homeobox domain		50140
133IPR000070
Pectinesterase, catalytic		5051
134IPR015300
DNA-binding pseudobarrel domain		50107
135IPR001932
Protein phosphatase 2C (PP2C)-like domain		50291
136IPR013525
ABC-2 type transporter		4862
137IPR003960
ATPase, AAA-type, conserved site		4852
138IPR000210
BTB/POZ domain		48122
139IPR003441
NAC domain		47138
140IPR000620
Drug/metabolite transporter		4779
141IPR000743
Glycoside hydrolase, family 28		4767
142IPR000873
AMP-dependent synthetase/ligase		4646
143IPR015655
Protein phosphatase 2C		4673
144IPR029052
Metallo-dependent phosphatase-like		46114
145IPR010259
Proteinase inhibitor I9		4556
146IPR027640
Kinesin-like protein		45123
147IPR016135
Ubiquitin-conjugating enzyme/RWD-like		4592
148IPR001752
Kinesin, motor domain		45336
149IPR001806
Small GTPase superfamily		4547
150IPR008949
Terpenoid synthase		4488
151IPR001563
Peptidase S10, serine carboxypeptidase		44195
152IPR016181
Acyl-CoA N-acyltransferase		4499
153IPR016039
Thiolase-like		44156
154IPR019786
Zinc finger, PHD-type, conserved site		4448
155IPR006045
Cupin 1		4497
156IPR012341
Six-hairpin glycosidase		4445
157IPR011993
Pleckstrin homology-like domain		4485
158IPR005202
Transcription factor GRAS		4389
159IPR007527
Zinc finger, SWIM-type		4378
160IPR006447
Myb domain, plants		4242
161IPR011527
ABC transporter type 1, transmembrane domain		42200
162IPR001220
Legume lectin domain		4243
163IPR004843
Phosphoesterase domain		4141
164IPR006564
Zinc finger, PMZ-type		4141
165IPR023828
Peptidase S8, subtilisin, Ser-active site		4141
166IPR018253
DnaJ domain, conserved site		4141
167IPR004158
Protein of unknown function DUF247, plant		4141
168IPR014014
RNA helicase, DEAD-box type, Q motif		4040
169IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4069
170IPR029045
ClpP/crotonase-like domain		40105
171IPR006501
Pectinesterase inhibitor domain		40187
172IPR001701
Glycoside hydrolase, family 9		4040
173IPR003663
Sugar/inositol transporter		40195
174IPR000626
Ubiquitin domain		3990
175IPR008978
HSP20-like chaperone		3976
176IPR013783
Immunoglobulin-like fold		3946
177IPR005829
Sugar transporter, conserved site		3960
178IPR003245
Plastocyanin-like		39105
179IPR008979
Galactose-binding domain-like		3991
180IPR000490
Glycoside hydrolase, family 17		3957
181IPR015915
Kelch-type beta propeller		3951
182IPR014756
Immunoglobulin E-set		3943
183IPR003613
U box domain		39115
184IPR029962
Trichome birefringence-like family		3844
185IPR004088
K Homology domain, type 1		38289
186IPR013149
Alcohol dehydrogenase, C-terminal		3737
187IPR026057
PC-Esterase		3739
188IPR004864
Late embryogenesis abundant protein, LEA-14		3739
189IPR014720
Double-stranded RNA-binding domain		37137
190IPR001214
SET domain		37100
191IPR013128
Peptidase C1A, papain		3637
192IPR000330
SNF2-related		3638
193IPR000120
Amidase		3636
194IPR032867
DYW domain		3636
195IPR004827
Basic-leucine zipper domain		36126
196IPR000048
IQ motif, EF-hand binding site		36237
197IPR000182
GNAT domain		3461
198IPR004873
BURP domain		3482
199IPR001929
Germin		3498
200IPR000608
Ubiquitin-conjugating enzyme, E2		3468
201IPR023393
START-like domain		3434
202IPR023631
Amidase signature domain		34100
203IPR002100
Transcription factor, MADS-box		34242
204IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3436
205IPR017877
Myb-like domain		3439
206IPR003340
B3 DNA binding domain		33113
207IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3344
208IPR009060
UBA-like		3338
209IPR003137
Protease-associated domain, PA		3333
210IPR009009
RlpA-like double-psi beta-barrel domain		3389
211IPR020845
AMP-binding, conserved site		3333
212IPR003657
DNA-binding WRKY		33195
213IPR006073
GTP binding domain		3383
214IPR009000
Translation protein, beta-barrel domain		3236
215IPR006652
Kelch repeat type 1		32104
216IPR025846
PMR5 N-terminal domain		3232
217IPR019378
GDP-fucose protein O-fucosyltransferase		3232
218IPR000668
Peptidase C1A, papain C-terminal		32118
219IPR001757
Cation-transporting P-type ATPase		3297
220IPR006121
Heavy metal-associated domain, HMA		31105
221IPR004263
Exostosin-like		3131
222IPR012675
Beta-grasp domain		3131
223IPR033131
Pectinesterase, Asp active site		3131
224IPR003594
Histidine kinase-like ATPase, ATP-binding domain		31117
225IPR002902
Gnk2-homologous domain		31116
226IPR011012
Longin-like domain		3131
227IPR003855
K+ potassium transporter		3148
228IPR000757
Glycoside hydrolase, family 16		3160
229IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		3150
230IPR015916
Galactose oxidase, beta-propeller		3032
231IPR019821
Kinesin, motor region, conserved site		3030
232IPR002068
Alpha crystallin/Hsp20 domain		3057
233IPR001509
NAD-dependent epimerase/dehydratase		3030
234IPR002423
Chaperonin Cpn60/TCP-1		3037
235IPR013763
Cyclin-like		30129
236IPR023299
P-type ATPase, cytoplasmic domain N		3053
237IPR004087
K Homology domain		3067
238IPR011043
Galactose oxidase/kelch, beta-propeller		3034
239IPR003676
Auxin-induced protein, ARG7		3030
240IPR006153
Cation/H+ exchanger		2929
241IPR001360
Glycoside hydrolase, family 1		29172
242IPR008991
Translation protein SH3-like domain		2932
243IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2954
244IPR012946
X8 domain		2958
245IPR006553
Leucine-rich repeat, cysteine-containing subtype		29226
246IPR013154
Alcohol dehydrogenase GroES-like		2929
247IPR020904
Short-chain dehydrogenase/reductase, conserved site		2929
248IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		29122
249IPR002067
Mitochondrial carrier protein		29140
250IPR024788
Malectin-like carbohydrate-binding domain		2929
251IPR008942
ENTH/VHS		2855
252IPR013601
FAE1/Type III polyketide synthase-like protein		2829
253IPR029000
Cyclophilin-like domain		2858
254IPR001357
BRCT domain		28162
255IPR008250
P-type ATPase, A domain		2866
256IPR005630
Terpene synthase, metal-binding domain		2830
257IPR027409
GroEL-like apical domain		2853
258IPR018303
P-type ATPase, phosphorylation site		2828
259IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2872
260IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		27146
261IPR000858
S-locus glycoprotein		2727
262IPR016166
FAD-binding, type 2		2754
263IPR018289
MULE transposase domain		2727
264IPR003008
Tubulin/FtsZ, GTPase domain		27105
265IPR031107
Small heat shock protein HSP20		2728
266IPR002109
Glutaredoxin		2756
267IPR024752
Myb/SANT-like domain		2727
268IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		2727
269IPR023210
NADP-dependent oxidoreductase domain		2779
270IPR001395
Aldo/keto reductase		2736
271IPR002921
Lipase, class 3		2626
272IPR006016
UspA		2626
273IPR006626
Parallel beta-helix repeat		26118
274IPR004853
Triose-phosphate transporter domain		2626
275IPR013216
Methyltransferase type 11		2626
276IPR029061
Thiamin diphosphate-binding fold		2683
277IPR005135
Endonuclease/exonuclease/phosphatase		2694
278IPR027356
NPH3 domain		2650
279IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		2626
280IPR026892
Glycoside hydrolase family 3		2633
281IPR004839
Aminotransferase, class I/classII		2626
282IPR011006
CheY-like superfamily		2630
283IPR022796
Chlorophyll A-B binding protein		2627
284IPR004813
Oligopeptide transporter, OPT superfamily		2648
285IPR011706
Multicopper oxidase, type 2		2626
286IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2626
287IPR015797
NUDIX hydrolase domain-like		2654
288IPR025287
Wall-associated receptor kinase galacturonan-binding domain		2525
289IPR032710
NTF2-like domain		2543
290IPR024171
S-receptor-like serine/threonine-protein kinase		2525
291IPR027413
GroEL-like equatorial domain		2547
292IPR022742
Putative lysophospholipase		2525
293IPR002035
von Willebrand factor, type A		2570
294IPR004046
Glutathione S-transferase, C-terminal		2525
295IPR002495
Glycosyl transferase, family 8		2525
296IPR028082
Periplasmic binding protein-like I		2552
297IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2537
298IPR001906
Terpene synthase, N-terminal domain		2548
299IPR001828
Extracellular ligand-binding receptor		2525
300IPR002912
ACT domain		2558
301IPR011707
Multicopper oxidase, type 3		2525
302IPR023329
Chlorophyll a/b binding protein domain		2527
303IPR015947
PUA-like domain		2536
304IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		2525
305IPR001789
Signal transduction response regulator, receiver domain		2570
306IPR001117
Multicopper oxidase, type 1		2424
307IPR025322
Protein of unknown function DUF4228, plant		2424
308IPR000217
Tubulin		24146
309IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2425
310IPR011701
Major facilitator superfamily		2424
311IPR017451
F-box associated interaction domain		2425
312IPR003609
Apple-like		2447
313IPR026961
PGG domain		2424
314IPR007125
Histone core		2424
315IPR017970
Homeobox, conserved site		2424
316IPR000644
CBS domain		24132
317IPR025660
Cysteine peptidase, histidine active site		2424
318IPR001251
CRAL-TRIO domain		23111
319IPR010920
Like-Sm (LSM) domain		2323
320IPR029021
Protein-tyrosine phosphatase-like		2358
321IPR011016
Zinc finger, RING-CH-type		2353
322IPR001279
Beta-lactamase-like		2381
323IPR000408
Regulator of chromosome condensation, RCC1		23380
324IPR007112
Expansin/pollen allergen, DPBB domain		2341
325IPR005150
Cellulose synthase		2329
326IPR004883
Lateral organ boundaries, LOB		2344
327IPR005746
Thioredoxin		2328
328IPR029062
Class I glutamine amidotransferase-like		2356
329IPR019780
Germin, manganese binding site		2323
330IPR016159
Cullin repeat-like-containing domain		2331
331IPR033389
AUX/IAA domain		2224
332IPR001344
Chlorophyll A-B binding protein, plant		2223
333IPR000795
Elongation factor, GTP-binding domain		22116
334IPR023271
Aquaporin-like		2244
335IPR029056
Ribokinase-like		2247
336IPR023313
Ubiquitin-conjugating enzyme, active site		2222
337IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2261
338IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		2222
339IPR008480
Protein of unknown function DUF761, plant		2222
340IPR000425
Major intrinsic protein		22178
341IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2225
342IPR020843
Polyketide synthase, enoylreductase domain		2222
343IPR002937
Amine oxidase		2224
344IPR000528
Plant lipid transfer protein/Par allergen		2194
345IPR025110
AMP-binding enzyme C-terminal domain		2121
346IPR006195
Aminoacyl-tRNA synthetase, class II		2121
347IPR013088
Zinc finger, NHR/GATA-type		2121
348IPR001296
Glycosyl transferase, family 1		2121
349IPR001969
Aspartic peptidase, active site		2127
350IPR000101
Gamma-glutamyltranspeptidase		21133
351IPR001353
Proteasome, subunit alpha/beta		2121
352IPR011013
Galactose mutarotase-like domain		2125
353IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2121
354IPR016167
FAD-binding, type 2, subdomain 1		2121
355IPR000169
Cysteine peptidase, cysteine active site		2121
356IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		2121
357IPR000086
NUDIX hydrolase domain		2139
358IPR025661
Cysteine peptidase, asparagine active site		2121
359IPR029033
Histidine phosphatase superfamily		2158
360IPR002913
START domain		2152
361IPR004274
NLI interacting factor		2161
362IPR000727
Target SNARE coiled-coil domain		2053
363IPR002772
Glycoside hydrolase family 3 C-terminal domain		2061
364IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		2034
365IPR018392
LysM domain		2071
366IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2040
367IPR001478
PDZ domain		2079
368IPR010989
t-SNARE		2022
369IPR001320
Ionotropic glutamate receptor		2037
370IPR014722
Ribosomal protein L2 domain 2		2020
371IPR006094
FAD linked oxidase, N-terminal		2020
372IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2028
373IPR013780
Glycosyl hydrolase, family 13, all-beta		2020
374IPR001638
Extracellular solute-binding protein, family 3		2020
375IPR011042
Six-bladed beta-propeller, TolB-like		2026
376IPR001487
Bromodomain		20147
377IPR018202
Peptidase S10, serine carboxypeptidase, active site		2020
378IPR000679
Zinc finger, GATA-type		2068
379IPR001041
2Fe-2S ferredoxin-type domain		2049
380IPR001764
Glycoside hydrolase, family 3, N-terminal		2068
381IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		1962
382IPR001305
Heat shock protein DnaJ, cysteine-rich domain		1948
383IPR024709
O-fucosyltransferase, plant		1919
384IPR003347
JmjC domain		1948
385IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		1947
386IPR008280
Tubulin/FtsZ, C-terminal		1919
387IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		1938
388IPR011074
CRAL/TRIO, N-terminal domain		1941
389IPR031052
FHY3/FAR1 family		1921
390IPR003406
Glycosyl transferase, family 14		1919
391IPR020103
Pseudouridine synthase, catalytic domain		1931
392IPR023410
14-3-3 domain		1949
393IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		1922
394IPR021099
Plant organelle RNA recognition domain		1920
395IPR033443
Pentacotripeptide-repeat region of PROPR		1920
396IPR006671
Cyclin, N-terminal		1929
397IPR002487
Transcription factor, K-box		1938
398IPR008974
TRAF-like		1937
399IPR029060
PIN domain-like		1837
400IPR016461
Caffeate O-methyltransferase (COMT) family		1823
401IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		1848
402IPR009071
High mobility group box domain		1885
403IPR000717
Proteasome component (PCI) domain		1832
404IPR002659
Glycosyl transferase, family 31		1835
405IPR005162
Retrotransposon gag domain		1818
406IPR004776
Auxin efflux carrier		1818
407IPR001876
Zinc finger, RanBP2-type		18138
408IPR022357
Major intrinsic protein, conserved site		1818
409IPR001849
Pleckstrin homology domain		1839
410IPR029069
HotDog domain		1851
411IPR003851
Zinc finger, Dof-type		1869
412IPR004314
Domain of unknown function DUF239		1818
413IPR017927
Ferredoxin reductase-type FAD-binding domain		1717
414IPR010402
CCT domain		1734
415IPR006594
LisH dimerisation motif		1734
416IPR017938
Riboflavin synthase-like beta-barrel		1721
417IPR021133
HEAT, type 2		1742
418IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		1717
419IPR003034
SAP domain		1765
420IPR007118
Expansin/Lol pI		1781
421IPR000315
Zinc finger, B-box		1760
422IPR004332
Transposase, MuDR, plant		1717
423IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1717
424IPR001272
Phosphoenolpyruvate carboxykinase, ATP-utilising		1721
425IPR004320
Protein of unknown function DUF241, plant		1720
426IPR011611
Carbohydrate kinase PfkB		1719
427IPR001763
Rhodanese-like domain		1775
428IPR013816
ATP-grasp fold, subdomain 2		1720
429IPR032308
Jas TPL-binding domain		1717
430IPR003958
Transcription factor CBF/NF-Y/archaeal histone		1717
431IPR008266
Tyrosine-protein kinase, active site		1717
432IPR008263
Glycoside hydrolase, family 16, active site		1717
433IPR008030
NmrA-like		1717
434IPR001077
O-methyltransferase, family 2		1718
435IPR020946
Flavin monooxygenase-like		1719
436IPR006566
FBD domain		1723
437IPR013126
Heat shock protein 70 family		17111
438IPR023298
P-type ATPase, transmembrane domain		1737
439IPR027410
TCP-1-like chaperonin intermediate domain		1730
440IPR025558
Domain of unknown function DUF4283		1717
441IPR004000
Actin-related protein		1693
442IPR000782
FAS1 domain		1678
443IPR018490
Cyclic nucleotide-binding-like		1617
444IPR013328
Dehydrogenase, multihelical		1619
445IPR025659
Tubby C-terminal-like domain		1622
446IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1616
447IPR001163
Ribonucleoprotein LSM domain		1631
448IPR000253
Forkhead-associated (FHA) domain		1652
449IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		1616
450IPR001938
Thaumatin		16178
451IPR002293
Amino acid/polyamine transporter I		1652
452IPR002123
Phospholipid/glycerol acyltransferase		1632
453IPR014044
CAP domain		1662
454IPR003689
Zinc/iron permease		1618
455IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		1620
456IPR004147
UbiB domain		1616
457IPR000642
Peptidase M41		1616
458IPR000595
Cyclic nucleotide-binding domain		1646
459IPR006439
HAD hydrolase, subfamily IA		1646
460IPR017998
Chaperone tailless complex polypeptide 1 (TCP-1)		1660
461IPR029064
50S ribosomal protein L30e-like		1632
462IPR003100
Argonaute/Dicer protein, PAZ domain		1561
463IPR007502
Helicase-associated domain		1530
464IPR007493
Protein of unknown function DUF538		1545
465IPR008984
SMAD/FHA domain		1516
466IPR011237
Peptidase M16 domain		1535
467IPR013581
Plant PDR ABC transporter associated		1515
468IPR027725
Heat shock transcription factor family		1520
469IPR005333
Transcription factor, TCP		1515
470IPR017887
Transcription factor TCP subgroup		1515
471IPR033124
Serine carboxypeptidases, histidine active site		1515
472IPR002938
Monooxygenase, FAD-binding		1518
473IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		1515
474IPR033275
E3 ubiquitin-protein ligase MARCH-like		1517
475IPR015712
DNA-directed RNA polymerase, subunit 2		1520
476IPR002129
Pyridoxal phosphate-dependent decarboxylase		1516
477IPR011053
Single hybrid motif		1515
478IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		1575
479IPR013035
Phosphoenolpyruvate carboxykinase, C-terminal		1517
480IPR025875
Leucine rich repeat 4		1515
481IPR001890
RNA-binding, CRM domain		15159
482IPR005821
Ion transport domain		1515
483IPR011004
Trimeric LpxA-like		1517
484IPR002933
Peptidase M20		1515
485IPR002194
Chaperonin TCP-1, conserved site		1531
486IPR003604
Zinc finger, U1-type		1519
487IPR029006
ADF-H/Gelsolin-like domain		1530
488IPR013094
Alpha/beta hydrolase fold-3		1516
489IPR002641
Patatin/Phospholipase A2-related		1515
490IPR005824
KOW		1537
491IPR013809
Epsin-like, N-terminal		1532
492IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		1515
493IPR008889
VQ		1515
494IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		1515
495IPR022702
DNA (cytosine-5)-methyltransferase 1, replication foci domain		1532
496IPR025610
Transcription factor MYC/MYB N-terminal		1515
497IPR004294
Carotenoid oxygenase		1432
498IPR006689
Small GTPase superfamily, ARF/SAR type		1461
499IPR000467
G-patch domain		1437
500IPR000308
14-3-3 protein		1475
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata.html b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata.html new file mode 100644 index 00000000..820aec0b --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata.html @@ -0,0 +1,779 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:v.1.0, Dec 2008
Database version:86.10
Base Pairs:206,667,935
Golden Path Length:206,667,935
Genebuild by: JGI
Genebuild method: Imported from JGI-Phytozome
Genebuild started: Dec 2008
Genebuild released: Dec 2008
Genebuild last updated/patched: Dec 2008
Genebuild version: 2008-12-Araly1.0
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		32,667
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:32,667
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
8 sequences
+
+ +
+ + + +
SequenceLength (bp)
133132539
219320864
324464547
423328337
521221946
625113588
724649197
822951293
+
+
scaffold
+
695 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaffold_133132539
scaffold_219320864
scaffold_324464547
scaffold_423328337
scaffold_521221946
scaffold_625113588
scaffold_724649197
scaffold_822951293
scaffold_91906741
scaffold_10461865
scaffold_11440609
scaffold_13274490
scaffold_14361337
scaffold_15269926
scaffold_16170080
scaffold_17170241
scaffold_18163736
scaffold_19129820
scaffold_20100232
scaffold_21154816
scaffold_2277967
scaffold_2395112
scaffold_2472324
scaffold_2576307
scaffold_26171326
scaffold_2779363
scaffold_2882702
scaffold_2977981
scaffold_31104288
scaffold_3267898
scaffold_33127197
scaffold_3482892
scaffold_3585588
scaffold_3655443
scaffold_3750885
scaffold_3854598
scaffold_3956741
scaffold_4183393
scaffold_4358977
scaffold_4750189
scaffold_4882330
scaffold_5160900
scaffold_5257915
scaffold_5342563
scaffold_5459709
scaffold_5735077
scaffold_5858233
scaffold_5960404
scaffold_6054680
scaffold_6137089
scaffold_6330383
scaffold_6451199
scaffold_6548666
scaffold_6628436
scaffold_6842762
scaffold_7030586
scaffold_7128414
scaffold_7227939
scaffold_7326592
scaffold_7430081
scaffold_7626132
scaffold_7726910
scaffold_8044312
scaffold_8324864
scaffold_8447761
scaffold_8524006
scaffold_8647099
scaffold_8750767
scaffold_8824147
scaffold_8922846
scaffold_9022400
scaffold_9122377
scaffold_9241166
scaffold_9621493
scaffold_9722403
scaffold_9820962
scaffold_9921256
scaffold_10020959
scaffold_10320430
scaffold_10620070
scaffold_10820787
scaffold_10942950
scaffold_11020827
scaffold_11219564
scaffold_11319435
scaffold_11419422
scaffold_11519382
scaffold_11721951
scaffold_11819913
scaffold_12019368
scaffold_12118658
scaffold_12218722
scaffold_12319715
scaffold_12518511
scaffold_12619147
scaffold_12818776
scaffold_12918393
scaffold_13018728
scaffold_13218203
scaffold_13318967
scaffold_13519286
scaffold_13618177
scaffold_13718049
scaffold_13817628
scaffold_13917624
scaffold_14117526
scaffold_14217620
scaffold_14317394
scaffold_14442461
scaffold_14617905
scaffold_14916847
scaffold_15117353
scaffold_15219386
scaffold_15816071
scaffold_15916148
scaffold_16016358
scaffold_16117702
scaffold_16315971
scaffold_16415851
scaffold_16515836
scaffold_16616014
scaffold_16749487
scaffold_16916599
scaffold_17015673
scaffold_17215141
scaffold_17315208
scaffold_17614793
scaffold_17714777
scaffold_17815941
scaffold_17914583
scaffold_18014826
scaffold_18114397
scaffold_18414860
scaffold_18541385
scaffold_18814062
scaffold_18914063
scaffold_19014608
scaffold_19114737
scaffold_19313678
scaffold_19514542
scaffold_19614784
scaffold_19713548
scaffold_19914456
scaffold_20114150
scaffold_20312995
scaffold_20513037
scaffold_20612758
scaffold_20712741
scaffold_20812734
scaffold_20913614
scaffold_21012820
scaffold_21113490
scaffold_21212623
scaffold_21312589
scaffold_21412939
scaffold_21512671
scaffold_21612667
scaffold_21912503
scaffold_22012567
scaffold_22112465
scaffold_22214935
scaffold_22312436
scaffold_22512774
scaffold_22614339
scaffold_22812137
scaffold_22914132
scaffold_23012195
scaffold_23112023
scaffold_23311955
scaffold_23413216
scaffold_23512746
scaffold_23611975
scaffold_23911778
scaffold_24011761
scaffold_24111720
scaffold_24212482
scaffold_24311791
scaffold_24411945
scaffold_24611661
scaffold_24711656
scaffold_24811543
scaffold_24911536
scaffold_25011642
scaffold_25111483
scaffold_25211573
scaffold_25311547
scaffold_25512066
scaffold_25811345
scaffold_25911642
scaffold_26111263
scaffold_26211236
scaffold_26411275
scaffold_26511173
scaffold_26611173
scaffold_26711253
scaffold_26811135
scaffold_26911233
scaffold_27011521
scaffold_27111518
scaffold_27511334
scaffold_27711163
scaffold_27811661
scaffold_27911393
scaffold_28110755
scaffold_28310573
scaffold_28410500
scaffold_28510478
scaffold_28611290
scaffold_28710534
scaffold_28810982
scaffold_28911519
scaffold_29010597
scaffold_29210276
scaffold_29310266
scaffold_29410363
scaffold_29510362
scaffold_29810202
scaffold_29910268
scaffold_30010133
scaffold_30113661
scaffold_30210227
scaffold_30310106
scaffold_30410091
scaffold_30510182
scaffold_30710021
scaffold_3109954
scaffold_31111111
scaffold_31510914
scaffold_3199767
scaffold_3209724
scaffold_3229656
scaffold_32313369
scaffold_3259588
scaffold_32710118
scaffold_3309444
scaffold_3329416
scaffold_3349371
scaffold_3359336
scaffold_3379326
scaffold_3399323
scaffold_3409319
scaffold_3419405
scaffold_3429505
scaffold_3439298
scaffold_3449289
scaffold_34510120
scaffold_3469256
scaffold_34711265
scaffold_3489251
scaffold_3499250
scaffold_3509246
scaffold_3519344
scaffold_3529205
scaffold_3549157
scaffold_3559149
scaffold_35710030
scaffold_3589041
scaffold_3619014
scaffold_3639090
scaffold_3649531
scaffold_3658943
scaffold_3668942
scaffold_3689003
scaffold_3719041
scaffold_3728876
scaffold_37411842
scaffold_3758855
scaffold_3769273
scaffold_3788822
scaffold_3798803
scaffold_3808802
scaffold_3818802
scaffold_3838774
scaffold_3848774
scaffold_3858873
scaffold_3868868
scaffold_38738674
scaffold_3889797
scaffold_3908733
scaffold_3968738
scaffold_3978535
scaffold_3988508
scaffold_4009516
scaffold_4018402
scaffold_4028929
scaffold_4038363
scaffold_4088592
scaffold_4098939
scaffold_4128224
scaffold_4138084
scaffold_4158283
scaffold_4168111
scaffold_41711063
scaffold_4198366
scaffold_4267840
scaffold_4277728
scaffold_4287726
scaffold_4297683
scaffold_4318404
scaffold_4337762
scaffold_4357656
scaffold_4367748
scaffold_4397615
scaffold_4418626
scaffold_4437567
scaffold_4467466
scaffold_4477466
scaffold_4497416
scaffold_4508167
scaffold_4517539
scaffold_4537712
scaffold_4558208
scaffold_4577818
scaffold_4607398
scaffold_4617174
scaffold_4627632
scaffold_4637147
scaffold_4648265
scaffold_4677598
scaffold_4687083
scaffold_4697057
scaffold_4707167
scaffold_4717831
scaffold_4727204
scaffold_4747843
scaffold_4757365
scaffold_4778359
scaffold_4807093
scaffold_4816892
scaffold_4827203
scaffold_4847775
scaffold_4857120
scaffold_4866821
scaffold_4877116
scaffold_4887089
scaffold_4897466
scaffold_4916784
scaffold_4927480
scaffold_4937252
scaffold_4966643
scaffold_5006608
scaffold_5016594
scaffold_5047398
scaffold_5057365
scaffold_5076505
scaffold_5096900
scaffold_5106553
scaffold_5126411
scaffold_5166382
scaffold_5196361
scaffold_5206360
scaffold_5256326
scaffold_5277565
scaffold_5316372
scaffold_5326269
scaffold_5357120
scaffold_5407151
scaffold_5487813
scaffold_5497074
scaffold_5517366
scaffold_5526083
scaffold_5546283
scaffold_5576061
scaffold_5586765
scaffold_5626014
scaffold_5646109
scaffold_5656009
scaffold_5668876
scaffold_5695983
scaffold_5735973
scaffold_5755959
scaffold_5766219
scaffold_5795937
scaffold_5805936
scaffold_5825927
scaffold_5845890
scaffold_5856689
scaffold_5875857
scaffold_5887625
scaffold_5895841
scaffold_5915806
scaffold_5926190
scaffold_5946032
scaffold_5956717
scaffold_5976031
scaffold_6026162
scaffold_6035688
scaffold_6045673
scaffold_6076542
scaffold_6085644
scaffold_6106315
scaffold_6126294
scaffold_6145576
scaffold_6155574
scaffold_6165563
scaffold_6176537
scaffold_6248921
scaffold_6255482
scaffold_6265482
scaffold_6275482
scaffold_6285459
scaffold_6295457
scaffold_6305629
scaffold_6315424
scaffold_6356847
scaffold_6365373
scaffold_6375829
scaffold_6385368
scaffold_6395820
scaffold_6426019
scaffold_6456504
scaffold_6465493
scaffold_6495283
scaffold_6515261
scaffold_6535252
scaffold_6555225
scaffold_6585205
scaffold_6595359
scaffold_6615160
scaffold_6625156
scaffold_6635148
scaffold_6645148
scaffold_6655827
scaffold_6665241
scaffold_6675140
scaffold_6685132
scaffold_6695128
scaffold_6705121
scaffold_6715118
scaffold_6725491
scaffold_6745112
scaffold_6756837
scaffold_6775864
scaffold_6785083
scaffold_6795059
scaffold_6805240
scaffold_6815213
scaffold_6825054
scaffold_6835141
scaffold_6845838
scaffold_6855534
scaffold_6865026
scaffold_6885023
scaffold_6934983
scaffold_6945113
scaffold_6955175
scaffold_6974979
scaffold_6995067
scaffold_7004965
scaffold_7014959
scaffold_7024958
scaffold_7046290
scaffold_7055366
scaffold_7067009
scaffold_7074917
scaffold_7104912
scaffold_7114872
scaffold_7134863
scaffold_7154861
scaffold_7164853
scaffold_7175243
scaffold_7195313
scaffold_7214834
scaffold_7234825
scaffold_7265424
scaffold_7274814
scaffold_7284797
scaffold_7294780
scaffold_7315275
scaffold_7334746
scaffold_7344745
scaffold_7354737
scaffold_7364732
scaffold_7384726
scaffold_7394724
scaffold_7404713
scaffold_7414712
scaffold_7444703
scaffold_7464685
scaffold_7474673
scaffold_7485666
scaffold_7524661
scaffold_7534660
scaffold_7554645
scaffold_7564643
scaffold_7594630
scaffold_7615050
scaffold_7624621
scaffold_7634616
scaffold_7664606
scaffold_7694691
scaffold_7706232
scaffold_7714584
scaffold_7724582
scaffold_7734573
scaffold_7764960
scaffold_7774536
scaffold_7794521
scaffold_7804662
scaffold_7814495
scaffold_7824595
scaffold_7834478
scaffold_7844474
scaffold_7864606
scaffold_7874568
scaffold_7884458
scaffold_7904554
scaffold_7924443
scaffold_7934441
scaffold_7955066
scaffold_7964429
scaffold_7974423
scaffold_7984415
scaffold_8014509
scaffold_8024396
scaffold_8044377
scaffold_8054370
scaffold_8076854
scaffold_8105651
scaffold_8114562
scaffold_8124514
scaffold_8134331
scaffold_8144539
scaffold_8154310
scaffold_8174298
scaffold_8194465
scaffold_8234267
scaffold_8254247
scaffold_8284207
scaffold_8294347
scaffold_8304194
scaffold_8314344
scaffold_8324187
scaffold_8344178
scaffold_8354174
scaffold_8374626
scaffold_8384523
scaffold_8405829
scaffold_8434275
scaffold_8454512
scaffold_8484102
scaffold_8494099
scaffold_8514097
scaffold_8524092
scaffold_8534089
scaffold_8554439
scaffold_8584066
scaffold_8614139
scaffold_8624575
scaffold_8644516
scaffold_8654494
scaffold_8664016
scaffold_8675049
scaffold_8684182
scaffold_8714285
scaffold_8723968
scaffold_8753940
scaffold_8774368
scaffold_8783930
scaffold_8793924
scaffold_8804021
scaffold_8813916
scaffold_8824320
scaffold_8833909
scaffold_8844431
scaffold_8874269
scaffold_8904249
scaffold_8914007
scaffold_8933862
scaffold_8943855
scaffold_8954136
scaffold_8963846
scaffold_9004145
scaffold_9014359
scaffold_9025000
scaffold_9034408
scaffold_9045088
scaffold_9054260
scaffold_9084028
scaffold_9114098
scaffold_9123771
scaffold_9153754
scaffold_9183747
scaffold_9193737
scaffold_9204123
scaffold_9243704
scaffold_9283697
scaffold_9363647
scaffold_9374338
scaffold_9383779
scaffold_9393631
scaffold_9403938
scaffold_9413726
scaffold_9453617
scaffold_9463616
scaffold_9476058
scaffold_9504273
scaffold_9543584
scaffold_9553571
scaffold_9584209
scaffold_9603538
scaffold_9614838
scaffold_9624142
scaffold_9633949
scaffold_9643891
scaffold_9653785
scaffold_9684042
scaffold_9704154
scaffold_9714079
scaffold_9753568
scaffold_9764054
scaffold_9774214
scaffold_9784265
scaffold_9793792
scaffold_9814203
scaffold_9823429
scaffold_9833426
scaffold_9843958
scaffold_9864114
scaffold_9874148
scaffold_9894061
scaffold_9904503
scaffold_9913657
scaffold_9923872
scaffold_9933636
scaffold_9944210
scaffold_9963769
scaffold_9983458
scaffold_9993250
scaffold_10003807
scaffold_10013881
scaffold_10033794
scaffold_10053927
scaffold_10063877
scaffold_10073901
scaffold_10083858
scaffold_10103854
scaffold_10123507
scaffold_10143862
scaffold_10153932
scaffold_10173499
scaffold_10194049
scaffold_10203919
scaffold_10213008
scaffold_10223679
scaffold_10253368
scaffold_10293768
scaffold_10313861
scaffold_10323379
scaffold_10333660
scaffold_10343146
scaffold_10403746
scaffold_10413612
scaffold_10433621
scaffold_10442691
scaffold_10463782
scaffold_10483927
scaffold_10523641
scaffold_10534104
scaffold_10543622
scaffold_10563510
scaffold_10573517
scaffold_10583585
scaffold_10613854
scaffold_10643571
scaffold_10693355
scaffold_10703525
scaffold_10723249
scaffold_10743416
scaffold_10764311
scaffold_10783595
scaffold_10801964
scaffold_10823428
scaffold_10841840
scaffold_10853303
scaffold_10861720
scaffold_10873400
scaffold_10891632
scaffold_10901576
scaffold_10911567
scaffold_10941447
scaffold_10951425
scaffold_10961413
scaffold_10973259
scaffold_10991362
scaffold_11021249
scaffold_11051194
scaffold_11061174
scaffold_11091083
scaffold_11111078
scaffold_11121047
scaffold_11131037
scaffold_11161032
scaffold_11171017
scaffold_11181005
+
+
chunk2677 sequences
+ +

Other

+ + + + + +
FGENESH gene predictions:30,044
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata_IPtop500.html new file mode 100644 index 00000000..b1cea646 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_lyrata_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		11933159
2IPR011009
Protein kinase-like domain		11421253
3IPR000719
Protein kinase, catalytic domain		10642572
4IPR001810
F-box domain, cyclin-like		7992529
5IPR008271
Serine/threonine-protein kinase, active site		791793
6IPR032675
Leucine-rich repeat domain, L domain-like		7781978
7IPR013083
Zinc finger, RING/FYVE/PHD-type		726783
8IPR017441
Protein kinase, ATP binding site		654655
9IPR011990
Tetratricopeptide-like helical		5981975
10IPR013320
Concanavalin A-like lectin/glucanase, subgroup		518701
11IPR002885
Pentatricopeptide repeat		50311488
12IPR001841
Zinc finger, RING-type		4821128
13IPR017451
F-box associated interaction domain		444476
14IPR009057
Homeodomain-like		4311032
15IPR016024
Armadillo-type fold		396929
16IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		387589
17IPR016040
NAD(P)-binding domain		376884
18IPR029058
Alpha/Beta hydrolase fold		359859
19IPR012340
Nucleic acid-binding, OB-fold		358524
20IPR012677
Nucleotide-binding, alpha-beta plait		3431050
21IPR001611
Leucine-rich repeat		3351668
22IPR011989
Armadillo-like helical		305599
23IPR015943
WD40/YVTN repeat-like-containing domain		294493
24IPR000504
RNA recognition motif domain		2891342
25IPR001005
SANT/Myb domain		289803
26IPR003593
AAA+ ATPase domain		288374
27IPR011991
Winged helix-turn-helix DNA-binding domain		275446
28IPR017986
WD40-repeat-containing domain		273693
29IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		272705
30IPR012336
Thioredoxin-like fold		271612
31IPR001128
Cytochrome P450		2551534
32IPR001680
WD40 repeat		2532703
33IPR017930
Myb domain		239386
34IPR020846
Major facilitator superfamily domain		237456
35IPR017853
Glycoside hydrolase, superfamily		235256
36IPR006527
F-box associated domain, type 1		231244
37IPR002401
Cytochrome P450, E-class, group I		2171450
38IPR017972
Cytochrome P450, conserved site		215216
39IPR013210
Leucine-rich repeat-containing N-terminal, type 2		212218
40IPR013187
F-box associated domain, type 3		206215
41IPR013781
Glycoside hydrolase, catalytic domain		202220
42IPR011992
EF-hand-like domain		197480
43IPR002182
NB-ARC		195201
44IPR003871
Domain of unknown function DUF223		182188
45IPR011050
Pectin lyase fold/virulence factor		174180
46IPR012334
Pectin lyase fold		174181
47IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		170800
48IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		170772
49IPR002048
Calcium-binding EF-hand		1681192
50IPR023214
HAD-like domain		166464
51IPR007087
Zinc finger, C2H2		162514
52IPR019775
WD40 repeat, conserved site		162284
53IPR016177
DNA-binding, integrase-type		161177
54IPR003591
Leucine-rich repeat, typical subtype		1561073
55IPR001471
AP2/ERF domain		151915
56IPR018247
EF-Hand 1, calcium-binding site		151391
57IPR006652
Kelch repeat type 1		151409
58IPR001650
Helicase, C-terminal		148439
59IPR015916
Galactose oxidase, beta-propeller		147157
60IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		147178
61IPR014001
Helicase, superfamily 1/2, ATP-binding domain		147290
62IPR029044
Nucleotide-diphospho-sugar transferases		146346
63IPR029071
Ubiquitin-related domain		141209
64IPR015300
DNA-binding pseudobarrel domain		141450
65IPR012337
Ribonuclease H-like domain		137264
66IPR005225
Small GTP-binding protein domain		134135
67IPR006501
Pectinesterase inhibitor		132618
68IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		129328
69IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		127541
70IPR008974
TRAF-like		127303
71IPR013026
Tetratricopeptide repeat-containing domain		124166
72IPR003441
No apical meristem (NAM) protein		122379
73IPR003959
ATPase, AAA-type, core		122149
74IPR003340
B3 DNA binding domain		121536
75IPR001623
DnaJ domain		120800
76IPR003439
ABC transporter-like		120345
77IPR019734
Tetratricopeptide repeat		119849
78IPR005123
Oxoglutarate/iron-dependent dioxygenase		119216
79IPR000008
C2 calcium-dependent membrane targeting		118793
80IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		116272
81IPR013830
SGNH hydrolase-type esterase domain		109343
82IPR013785
Aldolase-type TIM barrel		107124
83IPR027443
Isopenicillin N synthase-like		106112
84IPR011043
Galactose oxidase/kelch, beta-propeller		106122
85IPR009072
Histone-fold		106218
86IPR008972
Cupredoxin		103398
87IPR011011
Zinc finger, FYVE/PHD-type		103121
88IPR006566
FBD domain		102165
89IPR017907
Zinc finger, RING-type, conserved site		102102
90IPR014710
RmlC-like jelly roll fold		101120
91IPR001087
Lipase, GDSL		98105
92IPR002083
MATH/TRAF domain		98350
93IPR000626
Ubiquitin domain		97417
94IPR005174
Protein of unknown function DUF295		9798
95IPR008502
Prolamin-like domain		9699
96IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		9599
97IPR020472
G-protein beta WD-40 repeat		95285
98IPR011333
BTB/POZ fold		95100
99IPR015424
Pyridoxal phosphate-dependent transferase		95106
100IPR010255
Haem peroxidase		9495
101IPR001806
Small GTPase superfamily		9496
102IPR013101
Leucine-rich repeat 2		9297
103IPR000073
Alpha/beta hydrolase fold-1		92185
104IPR032867
DYW domain		9293
105IPR013766
Thioredoxin domain		91167
106IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		9194
107IPR002016
Haem peroxidase, plant/fungal/bacterial		90564
108IPR011713
Leucine-rich repeat 3		9093
109IPR006447
Myb domain, plants		8990
110IPR026992
Non-haem dioxygenase N-terminal domain		8888
111IPR001932
Protein phosphatase 2C (PP2C)-like		88516
112IPR015915
Kelch-type beta propeller		87101
113IPR000270
Phox/Bem1p		87143
114IPR027640
Kinesin-like protein		86208
115IPR017871
ABC transporter, conserved site		86111
116IPR001356
Homeobox domain		86224
117IPR015500
Peptidase S8, subtilisin-related		85290
118IPR015880
Zinc finger, C2H2-like		85221
119IPR010264
Plant self-incompatibility S1		8487
120IPR001965
Zinc finger, PHD-type		84130
121IPR000225
Armadillo		84674
122IPR002347
Glucose/ribitol dehydrogenase		83729
123IPR023393
START-like domain		8389
124IPR021109
Aspartic peptidase		83242
125IPR002902
Gnk2-homologous domain		82292
126IPR023213
Chloramphenicol acetyltransferase-like domain		82151
127IPR002100
Transcription factor, MADS-box		82547
128IPR001752
Kinesin, motor domain		82536
129IPR015655
Protein phosphatase 2C		81133
130IPR003657
DNA-binding WRKY		81459
131IPR011993
Pleckstrin homology-like domain		81158
132IPR001461
Peptidase A1		80216
133IPR000209
Peptidase S8/S53 domain		80408
134IPR020568
Ribosomal protein S5 domain 2-type fold		7993
135IPR004827
Basic-leucine zipper domain		79291
136IPR029052
Metallo-dependent phosphatase-like		78181
137IPR000571
Zinc finger, CCCH-type		78647
138IPR005828
General substrate transporter		7784
139IPR020683
Ankyrin repeat-containing domain		77294
140IPR006121
Heavy metal-associated domain, HMA		75226
141IPR000070
Pectinesterase, catalytic		7580
142IPR019786
Zinc finger, PHD-type, conserved site		7485
143IPR033121
Peptidase family A1 domain		7482
144IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		7480
145IPR003613
U box domain		73212
146IPR003676
Auxin responsive SAUR protein		7373
147IPR000823
Plant peroxidase		73620
148IPR003480
Transferase		7379
149IPR010987
Glutathione S-transferase, C-terminal-like		72211
150IPR004314
Domain of unknown function DUF239		7279
151IPR004843
Metallophosphoesterase domain		7171
152IPR011051
RmlC-like cupin domain		7075
153IPR016181
Acyl-CoA N-acyltransferase		69155
154IPR000210
BTB/POZ domain		69181
155IPR032861
Xylanase inhibitor, N-terminal		6970
156IPR008979
Galactose-binding domain-like		69180
157IPR013763
Cyclin-like		68314
158IPR019793
Peroxidases heam-ligand binding site		6868
159IPR023828
Peptidase S8, subtilisin, Ser-active site		6869
160IPR023395
Mitochondrial carrier domain		68143
161IPR012946
X8 domain		67138
162IPR019787
Zinc finger, PHD-finger		67119
163IPR018108
Mitochondrial substrate/solute carrier		67366
164IPR010259
Proteinase inhibitor I9		6698
165IPR000048
IQ motif, EF-hand binding site		66431
166IPR000743
Glycoside hydrolase, family 28		66111
167IPR003960
ATPase, AAA-type, conserved site		6571
168IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		6599
169IPR025521
Domain of unknown function DUF4409		6569
170IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		64102
171IPR016135
Ubiquitin-conjugating enzyme/RWD-like		64128
172IPR001480
Bulb-type lectin domain		64340
173IPR002110
Ankyrin repeat		64268
174IPR032799
Xylanase inhibitor, C-terminal		6364
175IPR029055
Nucleophile aminohydrolases, N-terminal		62124
176IPR006462
Protein of unknown function DUF626, Arabidopsis thaliana		62108
177IPR001220
Legume lectin domain		6263
178IPR001360
Glycoside hydrolase, family 1		61374
179IPR016166
FAD-binding, type 2		61115
180IPR002528
Multi antimicrobial extrusion protein		61170
181IPR019794
Peroxidase, active site		6161
182IPR004045
Glutathione S-transferase, N-terminal		61124
183IPR005829
Sugar transporter, conserved site		6097
184IPR000668
Peptidase C1A, papain C-terminal		60202
185IPR003245
Plastocyanin-like		59200
186IPR031127
E3 ubiquitin ligase RBR family		5962
187IPR000109
Proton-dependent oligopeptide transporter family		58120
188IPR000490
Glycoside hydrolase, family 17		58101
189IPR003594
Histidine kinase-like ATPase, ATP-binding domain		57205
190IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5757
191IPR006626
Parallel beta-helix repeat		56266
192IPR003609
Apple-like		54141
193IPR014014
RNA helicase, DEAD-box type, Q motif		5454
194IPR003663
Sugar/inositol transporter		54306
195IPR001878
Zinc finger, CCHC-type		54345
196IPR015947
PUA-like domain		5467
197IPR002109
Glutaredoxin		53109
198IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		5356
199IPR002867
Zinc finger, C6HC-type		52156
200IPR000858
S-locus glycoprotein		5252
201IPR008949
Terpenoid synthase		51104
202IPR013057
Amino acid transporter, transmembrane		5152
203IPR001563
Peptidase S10, serine carboxypeptidase		50285
204IPR019821
Kinesin, motor region, conserved site		5050
205IPR000608
Ubiquitin-conjugating enzyme, E2		50100
206IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		5055
207IPR018253
DnaJ domain, conserved site		5050
208IPR033389
AUX/IAA domain		4954
209IPR008978
HSP20-like chaperone		4998
210IPR009060
UBA-like		4956
211IPR004864
Late embryogenesis abundant protein, LEA-14		4950
212IPR007125
Histone core		4951
213IPR016167
FAD-binding, type 2, subdomain 1		4949
214IPR006094
FAD linked oxidase, N-terminal		4949
215IPR016159
Cullin repeat-like-containing domain		4968
216IPR030184
WAT1-related protein		4950
217IPR014756
Immunoglobulin E-set		4954
218IPR026057
PC-Esterase		4849
219IPR008928
Six-hairpin glycosidase-like		4859
220IPR001214
SET domain		48130
221IPR008942
ENTH/VHS		4789
222IPR029962
Trichome birefringence-like family		4760
223IPR004883
Lateral organ boundaries, LOB		4793
224IPR023299
P-type ATPase, cytoplasmic domain N		4796
225IPR029062
Class I glutamine amidotransferase-like		47118
226IPR010851
S locus-related glycoprotein 1 binding pollen coat		4646
227IPR022742
Alpha/beta hydrolase, N-terminal		4646
228IPR003690
Mitochodrial transcription termination factor-related		46357
229IPR025846
PMR5 N-terminal domain		4646
230IPR001229
Mannose-binding lectin		46499
231IPR011032
GroES-like		4599
232IPR033131
Pectinesterase, Asp active site		4545
233IPR011006
CheY-like superfamily		4549
234IPR001757
Cation-transporting P-type ATPase		45140
235IPR000620
Drug/metabolite transporter		4579
236IPR001789
Signal transduction response regulator, receiver domain		45135
237IPR006153
Cation/H+ exchanger		4444
238IPR011701
Major facilitator superfamily		4444
239IPR008250
P-type ATPase, A domain		4495
240IPR011527
ABC transporter, transmembrane domain, type 1		44238
241IPR005746
Thioredoxin		4452
242IPR002921
Lipase, class 3		4344
243IPR006016
UspA		4344
244IPR010920
Like-Sm (LSM) domain		4344
245IPR013128
Peptidase C1A, papain		4343
246IPR008991
Translation protein SH3-like domain		4344
247IPR023271
Aquaporin-like		4389
248IPR006553
Leucine-rich repeat, cysteine-containing subtype		43305
249IPR004839
Aminotransferase, class I/classII		4343
250IPR018303
P-type ATPase, phosphorylation site		4343
251IPR000425
Major intrinsic protein		43339
252IPR006525
Cystatin-related, plant		4347
253IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		43103
254IPR003614
Knottin		4396
255IPR000182
GNAT domain		4278
256IPR004263
Exostosin-like		4242
257IPR006045
Cupin 1		42100
258IPR019378
GDP-fucose protein O-fucosyltransferase		4242
259IPR002495
Glycosyl transferase, family 8		4245
260IPR006671
Cyclin, N-terminal		4267
261IPR011042
Six-bladed beta-propeller, TolB-like		4256
262IPR017877
Myb-like domain		4256
263IPR010402
CCT domain		4182
264IPR004853
Domain of unknown function DUF250		4141
265IPR029000
Cyclophilin-like domain		4187
266IPR011016
Zinc finger, RING-CH-type		4197
267IPR000330
SNF2-related		4141
268IPR001969
Peptidase aspartic, active site		4159
269IPR024768
Meiosis arrest female protein 1		4144
270IPR029045
ClpP/crotonase-like domain		41109
271IPR002067
Mitochondrial carrier protein		41205
272IPR021139
NYN domain, limkain-b1-type		4146
273IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		4141
274IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		4141
275IPR001117
Multicopper oxidase, type 1		4040
276IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		40221
277IPR013525
ABC-2 type transporter		4054
278IPR000873
AMP-dependent synthetase/ligase		4042
279IPR003137
Protease-associated domain, PA		4040
280IPR025886
Phloem protein 2-like		4040
281IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4040
282IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		4040
283IPR011706
Multicopper oxidase, type 2		4040
284IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4051
285IPR032710
NTF2-like domain		3970
286IPR011012
Longin-like domain		3939
287IPR004088
K Homology domain, type 1		39297
288IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3939
289IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3939
290IPR024788
Malectin-like carbohydrate-binding domain		3942
291IPR002487
Transcription factor, K-box		3977
292IPR000757
Glycoside hydrolase, family 16		3978
293IPR015797
NUDIX hydrolase domain-like		3979
294IPR006195
Aminoacyl-tRNA synthetase, class II		3838
295IPR001251
CRAL-TRIO domain		38181
296IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3839
297IPR029021
Protein-tyrosine phosphatase-like		3887
298IPR016039
Thiolase-like		38169
299IPR027725
Heat shock transcription factor family		3844
300IPR009009
Barwin-related endoglucanase		38113
301IPR013783
Immunoglobulin-like fold		3843
302IPR002423
Chaperonin Cpn60/TCP-1		3839
303IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3862
304IPR000232
Heat shock factor (HSF)-type, DNA-binding		38188
305IPR011707
Multicopper oxidase, type 3		3838
306IPR002068
Alpha crystallin/Hsp20 domain		3761
307IPR001509
NAD-dependent epimerase/dehydratase		3737
308IPR005135
Endonuclease/exonuclease/phosphatase		37137
309IPR016455
Xyloglucan endotransglucosylase/hydrolase		3737
310IPR005202
Transcription factor GRAS		3778
311IPR000727
Target SNARE coiled-coil domain		3698
312IPR000315
Zinc finger, B-box		36136
313IPR024171
S-receptor-like serine/threonine-protein kinase		3636
314IPR017970
Homeobox, conserved site		3636
315IPR008801
Rapid ALkalinization Factor		3636
316IPR013149
Alcohol dehydrogenase, C-terminal		3535
317IPR004367
Cyclin, C-terminal domain		3563
318IPR007112
Expansin/pollen allergen, DPBB domain		3568
319IPR003406
Glycosyl transferase, family 14		3536
320IPR023313
Ubiquitin-conjugating enzyme, active site		3535
321IPR020845
AMP-binding, conserved site		3537
322IPR002035
von Willebrand factor, type A		3586
323IPR022357
Major intrinsic protein, conserved site		3535
324IPR000916
Bet v I domain		3577
325IPR000644
Cystathionine beta-synthase, core		35189
326IPR002912
ACT domain		3591
327IPR018957
Zinc finger, C3HC4 RING-type		3434
328IPR020904
Short-chain dehydrogenase/reductase, conserved site		3434
329IPR008480
Protein of unknown function DUF761, plant		3434
330IPR001849
Pleckstrin homology domain		3478
331IPR003851
Zinc finger, Dof-type		34136
332IPR000086
NUDIX hydrolase domain		3466
333IPR029006
ADF-H/Gelsolin-like domain		3459
334IPR008889
VQ		3434
335IPR018490
Cyclic nucleotide-binding-like		3334
336IPR025659
Tubby C-terminal-like domain		3336
337IPR013216
Methyltransferase type 11		3335
338IPR003822
Paired amphipathic helix		33231
339IPR011013
Galactose mutarotase-like domain		3341
340IPR015813
Pyruvate/Phosphoenolpyruvate kinase		3389
341IPR003311
AUX/IAA protein		3337
342IPR007117
Expansin, cellulose-binding-like domain		33136
343IPR014720
Double-stranded RNA-binding domain		33119
344IPR006073
GTP binding domain		3389
345IPR010666
Zinc finger, GRF-type		3233
346IPR025287
Wall-associated receptor kinase galacturonan-binding domain		3232
347IPR001929
Germin		3294
348IPR007118
Expansin/Lol pI		32187
349IPR000795
Elongation factor, GTP-binding domain		32167
350IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3233
351IPR005150
Cellulose synthase		3240
352IPR027409
GroEL-like apical domain		3262
353IPR000595
Cyclic nucleotide-binding domain		3284
354IPR012341
Six-hairpin glycosidase		3233
355IPR017927
Ferredoxin reductase-type FAD-binding domain		3131
356IPR017938
Riboflavin synthase-like beta-barrel		3134
357IPR013201
Proteinase inhibitor I29, cathepsin propeptide		3161
358IPR001296
Glycosyl transferase, family 1		3131
359IPR012675
Beta-grasp domain		3131
360IPR001353
Proteasome, subunit alpha/beta		3131
361IPR011074
CRAL/TRIO, N-terminal domain		3181
362IPR014722
Ribosomal protein L2 domain 2		3131
363IPR017937
Thioredoxin, conserved site		3138
364IPR009003
Trypsin-like cysteine/serine peptidase domain		3134
365IPR001313
Pumilio RNA-binding repeat		31423
366IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3180
367IPR005175
Domain of unknown function DUF296		3164
368IPR006689
Small GTPase superfamily, ARF/SAR type		30130
369IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		3086
370IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		3048
371IPR012951
Berberine/berberine-like		3030
372IPR001938
Thaumatin		30337
373IPR013154
Alcohol dehydrogenase GroES-like		3030
374IPR010989
t-SNARE		3033
375IPR017926
Glutamine amidotransferase type 1		3055
376IPR001487
Bromodomain		30226
377IPR025660
Cysteine peptidase, histidine active site		3030
378IPR029064
50S ribosomal protein L30e-like		3055
379IPR025322
Protein of unknown function DUF4228		2929
380IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2973
381IPR029061
Thiamin diphosphate-binding fold		2989
382IPR001944
Glycoside hydrolase, family 35		29197
383IPR000169
Cysteine peptidase, cysteine active site		2929
384IPR013126
Heat shock protein 70 family		29200
385IPR013955
Replication factor A, C-terminal		2929
386IPR029047
Heat shock protein 70kD, peptide-binding domain		2961
387IPR018202
Peptidase S10, serine carboxypeptidase, active site		2929
388IPR029033
Histidine phosphatase superfamily		2983
389IPR004274
NLI interacting factor		2989
390IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2892
391IPR019956
Ubiquitin subgroup		2881
392IPR013088
Zinc finger, NHR/GATA-type		2828
393IPR001478
PDZ domain		28102
394IPR005821
Ion transport domain		2829
395IPR004087
K Homology domain		2872
396IPR020843
Polyketide synthase, enoylreductase		2828
397IPR023210
NADP-dependent oxidoreductase domain		2881
398IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		2852
399IPR000679
Zinc finger, GATA-type		28111
400IPR006594
LisH dimerisation motif		2756
401IPR025110
Domain of unknown function DUF4009		2729
402IPR024593
Domain of unknown function DUF3444		2740
403IPR000782
FAS1 domain		27156
404IPR003954
RNA recognition motif domain, eukaryote		2752
405IPR004162
E3 ubiquitin-protein ligase SINA like		2727
406IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		2727
407IPR001163
Ribonucleoprotein LSM domain		2753
408IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2728
409IPR001279
Beta-lactamase-like		27103
410IPR027413
GroEL-like equatorial domain		2748
411IPR027356
NPH3 domain		2755
412IPR029056
Ribokinase-like		2762
413IPR001283
Allergen V5/Tpx-1-related		27129
414IPR014044
CAP domain		27107
415IPR031107
Small heat shock protein HSP20		2727
416IPR004046
Glutathione S-transferase, C-terminal		2727
417IPR028082
Periplasmic binding protein-like I		2735
418IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2737
419IPR001828
Extracellular ligand-binding receptor		2728
420IPR023298
P-type ATPase, transmembrane domain		2753
421IPR000061
SWAP/Surp		27252
422IPR001395
Aldo/keto reductase		2738
423IPR003347
JmjC domain		2669
424IPR000253
Forkhead-associated (FHA) domain		2680
425IPR005630
Terpene synthase, metal-binding domain		2626
426IPR022812
Dynamin superfamily		26141
427IPR000408
Regulator of chromosome condensation, RCC1		26496
428IPR004265
Plant disease resistance response protein		2626
429IPR002963
Expansin		26222
430IPR001320
Ionotropic glutamate receptor		2653
431IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2626
432IPR013323
SIAH-type domain		2626
433IPR025661
Cysteine peptidase, asparagine active site		2626
434IPR001638
Extracellular solute-binding protein, family 3		2626
435IPR013809
Epsin-like, N-terminal		2653
436IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		26228
437IPR018082
AmbAllergen		26187
438IPR000528
Plant lipid transfer protein/Par allergen		25107
439IPR008984
SMAD/FHA domain		2526
440IPR021820
S-locus receptor kinase, C-terminal		2525
441IPR005333
Transcription factor, TCP		2525
442IPR017887
Transcription factor TCP subgroup		2525
443IPR002022
Pectate lyase/Amb allergen		2550
444IPR004140
Exocyst complex protein Exo70		2552
445IPR033275
E3 ubiquitin-protein ligase MARCH-like		2531
446IPR016021
MIF4-like, type 1/2/3		2546
447IPR003008
Tubulin/FtsZ, GTPase domain		25108
448IPR014002
Tudor-like, plant		2564
449IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2528
450IPR001701
Glycoside hydrolase, family 9		2525
451IPR025486
Domain of unknown function DUF4378		2525
452IPR023329
Chlorophyll a/b binding protein domain		2528
453IPR024156
Small GTPase superfamily, ARF type		2525
454IPR033133
Pumilio homology domain		2424
455IPR004041
NAF domain		2424
456IPR004316
SWEET sugar transporter		2444
457IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2457
458IPR024709
O-fucosyltransferase, plant		2424
459IPR018451
NAF/FISL domain		2424
460IPR000717
Proteasome component (PCI) domain		2443
461IPR002659
Glycosyl transferase, family 31		2447
462IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2448
463IPR033124
Serine carboxypeptidases, histidine active site		2424
464IPR011332
Ribosomal protein, zinc-binding domain		2424
465IPR006459
Uncharacterised protein family UPF0497, trans-membrane plant subgroup		2424
466IPR022796
Chlorophyll A-B binding protein		2425
467IPR004154
Anticodon-binding		2454
468IPR004146
DC1		2444
469IPR019780
Germin, manganese binding site		2424
470IPR006458
Ovate protein family, C-terminal		2467
471IPR001906
Terpene synthase, N-terminal domain		2447
472IPR000195
Rab-GTPase-TBC domain		24146
473IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		2448
474IPR006703
AIG1-type guanine nucleotide-binding (G) domain		2448
475IPR011905
Glutaredoxin-like, plant II		2424
476IPR029060
PIN domain-like		2345
477IPR003106
Leucine zipper, homeobox-associated		2332
478IPR006593
Cytochrome b561/ferric reductase transmembrane		2365
479IPR005299
SAM dependent carboxyl methyltransferase		2323
480IPR009071
High mobility group (HMG) box domain		23106
481IPR018150
Aminoacyl-tRNA synthetase, class II (D/K/N)-like		2336
482IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		2339
483IPR001025
Bromo adjacent homology (BAH) domain		2376
484IPR006379
HAD-superfamily hydrolase, subfamily IIB		2323
485IPR003689
Zinc/iron permease		2324
486IPR001876
Zinc finger, RanBP2-type		23201
487IPR006012
Syntaxin/epimorphin, conserved site		2323
488IPR016161
Aldehyde/histidinol dehydrogenase		2323
489IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		2372
490IPR030182
Purine permease, plant		2323
491IPR001940
Peptidase S1C		2294
492IPR013601
FAE1/Type III polyketide synthase-like protein		2222
493IPR008971
HSP40/DnaJ peptide-binding		2252
494IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2242
495IPR002403
Cytochrome P450, E-class, group IV		22110
496IPR000014
PAS domain		22117
497IPR019954
Ubiquitin conserved site		2272
498IPR007493
Protein of unknown function DUF538		2266
499IPR006043
Xanthine/uracil/vitamin C permease		2248
500IPR005508
Protein of unknown function DUF313		2223
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_thaliana.html b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_thaliana.html new file mode 100644 index 00000000..ac1c4865 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Arabidopsis_thaliana.html @@ -0,0 +1,69 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:TAIR10, Sep 2010
Database version:87.11
Base Pairs:135,670,229
Golden Path Length:119,667,750
Genebuild by: TAIR
Genebuild method: Imported from TAIR
Genebuild started: Sep 2010
Genebuild released: Sep 2010
Genebuild last updated/patched: Sep 2010
Genebuild version: 2016-06-Araport11
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		27,655
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:54,013
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
7 sequences
+
+ +
+ + + +
SequenceLength (bp)
130427671
219698289
323459830
418585056
526975502
Mt366924
Pt154478
+
+
contig1613 sequences
+ +

Other

+ + + + + +
FGENESH gene predictions:20,579
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		11095304
2IPR011009
Protein kinase-like domain		10821957
3IPR000719
Protein kinase, catalytic domain		10374139
4IPR008271
Serine/threonine-protein kinase, active site		8051317
5IPR032675
Leucine-rich repeat domain, L domain-like		7933371
6IPR013083
Zinc finger, RING/FYVE/PHD-type		7501219
7IPR001810
F-box domain, cyclin-like		6882523
8IPR017441
Protein kinase, ATP binding site		6801057
9IPR011990
Tetratricopeptide-like helical		5922566
10IPR013320
Concanavalin A-like lectin/glucanase, subgroup		5161078
11IPR002885
Pentatricopeptide repeat		47114397
12IPR001841
Zinc finger, RING-type		4671465
13IPR009057
Homeodomain-like		4351540
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		400971
15IPR016040
NAD(P)-binding domain		3721424
16IPR016024
Armadillo-type fold		3711496
17IPR001611
Leucine-rich repeat		3642696
18IPR029058
Alpha/Beta hydrolase fold		3381416
19IPR003593
AAA+ ATPase domain		320660
20IPR012677
Nucleotide-binding, alpha-beta plait		2891527
21IPR011989
Armadillo-like helical		286918
22IPR015943
WD40/YVTN repeat-like-containing domain		282800
23IPR001005
SANT/Myb domain		2821112
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		2691108
25IPR017451
F-box associated interaction domain		264301
26IPR017986
WD40-repeat-containing domain		2591085
27IPR000504
RNA recognition motif domain		2581971
28IPR012336
Thioredoxin-like fold		253792
29IPR001128
Cytochrome P450		2512077
30IPR001680
WD40 repeat		2384185
31IPR011991
Winged helix-turn-helix DNA-binding domain		232604
32IPR002401
Cytochrome P450, E-class, group I		2292055
33IPR017930
Myb domain		229540
34IPR017972
Cytochrome P450, conserved site		225275
35IPR020846
Major facilitator superfamily domain		224715
36IPR013210
Leucine-rich repeat-containing N-terminal, type 2		217287
37IPR017853
Glycoside hydrolase, superfamily		215397
38IPR011992
EF-hand-like domain		195749
39IPR013781
Glycoside hydrolase, catalytic domain		183316
40IPR006566
FBD domain		175330
41IPR003591
Leucine-rich repeat, typical subtype		1701756
42IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		1691402
43IPR002048
Calcium-binding EF-hand		1651742
44IPR002182
NB-ARC		165330
45IPR011050
Pectin lyase fold/virulence factor		164207
46IPR012334
Pectin lyase fold		164208
47IPR016177
DNA-binding, integrase-type		158250
48IPR023214
HAD-like domain		156698
49IPR006527
F-box associated domain, type 1		154168
50IPR007087
Zinc finger, C2H2		151685
51IPR018247
EF-Hand 1, calcium-binding site		151562
52IPR004146
DC1		151864
53IPR014001
Helicase, superfamily 1/2, ATP-binding domain		151551
54IPR019775
WD40 repeat, conserved site		149404
55IPR001650
Helicase, C-terminal		147786
56IPR001471
AP2/ERF domain		1461252
57IPR029044
Nucleotide-diphospho-sugar transferases		144470
58IPR012337
Ribonuclease H-like domain		140377
59IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		1401323
60IPR029071
Ubiquitin-related domain		135243
61IPR001965
Zinc finger, PHD-type		135456
62IPR012340
Nucleic acid-binding, OB-fold		132275
63IPR013101
Leucine-rich repeat 2		130191
64IPR013026
Tetratricopeptide repeat-containing domain		129266
65IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		128825
66IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		126351
67IPR005123
Oxoglutarate/iron-dependent dioxygenase		125363
68IPR006501
Pectinesterase inhibitor		125679
69IPR015300
DNA-binding pseudobarrel domain		125751
70IPR005225
Small GTP-binding protein domain		124159
71IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		123227
72IPR020683
Ankyrin repeat-containing domain		121924
73IPR003959
ATPase, AAA-type, core		120202
74IPR000008
C2 calcium-dependent membrane targeting		1181149
75IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		118378
76IPR003439
ABC transporter-like		118593
77IPR019734
Tetratricopeptide repeat		1171391
78IPR003441
No apical meristem (NAM) protein		115511
79IPR001623
DnaJ domain		1151231
80IPR013830
SGNH hydrolase-type esterase domain		114467
81IPR003340
B3 DNA binding domain		112992
82IPR002100
Transcription factor, MADS-box		1101205
83IPR013187
F-box associated domain, type 3		109127
84IPR015916
Galactose oxidase, beta-propeller		108125
85IPR006652
Kelch repeat type 1		108380
86IPR002110
Ankyrin repeat		1081246
87IPR027443
Isopenicillin N synthase-like		107178
88IPR001087
Lipase, GDSL		105146
89IPR011011
Zinc finger, FYVE/PHD-type		105237
90IPR020472
G-protein beta WD-40 repeat		103438
91IPR014710
RmlC-like jelly roll fold		102190
92IPR011333
BTB/POZ fold		101166
93IPR026992
Non-haem dioxygenase N-terminal domain		97139
94IPR001356
Homeobox domain		97371
95IPR008974
TRAF-like		97377
96IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		95159
97IPR017907
Zinc finger, RING-type, conserved site		95152
98IPR000073
Alpha/beta hydrolase fold-1		94339
99IPR013785
Aldolase-type TIM barrel		93192
100IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		92150
101IPR015424
Pyridoxal phosphate-dependent transferase		92161
102IPR000626
Ubiquitin domain		91447
103IPR017871
ABC transporter, conserved site		91191
104IPR011043
Galactose oxidase/kelch, beta-propeller		91121
105IPR008972
Cupredoxin		90485
106IPR032867
DYW domain		90105
107IPR002347
Glucose/ribitol dehydrogenase		891368
108IPR008502
Prolamin-like domain		8991
109IPR013766
Thioredoxin domain		86229
110IPR006447
Myb domain, plants		86135
111IPR000270
Phox/Bem1p		86216
112IPR011713
Leucine-rich repeat 3		86239
113IPR002902
Gnk2-homologous domain		85556
114IPR011993
Pleckstrin homology-like domain		85279
115IPR023393
START-like domain		84133
116IPR010255
Haem peroxidase		83110
117IPR001806
Small GTPase superfamily		83113
118IPR019786
Zinc finger, PHD-type, conserved site		82160
119IPR009072
Histone-fold		82204
120IPR001932
Protein phosphatase 2C (PP2C)-like		82870
121IPR002016
Haem peroxidase, plant/fungal/bacterial		81671
122IPR000225
Armadillo		81944
123IPR002083
MATH/TRAF domain		78472
124IPR003676
Auxin responsive SAUR protein		7884
125IPR015880
Zinc finger, C2H2-like		77360
126IPR015655
Protein phosphatase 2C		76225
127IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		76132
128IPR000210
BTB/POZ domain		75292
129IPR024788
Malectin-like carbohydrate-binding domain		74120
130IPR004827
Basic-leucine zipper domain		74442
131IPR000571
Zinc finger, CCCH-type		741083
132IPR003657
DNA-binding WRKY		73715
133IPR011051
RmlC-like cupin domain		73117
134IPR000823
Plant peroxidase		73740
135IPR021109
Aspartic peptidase		72339
136IPR023213
Chloramphenicol acetyltransferase-like domain		72145
137IPR005828
General substrate transporter		71128
138IPR006121
Heavy metal-associated domain, HMA		70313
139IPR019793
Peroxidases heam-ligand binding site		7081
140IPR033121
Peptidase family A1 domain		70118
141IPR001461
Peptidase A1		70323
142IPR029052
Metallo-dependent phosphatase-like		70276
143IPR000048
IQ motif, EF-hand binding site		70943
144IPR003960
ATPase, AAA-type, conserved site		69100
145IPR019787
Zinc finger, PHD-finger		68225
146IPR010987
Glutathione S-transferase, C-terminal-like		68261
147IPR000070
Pectinesterase, catalytic		6880
148IPR004843
Metallophosphoesterase domain		67108
149IPR020568
Ribosomal protein S5 domain 2-type fold		67126
150IPR000743
Glycoside hydrolase, family 28		67139
151IPR012946
X8 domain		66182
152IPR027640
Kinesin-like protein		65431
153IPR032799
Xylanase inhibitor, C-terminal		6591
154IPR015915
Kelch-type beta propeller		65117
155IPR003613
U box domain		65253
156IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		64147
157IPR032861
Xylanase inhibitor, N-terminal		6495
158IPR010264
Plant self-incompatibility S1		6466
159IPR004045
Glutathione S-transferase, N-terminal		63155
160IPR003480
Transferase		6368
161IPR006626
Parallel beta-helix repeat		62363
162IPR013763
Cyclin-like		62512
163IPR008979
Galactose-binding domain-like		62288
164IPR001752
Kinesin, motor domain		611027
165IPR018108
Mitochondrial substrate/solute carrier		59487
166IPR019794
Peroxidase, active site		5965
167IPR023395
Mitochondrial carrier domain		59178
168IPR005174
Protein of unknown function DUF295		5865
169IPR015500
Peptidase S8, subtilisin-related		58326
170IPR016135
Ubiquitin-conjugating enzyme/RWD-like		57199
171IPR005829
Sugar transporter, conserved site		57157
172IPR002528
Multi antimicrobial extrusion protein		57254
173IPR023828
Peptidase S8, subtilisin, Ser-active site		5677
174IPR000209
Peptidase S8/S53 domain		56450
175IPR014014
RNA helicase, DEAD-box type, Q motif		5579
176IPR001878
Zinc finger, CCHC-type		55525
177IPR008949
Terpenoid synthase		54158
178IPR001563
Peptidase S10, serine carboxypeptidase		54607
179IPR016181
Acyl-CoA N-acyltransferase		54189
180IPR010259
Proteinase inhibitor I9		54117
181IPR001220
Legume lectin domain		5467
182IPR000109
Proton-dependent oligopeptide transporter family		53149
183IPR018253
DnaJ domain, conserved site		5380
184IPR003663
Sugar/inositol transporter		53479
185IPR016166
FAD-binding, type 2		52139
186IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5271
187IPR008978
HSP20-like chaperone		51121
188IPR019821
Kinesin, motor region, conserved site		51110
189IPR009060
UBA-like		5194
190IPR000490
Glycoside hydrolase, family 17		51124
191IPR004314
Domain of unknown function DUF239		5158
192IPR001229
Mannose-binding lectin		50988
193IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		50188
194IPR001480
Bulb-type lectin domain		49540
195IPR017877
Myb-like domain		4985
196IPR000608
Ubiquitin-conjugating enzyme, E2		48163
197IPR008250
P-type ATPase, A domain		48166
198IPR029055
Nucleophile aminohydrolases, N-terminal		48147
199IPR033131
Pectinesterase, Asp active site		4855
200IPR008928
Six-hairpin glycosidase-like		4886
201IPR023299
P-type ATPase, cytoplasmic domain N		48144
202IPR001757
Cation-transporting P-type ATPase		48276
203IPR030184
WAT1-related protein		48104
204IPR002109
Glutaredoxin		48114
205IPR001214
SET domain		48231
206IPR001360
Glycoside hydrolase, family 1		47611
207IPR026057
PC-Esterase		4774
208IPR004864
Late embryogenesis abundant protein, LEA-14		4752
209IPR025521
Domain of unknown function DUF4409		4753
210IPR018303
P-type ATPase, phosphorylation site		4771
211IPR014756
Immunoglobulin E-set		4797
212IPR000620
Drug/metabolite transporter		47142
213IPR011032
GroES-like		46165
214IPR013057
Amino acid transporter, transmembrane		4669
215IPR011527
ABC transporter, transmembrane domain, type 1		46466
216IPR025846
PMR5 N-terminal domain		4669
217IPR033389
AUX/IAA domain		4588
218IPR029962
Trichome birefringence-like family		4589
219IPR000873
AMP-dependent synthetase/ligase		4569
220IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4575
221IPR008942
ENTH/VHS		44117
222IPR006016
UspA		4464
223IPR003245
Plastocyanin-like		44156
224IPR006094
FAD linked oxidase, N-terminal		4457
225IPR004883
Lateral organ boundaries, LOB		4390
226IPR017970
Homeobox, conserved site		4361
227IPR016167
FAD-binding, type 2, subdomain 1		4358
228IPR001789
Signal transduction response regulator, receiver domain		43180
229IPR002921
Lipase, class 3		4266
230IPR010851
S locus-related glycoprotein 1 binding pollen coat		4242
231IPR003609
Apple-like		42286
232IPR006045
Cupin 1		42134
233IPR002219
Protein kinase C-like, phorbol ester/diacylglycerol binding		42185
234IPR006671
Cyclin, N-terminal		42131
235IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		4275
236IPR015947
PUA-like domain		4281
237IPR001117
Multicopper oxidase, type 1		4159
238IPR006153
Cation/H+ exchanger		4152
239IPR013525
ABC-2 type transporter		4194
240IPR004853
Domain of unknown function DUF250		4171
241IPR010920
Like-Sm (LSM) domain		4161
242IPR011701
Major facilitator superfamily		4186
243IPR000330
SNF2-related		4192
244IPR003137
Protease-associated domain, PA		4158
245IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4168
246IPR026961
PGG domain		4171
247IPR022742
Alpha/beta hydrolase, N-terminal		4168
248IPR003594
Histidine kinase-like ATPase, ATP-binding domain		41236
249IPR004839
Aminotransferase, class I/classII		4165
250IPR011006
CheY-like superfamily		4169
251IPR019378
GDP-fucose protein O-fucosyltransferase		4153
252IPR011706
Multicopper oxidase, type 2		4159
253IPR031127
E3 ubiquitin ligase RBR family		4159
254IPR011042
Six-bladed beta-propeller, TolB-like		4171
255IPR010402
CCT domain		40118
256IPR013783
Immunoglobulin-like fold		4083
257IPR006553
Leucine-rich repeat, cysteine-containing subtype		40325
258IPR002495
Glycosyl transferase, family 8		4058
259IPR016159
Cullin repeat-like-containing domain		4069
260IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4088
261IPR002487
Transcription factor, K-box		40223
262IPR002867
Zinc finger, C6HC-type		39180
263IPR011016
Zinc finger, RING-CH-type		39159
264IPR004263
Exostosin-like		3955
265IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		3963
266IPR020845
AMP-binding, conserved site		3961
267IPR002035
von Willebrand factor, type A		39172
268IPR002067
Mitochondrial carrier protein		39268
269IPR011707
Multicopper oxidase, type 3		3956
270IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3946
271IPR003614
Knottin		3991
272IPR032710
NTF2-like domain		38118
273IPR002068
Alpha crystallin/Hsp20 domain		3872
274IPR013216
Methyltransferase type 11		3847
275IPR009009
Barwin-related endoglucanase		38165
276IPR023271
Aquaporin-like		38112
277IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		3854
278IPR011012
Longin-like domain		3851
279IPR000182
GNAT domain		37104
280IPR000858
S-locus glycoprotein		3790
281IPR013149
Alcohol dehydrogenase, C-terminal		3763
282IPR001969
Peptidase aspartic, active site		37108
283IPR007112
Expansin/pollen allergen, DPBB domain		37105
284IPR020904
Short-chain dehydrogenase/reductase, conserved site		3753
285IPR005746
Thioredoxin		3757
286IPR000425
Major intrinsic protein		37435
287IPR000727
Target SNARE coiled-coil domain		36143
288IPR024171
S-receptor-like serine/threonine-protein kinase		3671
289IPR001509
NAD-dependent epimerase/dehydratase		3657
290IPR005135
Endonuclease/exonuclease/phosphatase		36323
291IPR003690
Mitochodrial transcription termination factor-related		36373
292IPR007125
Histone core		3638
293IPR029045
ClpP/crotonase-like domain		36151
294IPR008801
Rapid ALkalinization Factor		3636
295IPR004088
K Homology domain, type 1		36506
296IPR000668
Peptidase C1A, papain C-terminal		36191
297IPR003851
Zinc finger, Dof-type		36188
298IPR002913
START domain		36160
299IPR001251
CRAL-TRIO domain		35322
300IPR007118
Expansin/Lol pI		35277
301IPR013128
Peptidase C1A, papain		3545
302IPR016039
Thiolase-like		35222
303IPR001849
Pleckstrin homology domain		35138
304IPR007117
Expansin, cellulose-binding-like domain		35201
305IPR015797
NUDIX hydrolase domain-like		35148
306IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3446
307IPR000315
Zinc finger, B-box		34190
308IPR005202
Transcription factor GRAS		3486
309IPR002912
ACT domain		34167
310IPR012341
Six-hairpin glycosidase		3451
311IPR018490
Cyclic nucleotide-binding-like		3362
312IPR025287
Wall-associated receptor kinase galacturonan-binding domain		3342
313IPR029000
Cyclophilin-like domain		33106
314IPR008991
Translation protein SH3-like domain		3342
315IPR005630
Terpene synthase, metal-binding domain		3349
316IPR016455
Xyloglucan endotransglucosylase/hydrolase		3339
317IPR027356
NPH3 domain		33120
318IPR003406
Glycosyl transferase, family 14		3350
319IPR017937
Thioredoxin, conserved site		3358
320IPR000644
Cystathionine beta-synthase, core		33252
321IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3341
322IPR000757
Glycoside hydrolase, family 16		3384
323IPR025110
Domain of unknown function DUF4009		3240
324IPR025659
Tubby C-terminal-like domain		3258
325IPR023313
Ubiquitin-conjugating enzyme, active site		3254
326IPR022357
Major intrinsic protein, conserved site		3248
327IPR029062
Class I glutamine amidotransferase-like		32140
328IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3253
329IPR000595
Cyclic nucleotide-binding domain		32163
330IPR008889
VQ		3238
331IPR005175
Domain of unknown function DUF296		3272
332IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		31155
333IPR001929
Germin		31113
334IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		31255
335IPR012675
Beta-grasp domain		3144
336IPR011074
CRAL/TRIO, N-terminal domain		31126
337IPR004367
Cyclin, C-terminal domain		3191
338IPR001906
Terpene synthase, N-terminal domain		3191
339IPR006073
GTP binding domain		31124
340IPR017927
Ferredoxin reductase-type FAD-binding domain		3055
341IPR017938
Riboflavin synthase-like beta-barrel		3054
342IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		30123
343IPR013088
Zinc finger, NHR/GATA-type		3034
344IPR029021
Protein-tyrosine phosphatase-like		30136
345IPR013201
Proteinase inhibitor I29, cathepsin propeptide		3073
346IPR001296
Glycosyl transferase, family 1		3041
347IPR025886
Phloem protein 2-like		3040
348IPR011013
Galactose mutarotase-like domain		3081
349IPR005821
Ion transport domain		3057
350IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3074
351IPR000086
NUDIX hydrolase domain		30120
352IPR014720
Double-stranded RNA-binding domain		30184
353IPR020843
Polyketide synthase, enoylreductase		3040
354IPR018202
Peptidase S10, serine carboxypeptidase, active site		3045
355IPR000679
Zinc finger, GATA-type		30133
356IPR006594
LisH dimerisation motif		29113
357IPR008480
Protein of unknown function DUF761, plant		2930
358IPR027923
Hydrophobic seed protein		2932
359IPR000916
Bet v I domain		2985
360IPR003311
AUX/IAA protein		2954
361IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		29151
362IPR001487
Bromodomain		29362
363IPR025322
Protein of unknown function DUF4228		2831
364IPR018957
Zinc finger, C3HC4 RING-type		2849
365IPR000795
Elongation factor, GTP-binding domain		28215
366IPR013154
Alcohol dehydrogenase GroES-like		2847
367IPR015813
Pyruvate/Phosphoenolpyruvate kinase		28108
368IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2847
369IPR004087
K Homology domain		28126
370IPR000169
Cysteine peptidase, cysteine active site		2836
371IPR023298
P-type ATPase, transmembrane domain		28100
372IPR025660
Cysteine peptidase, histidine active site		2832
373IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		2770
374IPR012951
Berberine/berberine-like		2733
375IPR001279
Beta-lactamase-like		27193
376IPR008265
Lipase, GDSL, active site		2736
377IPR003822
Paired amphipathic helix		27341
378IPR010989
t-SNARE		2744
379IPR004265
Plant disease resistance response protein		2729
380IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2740
381IPR004014
Cation-transporting P-type ATPase, N-terminal		2771
382IPR020946
Flavin monooxygenase-like		2764
383IPR031107
Small heat shock protein HSP20		2729
384IPR001701
Glycoside hydrolase, family 9		2738
385IPR004158
Protein of unknown function DUF247, plant		2743
386IPR004274
NLI interacting factor		27115
387IPR004041
NAF domain		2640
388IPR000782
FAS1 domain		26170
389IPR024709
O-fucosyltransferase, plant		2636
390IPR018451
NAF/FISL domain		2639
391IPR001163
Ribonucleoprotein LSM domain		2670
392IPR002022
Pectate lyase/Amb allergen		2668
393IPR005150
Cellulose synthase		2653
394IPR022796
Chlorophyll A-B binding protein		2636
395IPR029006
ADF-H/Gelsolin-like domain		26100
396IPR025661
Cysteine peptidase, asparagine active site		2629
397IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		26375
398IPR018082
AmbAllergen		26236
399IPR029060
PIN domain-like		25112
400IPR000528
Plant lipid transfer protein/Par allergen		25142
401IPR019956
Ubiquitin subgroup		2592
402IPR005299
SAM dependent carboxyl methyltransferase		2543
403IPR029061
Thiamin diphosphate-binding fold		25132
404IPR001938
Thaumatin		25444
405IPR029056
Ribokinase-like		2589
406IPR024768
Meiosis arrest female protein 1		2544
407IPR014002
Tudor-like, plant		25108
408IPR002963
Expansin		25294
409IPR014722
Ribosomal protein L2 domain 2		2532
410IPR004046
Glutathione S-transferase, C-terminal		2533
411IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2544
412IPR019780
Germin, manganese binding site		2530
413IPR001313
Pumilio RNA-binding repeat		25590
414IPR013809
Epsin-like, N-terminal		2571
415IPR029033
Histidine phosphatase superfamily		25162
416IPR017884
SANT domain		2439
417IPR006689
Small GTPase superfamily, ARF/SAR type		24137
418IPR025753
AAA-type ATPase, N-terminal domain		2430
419IPR003954
RNA recognition motif domain, eukaryote		2457
420IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2473
421IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2434
422IPR027725
Heat shock transcription factor family		2432
423IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2466
424IPR005333
Transcription factor, TCP		2431
425IPR017887
Transcription factor TCP subgroup		2430
426IPR001353
Proteasome, subunit alpha/beta		2435
427IPR000408
Regulator of chromosome condensation, RCC1		24995
428IPR006459
Uncharacterised protein family UPF0497, trans-membrane plant subgroup		2426
429IPR001876
Zinc finger, RanBP2-type		24304
430IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2445
431IPR025486
Domain of unknown function DUF4378		2440
432IPR000232
Heat shock factor (HSF)-type, DNA-binding		24145
433IPR023329
Chlorophyll a/b binding protein domain		2439
434IPR033133
Pumilio homology domain		2331
435IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2385
436IPR021820
S-locus receptor kinase, C-terminal		2351
437IPR002423
Chaperonin Cpn60/TCP-1		2338
438IPR004140
Exocyst complex protein Exo70		2356
439IPR012552
DVL		2323
440IPR033275
E3 ubiquitin-protein ligase MARCH-like		2357
441IPR016021
MIF4-like, type 1/2/3		2348
442IPR006379
HAD-superfamily hydrolase, subfamily IIB		2336
443IPR027409
GroEL-like apical domain		2375
444IPR014044
CAP domain		2393
445IPR006012
Syntaxin/epimorphin, conserved site		2338
446IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2340
447IPR001944
Glycoside hydrolase, family 35		23361
448IPR000195
Rab-GTPase-TBC domain		23315
449IPR003388
Reticulon		2385
450IPR007527
Zinc finger, SWIM-type		2376
451IPR010682
Plant self-incompatibility response		2324
452IPR021139
NYN domain, limkain-b1-type		2337
453IPR006703
AIG1-type guanine nucleotide-binding (G) domain		2362
454IPR025558
Domain of unknown function DUF4283		2323
455IPR010525
Auxin response factor		2342
456IPR007502
Helicase-associated domain		2268
457IPR006195
Aminoacyl-tRNA synthetase, class II		2232
458IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2224
459IPR019954
Ubiquitin conserved site		2265
460IPR007493
Protein of unknown function DUF538		2278
461IPR008984
SMAD/FHA domain		2242
462IPR009071
High mobility group (HMG) box domain		22192
463IPR000253
Forkhead-associated (FHA) domain		22123
464IPR026960
Reverse transcriptase zinc-binding domain		2225
465IPR001478
PDZ domain		22140
466IPR006462
Protein of unknown function DUF626, Arabidopsis thaliana		2262
467IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		2259
468IPR033124
Serine carboxypeptidases, histidine active site		2227
469IPR017926
Glutamine amidotransferase type 1		2262
470IPR011332
Ribosomal protein, zinc-binding domain		2224
471IPR013078
Histidine phosphatase superfamily, clade-1		2274
472IPR029057
Phosphoribosyltransferase-like		22103
473IPR001283
Allergen V5/Tpx-1-related		22116
474IPR025875
Leucine rich repeat 4		2244
475IPR001232
SKP1 component		2224
476IPR029069
HotDog domain		2280
477IPR015425
Actin-binding FH2		22107
478IPR013094
Alpha/beta hydrolase fold-3		2224
479IPR018097
EGF-like calcium-binding, conserved site		2226
480IPR023210
NADP-dependent oxidoreductase domain		22106
481IPR011709
Domain of unknown function DUF1605		2230
482IPR001041
2Fe-2S ferredoxin-type domain		2274
483IPR001395
Aldo/keto reductase		2248
484IPR025610
Transcription factor MYC/MYB N-terminal		2239
485IPR013601
FAE1/Type III polyketide synthase-like protein		2125
486IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2147
487IPR003106
Leucine zipper, homeobox-associated		2139
488IPR001357
BRCT domain		21297
489IPR003347
JmjC domain		21101
490IPR008422
Homeobox KN domain		2130
491IPR002659
Glycosyl transferase, family 31		2165
492IPR001763
Rhodanese-like domain		21207
493IPR018289
MULE transposase domain		2135
494IPR008266
Tyrosine-protein kinase, active site		2140
495IPR001025
Bromo adjacent homology (BAH) domain		21123
496IPR016072
SKP1 component, dimerisation		2144
497IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		2197
498IPR017923
Transcription factor IIS, N-terminal		2181
499IPR006595
CTLH, C-terminal LisH motif		2194
500IPR011905
Glutaredoxin-like, plant II		2122
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris.html b/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris.html new file mode 100644 index 00000000..8e934c60 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris.html @@ -0,0 +1,67 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:RefBeet-1.2.2, Jul 2015
Database version:86.2
Base Pairs:517,420,803
Golden Path Length:566,181,630
Genebuild by: EnsemblPlants
Genebuild method: Generated from ENA annotation
Genebuild started: Jan 2014
Genebuild released: Jan 2014
Genebuild last updated/patched: Jul 2015
Genebuild version: 2015-07-ENA
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		26,521
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:28,721
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
9 sequences
+
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+ + + +
SequenceLength (bp)
134941034
240393389
326577699
433024243
552461754
660962716
744152522
838796167
945274173
+
+
supercontig40405 sequences
contig71207 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris_IPtop500.html new file mode 100644 index 00000000..ec158175 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Beta_vulgaris_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		9865874
2IPR011009
Protein kinase-like domain		8322054
3IPR000719
Protein kinase domain		7564036
4IPR011990
Tetratricopeptide-like helical domain		5903946
5IPR032675
Leucine-rich repeat domain, L domain-like		5543948
6IPR008271
Serine/threonine-protein kinase, active site		5211134
7IPR017441
Protein kinase, ATP binding site		4811060
8IPR002885
Pentatricopeptide repeat		46824418
9IPR013083
Zinc finger, RING/FYVE/PHD-type		4601108
10IPR013320
Concanavalin A-like lectin/glucanase domain		4231166
11IPR016024
Armadillo-type fold		3201596
12IPR016040
NAD(P)-binding domain		3041486
13IPR001611
Leucine-rich repeat		3023834
14IPR001841
Zinc finger, RING-type		2861444
15IPR001810
F-box domain		2671636
16IPR015943
WD40/YVTN repeat-like-containing domain		266932
17IPR029058
Alpha/Beta hydrolase fold		2621416
18IPR009057
Homeodomain-like		2621302
19IPR011989
Armadillo-like helical		2541086
20IPR017986
WD40-repeat-containing domain		2521316
21IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		2471428
22IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		234820
23IPR012677
Nucleotide-binding alpha-beta plait domain		2311646
24IPR003593
AAA+ ATPase domain		228654
25IPR001680
WD40 repeat		2215078
26IPR012336
Thioredoxin-like fold		2161082
27IPR020846
Major facilitator superfamily domain		214912
28IPR000504
RNA recognition motif domain		2062236
29IPR001128
Cytochrome P450		1932118
30IPR017853
Glycoside hydrolase superfamily		191482
31IPR012337
Ribonuclease H-like domain		191716
32IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		187408
33IPR020683
Ankyrin repeat-containing domain		1672098
34IPR001005
SANT/Myb domain		159876
35IPR002110
Ankyrin repeat		1572706
36IPR003591
Leucine-rich repeat, typical subtype		1562278
37IPR013781
Glycoside hydrolase, catalytic domain		152362
38IPR011991
Winged helix-turn-helix DNA-binding domain		150580
39IPR002401
Cytochrome P450, E-class, group I		1461578
40IPR014710
RmlC-like jelly roll fold		145338
41IPR023214
HAD-like domain		143862
42IPR019775
WD40 repeat, conserved site		135514
43IPR011992
EF-hand domain pair		131686
44IPR002182
NB-ARC		128280
45IPR014001
Helicase superfamily 1/2, ATP-binding domain		128604
46IPR001650
Helicase, C-terminal		127910
47IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		127726
48IPR013026
Tetratricopeptide repeat-containing domain		124346
49IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		1231164
50IPR017930
Myb domain		118388
51IPR002048
EF-hand domain		1151518
52IPR023753
FAD/NAD(P)-binding domain		1141024
53IPR003439
ABC transporter-like		114654
54IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		113304
55IPR005123
Oxoglutarate/iron-dependent dioxygenase		111436
56IPR019734
Tetratricopeptide repeat		1101846
57IPR002016
Haem peroxidase, plant/fungal/bacterial		1101498
58IPR010255
Haem peroxidase		110232
59IPR012340
Nucleic acid-binding, OB-fold		109328
60IPR018247
EF-Hand 1, calcium-binding site		108500
61IPR027443
Isopenicillin N synthase-like		104234
62IPR017972
Cytochrome P450, conserved site		104216
63IPR011051
RmlC-like cupin domain		103232
64IPR016177
DNA-binding domain		102258
65IPR011050
Pectin lyase fold/virulence factor		102216
66IPR012334
Pectin lyase fold		102214
67IPR007087
Zinc finger, C2H2		99612
68IPR029044
Nucleotide-diphospho-sugar transferases		98490
69IPR003959
ATPase, AAA-type, core		98252
70IPR013785
Aldolase-type TIM barrel		95256
71IPR029071
Ubiquitin-related domain		94244
72IPR005225
Small GTP-binding protein domain		93200
73IPR000823
Plant peroxidase		931630
74IPR011011
Zinc finger, FYVE/PHD-type		92236
75IPR015424
Pyridoxal phosphate-dependent transferase		92210
76IPR001623
DnaJ domain		911364
77IPR026992
Non-haem dioxygenase N-terminal domain		91192
78IPR013830
SGNH hydrolase-type esterase domain		91562
79IPR001878
Zinc finger, CCHC-type		911024
80IPR000008
C2 domain		901408
81IPR001471
AP2/ERF domain		891162
82IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		87190
83IPR020472
G-protein beta WD-40 repeat		85552
84IPR017451
F-box associated interaction domain		82174
85IPR019793
Peroxidases heam-ligand binding site		81168
86IPR017871
ABC transporter, conserved site		81210
87IPR011545
DEAD/DEAH box helicase domain		81202
88IPR032867
DYW domain		81164
89IPR021109
Aspartic peptidase domain		80424
90IPR006045
Cupin 1		80372
91IPR001087
GDSL lipase/esterase		78172
92IPR019794
Peroxidase, active site		77158
93IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		75342
94IPR005828
Major facilitator, sugar transporter-like		74176
95IPR000571
Zinc finger, CCCH-type		731394
96IPR008972
Cupredoxin		71558
97IPR023213
Chloramphenicol acetyltransferase-like domain		71258
98IPR001965
Zinc finger, PHD-type		71232
99IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		69150
100IPR015300
DNA-binding pseudobarrel domain		69442
101IPR013766
Thioredoxin domain		66278
102IPR010987
Glutathione S-transferase, C-terminal-like		66416
103IPR001929
Germin		65388
104IPR011993
PH domain-like		64274
105IPR001932
PPM-type phosphatase domain		64806
106IPR003480
Transferase		64134
107IPR000225
Armadillo		641060
108IPR003340
B3 DNA binding domain		63614
109IPR002347
Short-chain dehydrogenase/reductase SDR		631266
110IPR000073
Alpha/beta hydrolase fold-1		62304
111IPR023395
Mitochondrial carrier domain		62304
112IPR000626
Ubiquitin domain		61422
113IPR023393
START-like domain		61134
114IPR002902
Gnk2-homologous domain		61516
115IPR018108
Mitochondrial substrate/solute carrier		61752
116IPR017907
Zinc finger, RING-type, conserved site		61134
117IPR009072
Histone-fold		60252
118IPR026057
PC-Esterase		59130
119IPR019787
Zinc finger, PHD-finger		59226
120IPR019786
Zinc finger, PHD-type, conserved site		58148
121IPR020568
Ribosomal protein S5 domain 2-type fold		58164
122IPR011333
SKP1/BTB/POZ domain		58136
123IPR029962
Trichome birefringence-like family		57150
124IPR026961
PGG domain		57126
125IPR001461
Aspartic peptidase A1 family		57342
126IPR029052
Metallo-dependent phosphatase-like		57306
127IPR001356
Homeobox domain		57348
128IPR004045
Glutathione S-transferase, N-terminal		56228
129IPR003960
ATPase, AAA-type, conserved site		55126
130IPR015655
Protein phosphatase 2C family		55188
131IPR033121
Peptidase family A1 domain		55138
132IPR016181
Acyl-CoA N-acyltransferase		54268
133IPR003441
NAC domain		54356
134IPR000270
PB1 domain		54196
135IPR015880
Zinc finger, C2H2-like		54326
136IPR004843
Calcineurin-like phosphoesterase domain, apaH type		53112
137IPR008978
HSP20-like chaperone		53230
138IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		52116
139IPR000109
Proton-dependent oligopeptide transporter family		52232
140IPR013057
Amino acid transporter, transmembrane domain		52110
141IPR003613
U box domain		52346
142IPR001806
Small GTPase superfamily		52114
143IPR001752
Kinesin motor domain		51986
144IPR006121
Heavy metal-associated domain, HMA		50360
145IPR000210
BTB/POZ domain		50262
146IPR006447
Myb domain, plants		50120
147IPR027640
Kinesin-like protein		50376
148IPR018253
DnaJ domain, conserved site		50108
149IPR006501
Pectinesterase inhibitor domain		49464
150IPR001480
Bulb-type lectin domain		49558
151IPR008979
Galactose-binding domain-like		48260
152IPR025846
PMR5 N-terminal domain		48104
153IPR004827
Basic-leucine zipper domain		48388
154IPR003676
Small auxin-up RNA		4896
155IPR032799
Xylanase inhibitor, C-terminal		47102
156IPR016135
Ubiquitin-conjugating enzyme/RWD-like		47190
157IPR005829
Sugar transporter, conserved site		47184
158IPR014014
RNA helicase, DEAD-box type, Q motif		46100
159IPR032861
Xylanase inhibitor, N-terminal		46100
160IPR002528
Multi antimicrobial extrusion protein		46268
161IPR011527
ABC transporter type 1, transmembrane domain		46478
162IPR003657
WRKY domain		46584
163IPR000490
Glycoside hydrolase family 17		46146
164IPR002068
Alpha crystallin/Hsp20 domain		45176
165IPR015500
Peptidase S8, subtilisin-related		45318
166IPR001214
SET domain		45266
167IPR000048
IQ motif, EF-hand binding site		45650
168IPR011032
GroES-like		44180
169IPR011701
Major facilitator superfamily		4496
170IPR003594
Histidine kinase-like ATPase, C-terminal domain		44380
171IPR002100
Transcription factor, MADS-box		44906
172IPR023299
P-type ATPase, cytoplasmic domain N		44184
173IPR008250
P-type ATPase, A domain		43188
174IPR000742
EGF-like domain		43272
175IPR003663
Sugar/inositol transporter		43530
176IPR000743
Glycoside hydrolase, family 28		43160
177IPR018490
Cyclic nucleotide-binding-like		4296
178IPR000873
AMP-dependent synthetase/ligase		4296
179IPR013763
Cyclin-like		42512
180IPR018303
P-type ATPase, phosphorylation site		4288
181IPR001757
P-type ATPase		42298
182IPR002109
Glutaredoxin		42172
183IPR014756
Immunoglobulin E-set		4298
184IPR009009
RlpA-like protein, double-psi beta-barrel domain		41234
185IPR000070
Pectinesterase, catalytic		4182
186IPR000209
Peptidase S8/S53 domain		41442
187IPR016039
Thiolase-like		40374
188IPR003656
Zinc finger, BED-type		40220
189IPR000595
Cyclic nucleotide-binding domain		40230
190IPR000182
GNAT domain		39156
191IPR006626
Parallel beta-helix repeat		39398
192IPR010920
LSM domain		3980
193IPR008906
HAT, C-terminal dimerisation domain		3984
194IPR029055
Nucleophile aminohydrolases, N-terminal		39168
195IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		39136
196IPR000863
Sulfotransferase domain		3982
197IPR013094
Alpha/beta hydrolase fold-3		3986
198IPR000330
SNF2-related, N-terminal domain		3898
199IPR016166
FAD-binding, type 2		38156
200IPR008928
Six-hairpin glycosidase-like		3898
201IPR004088
K Homology domain, type 1		38600
202IPR009060
UBA-like		37108
203IPR000608
Ubiquitin-conjugating enzyme E2		37148
204IPR009000
Translation protein, beta-barrel domain		3788
205IPR005162
Retrotransposon gag domain		3774
206IPR011006
CheY-like superfamily		37110
207IPR031107
Small heat shock protein HSP20		3780
208IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		3798
209IPR006566
FBD domain		37130
210IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		3778
211IPR006073
GTP binding domain		37192
212IPR001789
Signal transduction response regulator, receiver domain		37280
213IPR019821
Kinesin motor domain, conserved site		3694
214IPR005135
Endonuclease/exonuclease/phosphatase		36280
215IPR012946
X8 domain		36148
216IPR007112
Expansin/pollen allergen, DPBB domain		36122
217IPR002035
von Willebrand factor, type A		36242
218IPR000644
CBS domain		36356
219IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3686
220IPR006016
UspA		3578
221IPR025525
hAT-like transposase, RNase-H fold		3574
222IPR003245
Phytocyanin domain		35200
223IPR002085
Alcohol dehydrogenase superfamily, zinc-type		3590
224IPR015947
PUA-like domain		3598
225IPR015916
Galactose oxidase, beta-propeller		3486
226IPR001563
Peptidase S10, serine carboxypeptidase		34356
227IPR023828
Peptidase S8, subtilisin, Ser-active site		3472
228IPR020845
AMP-binding, conserved site		3480
229IPR011706
Multicopper oxidase, type 2		3470
230IPR001117
Multicopper oxidase, type 1		3368
231IPR008949
Isoprenoid synthase domain		33138
232IPR013525
ABC-2 type transporter		3394
233IPR004853
Sugar phosphate transporter domain		3368
234IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		33108
235IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		3372
236IPR006553
Leucine-rich repeat, cysteine-containing subtype		33544
237IPR004864
Late embryogenesis abundant protein, LEA-14		3370
238IPR029045
ClpP/crotonase-like domain		33182
239IPR011043
Galactose oxidase/kelch, beta-propeller		3380
240IPR024752
Myb/SANT-like domain		3372
241IPR002487
Transcription factor, K-box		33184
242IPR011707
Multicopper oxidase, type 3		3366
243IPR017877
Myb-like domain		3394
244IPR029021
Protein-tyrosine phosphatase-like		32204
245IPR013783
Immunoglobulin-like fold		3280
246IPR004839
Aminotransferase, class I/classII		3266
247IPR011012
Longin-like domain		3266
248IPR016167
FAD-binding, type 2, subdomain 1		3268
249IPR006094
FAD linked oxidase, N-terminal		3266
250IPR002067
Mitochondrial carrier protein		32326
251IPR016161
Aldehyde/histidinol dehydrogenase		3274
252IPR014720
Double-stranded RNA-binding domain		32328
253IPR002912
ACT domain		32160
254IPR011042
Six-bladed beta-propeller, TolB-like		3298
255IPR000757
Glycoside hydrolase family 16		32128
256IPR000727
Target SNARE coiled-coil homology domain		31160
257IPR007118
Expansin/Lol pI		31330
258IPR008991
Translation protein SH3-like domain		3164
259IPR001969
Aspartic peptidase, active site		31100
260IPR004263
Exostosin-like		3172
261IPR019378
GDP-fucose protein O-fucosyltransferase		3170
262IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3162
263IPR015915
Kelch-type beta propeller		3180
264IPR007117
Expansin, cellulose-binding-like domain		31248
265IPR015590
Aldehyde dehydrogenase domain		3172
266IPR013149
Alcohol dehydrogenase, C-terminal		3060
267IPR027806
Harbinger transposase-derived nuclease domain		3062
268IPR001881
EGF-like calcium-binding domain		30152
269IPR016455
Xyloglucan endotransglucosylase/hydrolase		3060
270IPR033131
Pectinesterase, Asp active site		3060
271IPR000222
PPM-type phosphatase, divalent cation binding		3074
272IPR000916
Bet v I/Major latex protein		30104
273IPR004087
K Homology domain		30150
274IPR001229
Jacalin-like lectin domain		30414
275IPR016163
Aldehyde dehydrogenase, C-terminal		3068
276IPR002921
Fungal lipase-like domain		2962
277IPR008942
ENTH/VHS		29126
278IPR000858
S-locus glycoprotein domain		2962
279IPR016461
O-methyltransferase COMT-type		29106
280IPR001251
CRAL-TRIO lipid binding domain		29276
281IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2964
282IPR013216
Methyltransferase type 11		2964
283IPR003609
PAN/Apple domain		29134
284IPR011013
Galactose mutarotase-like domain		2986
285IPR008480
Protein of unknown function DUF761, plant		2958
286IPR005746
Thioredoxin		2978
287IPR001849
Pleckstrin homology domain		29132
288IPR000620
EamA domain		29108
289IPR025558
Domain of unknown function DUF4283		2960
290IPR020904
Short-chain dehydrogenase/reductase, conserved site		2858
291IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		2872
292IPR001077
O-methyltransferase, family 2		2860
293IPR005202
Transcription factor GRAS		28112
294IPR006671
Cyclin, N-terminal		28124
295IPR018097
EGF-like calcium-binding, conserved site		2858
296IPR012341
Six-hairpin glycosidase		2866
297IPR033389
AUX/IAA domain		2762
298IPR032710
NTF2-like domain		2790
299IPR023271
Aquaporin-like		27108
300IPR013154
Alcohol dehydrogenase, N-terminal		2754
301IPR006652
Kelch repeat type 1		27220
302IPR003690
Transcription termination factor, mitochondrial/chloroplastic		27398
303IPR005174
Domain unknown function DUF295		2760
304IPR000425
Major intrinsic protein		27452
305IPR001220
Legume lectin domain		2756
306IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2796
307IPR030184
WAT1-related protein		2764
308IPR028889
Ubiquitin specific protease domain		2768
309IPR016162
Aldehyde dehydrogenase N-terminal domain		2764
310IPR006594
LIS1 homology motif		26110
311IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		26366
312IPR029000
Cyclophilin-like domain		26122
313IPR003137
PA domain		2654
314IPR001296
Glycosyl transferase, family 1		2660
315IPR025836
Zinc knuckle CX2CX4HX4C		2656
316IPR020103
Pseudouridine synthase, catalytic domain		2690
317IPR005821
Ion transport domain		2658
318IPR022357
Major intrinsic protein, conserved site		2652
319IPR004046
Glutathione S-transferase, C-terminal		2654
320IPR017937
Thioredoxin, conserved site		2662
321IPR002495
Glycosyl transferase, family 8		2656
322IPR007527
Zinc finger, SWIM-type		26106
323IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		26172
324IPR011016
Zinc finger, RING-CH-type		25118
325IPR019557
Aminotransferase-like, plant mobile domain		2552
326IPR002423
Chaperonin Cpn60/TCP-1 family		2550
327IPR000795
Transcription factor, GTP-binding domain		25288
328IPR010989
t-SNARE		2556
329IPR004265
Plant disease resistance response protein		2550
330IPR022742
Serine aminopeptidase, S33		2566
331IPR000152
EGF-type aspartate/asparagine hydroxylation site		2552
332IPR014044
CAP domain		25188
333IPR014722
Ribosomal protein L2 domain 2		2552
334IPR023298
P-type ATPase, transmembrane domain		25110
335IPR012967
Plant methyltransferase dimerisation		2552
336IPR004274
FCP1 homology domain		25156
337IPR006689
Small GTPase superfamily, ARF/SAR type		24222
338IPR025110
AMP-binding enzyme C-terminal domain		2456
339IPR019956
Ubiquitin		24132
340IPR006153
Cation/H+ exchanger		2450
341IPR018200
Ubiquitin specific protease, conserved site		24104
342IPR001279
Metallo-beta-lactamase		24190
343IPR001938
Thaumatin		24514
344IPR012675
Beta-grasp domain		2448
345IPR003406
Glycosyl transferase, family 14		2450
346IPR008263
Glycoside hydrolase, family 16, active site		2448
347IPR007125
Histone H2A/H2B/H3		2448
348IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		2460
349IPR024788
Malectin-like carbohydrate-binding domain		2450
350IPR015797
NUDIX hydrolase domain-like		2498
351IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		24106
352IPR006702
Domain of unknown function DUF588		2448
353IPR003614
Knottin, scorpion toxin-like		24132
354IPR010402
CCT domain		23112
355IPR011065
Kunitz inhibitor ST1-like		2346
356IPR006904
Protein of unknown function DUF716 (TMEM45)		2368
357IPR001024
PLAT/LH2 domain		23194
358IPR001305
Heat shock protein DnaJ, cysteine-rich domain		23132
359IPR001357
BRCT domain		23350
360IPR000253
Forkhead-associated (FHA) domain		23152
361IPR004320
Protein of unknown function DUF241, plant		2346
362IPR027356
NPH3 domain		2396
363IPR031052
FHY3/FAR1 family		2362
364IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		23112
365IPR004883
Lateral organ boundaries, LOB		2392
366IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		23212
367IPR017970
Homeobox, conserved site		2350
368IPR001876
Zinc finger, RanBP2-type		23492
369IPR029069
HotDog domain		23142
370IPR029062
Class I glutamine amidotransferase-like		23124
371IPR016159
Cullin repeat-like-containing domain		2364
372IPR016197
Chromo domain-like		2368
373IPR002160
Proteinase inhibitor I3, Kunitz legume		23190
374IPR015940
Ubiquitin-associated domain		22210
375IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		22118
376IPR029061
Thiamin diphosphate-binding fold		22170
377IPR001478
PDZ domain		22170
378IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2280
379IPR004312
Arabidopsis retrotransposon Orf1		2246
380IPR011074
CRAL/TRIO, N-terminal domain		22116
381IPR005150
Cellulose synthase		2266
382IPR027409
GroEL-like apical domain		2288
383IPR004158
Protein of unknown function DUF247, plant		2244
384IPR000086
NUDIX hydrolase domain		2280
385IPR020843
Polyketide synthase, enoylreductase domain		2244
386IPR008889
VQ		2244
387IPR006527
F-box associated domain, type 1		2246
388IPR025322
Protein of unknown function DUF4228, plant		2144
389IPR017938
Riboflavin synthase-like beta-barrel		2154
390IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		21114
391IPR024709
O-fucosyltransferase, plant		2148
392IPR029510
Aldehyde dehydrogenase, glutamic acid active site		2144
393IPR001163
LSM domain, eukaryotic/archaea-type		2182
394IPR004014
Cation-transporting P-type ATPase, N-terminal		2180
395IPR023313
Ubiquitin-conjugating enzyme, active site		2142
396IPR022796
Chlorophyll A-B binding protein		2144
397IPR033443
Pentacotripeptide-repeat region of PROPR		2150
398IPR019780
Germin, manganese binding site		2142
399IPR013780
Glycosyl hydrolase, all-beta		2146
400IPR003851
Zinc finger, Dof-type		21174
401IPR023210
NADP-dependent oxidoreductase domain		21188
402IPR001487
Bromodomain		21362
403IPR002937
Amine oxidase		2156
404IPR029033
Histidine phosphatase superfamily		21136
405IPR023329
Chlorophyll a/b binding protein domain		2148
406IPR001395
Aldo/keto reductase/potassium channel subunit beta		2194
407IPR017927
Ferredoxin reductase-type FAD-binding domain		2046
408IPR017884
SANT domain		2050
409IPR029060
PIN domain-like		2080
410IPR002156
Ribonuclease H domain		2044
411IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2040
412IPR008984
SMAD/FHA domain		2048
413IPR003347
JmjC domain		20116
414IPR024171
S-receptor-like serine/threonine-protein kinase		2040
415IPR004161
Translation elongation factor EFTu-like, domain 2		2042
416IPR006564
Zinc finger, PMZ-type		2046
417IPR001763
Rhodanese-like domain		20192
418IPR000408
Regulator of chromosome condensation, RCC1		20838
419IPR002293
Amino acid/polyamine transporter I		20152
420IPR001025
Bromo adjacent homology (BAH) domain		20140
421IPR008963
Purple acid phosphatase-like, N-terminal		2042
422IPR000668
Peptidase C1A, papain C-terminal		20178
423IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		2048
424IPR015914
Purple acid phosphatase, N-terminal		2084
425IPR011905
Glutaredoxin-like, plant II		2040
426IPR004330
FAR1 DNA binding domain		2046
427IPR018202
Serine carboxypeptidase, serine active site		2042
428IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		1970
429IPR000953
Chromo/chromo shadow domain		1998
430IPR001440
Tetratricopeptide repeat 1		1958
431IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1942
432IPR013128
Peptidase C1A		1940
433IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		1940
434IPR029472
Gag-polypeptide of LTR copia-type		1938
435IPR001353
Proteasome, subunit alpha/beta		1938
436IPR027413
GroEL-like equatorial domain		1970
437IPR029056
Ribokinase-like		1996
438IPR002355
Multicopper oxidase, copper-binding site		1940
439IPR002123
Phospholipid/glycerol acyltransferase		1986
440IPR013078
Histidine phosphatase superfamily, clade-1		1972
441IPR002963
Expansin		19326
442IPR004776
Membrane transport protein		1942
443IPR000169
Cysteine peptidase, cysteine active site		1938
444IPR003616
Post-SET domain		1966
445IPR004147
UbiB domain		1946
446IPR013126
Heat shock protein 70 family		19250
447IPR029006
ADF-H/Gelsolin-like domain		1970
448IPR016138
Ribosome-inactivating protein, subdomain 1		1938
449IPR005175
PPC domain		1976
450IPR001574
Ribosome-inactivating protein		1976
451IPR007502
Helicase-associated domain		1880
452IPR000528
Plant lipid transfer protein/Par allergen		18176
453IPR004041
NAF domain		1836
454IPR013601
FAE1/Type III polyketide synthase-like protein		1836
455IPR025659
Tubby C-terminal-like domain		1840
456IPR006195
Aminoacyl-tRNA synthetase, class II		1836
457IPR001360
Glycoside hydrolase family 1		18304
458IPR033138
Multicopper oxidases, conserved site		1838
459IPR007493
Protein of unknown function DUF538		18114
460IPR018451
NAF/FISL domain		1836
461IPR003854
Gibberellin regulated protein		1840
462IPR005299
SAM dependent carboxyl methyltransferase		1838
463IPR000315
B-box-type zinc finger		18158
464IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		1880
465IPR005630
Terpene synthase, metal-binding domain		1838
466IPR023346
Lysozyme-like domain		1836
467IPR013816
ATP-grasp fold, subdomain 2		1844
468IPR004367
Cyclin, C-terminal domain		18100
469IPR004252
Probable transposase, Ptta/En/Spm, plant		1838
470IPR016021
MIF4G-like domain		1872
471IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		1838
472IPR003008
Tubulin/FtsZ, GTPase domain		18146
473IPR008266
Tyrosine-protein kinase, active site		1842
474IPR003107
HAT (Half-A-TPR) repeat		18250
475IPR027923
Hydrophobic seed protein		1836
476IPR001701
Glycoside hydrolase family 9		1838
477IPR003311
AUX/IAA protein		1852
478IPR010658
Nodulin-like		1846
479IPR011709
Domain of unknown function DUF1605		1840
480IPR008974
TRAF-like		1884
481IPR024156
Small GTPase superfamily, ARF type		1840
482IPR022764
Peptidase S54, rhomboid domain		1776
483IPR021133
HEAT, type 2		1790
484IPR004000
Actin family		17240
485IPR000782
FAS1 domain		17220
486IPR008971
HSP40/DnaJ peptide-binding		1796
487IPR013328
6-phosphogluconate dehydrogenase, domain 2		1742
488IPR013187
F-box associated domain, type 3		1738
489IPR032872
Wall-associated receptor kinase, C-terminal		1738
490IPR018499
Tetraspanin/Peripherin		1734
491IPR013201
Cathepsin propeptide inhibitor domain (I29)		1768
492IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		1734
493IPR001344
Chlorophyll A-B binding protein, plant		1740
494IPR027725
Heat shock transcription factor family		1740
495IPR033124
Serine carboxypeptidases, histidine active site		1736
496IPR011332
Zinc-binding ribosomal protein		1734
497IPR029057
Phosphoribosyltransferase-like		17104
498IPR006685
Mechanosensitive ion channel MscS		1738
499IPR003604
Zinc finger, U1-type		1758
500IPR001906
Terpene synthase, N-terminal domain		1772
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon.html b/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon.html new file mode 100644 index 00000000..c6e59682 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon.html @@ -0,0 +1,132 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Brachypodium_distachyon_v3.0,
Database version:87.4
Base Pairs:270,739,461
Golden Path Length:271,163,419
Genebuild by: 23
Genebuild method: Generated from ENA annotation
Genebuild started: Feb 2010
Genebuild released: Feb 2010
Genebuild last updated/patched: Jan 2018
Genebuild version: 2018-01ENA
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		34,310
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:52,972
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
5 sequences
+
+ +
+ + + +
SequenceLength (bp)
175071545
259130575
359640145
448594894
528630136
+
+
supercontig
+
14 sequences
+
+ +
+ + + +
SequenceLength (bp)
Bd1_centromere_containing_Bradi1g4143046184
KZ62296137944854
KZ62296237026691
KZ62296328806913
KZ62296430223662
KZ62296525257007
KZ62296634283138
KZ62296720746583
KZ62296827748311
KZ62296928630136
KZ62297123566
KZ62297220560
KZ6229733881
KZ6229741933
+
+
contig
+
35 sequences
+
+ +
+ + + +
SequenceLength (bp)
ADDN03000001.137944854
ADDN03000002.137026691
ADDN03000003.146184
ADDN03000004.128806913
ADDN03000005.17768011
ADDN03000006.122455551
ADDN03000007.15784013
ADDN03000008.15572341
ADDN03000009.111559585
ADDN03000010.12340768
ADDN03000011.16773729
ADDN03000012.121988513
ADDN03000013.13495206
ADDN03000014.12015490
ADDN03000015.14338684
ADDN03000016.1213136
ADDN03000017.11511003
ADDN03000018.15851646
ADDN03000019.18362613
ADDN03000020.185982
ADDN03000021.11361
ADDN03000022.1380649
ADDN03000023.12496173
ADDN03000024.12614295
ADDN03000025.13877062
ADDN03000026.11279736
ADDN03000027.114353953
ADDN03000028.13116692
ADDN03000029.17099263
ADDN03000030.1633545
ADDN03000031.120895879
ADDN03000032.123566
ADDN03000033.120560
ADDN03000034.13881
ADDN03000035.11933
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon_IPtop500.html new file mode 100644 index 00000000..27a83b3e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brachypodium_distachyon_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		13212578
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		12803463
3IPR000719
 		126517286
4IPR032675
 		10166172
5IPR008271
Serine/threonine-protein kinase, active site		10011808
6IPR017441
Protein kinase, ATP binding site		8821602
7IPR036047
F-box-like domain superfamily		7881130
8IPR013083
 		7402950
9IPR011990
 		71213992
10IPR001810
 		5304155
11IPR002885
 		48135222
12IPR001841
 		4793584
13IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		4071157
14IPR029058
 		4002826
15IPR009057
Homeobox-like domain superfamily		375692
16IPR001611
 		3749237
17IPR016024
Armadillo-type fold		3551903
18IPR036291
NAD(P)-binding domain superfamily		349626
19IPR002182
NB-ARC		340655
20IPR003593
AAA+ ATPase domain		293731
21IPR035979
RNA-binding domain superfamily		293877
22IPR012677
 		2871902
23IPR036396
 		2702205
24IPR000504
 		2707770
25IPR001128
Cytochrome P450		2641464
26IPR001005
SANT/Myb domain		2631512
27IPR036259
MFS transporter superfamily		254779
28IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		252381
29IPR015943
 		2512337
30IPR036249
Thioredoxin-like superfamily		248397
31IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		242639
32IPR003591
Leucine-rich repeat, typical subtype		2412487
33IPR036322
WD40-repeat-containing domain superfamily		236791
34IPR002401
Cytochrome P450, E-class, group I		2321868
35IPR001680
 		23114793
36IPR011989
 		2301328
37IPR017853
Glycoside hydrolase superfamily		229384
38IPR017972
Cytochrome P450, conserved site		224286
39IPR038005
Virus X resistance protein-like, coiled-coil domain		212350
40IPR038765
Papain-like cysteine peptidase superfamily		209461
41IPR017986
 		2081470
42IPR017930
 		204974
43IPR011333
SKP1/BTB/POZ domain superfamily		203297
44IPR020846
 		1851162
45IPR000210
 		1831926
46IPR008974
 		1811260
47IPR016177
DNA-binding domain superfamily		180353
48IPR001471
 		1674347
49IPR036955
 		167867
50IPR036691
 		1661188
51IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		165186
52IPR036638
 		1611518
53IPR011992
EF-hand domain pair		161263
54IPR013087
 		1603255
55IPR031052
FHY3/FAR1 family		157284
56IPR011598
 		1572730
57IPR012337
Ribonuclease H-like superfamily		156300
58IPR036388
 		154574
59IPR002016
 		1543585
60IPR010255
Haem peroxidase		154185
61IPR014001
 		1541310
62IPR002048
 		1514827
63IPR036390
Winged helix DNA-binding domain superfamily		150256
64IPR001650
 		1492574
65IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		149240
66IPR012340
Nucleic acid-binding, OB-fold		146406
67IPR036412
HAD-like superfamily		146452
68IPR000823
Plant peroxidase		1441314
69IPR029044
 		1431154
70IPR019775
WD40 repeat, conserved site		143502
71IPR036236
Zinc finger C2H2 superfamily		141325
72IPR019793
Peroxidases heam-ligand binding site		140160
73IPR002083
 		1381374
74IPR018247
EF-Hand 1, calcium-binding site		137462
75IPR036188
 		1371710
76IPR020683
 		1372118
77IPR036093
 		1371134
78IPR036770
 		1371438
79IPR003441
 		1361119
80IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		135147
81IPR002110
 		1336087
82IPR023214
 		132868
83IPR033905
Secretory peroxidase		131146
84IPR035595
UDP-glycosyltransferase family, conserved site		128148
85IPR036397
 		127603
86IPR036514
 		126330
87IPR003959
ATPase, AAA-type, core		125247
88IPR011011
Zinc finger, FYVE/PHD-type		124291
89IPR003439
 		1242289
90IPR019734
 		1235601
91IPR008972
 		120998
92IPR013026
 		120954
93IPR004330
FAR1 DNA binding domain		119185
94IPR014729
 		117458
95IPR019794
Peroxidase, active site		117130
96IPR029071
Ubiquitin-like domain superfamily		116238
97IPR023213
 		114478
98IPR036869
 		113728
99IPR018289
MULE transposase domain		112162
100IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		112178
101IPR001087
GDSL lipase/esterase		111144
102IPR034090
BPM, C-terminal		107117
103IPR005123
 		106831
104IPR014710
 		106374
105IPR001623
 		1052138
106IPR007527
 		104717
107IPR005225
Small GTP-binding protein domain		102147
108IPR024752
Myb/SANT-like domain		101112
109IPR009072
 		101747
110IPR001878
 		1012424
111IPR005174
Domain unknown function DUF295		99115
112IPR003480
Transferase		99110
113IPR013785
 		98483
114IPR035669
GDSL lipase/esterase-like, plant		97120
115IPR017871
ABC transporter, conserved site		97249
116IPR015424
Pyridoxal phosphate-dependent transferase		97153
117IPR036875
Zinc finger, CCHC-type superfamily		97213
118IPR026960
Reverse transcriptase zinc-binding domain		96101
119IPR001356
 		961956
120IPR036426
 		95634
121IPR021109
 		94662
122IPR017907
Zinc finger, RING-type, conserved site		94169
123IPR015300
 		941344
124IPR035892
 		93540
125IPR036457
 		93734
126IPR011676
Domain of unknown function DUF1618		93130
127IPR001461
Aspartic peptidase A1 family		93278
128IPR015421
 		92408
129IPR027443
 		92256
130IPR036282
Glutathione S-transferase, C-terminal domain superfamily		92114
131IPR001965
Zinc finger, PHD-type		92343
132IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		91133
133IPR006447
Myb domain, plants		91163
134IPR011545
DEAD/DEAH box helicase domain		91175
135IPR001932
 		912085
136IPR003340
 		903765
137IPR032867
DYW domain		90136
138IPR036576
 		891020
139IPR000073
Alpha/beta hydrolase fold-1		89265
140IPR003657
 		891518
141IPR001480
 		89780
142IPR024171
S-receptor-like serine/threonine-protein kinase		88165
143IPR000626
 		871449
144IPR000008
 		871520
145IPR002347
Short-chain dehydrogenase/reductase SDR		87824
146IPR020472
G-protein beta WD-40 repeat		87552
147IPR006566
FBD domain		86126
148IPR004827
 		861608
149IPR011050
Pectin lyase fold/virulence factor		85114
150IPR004045
 		84585
151IPR036908
 		84348
152IPR005828
Major facilitator, sugar transporter-like		83193
153IPR033121
 		83218
154IPR012334
 		83222
155IPR032861
Xylanase inhibitor, N-terminal		8298
156IPR000109
Proton-dependent oligopeptide transporter family		81296
157IPR032799
Xylanase inhibitor, C-terminal		8095
158IPR002100
 		801917
159IPR010987
 		80192
160IPR011051
RmlC-like cupin domain superfamily		80105
161IPR015422
 		80525
162IPR036879
 		80621
163IPR026992
Non-haem dioxygenase N-terminal domain		78108
164IPR000270
 		78816
165IPR003609
 		77640
166IPR025315
Domain of unknown function DUF4220		77116
167IPR015655
Protein phosphatase 2C family		76148
168IPR029466
No apical meristem-associated, C-terminal domain		7581
169IPR017451
F-box associated interaction domain		75104
170IPR001563
Peptidase S10, serine carboxypeptidase		74553
171IPR003960
ATPase, AAA-type, conserved site		74133
172IPR006121
 		73837
173IPR036163
Heavy metal-associated domain superfamily		73119
174IPR000571
 		732475
175IPR000858
S-locus glycoprotein domain		72114
176IPR007658
Protein of unknown function DUF594		72103
177IPR019787
 		72550
178IPR003245
 		71642
179IPR013783
 		70314
180IPR013766
 		70615
181IPR011993
 		69282
182IPR006564
Zinc finger, PMZ-type		68108
183IPR005829
Sugar transporter, conserved site		68193
184IPR001220
Legume lectin domain		68173
185IPR019786
Zinc finger, PHD-type, conserved site		67136
186IPR003613
 		671068
187IPR035513
 		66260
188IPR036749
 		66276
189IPR016135
 		66566
190IPR036961
 		66681
191IPR007117
 		66276
192IPR000225
 		662499
193IPR038408
 		65372
194IPR002902
 		65738
195IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		6478
196IPR012871
Protein of unknown function DUF1677, Oryza sativa		6480
197IPR036852
 		641053
198IPR006501
Pectinesterase inhibitor domain		64152
199IPR000209
Peptidase S8/S53 domain		6483
200IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		63110
201IPR000742
 		63492
202IPR005202
 		63312
203IPR015500
Peptidase S8, subtilisin-related		63238
204IPR026961
PGG domain		62179
205IPR007112
 		62246
206IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6268
207IPR008979
 		61508
208IPR036915
Cyclin-like superfamily		61172
209IPR013094
Alpha/beta hydrolase fold-3		6165
210IPR003676
Small auxin-up RNA		6161
211IPR037045
 		61148
212IPR007118
Expansin/Lol pI		60367
213IPR009009
RlpA-like protein, double-psi beta-barrel domain		6063
214IPR005135
Endonuclease/exonuclease/phosphatase		60108
215IPR022059
Protein of unknown function DUF3615		60114
216IPR003663
Sugar/inositol transporter		60507
217IPR001806
Small GTPase superfamily		6079
218IPR001881
EGF-like calcium-binding domain		59119
219IPR020568
Ribosomal protein S5 domain 2-type fold		59127
220IPR029052
 		59196
221IPR034197
Cucumisin-like catalytic domain		5875
222IPR000490
Glycoside hydrolase family 17		58129
223IPR018097
EGF-like calcium-binding, conserved site		5789
224IPR000048
 		572712
225IPR036640
 		561473
226IPR000608
 		56660
227IPR003653
 		56435
228IPR018108
 		561168
229IPR011527
 		561449
230IPR023395
 		56466
231IPR004158
Protein of unknown function DUF247, plant		5688
232IPR027640
Kinesin-like protein		55162
233IPR001752
 		552805
234IPR004265
Dirigent protein		5458
235IPR013057
Amino acid transporter, transmembrane domain		5493
236IPR030184
WAT1-related protein		5486
237IPR017877
 		54280
238IPR014014
 		53164
239IPR006045
Cupin 1		53138
240IPR036465
 		53312
241IPR015915
 		53543
242IPR000620
EamA domain		53141
243IPR016039
 		52675
244IPR001214
 		521179
245IPR003137
PA domain		5166
246IPR023828
Peptidase S8, subtilisin, Ser-active site		5169
247IPR018253
DnaJ domain, conserved site		5177
248IPR036855
Zinc finger, CCCH-type superfamily		51206
249IPR002528
Multi antimicrobial extrusion protein		50253
250IPR004046
Glutathione S-transferase, C-terminal		5062
251IPR011042
 		50260
252IPR026057
PC-Esterase		4983
253IPR038718
 		49310
254IPR009003
Peptidase S1, PA clan		49139
255IPR016181
Acyl-CoA N-acyltransferase		4882
256IPR013128
Peptidase C1A		4868
257IPR000330
SNF2-related, N-terminal domain		48132
258IPR000873
AMP-dependent synthetase/ligase		4880
259IPR001938
 		48748
260IPR011006
CheY-like superfamily		4872
261IPR001789
 		48825
262IPR011032
GroES-like superfamily		47101
263IPR001509
NAD-dependent epimerase/dehydratase		4767
264IPR009000
Translation protein, beta-barrel domain superfamily		4770
265IPR025846
PMR5 N-terminal domain		4772
266IPR011706
Multicopper oxidase, type 2		4758
267IPR036318
FAD-binding, type 2-like superfamily		4665
268IPR012946
X8 domain		46132
269IPR006553
Leucine-rich repeat, cysteine-containing subtype		46654
270IPR013763
Cyclin-like		46223
271IPR017970
Homeobox, conserved site		4689
272IPR008978
 		45234
273IPR011701
Major facilitator superfamily		4586
274IPR029962
Trichome birefringence-like family		4574
275IPR023393
 		45144
276IPR000222
PPM-type phosphatase, divalent cation binding		4582
277IPR000668
Peptidase C1A, papain C-terminal		45237
278IPR002109
 		45315
279IPR023298
P-type ATPase, transmembrane domain superfamily		45259
280IPR024788
Malectin-like carbohydrate-binding domain		4574
281IPR011707
Multicopper oxidase, type 3		4551
282IPR002921
Fungal lipase-like domain		4474
283IPR001117
Multicopper oxidase, type 1		4454
284IPR008250
P-type ATPase, A domain superfamily		44111
285IPR029055
 		44230
286IPR016166
 		44183
287IPR001757
P-type ATPase		44279
288IPR013201
Cathepsin propeptide inhibitor domain (I29)		43108
289IPR008928
Six-hairpin glycosidase superfamily		4398
290IPR007125
Histone H2A/H2B/H3		4347
291IPR020845
AMP-binding, conserved site		4372
292IPR018303
P-type ATPase, phosphorylation site		4388
293IPR023299
 		43507
294IPR014756
Immunoglobulin E-set		43109
295IPR000743
Glycoside hydrolase, family 28		4386
296IPR033389
AUX/IAA domain		4299
297IPR008942
 		42276
298IPR000182
 		42224
299IPR033896
MADS MEF2-like		4267
300IPR036890
 		42400
301IPR011043
Galactose oxidase/kelch, beta-propeller		4269
302IPR002912
 		42330
303IPR012341
 		42207
304IPR025558
Domain of unknown function DUF4283		4246
305IPR008949
 		41364
306IPR013525
ABC-2 type transporter		41105
307IPR004162
E3 ubiquitin-protein ligase SIN-like		4169
308IPR036612
 		41876
309IPR016159
Cullin repeat-like-containing domain superfamily		4175
310IPR003690
Transcription termination factor, mitochondrial/chloroplastic		40357
311IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		40107
312IPR028889
 		40214
313IPR009060
UBA-like superfamily		3985
314IPR029021
 		39296
315IPR001969
Aspartic peptidase, active site		3970
316IPR011012
Longin-like domain superfamily		3966
317IPR006094
FAD linked oxidase, N-terminal		3945
318IPR010402
 		38399
319IPR025322
Protein of unknown function DUF4228, plant		3842
320IPR004853
Sugar phosphate transporter domain		3877
321IPR033124
Serine carboxypeptidases, histidine active site		3850
322IPR020904
Short-chain dehydrogenase/reductase, conserved site		3846
323IPR038538
 		38142
324IPR006671
Cyclin, N-terminal		3893
325IPR018202
Serine carboxypeptidase, serine active site		3859
326IPR019956
Ubiquitin		37130
327IPR001929
Germin		37111
328IPR006626
Parallel beta-helix repeat		37257
329IPR022742
Serine aminopeptidase, S33		3762
330IPR003594
Histidine kinase/HSP90-like ATPase		37147
331IPR000644
 		37870
332IPR008889
VQ		3737
333IPR014721
 		37156
334IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		37131
335IPR006016
UspA		3646
336IPR018200
Ubiquitin specific protease, conserved site		36149
337IPR015947
PUA-like superfamily		3696
338IPR037176
 		36168
339IPR001360
Glycoside hydrolase family 1		35394
340IPR019821
Kinesin motor domain, conserved site		3596
341IPR013149
Alcohol dehydrogenase, C-terminal		3562
342IPR007493
Protein of unknown function DUF538		3589
343IPR000152
EGF-type aspartate/asparagine hydroxylation site		3566
344IPR036758
 		35178
345IPR029045
ClpP/crotonase-like domain superfamily		3561
346IPR019378
GDP-fucose protein O-fucosyltransferase		3591
347IPR000169
Cysteine peptidase, cysteine active site		3543
348IPR025660
Cysteine peptidase, histidine active site		3540
349IPR002487
 		35357
350IPR006073
GTP binding domain		35155
351IPR027214
Cystatin		3439
352IPR002068
 		34176
353IPR011016
 		34891
354IPR013216
Methyltransferase type 11		3455
355IPR004263
Exostosin-like		3457
356IPR002355
Multicopper oxidase, copper-binding site		3441
357IPR004839
Aminotransferase, class I/classII		3454
358IPR004088
K Homology domain, type 1		34161
359IPR004087
K Homology domain		34168
360IPR002495
Glycosyl transferase, family 8		3459
361IPR013780
 		34128
362IPR006458
 		34200
363IPR006702
Casparian strip membrane protein domain		3440
364IPR032710
NTF2-like domain superfamily		3346
365IPR010920
LSM domain superfamily		3355
366IPR002659
Glycosyl transferase, family 31		3394
367IPR000795
 		33894
368IPR023271
 		33154
369IPR034294
Aquaporin transporter		3339
370IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		3341
371IPR008480
Protein of unknown function DUF761, plant		3334
372IPR000425
Major intrinsic protein		33281
373IPR016040
NAD(P)-binding domain		3242
374IPR013187
F-box associated domain, type 3		3250
375IPR038933
Ovate protein family		3239
376IPR013154
Alcohol dehydrogenase, N-terminal		3257
377IPR008266
Tyrosine-protein kinase, active site		3254
378IPR003406
Glycosyl transferase, family 14		3241
379IPR023313
Ubiquitin-conjugating enzyme, active site		3255
380IPR002963
Expansin		32274
381IPR002035
 		32252
382IPR000757
 		32222
383IPR000864
Proteinase inhibitor I13, potato inhibitor I		31166
384IPR001251
 		31658
385IPR000717
 		31220
386IPR016455
Xyloglucan endotransglucosylase/hydrolase		3134
387IPR036865
 		31332
388IPR013010
 		31126
389IPR001849
 		31254
390IPR002067
Mitochondrial carrier protein		31299
391IPR013126
Heat shock protein 70 family		31355
392IPR036354
Proteinase inhibitor I13, potato inhibitor I superfamily		3132
393IPR025661
Cysteine peptidase, asparagine active site		3135
394IPR020843
Polyketide synthase, enoylreductase domain		3153
395IPR000070
Pectinesterase, catalytic		3137
396IPR000010
Cystatin domain		3170
397IPR000727
 		30214
398IPR025110
AMP-binding enzyme, C-terminal domain		3046
399IPR004041
NAF domain		3061
400IPR018490
Cyclic nucleotide-binding-like		3064
401IPR002130
 		30915
402IPR025659
 		30152
403IPR029000
 		30212
404IPR033138
Multicopper oxidases, conserved site		3033
405IPR018451
 		30180
406IPR000315
 		30621
407IPR001296
Glycosyl transferase, family 1		3057
408IPR034161
Pepsin-like domain, plant		3034
409IPR001594
Palmitoyltransferase, DHHC domain		3071
410IPR004320
Protein of unknown function DUF241, plant		3032
411IPR038770
 		3068
412IPR011332
Zinc-binding ribosomal protein		3035
413IPR034288
Laccase, first cupredoxin domain		3033
414IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		3058
415IPR004813
Oligopeptide transporter, OPT superfamily		3085
416IPR022357
Major intrinsic protein, conserved site		3032
417IPR000595
 		30410
418IPR036034
PDZ superfamily		3057
419IPR004141
Strictosidine synthase		2939
420IPR036378
 		29162
421IPR006153
Cation/H+ exchanger		2932
422IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2936
423IPR013088
 		29120
424IPR006652
Kelch repeat type 1		29173
425IPR022796
Chlorophyll A-B binding protein		2936
426IPR034285
Laccase, second cupredoxin domain		2935
427IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2974
428IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2934
429IPR003851
 		29468
430IPR009091
 		29356
431IPR000679
 		29420
432IPR002913
 		29426
433IPR010666
Zinc finger, GRF-type		2832
434IPR013601
FAE1/Type III polyketide synthase-like protein		2832
435IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2864
436IPR008991
Translation protein SH3-like domain superfamily		2833
437IPR004140
Exocyst complex component Exo70		2878
438IPR002123
Phospholipid/glycerol acyltransferase		2880
439IPR011013
Galactose mutarotase-like domain superfamily		2843
440IPR000960
Flavin monooxygenase FMO		28181
441IPR004883
 		28184
442IPR033443
Pentacotripeptide-repeat region of PRORP		2863
443IPR003855
Potassium transporter		28163
444IPR005175
 		28258
445IPR000782
 		27202
446IPR024709
Putative O-fucosyltransferase, plant		27136
447IPR036186
Serpin superfamily		2736
448IPR008422
Homeobox KN domain		2754
449IPR002423
Chaperonin Cpn60/TCP-1 family		2748
450IPR007650
 		27152
451IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2772
452IPR027356
 		27240
453IPR000215
Serpin family		2735
454IPR036866
 		27390
455IPR016167
 		27126
456IPR027409
 		27192
457IPR005821
Ion transport domain		2761
458IPR018121
Seven-in-absentia protein, TRAF-like domain		2737
459IPR017937
Thioredoxin, conserved site		2744
460IPR019780
Germin, manganese binding site		2727
461IPR003311
AUX/IAA protein		2762
462IPR004314
Neprosin		2733
463IPR023796
Serpin domain		2764
464IPR010525
Auxin response factor		2759
465IPR017927
 		2699
466IPR017938
Riboflavin synthase-like beta-barrel		2639
467IPR019954
Ubiquitin conserved site		2668
468IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		26144
469IPR023753
FAD/NAD(P)-binding domain		2643
470IPR012675
 		2668
471IPR018181
Heat shock protein 70, conserved site		2668
472IPR031112
AP2-like ethylene-responsive transcription factor		2676
473IPR006694
Fatty acid hydroxylase		2638
474IPR005150
Cellulose synthase		2673
475IPR036273
CRAL/TRIO, N-terminal domain superfamily		2675
476IPR036537
 		26210
477IPR005746
Thioredoxin		2668
478IPR001876
 		26796
479IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2660
480IPR036427
 		26216
481IPR006439
HAD hydrolase, subfamily IA		26138
482IPR005069
Nucleotide-diphospho-sugar transferase		2641
483IPR015797
NUDIX hydrolase-like domain superfamily		2646
484IPR017884
 		25102
485IPR005795
Major pollen allergen Lol pI		25183
486IPR017946
 		25366
487IPR008984
SMAD/FHA domain superfamily		2544
488IPR027725
Heat shock transcription factor family		2554
489IPR009030
Growth factor receptor cysteine-rich domain superfamily		2535
490IPR036010
2Fe-2S ferredoxin-like superfamily		2530
491IPR000408
 		251938
492IPR004367
Cyclin, C-terminal domain		2564
493IPR029062
 		25190
494IPR029047
 		25134
495IPR003100
 		24477
496IPR036085
PAZ domain superfamily		2485
497IPR015940
 		24322
498IPR036965
 		24204
499IPR001357
 		24696
500IPR036420
 		24402
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_napus.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_napus.html new file mode 100644 index 00000000..4f8b6470 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_napus.html @@ -0,0 +1,44 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AST_PRJEB5043_v1, Sep 2015
Database version:86.1
Base Pairs:738,357,821
Golden Path Length:848,200,303
Genebuild by: EnsemblPlants
Genebuild method: Generated from ENA annotation
Genebuild started: Jul 2007
Genebuild released: Jul 2007
Genebuild last updated/patched: Sep 2015
Genebuild version: 2015-09-ENA
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		101,040
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:101,040
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Coordinate Systems

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supercontig20899 sequences
contig44187 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_napus_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_napus_IPtop500.html new file mode 100644 index 00000000..50760b70 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_napus_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		37187996
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		354418472
3IPR000719
Protein kinase domain		344416580
4IPR008271
Serine/threonine-protein kinase, active site		25605172
5IPR032675
Leucine-rich repeat domain, L domain-like		247312604
6IPR013083
Zinc finger, RING/FYVE/PHD-type		21434560
7IPR017441
Protein kinase, ATP binding site		21354300
8IPR001810
F-box domain		176410238
9IPR013320
Concanavalin A-like lectin/glucanase domain		16184322
10IPR009057
Homeodomain-like		15207144
11IPR011990
Tetratricopeptide-like helical domain		13728638
12IPR001841
Zinc finger, RING-type		13576338
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		13293880
14IPR016040
NAD(P)-binding domain		11265250
15IPR001611
Leucine-rich repeat		112511194
16IPR016024
Armadillo-type fold		11104542
17IPR002885
Pentatricopeptide repeat		108743896
18IPR012340
Nucleic acid-binding, OB-fold		10072888
19IPR001005
SANT/Myb domain		9955374
20IPR012677
Nucleotide-binding alpha-beta plait domain		9935882
21IPR029058
Alpha/Beta hydrolase fold		9934756
22IPR011989
Armadillo-like helical		8753092
23IPR015943
WD40/YVTN repeat-like-containing domain		8592766
24IPR000504
RNA recognition motif domain		8507510
25IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		8384254
26IPR003593
AAA+ ATPase domain		8192080
27IPR017986
WD40-repeat-containing domain		8063908
28IPR017930
Myb domain		8042570
29IPR012336
Thioredoxin-like fold		7933536
30IPR001128
Cytochrome P450		7909222
31IPR011991
Winged helix-turn-helix DNA-binding domain		7802674
32IPR020846
Major facilitator superfamily domain		7542834
33IPR001680
WD40 repeat		74715834
34IPR017853
Glycoside hydrolase superfamily		6621424
35IPR011992
EF-hand domain pair		6343172
36IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		6301314
37IPR002401
Cytochrome P450, E-class, group I		6238170
38IPR017451
F-box associated interaction domain		6161266
39IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		6015304
40IPR017972
Cytochrome P450, conserved site		5981202
41IPR013781
Glycoside hydrolase, catalytic domain		5701236
42IPR016177
DNA-binding domain		5681236
43IPR012334
Pectin lyase fold		5561138
44IPR011050
Pectin lyase fold/virulence factor		5551144
45IPR001471
AP2/ERF domain		5406436
46IPR002048
EF-hand domain		5367512
47IPR003591
Leucine-rich repeat, typical subtype		5106498
48IPR012337
Ribonuclease H-like domain		5081652
49IPR018247
EF-Hand 1, calcium-binding site		4992418
50IPR023214
HAD-like domain		4962730
51IPR007087
Zinc finger, C2H2		4923326
52IPR002182
NB-ARC		463966
53IPR029044
Nucleotide-diphospho-sugar transferases		4522036
54IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		4521034
55IPR019775
WD40 repeat, conserved site		4241444
56IPR003441
NAC domain		4212536
57IPR023753
FAD/NAD(P)-binding domain		4023202
58IPR005123
Oxoglutarate/iron-dependent dioxygenase		3971506
59IPR006566
FBD domain		3941406
60IPR005225
Small GTP-binding protein domain		392788
61IPR014001
Helicase superfamily 1/2, ATP-binding domain		3911536
62IPR027443
Isopenicillin N synthase-like		389830
63IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		3863646
64IPR015300
DNA-binding pseudobarrel domain		3862392
65IPR001650
Helicase, C-terminal		3792234
66IPR000008
C2 domain		3724580
67IPR003959
ATPase, AAA-type, core		372860
68IPR029071
Ubiquitin-related domain		359796
69IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		3581672
70IPR015916
Galactose oxidase, beta-propeller		357756
71IPR020683
Ankyrin repeat-containing domain		3532998
72IPR013026
Tetratricopeptide repeat-containing domain		351894
73IPR008972
Cupredoxin		3432434
74IPR001356
Homeobox domain		3421840
75IPR003653
Ulp1 protease family, C-terminal catalytic domain		3411078
76IPR003439
ABC transporter-like		3401912
77IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		3361596
78IPR001623
DnaJ domain		3354710
79IPR006501
Pectinesterase inhibitor domain		3343230
80IPR015424
Pyridoxal phosphate-dependent transferase		334698
81IPR003340
B3 DNA binding domain		3332972
82IPR006652
Kelch repeat type 1		3241770
83IPR019734
Tetratricopeptide repeat		3214706
84IPR006527
F-box associated domain, type 1		321666
85IPR013830
SGNH hydrolase-type esterase domain		3191846
86IPR002100
Transcription factor, MADS-box		3174262
87IPR006447
Myb domain, plants		312624
88IPR002110
Ankyrin repeat		3123814
89IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		311650
90IPR013785
Aldolase-type TIM barrel		308688
91IPR026992
Non-haem dioxygenase N-terminal domain		304608
92IPR001806
Small GTPase superfamily		304636
93IPR020472
G-protein beta WD-40 repeat		2991794
94IPR000270
PB1 domain		296982
95IPR013955
Replication factor A, C-terminal		295594
96IPR014710
RmlC-like jelly roll fold		294698
97IPR010255
Haem peroxidase		294604
98IPR013187
F-box associated domain, type 3		292608
99IPR011011
Zinc finger, FYVE/PHD-type		286692
100IPR003657
WRKY domain		2863356
101IPR001932
PPM-type phosphatase domain		2863146
102IPR002016
Haem peroxidase, plant/fungal/bacterial		2833660
103IPR005828
Major facilitator, sugar transporter-like		282672
104IPR003676
Small auxin-up RNA		281566
105IPR008974
TRAF-like		2731362
106IPR001087
GDSL lipase/esterase		270544
107IPR023393
START-like domain		269564
108IPR002347
Short-chain dehydrogenase/reductase SDR		2674556
109IPR021109
Aspartic peptidase domain		2671528
110IPR015655
Protein phosphatase 2C family		267812
111IPR011333
SKP1/BTB/POZ domain		267578
112IPR004827
Basic-leucine zipper domain		2651896
113IPR015880
Zinc finger, C2H2-like		2641384
114IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		261568
115IPR001965
Zinc finger, PHD-type		258884
116IPR011545
DEAD/DEAH box helicase domain		257540
117IPR023213
Chloramphenicol acetyltransferase-like domain		251836
118IPR001461
Aspartic peptidase A1 family		2511384
119IPR013766
Thioredoxin domain		250950
120IPR000823
Plant peroxidase		2494158
121IPR009072
Histone-fold		246998
122IPR000073
Alpha/beta hydrolase fold-1		245966
123IPR002902
Gnk2-homologous domain		2431820
124IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		239708
125IPR015410
Domain of unknown function DUF1985		238488
126IPR017907
Zinc finger, RING-type, conserved site		238476
127IPR002528
Multi antimicrobial extrusion protein		2351148
128IPR017871
ABC transporter, conserved site		234608
129IPR033121
Peptidase family A1 domain		234522
130IPR029052
Metallo-dependent phosphatase-like		2331048
131IPR016135
Ubiquitin-conjugating enzyme/RWD-like		232926
132IPR019793
Peroxidases heam-ligand binding site		229458
133IPR000048
IQ motif, EF-hand binding site		2282770
134IPR000626
Ubiquitin domain		2231178
135IPR000070
Pectinesterase, catalytic		223462
136IPR013763
Cyclin-like		2222060
137IPR023395
Mitochondrial carrier domain		222944
138IPR006121
Heavy metal-associated domain, HMA		2211342
139IPR003480
Transferase		220470
140IPR027640
Kinesin-like protein		2181082
141IPR000571
Zinc finger, CCCH-type		2183916
142IPR013101
Leucine-rich repeat 2		217478
143IPR000743
Glycoside hydrolase, family 28		216738
144IPR011993
PH domain-like		216872
145IPR000109
Proton-dependent oligopeptide transporter family		214882
146IPR003960
ATPase, AAA-type, conserved site		214458
147IPR018108
Mitochondrial substrate/solute carrier		2122268
148IPR015915
Kelch-type beta propeller		212492
149IPR000225
Armadillo		2113570
150IPR002083
MATH/TRAF domain		2091542
151IPR011713
Leucine-rich repeat 3		209436
152IPR004843
Calcineurin-like phosphoesterase domain, apaH type		207416
153IPR000210
BTB/POZ domain		2071044
154IPR032861
Xylanase inhibitor, N-terminal		207422
155IPR019794
Peroxidase, active site		206412
156IPR010987
Glutathione S-transferase, C-terminal-like		2061132
157IPR001878
Zinc finger, CCHC-type		2052182
158IPR032799
Xylanase inhibitor, C-terminal		204408
159IPR003613
U box domain		2031194
160IPR030184
WAT1-related protein		201408
161IPR000608
Ubiquitin-conjugating enzyme E2		200802
162IPR029055
Nucleophile aminohydrolases, N-terminal		197740
163IPR019786
Zinc finger, PHD-type, conserved site		195448
164IPR011051
RmlC-like cupin domain		195414
165IPR020568
Ribosomal protein S5 domain 2-type fold		192458
166IPR008978
HSP20-like chaperone		190690
167IPR005829
Sugar transporter, conserved site		189588
168IPR024788
Malectin-like carbohydrate-binding domain		189406
169IPR003245
Phytocyanin domain		1831116
170IPR010264
Plant self-incompatibility S1		183370
171IPR001220
Legume lectin domain		182394
172IPR000620
EamA domain		180612
173IPR013057
Amino acid transporter, transmembrane domain		179368
174IPR023299
P-type ATPase, cytoplasmic domain N		178670
175IPR032867
DYW domain		178358
176IPR001360
Glycoside hydrolase family 1		1772128
177IPR019787
Zinc finger, PHD-finger		177638
178IPR008979
Galactose-binding domain-like		177994
179IPR004045
Glutathione S-transferase, N-terminal		177706
180IPR001752
Kinesin motor domain		1762704
181IPR003663
Sugar/inositol transporter		1761832
182IPR025558
Domain of unknown function DUF4283		175350
183IPR005135
Endonuclease/exonuclease/phosphatase		1741038
184IPR002487
Transcription factor, K-box		174686
185IPR002109
Glutaredoxin		171688
186IPR001757
P-type ATPase		1691156
187IPR008250
P-type ATPase, A domain		168712
188IPR014756
Immunoglobulin E-set		168356
189IPR011043
Galactose oxidase/kelch, beta-propeller		167378
190IPR006626
Parallel beta-helix repeat		1661580
191IPR012946
X8 domain		166662
192IPR015500
Peptidase S8, subtilisin-related		1661154
193IPR004146
DC1		1611044
194IPR004314
Domain of unknown function DUF239		161340
195IPR000490
Glycoside hydrolase family 17		159528
196IPR011006
CheY-like superfamily		158346
197IPR003871
Domain of unknown function DUF223		156312
198IPR001789
Signal transduction response regulator, receiver domain		156924
199IPR033131
Pectinesterase, Asp active site		155310
200IPR003851
Zinc finger, Dof-type		1541212
201IPR006016
UspA		153310
202IPR004853
Sugar phosphate transporter domain		153306
203IPR011016
Zinc finger, RING-CH-type		153744
204IPR017970
Homeobox, conserved site		153306
205IPR001563
Peptidase S10, serine carboxypeptidase		1521584
206IPR026057
PC-Esterase		151310
207IPR014014
RNA helicase, DEAD-box type, Q motif		151306
208IPR008949
Isoprenoid synthase domain		150606
209IPR029962
Trichome birefringence-like family		149380
210IPR010920
LSM domain		148304
211IPR018303
P-type ATPase, phosphorylation site		148296
212IPR006671
Cyclin, N-terminal		148446
213IPR000209
Peptidase S8/S53 domain		1481588
214IPR033389
AUX/IAA domain		147332
215IPR004839
Aminotransferase, class I/classII		147304
216IPR018253
DnaJ domain, conserved site		147294
217IPR002495
Glycosyl transferase, family 8		147294
218IPR011012
Longin-like domain		146292
219IPR001480
Bulb-type lectin domain		1461570
220IPR017877
Myb-like domain		146360
221IPR016039
Thiolase-like		1421232
222IPR008928
Six-hairpin glycosidase-like		142326
223IPR009060
UBA-like		141332
224IPR009000
Translation protein, beta-barrel domain		141304
225IPR000425
Major intrinsic protein		1402140
226IPR016181
Acyl-CoA N-acyltransferase		139598
227IPR023271
Aquaporin-like		139552
228IPR009009
RlpA-like protein, double-psi beta-barrel domain		138804
229IPR016166
FAD-binding, type 2		138536
230IPR025521
Domain of unknown function DUF4409		138284
231IPR000668
Peptidase C1A, papain C-terminal		1381050
232IPR003609
PAN/Apple domain		136754
233IPR004864
Late embryogenesis abundant protein, LEA-14		136278
234IPR004883
Lateral organ boundaries, LOB		136540
235IPR008942
ENTH/VHS		134530
236IPR010402
CCT domain		134534
237IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		134434
238IPR025846
PMR5 N-terminal domain		134272
239IPR005174
Domain unknown function DUF295		133268
240IPR011527
ABC transporter type 1, transmembrane domain		1331334
241IPR000873
AMP-dependent synthetase/ligase		132278
242IPR023828
Peptidase S8, subtilisin, Ser-active site		131264
243IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		131264
244IPR006702
Domain of unknown function DUF588		130262
245IPR019821
Kinesin motor domain, conserved site		129258
246IPR003406
Glycosyl transferase, family 14		129270
247IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		129266
248IPR000222
PPM-type phosphatase, divalent cation binding		128256
249IPR023313
Ubiquitin-conjugating enzyme, active site		128256
250IPR019378
GDP-fucose protein O-fucosyltransferase		128260
251IPR016159
Cullin repeat-like-containing domain		128338
252IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		127266
253IPR026960
Reverse transcriptase zinc-binding domain		127254
254IPR007112
Expansin/pollen allergen, DPBB domain		127492
255IPR002067
Mitochondrial carrier protein		1271208
256IPR001117
Multicopper oxidase, type 1		126252
257IPR013128
Peptidase C1A		126258
258IPR011706
Multicopper oxidase, type 2		126254
259IPR013088
Zinc finger, NHR/GATA-type		125250
260IPR008991
Translation protein SH3-like domain		125260
261IPR029045
ClpP/crotonase-like domain		125616
262IPR001251
CRAL-TRIO lipid binding domain		1241172
263IPR001214
SET domain		124658
264IPR011707
Multicopper oxidase, type 3		124250
265IPR004263
Exostosin-like		123250
266IPR015947
PUA-like domain		123324
267IPR001229
Jacalin-like lectin domain		1232492
268IPR006153
Cation/H+ exchanger		122258
269IPR013525
ABC-2 type transporter		122312
270IPR013783
Immunoglobulin-like fold		122268
271IPR000679
Zinc finger, GATA-type		122962
272IPR002913
START domain		122654
273IPR007118
Expansin/Lol pI		1211336
274IPR006553
Leucine-rich repeat, cysteine-containing subtype		1211716
275IPR005175
PPC domain		121480
276IPR002068
Alpha crystallin/Hsp20 domain		120416
277IPR003594
Histidine kinase-like ATPase, C-terminal domain		120918
278IPR007117
Expansin, cellulose-binding-like domain		120950
279IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		119652
280IPR015797
NUDIX hydrolase domain-like		119478
281IPR000858
S-locus glycoprotein domain		118238
282IPR008502
Prolamin-like domain		118242
283IPR008889
VQ		118236
284IPR002423
Chaperonin Cpn60/TCP-1 family		116240
285IPR022742
Serine aminopeptidase, S33		116236
286IPR004088
K Homology domain, type 1		1161682
287IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		115446
288IPR011032
GroES-like		114468
289IPR025836
Zinc knuckle CX2CX4HX4C		114246
290IPR004367
Cyclin, C-terminal domain		114422
291IPR002921
Fungal lipase-like domain		113230
292IPR001969
Aspartic peptidase, active site		113324
293IPR006094
FAD linked oxidase, N-terminal		113228
294IPR011042
Six-bladed beta-propeller, TolB-like		113296
295IPR025322
Protein of unknown function DUF4228, plant		112224
296IPR000863
Sulfotransferase domain		112262
297IPR022357
Major intrinsic protein, conserved site		112224
298IPR000727
Target SNARE coiled-coil homology domain		111598
299IPR011701
Major facilitator superfamily		111224
300IPR000330
SNF2-related, N-terminal domain		111232
301IPR005746
Thioredoxin		111254
302IPR002035
von Willebrand factor, type A		111634
303IPR023298
P-type ATPase, transmembrane domain		111480
304IPR003311
AUX/IAA protein		109230
305IPR002912
ACT domain		109578
306IPR032710
NTF2-like domain		108368
307IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		108216
308IPR021139
NYN domain, limkain-b1-type		107252
309IPR029021
Protein-tyrosine phosphatase-like		106486
310IPR020904
Short-chain dehydrogenase/reductase, conserved site		106214
311IPR006045
Cupin 1		106508
312IPR000644
CBS domain		1061254
313IPR029033
Histidine phosphatase superfamily		106562
314IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		105212
315IPR000315
B-box-type zinc finger		104844
316IPR008906
HAT, C-terminal dimerisation domain		104208
317IPR007125
Histone H2A/H2B/H3		104208
318IPR005202
Transcription factor GRAS		104416
319IPR028889
Ubiquitin specific protease domain		103206
320IPR012341
Six-hairpin glycosidase		103230
321IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		1031630
322IPR024768
Meiosis arrest female protein 1		102220
323IPR002085
Alcohol dehydrogenase superfamily, zinc-type		102266
324IPR027413
GroEL-like equatorial domain		101358
325IPR008480
Protein of unknown function DUF761, plant		101202
326IPR004993
GH3 family		101412
327IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		101204
328IPR000182
GNAT domain		100368
329IPR018490
Cyclic nucleotide-binding-like		100206
330IPR014722
Ribosomal protein L2 domain 2		100200
331IPR011074
CRAL/TRIO, N-terminal domain		99502
332IPR033275
E3 ubiquitin-protein ligase MARCH-like		99244
333IPR001849
Pleckstrin homology domain		99428
334IPR017937
Thioredoxin, conserved site		99246
335IPR002022
Pectate lyase/Amb allergen		98384
336IPR000232
Heat shock factor (HSF)-type, DNA-binding		98970
337IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		98468
338IPR012675
Beta-grasp domain		97196
339IPR016167
FAD-binding, type 2, subdomain 1		97196
340IPR000086
NUDIX hydrolase domain		97382
341IPR000595
Cyclic nucleotide-binding domain		97470
342IPR000757
Glycoside hydrolase family 16		97388
343IPR018082
AmbAllergen		971402
344IPR018200
Ubiquitin specific protease, conserved site		96318
345IPR018957
Zinc finger, C3HC4 RING-type		96192
346IPR006462
Protein MS5		96314
347IPR027356
NPH3 domain		96404
348IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		96508
349IPR029062
Class I glutamine amidotransferase-like		96498
350IPR001944
Glycoside hydrolase, family 35		961348
351IPR027409
GroEL-like apical domain		95376
352IPR010713
Xyloglucan endo-transglycosylase, C-terminal		95190
353IPR011013
Galactose mutarotase-like domain		94240
354IPR006073
GTP binding domain		94552
355IPR017938
Riboflavin synthase-like beta-barrel		93198
356IPR029000
Cyclophilin-like domain		93380
357IPR010989
t-SNARE		93202
358IPR020845
AMP-binding, conserved site		93190
359IPR006689
Small GTPase superfamily, ARF/SAR type		92742
360IPR004041
NAF domain		92184
361IPR018451
NAF/FISL domain		92184
362IPR026961
PGG domain		92186
363IPR002963
Expansin		921516
364IPR031127
E3 ubiquitin ligase RBR family		92194
365IPR029064
50S ribosomal protein L30e-like		92362
366IPR013201
Cathepsin propeptide inhibitor domain (I29)		91362
367IPR001353
Proteasome, subunit alpha/beta		91190
368IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		91266
369IPR013216
Methyltransferase type 11		90180
370IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		89966
371IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		89356
372IPR013126
Heat shock protein 70 family		891024
373IPR029006
ADF-H/Gelsolin-like domain		89382
374IPR024752
Myb/SANT-like domain		89202
375IPR017927
Ferredoxin reductase-type FAD-binding domain		88176
376IPR025659
Tubby C-terminal-like domain		88190
377IPR001163
LSM domain, eukaryotic/archaea-type		88336
378IPR003137
PA domain		88176
379IPR029056
Ribokinase-like		88376
380IPR002867
IBR domain		87596
381IPR027725
Heat shock transcription factor family		87214
382IPR001938
Thaumatin		871794
383IPR004140
Exocyst complex protein Exo70		87366
384IPR025476
Helitron helicase-like domain		87176
385IPR006594
LIS1 homology motif		86380
386IPR016455
Xyloglucan endotransglucosylase/hydrolase		86172
387IPR003008
Tubulin/FtsZ, GTPase domain		86676
388IPR005821
Ion transport domain		86182
389IPR004087
K Homology domain		86414
390IPR001701
Glycoside hydrolase family 9		86178
391IPR025661
Cysteine peptidase, asparagine active site		86172
392IPR003690
Transcription termination factor, mitochondrial/chloroplastic		851178
393IPR022796
Chlorophyll A-B binding protein		85180
394IPR005299
SAM dependent carboxyl methyltransferase		84190
395IPR014002
Agenet domain, plant type		84394
396IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		83166
397IPR005630
Terpene synthase, metal-binding domain		83184
398IPR001077
O-methyltransferase, family 2		83170
399IPR017884
SANT domain		82172
400IPR025110
AMP-binding enzyme C-terminal domain		82164
401IPR027923
Hydrophobic seed protein		82166
402IPR000169
Cysteine peptidase, cysteine active site		82164
403IPR011905
Glutaredoxin-like, plant II		82164
404IPR023329
Chlorophyll a/b binding protein domain		82182
405IPR007493
Protein of unknown function DUF538		81492
406IPR000717
Proteasome component (PCI) domain		81296
407IPR010285
DNA helicase Pif1-like		81190
408IPR029061
Thiamin diphosphate-binding fold		81500
409IPR008266
Tyrosine-protein kinase, active site		81162
410IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		81162
411IPR031107
Small heat shock protein HSP20		81162
412IPR001487
Bromodomain		811034
413IPR003614
Knottin, scorpion toxin-like		81386
414IPR000782
FAS1 domain		80936
415IPR003106
Leucine zipper, homeobox-associated		80220
416IPR016461
O-methyltransferase COMT-type		80266
417IPR010851
S locus-related glycoprotein 1 binding pollen coat protein		80160
418IPR000408
Regulator of chromosome condensation, RCC1		802846
419IPR004014
Cation-transporting P-type ATPase, N-terminal		80298
420IPR015940
Ubiquitin-associated domain		79526
421IPR004000
Actin family		791066
422IPR006195
Aminoacyl-tRNA synthetase, class II		79158
423IPR025875
Leucine rich repeat 4		79164
424IPR025486
Domain of unknown function DUF4378		79158
425IPR001313
Pumilio RNA-binding repeat		792228
426IPR033133
Pumilio homology domain		78156
427IPR006459
Casparian strip membrane protein		78156
428IPR004046
Glutathione S-transferase, C-terminal		78156
429IPR029993
Plant galacturonosyltransferase GAUT		78158
430IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		78302
431IPR017392
AP2/ERF transcription factor ERF/PTI6		77178
432IPR005150
Cellulose synthase		77206
433IPR003388
Reticulon		77298
434IPR014720
Double-stranded RNA-binding domain		77562
435IPR013809
ENTH domain		77316
436IPR018202
Serine carboxypeptidase, serine active site		77154
437IPR004331
SPX domain		76350
438IPR005333
Transcription factor, TCP		76152
439IPR011332
Zinc-binding ribosomal protein		76154
440IPR000916
Bet v I/Major latex protein		76310
441IPR008395
Agenet-like domain		76192
442IPR017887
Transcription factor TCP subgroup		75150
443IPR008801
Rapid ALkalinization Factor		75152
444IPR000195
Rab-GTPase-TBC domain		75780
445IPR025660
Cysteine peptidase, histidine active site		75152
446IPR013149
Alcohol dehydrogenase, C-terminal		74148
447IPR001344
Chlorophyll A-B binding protein, plant		74158
448IPR000795
Transcription factor, GTP-binding domain		74760
449IPR021720
Malectin		74156
450IPR001876
Zinc finger, RanBP2-type		741192
451IPR002160
Proteinase inhibitor I3, Kunitz legume		74572
452IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		73146
453IPR013078
Histidine phosphatase superfamily, clade-1		73300
454IPR029069
HotDog domain		73418
455IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		73172
456IPR000528
Plant lipid transfer protein/Par allergen		72626
457IPR011065
Kunitz inhibitor ST1-like		72146
458IPR000217
Tubulin		72986
459IPR009071
High mobility group box domain		72640
460IPR008422
Homeobox KN domain		72144
461IPR003656
Zinc finger, BED-type		72278
462IPR031330
Glycoside hydrolase 35, catalytic domain		72156
463IPR028082
Periplasmic binding protein-like I		72194
464IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		72180
465IPR001906
Terpene synthase, N-terminal domain		72290
466IPR025064
Domain of unknown function DUF4005		72144
467IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		71242
468IPR006694
Fatty acid hydroxylase		71142
469IPR024709
O-fucosyltransferase, plant		70140
470IPR004161
Translation elongation factor EFTu-like, domain 2		70140
471IPR002659
Glycosyl transferase, family 31		70274
472IPR001296
Glycosyl transferase, family 1		70140
473IPR013154
Alcohol dehydrogenase, N-terminal		70140
474IPR004265
Plant disease resistance response protein		70142
475IPR001320
Ionotropic glutamate receptor		70256
476IPR003689
Zinc/iron permease		70154
477IPR016161
Aldehyde/histidinol dehydrogenase		70142
478IPR001828
Receptor, ligand binding region		70144
479IPR010399
Tify domain		70412
480IPR012967
Plant methyltransferase dimerisation		70140
481IPR029048
Heat shock protein 70kD, C-terminal domain		70276
482IPR009038
GOLD domain		69370
483IPR029057
Phosphoribosyltransferase-like		69362
484IPR004316
SWEET sugar transporter		68262
485IPR025753
AAA-type ATPase, N-terminal domain		68136
486IPR012951
Berberine/berberine-like		68136
487IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		68368
488IPR025422
Transcription factor TGA like domain		68136
489IPR000047
Helix-turn-helix motif		68272
490IPR011053
Single hybrid motif		68140
491IPR013094
Alpha/beta hydrolase fold-3		68140
492IPR005804
Fatty acid desaturase domain		68140
493IPR004274
FCP1 homology domain		68400
494IPR025610
Transcription factor MYC/MYB N-terminal		68150
495IPR021133
HEAT, type 2		67324
496IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		67322
497IPR001279
Metallo-beta-lactamase		67500
498IPR007650
Zf-FLZ domain		67134
499IPR011611
Carbohydrate kinase PfkB		67146
500IPR031112
AP2-like ethylene-responsive transcription factor		67158
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea.html new file mode 100644 index 00000000..4cdad0c9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea.html @@ -0,0 +1,63 @@ + +

Summary

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Assembly:v2.1, May 2014
Database version:86.1
Base Pairs:488,535,107
Golden Path Length:488,622,507
Genebuild by: CanSeq
Genebuild method: Import
Genebuild started: May 2014
Genebuild released: May 2014
Genebuild last updated/patched: May 2014
Genebuild version: v2.1
+

Gene counts

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Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		59,225
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:59,225
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Coordinate Systems

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chromosome
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9 sequences
+
+ +
+ + + +
SequenceLength (bp)
C143764888
C252886895
C364984695
C453719093
C546902585
C639822476
C748366697
C841758685
C954679868
+
+
scaffold33802 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea_IPtop500.html new file mode 100644 index 00000000..f1104909 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_oleracea_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		21655912
2IPR011009
Protein kinase-like domain		20362200
3IPR000719
Protein kinase domain		18664484
4IPR032675
Leucine-rich repeat domain, L domain-like		14484054
5IPR008271
Serine/threonine-protein kinase, active site		13681386
6IPR017441
Protein kinase, ATP binding site		11241138
7IPR013083
Zinc finger, RING/FYVE/PHD-type		11011173
8IPR006912
Harbinger transposase-derived protein		10631257
9IPR001810
F-box domain		10383077
10IPR009057
Homeodomain-like		10112113
11IPR013320
Concanavalin A-like lectin/glucanase domain		8751181
12IPR011990
Tetratricopeptide-like helical domain		7712447
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		7191013
14IPR001841
Zinc finger, RING-type		6971612
15IPR001611
Leucine-rich repeat		6463638
16IPR004252
Probable transposase, Ptta/En/Spm, plant		634637
17IPR012340
Nucleic acid-binding, OB-fold		600878
18IPR016040
NAD(P)-binding domain		5981410
19IPR016024
Armadillo-type fold		5961258
20IPR002885
Pentatricopeptide repeat		59312800
21IPR015410
Domain of unknown function DUF1985		561573
22IPR029058
Alpha/Beta hydrolase fold		5381282
23IPR012677
Nucleotide-binding alpha-beta plait domain		5251575
24IPR001005
SANT/Myb domain		5181420
25IPR012337
Ribonuclease H-like domain		500770
26IPR017877
Myb-like domain		486511
27IPR003593
AAA+ ATPase domain		467605
28IPR011989
Armadillo-like helical		464831
29IPR029466
No apical meristem-associated, C-terminal domain		456457
30IPR000504
RNA recognition motif domain		4521993
31IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		4521099
32IPR001128
Cytochrome P450		4512592
33IPR015943
WD40/YVTN repeat-like-containing domain		448728
34IPR017930
Myb domain		427688
35IPR011991
Winged helix-turn-helix DNA-binding domain		424714
36IPR017451
F-box associated interaction domain		419445
37IPR017986
WD40-repeat-containing domain		412998
38IPR012336
Thioredoxin-like fold		399894
39IPR020846
Major facilitator superfamily domain		396749
40IPR001680
WD40 repeat		3894063
41IPR017853
Glycoside hydrolase superfamily		374409
42IPR003653
Ulp1 protease family, C-terminal catalytic domain		367614
43IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		353373
44IPR002401
Cytochrome P450, E-class, group I		3462251
45IPR001878
Zinc finger, CCHC-type		3311438
46IPR013781
Glycoside hydrolase, catalytic domain		330361
47IPR012334
Pectin lyase fold		329337
48IPR002182
NB-ARC		328358
49IPR017972
Cytochrome P450, conserved site		327332
50IPR011050
Pectin lyase fold/virulence factor		324332
51IPR003591
Leucine-rich repeat, typical subtype		3232189
52IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		3181392
53IPR016177
DNA-binding domain		312339
54IPR011992
EF-hand domain pair		308773
55IPR001471
AP2/ERF domain		2961779
56IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		2711349
57IPR007087
Zinc finger, C2H2		270868
58IPR002048
EF-hand domain		2641827
59IPR023214
HAD-like domain		259706
60IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		247289
61IPR029044
Nucleotide-diphospho-sugar transferases		246555
62IPR018247
EF-Hand 1, calcium-binding site		241592
63IPR027443
Isopenicillin N synthase-like		236254
64IPR006527
F-box associated domain, type 1		236250
65IPR019775
WD40 repeat, conserved site		233403
66IPR003441
NAC domain		231682
67IPR005123
Oxoglutarate/iron-dependent dioxygenase		225416
68IPR006566
FBD domain		225413
69IPR015916
Galactose oxidase, beta-propeller		216237
70IPR010285
DNA helicase Pif1-like		216254
71IPR014001
Helicase superfamily 1/2, ATP-binding domain		215417
72IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		213854
73IPR015300
DNA-binding pseudobarrel domain		206631
74IPR001650
Helicase, C-terminal		203601
75IPR003959
ATPase, AAA-type, core		203235
76IPR006652
Kelch repeat type 1		202560
77IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		199475
78IPR000008
C2 domain		1961230
79IPR013026
Tetratricopeptide repeat-containing domain		193245
80IPR021109
Aspartic peptidase domain		191459
81IPR006501
Pectinesterase inhibitor domain		191929
82IPR005225
Small GTP-binding protein domain		190192
83IPR001356
Homeobox domain		190511
84IPR003439
ABC transporter-like		189530
85IPR008972
Cupredoxin		188681
86IPR020683
Ankyrin repeat-containing domain		187800
87IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		187424
88IPR025558
Domain of unknown function DUF4283		186187
89IPR003340
B3 DNA binding domain		185816
90IPR013187
F-box associated domain, type 3		183188
91IPR026992
Non-haem dioxygenase N-terminal domain		182183
92IPR029071
Ubiquitin-related domain		181213
93IPR015424
Pyridoxal phosphate-dependent transferase		178188
94IPR013830
SGNH hydrolase-type esterase domain		177484
95IPR002100
Transcription factor, MADS-box		1751170
96IPR001623
DnaJ domain		1711212
97IPR019734
Tetratricopeptide repeat		1671202
98IPR002110
Ankyrin repeat		1671052
99IPR008974
TRAF-like		165409
100IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		161168
101IPR006447
Myb domain, plants		160160
102IPR000270
PB1 domain		160266
103IPR025476
Helitron helicase-like domain		160170
104IPR008906
HAT dimerisation domain, C-terminal		159159
105IPR005135
Endonuclease/exonuclease/phosphatase		155397
106IPR005828
Major facilitator, sugar transporter-like		154169
107IPR005162
Retrotransposon gag domain		154159
108IPR013955
Replication factor A, C-terminal		154154
109IPR013101
Leucine-rich repeat 2		152171
110IPR003676
Small auxin-up RNA		152152
111IPR014710
RmlC-like jelly roll fold		151176
112IPR020472
G-protein beta WD-40 repeat		151453
113IPR003657
WRKY domain		151878
114IPR001932
PPM-type phosphatase domain		150812
115IPR013785
Aldolase-type TIM barrel		149175
116IPR023393
START-like domain		149153
117IPR011545
DEAD/DEAH box helicase domain		146152
118IPR002902
Gnk2-homologous domain		145546
119IPR011333
POZ domain		145155
120IPR011011
Zinc finger, FYVE/PHD-type		143174
121IPR010255
Haem peroxidase		143146
122IPR001806
Small GTPase superfamily		143152
123IPR001087
GDSL lipase/esterase		138140
124IPR002016
Haem peroxidase, plant/fungal/bacterial		137880
125IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		136151
126IPR002347
Glucose/ribitol dehydrogenase		1351064
127IPR000070
Pectinesterase, catalytic		135140
128IPR015880
Zinc finger, C2H2-like		135354
129IPR015655
Protein phosphatase 2C		134214
130IPR004827
Basic-leucine zipper domain		134481
131IPR011713
Leucine-rich repeat 3		134149
132IPR002083
MATH/TRAF domain		133453
133IPR001965
Zinc finger, PHD-type		132225
134IPR009072
Histone-fold		132261
135IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		131188
136IPR001461
Aspartic peptidase		131370
137IPR023213
Chloramphenicol acetyltransferase-like domain		129226
138IPR013763
Cyclin-like		128563
139IPR017907
Zinc finger, RING-type, conserved site		128128
140IPR013766
Thioredoxin domain		127241
141IPR007527
Zinc finger, SWIM-type		127247
142IPR000073
Alpha/beta hydrolase fold-1		126249
143IPR002528
Multi antimicrobial extrusion protein		126307
144IPR017871
ABC transporter, conserved site		126163
145IPR027640
Kinesin-like protein		124307
146IPR015915
Kelch-type beta propeller		124143
147IPR006564
Zinc finger, PMZ-type		123124
148IPR029052
Metallo-dependent phosphatase-like		123283
149IPR000823
Plant peroxidase		1231011
150IPR000225
Armadillo		123979
151IPR003871
Domain of unknown function DUF223		120121
152IPR000048
IQ motif, EF-hand binding site		120705
153IPR000743
Glycoside hydrolase, family 28		119207
154IPR011993
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)		119234
155IPR033121
Peptidase family A1 domain		118132
156IPR006121
Heavy metal-associated domain, HMA		116347
157IPR000571
Zinc finger, CCCH-type		1161039
158IPR000626
Ubiquitin domain		115343
159IPR000109
Proton-dependent oligopeptide transporter family		115230
160IPR003960
ATPase, AAA-type, conserved site		114123
161IPR016135
Ubiquitin-conjugating enzyme/RWD-like		114229
162IPR023395
Mitochondrial carrier domain		114246
163IPR018108
Mitochondrial substrate/solute carrier		113583
164IPR004314
Domain of unknown function DUF239		113126
165IPR001360
Glycoside hydrolase, family 1		111589
166IPR000210
BTB/POZ domain		110277
167IPR032799
Xylanase inhibitor, C-terminal		110110
168IPR003480
Transferase		110120
169IPR004843
Calcineurin-like phosphoesterase domain, apaH type		109110
170IPR026960
Reverse transcriptase zinc-binding domain		109110
171IPR019793
Peroxidases heam-ligand binding site		109109
172IPR029055
Nucleophile aminohydrolases, N-terminal		108198
173IPR001220
Legume lectin domain		107112
174IPR024788
Malectin-like carbohydrate-binding domain		107115
175IPR011043
Galactose oxidase/kelch, beta-propeller		106122
176IPR032861
Xylanase inhibitor, N-terminal		105106
177IPR011051
RmlC-like cupin domain		105113
178IPR003613
U box domain		105311
179IPR008978
HSP20-like chaperone		103195
180IPR020568
Ribosomal protein S5 domain 2-type fold		103119
181IPR010987
Glutathione S-transferase, C-terminal-like		103283
182IPR005174
Domain unknown function DUF295		102104
183IPR019794
Peroxidase, active site		101101
184IPR001752
Kinesin motor domain		101765
185IPR000608
Ubiquitin-conjugating enzyme E2		100198
186IPR003245
Phytocyanin domain		100324
187IPR030184
WAT1-related protein		100102
188IPR032867
DYW domain		9999
189IPR010264
Plant self-incompatibility S1		99101
190IPR004332
Transposase, MuDR, plant		9797
191IPR000620
EamA domain		97159
192IPR010666
Zinc finger, GRF-type		9699
193IPR008979
Galactose-binding domain-like		96262
194IPR023299
P-type ATPase, cytoplasmic domain N		96183
195IPR019786
Zinc finger, PHD-type, conserved site		95109
196IPR004146
DC1		95334
197IPR025836
Zinc knuckle CX2CX4HX4C		93109
198IPR001480
Bulb-type lectin domain		93527
199IPR001757
P-type ATPase		92302
200IPR019787
Zinc finger, PHD-finger		91158
201IPR002109
Glutaredoxin		91185
202IPR005829
Sugar transporter, conserved site		90140
203IPR006626
Parallel beta-helix repeat		89415
204IPR008949
Isoprenoid synthase domain		88182
205IPR013057
Amino acid transporter, transmembrane domain		8890
206IPR002487
Transcription factor, K-box		88171
207IPR033131
Pectinesterase, Asp active site		8787
208IPR004045
Glutathione S-transferase, N-terminal		87173
209IPR000490
Glycoside hydrolase, family 17		87141
210IPR018289
MULE transposase domain		8687
211IPR006671
Cyclin, N-terminal		86124
212IPR008250
P-type ATPase, A domain		85176
213IPR002495
Glycosyl transferase, family 8		8484
214IPR026057
PC-Esterase		8386
215IPR014014
RNA helicase, DEAD-box type, Q motif		8384
216IPR012946
X8 domain		83165
217IPR016166
FAD-binding, type 2		83161
218IPR014756
Immunoglobulin E-set		8388
219IPR003663
Sugar/inositol transporter		83456
220IPR011006
CheY-like superfamily		8289
221IPR029962
Trichome birefringence-like family		81105
222IPR003609
PAN/Apple domain		81227
223IPR000668
Peptidase C1A, papain C-terminal		81296
224IPR015500
Peptidase S8, subtilisin-related		81287
225IPR033389
AUX/IAA domain		8092
226IPR006016
UspA		8080
227IPR017970
Homeobox, conserved site		8080
228IPR018253
DnaJ domain, conserved site		8080
229IPR001789
Signal transduction response regulator, receiver domain		80231
230IPR001563
Peptidase S10, serine carboxypeptidase		79401
231IPR025521
Domain of unknown function DUF4409		7980
232IPR004839
Aminotransferase, class I/classII		7982
233IPR003851
Zinc finger, Dof-type		79309
234IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		7980
235IPR004864
Late embryogenesis abundant protein, LEA-14		7778
236IPR009060
UBA-like		7686
237IPR016039
Thiolase-like		76314
238IPR009009
RlpA-like double-psi beta-barrel domain		76223
239IPR011527
ABC transporter type 1, transmembrane domain		76378
240IPR019821
Kinesin motor domain, conserved site		7575
241IPR000858
S-locus glycoprotein domain		7477
242IPR010920
LSM domain		7474
243IPR013128
Peptidase C1A		7478
244IPR000873
AMP-dependent synthetase/ligase		7476
245IPR004883
Lateral organ boundaries, LOB		74148
246IPR000209
Peptidase S8/S53 domain		74405
247IPR011016
Zinc finger, RING-CH-type		73185
248IPR025398
Domain of unknown function DUF4371		7394
249IPR024752
Myb/SANT-like domain		7379
250IPR001117
Multicopper oxidase, type 1		7272
251IPR008928
Six-hairpin glycosidase-like		7281
252IPR018303
P-type ATPase, phosphorylation site		7272
253IPR006702
Domain of unknown function DUF588		7272
254IPR006462
Protein of unknown function DUF626		71114
255IPR007112
Expansin/pollen allergen, DPBB domain		71135
256IPR025846
PMR5 N-terminal domain		7172
257IPR011706
Multicopper oxidase, type 2		7172
258IPR016159
Cullin repeat-like-containing domain		71105
259IPR009000
Translation protein, beta-barrel domain		7076
260IPR024768
Meiosis arrest female protein 1		7073
261IPR000425
Major intrinsic protein		70514
262IPR023298
P-type ATPase, transmembrane domain		70129
263IPR021139
NYN domain, limkain-b1-type		7089
264IPR016181
Acyl-CoA N-acyltransferase		69149
265IPR001969
Aspartic peptidase, active site		6990
266IPR011707
Multicopper oxidase, type 3		6969
267IPR010402
CCT domain		68136
268IPR007118
Expansin/Lol pI		68369
269IPR000863
Sulfotransferase domain		6874
270IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		6872
271IPR001229
Jacalin-like lectin domain		68683
272IPR023271
Aquaporin-like		67134
273IPR006094
FAD linked oxidase, N-terminal		6770
274IPR000222
PPM-type phosphatase, divalent cation binding		6666
275IPR011012
Longin-like domain		6667
276IPR023828
Peptidase S8, subtilisin, Ser-active site		6667
277IPR007117
Expansin, cellulose-binding-like domain		66264
278IPR004853
Sugar phosphate transporter domain		6566
279IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		65107
280IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		6566
281IPR002423
Chaperonin Cpn60/TCP-1 family		6571
282IPR004263
Exostosin-like		6569
283IPR004367
Cyclin, C-terminal domain		65121
284IPR003406
Glycosyl transferase, family 14		6568
285IPR008502
Prolamin-like domain		6570
286IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		65120
287IPR008942
ENTH/VHS		64131
288IPR006553
Leucine-rich repeat, cysteine-containing subtype		64441
289IPR022742
Serine aminopeptidase, S33		6466
290IPR008889
VQ		6464
291IPR002068
Alpha crystallin/Hsp20 domain		63103
292IPR006045
Cupin 1		63143
293IPR019378
GDP-fucose protein O-fucosyltransferase		6363
294IPR015947
PUA-like domain		6385
295IPR013088
Zinc finger, NHR/GATA-type		6262
296IPR008991
Translation protein SH3-like domain		6265
297IPR013783
Immunoglobulin-like fold		6268
298IPR029045
ClpP/crotonase-like domain		62153
299IPR013525
ABC-2 type transporter		6182
300IPR011042
Six-bladed beta-propeller, TolB-like		6180
301IPR000679
Zinc finger, GATA-type		61242
302IPR002921
Fungal lipase-like domain		6062
303IPR011032
GroES-like		60125
304IPR006153
Cation/H+ exchanger		6063
305IPR026961
PGG domain		6063
306IPR003594
Histidine kinase-like ATPase, C-terminal domain		60232
307IPR002067
Mitochondrial carrier protein		60285
308IPR015797
NUDIX hydrolase domain-like		60122
309IPR018290
MULE transposase, N-terminal all-beta domain		6060
310IPR011701
Major facilitator superfamily		5960
311IPR027413
GroEL-like equatorial domain		59106
312IPR023313
Ubiquitin-conjugating enzyme, active site		5960
313IPR004088
K Homology domain, type 1		59420
314IPR002913
START domain		59162
315IPR025322
Protein of unknown function DUF4228, plant		5858
316IPR001251
CRAL-TRIO lipid binding domain		58285
317IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		5858
318IPR005175
PPC domain		58115
319IPR018082
AmbAllergen		58381
320IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		57132
321IPR008480
Protein of unknown function DUF761, plant		5757
322IPR003311
AUX/IAA protein		5761
323IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		5759
324IPR000315
B-box-type zinc finger		56215
325IPR000330
SNF2-related, N-terminal domain		5658
326IPR027409
GroEL-like apical domain		56114
327IPR005202
Transcription factor GRAS		56111
328IPR002035
von Willebrand factor, type A		56164
329IPR000232
Heat shock factor (HSF)-type, DNA-binding		56264
330IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		55161
331IPR022357
Major intrinsic protein, conserved site		5555
332IPR004993
GH3 family		55125
333IPR028889
Ubiquitin specific protease domain		5555
334IPR001214
SET domain		55149
335IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		54274
336IPR029000
Cyclophilin-like domain		54113
337IPR002022
Pectate lyase/Amb allergen		54104
338IPR002963
Expansin		54430
339IPR016167
FAD-binding, type 2, subdomain 1		5455
340IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		5477
341IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		54425
342IPR000727
Target SNARE coiled-coil homology domain		53140
343IPR013201
Cathepsin propeptide inhibitor domain (I29)		53108
344IPR014002
Agenet domain, plant type		53123
345IPR010713
Xyloglucan endo-transglycosylase, C-terminal		5353
346IPR031127
E3 ubiquitin ligase RBR family		5358
347IPR002912
ACT domain		53137
348IPR012341
Six-hairpin glycosidase		5360
349IPR000757
Glycoside hydrolase, family 16		53103
350IPR000182
GNAT domain		5296
351IPR018200
Ubiquitin specific protease, conserved site		5286
352IPR029021
Protein-tyrosine phosphatase-like		52123
353IPR001353
Proteasome, subunit alpha/beta		5253
354IPR007125
Histone H2A/H2B/H3		5252
355IPR002085
Alcohol dehydrogenase superfamily, zinc-type		5269
356IPR017938
Riboflavin synthase-like beta-barrel		5158
357IPR005630
Terpene synthase, metal-binding domain		5154
358IPR001938
Thaumatin		51539
359IPR011074
CRAL/TRIO, N-terminal domain		51129
360IPR033275
E3 ubiquitin-protein ligase MARCH-like		5162
361IPR001077
O-methyltransferase, family 2		5152
362IPR005746
Thioredoxin		5159
363IPR000916
Bet v I/Major latex protein		5199
364IPR000644
CBS domain		51309
365IPR007021
Domain of unknown function DUF659		5152
366IPR006594
LIS1 homology motif		50109
367IPR011065
Kunitz inhibitor ST1-like		5051
368IPR004041
NAF domain		5050
369IPR016461
O-methyltransferase COMT-type		5079
370IPR018451
NAF/FISL domain		5050
371IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		5050
372IPR027725
Heat shock transcription factor family		5062
373IPR027356
NPH3 domain		50101
374IPR003008
Tubulin/FtsZ, GTPase domain		50190
375IPR020904
Short-chain dehydrogenase/reductase, conserved site		5050
376IPR020845
AMP-binding, conserved site		5050
377IPR001849
Pleckstrin homology domain		50111
378IPR017937
Thioredoxin, conserved site		5063
379IPR000086
NUDIX hydrolase domain		50100
380IPR003840
DNA helicase		4949
381IPR003106
Leucine zipper, homeobox-associated		4970
382IPR025287
Wall-associated receptor kinase galacturonan-binding domain		4949
383IPR032710
NTF2-like domain		4984
384IPR002867
IBR domain		49154
385IPR024171
S-receptor-like serine/threonine-protein kinase		4949
386IPR029061
Thiamin diphosphate-binding fold		49147
387IPR004312
Arabidopsis retrotransposon Orf1		4956
388IPR003690
Mitochodrial transcription termination factor		49338
389IPR013094
Alpha/beta hydrolase fold-3		4949
390IPR006689
Small GTPase superfamily, ARF/SAR type		48175
391IPR018490
Cyclic nucleotide-binding-like		4849
392IPR018957
Zinc finger, C3HC4 RING-type		4848
393IPR013216
Methyltransferase type 11		4848
394IPR003137
PA domain		4849
395IPR010989
t-SNARE		4852
396IPR014722
Ribosomal protein L2 domain 2		4849
397IPR013126
Heat shock protein 70 family		48314
398IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		4890
399IPR025661
Cysteine peptidase, asparagine active site		4849
400IPR002160
Proteinase inhibitor I3, Kunitz legume		48174
401IPR006073
GTP binding domain		48139
402IPR012675
Beta-grasp domain		4747
403IPR029062
Class I glutamine amidotransferase-like		47121
404IPR029993
Plant galacturonosyltransferase GAUT		4747
405IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		47113
406IPR004000
Actin family		46276
407IPR025659
Tubby C-terminal-like domain		4652
408IPR000217
Tubulin		46275
409IPR016455
Xyloglucan endotransglucosylase/hydrolase		4646
410IPR027923
Hydrophobic seed protein		4647
411IPR000169
Cysteine peptidase, cysteine active site		4647
412IPR001701
Glycoside hydrolase, family 9		4649
413IPR029033
Histidine phosphatase superfamily		46136
414IPR017927
Ferredoxin reductase-type FAD-binding domain		4546
415IPR000782
FAS1 domain		45259
416IPR025525
hAT-like transposase, RNase-H fold		4545
417IPR005299
SAM dependent carboxyl methyltransferase		4549
418IPR003656
Zinc finger, BED-type		4592
419IPR004140
Exocyst complex protein Exo70		4595
420IPR011013
Galactose mutarotase-like domain		4557
421IPR021720
Malectin		4548
422IPR004014
Cation-transporting P-type ATPase, N-terminal		4586
423IPR029006
ADF-H/Gelsolin-like domain		4595
424IPR007493
Protein of unknown function DUF538		44130
425IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		4490
426IPR029056
Ribokinase-like		4494
427IPR005150
Cellulose synthase		4456
428IPR000595
Cyclic nucleotide-binding domain		44105
429IPR011905
Glutaredoxin-like, plant II		4444
430IPR025660
Cysteine peptidase, histidine active site		4446
431IPR008395
Agenet-like domain		4456
432IPR029048
Heat shock protein 70kD, C-terminal domain		4484
433IPR017884
SANT domain		4345
434IPR015940
Ubiquitin-associated domain		43137
435IPR001163
LSM domain, eukaryotic/archaea-type		4380
436IPR006459
Casparian strip membrane protein		4343
437IPR016161
Aldehyde/histidinol dehydrogenase		4344
438IPR003614
Knottin, scorpion toxin-like		43101
439IPR000717
Proteasome component (PCI) domain		4276
440IPR000795
Transcription factor, GTP-binding domain		42226
441IPR005821
Ion transport domain		4244
442IPR004087
K Homology domain		4299
443IPR001944
Glycoside hydrolase, family 35		42334
444IPR028082
Periplasmic binding protein-like I		4257
445IPR001906
Terpene synthase, N-terminal domain		4282
446IPR025486
Domain of unknown function DUF4378		4242
447IPR012967
Plant methyltransferase dimerisation		4242
448IPR029064
50S ribosomal protein L30e-like		4282
449IPR006195
Aminoacyl-tRNA synthetase, class II		4141
450IPR004331
SPX domain		4194
451IPR005333
Transcription factor, TCP		4141
452IPR017887
Transcription factor TCP subgroup		4141
453IPR009038
GOLD domain		41105
454IPR001828
Receptor, ligand binding region		4145
455IPR018202
Peptidase S10, serine carboxypeptidase, active site		4141
456IPR010525
Auxin response factor		4141
457IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		4069
458IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		40105
459IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		4040
460IPR022796
Chlorophyll A-B binding protein		4043
461IPR025875
Leucine rich repeat 4		4041
462IPR004046
Glutathione S-transferase, C-terminal		4041
463IPR000195
Rab-GTPase-TBC domain		40201
464IPR005804
Fatty acid desaturase domain		4041
465IPR009071
High mobility group box domain		39159
466IPR008422
Homeobox KN domain		3939
467IPR008280
Tubulin/FtsZ, C-terminal		3939
468IPR017392
AP2/ERF transcription factor ERF/PTI6		3945
469IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		3939
470IPR001320
Ionotropic glutamate receptor		3980
471IPR003689
Zinc/iron permease		3943
472IPR031107
Small heat shock protein HSP20		3940
473IPR008801
Rapid ALkalinization Factor		3939
474IPR001876
Zinc finger, RanBP2-type		39314
475IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		3945
476IPR014720
Double-stranded RNA-binding domain		39144
477IPR001313
Pumilio RNA-binding repeat		39556
478IPR001487
Bromodomain		39253
479IPR033133
Pumilio homology domain		3838
480IPR025110
AMP-binding enzyme C-terminal domain		3838
481IPR001929
Germin		38109
482IPR012951
Berberine/berberine-like		3838
483IPR003347
JmjC domain		38100
484IPR001296
Glycosyl transferase, family 1		3838
485IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		3870
486IPR013154
Alcohol dehydrogenase, N-terminal		3838
487IPR000408
Regulator of chromosome condensation, RCC1		38676
488IPR006694
Fatty acid hydroxylase		3838
489IPR000047
Helix-turn-helix motif		3876
490IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		3851
491IPR029047
Heat shock protein 70kD, peptide-binding domain		3882
492IPR013809
ENTH domain		3879
493IPR023329
Chlorophyll a/b binding protein domain		3842
494IPR004274
FCP1 homology domain		38112
495IPR021133
HEAT, type 2		3783
496IPR013601
FAE1/Type III polyketide synthase-like protein		3741
497IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3737
498IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		3785
499IPR025753
AAA-type ATPase, N-terminal domain		3737
500IPR021820
S-locus receptor kinase, C-terminal		3737
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diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa.html new file mode 100644 index 00000000..93e51f5e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa.html @@ -0,0 +1,72 @@ + +

Summary

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Assembly:IVFCAASv1, Aug 2009
Database version:86.1
Base Pairs:283,822,785
Golden Path Length:283,822,783
Genebuild by: IVFCAAS
Genebuild method: Imported from IVFCAAS by BrassEnsembl
Genebuild started: Mar 2012
Genebuild released: Apr 2012
Genebuild last updated/patched: May 2012
Genebuild version: bra_v1.01_SP2010_01
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Gene counts

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Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		41,018
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		817
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:42,853
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Coordinate Systems

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chromosome
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10 sequences
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+ + + +
SequenceLength (bp)
A0128605136
A0227846329
A0331715688
A0418965343
A0523939834
A0626271742
A0722586724
A0821594650
A0937120481
A1017594535
+
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scaffold40357 sequences
contig40550 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa_IPtop500.html new file mode 100644 index 00000000..ca22b40f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Brassica_rapa_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		17541911
2IPR000719
Protein kinase, catalytic domain		16444014
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		15884253
4IPR008271
Serine/threonine-protein kinase, active site		12491264
5IPR032675
Leucine-rich repeat domain, L domain-like		10553003
6IPR017441
Protein kinase, ATP binding site		10491062
7IPR013083
Zinc finger, RING/FYVE/PHD-type		10321099
8IPR001810
F-box domain, cyclin-like		7932339
9IPR013320
Concanavalin A-like lectin/glucanase, subgroup		7911043
10IPR009057
Homeodomain-like		7421757
11IPR011990
Tetratricopeptide-like helical		6802201
12IPR001841
Zinc finger, RING-type		6571529
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		640928
14IPR016040
NAD(P)-binding domain		5451277
15IPR016024
Armadillo-type fold		5331175
16IPR001611
Leucine-rich repeat		5193140
17IPR002885
Pentatricopeptide repeat		50911421
18IPR001005
SANT domain, DNA binding		4851343
19IPR029058
Alpha/Beta hydrolase fold		4661150
20IPR012677
Nucleotide-binding, alpha-beta plait		4621393
21IPR003593
ATPase, AAA+ type, core		415544
22IPR011989
Armadillo-like helical		414773
23IPR015943
WD40/YVTN repeat-like-containing domain		411667
24IPR017930
Transcription regulator HTH, Myb-type, DNA-binding		396644
25IPR000504
RNA recognition motif domain		3931771
26IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		386995
27IPR017986
WD40-repeat-containing domain		384944
28IPR012336
Thioredoxin-like fold		379858
29IPR011991
Winged helix-turn-helix transcription repressor DNA-binding		379650
30IPR001680
WD40 repeat		3613973
31IPR020846
Major facilitator superfamily domain		356699
32IPR001128
Cytochrome P450		3552252
33IPR017853
Glycoside hydrolase, superfamily		319357
34IPR002401
Cytochrome P450, E-class, group I		3182138
35IPR017451
F-box associated interaction domain		317321
36IPR013210
Leucine-rich repeat-containing N-terminal, type 2		306323
37IPR017972
Cytochrome P450, conserved site		305307
38IPR016177
DNA-binding, integrase-type		304330
39IPR011992
EF-hand-like domain		300748
40IPR001471
Pathogenesis-related transcriptional factor/ERF, DNA-binding		2891751
41IPR011598
Helix-loop-helix DNA-binding		2861281
42IPR003591
Leucine-rich repeat, typical subtype		2691861
43IPR011050
Pectin lyase fold/virulence factor		268278
44IPR013781
Glycoside hydrolase, subgroup, catalytic domain		268300
45IPR012334
Pectin lyase fold		268275
46IPR002048
Calcium-binding EF-hand		2571842
47IPR012340
Nucleic acid-binding, OB-fold		251361
48IPR007087
Zinc finger, C2H2		243824
49IPR023214
HAD-like domain		240677
50IPR018247
EF-Hand 1, calcium-binding site		238599
51IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		221258
52IPR029044
Nucleotide-diphospho-sugar transferases		220511
53IPR019775
WD40 repeat, conserved site		212376
54IPR015300
DNA-binding pseudobarrel domain		211689
55IPR003441
No apical meristem (NAM) protein		205618
56IPR005123
Oxoglutarate/iron-dependent oxygenase		204387
57IPR002182
NB-ARC		202218
58IPR001650
Helicase, C-terminal		199590
59IPR005225
Small GTP-binding protein domain		199200
60IPR014001
DEAD-like helicase		199399
61IPR003340
B3 DNA binding domain		193893
62IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		187787
63IPR027443
Isopenicillin N synthase-like		187198
64IPR000008
C2 calcium-dependent membrane targeting		1821188
65IPR015916
Galactose oxidase, beta-propeller		181190
66IPR003959
ATPase, AAA-type, core		173200
67IPR013026
Tetratricopeptide repeat-containing		170223
68IPR001356
Homeobox domain		169457
69IPR006501
Pectinesterase inhibitor		168810
70IPR001623
Heat shock protein DnaJ, N-terminal		1651165
71IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		164802
72IPR020683
Ankyrin repeat-containing domain		162704
73IPR002100
Transcription factor, MADS-box		1621107
74IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		162411
75IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage		162389
76IPR015424
Pyridoxal phosphate-dependent transferase, major domain		161170
77IPR003439
ABC transporter-like		160478
78IPR008972
Cupredoxin		159607
79IPR026992
Non-haem dioxygenase N-terminal domain		159159
80IPR019734
Tetratricopeptide repeat		1581147
81IPR013187
F-box associated domain, type 3		158160
82IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		154163
83IPR029071
Ubiquitin-related domain		154169
84IPR013830
Esterase, SGNH hydrolase-type		154463
85IPR006652
Kelch repeat type 1		152423
86IPR020472
G-protein beta WD-40 repeat		151453
87IPR001806
Small GTPase superfamily		150158
88IPR006447
Myb-like DNA-binding domain, SHAQKYF class		149149
89IPR003657
DNA-binding WRKY		147863
90IPR002110
Ankyrin repeat		147940
91IPR000270
Phox/Bem1p		146252
92IPR013785
Aldolase-type TIM barrel		144172
93IPR006527
F-box associated domain, type 1		144145
94IPR003676
Auxin responsive SAUR protein		142143
95IPR011011
Zinc finger, FYVE/PHD-type		141171
96IPR014710
RmlC-like jelly roll fold		140165
97IPR001932
Protein phosphatase 2C-like		138778
98IPR001087
Lipase, GDSL		137139
99IPR023393
START-like domain		133142
100IPR004827
Basic-leucine zipper domain		133467
101IPR005828
General substrate transporter		132151
102IPR011333
BTB/POZ fold		132141
103IPR006566
FBD domain		132248
104IPR008974
TRAF-like		132322
105IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		131137
106IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		131146
107IPR010255
Haem peroxidase		131136
108IPR015880
Zinc finger, C2H2-like		131339
109IPR012337
Ribonuclease H-like domain		130248
110IPR015655
Protein phosphatase 2C		130205
111IPR001965
Zinc finger, PHD-type		129209
112IPR002347
Glucose/ribitol dehydrogenase		1281177
113IPR002016
Haem peroxidase, plant/fungal/bacterial		127853
114IPR000073
Alpha/beta hydrolase fold-1		125262
115IPR013087
Zinc finger, C2H2-type/integrase, DNA-binding		124184
116IPR023213
Chloramphenicol acetyltransferase-like domain		122218
117IPR013766
Thioredoxin domain		121229
118IPR017871
ABC transporter, conserved site		118155
119IPR011043
Galactose oxidase/kelch, beta-propeller		116131
120IPR009072
Histone-fold		116232
121IPR000823
Plant peroxidase		116992
122IPR021109
Peptidase aspartic		115347
123IPR000571
Zinc finger, CCCH-type		1151055
124IPR011993
Pleckstrin homology-type		115222
125IPR002902
Gnk2-homologous domain		113434
126IPR017907
Zinc finger, RING-type, conserved site		113113
127IPR019793
Peroxidases heam-ligand binding site		112112
128IPR000070
Pectinesterase, catalytic		112114
129IPR001461
Peptidase A1		111317
130IPR016135
Ubiquitin-conjugating enzyme/RWD-like		110217
131IPR000225
Armadillo		110950
132IPR002528
Multi antimicrobial extrusion protein		108292
133IPR029052
Metallo-dependent phosphatase-like		108247
134IPR003480
Transferase		108111
135IPR033121
Peptidase family A1 domain		106120
136IPR003613
U box domain		105306
137IPR000048
IQ motif, EF-hand binding site		105678
138IPR006121
Heavy metal-associated domain, HMA		104336
139IPR000210
BTB/POZ domain		103266
140IPR013763
Cyclin-like		102498
141IPR019786
Zinc finger, PHD-type, conserved site		101117
142IPR015915
Kelch-type beta propeller		101116
143IPR004843
Metallophosphoesterase domain		99100
144IPR000109
Oligopeptide transporter		99204
145IPR003960
ATPase, AAA-type, conserved site		99108
146IPR027640
Kinesin-like protein		99264
147IPR010987
Glutathione S-transferase, C-terminal-like		99283
148IPR000743
Glycoside hydrolase, family 28		99171
149IPR002083
MATH/TRAF domain		98373
150IPR023395
Mitochondrial carrier domain		97212
151IPR018108
Mitochondrial substrate/solute carrier		96541
152IPR000608
Ubiquitin-conjugating enzyme, E2		95190
153IPR032799
Xylanase inhibitor, C-terminal		9495
154IPR019794
Peroxidase, active site		9494
155IPR011051
Cupin, RmlC-type		94102
156IPR032861
Xylanase inhibitor, N-terminal		9394
157IPR020568
Ribosomal protein S5 domain 2-type fold		93115
158IPR008978
HSP20-like chaperone		92173
159IPR032867
DYW domain		9293
160IPR000626
Ubiquitin domain		90227
161IPR013101
Leucine-rich repeat 2		90102
162IPR019787
Zinc finger, PHD-finger		90158
163IPR002109
Glutaredoxin		89179
164IPR001752
Kinesin, motor domain		89705
165IPR001878
Zinc finger, CCHC-type		89510
166IPR030184
WAT1-related protein		8788
167IPR014014
RNA helicase, DEAD-box type, Q motif		8686
168IPR029055
Nucleophile aminohydrolases, N-terminal		85165
169IPR005829
Sugar transporter, conserved site		85130
170IPR003245
Plastocyanin-like		85272
171IPR002487
Transcription factor, K-box		85169
172IPR008979
Galactose-binding domain-like		84240
173IPR014756
Immunoglobulin E-set		8489
174IPR024788
Malectin-like carbohydrate-binding domain		8487
175IPR013057
Amino acid transporter, transmembrane		8393
176IPR004045
Glutathione S-transferase, N-terminal		83168
177IPR000620
Drug/metabolite transporter		83141
178IPR011713
Leucine-rich repeat 3		8386
179IPR001360
Glycoside hydrolase, family 1		82537
180IPR006626
Parallel beta-helix repeat		80389
181IPR006016
UspA		7981
182IPR009060
UBA-like		7991
183IPR033131
Pectinesterase, Asp active site		7979
184IPR012946
X8 domain		78156
185IPR001220
Legume lectin, beta chain		7879
186IPR000490
Glycoside hydrolase, family 17		78132
187IPR003663
Sugar/inositol transporter		78415
188IPR004864
Late embryogenesis abundant protein, LEA-14		7678
189IPR003851
Zinc finger, Dof-type		76296
190IPR008250
ATPase, P-type, ATPase-associated domain		75168
191IPR018253
Heat shock protein DnaJ, conserved site		7575
192IPR023299
ATPase, P-type, cytoplasmic domain N		74142
193IPR001480
Bulb-type lectin domain		74416
194IPR015500
Peptidase S8, subtilisin-related		74282
195IPR026057
PC-Esterase		7375
196IPR011006
CheY-like superfamily		7382
197IPR017970
Homeobox, conserved site		7373
198IPR005174
Protein of unknown function DUF295		7374
199IPR018303
ATPase, P-type phosphorylation site		7373
200IPR001757
ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter		73269
201IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		7277
202IPR000668
Peptidase C1A, papain C-terminal		72268
203IPR002495
Glycosyl transferase, family 8		7273
204IPR029962
Trichome birefringence-like family		7195
205IPR004839
Aminotransferase, class I/classII		7174
206IPR025846
PMR5 N-terminal domain		7171
207IPR006671
Cyclin, N-terminal		71112
208IPR004314
Glucoamylase, putatuve		7182
209IPR033389
AUX/IAA domain		7080
210IPR010920
Like-Sm ribonucleoprotein (LSM)-related domain		7071
211IPR016039
Thiolase-like		70299
212IPR016166
FAD-binding, type 2		70136
213IPR001789
Signal transduction response regulator, receiver domain		70210
214IPR019821
Kinesin, motor region, conserved site		6969
215IPR011016
Zinc finger, RING-CH-type		69161
216IPR011012
Longin-like domain		6970
217IPR008928
Six-hairpin glycosidase-like		6978
218IPR000209
Peptidase S8/S53, subtilisin/kexin/sedolisin		69382
219IPR008942
ENTH/VHS		68135
220IPR003609
Apple-like		68198
221IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		6868
222IPR008949
Terpenoid synthase		67147
223IPR016181
Acyl-CoA N-acyltransferase		67145
224IPR010402
CCT domain		66131
225IPR004883
Lateral organ boundaries, LOB		66131
226IPR023828
Peptidase S8, subtilisin, Ser-active site		6667
227IPR004853
Domain of unknown function DUF250		6566
228IPR013128
Peptidase C1A, papain		6567
229IPR011706
Multicopper oxidase, type 2		6565
230IPR001117
Multicopper oxidase, type 1		6465
231IPR010259
Proteinase inhibitor I9, subtilisin propeptide		64108
232IPR023313
Ubiquitin-conjugating enzyme, active site		6464
233IPR011707
Multicopper oxidase, type 3		6464
234IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		6465
235IPR000858
S-locus glycoprotein		6366
236IPR002068
Heat shock protein Hsp20		63111
237IPR009009
Barwin-related endoglucanase		63185
238IPR011527
ABC transporter, transmembrane domain, type 1		63342
239IPR001214
SET domain		63165
240IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		6367
241IPR001563
Peptidase S10, serine carboxypeptidase		62358
242IPR006153
Cation/H+ exchanger		6264
243IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		6262
244IPR011701
Major facilitator superfamily		6162
245IPR000425
Major intrinsic protein		61494
246IPR013088
Zinc finger, NHR/GATA-type		6060
247IPR023271
Aquaporin-like		60122
248IPR007112
Expansin/pollen allergen, DPBB domain		60115
249IPR004146
DC1		60206
250IPR016159
Cullin repeat-like-containing domain		6082
251IPR017877
Myb-like domain		6080
252IPR000727
Target SNARE coiled-coil domain		59159
253IPR013525
ABC-2 type transporter		5979
254IPR008991
Translation protein SH3-like		5961
255IPR013783
Immunoglobulin-like fold		5966
256IPR004263
Exostosin-like		5960
257IPR006553
Leucine-rich repeat, cysteine-containing subtype		59427
258IPR019378
GDP-fucose protein O-fucosyltransferase		5960
259IPR002067
Mitochondrial carrier protein		59287
260IPR005175
Domain of unknown function DUF296		59117
261IPR025322
Protein of unknown function DUF4228		5858
262IPR007118
Expansin/Lol pI		58327
263IPR006094
FAD linked oxidase, N-terminal		5858
264IPR000679
Zinc finger, GATA-type		58226
265IPR001251
CRAL-TRIO domain		57276
266IPR004159
Protein of unknown function DUF248, methyltransferase putative		5758
267IPR000873
AMP-dependent synthetase/ligase		5758
268IPR001509
NAD-dependent epimerase/dehydratase		5758
269IPR022742
Alpha/beta hydrolase, N-terminal		5759
270IPR002035
von Willebrand factor, type A		57161
271IPR002913
Lipid-binding START		57159
272IPR015797
NUDIX hydrolase domain-like		57116
273IPR002921
Lipase, class 3		5656
274IPR011032
GroES-like		56118
275IPR003406
Glycosyl transferase, family 14		5660
276IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		5656
277IPR029045
ClpP/crotonase-like domain		56144
278IPR007117
Pollen allergen/expansin, C-terminal		56225
279IPR008889
VQ		5656
280IPR001229
Mannose-binding lectin		56680
281IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		55161
282IPR003594
ATPase-like, ATP-binding domain		55218
283IPR011042
Six-bladed beta-propeller, TolB-like		5571
284IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		5556
285IPR015947
PUA-like domain		5572
286IPR032710
NTF2-like domain		5493
287IPR004367
Cyclin, C-terminal		54103
288IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		5454
289IPR000330
SNF2-related		5353
290IPR008480
Protein of unknown function DUF761, plant		5353
291IPR006045
Cupin 1		53130
292IPR010713
Xyloglucan endo-transglycosylase, C-terminal		5353
293IPR000757
Glycoside hydrolase, family 16		53107
294IPR008930
Terpenoid cylases/protein prenyltransferase alpha-alpha toroid		53103
295IPR001969
Peptidase aspartic, active site		5278
296IPR020904
Short-chain dehydrogenase/reductase, conserved site		5252
297IPR000863
Sulfotransferase domain		5256
298IPR022357
Major intrinsic protein, conserved site		5252
299IPR003311
AUX/IAA protein		5255
300IPR000232
Heat shock factor (HSF)-type, DNA-binding		52260
301IPR010264
Plant self-incompatibility S1		5254
302IPR011074
CRAL/TRIO, N-terminal domain		51131
303IPR016167
FAD-binding, type 2, subdomain 1		5151
304IPR000644
Cystathionine beta-synthase, core		51307
305IPR002912
Amino acid-binding ACT		51137
306IPR012341
Six-hairpin glycosidase		5154
307IPR029021
Protein-tyrosine phosphatase-like		50119
308IPR000315
Zinc finger, B-box		50205
309IPR005135
Endonuclease/exonuclease/phosphatase		50198
310IPR025521
Domain of unknown function DUF4409		5052
311IPR020845
AMP-binding, conserved site		5050
312IPR004088
K Homology, type 1		50398
313IPR000182
GCN5-related N-acetyltransferase (GNAT) domain		4991
314IPR018490
Cyclic nucleotide-binding-like		4950
315IPR013201
Proteinase inhibitor I29, cathepsin propeptide		4997
316IPR002423
Chaperonin Cpn60/TCP-1		4953
317IPR002022
Pectate lyase/Amb allergen		4997
318IPR005746
Thioredoxin		4958
319IPR017937
Thioredoxin, conserved site		4960
320IPR000086
NUDIX hydrolase domain		4997
321IPR013955
Replication factor A, C-terminal		4949
322IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		49406
323IPR018082
AmbAllergen		49368
324IPR004041
NAF domain		4849
325IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		4881
326IPR027725
Heat shock transcription factor family		4860
327IPR027356
NPH3 domain		48101
328IPR007125
Histone core		4848
329IPR005202
Transcription factor GRAS		4897
330IPR031127
E3 ubiquitin ligase RBR family		4852
331IPR002867
Zinc finger, C6HC-type		47166
332IPR025659
Tubby C-terminal-like domain		4753
333IPR018451
NAF/FISL domain		4748
334IPR003137
Protease-associated domain, PA		4748
335IPR010989
t-SNARE		4751
336IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		46149
337IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		4692
338IPR016455
Xyloglucan endotransglucosylase/hydrolase		4646
339IPR011013
Glycoside hydrolase-type carbohydrate-binding		4658
340IPR005821
Ion transport		4648
341IPR014722
Translation protein SH3-like, subgroup		4646
342IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4660
343IPR000595
Cyclic nucleotide-binding domain		46111
344IPR017938
Riboflavin synthase-like beta-barrel		4548
345IPR029000
Cyclophilin-like domain		4590
346IPR013216
Methyltransferase type 11		4545
347IPR012675
Beta-grasp fold, ferredoxin-type		4545
348IPR003690
Mitochodrial transcription termination factor-related		45315
349IPR001849
Pleckstrin homology domain		45104
350IPR029062
Class I glutamine amidotransferase-like		45121
351IPR004993
GH3 auxin-responsive promoter		4595
352IPR001487
Bromodomain		45309
353IPR017927
Ferredoxin reductase-type FAD-binding domain		4444
354IPR000782
FAS1 domain		44258
355IPR001353
Proteasome, subunit alpha/beta		4446
356IPR023298
ATPase, P-type, transmembrane domain		44103
357IPR025661
Cysteine peptidase, asparagine active site		4444
358IPR029033
Histidine phosphatase superfamily		44127
359IPR006073
GTP binding domain		44129
360IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		43244
361IPR000795
Protein synthesis factor, GTP-binding		43231
362IPR033275
E3 ubiquitin-protein ligase MARCH-like		4355
363IPR027409
GroEL-like apical domain		4388
364IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		4365
365IPR001701
Glycoside hydrolase, family 9		4343
366IPR029006
ADF-H/Gelsolin-like domain		4393
367IPR021139
NYN domain, limkain-b1-type		4351
368IPR011905
Glutaredoxin-like, plant II		4343
369IPR003106
Leucine zipper, homeobox-associated		4261
370IPR001163
Like-Sm ribonucleoprotein (LSM) domain		4280
371IPR027413
GroEL-like equatorial domain		4282
372IPR002963
Expansin		42353
373IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		4242
374IPR007493
Protein of unknown function DUF538		41123
375IPR026961
PGG domain		4141
376IPR008266
Tyrosine-protein kinase, active site		4141
377IPR015813
Pyruvate/Phosphoenolpyruvate kinase		41122
378IPR022796
Chlorophyll A-B binding protein		4145
379IPR000169
Peptidase, cysteine peptidase active site		4141
380IPR009091
Regulator of chromosome condensation/beta-lactamase-inhibitor protein II		41100
381IPR025660
Cysteine peptidase, histidine active site		4141
382IPR025558
Domain of unknown function DUF4283		4141
383IPR017884
SANT, eukarya		4043
384IPR006594
LisH dimerisation motif		4091
385IPR006195
Aminoacyl-tRNA synthetase, class II		4040
386IPR018957
Zinc finger, C3HC4 RING-type		4040
387IPR001938
Thaumatin, pathogenesis-related		40410
388IPR031107
Small heat shock protein HSP20		4040
389IPR000916
Bet v I domain		4084
390IPR004087
K Homology		40101
391IPR013094
Alpha/beta hydrolase fold-3		4042
392IPR023329
Chlorophyll a/b binding protein domain		4043
393IPR004331
SPX, N-terminal		3987
394IPR005299
SAM dependent carboxyl methyltransferase		3943
395IPR005333
Transcription factor, TCP		3939
396IPR004140
Exo70 exocyst complex subunit		3982
397IPR017392
AP2/ERF transcription factor ERF/PTI6		3944
398IPR004265
Plant disease resistance response protein		3939
399IPR006459
Uncharacterised protein family UPF0497, trans-membrane plant subgroup		3939
400IPR006012
Syntaxin/epimorphin, conserved site		3939
401IPR001313
Pumilio RNA-binding repeat		39565
402IPR033133
Pumilio homology domain		3838
403IPR006689
Small GTPase superfamily, ARF/SAR type		38180
404IPR025110
Domain of unknown function DUF4009		3838
405IPR017887
Transcription factor TCP subgroup		3838
406IPR024768
Meiosis arrest female protein 1		3843
407IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3838
408IPR009038
GOLD domain		3898
409IPR025875
Leucine rich repeat 4		3839
410IPR008502
Protein of unknown function DUF784		3840
411IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3845
412IPR018202
Peptidase S10, serine carboxypeptidase, active site		3838
413IPR029064
50S ribosomal protein L30e-like		3875
414IPR025287
Wall-associated receptor kinase galacturonan-binding domain		3737
415IPR009071
High mobility group, superfamily		37160
416IPR000717
Proteasome component (PCI) domain		3768
417IPR024171
S-receptor-like serine/threonine-protein kinase		3737
418IPR001296
Glycosyl transferase, family 1		3737
419IPR005630
Terpene synthase, metal-binding domain		3742
420IPR000408
Regulator of chromosome condensation, RCC1		37684
421IPR003008
Tubulin/FtsZ, GTPase domain		37158
422IPR004014
ATPase, P-type cation-transporter, N-terminal		3769
423IPR004046
Glutathione S-transferase, C-terminal		3737
424IPR001944
Glycoside hydrolase, family 35		37301
425IPR025486
Domain of unknown function DUF4378		3737
426IPR014720
Double-stranded RNA-binding-like		37146
427IPR024752
Myb/SANT-like domain		3743
428IPR013809
Epsin-like, N-terminal		3776
429IPR013149
Alcohol dehydrogenase, C-terminal		3636
430IPR012951
Berberine/berberine-like		3636
431IPR004161
Translation elongation factor EFTu/EF1A, domain 2		3636
432IPR021720
Malectin		3636
433IPR005150
Cellulose synthase		3646
434IPR027923
Hydrophobic seed protein		3636
435IPR001077
O-methyltransferase, family 2		3636
436IPR001876
Zinc finger, RanBP2-type		36295
437IPR001906
Terpene synthase-like		3672
438IPR000195
Rab-GAP/TBC domain		36194
439IPR029048
Heat shock protein 70kD, C-terminal domain		3667
440IPR004274
NLI interacting factor		36108
441IPR025064
Domain of unknown function DUF4005		3636
442IPR000528
Plant lipid transfer protein/Par allergen		35150
443IPR011065
Kunitz inhibitor ST1-like		3536
444IPR016461
O-methyltransferase, COMT, eukaryota		3567
445IPR025753
AAA-type ATPase, N-terminal domain		3536
446IPR008422
Homeobox KN domain		3535
447IPR029061
Thiamin diphosphate-binding fold		35115
448IPR007650
Protein of unknown function DUF581		3535
449IPR013154
Alcohol dehydrogenase GroES-like		3535
450IPR014002
Tudor-like, plant		3589
451IPR003388
Reticulon		3567
452IPR001926
Pyridoxal phosphate-dependent enzyme, beta subunit		3574
453IPR010399
Tify domain		35103
454IPR002160
Proteinase inhibitor I3, Kunitz legume		35152
455IPR005804
Fatty acid desaturase, type 1		3535
456IPR008971
HSP40/DnaJ peptide-binding		3482
457IPR004316
RAG1-activating protein-1-related		3464
458IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		3496
459IPR002659
Glycosyl transferase, family 31		3466
460IPR001344
Chlorophyll A-B binding protein, plant		3437
461IPR006462
Protein of unknown function DUF626, Arabidopsis thaliana		3460
462IPR025836
Zinc knuckle CX2CX4HX4C		3436
463IPR029056
Ribokinase-like		3474
464IPR003689
Zinc/iron permease		3439
465IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		3491
466IPR013126
Heat shock protein 70		34259
467IPR012967
Plant methyltransferase dimerisation		3434
468IPR010525
Auxin response factor		3435
469IPR021133
HEAT, type 2		3378
470IPR004000
Actin family		33227
471IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3361
472IPR001929
Germin		3399
473IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		3335
474IPR008280
Tubulin/FtsZ, C-terminal		3333
475IPR020084
NUDIX hydrolase, conserved site		3333
476IPR011047
Quinonprotein alcohol dehydrogenase-like		3357
477IPR002123
Phospholipid/glycerol acyltransferase		3365
478IPR011053
Single hybrid motif		3335
479IPR013078
Histidine phosphatase superfamily, clade-1		3366
480IPR008263
Glycoside hydrolase, family 16, active site		3333
481IPR006379
HAD-superfamily hydrolase, subfamily IIB		3333
482IPR008801
Rapid ALkalinization Factor		3333
483IPR029993
Plant galacturonosyltransferase GAUT		3334
484IPR029047
Heat shock protein 70kD, peptide-binding domain		3370
485IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		3382
486IPR013601
FAE1/Type III polyketide synthase-like protein		3232
487IPR007612
Protein of unknown function DUF567		3232
488IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3232
489IPR000217
Tubulin		32257
490IPR001279
Beta-lactamase-like		32121
491IPR021820
S-locus receptor kinase, C-terminal		3232
492IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		3251
493IPR029057
Phosphoribosyltransferase-like		3282
494IPR014044
CAP domain		32125
495IPR002939
Chaperone DnaJ, C-terminal		3232
496IPR004838
Aminotransferases, class-I, pyridoxal-phosphate-binding site		3232
497IPR024156
Small GTPase superfamily, ARF type		3232
498IPR001305
Heat shock protein DnaJ, cysteine-rich domain		3174
499IPR024709
O-fucosyltransferase, plant		3131
500IPR008984
SMAD/FHA domain		3132
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii.html b/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii.html new file mode 100644 index 00000000..973165dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii.html @@ -0,0 +1,48 @@ + +

Summary

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Assembly:v3.1, Nov 2007
Database version:86.1
Base Pairs:120,404,952
Golden Path Length:120,404,952
Genebuild by: JGI
Genebuild method: Generated from ENA and UniProtKB annotation
Genebuild started: Nov 2012
Genebuild released: Nov 2012
Genebuild last updated/patched: Nov 2012
Genebuild version: 2007-11-ENA
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		14,416
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		15
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:14,560
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Coordinate Systems

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supercontig1558 sequences
contig1558 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii_IPtop500.html new file mode 100644 index 00000000..22abbb7f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Chlamydomonas_reinhardtii_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		6271963
2IPR011009
Protein kinase-like domain		620840
3IPR000719
Protein kinase, catalytic domain		5241281
4IPR008271
Serine/threonine-protein kinase, active site		327332
5IPR017441
Protein kinase, ATP binding site		220227
6IPR015943
WD40/YVTN repeat-like-containing domain		208378
7IPR016040
NAD(P)-binding domain		192489
8IPR017986
WD40-repeat-containing domain		175443
9IPR032675
Leucine-rich repeat domain, L domain-like		175423
10IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		172435
11IPR020683
Ankyrin repeat-containing domain		169771
12IPR001680
WD40 repeat		1661700
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		165272
14IPR003593
AAA+ ATPase domain		153211
15IPR016024
Armadillo-type fold		142320
16IPR011990
Tetratricopeptide-like helical		141430
17IPR029058
Alpha/Beta hydrolase fold		140369
18IPR013083
Zinc finger, RING/FYVE/PHD-type		137145
19IPR029787
Nucleotide cyclase		123208
20IPR001054
Adenylyl cyclase class-3/4/guanylyl cyclase		120481
21IPR011989
Armadillo-like helical		118251
22IPR009072
Histone-fold		117233
23IPR012336
Thioredoxin-like fold		111267
24IPR011992
EF-hand-like domain		111305
25IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		107456
26IPR002048
Calcium-binding EF-hand		101537
27IPR002110
Ankyrin repeat		100852
28IPR012677
Nucleotide-binding, alpha-beta plait		96269
29IPR018247
EF-Hand 1, calcium-binding site		95180
30IPR019775
WD40 repeat, conserved site		92176
31IPR001650
Helicase, C-terminal		87243
32IPR000504
RNA recognition motif domain		81328
33IPR014001
Helicase, superfamily 1/2, ATP-binding domain		81153
34IPR007125
Histone core		8080
35IPR023214
HAD-like domain		79231
36IPR001611
Leucine-rich repeat		76347
37IPR003439
ABC transporter-like		69171
38IPR019734
Tetratricopeptide repeat		67458
39IPR001623
DnaJ domain		64466
40IPR003959
ATPase, AAA-type, core		6482
41IPR024616
Pherophorin		6395
42IPR013026
Tetratricopeptide repeat-containing domain		6385
43IPR013785
Aldolase-type TIM barrel		6273
44IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		6279
45IPR012340
Nucleic acid-binding, OB-fold		6181
46IPR001841
Zinc finger, RING-type		61134
47IPR020846
Major facilitator superfamily domain		58128
48IPR029044
Nucleotide-diphospho-sugar transferases		54107
49IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		5456
50IPR013766
Thioredoxin domain		5291
51IPR011991
Winged helix-turn-helix DNA-binding domain		5296
52IPR015424
Pyridoxal phosphate-dependent transferase		5161
53IPR013783
Immunoglobulin-like fold		5077
54IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		4957
55IPR014756
Immunoglobulin E-set		4962
56IPR020472
G-protein beta WD-40 repeat		48144
57IPR029071
Ubiquitin-related domain		4854
58IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		4790
59IPR005225
Small GTP-binding protein domain		4750
60IPR009057
Homeodomain-like		47102
61IPR012337
Ribonuclease H-like domain		4687
62IPR002893
Zinc finger, MYND-type		4582
63IPR017871
ABC transporter, conserved site		4452
64IPR014710
RmlC-like jelly roll fold		4379
65IPR018108
Mitochondrial substrate/solute carrier		43246
66IPR023395
Mitochondrial carrier domain		43108
67IPR029052
Metallo-dependent phosphatase-like		43109
68IPR016181
Acyl-CoA N-acyltransferase		4290
69IPR001810
F-box domain, cyclin-like		4288
70IPR017853
Glycoside hydrolase, superfamily		4256
71IPR002347
Glucose/ribitol dehydrogenase		39273
72IPR008752
Peptidase M11, gametolysin		3840
73IPR013032
EGF-like, conserved site		38105
74IPR013781
Glycoside hydrolase, catalytic domain		3849
75IPR011333
BTB/POZ fold		3839
76IPR018297
Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site		3838
77IPR000626
Ubiquitin domain		3797
78IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		3745
79IPR001190
Speract/scavenger receptor		37252
80IPR022796
Chlorophyll A-B binding protein		3638
81IPR017448
Speract/scavenger receptor-related		36236
82IPR001214
SET domain		3677
83IPR011701
Major facilitator superfamily		3538
84IPR003960
ATPase, AAA-type, conserved site		3539
85IPR011050
Pectin lyase fold/virulence factor		3589
86IPR027640
Kinesin-like protein		3572
87IPR018253
DnaJ domain, conserved site		3535
88IPR001752
Kinesin, motor domain		35262
89IPR001932
Protein phosphatase 2C (PP2C)-like		35195
90IPR020568
Ribosomal protein S5 domain 2-type fold		3442
91IPR005821
Ion transport domain		3463
92IPR032710
NTF2-like domain		3363
93IPR004263
Exostosin-like		3337
94IPR000210
BTB/POZ domain		3398
95IPR014014
RNA helicase, DEAD-box type, Q motif		3333
96IPR006598
Lipopolysaccharide-modifying protein		3356
97IPR000182
GNAT domain		3155
98IPR001128
Cytochrome P450		31226
99IPR001005
SANT/Myb domain		3175
100IPR000558
Histone H2B		30237
101IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		3032
102IPR000048
IQ motif, EF-hand binding site		30227
103IPR023329
Chlorophyll a/b binding protein domain		3034
104IPR029000
Cyclophilin-like domain		2963
105IPR000008
C2 calcium-dependent membrane targeting		29140
106IPR008266
Tyrosine-protein kinase, active site		2929
107IPR003591
Leucine-rich repeat, typical subtype		29182
108IPR006502
Protein of unknown function DUF506, plant		2947
109IPR006626
Parallel beta-helix repeat		28299
110IPR016135
Ubiquitin-conjugating enzyme/RWD-like		2856
111IPR008979
Galactose-binding domain-like		2865
112IPR000742
Epidermal growth factor-like domain		2856
113IPR002073
3'5'-cyclic nucleotide phosphodiesterase, catalytic domain		2857
114IPR018490
Cyclic nucleotide-binding-like		2754
115IPR005123
Oxoglutarate/iron-dependent dioxygenase		2747
116IPR029055
Nucleophile aminohydrolases, N-terminal		2753
117IPR000164
Histone H3		27272
118IPR001763
Rhodanese-like domain		27133
119IPR017972
Cytochrome P450, conserved site		2727
120IPR004843
Metallophosphoesterase domain		2626
121IPR000014
PAS domain		26128
122IPR029021
Protein-tyrosine phosphatase-like		2665
123IPR005135
Endonuclease/exonuclease/phosphatase		2686
124IPR000073
Alpha/beta hydrolase fold-1		2651
125IPR011011
Zinc finger, FYVE/PHD-type		2626
126IPR002035
von Willebrand factor, type A		2678
127IPR009003
Trypsin-like cysteine/serine peptidase domain		2631
128IPR017930
Myb domain		2639
129IPR000608
Ubiquitin-conjugating enzyme, E2		2548
130IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2538
131IPR001344
Chlorophyll A-B binding protein, plant		2526
132IPR002119
Histone H2A		25140
133IPR029045
ClpP/crotonase-like domain		2574
134IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2540
135IPR015915
Kelch-type beta propeller		2542
136IPR000595
Cyclic nucleotide-binding domain		2574
137IPR006073
GTP binding domain		2578
138IPR023088
3'5'-cyclic nucleotide phosphodiesterase		24121
139IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		24149
140IPR004853
Domain of unknown function DUF250		2425
141IPR010920
Like-Sm (LSM) domain		2424
142IPR000330
SNF2-related		2429
143IPR008250
P-type ATPase, A domain		2455
144IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2441
145IPR032458
Histone H2A conserved site		2424
146IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2356
147IPR019821
Kinesin, motor region, conserved site		2323
148IPR001951
Histone H4		23150
149IPR017907
Zinc finger, RING-type, conserved site		2324
150IPR003613
U box domain		2363
151IPR011043
Galactose oxidase/kelch, beta-propeller		2327
152IPR017850
Alkaline-phosphatase-like, core domain		2352
153IPR006620
Prolyl 4-hydroxylase, alpha subunit		2222
154IPR013320
Concanavalin A-like lectin/glucanase, subgroup		2244
155IPR013216
Methyltransferase type 11		2222
156IPR032454
Histone H2A, C-terminal domain		2222
157IPR000795
Elongation factor, GTP-binding domain		22107
158IPR013763
Cyclin-like		2295
159IPR003594
Histidine kinase-like ATPase, ATP-binding domain		2285
160IPR017849
Alkaline phosphatase-like, alpha/beta/alpha		2248
161IPR015655
Protein phosphatase 2C		2241
162IPR001757
Cation-transporting P-type ATPase		2270
163IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2225
164IPR000225
Armadillo		22137
165IPR001279
Beta-lactamase-like		2182
166IPR012675
Beta-grasp domain		2121
167IPR013816
ATP-grasp fold, subdomain 2		2126
168IPR019809
Histone H4, conserved site		2121
169IPR004333
Transcription factor, SBP-box		2185
170IPR018303
P-type ATPase, phosphorylation site		2121
171IPR029033
Histidine phosphatase superfamily		2156
172IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		2122
173IPR005069
Nucleotide-diphospho-sugar transferase		2121
174IPR015797
NUDIX hydrolase domain-like		2144
175IPR011032
GroES-like		2052
176IPR000387
Protein-tyrosine/Dual specificity phosphatase		2020
177IPR011012
Longin-like domain		2020
178IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2020
179IPR011527
ABC transporter, transmembrane domain, type 1		2078
180IPR010987
Glutathione S-transferase, C-terminal-like		2057
181IPR001202
WW domain		2091
182IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2054
183IPR015947
PUA-like domain		2029
184IPR013525
ABC-2 type transporter		1925
185IPR023299
P-type ATPase, cytoplasmic domain N		1948
186IPR026983
Dynein heavy chain		1941
187IPR017937
Thioredoxin, conserved site		1923
188IPR023210
NADP-dependent oxidoreductase domain		1965
189IPR001395
Aldo/keto reductase		1928
190IPR012334
Pectin lyase fold		1949
191IPR013328
Dehydrogenase, multihelical		1820
192IPR001251
CRAL-TRIO domain		1886
193IPR000253
Forkhead-associated (FHA) domain		1855
194IPR002401
Cytochrome P450, E-class, group I		18100
195IPR015202
Domain of unknown function DUF1929		1818
196IPR000917
Sulfatase		1820
197IPR004045
Glutathione S-transferase, N-terminal		1833
198IPR000668
Peptidase C1A, papain C-terminal		1862
199IPR006311
Twin-arginine translocation pathway, signal sequence		1818
200IPR000209
Peptidase S8/S53 domain		1884
201IPR000782
FAS1 domain		17149
202IPR008978
HSP20-like chaperone		1745
203IPR009060
UBA-like		1720
204IPR013128
Peptidase C1A, papain		1727
205IPR008972
Cupredoxin		1783
206IPR001509
NAD-dependent epimerase/dehydratase		1717
207IPR007197
Radical SAM		1717
208IPR001478
PDZ domain		1763
209IPR013078
Histidine phosphatase superfamily, clade-1		1735
210IPR004839
Aminotransferase, class I/classII		1717
211IPR024079
Metallopeptidase, catalytic domain		1720
212IPR000945
Dopamine beta-hydroxylase-related		1719
213IPR024743
Dynein heavy chain, coiled coil stalk		1717
214IPR029062
Class I glutamine amidotransferase-like		1735
215IPR002067
Mitochondrial carrier protein		1779
216IPR011051
RmlC-like cupin domain		1718
217IPR004273
Dynein heavy chain domain		1721
218IPR000571
Zinc finger, CCCH-type		1790
219IPR006689
Small GTPase superfamily, ARF/SAR type		1669
220IPR015916
Galactose oxidase, beta-propeller		1616
221IPR008991
Translation protein SH3-like domain		1616
222IPR001163
Ribonucleoprotein LSM domain		1631
223IPR001296
Glycosyl transferase, family 1		1616
224IPR001353
Proteasome, subunit alpha/beta		1616
225IPR002938
Monooxygenase, FAD-binding		1617
226IPR013584
RAP domain		1652
227IPR005746
Thioredoxin		1620
228IPR000086
NUDIX hydrolase domain		1629
229IPR023298
P-type ATPase, transmembrane domain		1638
230IPR015500
Peptidase S8, subtilisin-related		1679
231IPR011993
Pleckstrin homology-like domain		1629
232IPR001806
Small GTPase superfamily		1617
233IPR024317
Dynein heavy chain, P-loop containing D4 domain		1617
234IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		1542
235IPR013784
Carbohydrate-binding-like fold		1518
236IPR003347
JmjC domain		1529
237IPR017941
Rieske [2Fe-2S] iron-sulphur domain		1557
238IPR013602
Dynein heavy chain, domain-2		1518
239IPR016177
DNA-binding, integrase-type		1521
240IPR000408
Regulator of chromosome condensation, RCC1		15138
241IPR020103
Pseudouridine synthase, catalytic domain		1519
242IPR011704
ATPase, dynein-related, AAA domain		1519
243IPR013830
SGNH hydrolase-type esterase domain		1539
244IPR004147
UbiB domain		1516
245IPR016130
Protein-tyrosine phosphatase, active site		1515
246IPR001965
Zinc finger, PHD-type		1519
247IPR016187
C-type lectin fold		1564
248IPR024156
Small GTPase superfamily, ARF type		1515
249IPR002921
Lipase, class 3		1414
250IPR022764
Peptidase S54, rhomboid domain		1428
251IPR003035
Plant regulator RWP-RK		1428
252IPR006195
Aminoacyl-tRNA synthetase, class II		1415
253IPR001357
BRCT domain		1459
254IPR008984
SMAD/FHA domain		1415
255IPR016039
Thiolase-like		14109
256IPR000873
AMP-dependent synthetase/ligase		1418
257IPR000340
Dual specificity phosphatase, catalytic domain		1414
258IPR023393
START-like domain		1414
259IPR001471
AP2/ERF domain		1481
260IPR032466
Metal-dependent hydrolase		1417
261IPR011074
CRAL/TRIO, N-terminal domain		1425
262IPR019787
Zinc finger, PHD-finger		1421
263IPR001199
Cytochrome b5-like heme/steroid binding domain		1488
264IPR022742
Alpha/beta hydrolase, N-terminal		1415
265IPR003582
Metridin-like ShK toxin		1437
266IPR015813
Pyruvate/Phosphoenolpyruvate kinase		1470
267IPR001283
Allergen V5/Tpx-1-related		1458
268IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		1418
269IPR006843
Plastid lipid-associated protein/fibrillin conserved domain		1417
270IPR029028
Alpha/beta knot methyltransferases		1418
271IPR014044
CAP domain		1456
272IPR013815
ATP-grasp fold, subdomain 1		1419
273IPR004088
K Homology domain, type 1		1459
274IPR029026
tRNA (guanine-N1-)-methyltransferase, N-terminal		1417
275IPR002085
Alcohol dehydrogenase superfamily, zinc-type		1424
276IPR000195
Rab-GTPase-TBC domain		1468
277IPR002937
Amine oxidase		1414
278IPR001041
2Fe-2S ferredoxin-type domain		1438
279IPR000727
Target SNARE coiled-coil domain		1330
280IPR027295
Quinonprotein alcohol dehydrogenase-like domain		1324
281IPR011016
Zinc finger, RING-CH-type		1334
282IPR011629
Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal		1351
283IPR027359
Voltage-dependent channel, four helix bundle domain		1339
284IPR023801
Histone deacetylase domain		1328
285IPR002423
Chaperonin Cpn60/TCP-1		1313
286IPR006553
Leucine-rich repeat, cysteine-containing subtype		1352
287IPR027413
GroEL-like equatorial domain		1326
288IPR022812
Dynamin superfamily		1366
289IPR011761
ATP-grasp fold		1314
290IPR013154
Alcohol dehydrogenase GroES-like		1313
291IPR007087
Zinc finger, C2H2		1325
292IPR029056
Ribokinase-like		1331
293IPR020904
Short-chain dehydrogenase/reductase, conserved site		1313
294IPR002528
Multi antimicrobial extrusion protein		1328
295IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		1316
296IPR027409
GroEL-like apical domain		1327
297IPR020892
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site		1313
298IPR016186
C-type lectin-like		1368
299IPR002044
Carbohydrate binding module family 20		1346
300IPR014722
Ribosomal protein L2 domain 2		1313
301IPR031157
Tr-type G domain, conserved site		1313
302IPR016161
Aldehyde/histidinol dehydrogenase		1313
303IPR000644
Cystathionine beta-synthase, core		1350
304IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		1313
305IPR002889
Carbohydrate-binding WSC		1354
306IPR009880
Glyoxal oxidase, N-terminal		1313
307IPR007248
Mpv17/PMP22		1325
308IPR001878
Zinc finger, CCHC-type		1328
309IPR017927
Ferredoxin reductase-type FAD-binding domain		1212
310IPR010095
Transposase IS605, OrfB, C-terminal		1212
311IPR017938
Riboflavin synthase-like beta-barrel		1214
312IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		1232
313IPR016123
Mog1/PsbP, alpha/beta/alpha sandwich		1226
314IPR001305
Heat shock protein DnaJ, cysteine-rich domain		1225
315IPR003864
Domain of unknown function DUF221		1212
316IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1212
317IPR000717
Proteasome component (PCI) domain		1222
318IPR003609
Apple-like		1252
319IPR002562
3'-5' exonuclease domain		1215
320IPR029016
GAF domain-like		1222
321IPR003107
RNA-processing protein, HAT helix		1298
322IPR011053
Single hybrid motif		1214
323IPR004014
Cation-transporting P-type ATPase, N-terminal		1222
324IPR023313
Ubiquitin-conjugating enzyme, active site		1212
325IPR000286
Histone deacetylase superfamily		1238
326IPR029057
Phosphoribosyltransferase-like		1231
327IPR023828
Peptidase S8, subtilisin, Ser-active site		1212
328IPR012292
Globin, structural domain		1217
329IPR024607
Sulfatase, conserved site		1217
330IPR006671
Cyclin, N-terminal		1219
331IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		1225
332IPR011042
Six-bladed beta-propeller, TolB-like		1217
333IPR000679
Zinc finger, GATA-type		1237
334IPR016163
Aldehyde dehydrogenase, C-terminal		1213
335IPR015353
Rubisco LS methyltransferase, substrate-binding domain		1132
336IPR003034
SAP domain		1140
337IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		1119
338IPR003607
HD/PDEase domain		1113
339IPR013088
Zinc finger, NHR/GATA-type		1114
340IPR000089
Biotin/lipoyl attachment		1124
341IPR002885
Pentatricopeptide repeat		11128
342IPR029061
Thiamin diphosphate-binding fold		1141
343IPR018392
Peptidoglycan-binding lysin domain		1142
344IPR009050
Globin-like		1115
345IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		1111
346IPR016021
MIF4-like, type 1/2/3		1117
347IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		1120
348IPR003008
Tubulin/FtsZ, GTPase domain		1150
349IPR000569
HECT domain		1147
350IPR019786
Zinc finger, PHD-type, conserved site		1111
351IPR004344
Tubulin-tyrosine ligase		1123
352IPR029039
Flavoprotein-like		1122
353IPR004154
Anticodon-binding		1127
354IPR003689
Zinc/iron permease		1112
355IPR015902
Glycoside hydrolase, family 13		1118
356IPR029069
HotDog domain		1130
357IPR013780
Glycosyl hydrolase, family 13, all-beta		1111
358IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		1146
359IPR013126
Heat shock protein 70 family		1173
360IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		1123
361IPR020843
Polyketide synthase, enoylreductase		1117
362IPR002912
ACT domain		1118
363IPR003409
MORN motif		11121
364IPR001487
Bromodomain		1180
365IPR005804
Fatty acid desaturase, type 1		1112
366IPR004274
NLI interacting factor		1134
367IPR001204
Phosphate transporter		1126
368IPR004294
Carotenoid oxygenase		1029
369IPR006638
Elongator protein 3/MiaB/NifB		1010
370IPR008254
Flavodoxin/nitric oxide synthase		1016
371IPR019956
Ubiquitin subgroup		1030
372IPR008971
HSP40/DnaJ peptide-binding		1023
373IPR006153
Cation/H+ exchanger		1011
374IPR002403
Cytochrome P450, E-class, group IV		1047
375IPR013149
Alcohol dehydrogenase, C-terminal		1016
376IPR024041
Ammonium transporter AmtB-like domain		1025
377IPR002350
Kazal domain		1093
378IPR002942
RNA-binding S4 domain		1038
379IPR009078
Ferritin/ribonucleotide reductase-like		1010
380IPR006068
Cation-transporting P-type ATPase, C-terminal		1011
381IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1010
382IPR032880
Calcium permeable stress-gated cation channel 1, N-terminal transmembrane domain		1011
383IPR008280
Tubulin/FtsZ, C-terminal		1010
384IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		1020
385IPR009030
Growth factor, receptor		1024
386IPR024950
Dual specificity phosphatase		1012
387IPR005828
General substrate transporter		1014
388IPR023271
Aquaporin-like		1014
389IPR000511
Cytochrome c/c1 haem-lyase		1018
390IPR006447
Myb domain, plants		1010
391IPR002123
Phospholipid/glycerol acyltransferase		1017
392IPR011332
Ribosomal protein, zinc-binding domain		1010
393IPR000850
Adenylate kinase		1069
394IPR002372
Pyrrolo-quinoline quinone repeat		1022
395IPR005829
Sugar transporter, conserved site		1012
396IPR001537
tRNA/rRNA methyltransferase, SpoU		1010
397IPR006461
Uncharacterised protein family Cys-rich		1019
398IPR011006
CheY-like superfamily		1010
399IPR006076
FAD dependent oxidoreductase		1010
400IPR009959
Polyketide cyclase SnoaL-like domain		1010
401IPR001494
Importin-beta, N-terminal		1029
402IPR026774
2'-5'-oligoadenylate synthase		1011
403IPR020946
Flavin monooxygenase-like		1014
404IPR006634
TRAM/LAG1/CLN8 homology domain		1023
405IPR001905
Ammonium transporter		1018
406IPR029020
Ammonium/urea transporter		1012
407IPR011004
Trimeric LpxA-like		1010
408IPR002939
Chaperone DnaJ, C-terminal		1010
409IPR001388
Synaptobrevin		1051
410IPR004827
Basic-leucine zipper domain		1022
411IPR000555
JAB1/Mov34/MPN/PAD-1		1019
412IPR016162
Aldehyde dehydrogenase, N-terminal		1011
413IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		1079
414IPR015590
Aldehyde dehydrogenase domain		1011
415IPR013122
Polycystin cation channel, PKD1/PKD2		1010
416IPR002683
Photosystem II PsbP, oxygen evolving complex		1010
417IPR003029
Ribosomal protein S1, RNA-binding domain		1029
418IPR001789
Signal transduction response regulator, receiver domain		1029
419IPR029060
PIN domain-like		918
420IPR027815
Domain of unknown function DUF4463		99
421IPR006593
Cytochrome b561/ferric reductase transmembrane		923
422IPR000953
Chromo domain/shadow		922
423IPR001486
Globin, truncated bacterial-like		911
424IPR011237
Peptidase M16 domain		920
425IPR009071
High mobility group (HMG) box domain		953
426IPR000961
AGC-kinase, C-terminal		912
427IPR005467
Signal transduction histidine kinase, core		99
428IPR007657
Glycosyltransferase AER61, uncharacterised		99
429IPR001907
ATP-dependent Clp protease proteolytic subunit		944
430IPR011611
Carbohydrate kinase PfkB		912
431IPR011044
Quinoprotein amine dehydrogenase, beta chain-like		914
432IPR013762
Integrase-like, catalytic core		910
433IPR003323
Ovarian tumour, otubain		916
434IPR006652
Kelch repeat type 1		930
435IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		917
436IPR007052
CS-like domain		919
437IPR013534
Starch synthase, catalytic domain		99
438IPR005162
Retrotransposon gag protein		99
439IPR012349
FMN-binding split barrel		917
440IPR013761
Sterile alpha motif/pointed domain		917
441IPR008928
Six-hairpin glycosidase-like		912
442IPR031167
OBG-type guanine nucleotide-binding (G) domain		99
443IPR004046
Glutathione S-transferase, C-terminal		99
444IPR004087
K Homology domain		913
445IPR022398
Peptidase S8, subtilisin, His-active site		99
446IPR018391
Pyrrolo-quinoline quinone beta-propeller repeat		950
447IPR023174
3'5'-cyclic nucleotide phosphodiesterase, conserved site		99
448IPR016185
Pre-ATP-grasp domain		918
449IPR011249
Metalloenzyme, LuxS/M16 peptidase-like		919
450IPR002109
Glutaredoxin		919
451IPR011054
Rudiment single hybrid motif		99
452IPR006047
Glycosyl hydrolase, family 13, catalytic domain		918
453IPR000594
UBA/THIF-type NAD/FAD binding fold		922
454IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		919
455IPR008974
TRAF-like		918
456IPR017896
4Fe-4S ferredoxin-type, iron-sulpur binding domain		917
457IPR003611
Intron-encoded nuclease 2		846
458IPR006594
LisH dimerisation motif		816
459IPR001433
Oxidoreductase FAD/NAD(P)-binding		88
460IPR000467
G-patch domain		822
461IPR021133
HEAT, type 2		822
462IPR001304
C-type lectin		8109
463IPR018506
Cytochrome b5, heme-binding site		88
464IPR029035
DHS-like NAD/FAD-binding domain		818
465IPR016064
ATP-NAD kinase-like domain		814
466IPR019954
Ubiquitin conserved site		813
467IPR000217
Tubulin		871
468IPR009022
Elongation factor G, III-V domain		817
469IPR001440
Tetratricopeptide TPR-1		89
470IPR017975
Tubulin, conserved site		88
471IPR023333
Proteasome B-type subunit		88
472IPR003440
Glycosyl transferase, family 48		812
473IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		822
474IPR020471
Aldo/keto reductase subgroup		831
475IPR009053
Prefoldin		816
476IPR013105
Tetratricopeptide TPR2		88
477IPR028427
Peptide methionine sulfoxide reductase		88
478IPR003495
CobW/HypB/UreG domain		88
479IPR020084
NUDIX hydrolase, conserved site		88
480IPR018181
Heat shock protein 70, conserved site		819
481IPR001269
tRNA-dihydrouridine synthase		815
482IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		820
483IPR017932
Glutamine amidotransferase type 2 domain		813
484IPR010989
t-SNARE		89
485IPR000640
Translation elongation factor EFG, V domain		820
486IPR001375
Peptidase S9, prolyl oligopeptidase, catalytic domain		89
487IPR008011
Complex 1 LYR protein		88
488IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		88
489IPR011060
Ribulose-phosphate binding barrel		88
490IPR011013
Galactose mutarotase-like domain		811
491IPR006050
DNA photolyase, N-terminal		824
492IPR011650
Peptidase M20, dimerisation domain		824
493IPR003690
Mitochodrial transcription termination factor-related		828
494IPR001208
Mini-chromosome maintenance, DNA-dependent ATPase		856
495IPR011641
Tyrosine-protein kinase ephrin type A/B receptor-like		859
496IPR000834
Peptidase M14, carboxypeptidase A		819
497IPR000994
Peptidase M24, structural domain		829
498IPR016193
Cytidine deaminase-like		810
499IPR009075
Acyl-CoA dehydrogenase/oxidase C-terminal		816
500IPR002933
Peptidase M20		88
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus.html b/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus.html new file mode 100644 index 00000000..3f901cb7 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus.html @@ -0,0 +1,994 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM35022v2, Sep 2015
Database version:86.1
Base Pairs:104,085,276
Golden Path Length:104,980,420
Genebuild by: ENA
Genebuild method: Generated from ENA annotation
Genebuild started: Mar 2013
Genebuild released: Mar 2013
Genebuild last updated/patched: Sep 2015
Genebuild version: 2015-09-ENA
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		9,807
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:9,841
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
Pt180086
+
+
supercontig
+
925 sequences
+
+ +
+ + + +
SequenceLength (bp)
HG0014591172314
HG001460665128
HG001461300717
HG0014625664
HG0014635656
HG0014645622
HG0014655568
HG0014665559
HG0014675549
HG0014685496
HG001469303938
HG0014705487
HG0014715485
HG0014725431
HG0014735413
HG0014745404
HG0014755381
HG0014765374
HG001477298319
HG0014785264
HG0014795234
HG0014805227
HG0014815220
HG0014825208
HG0014835136
HG0014845123
HG0014855111
HG0014865070
HG0014875060
HG0014885056
HG001489294128
HG0014905005
HG0014914969
HG0014924963
HG0014934958
HG0014944939
HG001495296477
HG0014964920
HG0014974883
HG0014984862
HG0014994859
HG0015004847
HG001501289684
HG0015024824
HG0015034820
HG0015044815
HG0015054799
HG0015064798
HG0015074790
HG001508292986
HG0015094747
HG0015104739
HG0015114710
HG001512288413
HG0015134651
HG0015144648
HG0015154628
HG0015164623
HG0015174623
HG0015184602
HG001519291777
HG0015204482
HG0015214468
HG0015224454
HG001523653314
HG001524292488
HG0015254419
HG0015264411
HG0015274381
HG0015284377
HG0015294374
HG0015304357
HG001531280524
HG0015324326
HG0015334323
HG0015344313
HG0015354311
HG0015364304
HG0015374280
HG0015384279
HG001539279107
HG0015404265
HG0015414240
HG0015424216
HG0015434201
HG0015444163
HG001545277726
HG0015464152
HG0015474137
HG0015484132
HG0015494108
HG0015504094
HG0015514092
HG0015524084
HG001553277209
HG0015544013
HG0015554007
HG0015563996
HG0015573993
HG0015583992
HG0015593990
HG0015603971
HG0015613957
HG0015623952
HG0015633946
HG0015643942
HG0015653926
HG001566271990
HG0015673894
HG0015683878
HG0015693861
HG0015703856
HG0015713854
HG0015723849
HG001573276997
HG0015743840
HG0015753818
HG0015763815
HG0015773804
HG0015783756
HG001579272142
HG0015803734
HG0015813728
HG0015823700
HG0015833682
HG0015843674
HG0015853672
HG0015863660
HG001587266119
HG0015883657
HG0015893639
HG0015903616
HG0015913594
HG001592640756
HG001593267289
HG0015943586
HG0015953547
HG0015963528
HG0015973524
HG0015983517
HG001599261143
HG0016003480
HG0016013420
HG0016023412
HG0016033388
HG0016043381
HG0016053376
HG001606262258
HG0016073353
HG0016083312
HG0016093306
HG0016103294
HG0016113282
HG0016123268
HG0016133254
HG0016143158
HG001615258760
HG0016163119
HG0016173092
HG0016183091
HG0016192962
HG0016202939
HG0016212870
HG0016222699
HG001623259167
HG0016242443
HG0016252432
HG0016262134
HG0016272013
HG001628257558
HG001629260365
HG001630256942
HG001631252368
HG001632252698
HG001633616057
HG001634252270
HG001635250633
HG001636243969
HG001637252481
HG001638248591
HG001639247392
HG001640242694
HG001641239798
HG001642613359
HG001643242511
HG001644240690
HG001645239018
HG001646239529
HG001647239481
HG001648243579
HG001649236013
HG001650236539
HG001651242307
HG001652233989
HG001653612141
HG001654232785
HG001655229897
HG001656229516
HG001657229092
HG001658232212
HG001659229401
HG001660230890
HG001661225884
HG001662225752
HG001663225436
HG001664599715
HG001665224131
HG001666225153
HG001667221055
HG001668220976
HG001669221296
HG001670220525
HG001671219000
HG001672223186
HG001673216670
HG001674215311
HG001675591990
HG001676214746
HG001677216577
HG001678212573
HG001679212105
HG001680211154
HG001681210423
HG001682209568
HG001683209992
HG001684208978
HG001685217300
HG001686208886
HG001687209518
HG001688209149
HG001689207211
HG001690206115
HG001691206110
HG001692205616
HG001693204788
HG001694214139
HG001695587116
HG001696203210
HG001697203276
HG001698202013
HG001699204210
HG001700203109
HG001701200320
HG001702202231
HG001703200930
HG001704199788
HG001705196612
HG0017061025594
HG001707584618
HG001708197591
HG001709203052
HG001710195162
HG001711195402
HG001712194670
HG001713200108
HG001714194532
HG001715195697
HG001716197115
HG001717194937
HG001718586499
HG001719191829
HG001720195570
HG001721190998
HG001722190524
HG001723190512
HG001724189222
HG001725195887
HG001726187631
HG001727188792
HG001728188369
HG001729574417
HG001730187623
HG001731187608
HG001732182062
HG001733189852
HG001734181656
HG001735179803
HG001736175820
HG001737180218
HG001738174768
HG001739571794
HG001740173149
HG001741175205
HG001742173327
HG001743171098
HG001744172550
HG001745172421
HG001746172211
HG001747173938
HG001748169618
HG001749168565
HG001750565704
HG001751167540
HG001752166719
HG001753164667
HG001754164968
HG001755164452
HG001756164442
HG001757161600
HG001758158911
HG001759157712
HG001760558271
HG001761158157
HG001762155817
HG001763155719
HG001764157070
HG001765153508
HG001766154274
HG001767150868
HG001768156148
HG001769557201
HG001770150346
HG001771150252
HG001772149386
HG001773149538
HG001774154226
HG001775151134
HG001776149076
HG001777148152
HG001778148348
HG001779147981
HG001780557879
HG001781149966
HG001782144973
HG001783144772
HG001784143036
HG001785143757
HG001786143159
HG001787143173
HG001788145631
HG001789143935
HG001790141625
HG001791146883
HG001792139113
HG001793139180
HG001794143237
HG001795137691
HG001796137313
HG001797136856
HG001798137528
HG001799135840
HG001800540206
HG001801134110
HG001802132028
HG001803135181
HG001804131214
HG001805130798
HG001806129724
HG001807957673
HG001808529288
HG001809129459
HG001810130177
HG001811129872
HG001812130942
HG001813129301
HG001814128236
HG001815127676
HG001816127591
HG001817128030
HG001818523105
HG001819126900
HG001820126328
HG001821125711
HG001822126164
HG001823125579
HG001824124699
HG001825124598
HG001826124523
HG001827123902
HG001828517557
HG001829122969
HG001830122262
HG001831123646
HG001832121627
HG001833120824
HG001834119938
HG001835119300
HG001836116854
HG001837121461
HG001838119155
HG001839114999
HG001840114462
HG001841114450
HG001842113266
HG001843506327
HG001844111547
HG001845111384
HG001846111568
HG001847110880
HG001848112589
HG001849110576
HG001850113025
HG001851111249
HG001852506013
HG001853107215
HG001854107275
HG001855106359
HG001856107589
HG001857107470
HG001858106443
HG001859105377
HG001860498982
HG001861105012
HG001862104846
HG001863104575
HG001864105401
HG001865106349
HG001866103294
HG001867103124
HG001868103090
HG001869104089
HG001870101844
HG001871500059
HG001872102039
HG001873101599
HG001874101786
HG001875100936
HG001876100578
HG001877101073
HG00187899869
HG00187999953
HG00188099945
HG001881101812
HG001882101539
HG00188398512
HG001884100927
HG00188597571
HG00188699018
HG00188797244
HG00188897154
HG00188999742
HG001890489189
HG00189196889
HG001892101218
HG00189395777
HG00189497697
HG00189595237
HG00189695148
HG00189796905
HG001898913059
HG001899485072
HG00190094330
HG00190193666
HG00190292618
HG00190394620
HG00190492724
HG00190591672
HG00190690096
HG001907468625
HG00190889372
HG00190989144
HG00191087918
HG00191186155
HG00191285865
HG00191385466
HG001914467017
HG00191585070
HG00191684861
HG00191784967
HG00191882845
HG00191982823
HG00192081743
HG00192181604
HG00192281496
HG00192381960
HG00192481201
HG00192579711
HG00192679642
HG00192781199
HG00192879401
HG00192979292
HG00193079427
HG00193178570
HG001932455627
HG00193378557
HG00193478677
HG00193578007
HG00193677867
HG00193776894
HG00193876565
HG00193975813
HG001940443916
HG00194175605
HG00194274987
HG00194375135
HG00194474574
HG00194574389
HG00194673942
HG00194773360
HG00194873530
HG001949440673
HG00195073070
HG00195177074
HG00195272670
HG00195372347
HG00195471947
HG00195571744
HG00195671477
HG00195770990
HG00195871176
HG001959438433
HG00196070795
HG00196170470
HG00196270133
HG00196371462
HG00196469979
HG00196569161
HG00196671266
HG001967444126
HG00196867666
HG00196967303
HG00197067829
HG00197166406
HG00197266213
HG00197365796
HG00197465276
HG001975441450
HG00197666927
HG00197764081
HG00197864253
HG00197963352
HG00198063069
HG00198165474
HG00198262117
HG001983830468
HG00198461516
HG00198561338
HG00198661296
HG00198761225
HG00198861600
HG00198960494
HG00199060448
HG00199160296
HG001992433925
HG00199360292
HG00199460378
HG00199560695
HG00199660010
HG00199762539
HG00199859668
HG00199964236
HG00200060198
HG00200158696
HG002002435350
HG00200358294
HG00200457984
HG00200557422
HG00200657610
HG00200757192
HG00200857494
HG00200955729
HG00201055496
HG00201155538
HG002012439109
HG00201355256
HG00201454671
HG00201554670
HG00201654426
HG00201753555
HG00201853507
HG00201953351
HG00202055430
HG00202153453
HG002022425369
HG00202354124
HG00202452926
HG00202554008
HG00202651669
HG00202750543
HG00202850172
HG00202949609
HG00203049450
HG002031425466
HG00203249021
HG00203348897
HG00203454572
HG00203548400
HG00203647520
HG00203747220
HG002038418573
HG00203948625
HG00204047001
HG00204146870
HG00204251526
HG00204346632
HG00204446204
HG00204547472
HG00204646193
HG00204746566
HG00204845892
HG00204945678
HG00205045631
HG00205146361
HG00205245155
HG00205344855
HG002054420008
HG00205544437
HG00205644358
HG00205744272
HG00205845259
HG00205943851
HG002060412374
HG00206142465
HG00206241621
HG00206342752
HG00206444518
HG00206541322
HG00206641044
HG00206743153
HG00206840692
HG00206940356
HG002070417207
HG00207140310
HG00207240131
HG00207342469
HG00207442613
HG00207539765
HG00207639545
HG00207739459
HG00207839191
HG002079414970
HG00208039170
HG00208139001
HG00208238421
HG00208339987
HG00208437962
HG00208537494
HG002086410170
HG00208737177
HG00208836878
HG00208936823
HG00209036798
HG00209136100
HG00209235689
HG00209335605
HG002094408713
HG00209542560
HG00209635231
HG00209735035
HG00209835118
HG00209934961
HG00210034355
HG00210135659
HG00210233885
HG002103406183
HG00210434246
HG00210533196
HG00210632924
HG00210732742
HG002108405443
HG00210932268
HG00211031593
HG00211131557
HG00211230996
HG00211330920
HG00211430744
HG00211533925
HG002116406852
HG00211730539
HG00211830594
HG00211930435
HG00212030179
HG00212130064
HG00212229929
HG00212328939
HG00212428936
HG00212529381
HG002126401796
HG00212728915
HG00212828713
HG00212928594
HG00213028538
HG00213128521
HG00213228562
HG00213327662
HG002134398315
HG00213527087
HG00213628246
HG00213726550
HG00213826238
HG00213937195
HG00214026610
HG002141393654
HG00214225815
HG00214325269
HG00214425181
HG00214524714
HG00214624750
HG002147390349
HG00214824574
HG00214924566
HG00215024410
HG00215123459
HG00215223158
HG00215323136
HG002154389098
HG00215523083
HG00215624903
HG00215724690
HG00215822924
HG00215922451
HG00216022184
HG00216122058
HG002162381262
HG00216321995
HG00216421773
HG00216521859
HG00216621563
HG00216721447
HG002168373441
HG00216921470
HG00217021401
HG00217125574
HG00217221253
HG00217321222
HG00217420949
HG00217521628
HG002176368492
HG00217720863
HG00217820706
HG00217920158
HG00218020026
HG00218119911
HG00218219957
HG00218320759
HG00218419740
HG002185363025
HG00218619591
HG00218719730
HG00218819226
HG00218919141
HG00219019106
HG00219119084
HG00219219003
HG00219318992
HG00219418912
HG002195358392
HG00219618706
HG00219718636
HG00219817834
HG00219918580
HG00220017401
HG002201358079
HG00220217218
HG00220317908
HG00220416993
HG00220518613
HG00220616630
HG00220716621
HG00220816577
HG002209356469
HG00221016564
HG00221116548
HG00221216529
HG00221316449
HG00221423004
HG00221516303
HG00221616276
HG00221716017
HG00221815688
HG002219357171
HG00222016296
HG00222115423
HG00222215419
HG00222315379
HG00222415377
HG00222515177
HG00222615125
HG002227698027
HG002228352171
HG00222915015
HG00223015085
HG00223114815
HG00223214751
HG00223314456
HG00223414335
HG00223514281
HG002236354508
HG00223714126
HG00223814097
HG00223913981
HG00224013864
HG00224113763
HG002242343747
HG00224313097
HG00224413096
HG00224512925
HG00224612916
HG00224712907
HG00224812886
HG00224912748
HG00225012742
HG002251342688
HG00225212448
HG00225312323
HG00225412303
HG00225512267
HG00225612245
HG00225713805
HG00225812177
HG00225912099
HG002260341256
HG00226111772
HG00226211762
HG00226311701
HG00226413050
HG00226511541
HG00226611648
HG002267342381
HG00226811304
HG00226911184
HG00227011275
HG00227111167
HG00227211536
HG00227311065
HG00227411048
HG00227511660
HG002276338745
HG00227710795
HG00227810700
HG00227910609
HG00228010558
HG00228110466
HG00228210439
HG00228310350
HG00228410330
HG002285338089
HG00228610161
HG00228710036
HG0022889760
HG0022899703
HG0022909701
HG0022919678
HG0022929606
HG0022939599
HG002294336146
HG0022959593
HG0022969546
HG0022979527
HG0022989253
HG0022999231
HG0023009192
HG002301333638
HG0023029136
HG0023039082
HG0023049049
HG0023059039
HG00230610301
HG0023078788
HG0023088776
HG002309685158
HG002310332307
HG0023118734
HG0023128708
HG0023138615
HG0023148550
HG0023158490
HG0023168489
HG0023178486
HG00231810422
HG0023198266
HG002320327877
HG0023218214
HG0023228108
HG0023238086
HG0023248045
HG0023257868
HG0023267867
HG0023277788
HG002328320184
HG0023297767
HG0023307613
HG0023317642
HG0023327531
HG002333317958
HG0023347432
HG0023357418
HG0023367303
HG0023377286
HG0023387194
HG002339316549
HG0023407170
HG0023417121
HG0023427051
HG0023437005
HG0023446998
HG0023456906
HG0023466902
HG0023476748
HG002348313126
HG0023496740
HG0023506724
HG0023516650
HG0023526642
HG0023536625
HG0023546523
HG002355307999
HG0023566437
HG0023576433
HG0023586390
HG0023596372
HG0023606282
HG0023616257
HG0023626195
HG002363308815
HG0023646185
HG0023656123
HG0023666100
HG0023676083
HG0023686041
HG0023696018
HG002370303913
HG0023716002
HG0023725945
HG0023735886
HG0023745883
HG0023755879
HG0023765867
HG0023775861
HG0023785814
HG002379302052
HG0023805800
HG0023815780
HG0023825687
HG0023835671
+
+
contig3242 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus_IPtop500.html new file mode 100644 index 00000000..cd770160 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Chondrus_crispus_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		5443011
2IPR011009
Protein kinase-like domain		223394
3IPR015943
WD40/YVTN repeat-like-containing domain		199608
4IPR017986
WD40-repeat-containing domain		181786
5IPR001680
WD40 repeat		1703639
6IPR000719
Protein kinase domain		164669
7IPR012337
Ribonuclease H-like domain		136330
8IPR011990
Tetratricopeptide-like helical domain		133705
9IPR016040
NAD(P)-binding domain		129658
10IPR016024
Armadillo-type fold		129669
11IPR019775
WD40 repeat, conserved site		120573
12IPR003593
AAA+ ATPase domain		116279
13IPR008271
Serine/threonine-protein kinase, active site		113177
14IPR001584
Integrase, catalytic core		100184
15IPR011989
Armadillo-like helical		96417
16IPR001650
Helicase, C-terminal		94465
17IPR017441
Protein kinase, ATP binding site		93149
18IPR009057
Homeodomain-like		91349
19IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		88454
20IPR014001
Helicase superfamily 1/2, ATP-binding domain		87287
21IPR020472
G-protein beta WD-40 repeat		84384
22IPR009072
Histone-fold		82155
23IPR013083
Zinc finger, RING/FYVE/PHD-type		77220
24IPR011991
Winged helix-turn-helix DNA-binding domain		72289
25IPR012336
Thioredoxin-like fold		69310
26IPR000164
Histone H3/CENP-A		68210
27IPR012340
Nucleic acid-binding, OB-fold		65181
28IPR029058
Alpha/Beta hydrolase fold		63296
29IPR011545
DEAD/DEAH box helicase domain		62106
30IPR002182
NB-ARC		5858
31IPR012677
Nucleotide-binding alpha-beta plait domain		56400
32IPR023214
HAD-like domain		56346
33IPR023753
FAD/NAD(P)-binding domain		53435
34IPR003959
ATPase, AAA-type, core		53125
35IPR010285
DNA helicase Pif1-like		5271
36IPR013785
Aldolase-type TIM barrel		50117
37IPR029044
Nucleotide-diphospho-sugar transferases		48215
38IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		48145
39IPR006597
Sel1-like repeat		48888
40IPR001841
Zinc finger, RING-type		48302
41IPR003439
ABC transporter-like		48223
42IPR020568
Ribosomal protein S5 domain 2-type fold		46112
43IPR025476
Helitron helicase-like domain		4648
44IPR007087
Zinc finger, C2H2		45255
45IPR000504
RNA recognition motif domain		45526
46IPR015424
Pyridoxal phosphate-dependent transferase		44114
47IPR025898
Tc3 transposase, DNA binding domain		4343
48IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		4298
49IPR005225
Small GTP-binding protein domain		4291
50IPR013026
Tetratricopeptide repeat-containing domain		42107
51IPR019734
Tetratricopeptide repeat		40710
52IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		40187
53IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3868
54IPR017871
ABC transporter, conserved site		3891
55IPR009000
Translation protein, beta-barrel domain		3672
56IPR015880
Zinc finger, C2H2-like		33136
57IPR020846
Major facilitator superfamily domain		31256
58IPR001005
SANT/Myb domain		31216
59IPR016181
Acyl-CoA N-acyltransferase		30131
60IPR002575
Aminoglycoside phosphotransferase		3031
61IPR032675
Leucine-rich repeat domain, L domain-like		29101
62IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		2980
63IPR003960
ATPase, AAA-type, conserved site		2855
64IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		2895
65IPR029045
ClpP/crotonase-like domain		28168
66IPR018108
Mitochondrial substrate/solute carrier		27349
67IPR023395
Mitochondrial carrier domain		27136
68IPR013766
Thioredoxin domain		2692
69IPR016135
Ubiquitin-conjugating enzyme/RWD-like		2699
70IPR016197
Chromo domain-like		2636
71IPR006912
Harbinger transposase-derived protein		2526
72IPR014014
RNA helicase, DEAD-box type, Q motif		2552
73IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		2560
74IPR029055
Nucleophile aminohydrolases, N-terminal		24105
75IPR029071
Ubiquitin-related domain		2472
76IPR010255
Haem peroxidase		2434
77IPR014756
Immunoglobulin E-set		2455
78IPR011042
Six-bladed beta-propeller, TolB-like		2446
79IPR012349
FMN-binding split barrel		2350
80IPR011527
ABC transporter type 1, transmembrane domain		23136
81IPR011993
PH domain-like		2369
82IPR000608
Ubiquitin-conjugating enzyme E2		2284
83IPR001279
Metallo-beta-lactamase		22140
84IPR000795
Transcription factor, GTP-binding domain		22212
85IPR001623
DnaJ domain		22431
86IPR000073
Alpha/beta hydrolase fold-1		2286
87IPR000953
Chromo/chromo shadow domain		2147
88IPR000330
SNF2-related, N-terminal domain		2133
89IPR023299
P-type ATPase, cytoplasmic domain N		2168
90IPR019791
Haem peroxidase, animal		21203
91IPR025724
GAG-pre-integrase domain		2121
92IPR000326
Phosphatidic acid phosphatase type 2/haloperoxidase		2060
93IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2042
94IPR006073
GTP binding domain		20132
95IPR000182
GNAT domain		1979
96IPR013783
Immunoglobulin-like fold		1946
97IPR017853
Glycoside hydrolase superfamily		1977
98IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		1936
99IPR002035
von Willebrand factor, type A		1998
100IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		1977
101IPR029052
Metallo-dependent phosphatase-like		1997
102IPR004827
Basic-leucine zipper domain		19105
103IPR001214
SET domain		1962
104IPR017930
Myb domain		1979
105IPR011992
EF-hand domain pair		19101
106IPR002563
Flavin reductase like domain		1933
107IPR006195
Aminoacyl-tRNA synthetase, class II		1835
108IPR011701
Major facilitator superfamily		1846
109IPR002347
Short-chain dehydrogenase/reductase SDR		18322
110IPR029061
Thiamin diphosphate-binding fold		18103
111IPR018247
EF-Hand 1, calcium-binding site		1852
112IPR011335
Restriction endonuclease type II-like		1831
113IPR000008
C2 domain		17135
114IPR008250
P-type ATPase, A domain		1767
115IPR004839
Aminotransferase, class I/classII		1737
116IPR001757
P-type ATPase		1750
117IPR010987
Glutathione S-transferase, C-terminal-like		17104
118IPR001128
Cytochrome P450		17144
119IPR004843
Calcineurin-like phosphoesterase domain, apaH type		1638
120IPR028992
Hedgehog/Intein (Hint) domain		1644
121IPR002048
EF-hand domain		16145
122IPR033247
Transketolase family		1630
123IPR013781
Glycoside hydrolase, catalytic domain		1655
124IPR016119
Bromoperoxidase/chloroperoxidase, C-terminal		1616
125IPR000225
Armadillo		16154
126IPR000626
Ubiquitin domain		15113
127IPR004045
Glutathione S-transferase, N-terminal		1557
128IPR018303
P-type ATPase, phosphorylation site		1524
129IPR001849
Pleckstrin homology domain		1537
130IPR028889
Ubiquitin specific protease domain		1533
131IPR001767
Hedgehog protein, Hint domain		1520
132IPR017938
Riboflavin synthase-like beta-barrel		1428
133IPR029000
Cyclophilin-like domain		1466
134IPR001357
BRCT domain		14118
135IPR009060
UBA-like		1433
136IPR010920
LSM domain		1437
137IPR008991
Translation protein SH3-like domain		1427
138IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1426
139IPR001353
Proteasome, subunit alpha/beta		1429
140IPR014710
RmlC-like jelly roll fold		1434
141IPR013816
ATP-grasp fold, subdomain 2		1433
142IPR003594
Histidine kinase-like ATPase, C-terminal domain		1487
143IPR020103
Pseudouridine synthase, catalytic domain		1442
144IPR023313
Ubiquitin-conjugating enzyme, active site		1427
145IPR011012
Longin-like domain		1433
146IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		1432
147IPR002067
Mitochondrial carrier protein		14196
148IPR001173
Glycosyltransferase 2-like		1423
149IPR002937
Amine oxidase		1429
150IPR006539
P-type ATPase, subfamily IV		1437
151IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		13159
152IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		1349
153IPR001163
LSM domain, eukaryotic/archaea-type		1363
154IPR002885
Pentatricopeptide repeat		13460
155IPR001478
PDZ domain		13105
156IPR012675
Beta-grasp domain		1330
157IPR003587
Hint domain N-terminal		1318
158IPR003107
HAT (Half-A-TPR) repeat		13244
159IPR020683
Ankyrin repeat-containing domain		13131
160IPR018253
DnaJ domain, conserved site		1331
161IPR005475
Transketolase-like, pyrimidine-binding domain		1341
162IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		1336
163IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		1342
164IPR001611
Leucine-rich repeat		13166
165IPR029033
Histidine phosphatase superfamily		1348
166IPR001878
Zinc finger, CCHC-type		1391
167IPR017927
Ferredoxin reductase-type FAD-binding domain		1221
168IPR012296
Nuclease, putative, TT1808		1216
169IPR011032
GroES-like		1268
170IPR008538
Domain of unknown function DUF820		1212
171IPR011041
Soluble quinoprotein glucose/sorbosone dehydrogenase		1218
172IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1229
173IPR000717
Proteasome component (PCI) domain		1255
174IPR000873
AMP-dependent synthetase/ligase		1232
175IPR002401
Cytochrome P450, E-class, group I		1298
176IPR005135
Endonuclease/exonuclease/phosphatase		1286
177IPR009050
Globin-like		1223
178IPR006447
Myb domain, plants		1229
179IPR001199
Cytochrome b5-like heme/steroid binding domain		12133
180IPR015847
Exoribonuclease, phosphorolytic domain 2		1238
181IPR002372
Pyrrolo-quinoline quinone repeat		1212
182IPR022967
RNA-binding domain, S1		1253
183IPR027409
GroEL-like apical domain		1248
184IPR011011
Zinc finger, FYVE/PHD-type		1229
185IPR029062
Class I glutamine amidotransferase-like		1256
186IPR009003
Peptidase S1, PA clan		1222
187IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		1212
188IPR001247
Exoribonuclease, phosphorolytic domain 1		1224
189IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		1248
190IPR003029
S1 domain		1292
191IPR021133
HEAT, type 2		1137
192IPR009022
Elongation factor G, III-V domain		1149
193IPR013216
Methyltransferase type 11		1128
194IPR002423
Chaperonin Cpn60/TCP-1 family		1124
195IPR027413
GroEL-like equatorial domain		1146
196IPR011761
ATP-grasp fold		1126
197IPR004443
YjeF N-terminal domain		1152
198IPR029057
Phosphoribosyltransferase-like		1164
199IPR010339
TIP49, C-terminal		1117
200IPR014722
Ribosomal protein L2 domain 2		1121
201IPR000644
CBS domain		11141
202IPR032976
YjeF N-terminal domain-containing protein, eukaryotes		1112
203IPR002110
Ankyrin repeat		11198
204IPR015797
NUDIX hydrolase domain-like		1159
205IPR006689
Small GTPase superfamily, ARF/SAR type		10107
206IPR002052
DNA methylase, N-6 adenine-specific, conserved site		1013
207IPR013328
6-phosphogluconate dehydrogenase, domain 2		1027
208IPR027408
PNPase/RNase PH domain		1021
209IPR018200
Ubiquitin specific protease, conserved site		1046
210IPR013320
Concanavalin A-like lectin/glucanase domain		1031
211IPR000089
Biotin/lipoyl attachment		1044
212IPR027238
RuvB-like		1012
213IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		1019
214IPR009030
Growth factor receptor cysteine-rich domain		1040
215IPR032466
Metal-dependent hydrolase		1018
216IPR001810
F-box domain		1096
217IPR001763
Rhodanese-like domain		10102
218IPR011060
Ribulose-phosphate binding barrel		1019
219IPR009014
Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II		1032
220IPR011053
Single hybrid motif		1026
221IPR011641
Tyrosine-protein kinase ephrin type A/B receptor-like		10133
222IPR004154
Anticodon-binding		1045
223IPR017937
Thioredoxin, conserved site		1025
224IPR031157
Tr-type G domain, conserved site		1019
225IPR002085
Alcohol dehydrogenase superfamily, zinc-type		1040
226IPR017907
Zinc finger, RING-type, conserved site		1035
227IPR001487
Bromodomain		10144
228IPR015947
PUA-like domain		1034
229IPR001932
PPM-type phosphatase domain		10117
230IPR012128
Phycobilisome, alpha/beta subunit		949
231IPR017884
SANT domain		918
232IPR010402
CCT domain		931
233IPR015940
Ubiquitin-associated domain		950
234IPR033248
Transketolase, C-terminal domain		914
235IPR029035
DHS-like NAD/FAD-binding domain		948
236IPR002909
IPT domain		926
237IPR004853
Sugar phosphate transporter domain		922
238IPR001297
Phycobilisome linker domain		948
239IPR001222
Zinc finger, TFIIS-type		946
240IPR002942
RNA-binding S4 domain		957
241IPR007197
Radical SAM		920
242IPR013763
Cyclin-like		999
243IPR017926
Glutamine amidotransferase		935
244IPR000640
Translation elongation factor EFG, V domain		948
245IPR002123
Phospholipid/glycerol acyltransferase		939
246IPR005331
Sulfotransferase		99
247IPR003406
Glycosyl transferase, family 14		915
248IPR013078
Histidine phosphatase superfamily, clade-1		928
249IPR001208
MCM domain		9112
250IPR007125
Histone H2A/H2B/H3		917
251IPR013815
ATP-grasp fold, subdomain 1		924
252IPR011051
RmlC-like cupin domain		918
253IPR004147
UbiB domain		917
254IPR002109
Glutaredoxin		936
255IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		932
256IPR000086
NUDIX hydrolase domain		942
257IPR014720
Double-stranded RNA-binding domain		930
258IPR001780
Ribosomal protein L35A		930
259IPR029047
Heat shock protein 70kD, peptide-binding domain		934
260IPR001404
Heat shock protein Hsp90 family		941
261IPR001965
Zinc finger, PHD-type		935
262IPR000594
THIF-type NAD/FAD binding fold		945
263IPR005069
Nucleotide-diphospho-sugar transferase		911
264IPR001806
Small GTPase superfamily		921
265IPR029064
50S ribosomal protein L30e-like		940
266IPR024156
Small GTPase superfamily, ARF type		921
267IPR029060
PIN domain-like		836
268IPR007502
Helicase-associated domain		830
269IPR001433
Oxidoreductase FAD/NAD(P)-binding		818
270IPR033762
MCM OB domain		816
271IPR032710
NTF2-like domain		826
272IPR003347
JmjC domain		830
273IPR007657
Glycosyltransferase AER61, uncharacterised		815
274IPR001296
Glycosyl transferase, family 1		818
275IPR013154
Alcohol dehydrogenase, N-terminal		825
276IPR019787
Zinc finger, PHD-finger		823
277IPR027640
Kinesin-like protein		872
278IPR016021
MIF4G-like domain		833
279IPR011650
Peptidase M20, dimerisation domain		832
280IPR023780
Chromo domain		810
281IPR020845
AMP-binding, conserved site		820
282IPR016193
Cytidine deaminase-like		817
283IPR004088
K Homology domain, type 1		882
284IPR002933
Peptidase M20		814
285IPR002194
Chaperonin TCP-1, conserved site		846
286IPR011333
SKP1/BTB/POZ domain		823
287IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		825
288IPR016185
Pre-ATP-grasp domain		841
289IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		873
290IPR000195
Rab-GTPase-TBC domain		874
291IPR013126
Heat shock protein 70 family		8126
292IPR031327
Mini-chromosome maintenance protein		816
293IPR006439
HAD hydrolase, subfamily IA		851
294IPR020843
Polyketide synthase, enoylreductase domain		821
295IPR000270
PB1 domain		824
296IPR017998
Chaperone tailless complex polypeptide 1 (TCP-1)		883
297IPR000477
Reverse transcriptase domain		813
298IPR001752
Kinesin motor domain		8175
299IPR000571
Zinc finger, CCCH-type		8170
300IPR023210
NADP-dependent oxidoreductase domain		866
301IPR000866
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant		812
302IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		843
303IPR001395
Aldo/keto reductase/potassium channel subunit beta		835
304IPR029048
Heat shock protein 70kD, C-terminal domain		830
305IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		816
306IPR005804
Fatty acid desaturase domain		817
307IPR000683
Oxidoreductase, N-terminal		716
308IPR006638
Elongator protein 3/MiaB/NifB		716
309IPR025110
AMP-binding enzyme C-terminal domain		717
310IPR000467
G-patch domain		736
311IPR004000
Actin family		7110
312IPR018506
Cytochrome b5, heme-binding site		713
313IPR013525
ABC-2 type transporter		724
314IPR008978
HSP20-like chaperone		730
315IPR008913
Zinc finger, CHY-type		716
316IPR013088
Zinc finger, NHR/GATA-type		715
317IPR002553
Clathrin/coatomer adaptor, adaptin-like, N-terminal		715
318IPR023333
Proteasome B-type subunit		715
319IPR017941
Rieske [2Fe-2S] iron-sulphur domain		744
320IPR002125
Cytidine and deoxycytidylate deaminases, zinc-binding		724
321IPR016039
Thiolase-like		768
322IPR002314
Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)		714
323IPR001907
ATP-dependent Clp protease proteolytic subunit		769
324IPR027005
Glycosyltransferase 39-like		710
325IPR011044
Quinoprotein amine dehydrogenase, beta chain-like		712
326IPR001374
R3H domain		762
327IPR027791
Galactosyltransferase, C-terminal		78
328IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		749
329IPR029056
Ribokinase-like		737
330IPR004875
DDE superfamily endonuclease domain		77
331IPR011332
Zinc-binding ribosomal protein		715
332IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		714
333IPR000639
Epoxide hydrolase-like		737
334IPR032630
P-type ATPase, C-terminal		710
335IPR006050
DNA photolyase, N-terminal		752
336IPR004039
Rubredoxin-type fold		714
337IPR017849
Alkaline phosphatase-like, alpha/beta/alpha		713
338IPR002935
O-methyltransferase, family 3		715
339IPR007696
DNA mismatch repair protein MutS, core		745
340IPR003591
Leucine-rich repeat, typical subtype		756
341IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		719
342IPR000994
Peptidase M24, structural domain		756
343IPR029028
Alpha/beta knot methyltransferases		720
344IPR005477
Deoxyxylulose-5-phosphate synthase		712
345IPR000426
Proteasome alpha-subunit, N-terminal domain		742
346IPR018525
Mini-chromosome maintenance, conserved site		714
347IPR029006
ADF-H/Gelsolin-like domain		715
348IPR001233
tRNA-splicing ligase, RtcB		726
349IPR000192
Aminotransferase class V domain		715
350IPR017850
Alkaline-phosphatase-like, core domain		716
351IPR015946
K homology domain-like, alpha/beta		714
352IPR000620
EamA domain		714
353IPR011709
Domain of unknown function DUF1605		713
354IPR023332
Proteasome A-type subunit		714
355IPR027410
TCP-1-like chaperonin intermediate domain		732
356IPR023562
Clp protease proteolytic subunit /Translocation-enhancing protein TepA		724
357IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		715
358IPR000432
DNA mismatch repair protein MutS, C-terminal		743
359IPR000679
Zinc finger, GATA-type		745
360IPR017972
Cytochrome P450, conserved site		713
361IPR000727
Target SNARE coiled-coil homology domain		650
362IPR006091
Acyl-CoA oxidase/dehydrogenase, central domain		614
363IPR006171
Toprim domain		632
364IPR000433
Zinc finger, ZZ-type		642
365IPR023404
Radical SAM, alpha/beta horseshoe		611
366IPR018490
Cyclic nucleotide-binding-like		611
367IPR008971
HSP40/DnaJ peptide-binding		639
368IPR006153
Cation/H+ exchanger		615
369IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		614
370IPR009025
DNA-directed RNA polymerase, RBP11-like dimerisation domain		622
371IPR032640
AMP-activated protein kinase, glycogen-binding domain		615
372IPR019821
Kinesin motor domain, conserved site		617
373IPR025714
Methyltransferase domain		69
374IPR013149
Alcohol dehydrogenase, C-terminal		622
375IPR000217
Tubulin		6131
376IPR013784
Carbohydrate-binding-like fold		612
377IPR001107
Band 7 domain		631
378IPR001305
Heat shock protein DnaJ, cysteine-rich domain		651
379IPR017975
Tubulin, conserved site		615
380IPR001091
Restriction/modification DNA-methylase		620
381IPR015720
TMP21-related		615
382IPR009008
Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain		629
383IPR029021
Protein-tyrosine phosphatase-like		638
384IPR004100
ATPase, F1 complex alpha/beta subunit, N-terminal domain		624
385IPR018215
ClpP, Ser active site		69
386IPR029065
Enolase C-terminal domain-like		615
387IPR001753
Crotonase superfamily		610
388IPR001373
Cullin, N-terminal		613
389IPR016050
Proteasome beta-type subunit, conserved site		612
390IPR001254
Serine proteases, trypsin domain		621
391IPR030960
3-dehydroquinate synthase domain		67
392IPR013155
Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding		613
393IPR032421
Protein O-mannosyl-transferase, C-terminal four TM domain		68
394IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		644
395IPR017921
Zinc finger, CTCHY-type		67
396IPR018150
Aminoacyl-tRNA synthetase, class II (D/K/N)-like		621
397IPR002300
Aminoacyl-tRNA synthetase, class Ia		617
398IPR021109
Aspartic peptidase domain		656
399IPR001451
Hexapeptide repeat		629
400IPR008280
Tubulin/FtsZ, C-terminal		616
401IPR022630
S-adenosylmethionine synthetase, C-terminal		68
402IPR006145
Pseudouridine synthase, RsuA/RluB/C/D/E/F		612
403IPR005101
Cryptochrome/DNA photolyase, FAD-binding domain		624
404IPR000210
BTB/POZ domain		641
405IPR022812
Dynamin superfamily		643
406IPR007235
Glycosyl transferase, family 28, C-terminal		610
407IPR002938
FAD-binding domain		612
408IPR010989
t-SNARE		618
409IPR004365
OB-fold nucleic acid binding domain, AA-tRNA synthetase-type		613
410IPR003323
OTU domain		626
411IPR016166
FAD-binding, type 2		622
412IPR013786
Acyl-CoA dehydrogenase/oxidase, N-terminal		622
413IPR001375
Peptidase S9, prolyl oligopeptidase, catalytic domain		616
414IPR003008
Tubulin/FtsZ, GTPase domain		671
415IPR020581
Glycine cleavage system P protein		618
416IPR006630
RNA-binding protein Lupus La		625
417IPR011013
Galactose mutarotase-like domain		615
418IPR016156
FAD/NAD-linked reductase, dimerisation domain		615
419IPR019786
Zinc finger, PHD-type, conserved site		617
420IPR009038
GOLD domain		634
421IPR020904
Short-chain dehydrogenase/reductase, conserved site		614
422IPR004160
Translation elongation factor EFTu/EF1A, C-terminal		611
423IPR002133
S-adenosylmethionine synthetase		618
424IPR003682
rRNA small subunit methyltransferase G		619
425IPR032678
tRNA synthetases class I, catalytic domain		610
426IPR024909
Cysteinyl-tRNA synthetase/mycothiol ligase		643
427IPR005937
26S proteasome subunit P45		612
428IPR015655
Protein phosphatase 2C family		617
429IPR007081
RNA polymerase Rpb1, domain 5		614
430IPR001709
Flavoprotein pyridine nucleotide cytochrome reductase		670
431IPR031167
OBG-type guanine nucleotide-binding (G) domain		614
432IPR004046
Glutathione S-transferase, C-terminal		616
433IPR009075
Acyl-CoA dehydrogenase/oxidase C-terminal		632
434IPR029026
tRNA (guanine-N1-)-methyltransferase, N-terminal		617
435IPR004038
Ribosomal protein L7Ae/L30e/S12e/Gadd45		613
436IPR005151
Tail specific protease		619
437IPR002941
DNA methylase N-4/N-6		66
438IPR004087
K Homology domain		622
439IPR023123
Tubulin, C-terminal		614
440IPR016161
Aldehyde/histidinol dehydrogenase		625
441IPR022636
S-adenosylmethionine synthetase superfamily		615
442IPR002939
Chaperone DnaJ, C-terminal		614
443IPR000760
Inositol monophosphatase		653
444IPR009100
Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain		615
445IPR023298
P-type ATPase, transmembrane domain		618
446IPR004364
Aminoacyl-tRNA synthetase, class II (D/K/N)		613
447IPR023779
Chromo domain, conserved site		67
448IPR008803
RHD3/Sey1		614
449IPR002912
ACT domain		629
450IPR002641
Patatin/Phospholipase A2-related		611
451IPR020003
ATPase, alpha/beta subunit, nucleotide-binding domain, active site		613
452IPR003342
Glycosyl transferase family 39/83		68
453IPR001012
UBX domain		628
454IPR000555
JAB1/MPN/MOV34 metalloenzyme domain		628
455IPR000903
Myristoyl-CoA:protein N-myristoyltransferase		610
456IPR004155
PBS lyase HEAT-like repeat		653
457IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		6111
458IPR017877
Myb-like domain		629
459IPR006141
Intein N-terminal splicing region		68
460IPR003395
RecF/RecN/SMC, N-terminal		613
461IPR005844
Alpha-D-phosphohexomutase, alpha/beta/alpha domain I		510
462IPR014284
RNA polymerase sigma-70 like domain		510
463IPR006554
Helicase-like, DEXD box c2 type		510
464IPR002921
Fungal lipase-like domain		58
465IPR003100
PAZ domain		514
466IPR001940
Peptidase S1C		558
467IPR013632
DNA recombination and repair protein Rad51, C-terminal		59
468IPR011258
BPG-independent PGAM, N-terminal		518
469IPR015927
Peptidase S24/S26A/S26B/S26C		512
470IPR012258
Acyl-CoA oxidase		57
471IPR006594
LIS1 homology motif		531
472IPR004240
Nonaspanin (TM9SF)		519
473IPR010614
DEAD2		510
474IPR008949
Isoprenoid synthase domain		524
475IPR000648
Oxysterol-binding protein		527
476IPR014371
Sterol O-acyltransferase, ACAT/DAG/ARE types		511
477IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		520
478IPR020810
Enolase, C-terminal TIM barrel domain		512
479IPR032781
ABC-transporter extension domain		57
480IPR000537
UbiA prenyltransferase family		511
481IPR027084
Dual specificity protein kinase TTK		58
482IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		59
483IPR002403
Cytochrome P450, E-class, group IV		557
484IPR030381
Dynamin-type guanine nucleotide-binding (G) domain		56
485IPR005517
Translation elongation factor EFG/EF2, domain IV		520
486IPR012678
Ribosomal protein L23/L15e core domain		59
487IPR028360
Peptidase S24/S26, beta-ribbon domain		514
488IPR015353
Rubisco LSMT, substrate-binding domain		524
489IPR000941
Enolase		547
490IPR001440
Tetratricopeptide repeat 1		516
491IPR003954
RNA recognition motif domain, eukaryote		530
492IPR003034
SAP domain		537
493IPR027806
Harbinger transposase-derived nuclease domain		55
494IPR004099
Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain		524
495IPR006592
RNA polymerase, N-terminal		510
496IPR006680
Amidohydrolase-related		510
497IPR009078
Ferritin-like superfamily		511
498IPR002655
Acyl-CoA oxidase, C-terminal		57
499IPR002068
Alpha crystallin/Hsp20 domain		517
500IPR006895
Zinc finger, Sec23/Sec24-type		517
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae.html b/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae.html new file mode 100644 index 00000000..83257e25 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae.html @@ -0,0 +1,112 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM9120v1, Nov 2008
Database version:86.1
Base Pairs:16,728,945
Golden Path Length:16,728,945
Genebuild by: ENA
Genebuild method: Generated from ENA and UniProtKB annotation
Genebuild started: May 2003
Genebuild released: May 2003
Genebuild last updated/patched: Nov 2008
Genebuild version: 2008-11-ENA
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		5,009
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		33
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:5,106
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
22 sequences
+
+ +
+ + + +
SequenceLength (bp)
1422616
2457013
3481791
4513455
5528682
6536163
7584452
8739753
9810151
10839707
11852849
12859119
13866983
14852727
15902900
16908485
171232258
181253087
191282939
201621617
Mito32211
Chloro149987
+
+
contig
+
22 sequences
+
+ +
+ + + +
SequenceLength (bp)
AB002583.1149987
AP006483.2422616
AP006484.2457013
AP006485.2481791
AP006486.2513455
AP006487.2528682
AP006488.2536163
AP006489.2584452
AP006490.2739753
AP006491.2810151
AP006492.2839707
AP006493.2852849
AP006494.2859119
AP006495.2866983
AP006496.2852727
AP006497.2902900
AP006498.2908485
AP006499.21232258
AP006500.21253087
AP006501.21282939
AP006502.21621617
D89861.132211
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae_IPtop500.html new file mode 100644 index 00000000..55996674 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Cyanidioschyzon_merolae_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		3251053
2IPR016040
NAD(P)-binding domain		137327
3IPR015943
WD40/YVTN repeat-like-containing domain		99186
4IPR003593
AAA+ ATPase domain		98121
5IPR017986
WD40-repeat-containing domain		91238
6IPR016024
Armadillo-type fold		87253
7IPR011009
Protein kinase-like domain		84128
8IPR001680
WD40 repeat		78773
9IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		77192
10IPR000719
Protein kinase, catalytic domain		69188
11IPR013083
Zinc finger, RING/FYVE/PHD-type		6271
12IPR011991
Winged helix-turn-helix DNA-binding domain		62115
13IPR011990
Tetratricopeptide-like helical		60213
14IPR001650
Helicase, C-terminal		56165
15IPR014001
Helicase, superfamily 1/2, ATP-binding domain		56109
16IPR011989
Armadillo-like helical		55120
17IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		5573
18IPR012340
Nucleic acid-binding, OB-fold		5574
19IPR008271
Serine/threonine-protein kinase, active site		5050
20IPR009057
Homeodomain-like		49120
21IPR012336
Thioredoxin-like fold		47103
22IPR019775
WD40 repeat, conserved site		4776
23IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		46213
24IPR029058
Alpha/Beta hydrolase fold		46134
25IPR013785
Aldolase-type TIM barrel		4550
26IPR017441
Protein kinase, ATP binding site		4444
27IPR023214
HAD-like domain		41139
28IPR003959
ATPase, AAA-type, core		4051
29IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		3941
30IPR012677
Nucleotide-binding, alpha-beta plait		39114
31IPR015424
Pyridoxal phosphate-dependent transferase		3947
32IPR001841
Zinc finger, RING-type		3879
33IPR020568
Ribosomal protein S5 domain 2-type fold		3651
34IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		3636
35IPR003439
ABC transporter-like		3582
36IPR001005
SANT/Myb domain		3585
37IPR005225
Small GTP-binding protein domain		3435
38IPR029044
Nucleotide-diphospho-sugar transferases		3276
39IPR018108
Mitochondrial substrate/solute carrier		31183
40IPR023395
Mitochondrial carrier domain		3176
41IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		3135
42IPR001623
DnaJ domain		29199
43IPR017871
ABC transporter, conserved site		2934
44IPR020472
G-protein beta WD-40 repeat		2781
45IPR019734
Tetratricopeptide repeat		26257
46IPR029055
Nucleophile aminohydrolases, N-terminal		2654
47IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		2528
48IPR000504
RNA recognition motif domain		25114
49IPR016181
Acyl-CoA N-acyltransferase		2452
50IPR013026
Tetratricopeptide repeat-containing domain		2438
51IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		2427
52IPR000182
GNAT domain		2237
53IPR002347
Glucose/ribitol dehydrogenase		22151
54IPR029045
ClpP/crotonase-like domain		2173
55IPR020846
Major facilitator superfamily domain		2143
56IPR015915
Kelch-type beta propeller		2130
57IPR000477
Reverse transcriptase		2139
58IPR010920
Like-Sm (LSM) domain		2022
59IPR014014
RNA helicase, DEAD-box type, Q motif		2020
60IPR012337
Ribonuclease H-like domain		2049
61IPR017930
Myb domain		2027
62IPR009072
Histone-fold		2038
63IPR000795
Elongation factor, GTP-binding domain		19102
64IPR003960
ATPase, AAA-type, conserved site		1920
65IPR016135
Ubiquitin-conjugating enzyme/RWD-like		1938
66IPR029052
Metallo-dependent phosphatase-like		1957
67IPR006073
GTP binding domain		1952
68IPR001305
Heat shock protein DnaJ, cysteine-rich domain		1841
69IPR004843
Metallophosphoesterase domain		1717
70IPR006195
Aminoacyl-tRNA synthetase, class II		1717
71IPR001163
Ribonucleoprotein LSM domain		1734
72IPR013766
Thioredoxin domain		1733
73IPR017853
Glycoside hydrolase, superfamily		1729
74IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		1721
75IPR002067
Mitochondrial carrier protein		1780
76IPR001965
Zinc finger, PHD-type		1721
77IPR000608
Ubiquitin-conjugating enzyme, E2		1632
78IPR008991
Translation protein SH3-like domain		1616
79IPR012675
Beta-grasp domain		1617
80IPR029071
Ubiquitin-related domain		1617
81IPR015797
NUDIX hydrolase domain-like		1637
82IPR028992
Hedgehog/Intein (Hint) domain		1546
83IPR001353
Proteasome, subunit alpha/beta		1516
84IPR007087
Zinc finger, C2H2		1556
85IPR013816
ATP-grasp fold, subdomain 2		1517
86IPR032675
Leucine-rich repeat domain, L domain-like		1531
87IPR004839
Aminotransferase, class I/classII		1515
88IPR011011
Zinc finger, FYVE/PHD-type		1516
89IPR000519
P-type trefoil		15134
90IPR029062
Class I glutamine amidotransferase-like		1539
91IPR001767
Hint domain		1515
92IPR007197
Radical SAM		1414
93IPR013783
Immunoglobulin-like fold		1418
94IPR013763
Cyclin-like		1452
95IPR000073
Alpha/beta hydrolase fold-1		1428
96IPR011012
Longin-like domain		1416
97IPR010987
Glutathione S-transferase, C-terminal-like		1435
98IPR000086
NUDIX hydrolase domain		1427
99IPR001657
Hedgehog protein		1345
100IPR002048
Calcium-binding EF-hand		1350
101IPR000330
SNF2-related		1313
102IPR029061
Thiamin diphosphate-binding fold		1342
103IPR001478
PDZ domain		1349
104IPR002423
Chaperonin Cpn60/TCP-1		1313
105IPR027413
GroEL-like equatorial domain		1327
106IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		1313
107IPR027409
GroEL-like apical domain		1326
108IPR018253
DnaJ domain, conserved site		1313
109IPR011527
ABC transporter, transmembrane domain, type 1		1346
110IPR000644
Cystathionine beta-synthase, core		1356
111IPR017907
Zinc finger, RING-type, conserved site		1313
112IPR011992
EF-hand-like domain		1331
113IPR013328
Dehydrogenase, multihelical		1216
114IPR004853
Domain of unknown function DUF250		1213
115IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1212
116IPR013216
Methyltransferase type 11		1212
117IPR011761
ATP-grasp fold		1214
118IPR018247
EF-Hand 1, calcium-binding site		1219
119IPR003587
Hint domain N-terminal		1212
120IPR020103
Pseudouridine synthase, catalytic domain		1226
121IPR023313
Ubiquitin-conjugating enzyme, active site		1212
122IPR014722
Ribosomal protein L2 domain 2		1212
123IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		1221
124IPR001806
Small GTPase superfamily		1213
125IPR011032
GroES-like		1123
126IPR006638
Elongator protein 3/MiaB/NifB		1111
127IPR029021
Protein-tyrosine phosphatase-like		1130
128IPR000089
Biotin/lipoyl attachment		1120
129IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1111
130IPR017926
Glutamine amidotransferase type 1		1120
131IPR003594
Histidine kinase-like ATPase, ATP-binding domain		1140
132IPR011060
Ribulose-phosphate binding barrel		1111
133IPR006050
DNA photolyase, N-terminal		1132
134IPR011053
Single hybrid motif		1112
135IPR020683
Ankyrin repeat-containing domain		1159
136IPR013781
Glycoside hydrolase, catalytic domain		1118
137IPR004154
Anticodon-binding		1127
138IPR013815
ATP-grasp fold, subdomain 1		1114
139IPR004045
Glutathione S-transferase, N-terminal		1121
140IPR004147
UbiB domain		1112
141IPR014756
Immunoglobulin E-set		1114
142IPR002912
ACT domain		1117
143IPR001611
Leucine-rich repeat		1149
144IPR015947
PUA-like domain		1118
145IPR000727
Target SNARE coiled-coil domain		1019
146IPR017938
Riboflavin synthase-like beta-barrel		1013
147IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		1020
148IPR008250
P-type ATPase, A domain		1029
149IPR023393
START-like domain		1010
150IPR001509
NAD-dependent epimerase/dehydratase		1010
151IPR001279
Beta-lactamase-like		1043
152IPR005101
DNA photolyase, FAD-binding/Cryptochrome, C-terminal		1017
153IPR014710
RmlC-like jelly roll fold		1014
154IPR027482
Sec1-like, domain 2		1024
155IPR002194
Chaperonin TCP-1, conserved site		1022
156IPR023299
P-type ATPase, cytoplasmic domain N		1020
157IPR016185
Pre-ATP-grasp domain		1023
158IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		1010
159IPR014720
Double-stranded RNA-binding domain		1014
160IPR001619
Sec1-like protein		1070
161IPR017998
Chaperone, tailless complex polypeptide 1		1049
162IPR002110
Ankyrin repeat		1097
163IPR027410
TCP-1-like chaperonin intermediate domain		1020
164IPR029064
50S ribosomal protein L30e-like		1019
165IPR015880
Zinc finger, C2H2-like		1033
166IPR006141
Intein splice site		1010
167IPR017927
Ferredoxin reductase-type FAD-binding domain		99
168IPR000626
Ubiquitin domain		923
169IPR017884
SANT domain		911
170IPR013784
Carbohydrate-binding-like fold		912
171IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		916
172IPR009060
UBA-like		910
173IPR011701
Major facilitator superfamily		99
174IPR000717
Proteasome component (PCI) domain		917
175IPR001451
Bacterial transferase hexapeptide repeat		915
176IPR005135
Endonuclease/exonuclease/phosphatase		935
177IPR009050
Globin-like		910
178IPR019787
Zinc finger, PHD-finger		916
179IPR006447
Myb domain, plants		99
180IPR002123
Phospholipid/glycerol acyltransferase		918
181IPR029057
Phosphoribosyltransferase-like		923
182IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		99
183IPR029028
Alpha/beta knot methyltransferases		913
184IPR018303
P-type ATPase, phosphorylation site		99
185IPR001757
Cation-transporting P-type ATPase		931
186IPR031157
Tr-type G domain, conserved site		99
187IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		918
188IPR001487
Bromodomain		963
189IPR002937
Amine oxidase		910
190IPR029033
Histidine phosphatase superfamily		925
191IPR001041
2Fe-2S ferredoxin-type domain		925
192IPR011993
Pleckstrin homology-like domain		921
193IPR017877
Myb-like domain		912
194IPR003029
Ribosomal protein S1, RNA-binding domain		926
195IPR012128
Phycobilisome, alpha/beta subunit		824
196IPR033762
MCM OB domain		88
197IPR013525
ABC-2 type transporter		88
198IPR009022
Elongation factor G, III-V domain		819
199IPR001357
BRCT domain		847
200IPR002942
RNA-binding S4 domain		831
201IPR011237
Peptidase M16 domain		820
202IPR000873
AMP-dependent synthetase/ligase		88
203IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		818
204IPR029056
Ribokinase-like		819
205IPR001199
Cytochrome b5-like heme/steroid binding domain		852
206IPR011332
Ribosomal protein, zinc-binding domain		88
207IPR003008
Tubulin/FtsZ, GTPase domain		851
208IPR000850
Adenylate kinase		847
209IPR003107
RNA-processing protein, HAT helix		858
210IPR007696
DNA mismatch repair protein MutS, core		827
211IPR001208
Mini-chromosome maintenance, DNA-dependent ATPase		855
212IPR022967
RNA-binding domain, S1		816
213IPR000994
Peptidase M24, structural domain		830
214IPR016193
Cytidine deaminase-like		88
215IPR004088
K Homology domain, type 1		821
216IPR029026
tRNA (guanine-N1-)-methyltransferase, N-terminal		810
217IPR017937
Thioredoxin, conserved site		88
218IPR011051
RmlC-like cupin domain		88
219IPR002085
Alcohol dehydrogenase superfamily, zinc-type		812
220IPR011249
Metalloenzyme, LuxS/M16 peptidase-like		825
221IPR031327
Mini-chromosome maintenance protein		88
222IPR001214
SET domain		819
223IPR000571
Zinc finger, CCCH-type		852
224IPR007863
Peptidase M16, C-terminal domain		810
225IPR000432
DNA mismatch repair protein MutS, C-terminal		823
226IPR033690
Adenylate kinase, conserved site		88
227IPR008942
ENTH/VHS		715
228IPR000683
Oxidoreductase, N-terminal		77
229IPR029060
PIN domain-like		717
230IPR006594
LisH dimerisation motif		712
231IPR008949
Terpenoid synthase		714
232IPR032710
NTF2-like domain		710
233IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		730
234IPR029035
DHS-like NAD/FAD-binding domain		720
235IPR000387
Protein-tyrosine/Dual specificity phosphatase		77
236IPR029000
Cyclophilin-like domain		714
237IPR025714
Methyltransferase domain		78
238IPR013149
Alcohol dehydrogenase, C-terminal		77
239IPR003034
SAP domain		720
240IPR003607
HD/PDEase domain		79
241IPR023333
Proteasome B-type subunit		77
242IPR002125
CMP/dCMP deaminase, zinc-binding		713
243IPR007861
DNA mismatch repair protein MutS, clamp		77
244IPR002314
Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain		77
245IPR002300
Aminoacyl-tRNA synthetase, class Ia		77
246IPR001296
Glycosyl transferase, family 1		77
247IPR012676
TGS-like		77
248IPR008280
Tubulin/FtsZ, C-terminal		79
249IPR013105
Tetratricopeptide TPR2		78
250IPR027005
Glycosyltransferase 39 like		77
251IPR020084
NUDIX hydrolase, conserved site		77
252IPR011257
DNA glycosylase		713
253IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		717
254IPR017932
Glutamine amidotransferase type 2 domain		710
255IPR001763
Rhodanese-like domain		736
256IPR010989
t-SNARE		79
257IPR004365
Nucleic acid binding, OB-fold, tRNA/helicase-type		77
258IPR000640
Translation elongation factor EFG, V domain		719
259IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		77
260IPR016055
Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III		736
261IPR004039
Rubredoxin-type fold		77
262IPR020904
Short-chain dehydrogenase/reductase, conserved site		77
263IPR001236
Lactate/malate dehydrogenase, N-terminal		77
264IPR013078
Histidine phosphatase superfamily, clade-1		714
265IPR015813
Pyruvate/Phosphoenolpyruvate kinase		721
266IPR013024
Butirosin biosynthesis, BtrG-like		712
267IPR008979
Galactose-binding domain-like		711
268IPR002044
Carbohydrate binding module family 20		724
269IPR011004
Trimeric LpxA-like		77
270IPR002035
von Willebrand factor, type A		718
271IPR005475
Transketolase-like, pyrimidine-binding domain		714
272IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		712
273IPR016161
Aldehyde/histidinol dehydrogenase		78
274IPR000426
Proteasome, alpha-subunit, N-terminal domain		721
275IPR033391
Fructose-1-6-bisphosphatase class I, N-terminal		77
276IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		715
277IPR000195
Rab-GTPase-TBC domain		737
278IPR004104
Oxidoreductase, C-terminal		77
279IPR018525
Mini-chromosome maintenance, conserved site		77
280IPR020843
Polyketide synthase, enoylreductase		77
281IPR011765
Peptidase M16, N-terminal		78
282IPR006968
Protein of unknown function DUF647		717
283IPR023332
Proteasome A-type subunit		77
284IPR000594
UBA/THIF-type NAD/FAD binding fold		719
285IPR000866
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant		77
286IPR022383
Lactate/malate dehydrogenase, C-terminal		77
287IPR001932
Protein phosphatase 2C (PP2C)-like		743
288IPR017896
4Fe-4S ferredoxin-type, iron-sulpur binding domain		716
289IPR003586
Hint domain C-terminal		77
290IPR005804
Fatty acid desaturase, type 1		77
291IPR015955
Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal		714
292IPR005844
Alpha-D-phosphohexomutase, alpha/beta/alpha domain I		66
293IPR015927
Peptidase S24/S26A/S26B/S26C		66
294IPR007502
Helicase-associated domain		611
295IPR006171
Toprim domain		615
296IPR001433
Oxidoreductase FAD/NAD(P)-binding		66
297IPR006689
Small GTPase superfamily, ARF/SAR type		623
298IPR000326
Phosphatidic acid phosphatase type 2/haloperoxidase		622
299IPR003316
Transcription factor E2F/dimerisation partner (TDP)		614
300IPR004000
Actin-related protein		641
301IPR008971
HSP40/DnaJ peptide-binding		616
302IPR000537
UbiA prenyltransferase family		66
303IPR006153
Cation/H+ exchanger		66
304IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		66
305IPR028360
Peptidase S24/S26, beta-ribbon domain		68
306IPR005024
Snf7 family		66
307IPR013088
Zinc finger, NHR/GATA-type		66
308IPR002553
Clathrin/coatomer adaptor, adaptin-like, N-terminal		66
309IPR009078
Ferritin/ribonucleotide reductase-like		66
310IPR009008
Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain		613
311IPR013320
Concanavalin A-like lectin/glucanase, subgroup		69
312IPR004100
ATPase, alpha/beta subunit, N-terminal		611
313IPR016039
Thiolase-like		637
314IPR033247
Transketolase family		69
315IPR013155
Valyl/Leucyl/Isoleucyl-tRNA synthetase, class I, anticodon-binding		66
316IPR032421
Protein O-mannosyl-transferase, C-terminal four TM domain		66
317IPR002885
Pentatricopeptide repeat		688
318IPR019759
Peptidase S24/S26A/S26B		66
319IPR018150
Aminoacyl-tRNA synthetase, class II (D/K/N)-like		69
320IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		612
321IPR006145
Pseudouridine synthase, RsuA/RluB/C/D/E/F		67
322IPR032466
Metal-dependent hydrolase		68
323IPR013154
Alcohol dehydrogenase GroES-like		66
324IPR003016
2-oxo acid dehydrogenase, lipoyl-binding site		67
325IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		617
326IPR019786
Zinc finger, PHD-type, conserved site		67
327IPR004360
Glyoxalase/fosfomycin resistance/dioxygenase domain		66
328IPR019489
Clp ATPase, C-terminal		612
329IPR007125
Histone core		66
330IPR024079
Metallopeptidase, catalytic domain		68
331IPR005937
26S proteasome subunit P45		66
332IPR005843
Alpha-D-phosphohexomutase, C-terminal		611
333IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		67
334IPR015902
Glycoside hydrolase, family 13		616
335IPR005746
Thioredoxin		611
336IPR031167
OBG-type guanine nucleotide-binding (G) domain		66
337IPR004038
Ribosomal protein L7Ae/L30e/S12e/Gadd45		66
338IPR029069
HotDog domain		615
339IPR006671
Cyclin, N-terminal		68
340IPR002939
Chaperone DnaJ, C-terminal		66
341IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		627
342IPR001356
Homeobox domain		615
343IPR013126
Heat shock protein 70 family		653
344IPR004364
Aminoacyl-tRNA synthetase, class II (D/K/N)		66
345IPR011054
Rudiment single hybrid motif		66
346IPR006047
Glycosyl hydrolase, family 13, catalytic domain		612
347IPR015946
K homology domain-like, alpha/beta		66
348IPR000620
Drug/metabolite transporter		69
349IPR029047
Heat shock protein 70kD, peptide-binding domain		612
350IPR005814
Aminotransferase class-III		623
351IPR020003
ATPase, alpha/beta subunit, nucleotide-binding domain, active site		66
352IPR003265
HhH-GPD domain		612
353IPR005479
Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain		623
354IPR016162
Aldehyde dehydrogenase, N-terminal		68
355IPR001557
L-lactate/malate dehydrogenase		634
356IPR001247
Exoribonuclease, phosphorolytic domain 1		69
357IPR002781
Transmembrane protein TauE like		614
358IPR000679
Zinc finger, GATA-type		620
359IPR017900
4Fe-4S ferredoxin, iron-sulphur binding, conserved site		68
360IPR015590
Aldehyde dehydrogenase domain		66
361IPR016163
Aldehyde dehydrogenase, C-terminal		66
362IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		66
363IPR027925
MCM N-terminal domain		66
364IPR004274
NLI interacting factor		618
365IPR003395
RecF/RecN/SMC, N-terminal		66
366IPR006554
Helicase-like, DEXD box c2 type		55
367IPR002921
Lipase, class 3		55
368IPR016102
Succinyl-CoA synthetase-like		511
369IPR001940
Peptidase S1C		529
370IPR022764
Peptidase S54, rhomboid domain		59
371IPR010614
DEAD2		56
372IPR000433
Zinc finger, ZZ-type		522
373IPR023404
Radical SAM, alpha/beta horseshoe		56
374IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		519
375IPR021133
HEAT, type 2		512
376IPR033248
Transketolase, C-terminal domain		55
377IPR031645
Vacuolar protein sorting-associated protein 13, C-terminal		55
378IPR027408
PNPase/RNase PH domain		59
379IPR012678
Ribosomal protein L23/L15e core domain		55
380IPR009025
DNA-directed RNA polymerase, RBP11-like		514
381IPR004821
Cytidyltransferase-like domain		59
382IPR001440
Tetratricopeptide TPR-1		57
383IPR001251
CRAL-TRIO domain		518
384IPR006115
6-phosphogluconate dehydrogenase, NADP-binding		55
385IPR029510
Aldehyde dehydrogenase, glutamic acid active site		55
386IPR011016
Zinc finger, RING-CH-type		510
387IPR016050
Proteasome, beta-type subunit, conserved site		55
388IPR014719
Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like		510
389IPR000297
Peptidyl-prolyl cis-trans isomerase, PpiC-type		510
390IPR000340
Dual specificity phosphatase, catalytic domain		55
391IPR004143
Biotin/lipoate A/B protein ligase		58
392IPR001943
UVR domain		513
393IPR000352
Peptide chain release factor class I/class II		59
394IPR008921
DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal		55
395IPR001907
ATP-dependent Clp protease proteolytic subunit		530
396IPR024950
Dual specificity phosphatase		57
397IPR005828
General substrate transporter		57
398IPR011611
Carbohydrate kinase PfkB		56
399IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		511
400IPR018181
Heat shock protein 70, conserved site		513
401IPR006553
Leucine-rich repeat, cysteine-containing subtype		541
402IPR029903
RmlD-like substrate binding domain		55
403IPR001810
F-box domain, cyclin-like		517
404IPR003337
Trehalose-phosphatase		511
405IPR000408
Regulator of chromosome condensation, RCC1		556
406IPR006694
Fatty acid hydroxylase		55
407IPR003323
Ovarian tumour, otubain		59
408IPR027640
Kinesin-like protein		520
409IPR016021
MIF4-like, type 1/2/3		512
410IPR016142
Citrate synthase-like, large alpha subdomain		55
411IPR006555
ATP-dependent helicase, C-terminal		510
412IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		59
413IPR008011
Complex 1 LYR protein		55
414IPR003958
Transcription factor CBF/NF-Y/archaeal histone		55
415IPR009014
Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II		510
416IPR016156
FAD/NAD-linked reductase, dimerisation		55
417IPR009038
GOLD domain		513
418IPR004160
Translation elongation factor EFTu/EF1A, C-terminal		55
419IPR000223
Peptidase S26A, signal peptidase I		523
420IPR014013
Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type		55
421IPR001537
tRNA/rRNA methyltransferase, SpoU		57
422IPR004014
Cation-transporting P-type ATPase, N-terminal		59
423IPR002478
Pseudouridine synthase/archaeosine transglycosylase		512
424IPR023213
Chloramphenicol acetyltransferase-like domain		55
425IPR006076
FAD dependent oxidoreductase		55
426IPR007109
Brix domain		518
427IPR006843
Plastid lipid-associated protein/fibrillin conserved domain		55
428IPR015655
Protein phosphatase 2C		516
429IPR001709
Flavoprotein pyridine nucleotide cytochrome reductase		526
430IPR000793
ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal		57
431IPR002020
Citrate synthase-like		537
432IPR005936
Peptidase, FtsH		510
433IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		510
434IPR005031
Streptomyces cyclase/dehydrase		55
435IPR000146
Fructose-1,6-bisphosphatase class 1/Sedoheputulose-1,7-bisphosphatase		512
436IPR000642
Peptidase M41		55
437IPR004095
TGS		55
438IPR016066
Alpha-D-phosphohexomutase, conserved site		55
439IPR002109
Glutaredoxin		59
440IPR005888
dTDP-glucose 4,6-dehydratase		55
441IPR011146
HIT-like domain		516
442IPR000322
Glycoside hydrolase, family 31		55
443IPR001048
Aspartate/glutamate/uridylate kinase		521
444IPR023170
Helix-turn-helix, base-excision DNA repair, C-terminal		55
445IPR029006
ADF-H/Gelsolin-like domain		58
446IPR009003
Trypsin-like cysteine/serine peptidase domain		56
447IPR023298
P-type ATPase, transmembrane domain		510
448IPR011037
Pyruvate kinase-like, insert domain		56
449IPR000192
Aminotransferase, class V/Cysteine desulfurase		55
450IPR001128
Cytochrome P450		533
451IPR008803
Root hair defective 3 GTP-binding		58
452IPR001752
Kinesin, motor domain		540
453IPR002641
Patatin/Phospholipase A2-related		55
454IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		515
455IPR001173
Glycosyl transferase, family 2		55
456IPR007248
Mpv17/PMP22		510
457IPR011709
Domain of unknown function DUF1605		55
458IPR000555
JAB1/Mov34/MPN/PAD-1		58
459IPR004861
Protein-tyrosine phosphatase, SIW14-like		55
460IPR023562
Clp protease proteolytic subunit /Translocation-enhancing protein TepA		510
461IPR018177
L-lactate dehydrogenase, active site		55
462IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		55
463IPR001078
2-oxoacid dehydrogenase acyltransferase, catalytic domain		55
464IPR029048
Heat shock protein 70kD, C-terminal domain		59
465IPR024156
Small GTPase superfamily, ARF type		55
466IPR002634
BolA protein		410
467IPR014284
RNA polymerase sigma-70 like domain		44
468IPR004217
Tim10/DDP family zinc finger		412
469IPR000878
Tetrapyrrole methylase		48
470IPR001270
Chaperonin ClpA/B		416
471IPR009019
K homology domain, prokaryotic type		44
472IPR000589
Ribosomal protein S15		412
473IPR013632
DNA recombination and repair protein Rad51, C-terminal		44
474IPR006133
DNA-directed DNA polymerase, family B, exonuclease domain		44
475IPR023267
RNA (C5-cytosine) methyltransferase		418
476IPR020805
Cell division protein FtsZ, conserved site		47
477IPR018506
Cytochrome b5, heme-binding site		44
478IPR010935
SMCs flexible hinge		412
479IPR002052
DNA methylase, N-6 adenine-specific, conserved site		44
480IPR011304
L-lactate dehydrogenase		44
481IPR030827
Inositol 2-dehydrogenase		44
482IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		44
483IPR002403
Cytochrome P450, E-class, group IV		423
484IPR004923
Iron permease FTR1		48
485IPR016064
ATP-NAD kinase-like domain		47
486IPR019821
Kinesin, motor region, conserved site		44
487IPR015353
Rubisco LS methyltransferase, substrate-binding domain		411
488IPR018422
Cation/H+ exchanger, CPA1 family		49
489IPR001697
Pyruvate kinase		431
490IPR024757
Cell division protein FtsZ, C-terminal		44
491IPR028343
Fructose-1,6-bisphosphatase		423
492IPR001606
ARID/BRIGHT DNA-binding domain		420
493IPR001222
Zinc finger, TFIIS-type		415
494IPR017975
Tubulin, conserved site		44
495IPR004099
Pyridine nucleotide-disulphide oxidoreductase, dimerisation		48
496IPR006134
DNA-directed DNA polymerase, family B, multifunctional domain		44
497IPR006592
RNA polymerase, N-terminal		44
498IPR000022
Carboxyl transferase		45
499IPR003347
JmjC domain		410
500IPR017941
Rieske [2Fe-2S] iron-sulphur domain		416
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria.html b/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria.html new file mode 100644 index 00000000..b5efe70f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria.html @@ -0,0 +1,1015 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM34128v1, Feb 2013
Database version:86.1
Base Pairs:13,419,354
Golden Path Length:13,712,004
Genebuild by: ENA
Genebuild method: Generated from ENA annotation
Genebuild started: Feb 2013
Genebuild released: Feb 2013
Genebuild last updated/patched: Feb 2013
Genebuild version: 2013-02-ENA
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		6,622
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:7,275
+ + +

Coordinate Systems

+ + + + + + + + +
supercontig
+
433 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaf_0465833
scaf_1309569
scaf_2300364
scaf_3289758
scaf_4278265
scaf_5291449
scaf_6274249
scaf_7268242
scaf_8249065
scaf_9254509
scaf_10227306
scaf_11221157
scaf_12208297
scaf_13208524
scaf_14243816
scaf_15207090
scaf_16203407
scaf_17202930
scaf_18190679
scaf_19190064
scaf_20200491
scaf_21185391
scaf_22184947
scaf_23177434
scaf_24176343
scaf_25183063
scaf_26172322
scaf_27182797
scaf_28205375
scaf_29165106
scaf_30162788
scaf_31160524
scaf_32160259
scaf_33163106
scaf_34174032
scaf_35158315
scaf_36153348
scaf_37155995
scaf_38151821
scaf_39150478
scaf_40149690
scaf_41169963
scaf_42147121
scaf_43144539
scaf_44145161
scaf_45132796
scaf_46132283
scaf_47131600
scaf_48121273
scaf_49118838
scaf_50120017
scaf_51109007
scaf_52108070
scaf_53107229
scaf_54102629
scaf_5598466
scaf_56118401
scaf_5793401
scaf_5891853
scaf_5991794
scaf_6091661
scaf_6189227
scaf_62104598
scaf_6385120
scaf_6469250
scaf_6563017
scaf_6657353
scaf_6755687
scaf_6847274
scaf_6944409
scaf_7037885
scaf_7117706
scaf_7217549
scaf_7317462
scaf_7443083
scaf_7516229
scaf_7616055
scaf_7715855
scaf_7815549
scaf_7915533
scaf_8014807
scaf_8114533
scaf_8214177
scaf_8314018
scaf_8413883
scaf_8513873
scaf_8613755
scaf_8713580
scaf_8813134
scaf_8912791
scaf_9012778
scaf_9112474
scaf_9212279
scaf_9311980
scaf_9411649
scaf_9511087
scaf_9611070
scaf_9711013
scaf_9810436
scaf_9910414
scaf_10010288
scaf_10110203
scaf_10210166
scaf_1039969
scaf_1049963
scaf_1059820
scaf_1069793
scaf_1079762
scaf_1089743
scaf_1099731
scaf_1109291
scaf_1119231
scaf_1129227
scaf_1139172
scaf_1149148
scaf_1158895
scaf_1168708
scaf_1178653
scaf_1188629
scaf_1198608
scaf_1208359
scaf_1218620
scaf_1228349
scaf_1238300
scaf_1248277
scaf_1258222
scaf_1268204
scaf_1278021
scaf_1287992
scaf_1297949
scaf_1307864
scaf_1317799
scaf_1327758
scaf_1337722
scaf_1347699
scaf_1357663
scaf_1367661
scaf_1377660
scaf_1387590
scaf_1397572
scaf_1407570
scaf_1417520
scaf_1427504
scaf_1437411
scaf_1447353
scaf_1457319
scaf_1467303
scaf_1477247
scaf_1487087
scaf_1497048
scaf_1507001
scaf_1517000
scaf_1526997
scaf_1536968
scaf_1546932
scaf_1556867
scaf_1566844
scaf_1576840
scaf_1586838
scaf_1596830
scaf_1606830
scaf_1616774
scaf_1626755
scaf_1636661
scaf_1646654
scaf_1656584
scaf_1666547
scaf_1676452
scaf_1686357
scaf_1696337
scaf_1706328
scaf_1716306
scaf_1726304
scaf_1736293
scaf_1746288
scaf_1756209
scaf_1766146
scaf_1776132
scaf_1786118
scaf_1796109
scaf_1806138
scaf_1816084
scaf_1826052
scaf_1836047
scaf_1846006
scaf_1856001
scaf_1865989
scaf_1875966
scaf_1885939
scaf_1895892
scaf_1905870
scaf_1915776
scaf_1925733
scaf_1935729
scaf_1945707
scaf_1955684
scaf_1965667
scaf_1975609
scaf_1985586
scaf_1995547
scaf_2005540
scaf_2015508
scaf_2025471
scaf_2035465
scaf_2045433
scaf_2055412
scaf_2065364
scaf_2075328
scaf_2085294
scaf_2095282
scaf_2105272
scaf_2115244
scaf_2125203
scaf_2135124
scaf_2145071
scaf_2155021
scaf_2165018
scaf_2175009
scaf_2184996
scaf_2194994
scaf_2204987
scaf_2214969
scaf_2224961
scaf_2234941
scaf_2244916
scaf_2254913
scaf_2264909
scaf_2274876
scaf_2284867
scaf_2294841
scaf_2304822
scaf_2314821
scaf_2324819
scaf_2334763
scaf_2344758
scaf_2354743
scaf_2364739
scaf_2374725
scaf_2384720
scaf_2394704
scaf_2404703
scaf_2414702
scaf_2424666
scaf_2434652
scaf_2444647
scaf_2454636
scaf_2464634
scaf_2474617
scaf_2484612
scaf_2494584
scaf_2504583
scaf_2514564
scaf_2524559
scaf_2534551
scaf_2544541
scaf_2554464
scaf_2564458
scaf_2574448
scaf_2584425
scaf_2594372
scaf_2604348
scaf_2614344
scaf_2624342
scaf_2634334
scaf_2644326
scaf_2654313
scaf_2664300
scaf_2674292
scaf_2684285
scaf_2694280
scaf_2704271
scaf_2714243
scaf_2724237
scaf_2734210
scaf_2744209
scaf_2754194
scaf_2764186
scaf_2774177
scaf_2784161
scaf_2794160
scaf_2804141
scaf_2814130
scaf_2824115
scaf_2834089
scaf_2844069
scaf_2854053
scaf_2864035
scaf_2874032
scaf_2884029
scaf_2894028
scaf_2904024
scaf_2914016
scaf_2923993
scaf_2933981
scaf_2943981
scaf_2953979
scaf_2963953
scaf_2973941
scaf_2983936
scaf_2993921
scaf_3003921
scaf_3013916
scaf_3023911
scaf_3033904
scaf_3043893
scaf_3053880
scaf_3063878
scaf_3073871
scaf_3083849
scaf_3093846
scaf_3103842
scaf_3113818
scaf_3123797
scaf_3133784
scaf_3143739
scaf_3153738
scaf_3163730
scaf_3173725
scaf_3183718
scaf_3193704
scaf_3203701
scaf_3213697
scaf_3223689
scaf_3233681
scaf_3243676
scaf_3253666
scaf_3263647
scaf_3273643
scaf_3283632
scaf_3293616
scaf_3303609
scaf_3313607
scaf_3323591
scaf_3333558
scaf_3343541
scaf_3353511
scaf_3363510
scaf_3373501
scaf_3383455
scaf_3393439
scaf_3403425
scaf_3413418
scaf_3423392
scaf_3433381
scaf_3443376
scaf_3453341
scaf_3463338
scaf_3473329
scaf_3483328
scaf_3493288
scaf_3503288
scaf_3513272
scaf_3523229
scaf_3533198
scaf_3543197
scaf_3553183
scaf_3563164
scaf_3573158
scaf_3583142
scaf_3593125
scaf_3603122
scaf_3613120
scaf_3623116
scaf_3633071
scaf_3643060
scaf_3653055
scaf_3663055
scaf_3673041
scaf_3683040
scaf_3693030
scaf_3703024
scaf_3713024
scaf_3723003
scaf_3732988
scaf_3742967
scaf_3752962
scaf_3762952
scaf_3772949
scaf_3782918
scaf_3792913
scaf_3802861
scaf_3812813
scaf_3822804
scaf_3832770
scaf_3842752
scaf_3852743
scaf_3862711
scaf_3872695
scaf_3882678
scaf_3892662
scaf_3902648
scaf_3912638
scaf_3922618
scaf_3932601
scaf_3942598
scaf_3952547
scaf_3962545
scaf_3972540
scaf_3982534
scaf_3992514
scaf_4002512
scaf_4012499
scaf_4022489
scaf_4032458
scaf_4042441
scaf_4052429
scaf_4062411
scaf_4072406
scaf_4082403
scaf_4092399
scaf_4102382
scaf_4112369
scaf_4122366
scaf_4132355
scaf_4142341
scaf_4152321
scaf_4162272
scaf_4172252
scaf_4182250
scaf_4192205
scaf_4202197
scaf_4212186
scaf_4222133
scaf_4232039
scaf_4242037
scaf_4252017
scaf_4261991
scaf_4271968
scaf_4281949
scaf_4291920
scaf_4301843
scaf_4311629
scaf_4321090
+
+
contig
+
518 sequences
+
+ +
+ + + +
SequenceLength (bp)
ADNM02000001.151433
ADNM02000002.1129758
ADNM02000003.1284602
ADNM02000004.1135011
ADNM02000005.167186
ADNM02000006.181476
ADNM02000007.125836
ADNM02000008.178419
ADNM02000009.1105352
ADNM02000010.1115798
ADNM02000011.1289758
ADNM02000012.1142073
ADNM02000013.19396
ADNM02000014.1126527
ADNM02000015.1141522
ADNM02000016.11168
ADNM02000017.120969
ADNM02000018.116647
ADNM02000019.195094
ADNM02000020.111120
ADNM02000021.1105590
ADNM02000022.1157499
ADNM02000023.114029
ADNM02000024.112126
ADNM02000025.1228192
ADNM02000026.1249065
ADNM02000027.163521
ADNM02000028.17486
ADNM02000029.14010
ADNM02000030.134335
ADNM02000031.12547
ADNM02000032.121020
ADNM02000033.126701
ADNM02000034.119799
ADNM02000035.118548
ADNM02000036.131506
ADNM02000037.1209776
ADNM02000038.117510
ADNM02000039.1221157
ADNM02000040.1208297
ADNM02000041.17590
ADNM02000042.148117
ADNM02000043.1151938
ADNM02000044.186337
ADNM02000045.198029
ADNM02000046.11029
ADNM02000047.14142
ADNM02000048.12714
ADNM02000049.11521
ADNM02000050.14359
ADNM02000051.18982
ADNM02000052.1111646
ADNM02000053.194628
ADNM02000054.144306
ADNM02000055.1158831
ADNM02000056.1202930
ADNM02000057.1190679
ADNM02000058.1190064
ADNM02000059.16274
ADNM02000060.1183218
ADNM02000061.1185391
ADNM02000062.1184947
ADNM02000063.1177434
ADNM02000064.1176343
ADNM02000065.142763
ADNM02000066.1132236
ADNM02000067.1172322
ADNM02000068.123381
ADNM02000069.169144
ADNM02000070.179795
ADNM02000071.115125
ADNM02000072.1150528
ADNM02000073.1165106
ADNM02000074.1162788
ADNM02000075.1160524
ADNM02000076.111128
ADNM02000077.1149111
ADNM02000078.18056
ADNM02000079.16982
ADNM02000080.11190
ADNM02000081.165973
ADNM02000082.175745
ADNM02000083.121502
ADNM02000084.118421
ADNM02000085.1116786
ADNM02000086.18678
ADNM02000087.125335
ADNM02000088.1295
ADNM02000089.1627
ADNM02000090.119984
ADNM02000091.18085
ADNM02000092.13744
ADNM02000093.127679
ADNM02000094.137834
ADNM02000095.15541
ADNM02000096.117144
ADNM02000097.1153348
ADNM02000098.124889
ADNM02000099.1128148
ADNM02000100.157767
ADNM02000101.194034
ADNM02000102.1150478
ADNM02000103.166463
ADNM02000104.183207
ADNM02000105.167292
ADNM02000106.181684
ADNM02000107.1147121
ADNM02000108.1144539
ADNM02000109.126457
ADNM02000110.1882
ADNM02000111.19966
ADNM02000112.1106688
ADNM02000113.1132796
ADNM02000114.140752
ADNM02000115.191404
ADNM02000116.1131600
ADNM02000117.1121273
ADNM02000118.1118838
ADNM02000119.191910
ADNM02000120.122241
ADNM02000121.123446
ADNM02000122.185541
ADNM02000123.1108070
ADNM02000124.1107229
ADNM02000125.1102629
ADNM02000126.170254
ADNM02000127.128192
ADNM02000128.110130
ADNM02000129.139206
ADNM02000130.146800
ADNM02000131.193401
ADNM02000132.191853
ADNM02000133.191794
ADNM02000134.191661
ADNM02000135.189227
ADNM02000136.112303
ADNM02000137.173836
ADNM02000138.185120
ADNM02000139.112239
ADNM02000140.11374
ADNM02000141.133198
ADNM02000142.17233
ADNM02000143.114596
ADNM02000144.111219
ADNM02000145.147828
ADNM02000146.125561
ADNM02000147.131772
ADNM02000148.155687
ADNM02000149.147274
ADNM02000150.144409
ADNM02000151.137885
ADNM02000152.117706
ADNM02000153.117549
ADNM02000154.117462
ADNM02000155.18152
ADNM02000156.19146
ADNM02000157.14817
ADNM02000158.111392
ADNM02000159.116055
ADNM02000160.115855
ADNM02000161.115549
ADNM02000162.115533
ADNM02000163.114807
ADNM02000164.114533
ADNM02000165.114177
ADNM02000166.114018
ADNM02000167.113883
ADNM02000168.113873
ADNM02000169.113755
ADNM02000170.113580
ADNM02000171.113134
ADNM02000172.112791
ADNM02000173.112778
ADNM02000174.112474
ADNM02000175.11929
ADNM02000176.110330
ADNM02000177.111980
ADNM02000178.111649
ADNM02000179.111087
ADNM02000180.111070
ADNM02000181.111013
ADNM02000182.110436
ADNM02000183.110414
ADNM02000184.110288
ADNM02000185.110203
ADNM02000186.110166
ADNM02000187.19969
ADNM02000188.19963
ADNM02000189.19820
ADNM02000190.19793
ADNM02000191.19762
ADNM02000192.19743
ADNM02000193.19731
ADNM02000194.19291
ADNM02000195.19231
ADNM02000196.19227
ADNM02000197.19172
ADNM02000198.19148
ADNM02000199.18895
ADNM02000200.18708
ADNM02000201.18653
ADNM02000202.18629
ADNM02000203.18608
ADNM02000204.18359
ADNM02000205.12830
ADNM02000206.15524
ADNM02000207.18349
ADNM02000208.18300
ADNM02000209.18277
ADNM02000210.18222
ADNM02000211.18204
ADNM02000212.18021
ADNM02000213.17992
ADNM02000214.17949
ADNM02000215.17864
ADNM02000216.17799
ADNM02000217.17758
ADNM02000218.17722
ADNM02000219.17699
ADNM02000220.17663
ADNM02000221.17661
ADNM02000222.17660
ADNM02000223.17590
ADNM02000224.17572
ADNM02000225.17570
ADNM02000226.17520
ADNM02000227.17504
ADNM02000228.17411
ADNM02000229.17353
ADNM02000230.17319
ADNM02000231.17303
ADNM02000232.17247
ADNM02000233.17087
ADNM02000234.17048
ADNM02000235.17001
ADNM02000236.17000
ADNM02000237.16997
ADNM02000238.16968
ADNM02000239.16932
ADNM02000240.16867
ADNM02000241.16844
ADNM02000242.16840
ADNM02000243.16838
ADNM02000244.16830
ADNM02000245.16830
ADNM02000246.16774
ADNM02000247.16755
ADNM02000248.16661
ADNM02000249.16654
ADNM02000250.16584
ADNM02000251.16547
ADNM02000252.16452
ADNM02000253.16357
ADNM02000254.16337
ADNM02000255.16328
ADNM02000256.16306
ADNM02000257.16304
ADNM02000258.16293
ADNM02000259.16288
ADNM02000260.16209
ADNM02000261.16146
ADNM02000262.16132
ADNM02000263.16118
ADNM02000264.16109
ADNM02000265.15329
ADNM02000266.1766
ADNM02000267.16084
ADNM02000268.16052
ADNM02000269.16047
ADNM02000270.16006
ADNM02000271.16001
ADNM02000272.15989
ADNM02000273.15966
ADNM02000274.15939
ADNM02000275.15892
ADNM02000276.15870
ADNM02000277.15776
ADNM02000278.15733
ADNM02000279.15729
ADNM02000280.15707
ADNM02000281.15684
ADNM02000282.15667
ADNM02000283.15609
ADNM02000284.15586
ADNM02000285.15547
ADNM02000286.15540
ADNM02000287.15508
ADNM02000288.15471
ADNM02000289.15465
ADNM02000290.15433
ADNM02000291.15412
ADNM02000292.15364
ADNM02000293.15328
ADNM02000294.15294
ADNM02000295.15282
ADNM02000296.15272
ADNM02000297.15244
ADNM02000298.15203
ADNM02000299.15124
ADNM02000300.15071
ADNM02000301.15021
ADNM02000302.15018
ADNM02000303.15009
ADNM02000304.14996
ADNM02000305.14994
ADNM02000306.14987
ADNM02000307.14969
ADNM02000308.14961
ADNM02000309.14941
ADNM02000310.14916
ADNM02000311.14913
ADNM02000312.14909
ADNM02000313.14876
ADNM02000314.14867
ADNM02000315.14841
ADNM02000316.14822
ADNM02000317.14821
ADNM02000318.14819
ADNM02000319.14763
ADNM02000320.14758
ADNM02000321.14743
ADNM02000322.14739
ADNM02000323.14725
ADNM02000324.14720
ADNM02000325.14704
ADNM02000326.14703
ADNM02000327.14702
ADNM02000328.14666
ADNM02000329.14652
ADNM02000330.14647
ADNM02000331.14636
ADNM02000332.14634
ADNM02000333.14617
ADNM02000334.14612
ADNM02000335.14584
ADNM02000336.14583
ADNM02000337.14564
ADNM02000338.14559
ADNM02000339.14551
ADNM02000340.14541
ADNM02000341.14464
ADNM02000342.14458
ADNM02000343.14448
ADNM02000344.14425
ADNM02000345.14372
ADNM02000346.14348
ADNM02000347.14344
ADNM02000348.14342
ADNM02000349.14334
ADNM02000350.14326
ADNM02000351.14313
ADNM02000352.14300
ADNM02000353.14292
ADNM02000354.14285
ADNM02000355.14280
ADNM02000356.14271
ADNM02000357.14243
ADNM02000358.14237
ADNM02000359.14210
ADNM02000360.14209
ADNM02000361.14194
ADNM02000362.14186
ADNM02000363.14177
ADNM02000364.14161
ADNM02000365.14160
ADNM02000366.14141
ADNM02000367.14130
ADNM02000368.14115
ADNM02000369.14089
ADNM02000370.14069
ADNM02000371.14053
ADNM02000372.14035
ADNM02000373.14032
ADNM02000374.14029
ADNM02000375.14028
ADNM02000376.14024
ADNM02000377.14016
ADNM02000378.13993
ADNM02000379.13981
ADNM02000380.13981
ADNM02000381.13979
ADNM02000382.13953
ADNM02000383.13941
ADNM02000384.13936
ADNM02000385.13921
ADNM02000386.13921
ADNM02000387.13916
ADNM02000388.13911
ADNM02000389.13904
ADNM02000390.13893
ADNM02000391.13880
ADNM02000392.13878
ADNM02000393.13871
ADNM02000394.13849
ADNM02000395.13846
ADNM02000396.13842
ADNM02000397.13818
ADNM02000398.13797
ADNM02000399.13784
ADNM02000400.13739
ADNM02000401.13738
ADNM02000402.13730
ADNM02000403.13725
ADNM02000404.13718
ADNM02000405.13704
ADNM02000406.13701
ADNM02000407.13697
ADNM02000408.13689
ADNM02000409.13681
ADNM02000410.13676
ADNM02000411.13666
ADNM02000412.13647
ADNM02000413.13643
ADNM02000414.13632
ADNM02000415.13616
ADNM02000416.13609
ADNM02000417.13607
ADNM02000418.13591
ADNM02000419.13558
ADNM02000420.13541
ADNM02000421.13511
ADNM02000422.13510
ADNM02000423.13501
ADNM02000424.13455
ADNM02000425.13439
ADNM02000426.13425
ADNM02000427.13418
ADNM02000428.13392
ADNM02000429.13381
ADNM02000430.13376
ADNM02000431.13341
ADNM02000432.13338
ADNM02000433.13329
ADNM02000434.13328
ADNM02000435.13288
ADNM02000436.13288
ADNM02000437.13272
ADNM02000438.13229
ADNM02000439.13198
ADNM02000440.13197
ADNM02000441.13183
ADNM02000442.13164
ADNM02000443.13158
ADNM02000444.13142
ADNM02000445.13125
ADNM02000446.13122
ADNM02000447.13120
ADNM02000448.13116
ADNM02000449.13071
ADNM02000450.13060
ADNM02000451.13055
ADNM02000452.13055
ADNM02000453.13041
ADNM02000454.13040
ADNM02000455.13030
ADNM02000456.13024
ADNM02000457.13024
ADNM02000458.13003
ADNM02000459.12988
ADNM02000460.12967
ADNM02000461.12962
ADNM02000462.12952
ADNM02000463.12949
ADNM02000464.12918
ADNM02000465.12913
ADNM02000466.12861
ADNM02000467.12813
ADNM02000468.12804
ADNM02000469.12770
ADNM02000470.12752
ADNM02000471.12743
ADNM02000472.12711
ADNM02000473.12695
ADNM02000474.12678
ADNM02000475.12662
ADNM02000476.12648
ADNM02000477.12638
ADNM02000478.12618
ADNM02000479.12601
ADNM02000480.12598
ADNM02000481.12547
ADNM02000482.12545
ADNM02000483.12540
ADNM02000484.12534
ADNM02000485.12514
ADNM02000486.12512
ADNM02000487.12499
ADNM02000488.12489
ADNM02000489.12458
ADNM02000490.12441
ADNM02000491.12429
ADNM02000492.12411
ADNM02000493.12406
ADNM02000494.12403
ADNM02000495.12399
ADNM02000496.12382
ADNM02000497.12369
ADNM02000498.12366
ADNM02000499.12355
ADNM02000500.12341
ADNM02000501.12321
ADNM02000502.12272
ADNM02000503.12252
ADNM02000504.12250
ADNM02000505.12205
ADNM02000506.12197
ADNM02000507.12186
ADNM02000508.12133
ADNM02000509.12039
ADNM02000510.12037
ADNM02000511.12017
ADNM02000512.11991
ADNM02000513.11968
ADNM02000514.11949
ADNM02000515.11920
ADNM02000516.11843
ADNM02000517.11629
ADNM02000518.11090
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria_IPtop500.html new file mode 100644 index 00000000..2275e455 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Galdieria_sulphuraria_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		4413011
2IPR016040
NAD(P)-binding domain		153658
3IPR015943
WD40/YVTN repeat-like-containing domain		146608
4IPR017986
WD40-repeat-containing domain		143786
5IPR001680
WD40 repeat		1223639
6IPR013083
Zinc finger, RING/FYVE/PHD-type		115220
7IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		112454
8IPR016024
Armadillo-type fold		112669
9IPR020846
Major facilitator superfamily domain		101256
10IPR003593
AAA+ ATPase domain		99279
11IPR011009
Protein kinase-like domain		96394
12IPR011990
Tetratricopeptide-like helical domain		90705
13IPR001841
Zinc finger, RING-type		82302
14IPR011989
Armadillo-like helical		80417
15IPR000719
Protein kinase domain		78669
16IPR011991
Winged helix-turn-helix DNA-binding domain		76289
17IPR012677
Nucleotide-binding alpha-beta plait domain		74400
18IPR019775
WD40 repeat, conserved site		72573
19IPR005828
Major facilitator, sugar transporter-like		6885
20IPR012336
Thioredoxin-like fold		65310
21IPR000504
RNA recognition motif domain		65526
22IPR012340
Nucleic acid-binding, OB-fold		65181
23IPR001650
Helicase, C-terminal		62465
24IPR008271
Serine/threonine-protein kinase, active site		59177
25IPR029058
Alpha/Beta hydrolase fold		59296
26IPR014001
Helicase superfamily 1/2, ATP-binding domain		59287
27IPR005829
Sugar transporter, conserved site		5779
28IPR013785
Aldolase-type TIM barrel		53117
29IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		53145
30IPR023214
HAD-like domain		52346
31IPR009057
Homeodomain-like		52349
32IPR017441
Protein kinase, ATP binding site		50149
33IPR023753
FAD/NAD(P)-binding domain		48435
34IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		4898
35IPR015424
Pyridoxal phosphate-dependent transferase		48114
36IPR029044
Nucleotide-diphospho-sugar transferases		44215
37IPR005225
Small GTP-binding protein domain		4491
38IPR003959
ATPase, AAA-type, core		44125
39IPR011545
DEAD/DEAH box helicase domain		42106
40IPR001005
SANT/Myb domain		42216
41IPR020568
Ribosomal protein S5 domain 2-type fold		40112
42IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		4080
43IPR003439
ABC transporter-like		40223
44IPR003663
Sugar/inositol transporter		40215
45IPR013026
Tetratricopeptide repeat-containing domain		39107
46IPR020472
G-protein beta WD-40 repeat		38384
47IPR029071
Ubiquitin-related domain		3772
48IPR019734
Tetratricopeptide repeat		35710
49IPR018108
Mitochondrial substrate/solute carrier		35349
50IPR023395
Mitochondrial carrier domain		35136
51IPR001623
DnaJ domain		33431
52IPR017853
Glycoside hydrolase superfamily		3377
53IPR017871
ABC transporter, conserved site		3391
54IPR016181
Acyl-CoA N-acyltransferase		30131
55IPR017930
Myb domain		3079
56IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		2860
57IPR009000
Translation protein, beta-barrel domain		2772
58IPR014014
RNA helicase, DEAD-box type, Q motif		2752
59IPR013766
Thioredoxin domain		2692
60IPR002067
Mitochondrial carrier protein		26196
61IPR004827
Basic-leucine zipper domain		26105
62IPR000626
Ubiquitin domain		25113
63IPR011701
Major facilitator superfamily		2546
64IPR029055
Nucleophile aminohydrolases, N-terminal		25105
65IPR002347
Short-chain dehydrogenase/reductase SDR		24322
66IPR032675
Leucine-rich repeat domain, L domain-like		24101
67IPR013781
Glycoside hydrolase, catalytic domain		2455
68IPR017907
Zinc finger, RING-type, conserved site		2435
69IPR009072
Histone-fold		24155
70IPR000182
GNAT domain		2379
71IPR003960
ATPase, AAA-type, conserved site		2355
72IPR016135
Ubiquitin-conjugating enzyme/RWD-like		2399
73IPR011032
GroES-like		2168
74IPR010920
LSM domain		2137
75IPR012337
Ribonuclease H-like domain		21330
76IPR029052
Metallo-dependent phosphatase-like		2197
77IPR006073
GTP binding domain		21132
78IPR004843
Calcineurin-like phosphoesterase domain, apaH type		2038
79IPR029045
ClpP/crotonase-like domain		20168
80IPR010987
Glutathione S-transferase, C-terminal-like		20104
81IPR000608
Ubiquitin-conjugating enzyme E2		1984
82IPR000795
Transcription factor, GTP-binding domain		19212
83IPR002085
Alcohol dehydrogenase superfamily, zinc-type		1940
84IPR014756
Immunoglobulin E-set		1955
85IPR011992
EF-hand domain pair		19101
86IPR003029
S1 domain		1992
87IPR009060
UBA-like		1833
88IPR001163
LSM domain, eukaryotic/archaea-type		1863
89IPR013057
Amino acid transporter, transmembrane domain		1822
90IPR004839
Aminotransferase, class I/classII		1837
91IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		1832
92IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		1836
93IPR016161
Aldehyde/histidinol dehydrogenase		1825
94IPR028889
Ubiquitin specific protease domain		1833
95IPR001611
Leucine-rich repeat		18166
96IPR013216
Methyltransferase type 11		1728
97IPR001810
F-box domain		1796
98IPR006447
Myb domain, plants		1729
99IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		1736
100IPR004045
Glutathione S-transferase, N-terminal		1757
101IPR015590
Aldehyde dehydrogenase domain		1723
102IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		16159
103IPR006195
Aminoacyl-tRNA synthetase, class II		1635
104IPR029000
Cyclophilin-like domain		1666
105IPR013149
Alcohol dehydrogenase, C-terminal		1622
106IPR001279
Metallo-beta-lactamase		16140
107IPR012675
Beta-grasp domain		1630
108IPR013154
Alcohol dehydrogenase, N-terminal		1625
109IPR000073
Alpha/beta hydrolase fold-1		1686
110IPR011012
Longin-like domain		1633
111IPR018253
DnaJ domain, conserved site		1631
112IPR016162
Aldehyde dehydrogenase N-terminal domain		1624
113IPR011993
PH domain-like		1669
114IPR016163
Aldehyde dehydrogenase, C-terminal		1622
115IPR018200
Ubiquitin specific protease, conserved site		1546
116IPR002048
EF-hand domain		15145
117IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1529
118IPR000717
Proteasome component (PCI) domain		1555
119IPR000873
AMP-dependent synthetase/ligase		1532
120IPR002885
Pentatricopeptide repeat		15460
121IPR001353
Proteasome, subunit alpha/beta		1529
122IPR013763
Cyclin-like		1599
123IPR008979
Galactose-binding domain-like		1541
124IPR022967
RNA-binding domain, S1		1553
125IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		1542
126IPR000644
CBS domain		15141
127IPR001752
Kinesin motor domain		15175
128IPR000571
Zinc finger, CCCH-type		15170
129IPR015797
NUDIX hydrolase domain-like		1559
130IPR020103
Pseudouridine synthase, catalytic domain		1442
131IPR020683
Ankyrin repeat-containing domain		14131
132IPR013761
Sterile alpha motif/pointed domain		1421
133IPR013328
6-phosphogluconate dehydrogenase, domain 2		1327
134IPR008991
Translation protein SH3-like domain		1327
135IPR029061
Thiamin diphosphate-binding fold		13103
136IPR001478
PDZ domain		13105
137IPR013816
ATP-grasp fold, subdomain 2		1333
138IPR003594
Histidine kinase-like ATPase, C-terminal domain		1387
139IPR023313
Ubiquitin-conjugating enzyme, active site		1327
140IPR029057
Phosphoribosyltransferase-like		1364
141IPR011527
ABC transporter type 1, transmembrane domain		13136
142IPR011011
Zinc finger, FYVE/PHD-type		1329
143IPR002110
Ankyrin repeat		13198
144IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		1348
145IPR008942
ENTH/VHS		1231
146IPR006689
Small GTPase superfamily, ARF/SAR type		12107
147IPR015940
Ubiquitin-associated domain		1250
148IPR001305
Heat shock protein DnaJ, cysteine-rich domain		1251
149IPR029510
Aldehyde dehydrogenase, glutamic acid active site		1214
150IPR000330
SNF2-related, N-terminal domain		1233
151IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1226
152IPR005135
Endonuclease/exonuclease/phosphatase		1286
153IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		1249
154IPR018247
EF-Hand 1, calcium-binding site		1252
155IPR027640
Kinesin-like protein		1272
156IPR003107
HAT (Half-A-TPR) repeat		12244
157IPR011053
Single hybrid motif		1226
158IPR020845
AMP-binding, conserved site		1220
159IPR002035
von Willebrand factor, type A		1298
160IPR004088
K Homology domain, type 1		1282
161IPR029062
Class I glutamine amidotransferase-like		1256
162IPR017937
Thioredoxin, conserved site		1225
163IPR000086
NUDIX hydrolase domain		1242
164IPR014720
Double-stranded RNA-binding domain		1230
165IPR020843
Polyketide synthase, enoylreductase domain		1221
166IPR002912
ACT domain		1229
167IPR023210
NADP-dependent oxidoreductase domain		1266
168IPR001395
Aldo/keto reductase/potassium channel subunit beta		1235
169IPR001806
Small GTPase superfamily		1221
170IPR000727
Target SNARE coiled-coil homology domain		1150
171IPR017938
Riboflavin synthase-like beta-barrel		1128
172IPR013525
ABC-2 type transporter		1124
173IPR004853
Sugar phosphate transporter domain		1122
174IPR001357
BRCT domain		11118
175IPR000089
Biotin/lipoyl attachment		1144
176IPR008250
P-type ATPase, A domain		1167
177IPR007197
Radical SAM		1120
178IPR001451
Hexapeptide repeat		1129
179IPR013783
Immunoglobulin-like fold		1146
180IPR002423
Chaperonin Cpn60/TCP-1 family		1124
181IPR027413
GroEL-like equatorial domain		1146
182IPR001763
Rhodanese-like domain		11102
183IPR003008
Tubulin/FtsZ, GTPase domain		1171
184IPR027409
GroEL-like apical domain		1148
185IPR013780
Glycosyl hydrolase, all-beta		1116
186IPR000791
Acetate transporter GPR1/FUN34/SatP family		1111
187IPR029064
50S ribosomal protein L30e-like		1140
188IPR025110
AMP-binding enzyme C-terminal domain		1017
189IPR003035
RWP-RK domain		1022
190IPR019821
Kinesin motor domain, conserved site		1017
191IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		1044
192IPR001296
Glycosyl transferase, family 1		1018
193IPR008280
Tubulin/FtsZ, C-terminal		1016
194IPR011761
ATP-grasp fold		1026
195IPR014710
RmlC-like jelly roll fold		1034
196IPR000408
Regulator of chromosome condensation, RCC1		10223
197IPR029039
Flavoprotein-like domain		1028
198IPR022796
Chlorophyll A-B binding protein		1016
199IPR004154
Anticodon-binding		1045
200IPR029028
Alpha/beta knot methyltransferases		1020
201IPR013815
ATP-grasp fold, subdomain 1		1024
202IPR014722
Ribosomal protein L2 domain 2		1021
203IPR004046
Glutathione S-transferase, C-terminal		1016
204IPR011333
SKP1/BTB/POZ domain		1023
205IPR004087
K Homology domain		1022
206IPR006671
Cyclin, N-terminal		1017
207IPR001965
Zinc finger, PHD-type		1035
208IPR002937
Amine oxidase		1029
209IPR015947
PUA-like domain		1034
210IPR001932
PPM-type phosphatase domain		10117
211IPR004274
FCP1 homology domain		1048
212IPR024156
Small GTPase superfamily, ARF type		1021
213IPR017927
Ferredoxin reductase-type FAD-binding domain		921
214IPR027267
Arfaptin homology (AH) domain/BAR domain		913
215IPR000683
Oxidoreductase, N-terminal		916
216IPR006638
Elongator protein 3/MiaB/NifB		916
217IPR006594
LIS1 homology motif		931
218IPR001433
Oxidoreductase FAD/NAD(P)-binding		918
219IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		949
220IPR009022
Elongation factor G, III-V domain		949
221IPR003954
RNA recognition motif domain, eukaryote		930
222IPR017975
Tubulin, conserved site		915
223IPR023393
START-like domain		914
224IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		919
225IPR021109
Aspartic peptidase domain		956
226IPR029056
Ribokinase-like		937
227IPR017926
Glutamine amidotransferase		935
228IPR002123
Phospholipid/glycerol acyltransferase		939
229IPR001375
Peptidase S9, prolyl oligopeptidase, catalytic domain		916
230IPR016156
FAD/NAD-linked reductase, dimerisation domain		915
231IPR006050
DNA photolyase, N-terminal		952
232IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		940
233IPR015902
Glycoside hydrolase, family 13		935
234IPR016160
Aldehyde dehydrogenase, cysteine active site		913
235IPR018303
P-type ATPase, phosphorylation site		924
236IPR011004
Trimeric LpxA-like		916
237IPR029026
tRNA (guanine-N1-)-methyltransferase, N-terminal		917
238IPR023299
P-type ATPase, cytoplasmic domain N		968
239IPR001757
P-type ATPase		950
240IPR002016
Haem peroxidase, plant/fungal/bacterial		981
241IPR031157
Tr-type G domain, conserved site		919
242IPR016185
Pre-ATP-grasp domain		941
243IPR010255
Haem peroxidase		934
244IPR009100
Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain		915
245IPR006047
Glycosyl hydrolase, family 13, catalytic domain		929
246IPR000836
Phosphoribosyltransferase domain		916
247IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		948
248IPR001173
Glycosyltransferase 2-like		923
249IPR001487
Bromodomain		9144
250IPR023329
Chlorophyll a/b binding protein domain		914
251IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		943
252IPR017884
SANT domain		818
253IPR029060
PIN domain-like		836
254IPR006091
Acyl-CoA oxidase/dehydrogenase, central domain		814
255IPR033762
MCM OB domain		816
256IPR004000
Actin family		8110
257IPR005025
NADPH-dependent FMN reductase-like		88
258IPR032710
NTF2-like domain		826
259IPR006140
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain		812
260IPR029035
DHS-like NAD/FAD-binding domain		848
261IPR032640
AMP-activated protein kinase, glycogen-binding domain		815
262IPR000217
Tubulin		8131
263IPR003034
SAP domain		837
264IPR005024
Snf7 family		812
265IPR004099
Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain		824
266IPR002942
RNA-binding S4 domain		857
267IPR013088
Zinc finger, NHR/GATA-type		815
268IPR023333
Proteasome B-type subunit		815
269IPR013320
Concanavalin A-like lectin/glucanase domain		831
270IPR029021
Protein-tyrosine phosphatase-like		838
271IPR029753
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site		819
272IPR009053
Prefoldin		825
273IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		810
274IPR001344
Chlorophyll A-B binding protein, plant		813
275IPR005101
Cryptochrome/DNA photolyase, FAD-binding domain		824
276IPR009050
Globin-like		823
277IPR007087
Zinc finger, C2H2		8255
278IPR010989
t-SNARE		818
279IPR006139
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain		812
280IPR006694
Fatty acid hydroxylase		812
281IPR001199
Cytochrome b5-like heme/steroid binding domain		8133
282IPR000640
Translation elongation factor EFG, V domain		848
283IPR015847
Exoribonuclease, phosphorolytic domain 2		838
284IPR013786
Acyl-CoA dehydrogenase/oxidase, N-terminal		822
285IPR011332
Zinc-binding ribosomal protein		815
286IPR011060
Ribulose-phosphate binding barrel		819
287IPR011013
Galactose mutarotase-like domain		815
288IPR019786
Zinc finger, PHD-type, conserved site		817
289IPR000850
Adenylate kinase/UMP-CMP kinase		871
290IPR020904
Short-chain dehydrogenase/reductase, conserved site		814
291IPR001208
MCM domain		8112
292IPR007125
Histone H2A/H2B/H3		817
293IPR000994
Peptidase M24, structural domain		856
294IPR033121
Peptidase family A1 domain		826
295IPR016193
Cytidine deaminase-like		817
296IPR009075
Acyl-CoA dehydrogenase/oxidase C-terminal		832
297IPR002194
Chaperonin TCP-1, conserved site		846
298IPR005475
Transketolase-like, pyrimidine-binding domain		841
299IPR023123
Tubulin, C-terminal		814
300IPR001461
Aspartic peptidase A1 family		872
301IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		825
302IPR033391
Fructose-1-6-bisphosphatase class I, N-terminal		813
303IPR004147
UbiB domain		817
304IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		873
305IPR002109
Glutaredoxin		836
306IPR000195
Rab-GTPase-TBC domain		874
307IPR031327
Mini-chromosome maintenance protein		816
308IPR006439
HAD hydrolase, subfamily IA		851
309IPR017998
Chaperone tailless complex polypeptide 1 (TCP-1)		883
310IPR005814
Aminotransferase class-III		845
311IPR001214
SET domain		862
312IPR007248
Mpv17/PMP22		824
313IPR000555
JAB1/MPN/MOV34 metalloenzyme domain		828
314IPR011042
Six-bladed beta-propeller, TolB-like		846
315IPR027410
TCP-1-like chaperonin intermediate domain		832
316IPR001247
Exoribonuclease, phosphorolytic domain 1		824
317IPR000594
THIF-type NAD/FAD binding fold		845
318IPR000679
Zinc finger, GATA-type		845
319IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		8111
320IPR033690
Adenylate kinase, conserved site		812
321IPR017877
Myb-like domain		829
322IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		816
323IPR005804
Fatty acid desaturase domain		817
324IPR010402
CCT domain		731
325IPR022764
Peptidase S54, rhomboid domain		726
326IPR007502
Helicase-associated domain		730
327IPR008949
Isoprenoid synthase domain		724
328IPR003316
E2F/DP family, winged-helix DNA-binding domain		726
329IPR000467
G-patch domain		736
330IPR000782
FAS1 domain		765
331IPR008971
HSP40/DnaJ peptide-binding		739
332IPR006153
Cation/H+ exchanger		715
333IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		714
334IPR027408
PNPase/RNase PH domain		721
335IPR008978
HSP20-like chaperone		730
336IPR019954
Ubiquitin conserved site		715
337IPR002553
Clathrin/coatomer adaptor, adaptin-like, N-terminal		715
338IPR000008
C2 domain		7135
339IPR009008
Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain		729
340IPR002125
Cytidine and deoxycytidylate deaminases, zinc-binding		724
341IPR016039
Thiolase-like		768
342IPR002314
Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)		714
343IPR007657
Glycosyltransferase AER61, uncharacterised		715
344IPR002300
Aminoacyl-tRNA synthetase, class Ia		717
345IPR012676
TGS-like		713
346IPR001969
Aspartic peptidase, active site		710
347IPR020084
NUDIX hydrolase, conserved site		711
348IPR000210
BTB/POZ domain		741
349IPR032466
Metal-dependent hydrolase		718
350IPR001374
R3H domain		762
351IPR019787
Zinc finger, PHD-finger		723
352IPR003337
Trehalose-phosphatase		721
353IPR002293
Amino acid/polyamine transporter I		723
354IPR003323
OTU domain		726
355IPR027482
Sec1-like, domain 2		726
356IPR016021
MIF4G-like domain		733
357IPR008011
Complex 1 LYR protein		79
358IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		714
359IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		710
360IPR004039
Rubredoxin-type fold		714
361IPR004360
Glyoxalase/fosfomycin resistance/dioxygenase domain		716
362IPR031330
Glycoside hydrolase 35, catalytic domain		711
363IPR007696
DNA mismatch repair protein MutS, core		745
364IPR006379
HAD-superfamily hydrolase, subfamily IIB		711
365IPR031167
OBG-type guanine nucleotide-binding (G) domain		714
366IPR004038
Ribosomal protein L7Ae/L30e/S12e/Gadd45		713
367IPR029069
HotDog domain		720
368IPR001944
Glycoside hydrolase, family 35		770
369IPR003604
Zinc finger, U1-type		714
370IPR000426
Proteasome alpha-subunit, N-terminal domain		742
371IPR011051
RmlC-like cupin domain		718
372IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		777
373IPR000146
Fructose-1,6-bisphosphatase class 1		728
374IPR002939
Chaperone DnaJ, C-terminal		714
375IPR013126
Heat shock protein 70 family		7126
376IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		732
377IPR003010
Carbon-nitrogen hydrolase		752
378IPR018525
Mini-chromosome maintenance, conserved site		714
379IPR000192
Aminotransferase class V domain		715
380IPR001128
Cytochrome P450		7144
381IPR001619
Sec1-like protein		758
382IPR015946
K homology domain-like, alpha/beta		714
383IPR022775
AP complex, mu/sigma subunit		714
384IPR023332
Proteasome A-type subunit		714
385IPR029033
Histidine phosphatase superfamily		748
386IPR001878
Zinc finger, CCHC-type		791
387IPR000432
DNA mismatch repair protein MutS, C-terminal		743
388IPR000225
Armadillo		7154
389IPR012128
Phycobilisome, alpha/beta subunit		649
390IPR015927
Peptidase S24/S26A/S26B/S26C		612
391IPR006133
DNA-directed DNA polymerase, family B, exonuclease domain		611
392IPR006171
Toprim domain		632
393IPR008254
Flavodoxin/nitric oxide synthase		616
394IPR000326
Phosphatidic acid phosphatase type 2/haloperoxidase		660
395IPR018506
Cytochrome b5, heme-binding site		613
396IPR024395
CLASP N-terminal domain		67
397IPR019956
Ubiquitin		625
398IPR028992
Hedgehog/Intein (Hint) domain		644
399IPR000537
UbiA prenyltransferase family		611
400IPR023179
GTP-binding protein, orthogonal bundle domain		610
401IPR029066
PLP-binding barrel		620
402IPR028360
Peptidase S24/S26, beta-ribbon domain		614
403IPR000741
Fructose-bisphosphate aldolase, class-I		610
404IPR028343
Fructose-1,6-bisphosphatase		651
405IPR001606
ARID DNA-binding domain		640
406IPR008984
SMAD/FHA domain		611
407IPR011237
Peptidase M16 domain		625
408IPR009078
Ferritin-like superfamily		611
409IPR004100
ATPase, F1 complex alpha/beta subunit, N-terminal domain		624
410IPR006204
GHMP kinase N-terminal domain		612
411IPR011016
Zinc finger, RING-CH-type		619
412IPR016050
Proteasome beta-type subunit, conserved site		612
413IPR033247
Transketolase family		630
414IPR000253
Forkhead-associated (FHA) domain		636
415IPR013838
Beta tubulin, autoregulation binding site		68
416IPR013155
Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding		613
417IPR018150
Aminoacyl-tRNA synthetase, class II (D/K/N)-like		621
418IPR027725
Heat shock transcription factor family		614
419IPR008921
DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal		611
420IPR018962
Domain of unknown function DUF1995		611
421IPR010994
RuvA domain 2-like		610
422IPR006145
Pseudouridine synthase, RsuA/RluB/C/D/E/F		612
423IPR008333
Oxidoreductase, FAD-binding domain		69
424IPR011611
Carbohydrate kinase PfkB		611
425IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		668
426IPR000868
Isochorismatase-like		623
427IPR003016
2-oxo acid dehydrogenase, lipoyl-binding site		612
428IPR004365
OB-fold nucleic acid binding domain, AA-tRNA synthetase-type		613
429IPR022742
Serine aminopeptidase, S33		610
430IPR016142
Citrate synthase-like, large alpha subdomain		68
431IPR009014
Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II		632
432IPR011650
Peptidase M20, dimerisation domain		632
433IPR013750
GHMP kinase, C-terminal domain		630
434IPR003406
Glycosyl transferase, family 14		615
435IPR002478
PUA domain		627
436IPR019489
Clp ATPase, C-terminal		622
437IPR002453
Beta tubulin		6104
438IPR011417
AP180 N-terminal homology (ANTH) domain		68
439IPR013024
Butirosin biosynthesis, BtrG-like		618
440IPR018936
Phosphatidylinositol 3/4-kinase, conserved site		616
441IPR008928
Six-hairpin glycosidase-like		617
442IPR005937
26S proteasome subunit P45		612
443IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		619
444IPR007081
RNA polymerase Rpb1, domain 5		614
445IPR001709
Flavoprotein pyridine nucleotide cytochrome reductase		670
446IPR002933
Peptidase M20		614
447IPR002020
Citrate synthase		663
448IPR019410
Lysine methyltransferase		68
449IPR005936
Peptidase, FtsH		622
450IPR007956
Malonyl-CoA decarboxylase		66
451IPR003675
CAAX amino terminal protease		610
452IPR011249
Metalloenzyme, LuxS/M16 peptidase-like		633
453IPR000642
Peptidase M41		611
454IPR004838
Aminotransferases, class-I, pyridoxal-phosphate-binding site		612
455IPR011335
Restriction endonuclease type II-like		631
456IPR000322
Glycoside hydrolase family 31		68
457IPR001048
Aspartate/glutamate/uridylate kinase		639
458IPR009003
Peptidase S1, PA clan		622
459IPR004364
Aminoacyl-tRNA synthetase, class II (D/K/N)		613
460IPR000232
Heat shock factor (HSF)-type, DNA-binding		639
461IPR007083
RNA polymerase Rpb1, domain 4		610
462IPR011765
Peptidase M16, N-terminal		611
463IPR006172
DNA-directed DNA polymerase, family B		631
464IPR029047
Heat shock protein 70kD, peptide-binding domain		634
465IPR020003
ATPase, alpha/beta subunit, nucleotide-binding domain, active site		613
466IPR006595
CTLH, C-terminal LisH motif		621
467IPR011709
Domain of unknown function DUF1605		613
468IPR005479
Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain		646
469IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		615
470IPR007863
Peptidase M16, C-terminal		613
471IPR029752
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1		67
472IPR029048
Heat shock protein 70kD, C-terminal domain		630
473IPR017896
4Fe-4S ferredoxin-type, iron-sulphur binding domain		626
474IPR027925
MCM N-terminal domain		611
475IPR003395
RecF/RecN/SMC, N-terminal		613
476IPR014284
RNA polymerase sigma-70 like domain		510
477IPR006554
Helicase-like, DEXD box c2 type		510
478IPR016102
Succinyl-CoA synthetase-like		518
479IPR001940
Peptidase S1C		558
480IPR010614
DEAD2		510
481IPR000433
Zinc finger, ZZ-type		542
482IPR023404
Radical SAM, alpha/beta horseshoe		511
483IPR021133
HEAT, type 2		537
484IPR000648
Oxysterol-binding protein		527
485IPR020548
Fructose-1,6-bisphosphatase, active site		58
486IPR033248
Transketolase, C-terminal domain		514
487IPR030827
Inositol 2-dehydrogenase		58
488IPR016461
O-methyltransferase COMT-type		59
489IPR005517
Translation elongation factor EFG/EF2, domain IV		520
490IPR000387
Tyrosine specific protein phosphatases domain		510
491IPR009006
Alanine racemase/group IV decarboxylase, C-terminal		516
492IPR000023
Phosphofructokinase domain		517
493IPR018422
Cation/H+ exchanger, CPA1 family		511
494IPR002207
Plant ascorbate peroxidase		548
495IPR001251
CRAL-TRIO lipid binding domain		542
496IPR003607
HD/PDEase domain		513
497IPR006134
DNA-directed DNA polymerase, family B, multifunctional domain		59
498IPR002173
Carbohydrate/puine kinase, PfkB, conserved site		59
499IPR006592
RNA polymerase, N-terminal		510
500IPR014782
Peptidase M1, membrane alanine aminopeptidase, N-terminal		544
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Glycine_max.html b/gramene/htdocs/ssi/species.weix/stats_Glycine_max.html new file mode 100644 index 00000000..ae47b2af --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Glycine_max.html @@ -0,0 +1,86 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:V1.0, Jan 2010
Database version:86.1
Base Pairs:973,344,380
Golden Path Length:973,344,380
Genebuild by: JGI
Genebuild method: Imported from JGI-Phytozome
Genebuild started: Jul 2012
Genebuild version: JGI-Glyma-1.1
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		54,174
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:73,319
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
20 sequences
+
+ +
+ + + +
SequenceLength (bp)
155915595
251656713
347781076
449243852
541936504
650722821
744683157
846995532
946843750
1050969635
1139172790
1240113140
1344408971
1449711204
1550939160
1637397385
1741906774
1862308140
1950589441
2046773167
+
+
scaffold1148 sequences
chunk10774 sequences
+ +

Other

+ + + + + +
FGENESH gene predictions:128,627
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		24813411
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		24518210
3IPR000719
Protein kinase, catalytic domain		23607193
4IPR008271
Serine/threonine-protein kinase, active site		17222204
5IPR032675
Leucine-rich repeat domain, L domain-like		16026346
6IPR017441
Protein kinase, ATP binding site		14461832
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		12671940
8IPR013083
Zinc finger, RING/FYVE/PHD-type		12071659
9IPR011990
Tetratricopeptide-like helical		10123917
10IPR009057
Homeodomain-like		10012778
11IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		9071658
12IPR002885
Pentatricopeptide repeat		88521032
13IPR001611
Leucine-rich repeat		8686661
14IPR016040
NAD(P)-binding domain		7632234
15IPR001841
Zinc finger, RING-type		7622128
16IPR016024
Armadillo-type fold		7201924
17IPR029058
Alpha/Beta hydrolase fold		6572102
18IPR001005
SANT/Myb domain		6501997
19IPR012677
Nucleotide-binding, alpha-beta plait		6272353
20IPR015943
WD40/YVTN repeat-like-containing domain		5751238
21IPR011989
Armadillo-like helical		5721316
22IPR013210
Leucine-rich repeat-containing N-terminal, type 2		566629
23IPR000504
RNA recognition motif domain		5523235
24IPR017986
WD40-repeat-containing domain		5361769
25IPR003593
AAA+ ATPase domain		532874
26IPR003591
Leucine-rich repeat, typical subtype		5314356
27IPR017930
Myb domain		529951
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		5121558
29IPR001680
WD40 repeat		4967103
30IPR001810
F-box domain, cyclin-like		4941505
31IPR017853
Glycoside hydrolase, superfamily		472661
32IPR012336
Thioredoxin-like fold		4691248
33IPR002182
NB-ARC		452557
34IPR011991
Winged helix-turn-helix DNA-binding domain		441926
35IPR001128
Cytochrome P450		4372900
36IPR020846
Major facilitator superfamily domain		4341066
37IPR012337
Ribonuclease H-like domain		397697
38IPR013781
Glycoside hydrolase, catalytic domain		388519
39IPR016177
DNA-binding, integrase-type		382485
40IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		3822129
41IPR011992
EF-hand-like domain		3781159
42IPR002401
Cytochrome P450, E-class, group I		3732734
43IPR001471
AP2/ERF domain		3602518
44IPR017972
Cytochrome P450, conserved site		345369
45IPR002048
Calcium-binding EF-hand		3332554
46IPR023214
HAD-like domain		3311288
47IPR019775
WD40 repeat, conserved site		316670
48IPR007087
Zinc finger, C2H2		3131052
49IPR018247
EF-Hand 1, calcium-binding site		309802
50IPR012340
Nucleic acid-binding, OB-fold		307552
51IPR005123
Oxoglutarate/iron-dependent dioxygenase		288631
52IPR011050
Pectin lyase fold/virulence factor		287333
53IPR012334
Pectin lyase fold		287341
54IPR029044
Nucleotide-diphospho-sugar transferases		280841
55IPR027443
Isopenicillin N synthase-like		280354
56IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		275712
57IPR020683
Ankyrin repeat-containing domain		2721564
58IPR013026
Tetratricopeptide repeat-containing domain		252421
59IPR014001
Helicase, superfamily 1/2, ATP-binding domain		250617
60IPR001650
Helicase, C-terminal		249915
61IPR003676
Auxin responsive SAUR protein		248249
62IPR003439
ABC transporter-like		242915
63IPR001623
DnaJ domain		2392045
64IPR002110
Ankyrin repeat		2392056
65IPR019734
Tetratricopeptide repeat		2362361
66IPR026992
Non-haem dioxygenase N-terminal domain		235277
67IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		2341089
68IPR001356
Homeobox domain		231762
69IPR013830
SGNH hydrolase-type esterase domain		227720
70IPR003959
ATPase, AAA-type, core		226310
71IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		225347
72IPR000008
C2 calcium-dependent membrane targeting		2231833
73IPR013785
Aldolase-type TIM barrel		219334
74IPR010285
DNA helicase PIF1, ATP-dependent		219288
75IPR010255
Haem peroxidase		213236
76IPR020472
G-protein beta WD-40 repeat		212780
77IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		2121319
78IPR005225
Small GTP-binding protein domain		211270
79IPR002016
Haem peroxidase, plant/fungal/bacterial		2091438
80IPR008972
Cupredoxin		208881
81IPR014710
RmlC-like jelly roll fold		208314
82IPR006447
Myb domain, plants		208269
83IPR015424
Pyridoxal phosphate-dependent transferase		206293
84IPR011011
Zinc finger, FYVE/PHD-type		204313
85IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		197268
86IPR029071
Ubiquitin-related domain		195331
87IPR015880
Zinc finger, C2H2-like		193541
88IPR032867
DYW domain		187199
89IPR000823
Plant peroxidase		1871584
90IPR003441
No apical meristem (NAM) protein		184683
91IPR000270
Phox/Bem1p		183374
92IPR003657
DNA-binding WRKY		1821266
93IPR001087
Lipase, GDSL		181201
94IPR021109
Aspartic peptidase		177623
95IPR008906
HAT dimerisation		175179
96IPR002100
Transcription factor, MADS-box		1751654
97IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		175425
98IPR006501
Pectinesterase inhibitor		174842
99IPR001932
Protein phosphatase 2C (PP2C)-like		1731314
100IPR006121
Heavy metal-associated domain, HMA		172620
101IPR000225
Armadillo		1721664
102IPR009072
Histone-fold		170368
103IPR017871
ABC transporter, conserved site		169277
104IPR001480
Bulb-type lectin domain		1661194
105IPR001461
Peptidase A1		165536
106IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		163197
107IPR000571
Zinc finger, CCCH-type		1631754
108IPR027640
Kinesin-like protein		162539
109IPR015655
Protein phosphatase 2C		162328
110IPR033121
Peptidase family A1 domain		161206
111IPR011333
BTB/POZ fold		161206
112IPR002347
Glucose/ribitol dehydrogenase		1601690
113IPR001965
Zinc finger, PHD-type		160376
114IPR013766
Thioredoxin domain		159358
115IPR023213
Chloramphenicol acetyltransferase-like domain		159329
116IPR019793
Peroxidases heam-ligand binding site		157171
117IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		155278
118IPR001752
Kinesin, motor domain		1551573
119IPR025476
Helitron helicase-like domain		153161
120IPR030184
WAT1-related protein		151189
121IPR017907
Zinc finger, RING-type, conserved site		151192
122IPR015300
DNA-binding pseudobarrel domain		151489
123IPR004827
Basic-leucine zipper domain		150746
124IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		149216
125IPR001806
Small GTPase superfamily		149204
126IPR005828
General substrate transporter		148206
127IPR011051
RmlC-like cupin domain		146191
128IPR003480
Transferase		146166
129IPR023393
START-like domain		144193
130IPR032799
Xylanase inhibitor, C-terminal		143167
131IPR002902
Gnk2-homologous domain		143782
132IPR000073
Alpha/beta hydrolase fold-1		143384
133IPR013057
Amino acid transporter, transmembrane		143172
134IPR032861
Xylanase inhibitor, N-terminal		143166
135IPR001878
Zinc finger, CCHC-type		1431088
136IPR000048
IQ motif, EF-hand binding site		1431396
137IPR018108
Mitochondrial substrate/solute carrier		141981
138IPR023395
Mitochondrial carrier domain		141391
139IPR000109
Proton-dependent oligopeptide transporter family		138315
140IPR003609
Apple-like		138540
141IPR019787
Zinc finger, PHD-finger		138322
142IPR015500
Peptidase S8, subtilisin-related		136540
143IPR011993
Pleckstrin homology-like domain		136395
144IPR003340
B3 DNA binding domain		134647
145IPR000858
S-locus glycoprotein		134198
146IPR003613
U box domain		134471
147IPR019786
Zinc finger, PHD-type, conserved site		133209
148IPR003960
ATPase, AAA-type, conserved site		132167
149IPR019794
Peroxidase, active site		130140
150IPR000626
Ubiquitin domain		129599
151IPR010987
Glutathione S-transferase, C-terminal-like		129411
152IPR000070
Pectinesterase, catalytic		128139
153IPR000209
Peptidase S8/S53 domain		128752
154IPR026057
PC-Esterase		127147
155IPR000620
Drug/metabolite transporter		125261
156IPR024171
S-receptor-like serine/threonine-protein kinase		124148
157IPR029962
Trichome birefringence-like family		124173
158IPR000210
BTB/POZ domain		124372
159IPR018253
DnaJ domain, conserved site		123159
160IPR029052
Metallo-dependent phosphatase-like		121397
161IPR013763
Cyclin-like		120711
162IPR005202
Transcription factor GRAS		119252
163IPR002528
Multi antimicrobial extrusion protein		118401
164IPR025846
PMR5 N-terminal domain		118130
165IPR008979
Galactose-binding domain-like		117389
166IPR008978
HSP20-like chaperone		116250
167IPR020568
Ribosomal protein S5 domain 2-type fold		116167
168IPR005135
Endonuclease/exonuclease/phosphatase		114473
169IPR008250
P-type ATPase, A domain		113316
170IPR005829
Sugar transporter, conserved site		112228
171IPR023299
P-type ATPase, cytoplasmic domain N		112295
172IPR011032
GroES-like		111276
173IPR016135
Ubiquitin-conjugating enzyme/RWD-like		110334
174IPR013525
ABC-2 type transporter		109194
175IPR004045
Glutathione S-transferase, N-terminal		109247
176IPR001757
Cation-transporting P-type ATPase		109480
177IPR004843
Metallophosphoesterase domain		108158
178IPR016181
Acyl-CoA N-acyltransferase		108302
179IPR000743
Glycoside hydrolase, family 28		108221
180IPR010259
Proteinase inhibitor I9		107185
181IPR017970
Homeobox, conserved site		107125
182IPR011527
ABC transporter, transmembrane domain, type 1		107704
183IPR009009
Barwin-related endoglucanase		106341
184IPR004864
Late embryogenesis abundant protein, LEA-14		106114
185IPR018303
P-type ATPase, phosphorylation site		106135
186IPR003663
Sugar/inositol transporter		106681
187IPR019821
Kinesin, motor region, conserved site		104140
188IPR014756
Immunoglobulin E-set		104140
189IPR014014
RNA helicase, DEAD-box type, Q motif		103120
190IPR011006
CheY-like superfamily		103160
191IPR002085
Alcohol dehydrogenase superfamily, zinc-type		103161
192IPR001789
Signal transduction response regulator, receiver domain		103404
193IPR011706
Multicopper oxidase, type 2		101113
194IPR001117
Multicopper oxidase, type 1		100112
195IPR013128
Peptidase C1A, papain		100108
196IPR033131
Pectinesterase, Asp active site		100103
197IPR000668
Peptidase C1A, papain C-terminal		100470
198IPR033389
AUX/IAA domain		99149
199IPR031052
FHY3/FAR1 family		99132
200IPR002487
Transcription factor, K-box		99305
201IPR015916
Galactose oxidase, beta-propeller		98115
202IPR000608
Ubiquitin-conjugating enzyme, E2		98306
203IPR029055
Nucleophile aminohydrolases, N-terminal		98241
204IPR023828
Peptidase S8, subtilisin, Ser-active site		98113
205IPR025558
Domain of unknown function DUF4283		9899
206IPR011707
Multicopper oxidase, type 3		97108
207IPR008942
ENTH/VHS		96233
208IPR001220
Legume lectin domain		96104
209IPR007021
Domain of unknown function DUF659		96105
210IPR026961
PGG domain		95114
211IPR002068
Alpha crystallin/Hsp20 domain		94184
212IPR017451
F-box associated interaction domain		94100
213IPR000873
AMP-dependent synthetase/ligase		94133
214IPR002109
Glutaredoxin		94216
215IPR001214
SET domain		94316
216IPR001563
Peptidase S10, serine carboxypeptidase		93618
217IPR012946
X8 domain		93232
218IPR003656
Zinc finger, BED-type predicted		93173
219IPR031107
Small heat shock protein HSP20		93104
220IPR016166
FAD-binding, type 2		92201
221IPR018289
MULE transposase domain		92105
222IPR003245
Plastocyanin-like		92266
223IPR000490
Glycoside hydrolase, family 17		92187
224IPR024788
Malectin-like carbohydrate-binding domain		92109
225IPR006553
Leucine-rich repeat, cysteine-containing subtype		91844
226IPR004883
Lateral organ boundaries, LOB		91200
227IPR002067
Mitochondrial carrier protein		91547
228IPR002921
Lipase, class 3		89112
229IPR001251
CRAL-TRIO domain		89555
230IPR016039
Thiolase-like		88456
231IPR019378
GDP-fucose protein O-fucosyltransferase		88106
232IPR006671
Cyclin, N-terminal		88168
233IPR013201
Proteinase inhibitor I29, cathepsin propeptide		87179
234IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		87125
235IPR007112
Expansin/pollen allergen, DPBB domain		87176
236IPR003137
Protease-associated domain, PA		8698
237IPR023271
Aquaporin-like		86216
238IPR006045
Cupin 1		86233
239IPR000425
Major intrinsic protein		86784
240IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		8697
241IPR017877
Myb-like domain		86130
242IPR003594
Histidine kinase-like ATPase, ATP-binding domain		85393
243IPR006652
Kelch repeat type 1		85345
244IPR004088
K Homology domain, type 1		841040
245IPR016159
Cullin repeat-like-containing domain		84124
246IPR004853
Domain of unknown function DUF250		83103
247IPR004263
Exostosin-like		8399
248IPR011012
Longin-like domain		83113
249IPR003871
Domain of unknown function DUF223		8285
250IPR013783
Immunoglobulin-like fold		81122
251IPR006094
FAD linked oxidase, N-terminal		8192
252IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		8198
253IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		8093
254IPR002495
Glycosyl transferase, family 8		80101
255IPR007527
Zinc finger, SWIM-type		80159
256IPR025661
Cysteine peptidase, asparagine active site		8082
257IPR000757
Glycoside hydrolase, family 16		80164
258IPR000182
GNAT domain		79186
259IPR006626
Parallel beta-helix repeat		79509
260IPR001969
Peptidase aspartic, active site		79139
261IPR008266
Tyrosine-protein kinase, active site		7989
262IPR003851
Zinc finger, Dof-type		79339
263IPR007117
Expansin, cellulose-binding-like domain		79358
264IPR025287
Wall-associated receptor kinase galacturonan-binding domain		7886
265IPR009060
UBA-like		78123
266IPR007118
Expansin/Lol pI		78493
267IPR011016
Zinc finger, RING-CH-type		78284
268IPR001509
NAD-dependent epimerase/dehydratase		78110
269IPR000782
FAS1 domain		77433
270IPR027356
NPH3 domain		77198
271IPR020845
AMP-binding, conserved site		77102
272IPR016161
Aldehyde/histidinol dehydrogenase		77113
273IPR002912
ACT domain		77273
274IPR025660
Cysteine peptidase, histidine active site		7779
275IPR025322
Protein of unknown function DUF4228		7679
276IPR005175
Domain of unknown function DUF296		76169
277IPR006016
UspA		7595
278IPR029061
Thiamin diphosphate-binding fold		74315
279IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		7492
280IPR008928
Six-hairpin glycosidase-like		74118
281IPR008889
VQ		7478
282IPR017884
SANT domain		7396
283IPR016167
FAD-binding, type 2, subdomain 1		7382
284IPR023298
P-type ATPase, transmembrane domain		73179
285IPR004087
K Homology domain		72261
286IPR000169
Cysteine peptidase, cysteine active site		7277
287IPR001360
Glycoside hydrolase, family 1		71462
288IPR011074
CRAL/TRIO, N-terminal domain		71243
289IPR015797
NUDIX hydrolase domain-like		71189
290IPR025525
Domain of unknown function DUF4413		7071
291IPR000315
Zinc finger, B-box		70338
292IPR013154
Alcohol dehydrogenase GroES-like		7087
293IPR005746
Thioredoxin		70109
294IPR002035
von Willebrand factor, type A		70264
295IPR004330
FAR1 DNA binding domain		7088
296IPR015590
Aldehyde dehydrogenase domain		70103
297IPR010920
Like-Sm (LSM) domain		6986
298IPR029021
Protein-tyrosine phosphatase-like		69251
299IPR000330
SNF2-related		6995
300IPR022357
Major intrinsic protein, conserved site		6988
301IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		69209
302IPR010402
CCT domain		68186
303IPR016162
Aldehyde dehydrogenase, N-terminal		68118
304IPR008974
TRAF-like		68199
305IPR000727
Target SNARE coiled-coil domain		67219
306IPR022742
Alpha/beta hydrolase, N-terminal		67116
307IPR029045
ClpP/crotonase-like domain		67253
308IPR000644
Cystathionine beta-synthase, core		67572
309IPR004158
Protein of unknown function DUF247, plant		6774
310IPR018202
Peptidase S10, serine carboxypeptidase, active site		6778
311IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		6783
312IPR008949
Terpenoid synthase		66159
313IPR006153
Cation/H+ exchanger		6676
314IPR003958
Transcription factor CBF/NF-Y/archaeal histone		6679
315IPR004839
Aminotransferase, class I/classII		6689
316IPR015915
Kelch-type beta propeller		66113
317IPR014720
Double-stranded RNA-binding domain		66364
318IPR002913
START domain		66256
319IPR016163
Aldehyde dehydrogenase, C-terminal		66100
320IPR004367
Cyclin, C-terminal domain		65143
321IPR005150
Cellulose synthase		65116
322IPR000595
Cyclic nucleotide-binding domain		65245
323IPR018490
Cyclic nucleotide-binding-like		64102
324IPR032710
NTF2-like domain		64145
325IPR013149
Alcohol dehydrogenase, C-terminal		6481
326IPR013088
Zinc finger, NHR/GATA-type		6466
327IPR011701
Major facilitator superfamily		6480
328IPR008991
Translation protein SH3-like domain		6485
329IPR001395
Aldo/keto reductase		64135
330IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		63429
331IPR029000
Cyclophilin-like domain		63155
332IPR008422
Homeobox KN domain		6377
333IPR020904
Short-chain dehydrogenase/reductase, conserved site		6372
334IPR015813
Pyruvate/Phosphoenolpyruvate kinase		63199
335IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		6378
336IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		6374
337IPR010713
Xyloglucan endo-transglycosylase, C-terminal		6369
338IPR000086
NUDIX hydrolase domain		63166
339IPR003311
AUX/IAA protein		63125
340IPR025110
Domain of unknown function DUF4009		6273
341IPR011013
Galactose mutarotase-like domain		6288
342IPR003406
Glycosyl transferase, family 14		6269
343IPR001849
Pleckstrin homology domain		62207
344IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		6276
345IPR013094
Alpha/beta hydrolase fold-3		6266
346IPR023210
NADP-dependent oxidoreductase domain		62297
347IPR000679
Zinc finger, GATA-type		62238
348IPR001296
Glycosyl transferase, family 1		6181
349IPR023313
Ubiquitin-conjugating enzyme, active site		61102
350IPR007125
Histone core		6163
351IPR025659
Tubby C-terminal-like domain		6087
352IPR006564
Zinc finger, PMZ-type		6071
353IPR002355
Multicopper oxidase, copper-binding site		6062
354IPR008480
Protein of unknown function DUF761, plant		6061
355IPR017937
Thioredoxin, conserved site		6090
356IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		60102
357IPR001487
Bromodomain		60544
358IPR006073
GTP binding domain		60174
359IPR006594
LisH dimerisation motif		59191
360IPR013216
Methyltransferase type 11		5975
361IPR004320
Protein of unknown function DUF241, plant		5960
362IPR003690
Mitochodrial transcription termination factor-related		59415
363IPR000742
Epidermal growth factor-like domain		59127
364IPR004046
Glutathione S-transferase, C-terminal		5966
365IPR003106
Leucine zipper, homeobox-associated		5891
366IPR033138
Multicopper oxidases, conserved site		5859
367IPR017392
AP2/ERF transcription factor ERF/PTI6		5882
368IPR005821
Ion transport domain		5884
369IPR010525
Auxin response factor		5880
370IPR001938
Thaumatin		57654
371IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		57123
372IPR001077
O-methyltransferase, family 2		5765
373IPR014722
Ribosomal protein L2 domain 2		5775
374IPR016461
Caffeate O-methyltransferase (COMT) family		56106
375IPR000907
Lipoxygenase		56125
376IPR029056
Ribokinase-like		56174
377IPR033275
E3 ubiquitin-protein ligase MARCH-like		56101
378IPR004265
Plant disease resistance response protein		5658
379IPR013819
Lipoxygenase, C-terminal		56356
380IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		5669
381IPR001944
Glycoside hydrolase, family 35		56543
382IPR015947
PUA-like domain		5687
383IPR001929
Germin		55161
384IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		55110
385IPR005333
Transcription factor, TCP		5555
386IPR004140
Exocyst complex protein Exo70		55135
387IPR000408
Regulator of chromosome condensation, RCC1		551115
388IPR029006
ADF-H/Gelsolin-like domain		55146
389IPR025398
Domain of unknown function DUF4371		5567
390IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		54241
391IPR004316
SWEET sugar transporter		54120
392IPR001024
Lipoxygenase, LH2		54264
393IPR003347
JmjC domain		54178
394IPR027725
Heat shock transcription factor family		5465
395IPR017887
Transcription factor TCP subgroup		5454
396IPR031112
AP2-like ethylene-responsive transcription factor		5480
397IPR004014
Cation-transporting P-type ATPase, N-terminal		54119
398IPR002963
Expansin		54521
399IPR011043
Galactose oxidase/kelch, beta-propeller		5477
400IPR017927
Ferredoxin reductase-type FAD-binding domain		5366
401IPR004041
NAF domain		5363
402IPR024709
O-fucosyltransferase, plant		5364
403IPR018451
NAF/FISL domain		5363
404IPR016455
Xyloglucan endotransglucosylase/hydrolase		5355
405IPR000232
Heat shock factor (HSF)-type, DNA-binding		53303
406IPR001305
Heat shock protein DnaJ, cysteine-rich domain		52177
407IPR013809
Epsin-like, N-terminal		52125
408IPR023329
Chlorophyll a/b binding protein domain		5270
409IPR017938
Riboflavin synthase-like beta-barrel		5175
410IPR012951
Berberine/berberine-like		5151
411IPR009071
High mobility group (HMG) box domain		51327
412IPR002423
Chaperonin Cpn60/TCP-1		5161
413IPR010989
t-SNARE		5174
414IPR002123
Phospholipid/glycerol acyltransferase		51131
415IPR006456
ZF-HD homeobox protein, Cys/His-rich dimerisation domain		51207
416IPR025486
Domain of unknown function DUF4378		5168
417IPR012341
Six-hairpin glycosidase		5166
418IPR008971
HSP40/DnaJ peptide-binding		49145
419IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		49137
420IPR018392
Peptidoglycan-binding lysin domain		49159
421IPR031330
Glycoside hydrolase 35, catalytic domain		4962
422IPR002939
Chaperone DnaJ, C-terminal		4959
423IPR013126
Heat shock protein 70 family		49451
424IPR020843
Polyketide synthase, enoylreductase		4953
425IPR017761
Laccase		4952
426IPR011042
Six-bladed beta-propeller, TolB-like		4973
427IPR025064
Domain of unknown function DUF4005		4960
428IPR004000
Actin-related protein		48348
429IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		48172
430IPR000795
Elongation factor, GTP-binding domain		48295
431IPR012675
Beta-grasp domain		4854
432IPR002083
MATH/TRAF domain		48188
433IPR025875
Leucine rich repeat 4		4855
434IPR002160
Proteinase inhibitor I3, Kunitz legume		48206
435IPR029033
Histidine phosphatase superfamily		48253
436IPR006689
Small GTPase superfamily, ARF/SAR type		47273
437IPR011065
Kunitz inhibitor ST1-like		4747
438IPR003337
Trehalose-phosphatase		47103
439IPR000639
Epoxide hydrolase-like		47267
440IPR003008
Tubulin/FtsZ, GTPase domain		47240
441IPR006459
Uncharacterised protein family UPF0497, trans-membrane plant subgroup		4755
442IPR001876
Zinc finger, RanBP2-type		47656
443IPR011004
Trimeric LpxA-like		4759
444IPR012967
Plant methyltransferase dimerisation		4752
445IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		47149
446IPR025610
Transcription factor MYC/MYB N-terminal		4759
447IPR001163
Ribonucleoprotein LSM domain		46109
448IPR020084
NUDIX hydrolase, conserved site		4660
449IPR011611
Carbohydrate kinase PfkB		4673
450IPR004333
Transcription factor, SBP-box		46229
451IPR008263
Glycoside hydrolase, family 16, active site		4648
452IPR029069
HotDog domain		46200
453IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		46545
454IPR003954
RNA recognition motif domain, eukaryote		45115
455IPR001279
Beta-lactamase-like		45216
456IPR008280
Tubulin/FtsZ, C-terminal		4549
457IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		45116
458IPR004326
Mlo-related protein		4556
459IPR004776
Auxin efflux carrier		4561
460IPR029062
Class I glutamine amidotransferase-like		45141
461IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		4587
462IPR029047
Heat shock protein 70kD, peptide-binding domain		45120
463IPR001440
Tetratricopeptide TPR-1		4472
464IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		4448
465IPR001199
Cytochrome b5-like heme/steroid binding domain		44351
466IPR006580
Zinc finger, TTF-type		4444
467IPR022796
Chlorophyll A-B binding protein		4456
468IPR019780
Germin, manganese binding site		4445
469IPR006458
Ovate protein family, C-terminal		44127
470IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		43159
471IPR029057
Phosphoribosyltransferase-like		43182
472IPR027409
GroEL-like apical domain		43103
473IPR024752
Myb/SANT-like domain		4363
474IPR000528
Plant lipid transfer protein/Par allergen		42194
475IPR000717
Proteasome component (PCI) domain		4299
476IPR001246
Lipoxygenase, plant		42407
477IPR027433
Lipoxygenase, domain 3		4251
478IPR022755
Zinc finger, double-stranded RNA binding		4248
479IPR033443
Pentacotripeptide-repeat region of PROPR		4259
480IPR000916
Bet v I domain		4273
481IPR001701
Glycoside hydrolase, family 9		4250
482IPR010658
Nodulin-like		4248
483IPR029048
Heat shock protein 70kD, C-terminal domain		4296
484IPR021133
HEAT, type 2		41127
485IPR002293
Amino acid/polyamine transporter I		41156
486IPR001164
Arf GTPase activating protein		41331
487IPR013780
Glycosyl hydrolase, family 13, all-beta		4160
488IPR029993
Plant galacturonosyltransferase GAUT		4153
489IPR032795
DUF3741-associated sequence motif		4155
490IPR011905
Glutaredoxin-like, plant II		4142
491IPR001902
Sulphate anion transporter		4079
492IPR007493
Protein of unknown function DUF538		40123
493IPR008984
SMAD/FHA domain		4049
494IPR000253
Forkhead-associated (FHA) domain		40153
495IPR005467
Signal transduction histidine kinase, core		4046
496IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		4054
497IPR005516
Remorin, C-terminal		4058
498IPR027413
GroEL-like equatorial domain		4083
499IPR022812
Dynamin superfamily		40296
500IPR032308
Jas TPL-binding domain		4065
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Hordeum_vulgare.html b/gramene/htdocs/ssi/species.weix/stats_Hordeum_vulgare.html new file mode 100644 index 00000000..269ff84a --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Hordeum_vulgare.html @@ -0,0 +1,87 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM32608v1, Mar 2012
Database version:86.2
Base Pairs:1,868,764,129
Golden Path Length:4,045,300,851
Genebuild by: IBSC_1.0
Genebuild method: Import
Genebuild started: May 2014
Genebuild version: IBSC_1.0
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		24,287
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		268
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:64,096
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
21 sequences
+
+ +
+ + + +
SequenceLength (bp)
1H_unordered26539468
2HL_unordered6814402
2HS_unordered4967457
3HL_unordered8271953
3HS_unordered6758297
4HL_unordered9496122
4HS_unordered7330345
5HL_unordered8650567
5HS_unordered3863000
6HL_unordered7404877
6HS_unordered5227695
7HL_unordered8976439
7HS_unordered6918872
1464124043
2628342783
3564427874
4544168226
5561411686
6538755036
7601597413
Pt115974
+
+
contig922536 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):19,474,539
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		110312654
2IPR011009
Protein kinase-like domain		10772790
3IPR000719
Protein kinase, catalytic domain		10305833
4IPR032675
Leucine-rich repeat domain, L domain-like		8295175
5IPR008271
Serine/threonine-protein kinase, active site		8001715
6IPR017441
Protein kinase, ATP binding site		6801366
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		6071445
8IPR013083
Zinc finger, RING/FYVE/PHD-type		5291042
9IPR011990
Tetratricopeptide-like helical		5265520
10IPR002885
Pentatricopeptide repeat		44515628
11IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		3621002
12IPR001611
Leucine-rich repeat		3443795
13IPR016040
NAD(P)-binding domain		3261542
14IPR001841
Zinc finger, RING-type		3171128
15IPR001810
F-box domain, cyclin-like		3151132
16IPR029058
Alpha/Beta hydrolase fold		3101756
17IPR016024
Armadillo-type fold		3051327
18IPR009057
Homeodomain-like		2981144
19IPR002182
NB-ARC		286613
20IPR001128
Cytochrome P450		2502425
21IPR015943
WD40/YVTN repeat-like-containing domain		247756
22IPR003591
Leucine-rich repeat, typical subtype		2362947
23IPR011989
Armadillo-like helical		234953
24IPR003593
AAA+ ATPase domain		2241258
25IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		2241265
26IPR017986
WD40-repeat-containing domain		2171049
27IPR013210
Leucine-rich repeat-containing N-terminal, type 2		216391
28IPR002401
Cytochrome P450, E-class, group I		2131810
29IPR026960
Reverse transcriptase zinc-binding domain		211217
30IPR020846
Major facilitator superfamily domain		210883
31IPR012677
Nucleotide-binding, alpha-beta plait		2072650
32IPR012336
Thioredoxin-like fold		205697
33IPR017853
Glycoside hydrolase, superfamily		202559
34IPR001005
SANT/Myb domain		200760
35IPR001680
WD40 repeat		1953382
36IPR017972
Cytochrome P450, conserved site		193272
37IPR000504
RNA recognition motif domain		1791672
38IPR005135
Endonuclease/exonuclease/phosphatase		174621
39IPR013781
Glycoside hydrolase, catalytic domain		162406
40IPR017930
Myb domain		159372
41IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		155529
42IPR000477
Reverse transcriptase		154246
43IPR012337
Ribonuclease H-like domain		142475
44IPR010255
Haem peroxidase		141233
45IPR011992
EF-hand-like domain		140568
46IPR002016
Haem peroxidase, plant/fungal/bacterial		1391236
47IPR011991
Winged helix-turn-helix transcription repressor DNA-binding		138472
48IPR002048
Calcium-binding EF-hand		1351195
49IPR011598
Helix-loop-helix DNA-binding		1311112
50IPR000823
Plant peroxidase		1271321
51IPR029044
Nucleotide-diphospho-sugar transferases		126613
52IPR007087
Zinc finger, C2H2		126520
53IPR023214
HAD-like domain		126887
54IPR018247
EF-Hand 1, calcium-binding site		124408
55IPR014001
Helicase, superfamily 1/2, ATP-binding domain		122545
56IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		119967
57IPR013830
Esterase, SGNH hydrolase-type		118536
58IPR019793
Peroxidases heam-ligand binding site		116153
59IPR003439
ABC transporter-like		115836
60IPR001650
Helicase, C-terminal		114716
61IPR005123
Oxoglutarate/iron-dependent dioxygenase		108347
62IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		106249
63IPR019775
WD40 repeat, conserved site		104370
64IPR027443
Isopenicillin N synthase-like		104199
65IPR016177
DNA-binding, integrase-type		102174
66IPR012340
Nucleic acid-binding, OB-fold		102706
67IPR001087
Lipase, GDSL		100149
68IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		100279
69IPR001480
Bulb-type lectin domain		991003
70IPR019794
Peroxidase, active site		98126
71IPR001471
AP2/ERF domain		96822
72IPR003609
Apple-like		94505
73IPR021109
Peptidase aspartic		94385
74IPR003959
ATPase, AAA-type, core		93232
75IPR011011
Zinc finger, FYVE/PHD-type		91269
76IPR013785
Aldolase-type TIM barrel		90229
77IPR023213
Chloramphenicol acetyltransferase-like domain		89197
78IPR032867
DYW domain		89132
79IPR013026
Tetratricopeptide repeat-containing domain		89456
80IPR019734
Tetratricopeptide repeat		882144
81IPR008972
Cupredoxin		88555
82IPR000858
S-locus glycoprotein		87169
83IPR020683
Ankyrin repeat-containing domain		87982
84IPR001623
Heat shock protein DnaJ, N-terminal		841037
85IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		84201
86IPR015424
Pyridoxal phosphate-dependent transferase, major domain		84218
87IPR014710
RmlC-like jelly roll fold		83160
88IPR003441
No apical meristem (NAM) protein		82423
89IPR011333
BTB/POZ fold		82156
90IPR000008
C2 calcium-dependent membrane targeting		811198
91IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		81187
92IPR017871
ABC transporter, conserved site		81251
93IPR031052
FHY3/FAR1 family		80189
94IPR002110
Ankyrin repeat		801338
95IPR003480
Transferase		79104
96IPR001461
Peptidase A1		78280
97IPR006447
Myb domain, plants		77150
98IPR015300
DNA-binding pseudobarrel domain		77487
99IPR010987
Glutathione S-transferase, C-terminal-like		76318
100IPR017907
Zinc finger, RING-type, conserved site		75140
101IPR024171
S-receptor-like serine/threonine-protein kinase		7496
102IPR033121
Peptidase family A1 domain		74130
103IPR001932
Protein phosphatase 2C-like		74871
104IPR003340
B3 DNA binding domain		73658
105IPR009072
Histone-fold		73188
106IPR026992
Non-haem dioxygenase N-terminal domain		72108
107IPR032861
Xylanase inhibitor, N-terminal		72113
108IPR003657
DNA-binding WRKY		71697
109IPR001965
Zinc finger, PHD-type		71283
110IPR002347
Glucose/ribitol dehydrogenase		701016
111IPR015655
Protein phosphatase 2C		69234
112IPR005225
Small GTP-binding protein domain		69120
113IPR000109
Oligopeptide transporter		68301
114IPR000210
BTB/POZ domain		68294
115IPR004045
Glutathione S-transferase, N-terminal		68192
116IPR001878
Zinc finger, CCHC-type		68641
117IPR008974
TRAF-like		68199
118IPR032799
Xylanase inhibitor, C-terminal		6698
119IPR000073
Alpha/beta hydrolase fold-1		66296
120IPR011050
Pectin lyase fold/virulence factor		65151
121IPR020472
G-protein beta WD-40 repeat		65353
122IPR004827
Basic-leucine zipper domain		65448
123IPR012334
Pectin lyase fold		65147
124IPR025287
Wall-associated receptor kinase galacturonan-binding domain		63112
125IPR011051
RmlC-like cupin domain		6297
126IPR005828
General substrate transporter		61146
127IPR029071
Ubiquitin-related domain		6099
128IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		60127
129IPR029052
Metallo-dependent phosphatase-like		60286
130IPR000270
Phox/Bem1p		60220
131IPR001356
Homeobox domain		59233
132IPR006121
Heavy metal-associated domain, HMA		58284
133IPR027640
Kinesin-like protein		57452
134IPR006501
Pectinesterase inhibitor		57272
135IPR015500
Peptidase S8, subtilisin-related		57335
136IPR015880
Zinc finger, C2H2-like		57291
137IPR003613
U box domain		56278
138IPR009009
Barwin-related endoglucanase		55217
139IPR001220
Legume lectin domain		5568
140IPR000571
Zinc finger, CCCH-type		55882
141IPR011993
Pleckstrin homology-like domain		55199
142IPR000209
Peptidase S8/S53, subtilisin/kexin/sedolisin		55498
143IPR003960
ATPase, AAA-type, conserved site		54112
144IPR013057
Amino acid transporter, transmembrane		54127
145IPR000490
Glycoside hydrolase, family 17		54129
146IPR013766
Thioredoxin domain		53157
147IPR019787
Zinc finger, PHD-finger		53233
148IPR018108
Mitochondrial substrate/solute carrier		53514
149IPR023395
Mitochondrial carrier domain		53252
150IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		52147
151IPR004843
Metallophosphoesterase domain		51100
152IPR005829
Sugar transporter, conserved site		51156
153IPR008979
Galactose-binding domain-like		51257
154IPR001752
Kinesin, motor domain		511229
155IPR011527
ABC transporter, transmembrane domain, type 1		50702
156IPR007527
Zinc finger, SWIM-type		50156
157IPR000225
Armadillo		50603
158IPR016039
Thiolase-like		48299
159IPR004864
Late embryogenesis abundant protein, LEA-14		4857
160IPR019786
Zinc finger, PHD-type, conserved site		48123
161IPR020568
Ribosomal protein S5 domain 2-type fold		48128
162IPR007117
Pollen allergen/expansin, C-terminal		48278
163IPR004330
FAR1 DNA binding domain		48112
164IPR013763
Cyclin-like		47429
165IPR003245
Plastocyanin-like		47155
166IPR023828
Peptidase S8, subtilisin, Ser-active site		4780
167IPR000048
IQ motif, EF-hand binding site		47818
168IPR013525
ABC-2 type transporter		46180
169IPR018289
MULE transposase domain		46103
170IPR007112
Expansin/pollen allergen, DPBB domain		46128
171IPR000742
Epidermal growth factor-like domain		46176
172IPR000873
AMP-dependent synthetase/ligase		45115
173IPR002902
Gnk2-homologous domain		45262
174IPR003676
Auxin responsive SAUR protein		4562
175IPR001806
Small GTPase superfamily		4582
176IPR007118
Expansin/Lol pI		44337
177IPR011701
Major facilitator superfamily		44100
178IPR026057
PC-Esterase		4480
179IPR001881
EGF-like calcium-binding		4499
180IPR008928
Six-hairpin glycosidase-like		44127
181IPR030184
WAT1-related protein		44106
182IPR003663
Sugar/inositol transporter		44382
183IPR024788
Malectin-like carbohydrate-binding domain		4473
184IPR008978
HSP20-like chaperone		43115
185IPR010259
Proteinase inhibitor I9		4388
186IPR023393
START-like domain		4377
187IPR001509
NAD-dependent epimerase/dehydratase		4367
188IPR012946
X8 domain		43138
189IPR000620
Drug/metabolite transporter		43123
190IPR001214
SET domain		43240
191IPR029055
Nucleophile aminohydrolases, N-terminal		42153
192IPR016166
FAD-binding, type 2		42132
193IPR002528
Multi antimicrobial extrusion protein		42239
194IPR013094
Alpha/beta hydrolase fold-3		4250
195IPR015916
Galactose oxidase, beta-propeller		4157
196IPR001563
Peptidase S10, serine carboxypeptidase		41559
197IPR029962
Trichome birefringence-like family		4183
198IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4181
199IPR016135
Ubiquitin-conjugating enzyme/RWD-like		41131
200IPR003690
Mitochodrial transcription termination factor-related		41361
201IPR017877
Myb-like domain		4167
202IPR006564
Zinc finger, PMZ-type		4079
203IPR001117
Multicopper oxidase, type 1		3973
204IPR016181
Acyl-CoA N-acyltransferase		39152
205IPR011006
CheY-like superfamily		3968
206IPR005174
Protein of unknown function DUF295		3947
207IPR002035
von Willebrand factor, type A		39223
208IPR006566
FBD domain		3959
209IPR004158
Protein of unknown function DUF247, plant		3958
210IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		3962
211IPR025315
Domain of unknown function DUF4220		3957
212IPR000626
Ubiquitin domain		38157
213IPR011032
GroES-like		38141
214IPR006553
Leucine-rich repeat, cysteine-containing subtype		38408
215IPR006045
Cupin 1		38105
216IPR031107
Small heat shock protein HSP20		3847
217IPR005202
Transcription factor GRAS		38102
218IPR023299
ATPase, P-type, cytoplasmic domain N		38243
219IPR001757
ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter		38362
220IPR002085
Alcohol dehydrogenase superfamily, zinc-type		3889
221IPR002109
Glutaredoxin		3884
222IPR018097
EGF-like calcium-binding, conserved site		3864
223IPR001789
Signal transduction response regulator, receiver domain		38175
224IPR000330
SNF2-related		3783
225IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		3765
226IPR018253
Heat shock protein DnaJ, conserved site		3766
227IPR025846
PMR5 N-terminal domain		3757
228IPR018303
ATPase, P-type phosphorylation site		37118
229IPR011706
Multicopper oxidase, type 2		3772
230IPR016159
Cullin repeat-like-containing domain		3767
231IPR002921
Lipase, class 3		3692
232IPR014014
RNA helicase, DEAD-box type, Q motif		3668
233IPR020845
AMP-binding, conserved site		3677
234IPR020635
Tyrosine-protein kinase, catalytic domain		3648
235IPR033389
AUX/IAA domain		3592
236IPR003137
Protease-associated domain, PA		3554
237IPR008250
ATPase, P-type, ATPase-associated domain		35245
238IPR004046
Glutathione S-transferase, C-terminal		3548
239IPR011707
Multicopper oxidase, type 3		3558
240IPR006016
UspA		3455
241IPR007658
Protein of unknown function DUF594		3447
242IPR002083
MATH/TRAF domain		34128
243IPR003594
ATPase-like, ATP-binding domain		34254
244IPR006652
Kelch repeat type 1		34172
245IPR004088
K Homology domain, type 1		34556
246IPR025659
Tubby C-terminal-like domain		3374
247IPR001251
CRAL-TRIO domain		33401
248IPR001969
Peptidase aspartic, active site		3394
249IPR013783
Immunoglobulin-like fold		3373
250IPR023271
Aquaporin-like		33118
251IPR022796
Chlorophyll A-B binding protein		3354
252IPR029045
ClpP/crotonase-like domain		33248
253IPR000644
Cystathionine beta-synthase, core		33396
254IPR025322
Protein of unknown function DUF4228		3240
255IPR004853
Domain of unknown function DUF250		3273
256IPR000608
Ubiquitin-conjugating enzyme, E2		3292
257IPR013128
Peptidase C1A, papain		3261
258IPR017451
F-box associated interaction domain		3242
259IPR011047
Quinonprotein alcohol dehydrogenase-like		3281
260IPR026961
PGG domain		32115
261IPR004265
Plant disease resistance response protein		3236
262IPR004839
Aminotransferase, class I/classII		3283
263IPR000425
Major intrinsic protein		32371
264IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3283
265IPR000743
Glycoside hydrolase, family 28		32114
266IPR000182
GNAT domain		31102
267IPR002068
Heat shock protein Hsp20		3174
268IPR013201
Proteinase inhibitor I29, cathepsin propeptide		3172
269IPR008266
Tyrosine-protein kinase, active site		3162
270IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		3174
271IPR019378
GDP-fucose protein O-fucosyltransferase		3183
272IPR002495
Glycosyl transferase, family 8		3165
273IPR006094
FAD linked oxidase, N-terminal		3150
274IPR028889
Ubiquitin specific protease domain		3175
275IPR014756
Immunoglobulin E-set		3160
276IPR004314
Domain of unknown function DUF239		3151
277IPR008949
Terpenoid synthase		30166
278IPR016461
O-methyltransferase, caffeic acid-type		3068
279IPR019821
Kinesin, motor region, conserved site		3086
280IPR013149
Alcohol dehydrogenase, C-terminal		3049
281IPR007657
Glycosyltransferase AER61, uncharacterised		3047
282IPR001296
Glycosyl transferase, family 1		3080
283IPR004263
Exostosin-like		3067
284IPR001077
O-methyltransferase, family 2		3044
285IPR000668
Peptidase C1A, papain C-terminal		30191
286IPR012341
Six-hairpin glycosidase		3064
287IPR000757
Glycoside hydrolase, family 16		3082
288IPR025110
Domain of unknown function DUF4009		2950
289IPR001360
Glycoside hydrolase, family 1		29460
290IPR004162
Seven-in-absentia protein, sina		2955
291IPR022742
Alpha/beta hydrolase, N-terminal		2961
292IPR002100
Transcription factor, MADS-box		29312
293IPR017927
Ferredoxin reductase-type FAD-binding domain		2859
294IPR010402
CCT domain		2893
295IPR017938
Riboflavin synthase-like beta-barrel		2880
296IPR001929
Germin		28108
297IPR002355
Multicopper oxidase, copper-binding site		2843
298IPR011012
Longin-like domain		2846
299IPR007125
Histone core		2831
300IPR008480
Protein of unknown function DUF761, plant		2828
301IPR015947
PUA-like domain		28100
302IPR004041
NAF domain		2744
303IPR032710
NTF2-like domain		2796
304IPR027806
Harbinger transposase-derived nuclease domain		2742
305IPR018451
NAF/FISL domain		2744
306IPR029021
Protein-tyrosine phosphatase-like		27127
307IPR008906
HAT dimerisation		2736
308IPR002423
Chaperonin Cpn60/TCP-1		2764
309IPR011676
Domain of unknown function DUF1618		2753
310IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2754
311IPR017970
Homeobox, conserved site		2736
312IPR016167
FAD-binding, type 2, subdomain 1		2739
313IPR022357
Major intrinsic protein, conserved site		2741
314IPR029062
Class I glutamine amidotransferase-like		27146
315IPR004087
K Homology domain		27126
316IPR006671
Cyclin, N-terminal		2788
317IPR013323
Seven In Absentia Homolog-type		2750
318IPR000070
Pectinesterase, catalytic		2755
319IPR006073
GTP binding domain		27159
320IPR025558
Domain of unknown function DUF4283		2727
321IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		2740
322IPR006626
Parallel beta-helix repeat		26230
323IPR007493
Protein of unknown function DUF538		26112
324IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		2671
325IPR013216
Methyltransferase type 11		2642
326IPR004320
Protein of unknown function DUF241, plant		2629
327IPR012675
Beta-grasp domain		2646
328IPR004140
Exo70 exocyst complex subunit		2681
329IPR027356
NPH3 domain		26100
330IPR011074
CRAL/TRIO, N-terminal domain		26157
331IPR001763
Rhodanese-like domain		26266
332IPR023296
Glycosyl hydrolase family 43, five-bladed beta-propellor domain		26122
333IPR027409
GroEL-like apical domain		26122
334IPR012967
Plant methyltransferase dimerisation		2637
335IPR002487
Transcription factor, K-box		2691
336IPR023329
Chlorophyll a/b binding protein domain		2649
337IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		26186
338IPR033138
Multicopper oxidases, conserved site		2537
339IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2561
340IPR001279
Beta-lactamase-like		25208
341IPR001344
Chlorophyll A-B binding protein, plant		2547
342IPR001938
Thaumatin, pathogenesis-related		25322
343IPR005746
Thioredoxin		2557
344IPR006458
Ovate protein family, C-terminal		2576
345IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2531
346IPR015915
Kelch-type beta propeller		2569
347IPR011042
Six-bladed beta-propeller, TolB-like		2551
348IPR008942
ENTH/VHS		2494
349IPR010920
Like-Sm (LSM) domain		2433
350IPR019557
Aminotransferase-like, plant mobile domain		2444
351IPR016455
Xyloglucan endotransglucosylase/hydrolase		2425
352IPR013154
Alcohol dehydrogenase GroES-like		2443
353IPR006694
Fatty acid hydroxylase		2444
354IPR013010
Zinc finger, SIAH-type		2442
355IPR004813
Oligopeptide transporter OPT superfamily		24104
356IPR025661
Cysteine peptidase, asparagine active site		2435
357IPR011043
Galactose oxidase/kelch, beta-propeller		2434
358IPR020843
Polyketide synthase, enoylreductase		2433
359IPR002912
ACT domain		2497
360IPR023210
NADP-dependent oxidoreductase domain		24189
361IPR001395
Aldo/keto reductase		2483
362IPR001229
Mannose-binding lectin		24278
363IPR013148
Glycosyl hydrolases family 32, N-terminal		2357
364IPR013601
FAE1/Type III polyketide synthase-like protein		2329
365IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		23176
366IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2349
367IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2331
368IPR009060
UBA-like		2347
369IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		2338
370IPR007650
Protein of unknown function DUF581		2335
371IPR001362
Glycoside hydrolase, family 32		2357
372IPR011013
Glycoside hydrolase-type carbohydrate-binding		2357
373IPR005150
Cellulose synthase		2381
374IPR003406
Glycosyl transferase, family 14		2339
375IPR022059
Protein of unknown function DUF3615		2341
376IPR002963
Expansin		23248
377IPR029069
HotDog domain		2390
378IPR000169
Cysteine peptidase, cysteine active site		2332
379IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2380
380IPR003851
Zinc finger, Dof-type		23133
381IPR013189
Glycosyl hydrolase family 32, C-terminal		23146
382IPR009003
Peptidase cysteine/serine, trypsin-like		2370
383IPR003855
K+ potassium transporter		2382
384IPR009091
Regulator of chromosome condensation/beta-lactamase-inhibitor protein II		23180
385IPR002937
Amine oxidase		2356
386IPR000782
FAS1 domain		22153
387IPR018490
Cyclic nucleotide-binding-like		2260
388IPR002659
Glycosyl transferase, family 31		2289
389IPR027725
Heat shock transcription factor family		2251
390IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2286
391IPR003656
Zinc finger, BED-type predicted		2277
392IPR033131
Pectinesterase, Asp active site		2240
393IPR000408
Regulator of chromosome condensation, RCC1		221239
394IPR004367
Cyclin, C-terminal		2281
395IPR002119
Histone H2A		22143
396IPR002293
Amino acid/polyamine transporter I		22152
397IPR020904
Short-chain dehydrogenase/reductase, conserved site		2241
398IPR000152
EGF-type aspartate/asparagine hydroxylation site		2242
399IPR000863
Sulfotransferase domain		2224
400IPR023313
Ubiquitin-conjugating enzyme, active site		2229
401IPR008963
Purple acid phosphatase-like, N-terminal		2236
402IPR005821
Ion transport domain		2261
403IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2249
404IPR002067
Mitochondrial carrier protein		22172
405IPR013126
Heat shock protein 70 family		22270
406IPR003311
AUX/IAA protein		2257
407IPR014720
Double-stranded RNA-binding-like		22163
408IPR000595
Cyclic nucleotide-binding domain		22141
409IPR015914
Purple acid phosphatase, N-terminal		2268
410IPR018202
Peptidase S10, serine carboxypeptidase, active site		2250
411IPR029033
Histidine phosphatase superfamily		22138
412IPR003614
Knottin		2263
413IPR000315
Zinc finger, B-box		21162
414IPR029061
Thiamin diphosphate-binding fold		21161
415IPR000795
Protein synthesis factor, GTP-binding		21205
416IPR033124
Serine carboxypeptidases, histidine active site		2145
417IPR006461
Uncharacterised protein family Cys-rich		2155
418IPR001876
Zinc finger, RanBP2-type		21389
419IPR019780
Germin, manganese binding site		2126
420IPR016161
Aldehyde/histidinol dehydrogenase		2155
421IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2169
422IPR001701
Glycoside hydrolase, family 9		2138
423IPR023298
ATPase, P-type, transmembrane domain		21126
424IPR025660
Cysteine peptidase, histidine active site		2132
425IPR005175
Domain of unknown function DUF296		2163
426IPR015797
NUDIX hydrolase domain-like		2194
427IPR000727
Target SNARE coiled-coil domain		2066
428IPR005795
Major pollen allergen Lol pI		20190
429IPR000528
Plant lipid transfer protein/Par allergen		2099
430IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		20194
431IPR002867
Zinc finger, C6HC-type		20121
432IPR001024
Lipoxygenase, LH2		20128
433IPR006912
Putative harbinger transposase-derived nuclease		2022
434IPR029000
Cyclophilin-like domain		2082
435IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		20123
436IPR001357
BRCT domain		20434
437IPR011016
Zinc finger, RING-CH-type		20130
438IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2038
439IPR004182
GRAM domain		2078
440IPR001353
Proteasome, subunit alpha/beta		2025
441IPR027413
GroEL-like equatorial domain		2062
442IPR029056
Ribokinase-like		20105
443IPR015813
Pyruvate/Phosphoenolpyruvate kinase		2088
444IPR020946
Flavin monooxygenase-like		2041
445IPR018121
Seven-in-absentia protein, TRAF-like domain		2035
446IPR001849
Pleckstrin homology domain		2086
447IPR017937
Thioredoxin, conserved site		2037
448IPR028871
Blue (type 1) copper protein, binding site		2023
449IPR029006
ADF-H/Gelsolin-like domain		2099
450IPR017761
Laccase		2034
451IPR016162
Aldehyde dehydrogenase, N-terminal		2042
452IPR001487
Bromodomain		20267
453IPR001041
2Fe-2S ferredoxin-type domain		2071
454IPR002913
Lipid-binding START		20114
455IPR006867
Domain of unknown function DUF632		2038
456IPR003100
Argonaute/Dicer protein, PAZ		19226
457IPR013328
Dehydrogenase, multihelical		1949
458IPR000717
Proteasome component (PCI) domain		1967
459IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1933
460IPR032454
Histone H2A, C-terminal domain		1927
461IPR018181
Heat shock protein 70, conserved site		1967
462IPR002123
Phospholipid/glycerol acyltransferase		1961
463IPR020103
Pseudouridine synthase, catalytic domain		19121
464IPR025875
Leucine rich repeats (2 copies)		1933
465IPR013771
Bifunctional trypsin/alpha-amylase inhibitor helical domain		1922
466IPR011004
Trimeric LpxA-like		1930
467IPR033443
Pentacotripeptide-repeat region of PROPR		1940
468IPR028082
Periplasmic binding protein-like I		19102
469IPR001906
Terpene synthase-like		19134
470IPR000195
Rab-GTPase-TBC domain		19215
471IPR031127
E3 ubiquitin ligase RBR family		1943
472IPR029047
Heat shock protein 70kD, peptide-binding domain		1970
473IPR015590
Aldehyde dehydrogenase domain		1945
474IPR010525
Auxin response factor		1951
475IPR016163
Aldehyde dehydrogenase, C-terminal		1941
476IPR007502
Helicase-associated domain		1878
477IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		18107
478IPR016064
ATP-NAD kinase, PpnK-type		1866
479IPR007612
LURP1-like domain		1831
480IPR001305
Heat shock protein DnaJ, cysteine-rich domain		18110
481IPR024709
O-fucosyltransferase, plant		1842
482IPR012951
Berberine/berberine-like		1821
483IPR003347
JmjC domain		1897
484IPR005630
Terpene synthase, metal-binding domain		1858
485IPR011257
DNA glycosylase		1886
486IPR026892
Glycoside hydrolase family 3		1850
487IPR003958
Transcription factor CBF/NF-Y/archaeal histone		1827
488IPR006015
Universal stress protein A		1857
489IPR002498
Phosphatidylinositol-4-phosphate 5-kinase, core		18177
490IPR029993
Plant galacturonosyltransferase GAUT		1850
491IPR001828
Extracellular ligand-binding receptor		1859
492IPR025486
Domain of unknown function DUF4378		1834
493IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		1887
494IPR000232
Heat shock factor (HSF)-type, DNA-binding		18149
495IPR027484
Phosphatidylinositol-4-phosphate 5-kinase, N-terminal domain		1855
496IPR011709
Domain of unknown function DUF1605		1835
497IPR029060
PIN domain-like		1783
498IPR004000
Actin family		17270
499IPR003106
Leucine zipper, homeobox-associated		1741
500IPR006195
Aminoacyl-tRNA synthetase, class II		1735
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Leersia_perrieri.html b/gramene/htdocs/ssi/species.weix/stats_Leersia_perrieri.html new file mode 100644 index 00000000..059c1ab8 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Leersia_perrieri.html @@ -0,0 +1,74 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Lperr_V1.4, Mar 2014
Database version:87.14
Base Pairs:266,687,832
Golden Path Length:266,687,832
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-OGE
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		29,078
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:40,939
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
132922458
226406337
329602667
423326293
520807039
621016138
722540073
820165712
915534364
1015557830
1121046960
1217761961
+
+
chunk2675 sequences
+ +

Other

+ + + + + +
FGENESH gene predictions:45,319
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		13812395
2IPR000719
Protein kinase domain		13153632
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		12825351
4IPR008271
Serine/threonine-protein kinase, active site		10381625
5IPR002290
Serine/threonine- /dual specificity protein kinase, catalytic domain		10301643
6IPR017441
Protein kinase, ATP binding site		8791351
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		6891112
8IPR013083
Zinc finger, RING/FYVE/PHD-type		656973
9IPR011990
Tetratricopeptide-like helical		5671800
10IPR001810
F-box domain		5332040
11IPR002885
Pentatricopeptide repeat		45514961
12IPR001611
Leucine-rich repeat		4433207
13IPR001841
Zinc finger, RING-type		3991340
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		397978
15IPR002182
NB-ARC		393679
16IPR016040
NAD(P)-binding domain		376698
17IPR009057
Homeodomain-like		3681040
18IPR029058
Alpha/Beta hydrolase fold		3581591
19IPR016024
Armadillo-type fold		3441284
20IPR001128
Cytochrome P450		3042359
21IPR003593
AAA+ ATPase domain		286570
22IPR012677
Nucleotide-binding, alpha-beta plait		270678
23IPR015943
WD40/YVTN repeat-like-containing domain		270665
24IPR013210
Leucine-rich repeat-containing N-terminal, type 2		269383
25IPR011989
Armadillo-like helical		265857
26IPR003591
Leucine-rich repeat, typical subtype		2472347
27IPR002401
Cytochrome P450, E-class, group I		2461765
28IPR017986
WD40-repeat-containing domain		245952
29IPR000504
RNA recognition motif domain		2451620
30IPR017972
Cytochrome P450, conserved site		245329
31IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		2431002
32IPR001680
WD40 repeat		2373779
33IPR016196
Major facilitator superfamily domain, general substrate transporter		231607
34IPR017853
Glycoside hydrolase, superfamily		228424
35IPR001005
SANT/Myb domain		228643
36IPR012336
Thioredoxin-like fold		225789
37IPR013781
Glycoside hydrolase, catalytic domain		188366
38IPR011992
EF-hand domain pair		176524
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		173581
40IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		173953
41IPR017930
Myb domain		170294
42IPR025875
Leucine rich repeat 4		169221
43IPR002048
EF-hand domain		1671182
44IPR016177
DNA-binding domain		167222
45IPR003441
NAC domain		166581
46IPR023214
HAD-like domain		164816
47IPR001471
AP2/ERF domain		1581047
48IPR007087
Zinc finger, C2H2		158523
49IPR011991
Winged helix-turn-helix DNA-binding domain		154238
50IPR011333
BTB/POZ fold		154478
51IPR018247
EF-Hand 1, calcium-binding site		150469
52IPR023213
Chloramphenicol acetyltransferase-like domain		144279
53IPR020683
Ankyrin repeat-containing domain		1431183
54IPR008985
Concanavalin A-like lectin/glucanases superfamily		139209
55IPR029044
Nucleotide-diphospho-sugar transferases		137455
56IPR014001
Helicase, superfamily 1/2, ATP-binding domain		136446
57IPR001650
Helicase, C-terminal		134660
58IPR002110
Ankyrin repeat		1341705
59IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		129214
60IPR019775
WD40 repeat, conserved site		127302
61IPR013026
Tetratricopeptide repeat-containing domain		125248
62IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		124317
63IPR003480
Transferase		124142
64IPR003439
ABC transporter-like		123601
65IPR019734
Tetratricopeptide repeat		1201331
66IPR003959
ATPase, AAA-type, core		119199
67IPR012340
Nucleic acid-binding, OB-fold		115462
68IPR001623
DnaJ domain		1121085
69IPR011011
Zinc finger, FYVE/PHD-type		111202
70IPR008974
TRAF-like		111193
71IPR013785
Aldolase-type TIM barrel		108219
72IPR005174
Protein of unknown function DUF295		107141
73IPR000210
BTB/POZ-like		106301
74IPR014710
RmlC-like jelly roll fold		106206
75IPR012337
Ribonuclease H-like domain		106338
76IPR013831
SGNH hydrolase-type esterase domain		106174
77IPR000008
C2 domain		1051034
78IPR001480
Bulb-type lectin domain		105694
79IPR013069
BTB/POZ		103163
80IPR001087
Lipase, GDSL		102151
81IPR003657
DNA-binding WRKY		100677
82IPR008972
Cupredoxin		99452
83IPR005225
Small GTP-binding protein domain		99149
84IPR011050
Pectin lyase fold/virulence factor		97110
85IPR012334
Pectin lyase fold		97115
86IPR001356
Homeobox domain		95312
87IPR006447
Myb domain, plants		94115
88IPR029071
Ubiquitin-related domain		94143
89IPR020846
Major facilitator superfamily domain		94149
90IPR005123
Oxoglutarate/iron-dependent dioxygenase		93363
91IPR021109
Aspartic peptidase domain		93419
92IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		92141
93IPR015424
Pyridoxal phosphate-dependent transferase		92156
94IPR001932
Protein phosphatase 2C (PP2C)-like domain		92724
95IPR025287
Wall-associated receptor kinase galacturonan-binding domain		91185
96IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		89150
97IPR015300
DNA-binding pseudobarrel domain		88383
98IPR001461
Aspartic peptidase		87316
99IPR009072
Histone-fold		87192
100IPR027443
Isopenicillin N synthase-like		86216
101IPR017871
ABC transporter, conserved site		86168
102IPR007658
Protein of unknown function DUF594		85103
103IPR000858
S-locus glycoprotein		83110
104IPR015880
Zinc finger, C2H2-like		83266
105IPR003609
Apple-like		82191
106IPR005828
General substrate transporter		82152
107IPR025315
Domain of unknown function DUF4220		82134
108IPR001965
Zinc finger, PHD-type		82189
109IPR002347
Glucose/ribitol dehydrogenase		81506
110IPR015655
Protein phosphatase 2C		81135
111IPR006501
Pectinesterase inhibitor domain		80348
112IPR017907
Zinc finger, RING-type, conserved site		80124
113IPR004827
Basic-leucine zipper domain		80401
114IPR011676
Domain of unknown function DUF1618		79106
115IPR003340
B3 DNA binding domain		78522
116IPR020472
G-protein beta WD-40 repeat		78333
117IPR006121
Heavy metal-associated domain, HMA		77266
118IPR011051
RmlC-like cupin domain		76135
119IPR002198
Short-chain dehydrogenase/reductase SDR		75327
120IPR003960
ATPase, AAA-type, conserved site		75120
121IPR002083
MATH		75320
122IPR013227
PAN-2 domain		7497
123IPR026992
Non-haem dioxygenase N-terminal domain		73155
124IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		73137
125IPR003613
U box domain		73183
126IPR001220
Legume lectin domain		7080
127IPR000109
Proton-dependent oligopeptide transporter family		69213
128IPR013763
Cyclin-like		69511
129IPR002100
Transcription factor, MADS-box		69680
130IPR000225
Armadillo		69782
131IPR010987
Glutathione S-transferase, C-terminal-like		68306
132IPR003579
Small GTPase superfamily, Rab type		68106
133IPR019787
Zinc finger, PHD-finger		67202
134IPR002902
Gnk2-homologous domain		66386
135IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		64123
136IPR016038
Thiolase-like, subgroup		63168
137IPR029052
Metallo-dependent phosphatase-like		63213
138IPR016039
Thiolase-like		62155
139IPR009009
RlpA-like double-psi beta-barrel domain		62141
140IPR000742
Epidermal growth factor-like domain		62257
141IPR015500
Peptidase S8, subtilisin-related		62274
142IPR000571
Zinc finger, CCCH-type		62647
143IPR001806
Small GTPase superfamily		62479
144IPR000626
Ubiquitin-like		61202
145IPR026961
PGG domain		61154
146IPR013766
Thioredoxin domain		6179
147IPR014733
Barwin-like endoglucanase		6177
148IPR027001
Caskin/Ankyrin repeat-containing protein		6179
149IPR012871
Protein of unknown function DUF1677, Oryza sativa		6089
150IPR001509
NAD-dependent epimerase/dehydratase		6099
151IPR019786
Zinc finger, PHD-type, conserved site		60105
152IPR004045
Glutathione S-transferase, N-terminal		60204
153IPR013057
Amino acid transporter, transmembrane		5974
154IPR000620
Drug/metabolite transporter		58128
155IPR000048
IQ motif, EF-hand binding site		58578
156IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5782
157IPR003137
Protease-associated domain, PA		5781
158IPR004864
Late embryogenesis abundant protein, LEA-14		5765
159IPR003245
Plastocyanin-like		57133
160IPR023395
Mitochondrial carrier domain		57169
161IPR000209
Peptidase S8/S53 domain		57431
162IPR018108
Mitochondrial substrate/solute carrier		56447
163IPR016159
Cullin repeat-like-containing domain		5695
164IPR011993
Pleckstrin homology-like domain		5683
165IPR027640
Kinesin-like protein		55104
166IPR020568
Ribosomal protein S5 domain 2-type fold		55102
167IPR013525
ABC-2 type transporter		54129
168IPR007112
Expansin/pollen allergen, DPBB domain		54119
169IPR016135
Ubiquitin-conjugating enzyme/RWD-like		54167
170IPR008979
Galactose-binding domain-like		54259
171IPR005202
Transcription factor GRAS		54124
172IPR000490
Glycoside hydrolase, family 17		54115
173IPR003578
Small GTPase superfamily, Rho type		5492
174IPR013094
Alpha/beta hydrolase fold-3		5463
175IPR001752
Kinesin, motor domain		54817
176IPR020849
Small GTPase superfamily, Ras type		5378
177IPR001881
EGF-like calcium-binding domain		53153
178IPR018097
EGF-like calcium-binding, conserved site		53100
179IPR013128
Peptidase C1A		5255
180IPR005829
Sugar transporter, conserved site		52133
181IPR006566
FBD domain		5261
182IPR003676
Auxin-induced protein, ARG7		5264
183IPR016181
Acyl-CoA N-acyltransferase		51181
184IPR010259
Proteinase inhibitor I9		5178
185IPR026057
PC-Esterase		5183
186IPR007117
Expansin, cellulose-binding-like domain		51240
187IPR008949
Terpenoid synthase		50160
188IPR002035
von Willebrand factor, type A		50199
189IPR002921
Lipase, class 3		4969
190IPR007118
Expansin/Lol pI		49280
191IPR024171
S-receptor-like serine/threonine-protein kinase		4958
192IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4977
193IPR007125
Histone core		4953
194IPR003663
Sugar/inositol transporter		49381
195IPR024788
Malectin-like carbohydrate-binding domain		49113
196IPR011032
GroES (chaperonin 10)-like		48168
197IPR001563
Peptidase S10, serine carboxypeptidase		48552
198IPR023393
START-like domain		4872
199IPR012946
X8		48120
200IPR002528
Multi antimicrobial extrusion protein		48220
201IPR011042
Six-bladed beta-propeller, TolB-like		4878
202IPR006016
UspA		4751
203IPR000873
AMP-dependent synthetase/ligase		4771
204IPR006553
Leucine-rich repeat, cysteine-containing subtype		47563
205IPR011527
ABC transporter type 1, transmembrane domain		47272
206IPR025846
PMR5 N-terminal domain		4774
207IPR017451
F-box associated interaction domain		4660
208IPR014014
RNA helicase, DEAD-box type, Q motif		4667
209IPR022059
Protein of unknown function DUF3615		4670
210IPR017970
Homeobox, conserved site		4649
211IPR023299
P-type ATPase, cytoplasmic domain N		46156
212IPR001757
Cation-transporting P-type ATPase		46697
213IPR004853
Triose-phosphate transporter domain		4568
214IPR000608
Ubiquitin-conjugating enzyme, E2		45129
215IPR008250
P-type ATPase, A domain		45208
216IPR029055
Nucleophile aminohydrolases, N-terminal		45105
217IPR003594
Histidine kinase-like ATPase, ATP-binding domain		45263
218IPR008928
Six-hairpin glycosidase-like		4580
219IPR023828
Peptidase S8, subtilisin, Ser-active site		4567
220IPR009003
Trypsin-like cysteine/serine peptidase domain		4583
221IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		45191
222IPR001140
ABC transporter, transmembrane domain		44131
223IPR013201
Proteinase inhibitor I29, cathepsin propeptide		4495
224IPR018253
DnaJ domain, conserved site		4459
225IPR006671
Cyclin, N-terminal		44108
226IPR004158
Protein of unknown function DUF247, plant		4457
227IPR011006
CheY-like superfamily		4362
228IPR020845
AMP-binding, conserved site		4360
229IPR018303
P-type ATPase, phosphorylation site		4376
230IPR004046
Glutathione S-transferase, C-terminal		4367
231IPR000668
Peptidase C1A, papain C-terminal		43209
232IPR003311
AUX/IAA protein		4367
233IPR000070
Pectinesterase, catalytic		4347
234IPR001214
SET domain		43162
235IPR017877
Myb-like domain		4370
236IPR008978
HSP20-like chaperone		42102
237IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4261
238IPR014756
Immunoglobulin E-set		4278
239IPR011525
Aux/IAA-ARF-dimerisation		4161
240IPR016166
FAD-binding, type 2		41109
241IPR006045
Cupin 1		41139
242IPR010255
Haem peroxidase		4161
243IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4156
244IPR000743
Glycoside hydrolase, family 28		4175
245IPR001789
Signal transduction response regulator, receiver domain		41160
246IPR008942
ENTH/VHS		40126
247IPR010402
CCT domain		40113
248IPR007493
Protein of unknown function DUF538		40138
249IPR011701
Major facilitator superfamily		4096
250IPR000330
SNF2-related		4066
251IPR013105
Tetratricopeptide TPR2		4070
252IPR011706
Multicopper oxidase, type 2		4049
253IPR002016
Haem peroxidase, plant/fungal/bacterial		40268
254IPR002912
ACT domain		40174
255IPR001117
Multicopper oxidase, type 1		3947
256IPR000182
GNAT domain		39102
257IPR025659
Tubby C-terminal-like domain		3970
258IPR009000
Translation protein, beta-barrel domain		3967
259IPR004140
Exocyst complex protein Exo70		3987
260IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3972
261IPR025322
Protein of unknown function DUF4228, plant		3839
262IPR006626
Parallel beta-helix repeat		38216
263IPR011016
Zinc finger, RING-CH-type		38110
264IPR001296
Glycosyl transferase, family 1		3862
265IPR001969
Aspartic peptidase, active site		3883
266IPR004883
Lateral organ boundaries, LOB		3875
267IPR002041
Ran GTPase		3877
268IPR002495
Glycosyl transferase, family 8		3852
269IPR000644
CBS domain		38326
270IPR004314
Domain of unknown function DUF239		3843
271IPR011043
Galactose oxidase/kelch, beta-propeller		3849
272IPR018202
Peptidase S10, serine carboxypeptidase, active site		38102
273IPR008889
VQ		3839
274IPR011707
Multicopper oxidase, type 3		3846
275IPR009060
UBA-like		3753
276IPR005135
Endonuclease/exonuclease/phosphatase		37199
277IPR013783
Immunoglobulin-like fold		3769
278IPR004263
Exostosin-like		3797
279IPR000073
Alpha/beta hydrolase fold-1		37150
280IPR000152
EGF-type aspartate/asparagine hydroxylation site		3774
281IPR011012
Longin-like domain		3755
282IPR013126
Heat shock protein 70 family		37292
283IPR025661
Cysteine peptidase, asparagine active site		3740
284IPR001878
Zinc finger, CCHC-type		37319
285IPR001251
CRAL-TRIO domain		36247
286IPR023271
Aquaporin-like		3692
287IPR004265
Plant disease resistance response protein		3647
288IPR008480
Protein of unknown function DUF761, plant		3636
289IPR000425
Major intrinsic protein		36359
290IPR004088
K Homology domain, type 1		36515
291IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3661
292IPR002487
Transcription factor, K-box		36115
293IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3662
294IPR029021
Protein-tyrosine phosphatase-like		35127
295IPR002109
Glutaredoxin		3572
296IPR015947
PUA-like domain		3559
297IPR000169
Cysteine peptidase, cysteine active site		3435
298IPR015915
Kelch-type beta propeller		3476
299IPR025660
Cysteine peptidase, histidine active site		3438
300IPR004041
NAF domain		3337
301IPR013149
Alcohol dehydrogenase, C-terminal		3353
302IPR018451
NAF/FISL domain		3337
303IPR001938
Thaumatin		33418
304IPR004367
Cyclin, C-terminal domain		3350
305IPR020904
Short-chain dehydrogenase/reductase, conserved site		3353
306IPR029045
ClpP/crotonase-like domain		33120
307IPR014044
CAP domain		33160
308IPR005746
Thioredoxin		3347
309IPR022357
Major intrinsic protein, conserved site		3339
310IPR006094
FAD linked oxidase, N-terminal		3339
311IPR002067
Mitochondrial carrier protein		33223
312IPR029047
Heat shock protein 70kD, peptide-binding domain		3376
313IPR024156
Small GTPase superfamily, ARF type		3377
314IPR015916
Galactose oxidase, beta-propeller		3240
315IPR006153
Cation/H+ exchanger		3252
316IPR019821
Kinesin, motor region, conserved site		3251
317IPR002659
Glycosyl transferase, family 31		3284
318IPR005630
Terpene synthase, metal-binding domain		3241
319IPR013154
Alcohol dehydrogenase GroES-like		3250
320IPR003406
Glycosyl transferase, family 14		3239
321IPR004839
Aminotransferase, class I/classII		3263
322IPR014720
Double-stranded RNA-binding domain		32296
323IPR018040
Pectinesterase, active site		3236
324IPR012341
Six-hairpin glycosidase		3255
325IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3241
326IPR000782
FAS1 domain		31172
327IPR002068
Alpha crystallin/Hsp20 domain		3165
328IPR006652
Kelch repeat type 1		31177
329IPR016167
FAD-binding, type 2, subdomain 1		3139
330IPR019378
GDP-fucose protein O-fucosyltransferase		3155
331IPR020843
Polyketide synthase, enoylreductase		3137
332IPR013027
FAD-dependent pyridine nucleotide-disulphide oxidoreductase		31137
333IPR018490
Cyclic nucleotide-binding-like		3057
334IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		3082
335IPR000795
Elongation factor, GTP-binding domain		30228
336IPR012675
Beta-grasp domain		3038
337IPR018181
Heat shock protein 70, conserved site		3075
338IPR003690
Mitochodrial transcription termination factor-related		30280
339IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		30137
340IPR004087
K Homology domain		30128
341IPR006458
Ovate protein family, C-terminal		3060
342IPR000823
Plant peroxidase		30219
343IPR025110
AMP-binding enzyme C-terminal domain		2942
344IPR001440
Tetratricopeptide TPR1		2950
345IPR001357
BRCT domain		29345
346IPR008991
Translation protein SH3-like domain		2934
347IPR002283
Isopenicillin N synthase		29120
348IPR011074
CRAL/TRIO, N-terminal domain		29118
349IPR002123
Phospholipid/glycerol acyltransferase		2956
350IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		29112
351IPR006041
Pollen Ole e 1 allergen/extensin		2933
352IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2839
353IPR013216
Methyltransferase type 11		2845
354IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2882
355IPR002423
Chaperonin Cpn60/TCP-1		28119
356IPR027356
NPH3 domain		2880
357IPR019793
Peroxidases heam-ligand binding site		2840
358IPR019794
Peroxidase, active site		2840
359IPR027409
GroEL-like apical domain		2871
360IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2850
361IPR017937
Thioredoxin, conserved site		2841
362IPR003851
Zinc finger, Dof-type		2889
363IPR023298
P-type ATPase, transmembrane domain		28128
364IPR000595
Cyclic nucleotide-binding domain		28143
365IPR000270
Phox/Bem1p		2886
366IPR006073
GTP binding domain		2896
367IPR017884
SANT domain		2742
368IPR000727
Target SNARE coiled-coil domain		2775
369IPR017938
Riboflavin synthase-like beta-barrel		2743
370IPR007650
Protein of unknown function DUF581		2730
371IPR002355
Multicopper oxidase, copper-binding site		2755
372IPR005150
Cellulose synthase		2757
373IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2785
374IPR002963
Expansin		27217
375IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2741
376IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2734
377IPR001906
Terpene synthase, N-terminal domain		2762
378IPR000757
Glycoside hydrolase, family 16		2734
379IPR023329
Chlorophyll a/b binding protein domain		2755
380IPR017927
Ferredoxin reductase-type FAD-binding domain		2635
381IPR000528
Plant lipid transfer protein/Par allergen		26119
382IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2630
383IPR000315
Zinc finger, B-box		26117
384IPR029061
Thiamin diphosphate-binding fold		26146
385IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2631
386IPR004014
Cation-transporting P-type ATPase, N-terminal		2689
387IPR000863
Sulfotransferase domain		2639
388IPR023313
Ubiquitin-conjugating enzyme, active site		2632
389IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2627
390IPR001077
O-methyltransferase, family 2		2639
391IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2633
392IPR003855
K+ potassium transporter		2668
393IPR005175
Domain of unknown function DUF296		2626
394IPR003100
Argonaute/Dicer protein, PAZ domain		25234
395IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2576
396IPR013601
FAE1/Type III polyketide synthase-like protein		2527
397IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2595
398IPR025753
AAA-type ATPase, N-terminal domain		2529
399IPR013088
Zinc finger, NHR/GATA-type		2537
400IPR010920
Like-Sm (LSM) domain		2544
401IPR008422
Homeobox KN domain		2528
402IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		2537
403IPR001279
Beta-lactamase-like		25161
404IPR027725
Heat shock transcription factor family		2528
405IPR001478
PDZ domain		25123
406IPR001353
Proteasome, subunit alpha/beta		2530
407IPR000408
Regulator of chromosome condensation, RCC1		25658
408IPR008266
Tyrosine-protein kinase, active site		2539
409IPR011013
Galactose mutarotase-like domain		2548
410IPR004813
Oligopeptide transporter, OPT superfamily		25117
411IPR001849
Pleckstrin homology domain		2593
412IPR013780
Glycosyl hydrolase, family 13, all-beta		2533
413IPR025486
Domain of unknown function DUF4378		2540
414IPR000232
Heat shock factor (HSF)-type, DNA-binding		25166
415IPR001223
Glycoside hydrolase, family 18, catalytic domain		2527
416IPR000679
Zinc finger, GATA-type		25134
417IPR002913
START domain		25108
418IPR015797
NUDIX hydrolase domain-like		2575
419IPR027709
Heat shock transcription factor, plant		2528
420IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		24240
421IPR016461
Caffeate O-methyltransferase (COMT) family		2440
422IPR027214
Cystatin		2425
423IPR007612
LURP1-like domain		2431
424IPR029000
Cyclophilin-like domain		2484
425IPR024709
O-fucosyltransferase, plant		2439
426IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2426
427IPR001763
Rhodanese-like domain		24152
428IPR002293
Amino acid/polyamine transporter I		2492
429IPR017923
Transcription factor IIS, N-terminal		24149
430IPR001701
Glycoside hydrolase, family 9		2431
431IPR029006
ADF-H/Gelsolin-like domain		24111
432IPR010525
Auxin response factor		2441
433IPR003106
Leucine zipper, homeobox-associated		2334
434IPR001929
Germin		2380
435IPR001360
Glycoside hydrolase, family 1		23338
436IPR003954
RNA recognition motif domain, eukaryote		2352
437IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2384
438IPR013581
Plant PDR ABC transporter associated		2342
439IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		2361
440IPR003337
Trehalose-phosphatase		2353
441IPR027923
Hydrophobic seed protein		2328
442IPR014722
Ribosomal protein L2 domain 2		2327
443IPR029062
Class I glutamine amidotransferase-like		2391
444IPR003388
Reticulon		2370
445IPR008971
HSP40/DnaJ peptide-binding		2282
446IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2222
447IPR006593
Cytochrome b561/ferric reductase transmembrane		2247
448IPR006195
Aminoacyl-tRNA synthetase, class II		2229
449IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2279
450IPR003347
JmjC domain		22110
451IPR007657
Glycosyltransferase AER61, uncharacterised		2235
452IPR000300
Inositol polyphosphate-related phosphatase		2230
453IPR008963
Purple acid phosphatase-like, N-terminal		2230
454IPR012967
Plant methyltransferase dimerisation		2229
455IPR029033
Histidine phosphatase superfamily		2297
456IPR001229
Mannose-binding lectin		22119
457IPR001099
Chalcone/stilbene synthase, N-terminal		2223
458IPR029048
Heat shock protein 70kD, C-terminal domain		2243
459IPR004274
NLI interacting factor		22107
460IPR006689
Small GTPase superfamily, ARF/SAR type		21130
461IPR018244
Allergen V5/Tpx-1-related, conserved site		2140
462IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		2129
463IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2132
464IPR002168
Lipase, GDXG, active site		2130
465IPR005333
Transcription factor, TCP		2124
466IPR005516
Remorin, C-terminal		2131
467IPR016455
Xyloglucan endotransglucosylase/hydrolase		2125
468IPR025422
Transcription factor TGA like domain		2140
469IPR006694
Fatty acid hydroxylase		2137
470IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2139
471IPR029481
ABC-transporter extracellular N-terminal domain		2138
472IPR005821
Ion transport domain		2134
473IPR001232
SKP1 component		2145
474IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2130
475IPR016161
Aldehyde/histidinol dehydrogenase		2139
476IPR002939
Chaperone DnaJ, C-terminal		2133
477IPR029059
Alpha/beta hydrolase fold-5		2128
478IPR020635
Tyrosine-protein kinase, catalytic domain		2135
479IPR000086
NUDIX hydrolase domain		2162
480IPR013323
SIAH-type domain		2132
481IPR006439
HAD hydrolase, subfamily IA		2189
482IPR015914
Purple acid phosphatase, N-terminal		2129
483IPR010399
Tify		2198
484IPR023210
NADP-dependent oxidoreductase domain		21143
485IPR001487
Bromodomain		21256
486IPR023796
Serpin domain		21117
487IPR001041
2Fe-2S ferredoxin-type domain		2169
488IPR001395
Aldo/keto reductase		2139
489IPR006867
Domain of unknown function DUF632		2132
490IPR006594
LisH dimerisation motif		2074
491IPR013328
Dehydrogenase, multihelical		2040
492IPR002867
Zinc finger, C6HC-type		20116
493IPR002403
Cytochrome P450, E-class, group IV		20134
494IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		2027
495IPR000717
Proteasome component (PCI) domain		2041
496IPR001163
Ribonucleoprotein LSM domain		2027
497IPR018221
Glycoside hydrolase, family 9, active site		2034
498IPR017887
Transcription factor TCP subgroup		2023
499IPR004320
Protein of unknown function DUF241, plant		2054
500IPR027413
GroEL-like equatorial domain		2045
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula.html b/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula.html new file mode 100644 index 00000000..bfff76e2 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula.html @@ -0,0 +1,70 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:MedtrA17_4.0, Jun 2014
Database version:86.2
Base Pairs:412,800,391
Golden Path Length:412,800,391
Genebuild by: IMGAG
Genebuild method: Generated from ENA annotation
Genebuild started: Jan 2015
Genebuild released: Aug 2011
Genebuild last updated/patched: Jun 2014
Genebuild version: 2014-06-EnsemblPlants
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		50,444
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		189
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:61,214
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
8 sequences
+
+ +
+ + + +
SequenceLength (bp)
152991155
245729672
355515152
456582383
543630510
635275713
749172423
845569985
+
+
supercontig2178 sequences
chunk4122 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula_IPtop500.html new file mode 100644 index 00000000..09df02c1 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Medicago_truncatula_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		23427152
2IPR032675
Leucine-rich repeat domain, L domain-like		23338112
3IPR011009
Protein kinase-like domain		17462290
4IPR000719
Protein kinase domain		16094749
5IPR001810
F-box domain		12603758
6IPR008271
Serine/threonine-protein kinase, active site		11741462
7IPR017441
Protein kinase, ATP binding site		10041216
8IPR013320
Concanavalin A-like lectin/glucanase domain		9511363
9IPR002182
NB-ARC		8021001
10IPR013083
Zinc finger, RING/FYVE/PHD-type		7761035
11IPR001611
Leucine-rich repeat		7605787
12IPR011990
Tetratricopeptide-like helical domain		7232731
13IPR002885
Pentatricopeptide repeat		71415956
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		6201077
15IPR009810
Late nodulin		592611
16IPR009057
Homeodomain-like		5481525
17IPR017451
F-box associated interaction domain		540553
18IPR016040
NAD(P)-binding domain		5311536
19IPR001841
Zinc finger, RING-type		5231389
20IPR003593
AAA+ ATPase domain		494871
21IPR013210
Leucine-rich repeat-containing N-terminal, type 2		486537
22IPR003591
Leucine-rich repeat, typical subtype		4853510
23IPR011991
Winged helix-turn-helix DNA-binding domain		484890
24IPR001128
Cytochrome P450		4502838
25IPR029058
Alpha/Beta hydrolase fold		4201280
26IPR016024
Armadillo-type fold		4111219
27IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		3872382
28IPR002401
Cytochrome P450, E-class, group I		3702646
29IPR017853
Glycoside hydrolase superfamily		360527
30IPR001005
SANT/Myb domain		3541079
31IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		3411038
32IPR012677
Nucleotide-binding alpha-beta plait domain		3381379
33IPR017972
Cytochrome P450, conserved site		338355
34IPR012340
Nucleic acid-binding, OB-fold		330515
35IPR011989
Armadillo-like helical		329808
36IPR015943
WD40/YVTN repeat-like-containing domain		327670
37IPR020846
Major facilitator superfamily domain		323780
38IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		322801
39IPR017986
WD40-repeat-containing domain		308948
40IPR013781
Glycoside hydrolase, catalytic domain		292404
41IPR012336
Thioredoxin-like fold		287743
42IPR017930
Myb domain		280512
43IPR000504
RNA recognition motif domain		2771735
44IPR001680
WD40 repeat		2723670
45IPR016177
DNA-binding domain		252313
46IPR012334
Pectin lyase fold		237258
47IPR011050
Pectin lyase fold/virulence factor		234251
48IPR011992
EF-hand domain pair		228748
49IPR001471
AP2/ERF domain		2271472
50IPR015300
DNA-binding pseudobarrel domain		224667
51IPR027443
Isopenicillin N synthase-like		222270
52IPR006566
FBD domain		222378
53IPR005123
Oxoglutarate/iron-dependent dioxygenase		221496
54IPR002048
EF-hand domain		2031578
55IPR023214
HAD-like domain		198790
56IPR003439
ABC transporter-like		198785
57IPR010285
DNA helicase Pif1 like		197238
58IPR001650
Helicase, C-terminal		193701
59IPR026992
Non-haem dioxygenase N-terminal domain		192225
60IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		1921131
61IPR023213
Chloramphenicol acetyltransferase-like domain		189328
62IPR014001
Helicase superfamily 1/2, ATP-binding domain		187468
63IPR018247
EF-Hand 1, calcium-binding site		186487
64IPR006527
F-box associated domain, type 1		182187
65IPR013830
SGNH hydrolase-type esterase domain		180563
66IPR001480
Bulb-type lectin domain		1801133
67IPR019775
WD40 repeat, conserved site		179376
68IPR020683
Ankyrin repeat-containing domain		172982
69IPR014710
RmlC-like jelly roll fold		171234
70IPR006501
Pectinesterase inhibitor domain		166716
71IPR003480
Transferase		166180
72IPR007087
Zinc finger, C2H2		164537
73IPR003959
ATPase, AAA-type, core		164253
74IPR029044
Nucleotide-diphospho-sugar transferases		162516
75IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		153823
76IPR002110
Ankyrin repeat		1521184
77IPR029071
Ubiquitin-related domain		151283
78IPR009072
Histone-fold		146301
79IPR000008
C2 domain		1451028
80IPR002100
Transcription factor, MADS-box		143991
81IPR010255
Haem peroxidase		143171
82IPR005135
Endonuclease/exonuclease/phosphatase		142454
83IPR003676
Auxin-induced protein, ARG7		142142
84IPR008972
Cupredoxin		141520
85IPR017871
ABC transporter, conserved site		140239
86IPR001087
Lipase, GDSL		139154
87IPR003340
B3 DNA binding domain		139667
88IPR003871
Domain of unknown function DUF223		138139
89IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		138204
90IPR002016
Haem peroxidase, plant/fungal/bacterial		138969
91IPR002347
Glucose/ribitol dehydrogenase		1311389
92IPR003609
Apple-like		131471
93IPR006553
Leucine-rich repeat, cysteine-containing subtype		131966
94IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		131328
95IPR011051
RmlC-like cupin domain		129172
96IPR011011
Zinc finger, FYVE/PHD-type		127207
97IPR000823
Plant peroxidase		1271081
98IPR013785
Aldolase-type TIM barrel		126209
99IPR011043
Galactose oxidase/kelch, beta-propeller		124148
100IPR015424
Pyridoxal phosphate-dependent transferase		124152
101IPR021109
Aspartic peptidase domain		123425
102IPR015500
Peptidase S8, subtilisin-related		123467
103IPR013026
Tetratricopeptide repeat-containing domain		123234
104IPR011333
BTB/POZ fold		122165
105IPR011545
DEAD/DEAH box helicase domain		121154
106IPR032867
DYW domain		121127
107IPR000858
S-locus glycoprotein		120168
108IPR005225
Small GTP-binding protein domain		120139
109IPR017907
Zinc finger, RING-type, conserved site		120145
110IPR001623
DnaJ domain		1191016
111IPR019734
Tetratricopeptide repeat		1161268
112IPR005828
General substrate transporter		115156
113IPR001461
Aspartic peptidase		115321
114IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		114140
115IPR000209
Peptidase S8/S53 domain		113638
116IPR001356
Homeobox domain		112369
117IPR025558
Domain of unknown function DUF4283		112112
118IPR000626
Ubiquitin domain		110612
119IPR000109
Proton-dependent oligopeptide transporter family		109246
120IPR003657
DNA-binding WRKY		109756
121IPR013126
Heat shock protein 70 family		109798
122IPR000070
Pectinesterase, catalytic		109115
123IPR031052
FHY3/FAR1 family		108118
124IPR006121
Heavy metal-associated domain, HMA		106361
125IPR006447
Myb domain, plants		106141
126IPR033121
Peptidase family A1 domain		106137
127IPR013057
Amino acid transporter, transmembrane		104128
128IPR019793
Peroxidases heam-ligand binding site		103114
129IPR032861
Xylanase inhibitor, N-terminal		101119
130IPR003441
NAC domain		100354
131IPR024171
S-receptor-like serine/threonine-protein kinase		100117
132IPR020472
G-protein beta WD-40 repeat		100372
133IPR001965
Zinc finger, PHD-type		100207
134IPR032799
Xylanase inhibitor, C-terminal		98111
135IPR000073
Alpha/beta hydrolase fold-1		98276
136IPR011527
ABC transporter type 1, transmembrane domain		97684
137IPR001806
Small GTPase superfamily		96121
138IPR012337
Ribonuclease H-like domain		95216
139IPR006045
Cupin 1		95242
140IPR000270
Phox/Bem1p		95213
141IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		94143
142IPR030184
WAT1-related protein		94127
143IPR029047
Heat shock protein 70kD, peptide-binding domain		94200
144IPR001932
Protein phosphatase 2C (PP2C)-like domain		94785
145IPR000225
Armadillo		941000
146IPR004158
Protein of unknown function DUF247, plant		93101
147IPR009000
Translation protein, beta-barrel domain		91122
148IPR002902
Gnk2-homologous domain		91430
149IPR010987
Glutathione S-transferase, C-terminal-like		90292
150IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		89112
151IPR011032
GroES (chaperonin 10)-like		88219
152IPR023393
START-like domain		88106
153IPR000571
Zinc finger, CCCH-type		87913
154IPR003960
ATPase, AAA-type, conserved site		86115
155IPR026961
PGG domain		86102
156IPR023828
Peptidase S8, subtilisin, Ser-active site		8596
157IPR015655
Protein phosphatase 2C		85197
158IPR001220
Legume lectin domain		8596
159IPR019787
Zinc finger, PHD-finger		84210
160IPR025287
Wall-associated receptor kinase galacturonan-binding domain		8386
161IPR000620
EamA domain		83196
162IPR023395
Mitochondrial carrier domain		82244
163IPR004045
Glutathione S-transferase, N-terminal		82180
164IPR011993
Pleckstrin homology-like domain		82211
165IPR011006
CheY-like superfamily		81120
166IPR003663
Sugar/inositol transporter		81526
167IPR013101
Leucine-rich repeat 2		8096
168IPR018181
Heat shock protein 70, conserved site		80212
169IPR018108
Mitochondrial substrate/solute carrier		80580
170IPR003245
Plastocyanin-like		80239
171IPR019794
Peroxidase, active site		8087
172IPR033131
Pectinesterase, Asp active site		7981
173IPR005829
Sugar transporter, conserved site		79169
174IPR016159
Cullin repeat-like-containing domain		79106
175IPR001789
Signal transduction response regulator, receiver domain		79295
176IPR009009
RlpA-like double-psi beta-barrel domain		78202
177IPR013766
Thioredoxin domain		78177
178IPR002085
Alcohol dehydrogenase superfamily, zinc-type		78117
179IPR004827
Basic-leucine zipper domain		78365
180IPR010264
Plant self-incompatibility S1		7878
181IPR015880
Zinc finger, C2H2-like		78208
182IPR008978
HSP20-like chaperone		77180
183IPR001214
SET domain		77265
184IPR000743
Glycoside hydrolase, family 28		77134
185IPR016039
Thiolase-like		76350
186IPR029052
Metallo-dependent phosphatase-like		76258
187IPR024788
Malectin-like carbohydrate-binding domain		76101
188IPR016181
Acyl-CoA N-acyltransferase		75183
189IPR001563
Peptidase S10, serine carboxypeptidase		74486
190IPR029048
Heat shock protein 70kD, C-terminal domain		74141
191IPR026057
PC-Esterase		7384
192IPR008266
Tyrosine-protein kinase, active site		7384
193IPR008949
Isoprenoid synthase domain		72164
194IPR029962
Trichome birefringence-like family		7298
195IPR013763
Cyclin-like		72415
196IPR019786
Zinc finger, PHD-type, conserved site		72120
197IPR002528
Multi antimicrobial extrusion protein		72237
198IPR004864
Late embryogenesis abundant protein, LEA-14		7178
199IPR008979
Galactose-binding domain-like		71232
200IPR027640
Kinesin-like protein		70238
201IPR004330
FAR1 DNA binding domain		7078
202IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		70170
203IPR007750
Protein of unknown function DUF674		6993
204IPR002109
Glutaredoxin		69135
205IPR001752
Kinesin motor domain		69630
206IPR004843
Calcineurin-like phosphoesterase domain, apaH type		68102
207IPR014756
Immunoglobulin E-set		68112
208IPR014014
RNA helicase, DEAD-box type, Q motif		6777
209IPR005202
Transcription factor GRAS		67137
210IPR000048
IQ motif, EF-hand binding site		67572
211IPR006626
Parallel beta-helix repeat		66338
212IPR020568
Ribosomal protein S5 domain 2-type fold		6699
213IPR005174
Protein of unknown function DUF295		6668
214IPR003613
U box domain		66249
215IPR016135
Ubiquitin-conjugating enzyme/RWD-like		65187
216IPR007125
Histone core		6566
217IPR013525
ABC-2 type transporter		64113
218IPR000873
AMP-dependent synthetase/ligase		6492
219IPR025846
PMR5 N-terminal domain		6471
220IPR016461
O-methyltransferase COMT-type		63118
221IPR013128
Peptidase C1A		6368
222IPR001077
O-methyltransferase, family 2		6370
223IPR023299
P-type ATPase, cytoplasmic domain N		63178
224IPR000668
Peptidase C1A, papain C-terminal		63254
225IPR024752
Myb/SANT-like domain		6376
226IPR000182
GNAT domain		62127
227IPR006153
Cation/H+ exchanger		6167
228IPR004883
Lateral organ boundaries, LOB		61126
229IPR013149
Alcohol dehydrogenase, C-terminal		6075
230IPR000210
BTB/POZ domain		60244
231IPR003323
Ovarian tumour, otubain		6085
232IPR003594
Histidine kinase-like ATPase, C-terminal domain		60261
233IPR020904
Short-chain dehydrogenase/reductase, conserved site		6065
234IPR000742
Epidermal growth factor-like domain		60114
235IPR018253
DnaJ domain, conserved site		6072
236IPR029045
ClpP/crotonase-like domain		60239
237IPR000490
Glycoside hydrolase, family 17		60119
238IPR001360
Glycoside hydrolase, family 1		59517
239IPR002068
Alpha crystallin/Hsp20 domain		59123
240IPR003690
Mitochodrial transcription termination factor		59462
241IPR016072
SKP1 component, dimerisation		59113
242IPR000528
Plant lipid transfer protein/Par allergen		58275
243IPR003614
Knottin, scorpion toxin-like		58153
244IPR000608
Ubiquitin-conjugating enzyme E2		57170
245IPR008250
P-type ATPase, A domain		57190
246IPR020845
AMP-binding, conserved site		5782
247IPR012967
Plant methyltransferase dimerisation		5763
248IPR001929
Germin		56169
249IPR005175
Domain of unknown function DUF296		56117
250IPR008974
TRAF-like		56133
251IPR015916
Galactose oxidase, beta-propeller		5564
252IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		5584
253IPR018303
P-type ATPase, phosphorylation site		5582
254IPR001232
S-phase kinase-associated protein 1-like		5557
255IPR001757
P-type ATPase		55296
256IPR011042
Six-bladed beta-propeller, TolB-like		5596
257IPR029055
Nucleophile aminohydrolases, N-terminal		54146
258IPR000795
Elongation factor, GTP-binding domain		54300
259IPR013154
Alcohol dehydrogenase GroES-like		5467
260IPR016166
FAD-binding, type 2		54116
261IPR031107
Small heat shock protein HSP20		5460
262IPR002035
von Willebrand factor, type A		54203
263IPR020843
Polyketide synthase, enoylreductase domain		5460
264IPR003137
Protease-associated domain, PA		5372
265IPR012946
X8 domain		53132
266IPR011706
Multicopper oxidase, type 2		5356
267IPR006671
Cyclin, N-terminal		53103
268IPR004873
BURP domain		52184
269IPR008928
Six-hairpin glycosidase-like		5294
270IPR004088
K Homology domain, type 1		52513
271IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5258
272IPR011707
Multicopper oxidase, type 3		5255
273IPR001117
Multicopper oxidase, type 1		5154
274IPR000330
SNF2-related		5168
275IPR017884
SANT domain		5064
276IPR013201
Proteinase inhibitor I29, cathepsin propeptide		50100
277IPR017970
Homeobox, conserved site		5054
278IPR011065
Kunitz inhibitor ST1-like		4950
279IPR016073
SKP1 component, POZ domain		4951
280IPR011701
Major facilitator superfamily		4959
281IPR005630
Terpene synthase, metal-binding domain		4960
282IPR001938
Thaumatin		49568
283IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		4988
284IPR008480
Protein of unknown function DUF761, plant		4949
285IPR000425
Major intrinsic protein		49510
286IPR002160
Proteinase inhibitor I3, Kunitz legume		49156
287IPR018202
Peptidase S10, serine carboxypeptidase, active site		4956
288IPR032710
NTF2-like domain		48105
289IPR004263
Exostosin-like		4863
290IPR023271
Aquaporin-like		48132
291IPR006094
FAD linked oxidase, N-terminal		4851
292IPR019780
Germin, manganese binding site		4849
293IPR002067
Mitochondrial carrier protein		48325
294IPR004314
Domain of unknown function DUF239		4854
295IPR019956
Ubiquitin		47186
296IPR009060
UBA-like		4769
297IPR004161
Translation elongation factor EFTu/EF1A, domain 2		4757
298IPR013783
Immunoglobulin-like fold		4781
299IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4766
300IPR011012
Longin-like domain		4760
301IPR002495
Glycosyl transferase, family 8		4763
302IPR001906
Terpene synthase, N-terminal domain		47108
303IPR015947
PUA-like domain		4769
304IPR001251
CRAL-TRIO domain		46320
305IPR013094
Alpha/beta hydrolase fold-3		4648
306IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4657
307IPR025659
Tubby C-terminal-like domain		4552
308IPR004853
Triose-phosphate transporter domain		4563
309IPR019821
Kinesin motor domain, conserved site		4553
310IPR013088
Zinc finger, NHR/GATA-type		4552
311IPR010920
Like-Sm (LSM) domain		4553
312IPR001969
Aspartic peptidase, active site		4584
313IPR004265
Plant disease resistance response protein		4545
314IPR007112
Expansin/pollen allergen, DPBB domain		4585
315IPR007117
Expansin, cellulose-binding-like domain		45187
316IPR023210
NADP-dependent oxidoreductase domain		45181
317IPR017877
Myb-like domain		4567
318IPR010525
Auxin response factor		4568
319IPR002921
Fungal lipase-like domain		4453
320IPR000782
FAS1 domain		44256
321IPR002867
Zinc finger, C6HC-type		44137
322IPR007118
Expansin/Lol pI		44251
323IPR025886
Phloem protein 2-like		4444
324IPR006652
Kelch repeat type 1		44171
325IPR025875
Leucine rich repeat 4		4449
326IPR019378
GDP-fucose protein O-fucosyltransferase		4452
327IPR031127
E3 ubiquitin ligase RBR family		4447
328IPR001487
Bromodomain		44398
329IPR023796
Serpin domain		44130
330IPR001395
Aldo/keto reductase		4479
331IPR001024
PLAT/LH2 domain		43214
332IPR008991
Translation protein SH3-like domain		4348
333IPR003822
Paired amphipathic helix		43290
334IPR004367
Cyclin, C-terminal domain		4388
335IPR013819
Lipoxygenase, C-terminal		43279
336IPR014720
Double-stranded RNA-binding domain		43230
337IPR008942
ENTH/VHS		4294
338IPR025110
AMP-binding enzyme C-terminal domain		4251
339IPR016167
FAD-binding, type 2, subdomain 1		4247
340IPR004046
Glutathione S-transferase, C-terminal		4246
341IPR012474
Frigida-like		4245
342IPR003851
Zinc finger, Dof-type		42172
343IPR011713
Leucine-rich repeat 3		4255
344IPR000679
Zinc finger, GATA-type		42170
345IPR000757
Glycoside hydrolase, family 16		4287
346IPR006594
LisH dimerisation motif		41109
347IPR006016
UspA		4149
348IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		4147
349IPR000644
CBS domain		41374
350IPR010713
Xyloglucan endo-transglycosylase, C-terminal		4143
351IPR015915
Kelch-type beta propeller		4160
352IPR001223
Glycoside hydrolase, family 18, catalytic domain		4142
353IPR002487
Transcription factor, K-box		41101
354IPR000010
Proteinase inhibitor I25, cystatin		4165
355IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		4145
356IPR000907
Lipoxygenase		4097
357IPR022742
Putative lysophospholipase		4053
358IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4061
359IPR004839
Aminotransferase, class I/classII		4046
360IPR002912
ACT domain		40131
361IPR033389
AUX/IAA domain		3957
362IPR010666
Zinc finger, GRF-type		3939
363IPR011016
Zinc finger, RING-CH-type		39149
364IPR005150
Cellulose synthase		3985
365IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3955
366IPR014722
Ribosomal protein L2 domain 2		3943
367IPR005746
Thioredoxin		3962
368IPR022357
Major intrinsic protein, conserved site		3955
369IPR028889
Ubiquitin specific protease domain		3955
370IPR002913
START domain		39125
371IPR018490
Cyclic nucleotide-binding-like		3848
372IPR029061
Thiamin diphosphate-binding fold		38161
373IPR016455
Xyloglucan endotransglucosylase/hydrolase		3839
374IPR033124
Serine carboxypeptidases, histidine active site		3841
375IPR004140
Exocyst complex protein Exo70		3886
376IPR000215
Serpin family		3841
377IPR016161
Aldehyde/histidinol dehydrogenase		3858
378IPR001568
Ribonuclease T2-like		38143
379IPR025660
Cysteine peptidase, histidine active site		3840
380IPR018957
Zinc finger, C3HC4 RING-type		3739
381IPR003347
JmjC domain		37162
382IPR029021
Protein-tyrosine phosphatase-like		37129
383IPR011074
CRAL/TRIO, N-terminal domain		37120
384IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		3746
385IPR000916
Bet v I domain		3757
386IPR004087
K Homology domain		37122
387IPR013780
Glycosyl hydrolase, family 13, all-beta		3746
388IPR023298
P-type ATPase, transmembrane domain		37115
389IPR025661
Cysteine peptidase, asparagine active site		3738
390IPR000595
Cyclic nucleotide-binding domain		37111
391IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		37119
392IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		3759
393IPR010402
CCT domain		3698
394IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		3638
395IPR001296
Glycosyl transferase, family 1		3643
396IPR027725
Heat shock transcription factor family		3647
397IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		3688
398IPR032000
Albumin I chain a		3638
399IPR025521
Domain of unknown function DUF4409		3640
400IPR000169
Cysteine peptidase, cysteine active site		3638
401IPR001878
Zinc finger, CCHC-type		36113
402IPR012341
Six-hairpin glycosidase		3650
403IPR000727
Target SNARE coiled-coil domain		35102
404IPR001547
Glycoside hydrolase, family 5		3536
405IPR018200
Ubiquitin specific protease, conserved site		3584
406IPR001373
Cullin, N-terminal		3548
407IPR018392
LysM domain		35114
408IPR002022
Pectate lyase/Amb allergen		3572
409IPR001739
Methyl-CpG DNA binding		35142
410IPR033443
Pentacotripeptide-repeat region of PROPR		3548
411IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		3569
412IPR008889
VQ		3535
413IPR006073
GTP binding domain		35111
414IPR018082
AmbAllergen		35246
415IPR015590
Aldehyde dehydrogenase domain		3557
416IPR017927
Ferredoxin reductase-type FAD-binding domain		3452
417IPR025322
Protein of unknown function DUF4228, plant		3437
418IPR001357
BRCT domain		34314
419IPR027356
NPH3 domain		3492
420IPR029056
Ribokinase-like		34119
421IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3438
422IPR011013
Galactose mutarotase-like domain		3453
423IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		34116
424IPR016163
Aldehyde dehydrogenase, C-terminal		3453
425IPR029000
Cyclophilin-like domain		3384
426IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		33143
427IPR001107
Band 7 protein		3382
428IPR004320
Protein of unknown function DUF241, plant		3333
429IPR031112
AP2-like ethylene-responsive transcription factor		3344
430IPR023795
Serpin, conserved site		3333
431IPR031157
Tr-type G domain, conserved site		3338
432IPR016162
Aldehyde dehydrogenase N-terminal domain		3360
433IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		32125
434IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		32240
435IPR012951
Berberine/berberine-like		3233
436IPR009071
High mobility group box domain		32147
437IPR001279
Beta-lactamase-like		32165
438IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		3242
439IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		32101
440IPR003406
Glycosyl transferase, family 14		3235
441IPR004014
Cation-transporting P-type ATPase, N-terminal		3287
442IPR002963
Expansin		32270
443IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3246
444IPR028919
Viral movement protein		3234
445IPR007728
Pre-SET domain		3197
446IPR017938
Riboflavin synthase-like beta-barrel		3156
447IPR013601
FAE1/Type III polyketide synthase-like protein		3132
448IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3156
449IPR013581
Plant PDR ABC transporter associated		3138
450IPR013216
Methyltransferase type 11		3144
451IPR000164
Histone H3/CENP-A		31256
452IPR001025
Bromo adjacent homology (BAH) domain		31129
453IPR001246
Lipoxygenase, plant		31309
454IPR027433
Lipoxygenase, domain 3		3142
455IPR029481
ABC-transporter extracellular N-terminal domain		3135
456IPR005821
Ion transport domain		3141
457IPR001849
Pleckstrin homology domain		31106
458IPR020834
Lipoxygenase, conserved site		3139
459IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3155
460IPR015797
NUDIX hydrolase domain-like		3193
461IPR007502
Helicase-associated domain		3071
462IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3030
463IPR001163
Ribonucleoprotein LSM domain		3065
464IPR021820
S-locus receptor kinase, C-terminal		3034
465IPR000408
Regulator of chromosome condensation, RCC1		30695
466IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		3036
467IPR000639
Epoxide hydrolase-like		30193
468IPR022796
Chlorophyll A-B binding protein		3034
469IPR029062
Class I glutamine amidotransferase-like		3098
470IPR013323
SIAH-type domain		3035
471IPR003409
MORN motif		30566
472IPR023329
Chlorophyll a/b binding protein domain		3036
473IPR004274
NLI interacting factor		30126
474IPR004041
NAF domain		2939
475IPR003106
Leucine zipper, homeobox-associated		2944
476IPR006195
Aminoacyl-tRNA synthetase, class II		2941
477IPR025753
AAA-type ATPase, N-terminal domain		2929
478IPR018451
NAF/FISL domain		2939
479IPR003105
SRA-YDG		29120
480IPR004162
E3 ubiquitin-protein ligase SINA like		2933
481IPR017392
Pathogenesis-related genes transcriptional activator PTI6		2939
482IPR032308
Jas TPL-binding domain		2940
483IPR008263
Glycoside hydrolase, family 16, active site		2930
484IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2932
485IPR029069
HotDog domain		2990
486IPR017937
Thioredoxin, conserved site		2936
487IPR003616
Post-SET domain		2949
488IPR001701
Glycoside hydrolase, family 9		2935
489IPR004141
Strictosidine synthase		2828
490IPR027214
Cystatin		2831
491IPR032872
Wall-associated receptor kinase, C-terminal		2830
492IPR011611
Carbohydrate kinase PfkB		2851
493IPR033275
E3 ubiquitin-protein ligase MARCH-like		2855
494IPR002293
Amino acid/polyamine transporter I		28123
495IPR004160
Translation elongation factor EFTu/EF1A, C-terminal		2835
496IPR025486
Domain of unknown function DUF4378		2831
497IPR000086
NUDIX hydrolase domain		2886
498IPR011709
Domain of unknown function DUF1605		2832
499IPR008395
Agenet-like domain		2834
500IPR004316
SWEET sugar transporter		2756
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata.html b/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata.html new file mode 100644 index 00000000..45c75689 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata.html @@ -0,0 +1,70 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:MA1, Aug 2012
Database version:86.1
Base Pairs:390,578,572
Golden Path Length:472,960,417
Genebuild by: Cirad
Genebuild method: Import
Genebuild started: Aug 2012
Genebuild released: Aug 2012
Genebuild last updated/patched: Aug 2012
Genebuild version: 2012-08-Cirad
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,525
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:37,579
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
chrUn_random141147818
127573629
222054697
330470407
430051516
529377369
634899179
728617404
835439739
934148863
1033665772
1125514024
+
+
scaffold7513 sequences
contig24424 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata_IPtop500.html new file mode 100644 index 00000000..76b83ef9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Musa_acuminata_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		15401697
2IPR000719
Protein kinase, catalytic domain		14393542
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		13093369
4IPR008271
Serine/threonine-protein kinase, active site		10441059
5IPR017441
Protein kinase, ATP binding site		843851
6IPR013083
Zinc finger, RING/FYVE/PHD-type		812857
7IPR009057
Homeodomain-like		7781881
8IPR032675
Leucine-rich repeat domain, L domain-like		7722224
9IPR013320
Concanavalin A-like lectin/glucanase, subgroup		625865
10IPR011990
Tetratricopeptide-like helical		6021786
11IPR001005
SANT/Myb domain		5211509
12IPR002885
Pentatricopeptide repeat		5149881
13IPR001841
Zinc finger, RING-type		5131171
14IPR001611
Leucine-rich repeat		5082537
15IPR016024
Armadillo-type fold		497953
16IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		492782
17IPR016040
NAD(P)-binding domain		4911154
18IPR017930
Myb domain		442733
19IPR012677
Nucleotide-binding, alpha-beta plait		3931196
20IPR011989
Armadillo-like helical		391651
21IPR029058
Alpha/Beta hydrolase fold		386946
22IPR015943
WD40/YVTN repeat-like-containing domain		361573
23IPR000504
RNA recognition motif domain		3571613
24IPR017986
WD40-repeat-containing domain		340844
25IPR011598
Helix-loop-helix domain		3291439
26IPR013210
Leucine-rich repeat-containing N-terminal, type 2		319331
27IPR001680
WD40 repeat		3173319
28IPR003591
Leucine-rich repeat, typical subtype		3031844
29IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		303758
30IPR012336
Thioredoxin-like fold		287666
31IPR016177
DNA-binding, integrase-type		285336
32IPR017853
Glycoside hydrolase, superfamily		283321
33IPR001471
AP2/ERF domain		2811775
34IPR003593
AAA+ ATPase domain		271352
35IPR001128
Cytochrome P450		2491545
36IPR020846
Major facilitator superfamily domain		245476
37IPR007087
Zinc finger, C2H2		242771
38IPR011991
Winged helix-turn-helix transcription repressor DNA-binding		240460
39IPR011992
EF-hand-like domain		237594
40IPR023214
HAD-like domain		224621
41IPR013781
Glycoside hydrolase, catalytic domain		224293
42IPR001810
F-box domain, cyclin-like		221508
43IPR029044
Nucleotide-diphospho-sugar transferases		220520
44IPR002048
Calcium-binding EF-hand		2111462
45IPR019775
WD40 repeat, conserved site		190316
46IPR018247
EF-Hand 1, calcium-binding site		190502
47IPR005225
Small GTP-binding protein domain		184186
48IPR001356
Homeobox domain		183493
49IPR002401
Cytochrome P450, E-class, group I		181947
50IPR003441
No apical meristem (NAM) protein		172516
51IPR017972
Cytochrome P450, conserved site		163164
52IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		158622
53IPR006447
Myb domain, plants		157157
54IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		155176
55IPR011050
Pectin lyase fold/virulence factor		153156
56IPR003657
DNA-binding WRKY		153886
57IPR012334
Pectin lyase fold		153176
58IPR014001
Helicase, superfamily 1/2, ATP-binding domain		151291
59IPR001623
Heat shock protein DnaJ, N-terminal		1481044
60IPR011011
Zinc finger, FYVE/PHD-type		147167
61IPR020683
Ankyrin repeat-containing domain		146662
62IPR013785
Aldolase-type TIM barrel		145180
63IPR001650
Helicase, C-terminal		142411
64IPR000270
Phox/Bem1p		142222
65IPR001806
Small GTPase superfamily		141144
66IPR003439
ABC transporter-like		139383
67IPR003959
ATPase, AAA-type, core		139167
68IPR012340
Nucleic acid-binding, OB-fold		138184
69IPR004827
Basic-leucine zipper domain		137480
70IPR015880
Zinc finger, C2H2-like		137360
71IPR015424
Pyridoxal phosphate-dependent transferase, major domain		136147
72IPR001932
Protein phosphatase 2C-like		134750
73IPR002110
Ankyrin repeat		132887
74IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		130147
75IPR014710
RmlC-like jelly roll fold		130160
76IPR029071
Ubiquitin-related domain		130144
77IPR010255
Haem peroxidase		129135
78IPR013026
Tetratricopeptide repeat-containing domain		129167
79IPR019734
Tetratricopeptide repeat		127937
80IPR000008
C2 calcium-dependent membrane targeting		127855
81IPR005123
Oxoglutarate/iron-dependent dioxygenase		126234
82IPR032867
DYW domain		125125
83IPR020472
G-protein beta WD-40 repeat		124372
84IPR002016
Haem peroxidase, plant/fungal/bacterial		123767
85IPR015655
Protein phosphatase 2C		122182
86IPR000225
Armadillo		120877
87IPR008972
Cupredoxin		118447
88IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		118200
89IPR012337
Ribonuclease H-like domain		117206
90IPR006121
Heavy metal-associated domain, HMA		116362
91IPR018108
Mitochondrial substrate/solute carrier		115589
92IPR023395
Mitochondrial carrier domain		115242
93IPR017907
Zinc finger, RING-type, conserved site		114114
94IPR009072
Histone-fold		114242
95IPR000571
Zinc finger, CCCH-type		113918
96IPR011333
BTB/POZ fold		112121
97IPR000823
Plant peroxidase		108738
98IPR027443
Isopenicillin N synthase-like		107117
99IPR015300
DNA-binding pseudobarrel domain		107233
100IPR003340
B3 DNA binding domain		106304
101IPR002182
NB-ARC		106112
102IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		106223
103IPR001965
Zinc finger, PHD-type		103138
104IPR016135
Ubiquitin-conjugating enzyme/RWD-like		102206
105IPR000048
IQ motif, EF-hand binding site		101594
106IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		99104
107IPR019793
Peroxidases heam-ligand binding site		98102
108IPR013830
Esterase, SGNH hydrolase-type		98307
109IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		98111
110IPR011993
Pleckstrin homology-like domain		98187
111IPR013766
Thioredoxin domain		96176
112IPR002347
Glucose/ribitol dehydrogenase		94746
113IPR017871
ABC transporter, conserved site		94120
114IPR017970
Homeobox, conserved site		9494
115IPR003613
U box domain		94275
116IPR000608
Ubiquitin-conjugating enzyme, E2		91182
117IPR015500
Peptidase S8, subtilisin-related		91270
118IPR000626
Ubiquitin domain		89249
119IPR023213
Chloramphenicol acetyltransferase-like domain		89179
120IPR011051
RmlC-like cupin domain		89102
121IPR013763
Cyclin-like		88406
122IPR019794
Peroxidase, active site		8892
123IPR001087
Lipase, GDSL		8787
124IPR000210
BTB/POZ domain		87214
125IPR019787
Zinc finger, PHD-finger		87153
126IPR000073
Alpha/beta hydrolase fold-1		85178
127IPR029052
Metallo-dependent phosphatase-like		84193
128IPR023393
START-like domain		8287
129IPR005828
General substrate transporter		82116
130IPR027640
Kinesin-like protein		82203
131IPR026992
Non-haem dioxygenase N-terminal domain		8283
132IPR000209
Peptidase S8/S53, subtilisin/kexin/sedolisin		82398
133IPR021109
Peptidase aspartic		81259
134IPR019786
Zinc finger, PHD-type, conserved site		8189
135IPR002100
Transcription factor, MADS-box		81621
136IPR001752
Kinesin, motor domain		80590
137IPR033389
AUX/IAA domain		7987
138IPR008949
Terpenoid synthase		79164
139IPR001461
Peptidase A1		78266
140IPR033121
Peptidase family A1 domain		7688
141IPR001757
ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter		76265
142IPR016039
Thiolase-like		75314
143IPR003960
ATPase, AAA-type, conserved site		7582
144IPR003480
Transferase		75110
145IPR008250
ATPase, P-type, ATPase-associated domain		74179
146IPR018253
Heat shock protein DnaJ, conserved site		7474
147IPR003851
Zinc finger, Dof-type		74295
148IPR009009
Barwin-related endoglucanase		73208
149IPR005202
Transcription factor GRAS		73168
150IPR023299
ATPase, P-type, cytoplasmic domain N		73143
151IPR004843
Metallophosphoesterase domain		7273
152IPR026057
PC-Esterase		7279
153IPR004883
Lateral organ boundaries, LOB		72144
154IPR018303
ATPase, P-type phosphorylation site		7272
155IPR010402
CCT domain		71142
156IPR010259
Proteinase inhibitor I9		7092
157IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		7070
158IPR020568
Ribosomal protein S5 domain 2-type fold		7082
159IPR006671
Cyclin, N-terminal		70100
160IPR029055
Nucleophile aminohydrolases, N-terminal		69140
161IPR013057
Amino acid transporter, transmembrane		6980
162IPR029962
Trichome birefringence-like family		6890
163IPR012946
X8 domain		68135
164IPR000109
Proton-dependent oligopeptide transporter family		67164
165IPR000070
Pectinesterase, catalytic		6684
166IPR017877
Myb-like domain		6680
167IPR032799
Xylanase inhibitor, C-terminal		6566
168IPR007112
Expansin/pollen allergen, DPBB domain		65119
169IPR032861
Xylanase inhibitor, N-terminal		6570
170IPR000490
Glycoside hydrolase, family 17		65124
171IPR011006
CheY-like superfamily		6467
172IPR002912
ACT domain		64169
173IPR000743
Glycoside hydrolase, family 28		6490
174IPR001789
Signal transduction response regulator, receiver domain		64186
175IPR016181
Acyl-CoA N-acyltransferase		63145
176IPR009060
UBA-like		6370
177IPR008928
Six-hairpin glycosidase-like		6375
178IPR010987
Glutathione S-transferase, C-terminal-like		63197
179IPR001480
Bulb-type lectin domain		63312
180IPR014756
Immunoglobulin E-set		6368
181IPR029006
ADF-H/Gelsolin-like domain		63106
182IPR024788
Malectin-like carbohydrate-binding domain		6376
183IPR008942
ENTH/VHS		62126
184IPR011016
Zinc finger, RING-CH-type		62158
185IPR005829
Sugar transporter, conserved site		62101
186IPR008979
Galactose-binding domain-like		62180
187IPR025846
PMR5 N-terminal domain		6262
188IPR000644
Cystathionine beta-synthase, core		62356
189IPR015916
Galactose oxidase, beta-propeller		6171
190IPR023313
Ubiquitin-conjugating enzyme, active site		6161
191IPR002495
Glycosyl transferase, family 8		6170
192IPR002067
Mitochondrial carrier protein		61293
193IPR002109
Glutaredoxin		61125
194IPR006016
UspA		6060
195IPR001251
CRAL-TRIO domain		60303
196IPR000873
AMP-dependent synthetase/ligase		6074
197IPR004045
Glutathione S-transferase, N-terminal		60130
198IPR002487
Transcription factor, K-box		60119
199IPR003106
Leucine zipper, homeobox-associated		5986
200IPR000315
Zinc finger, B-box		59223
201IPR003663
Sugar/inositol transporter		59263
202IPR007118
Expansin/Lol pI		58318
203IPR004333
Transcription factor, SBP-box		58233
204IPR006501
Pectinesterase inhibitor		58280
205IPR025287
Wall-associated receptor kinase galacturonan-binding domain		5769
206IPR004853
Domain of unknown function DUF250		5761
207IPR003245
Plastocyanin-like		57164
208IPR011527
ABC transporter, transmembrane domain, type 1		57275
209IPR029021
Protein-tyrosine phosphatase-like		56124
210IPR005135
Endonuclease/exonuclease/phosphatase		56221
211IPR006553
Leucine-rich repeat, cysteine-containing subtype		56452
212IPR031112
AP2-like ethylene-responsive transcription factor		5664
213IPR006652
Kelch repeat type 1		56166
214IPR003676
Auxin responsive SAUR protein		5659
215IPR000757
Glycoside hydrolase, family 16		56112
216IPR004367
Cyclin, C-terminal		55102
217IPR007117
Pollen allergen/expansin, C-terminal		55218
218IPR001117
Multicopper oxidase, type 1		5454
219IPR013525
ABC-2 type transporter		5471
220IPR008978
HSP20-like chaperone		54105
221IPR004864
Late embryogenesis abundant protein, LEA-14		5454
222IPR011706
Multicopper oxidase, type 2		5454
223IPR011032
GroES-like		53113
224IPR013088
Zinc finger, NHR/GATA-type		5353
225IPR008422
Homeobox KN domain		5353
226IPR014014
RNA helicase, DEAD-box type, Q motif		5353
227IPR011074
CRAL/TRIO, N-terminal domain		53145
228IPR000425
Major intrinsic protein		53395
229IPR004088
K Homology domain, type 1		53417
230IPR011707
Multicopper oxidase, type 3		5353
231IPR000679
Zinc finger, GATA-type		53200
232IPR005175
Domain of unknown function DUF296		53101
233IPR005630
Terpene synthase, metal-binding domain		5259
234IPR023271
Aquaporin-like		52105
235IPR011012
Longin-like domain		5252
236IPR019378
GDP-fucose protein O-fucosyltransferase		5254
237IPR010525
Auxin response factor		5252
238IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		5155
239IPR015813
Pyruvate/Phosphoenolpyruvate kinase		51148
240IPR002528
Multi antimicrobial extrusion protein		51124
241IPR029045
ClpP/crotonase-like domain		51132
242IPR002035
von Willebrand factor, type A		51149
243IPR010713
Xyloglucan endo-transglycosylase, C-terminal		5151
244IPR010399
Tify domain		51150
245IPR000620
Drug/metabolite transporter		5191
246IPR019821
Kinesin, motor region, conserved site		5050
247IPR003594
ATPase-like, ATP-binding domain		50189
248IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		5052
249IPR030184
WAT1-related protein		5054
250IPR002913
Lipid-binding START		50136
251IPR025322
Protein of unknown function DUF4228		4949
252IPR001563
Peptidase S10, serine carboxypeptidase		49257
253IPR032710
NTF2-like domain		4987
254IPR025659
Tubby C-terminal-like domain		4951
255IPR010920
Like-Sm (LSM) domain		4949
256IPR033275
E3 ubiquitin-protein ligase MARCH-like		4952
257IPR023828
Peptidase S8, subtilisin, Ser-active site		4949
258IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		4977
259IPR001509
NAD-dependent epimerase/dehydratase		4849
260IPR004839
Aminotransferase, class I/classII		4849
261IPR020845
AMP-binding, conserved site		4848
262IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		48120
263IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		4848
264IPR002921
Lipase, class 3		4747
265IPR016159
Cullin repeat-like-containing domain		4767
266IPR003311
AUX/IAA protein		4756
267IPR029061
Thiamin diphosphate-binding fold		46159
268IPR006045
Cupin 1		46121
269IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4656
270IPR004041
NAF domain		4545
271IPR001969
Peptidase aspartic, active site		4569
272IPR005333
Transcription factor, TCP		4546
273IPR013783
Immunoglobulin-like fold		4549
274IPR027356
NPH3 domain		4591
275IPR003406
Glycosyl transferase, family 14		4552
276IPR007125
Histone core		4546
277IPR022357
Major intrinsic protein, conserved site		4545
278IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4558
279IPR013126
Heat shock protein 70 family		45253
280IPR000182
GNAT domain		4481
281IPR006626
Parallel beta-helix repeat		44235
282IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		4447
283IPR018451
NAF/FISL domain		4444
284IPR009071
High mobility group, superfamily		44165
285IPR027725
Heat shock transcription factor family		4449
286IPR017887
Transcription factor TCP subgroup		4444
287IPR016166
FAD-binding, type 2		4475
288IPR008266
Tyrosine-protein kinase, active site		4445
289IPR005746
Thioredoxin		4453
290IPR001849
Pleckstrin homology domain		44103
291IPR004087
K Homology domain		44102
292IPR025486
Domain of unknown function DUF4378		4444
293IPR023298
ATPase, P-type, transmembrane domain		44110
294IPR008889
VQ		4444
295IPR012341
Six-hairpin glycosidase		4446
296IPR006594
LisH dimerisation motif		4388
297IPR011701
Major facilitator superfamily		4343
298IPR007657
Glycosyltransferase AER61, uncharacterised		4344
299IPR016455
Xyloglucan endotransglucosylase/hydrolase		4343
300IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		4343
301IPR000727
Target SNARE coiled-coil domain		42112
302IPR006689
Small GTPase superfamily, ARF/SAR type		42185
303IPR007650
Protein of unknown function DUF581		4242
304IPR000742
Epidermal growth factor-like domain		42117
305IPR000232
Heat shock factor (HSF)-type, DNA-binding		42238
306IPR018097
EGF-like calcium-binding, conserved site		4247
307IPR001214
SET domain		42105
308IPR018490
Cyclic nucleotide-binding-like		4142
309IPR013216
Methyltransferase type 11		4141
310IPR001296
Glycosyl transferase, family 1		4141
311IPR001881
EGF-like calcium-binding		4175
312IPR004263
Exostosin-like		4146
313IPR001938
Thaumatin, pathogenesis-related		41434
314IPR022742
Alpha/beta hydrolase, N-terminal		4143
315IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		4146
316IPR001220
Legume lectin domain		4162
317IPR029993
Plant galacturonosyltransferase GAUT		4145
318IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4142
319IPR025610
Transcription factor MYC/MYB N-terminal		4145
320IPR004240
Nonaspanin (TM9SF)		4097
321IPR006153
Cation/H+ exchanger		4046
322IPR016461
O-methyltransferase, caffeic acid-type		4061
323IPR008991
Translation protein SH3-like		4041
324IPR000330
SNF2-related		4045
325IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		4082
326IPR008480
Protein of unknown function DUF761, plant		4040
327IPR001906
Terpene synthase-like		4079
328IPR000595
Cyclic nucleotide-binding domain		40115
329IPR025110
Domain of unknown function DUF4009		3939
330IPR004000
Actin family		39272
331IPR000217
Tubulin		39222
332IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		3958
333IPR002423
Chaperonin Cpn60/TCP-1		3942
334IPR033131
Pectinesterase, Asp active site		3939
335IPR006694
Fatty acid hydroxylase		3939
336IPR003008
Tubulin/FtsZ, GTPase domain		39191
337IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		3939
338IPR005821
Ion transport domain		3939
339IPR001876
Zinc finger, RanBP2-type		39421
340IPR009091
Regulator of chromosome condensation/beta-lactamase-inhibitor protein II		39103
341IPR015797
NUDIX hydrolase domain-like		3977
342IPR017938
Riboflavin synthase-like beta-barrel		3845
343IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		38120
344IPR001077
O-methyltransferase, family 2		3838
345IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		38315
346IPR023329
Chlorophyll a/b binding protein domain		3844
347IPR017927
Ferredoxin reductase-type FAD-binding domain		3737
348IPR010989
t-SNARE		3740
349IPR003337
Trehalose-phosphatase		3771
350IPR002963
Expansin		37315
351IPR027409
GroEL-like apical domain		3776
352IPR013780
Glycosyl hydrolase, family 13, all-beta		3737
353IPR015915
Kelch-type beta propeller		3752
354IPR001878
Zinc finger, CCHC-type		37168
355IPR001395
Aldo/keto reductase		3757
356IPR013149
Alcohol dehydrogenase, C-terminal		3637
357IPR001305
Heat shock protein DnaJ, cysteine-rich domain		3699
358IPR001163
Ribonucleoprotein LSM domain		3667
359IPR002659
Glycosyl transferase, family 31		3669
360IPR008280
Tubulin/FtsZ, C-terminal		3636
361IPR011332
Ribosomal protein, zinc-binding domain		3636
362IPR004014
ATPase, P-type cation-transporter, N-terminal		3666
363IPR006379
HAD-superfamily hydrolase, subfamily IIB		3636
364IPR023210
NADP-dependent oxidoreductase domain		36114
365IPR018202
Peptidase S10, serine carboxypeptidase, active site		3636
366IPR013154
Alcohol dehydrogenase GroES-like		3535
367IPR002902
Gnk2-homologous domain		35131
368IPR020904
Short-chain dehydrogenase/reductase, conserved site		3536
369IPR001701
Glycoside hydrolase, family 9		3535
370IPR013094
Alpha/beta hydrolase fold-3		3555
371IPR001487
Bromodomain		35268
372IPR008974
TRAF-like		3570
373IPR015947
PUA-like domain		3551
374IPR013128
Peptidase C1A, papain		3434
375IPR006563
POX domain		3464
376IPR005150
Cellulose synthase		3463
377IPR001164
Arf GTPase activating protein		34204
378IPR017937
Thioredoxin, conserved site		3442
379IPR014720
Double-stranded RNA-binding-like		34139
380IPR025064
Domain of unknown function DUF4005		3434
381IPR013601
FAE1/Type III polyketide synthase-like protein		3339
382IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3334
383IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		33175
384IPR029000
Cyclophilin-like domain		3367
385IPR017975
Tubulin, conserved site		3333
386IPR002068
Alpha crystallin/Hsp20 domain		3362
387IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		3333
388IPR003137
Protease-associated domain, PA		3333
389IPR018467
CO/COL/TOC1, conserved site		3333
390IPR000300
Inositol polyphosphate-related phosphatase		3333
391IPR020946
Flavin monooxygenase-like		3336
392IPR004813
Oligopeptide transporter OPT superfamily		3383
393IPR006458
Ovate protein family, C-terminal		3397
394IPR003388
Reticulon		3362
395IPR000086
NUDIX hydrolase domain		3364
396IPR016130
Protein-tyrosine phosphatase, active site		3333
397IPR029047
Heat shock protein 70kD, peptide-binding domain		3373
398IPR012967
Plant methyltransferase dimerisation		3333
399IPR008971
HSP40/DnaJ peptide-binding		3280
400IPR001360
Glycoside hydrolase, family 1		32193
401IPR001697
Pyruvate kinase		32203
402IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		3287
403IPR003609
Apple-like		3276
404IPR001353
Proteasome, subunit alpha/beta		3233
405IPR027413
GroEL-like equatorial domain		3258
406IPR015793
Pyruvate kinase, barrel		3232
407IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		3232
408IPR000408
Regulator of chromosome condensation, RCC1		32559
409IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3232
410IPR022796
Chlorophyll A-B binding protein		3238
411IPR000668
Peptidase C1A, papain C-terminal		32132
412IPR000195
Rab-GTPase-TBC domain		32175
413IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		3269
414IPR001344
Chlorophyll A-B binding protein, plant		3131
415IPR000795
Protein synthesis factor, GTP-binding		31141
416IPR003690
Mitochodrial transcription termination factor-related		31209
417IPR000152
EGF-type aspartate/asparagine hydroxylation site		3136
418IPR004776
Auxin efflux carrier		3138
419IPR014722
Translation protein SH3-like, subgroup		3131
420IPR004176
Clp, N-terminal		31100
421IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3146
422IPR002939
Chaperone DnaJ, C-terminal		3131
423IPR020843
Polyketide synthase, enoylreductase		3131
424IPR013809
Epsin-like, N-terminal		3168
425IPR012317
Poly(ADP-ribose) polymerase, catalytic domain		3152
426IPR029064
50S ribosomal protein L30e-like		3166
427IPR024156
Small GTPase superfamily, ARF type		3131
428IPR029060
PIN domain-like		3053
429IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3030
430IPR007493
Protein of unknown function DUF538		3095
431IPR024709
O-fucosyltransferase, plant		3030
432IPR000717
Proteasome component (PCI) domain		3059
433IPR004140
Exo70 exocyst complex subunit		3063
434IPR000047
Helix-turn-helix motif		3060
435IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		3036
436IPR031107
Small heat shock protein HSP20		3030
437IPR022755
Zinc finger, double-stranded RNA binding		3030
438IPR029062
Class I glutamine amidotransferase-like		3069
439IPR006094
FAD linked oxidase, N-terminal		3034
440IPR017884
SANT domain		2932
441IPR018499
Tetraspanin/Peripherin		2929
442IPR011047
Quinonprotein alcohol dehydrogenase-like		2949
443IPR018181
Heat shock protein 70, conserved site		2953
444IPR029056
Ribokinase-like		2962
445IPR011013
Glycoside hydrolase-type carbohydrate-binding		2938
446IPR025875
Leucine rich repeats (2 copies)		2930
447IPR007123
Gelsolin domain		2980
448IPR006936
Domain of unknown function DUF640		2985
449IPR032795
DUF3741-associated sequence motif		2929
450IPR029033
Histidine phosphatase superfamily		2974
451IPR006073
GTP binding domain		2977
452IPR006867
Domain of unknown function DUF632		2929
453IPR029048
Heat shock protein 70kD, C-terminal domain		2956
454IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2878
455IPR000387
Protein-tyrosine/Dual-specificity phosphatase		2828
456IPR003954
RNA recognition motif domain, eukaryote		2855
457IPR000340
Dual specificity phosphatase, catalytic domain		2828
458IPR005516
Remorin, C-terminal		2828
459IPR014977
WRC domain		2855
460IPR002108
Actin-binding, cofilin/tropomyosin type		2882
461IPR017392
AP2/ERF transcription factor ERF/PTI6		2830
462IPR016167
FAD-binding, type 2, subdomain 1		2828
463IPR017904
ADF/Cofilin/Destrin		2830
464IPR011004
Trimeric LpxA-like		2831
465IPR004046
Glutathione S-transferase, C-terminal		2830
466IPR029069
HotDog domain		2877
467IPR001944
Glycoside hydrolase, family 35		28257
468IPR017923
Transcription factor IIS, N-terminal		28104
469IPR006868
Domain of unknown function DUF630		2828
470IPR000103
Pyridine nucleotide-disulphide oxidoreductase, class-II		2786
471IPR000782
FAS1 domain		27159
472IPR006593
Cytochrome b561/ferric reductase transmembrane		2780
473IPR001440
Tetratricopeptide TPR-1		2733
474IPR004182
GRAM domain		2751
475IPR015806
Pyruvate kinase, beta-barrel insert domain		2727
476IPR012675
Beta-grasp domain		2727
477IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		2764
478IPR016021
MIF4-like, type 1/2/3		2748
479IPR008263
Glycoside hydrolase, family 16, active site		2727
480IPR029057
Phosphoribosyltransferase-like		2772
481IPR006456
ZF-HD homeobox protein, Cys/His-rich dimerisation domain		27108
482IPR011037
Pyruvate kinase-like, insert domain		2729
483IPR013328
Dehydrogenase, multihelical		2632
484IPR004316
SWEET sugar transporter		2651
485IPR007612
LURP1-like domain		2626
486IPR006043
Xanthine/uracil/vitamin C permease		2666
487IPR003347
JmjC domain		2667
488IPR006734
Protein of unknown function DUF597		2626
489IPR024950
Dual specificity phosphatase		2629
490IPR033124
Serine carboxypeptidases, histidine active site		2626
491IPR026892
Glycoside hydrolase family 3		2640
492IPR002355
Multicopper oxidase, copper-binding site		2626
493IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		2646
494IPR031330
Glycoside hydrolase 35, catalytic domain		2626
495IPR004326
Mlo-related protein		2632
496IPR006461
Uncharacterised protein family Cys-rich		2652
497IPR008195
Ribosomal protein L34Ae		2666
498IPR023123
Tubulin, C-terminal		2626
499IPR016161
Aldehyde/histidinol dehydrogenase		2626
500IPR001202
WW/Rsp5/WWP		2692
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_aus.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_aus.html new file mode 100644 index 00000000..fd668628 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_aus.html @@ -0,0 +1,984 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM195236v1, Jan 2017
Database version:87.1
Base Pairs:362,186,697
Golden Path Length:362,279,097
Genebuild by: AGI
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Apr 2017
Genebuild version: 2017-04-AGI
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:53,073
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144711178
238372633
336762248
433558078
528792057
629772976
729936233
825527801
922277206
1020972683
1129032419
1222563585
+
+
contig
+
912 sequences
+
+ +
+ + + +
SequenceLength (bp)
LWDA01000401.1935262
LWDA01000402.157764
LWDA01000403.1220400
LWDA01000404.1459667
LWDA01000405.1699351
LWDA01000406.146735
LWDA01000407.1960482
LWDA01000408.1387905
LWDA01000409.12594928
LWDA01000410.1778538
LWDA01000411.11482448
LWDA01000412.1557008
LWDA01000413.11954785
LWDA01000414.1629064
LWDA01000415.1432566
LWDA01000416.127411
LWDA01000417.1154998
LWDA01000418.1436137
LWDA01000419.196875
LWDA01000420.1878887
LWDA01000421.1599651
LWDA01000422.155240
LWDA01000423.1282301
LWDA01000424.1306571
LWDA01000425.121298
LWDA01000426.1668621
LWDA01000427.1116630
LWDA01000428.1576703
LWDA01000429.131368
LWDA01000430.1415712
LWDA01000431.1169743
LWDA01000432.119108
LWDA01000433.1139804
LWDA01000434.1130566
LWDA01000435.11264367
LWDA01000436.1382311
LWDA01000437.13396561
LWDA01000438.154432
LWDA01000439.1462142
LWDA01000440.1230850
LWDA01000441.1158557
LWDA01000442.11327976
LWDA01000443.1542537
LWDA01000444.1406463
LWDA01000445.1527598
LWDA01000446.1405465
LWDA01000447.11993657
LWDA01000448.128135
LWDA01000449.1912479
LWDA01000450.187955
LWDA01000451.1907739
LWDA01000452.1233645
LWDA01000453.1309932
LWDA01000454.190897
LWDA01000455.1421112
LWDA01000456.12139717
LWDA01000457.130239
LWDA01000458.14079
LWDA01000459.12428675
LWDA01000460.12068923
LWDA01000461.1127181
LWDA01000462.1109476
LWDA01000463.1443832
LWDA01000464.11163804
LWDA01000465.11140059
LWDA01000466.11621447
LWDA01000467.1582584
LWDA01000468.11270836
LWDA01000469.1103989
LWDA01000470.1370404
LWDA01000471.11198260
LWDA01000472.121930
LWDA01000473.174696
LWDA01000474.1513544
LWDA01000475.1105601
LWDA01000476.119436
LWDA01000477.11034476
LWDA01000478.11469471
LWDA01000479.12294460
LWDA01000480.136168
LWDA01000481.1387959
LWDA01000482.1282035
LWDA01000483.193919
LWDA01000484.1425693
LWDA01000485.199053
LWDA01000486.1433377
LWDA01000487.11399696
LWDA01000488.130897
LWDA01000489.1248670
LWDA01000490.11168680
LWDA01000491.1139786
LWDA01000492.1472170
LWDA01000493.193448
LWDA01000494.1157072
LWDA01000495.1179059
LWDA01000496.1112223
LWDA01000497.1123424
LWDA01000498.1667875
LWDA01000499.1218286
LWDA01000500.116838
LWDA01000501.137557
LWDA01000502.1294206
LWDA01000503.1129360
LWDA01000504.1123861
LWDA01000505.123962
LWDA01000506.195128
LWDA01000507.1228668
LWDA01000508.151664
LWDA01000509.1453569
LWDA01000510.183031
LWDA01000511.1501261
LWDA01000512.11826620
LWDA01000513.139084
LWDA01000514.11237186
LWDA01000515.1164276
LWDA01000516.12017788
LWDA01000517.1292736
LWDA01000518.1798601
LWDA01000519.1653244
LWDA01000520.1795256
LWDA01000521.1154662
LWDA01000522.1609665
LWDA01000523.183294
LWDA01000524.11059367
LWDA01000525.1555021
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LWDA01001280.125764
LWDA01001281.1388804
LWDA01001282.1249118
LWDA01001283.1863279
LWDA01001284.1109120
LWDA01001285.1305179
LWDA01001286.123762
LWDA01001287.1160506
LWDA01001288.1273838
LWDA01001289.1211341
LWDA01001290.119887
LWDA01001291.159772
LWDA01001292.1239909
LWDA01001293.1225574
LWDA01001294.121779
LWDA01001295.1132037
LWDA01001296.1130335
LWDA01001297.1185647
LWDA01001298.1228192
LWDA01001299.1106124
LWDA01001300.11019563
LWDA01001301.1258088
LWDA01001302.1365340
LWDA01001303.113267
LWDA01001304.11920028
LWDA01001305.1131148
LWDA01001306.113248
LWDA01001307.1434058
LWDA01001308.12313420
LWDA01001309.1254692
LWDA01001310.1791548
LWDA01001311.1304856
LWDA01001312.1790250
+
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diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_aus_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_aus_IPtop500.html new file mode 100644 index 00000000..21988d51 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_aus_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		13042405
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		12546125
3IPR000719
Protein kinase domain		12413525
4IPR032675
Leucine-rich repeat domain, L domain-like		11416197
5IPR008271
Serine/threonine-protein kinase, active site		9901630
6IPR002290
Serine/threonine/dual specificity protein kinase, catalytic domain		9871658
7IPR017441
Protein kinase, ATP binding site		8531414
8IPR013320
Concanavalin A-like lectin/glucanase domain		7151427
9IPR013083
Zinc finger, RING/FYVE/PHD-type		6511148
10IPR001810
F-box domain		5672532
11IPR011990
Tetratricopeptide-like helical domain		5523411
12IPR002885
Pentatricopeptide repeat		43616619
13IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		428937
14IPR001611
Leucine-rich repeat		4103801
15IPR002182
NB-ARC		404705
16IPR001841
Zinc finger, RING-type		4001465
17IPR016040
NAD(P)-binding domain		3751534
18IPR016024
Armadillo-type fold		3431764
19IPR029058
Alpha/Beta hydrolase fold		3331428
20IPR009057
Homeobox domain-like		3181042
21IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		296445
22IPR003591
Leucine-rich repeat, typical subtype		2943050
23IPR001128
Cytochrome P450		2892506
24IPR012677
Nucleotide-binding alpha-beta plait domain		2871472
25IPR011989
Armadillo-like helical		2711089
26IPR003593
AAA+ ATPase domain		257651
27IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		2541167
28IPR000504
RNA recognition motif domain		2451816
29IPR015943
WD40/YVTN repeat-like-containing domain		240813
30IPR017853
Glycoside hydrolase superfamily		238476
31IPR002401
Cytochrome P450, E-class, group I		2342056
32IPR020846
Major facilitator superfamily domain		233826
33IPR012336
Thioredoxin-like fold		227884
34IPR017972
Cytochrome P450, conserved site		220336
35IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		215630
36IPR017986
WD40-repeat-containing domain		2121065
37IPR001680
WD40 repeat		2073948
38IPR013781
Glycoside hydrolase, catalytic domain		197365
39IPR001005
SANT/Myb domain		183579
40IPR011992
EF-hand domain pair		176643
41IPR011991
Winged helix-turn-helix DNA-binding domain		175436
42IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		1731050
43IPR002048
EF-hand domain		1581454
44IPR016177
DNA-binding domain		153270
45IPR023214
HAD-like domain		152765
46IPR011333
SKP1/BTB/POZ domain		149254
47IPR020683
Ankyrin repeat-containing domain		1481434
48IPR007087
Zinc finger, C2H2		145857
49IPR018247
EF-Hand 1, calcium-binding site		144466
50IPR003441
NAC domain		143558
51IPR001471
AP2/ERF domain		1421298
52IPR002110
Ankyrin repeat		1402143
53IPR023213
Chloramphenicol acetyltransferase-like domain		135298
54IPR029044
Nucleotide-diphospho-sugar transferases		133545
55IPR017930
Myb domain		131255
56IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		129367
57IPR013026
Tetratricopeptide repeat-containing domain		128314
58IPR001650
Helicase, C-terminal		127803
59IPR014001
Helicase superfamily 1/2, ATP-binding domain		127515
60IPR023753
FAD/NAD(P)-binding domain		126896
61IPR012340
Nucleic acid-binding, OB-fold		124534
62IPR019734
Tetratricopeptide repeat		1221815
63IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		122272
64IPR013830
SGNH hydrolase-type esterase domain		121461
65IPR019775
WD40 repeat, conserved site		118352
66IPR000210
BTB/POZ domain		116495
67IPR014710
RmlC-like jelly roll fold		114234
68IPR003439
ABC transporter-like		110720
69IPR003480
Transferase		110150
70IPR021109
Aspartic peptidase domain		108469
71IPR005174
Domain unknown function DUF295		108186
72IPR001623
DnaJ domain		1071177
73IPR008974
TRAF-like		106308
74IPR003959
ATPase, AAA-type, core		105194
75IPR013785
Aldolase-type TIM barrel		104218
76IPR001461
Aspartic peptidase A1 family		104365
77IPR000008
C2 domain		1031054
78IPR011011
Zinc finger, FYVE/PHD-type		102219
79IPR001087
GDSL lipase/esterase		101136
80IPR005123
Oxoglutarate/iron-dependent dioxygenase		101306
81IPR008972
Cupredoxin		100478
82IPR003657
WRKY domain		100726
83IPR025315
Domain of unknown function DUF4220		100132
84IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		96178
85IPR011050
Pectin lyase fold/virulence factor		96138
86IPR027443
Isopenicillin N synthase-like		96183
87IPR029071
Ubiquitin-related domain		96161
88IPR005225
Small GTP-binding protein domain		96133
89IPR015424
Pyridoxal phosphate-dependent transferase		96197
90IPR012334
Pectin lyase fold		95137
91IPR007658
Protein of unknown function DUF594		92125
92IPR001480
Bulb-type lectin domain		92901
93IPR001932
PPM-type phosphatase domain		921071
94IPR006447
Myb domain, plants		91143
95IPR032799
Xylanase inhibitor, C-terminal		91130
96IPR032861
Xylanase inhibitor, N-terminal		90126
97IPR001356
Homeobox domain		85337
98IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		84151
99IPR005828
Major facilitator, sugar transporter-like		84152
100IPR011051
RmlC-like cupin domain		84165
101IPR017907
Zinc finger, RING-type, conserved site		84141
102IPR015300
DNA-binding pseudobarrel domain		84343
103IPR004827
Basic-leucine zipper domain		83441
104IPR009072
Histone-fold		83211
105IPR032867
DYW domain		81144
106IPR001965
Zinc finger, PHD-type		81238
107IPR006121
Heavy metal-associated domain, HMA		80285
108IPR012337
Ribonuclease H-like domain		80368
109IPR015655
Protein phosphatase 2C family		80229
110IPR002347
Short-chain dehydrogenase/reductase SDR		79508
111IPR026992
Non-haem dioxygenase N-terminal domain		79124
112IPR002198
Short-chain dehydrogenase/reductase SDR		78311
113IPR017871
ABC transporter, conserved site		78201
114IPR001220
Legume lectin domain		7890
115IPR026961
PGG domain		77192
116IPR011545
DEAD/DEAH box helicase domain		77158
117IPR011676
Domain of unknown function DUF1618		76120
118IPR015880
Zinc finger, C2H2-like		76387
119IPR003609
PAN/Apple domain		75337
120IPR000109
Proton-dependent oligopeptide transporter family		74251
121IPR015422
Pyridoxal phosphate-dependent transferase, subdomain 2		74127
122IPR003340
B3 DNA binding domain		73453
123IPR004158
Protein of unknown function DUF247, plant		73111
124IPR002083
MATH/TRAF domain		72217
125IPR016039
Thiolase-like		71362
126IPR020472
G-protein beta WD-40 repeat		71381
127IPR011993
PH domain-like		71253
128IPR003613
U box domain		70355
129IPR000073
Alpha/beta hydrolase fold-1		69254
130IPR000225
Armadillo		68599
131IPR000858
S-locus glycoprotein domain		67117
132IPR017451
F-box associated interaction domain		6793
133IPR003960
ATPase, AAA-type, conserved site		67105
134IPR010987
Glutathione S-transferase, C-terminal-like		66300
135IPR006501
Pectinesterase inhibitor domain		66321
136IPR000270
PB1 domain		66181
137IPR015500
Peptidase S8, subtilisin-related		64324
138IPR003579
Small GTPase superfamily, Rab type		6386
139IPR000571
Zinc finger, CCCH-type		63856
140IPR013763
Cyclin-like		62550
141IPR018108
Mitochondrial substrate/solute carrier		61656
142IPR023395
Mitochondrial carrier domain		61303
143IPR016159
Cullin repeat-like-containing domain		61104
144IPR029052
Metallo-dependent phosphatase-like		61272
145IPR012871
Protein of unknown function DUF1677, Oryza sativa		6084
146IPR019787
Zinc finger, PHD-finger		60203
147IPR004864
Late embryogenesis abundant protein, LEA-14		6090
148IPR002100
Transcription factor, MADS-box		60585
149IPR013057
Amino acid transporter, transmembrane domain		59105
150IPR004045
Glutathione S-transferase, N-terminal		59172
151IPR000209
Peptidase S8/S53 domain		59462
152IPR013128
Peptidase C1A		5878
153IPR013766
Thioredoxin domain		5891
154IPR005829
Sugar transporter, conserved site		58155
155IPR003245
Phytocyanin domain		58186
156IPR003663
Sugar/inositol transporter		58428
157IPR024788
Malectin-like carbohydrate-binding domain		5896
158IPR000048
IQ motif, EF-hand binding site		581021
159IPR009009
RlpA-like protein, double-psi beta-barrel domain		57196
160IPR000742
EGF-like domain		57196
161IPR000626
Ubiquitin domain		56210
162IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5698
163IPR013087
Zinc finger C2H2-type		56161
164IPR019786
Zinc finger, PHD-type, conserved site		56122
165IPR013094
Alpha/beta hydrolase fold-3		5681
166IPR001806
Small GTPase superfamily		5678
167IPR026057
PC-Esterase		5572
168IPR002902
Gnk2-homologous domain		55411
169IPR016135
Ubiquitin-conjugating enzyme/RWD-like		55201
170IPR005202
Transcription factor GRAS		55163
171IPR010255
Haem peroxidase		5573
172IPR009003
Peptidase S1, PA clan		55144
173IPR020568
Ribosomal protein S5 domain 2-type fold		54128
174IPR002016
Haem peroxidase, plant/fungal/bacterial		54365
175IPR029962
Trichome birefringence-like family		5382
176IPR001509
NAD-dependent epimerase/dehydratase		5386
177IPR027640
Kinesin-like protein		53219
178IPR025846
PMR5 N-terminal domain		5367
179IPR000490
Glycoside hydrolase family 17		53116
180IPR020849
Small GTPase superfamily, Ras type		5272
181IPR023393
START-like domain		5297
182IPR008949
Isoprenoid synthase domain		51154
183IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		51101
184IPR003653
Ulp1 protease family, C-terminal catalytic domain		51149
185IPR007117
Expansin, cellulose-binding-like domain		51267
186IPR003578
Small GTPase superfamily, Rho type		5179
187IPR001752
Kinesin motor domain		51707
188IPR013201
Cathepsin propeptide inhibitor domain (I29)		50121
189IPR000222
PPM-type phosphatase, divalent cation binding		50108
190IPR008979
Galactose-binding domain-like		50265
191IPR002035
von Willebrand factor, type A		50235
192IPR002921
Fungal lipase-like domain		4972
193IPR011032
GroES-like		49199
194IPR001563
Peptidase S10, serine carboxypeptidase		49419
195IPR001881
EGF-like calcium-binding domain		49100
196IPR022059
Protein of unknown function DUF3615		4968
197IPR023828
Peptidase S8, subtilisin, Ser-active site		4974
198IPR006045
Cupin 1		49182
199IPR016181
Acyl-CoA N-acyltransferase		48160
200IPR013525
ABC-2 type transporter		48162
201IPR007112
Expansin/pollen allergen, DPBB domain		48109
202IPR002528
Multi antimicrobial extrusion protein		48262
203IPR018253
DnaJ domain, conserved site		4768
204IPR006566
FBD domain		4783
205IPR003676
Small auxin-up RNA		4775
206IPR004140
Exocyst complex component Exo70		46134
207IPR006016
UspA		4563
208IPR000608
Ubiquitin-conjugating enzyme E2		45145
209IPR024171
S-receptor-like serine/threonine-protein kinase		4553
210IPR000873
AMP-dependent synthetase/ligase		4591
211IPR003137
PA domain		4562
212IPR006553
Leucine-rich repeat, cysteine-containing subtype		45530
213IPR011527
ABC transporter type 1, transmembrane domain		45497
214IPR000668
Peptidase C1A, papain C-terminal		45247
215IPR018097
EGF-like calcium-binding, conserved site		4567
216IPR000620
EamA domain		45148
217IPR017877
Myb-like domain		4574
218IPR008978
HSP20-like chaperone		44103
219IPR012946
X8 domain		44132
220IPR016166
FAD-binding, type 2		44112
221IPR004088
K Homology domain, type 1		44575
222IPR007118
Expansin/Lol pI		43275
223IPR008928
Six-hairpin glycosidase-like		4380
224IPR006671
Cyclin, N-terminal		43124
225IPR030184
WAT1-related protein		4385
226IPR002109
Glutaredoxin		43129
227IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		43192
228IPR001117
Multicopper oxidase, type 1		4253
229IPR016461
O-methyltransferase COMT-type		4273
230IPR029055
Nucleophile aminohydrolases, N-terminal		42109
231IPR014014
RNA helicase, DEAD-box type, Q motif		4274
232IPR011706
Multicopper oxidase, type 2		4254
233IPR014756
Immunoglobulin E-set		4289
234IPR004853
Sugar phosphate transporter domain		4170
235IPR009000
Translation protein, beta-barrel domain		4172
236IPR017970
Homeobox, conserved site		4154
237IPR000070
Pectinesterase, catalytic		4160
238IPR001214
SET domain		41201
239IPR001878
Zinc finger, CCHC-type		41444
240IPR008889
VQ		4152
241IPR011707
Multicopper oxidase, type 3		4150
242IPR000743
Glycoside hydrolase, family 28		4189
243IPR010402
CCT domain		40132
244IPR000182
GNAT domain		40101
245IPR009060
UBA-like		4066
246IPR011701
Major facilitator superfamily		4071
247IPR013105
Tetratricopeptide repeat 2		4083
248IPR002041
Ran GTPase		4066
249IPR001077
O-methyltransferase, family 2		4045
250IPR023299
P-type ATPase, cytoplasmic domain N		40137
251IPR000823
Plant peroxidase		40317
252IPR015947
PUA-like domain		4078
253IPR025322
Protein of unknown function DUF4228, plant		3953
254IPR006626
Parallel beta-helix repeat		39282
255IPR008250
P-type ATPase, A domain		39158
256IPR004265
Plant disease resistance response protein		3960
257IPR011006
CheY-like superfamily		3970
258IPR020845
AMP-binding, conserved site		3968
259IPR002085
Alcohol dehydrogenase superfamily, zinc-type		3991
260IPR011042
Six-bladed beta-propeller, TolB-like		3965
261IPR015916
Galactose oxidase, beta-propeller		3857
262IPR025659
Tubby C-terminal-like domain		3872
263IPR001969
Aspartic peptidase, active site		3877
264IPR019793
Peroxidases heam-ligand binding site		3849
265IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3868
266IPR006702
Domain of unknown function DUF588		3842
267IPR000330
SNF2-related, N-terminal domain		3784
268IPR003594
Histidine kinase-like ATPase, C-terminal domain		37292
269IPR006652
Kelch repeat type 1		37249
270IPR001757
P-type ATPase		37501
271IPR002495
Glycosyl transferase, family 8		3755
272IPR001789
Signal transduction response regulator, receiver domain		37170
273IPR004041
NAF domain		3650
274IPR029021
Protein-tyrosine phosphatase-like		36151
275IPR013783
Immunoglobulin-like fold		3675
276IPR001938
Thaumatin		36423
277IPR011012
Longin-like domain		3648
278IPR019794
Peroxidase, active site		3647
279IPR029045
ClpP/crotonase-like domain		36193
280IPR000644
CBS domain		36348
281IPR028889
Ubiquitin specific protease domain		3681
282IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		3652
283IPR023271
Aquaporin-like		3593
284IPR007125
Histone H2A/H2B/H3		3540
285IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3580
286IPR018303
P-type ATPase, phosphorylation site		3561
287IPR000425
Major intrinsic protein		35327
288IPR002067
Mitochondrial carrier protein		35277
289IPR015915
Kelch-type beta propeller		3576
290IPR003311
AUX/IAA protein		3561
291IPR025661
Cysteine peptidase, asparagine active site		3545
292IPR012967
Plant methyltransferase dimerisation		3535
293IPR008942
ENTH/VHS		34124
294IPR018451
NAF/FISL domain		3448
295IPR002068
Alpha crystallin/Hsp20 domain		3478
296IPR013154
Alcohol dehydrogenase, N-terminal		3463
297IPR004087
K Homology domain		34136
298IPR002487
Transcription factor, K-box		3498
299IPR013149
Alcohol dehydrogenase, C-terminal		3361
300IPR011016
Zinc finger, RING-CH-type		33141
301IPR005630
Terpene synthase, metal-binding domain		3343
302IPR005135
Endonuclease/exonuclease/phosphatase		33291
303IPR004263
Exostosin-like		3348
304IPR004367
Cyclin, C-terminal domain		3357
305IPR004883
Lateral organ boundaries, LOB		3376
306IPR031107
Small heat shock protein HSP20		3341
307IPR004046
Glutathione S-transferase, C-terminal		3355
308IPR006094
FAD linked oxidase, N-terminal		3347
309IPR013126
Heat shock protein 70 family		33270
310IPR011043
Galactose oxidase/kelch, beta-propeller		3353
311IPR020843
Polyketide synthase, enoylreductase domain		3350
312IPR001440
Tetratricopeptide repeat 1		3271
313IPR000315
B-box-type zinc finger		32122
314IPR004839
Aminotransferase, class I/classII		3265
315IPR016167
FAD-binding, type 2, subdomain 1		3243
316IPR019378
GDP-fucose protein O-fucosyltransferase		3290
317IPR018202
Serine carboxypeptidase, serine active site		3262
318IPR012341
Six-hairpin glycosidase		3246
319IPR018490
Cyclic nucleotide-binding-like		3161
320IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3163
321IPR019821
Kinesin motor domain, conserved site		3147
322IPR007493
Protein of unknown function DUF538		31123
323IPR018200
Ubiquitin specific protease, conserved site		31115
324IPR008991
Translation protein SH3-like domain		3143
325IPR001296
Glycosyl transferase, family 1		3160
326IPR001594
Palmitoyltransferase, DHHC domain		3190
327IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		31117
328IPR002123
Phospholipid/glycerol acyltransferase		3197
329IPR008266
Tyrosine-protein kinase, active site		3148
330IPR020904
Short-chain dehydrogenase/reductase, conserved site		3143
331IPR005746
Thioredoxin		3145
332IPR022357
Major intrinsic protein, conserved site		3137
333IPR001906
Terpene synthase, N-terminal domain		3179
334IPR002912
ACT domain		31118
335IPR023329
Chlorophyll a/b binding protein domain		3177
336IPR024156
Small GTPase superfamily, ARF type		3168
337IPR000528
Plant lipid transfer protein/Par allergen		30155
338IPR013187
F-box associated domain, type 3		3041
339IPR031112
AP2-like ethylene-responsive transcription factor		3049
340IPR014044
CAP domain		30172
341IPR000169
Cysteine peptidase, cysteine active site		3040
342IPR006458
Ovate protein family, C-terminal		3087
343IPR004314
Neprosin		3033
344IPR018040
Pectinesterase, Tyr active site		3043
345IPR006311
Twin-arginine translocation pathway, signal sequence		3043
346IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2950
347IPR013088
Zinc finger, NHR/GATA-type		2947
348IPR000795
Transcription factor, GTP-binding domain		29225
349IPR002355
Multicopper oxidase, copper-binding site		2964
350IPR003406
Glycosyl transferase, family 14		2941
351IPR000863
Sulfotransferase domain		2937
352IPR002963
Expansin		29286
353IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		29166
354IPR008480
Protein of unknown function DUF761, plant		2946
355IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2975
356IPR000595
Cyclic nucleotide-binding domain		29156
357IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		29121
358IPR002937
Amine oxidase		2948
359IPR000679
Zinc finger, GATA-type		29162
360IPR001574
Ribosome-inactivating protein		2985
361IPR013601
FAE1/Type III polyketide synthase-like protein		2833
362IPR032710
NTF2-like domain		2861
363IPR006153
Cation/H+ exchanger		2850
364IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28140
365IPR018957
Zinc finger, C3HC4 RING-type		2841
366IPR005299
SAM dependent carboxyl methyltransferase		2847
367IPR002423
Chaperonin Cpn60/TCP-1 family		2846
368IPR012675
Beta-grasp domain		2840
369IPR005150
Cellulose synthase		2891
370IPR001849
Pleckstrin homology domain		28123
371IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		2859
372IPR001223
Glycoside hydrolase family 18, catalytic domain		2834
373IPR000757
Glycoside hydrolase family 16		2839
374IPR005175
PPC domain		2882
375IPR006073
GTP binding domain		28112
376IPR001099
Chalcone/stilbene synthase, N-terminal		2833
377IPR017927
Ferredoxin reductase-type FAD-binding domain		2738
378IPR000727
Target SNARE coiled-coil homology domain		2794
379IPR000782
FAS1 domain		27208
380IPR001251
CRAL-TRIO lipid binding domain		27240
381IPR010920
LSM domain		2740
382IPR001478
PDZ domain		27145
383IPR027356
NPH3 domain		2778
384IPR027409
GroEL-like apical domain		2780
385IPR003851
Zinc finger, Dof-type		27157
386IPR014720
Double-stranded RNA-binding domain		27291
387IPR025660
Cysteine peptidase, histidine active site		2739
388IPR010525
Auxin response factor		2750
389IPR025110
AMP-binding enzyme C-terminal domain		2642
390IPR017938
Riboflavin synthase-like beta-barrel		2643
391IPR015940
Ubiquitin-associated domain		26131
392IPR001929
Germin		26102
393IPR001360
Glycoside hydrolase family 1		26330
394IPR002659
Glycosyl transferase, family 31		2686
395IPR029061
Thiamin diphosphate-binding fold		26140
396IPR003337
Trehalose-phosphatase		2664
397IPR023313
Ubiquitin-conjugating enzyme, active site		2633
398IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2686
399IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2627
400IPR027923
Hydrophobic seed protein		2632
401IPR014722
Ribosomal protein L2 domain 2		2629
402IPR016138
Ribosome-inactivating protein, subdomain 1		2633
403IPR029047
Heat shock protein 70kD, peptide-binding domain		2666
404IPR015797
NUDIX hydrolase domain-like		2688
405IPR003106
Leucine zipper, homeobox-associated		2545
406IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		25230
407IPR029000
Cyclophilin-like domain		2599
408IPR013216
Methyltransferase type 11		2538
409IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2538
410IPR027725
Heat shock transcription factor family		2542
411IPR004320
Protein of unknown function DUF241, plant		2545
412IPR007650
Zf-FLZ domain		2534
413IPR001763
Rhodanese-like domain		25216
414IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2539
415IPR003690
Transcription termination factor, mitochondrial/chloroplastic		25220
416IPR000152
EGF-type aspartate/asparagine hydroxylation site		2540
417IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		2547
418IPR029062
Class I glutamine amidotransferase-like		25131
419IPR017937
Thioredoxin, conserved site		2542
420IPR012328
Chalcone/stilbene synthase, C-terminal		2527
421IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2532
422IPR002867
IBR domain		24118
423IPR004316
SWEET sugar transporter		2463
424IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2430
425IPR008999
Actin cross-linking		2432
426IPR000408
Regulator of chromosome condensation, RCC1		24748
427IPR006379
HAD-superfamily hydrolase, subfamily IIB		2430
428IPR005821
Ion transport domain		2450
429IPR029059
Alpha/beta hydrolase fold-5		2440
430IPR001701
Glycoside hydrolase family 9		2428
431IPR025486
Domain of unknown function DUF4378		2435
432IPR031127
E3 ubiquitin ligase RBR family		2450
433IPR023210
NADP-dependent oxidoreductase domain		24183
434IPR006867
Domain of unknown function DUF632		2438
435IPR001024
PLAT/LH2 domain		23115
436IPR008422
Homeobox KN domain		2334
437IPR018181
Heat shock protein 70, conserved site		2363
438IPR022812
Dynamin superfamily		23183
439IPR011013
Galactose mutarotase-like domain		2347
440IPR016072
SKP1 component, dimerisation		2364
441IPR022796
Chlorophyll A-B binding protein		2334
442IPR029069
HotDog domain		23119
443IPR000086
NUDIX hydrolase domain		2372
444IPR000232
Heat shock factor (HSF)-type, DNA-binding		23160
445IPR001487
Bromodomain		23320
446IPR002913
START domain		23121
447IPR001395
Aldo/keto reductase/potassium channel subunit beta		2364
448IPR018244
Allergen V5/Tpx-1-related, conserved site		2247
449IPR007612
LURP1-related protein domain		2229
450IPR001163
LSM domain, eukaryotic/archaea-type		2257
451IPR009030
Growth factor receptor cysteine-rich domain		2231
452IPR011074
CRAL/TRIO, N-terminal domain		22119
453IPR010989
SNARE		2236
454IPR002293
Amino acid/polyamine transporter I		22120
455IPR006459
Casparian strip membrane protein		2223
456IPR004776
Membrane transport protein		2235
457IPR001876
Zinc finger, RanBP2-type		22278
458IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2260
459IPR029993
Plant galacturonosyltransferase GAUT		2236
460IPR029006
ADF-H/Gelsolin-like domain		22114
461IPR023298
P-type ATPase, transmembrane domain		2286
462IPR006439
HAD hydrolase, subfamily IA		22111
463IPR006868
Domain of unknown function DUF630		2234
464IPR003855
Potassium transporter		2274
465IPR029033
Histidine phosphatase superfamily		22171
466IPR006689
Small GTPase superfamily, ARF/SAR type		21126
467IPR013328
6-phosphogluconate dehydrogenase, domain 2		2149
468IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		2130
469IPR013581
Plant PDR ABC transporter associated		2158
470IPR000717
Proteasome component (PCI) domain		2144
471IPR005516
Remorin, C-terminal		2136
472IPR014977
WRC domain		2153
473IPR001353
Proteasome, subunit alpha/beta		2126
474IPR023346
Lysozyme-like domain		2132
475IPR000300
Inositol polyphosphate-related phosphatase		2145
476IPR006461
PLAC8 motif-containing protein		2155
477IPR020946
Flavin monooxygenase-like		2138
478IPR019780
Germin, manganese binding site		2132
479IPR013780
Glycosyl hydrolase, all-beta		2138
480IPR017761
Laccase		2123
481IPR001229
Jacalin-like lectin domain		21184
482IPR029048
Heat shock protein 70kD, C-terminal domain		2148
483IPR000726
Glycoside hydrolase, family 19, catalytic		2050
484IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		2026
485IPR025753
AAA-type ATPase, N-terminal domain		2024
486IPR001357
BRCT domain		20247
487IPR009071
High mobility group box domain		2098
488IPR004161
Translation elongation factor EFTu-like, domain 2		2030
489IPR007657
Glycosyltransferase 61		2030
490IPR008914
Phosphatidylethanolamine-binding protein		2067
491IPR018221
Glycoside hydrolase family 9, His active site		2029
492IPR005333
Transcription factor, TCP		2030
493IPR017887
Transcription factor TCP subgroup		2030
494IPR002283
Isopenicillin N synthase		2078
495IPR025422
Transcription factor TGA like domain		2031
496IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2041
497IPR006694
Fatty acid hydroxylase		2027
498IPR000215
Serpin family		2030
499IPR003008
Tubulin/FtsZ, GTPase domain		20112
500IPR021720
Malectin		2080
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_brachyantha.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_brachyantha.html new file mode 100644 index 00000000..d3cfd797 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_brachyantha.html @@ -0,0 +1,109 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:263,195,077
Golden Path Length:263,195,077
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:41,684
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
59 sequences
+
+ +
+ + + +
SequenceLength (bp)
133554891
227476678
329856040
421827379
520245399
621974636
719450094
818299912
915506556
1016246320
1117534090
1216931956
UN-Ctg4456751
UN-Ctg45120491
UN-Ctg46705295
UN-Ctg47278345
UN-Ctg48232093
UN-Ctg49207166
UN-Ctg50201584
UN-Ctg51164390
UN-Ctg52155163
UN-Ctg53145019
UN-Ctg54106328
UN-Ctg5599473
UN-Ctg5692129
UN-Ctg5790675
UN-Ctg5887736
UN-Ctg5982649
UN-Ctg6082116
UN-Ctg6177768
UN-Ctg6277474
UN-Ctg6373099
UN-Ctg6464398
UN-Ctg6563165
UN-Ctg6659948
UN-Ctg6758844
UN-Ctg6857773
UN-Ctg6956880
UN-Ctg7052260
UN-Ctg7151046
UN-Ctg7249779
UN-Ctg7346557
UN-Ctg7446712
UN-Ctg7543054
UN-Ctg7641780
UN-Ctg7741140
UN-Ctg7840355
UN-Ctg7939538
UN-Ctg8037402
UN-Ctg8136362
UN-Ctg8236421
UN-Ctg8336016
UN-Ctg8435832
UN-Ctg8534500
UN-Ctg8630170
UN-Ctg8726420
UN-Ctg8823840
UN-Ctg8923378
UN-Ctg9021812
+
+
chunk2662 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_brachyantha_IPtop500.html similarity index 100% rename from gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop40.html rename to gramene/htdocs/ssi/species.weix/stats_Oryza_brachyantha_IPtop500.html diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina.html new file mode 100644 index 00000000..0345c851 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina.html @@ -0,0 +1,260 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:CGRFv1,
Database version:87.1
Base Pairs:404,338,695
Golden Path Length:404,338,695
Genebuild by: Maker
Genebuild method: Warelab Maker-P annotation
Genebuild started: Jul 2018
Genebuild version: 2018-07-Maker
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:53,931
+ + +

Coordinate Systems

+ + + + + + + + +
contig
+
210 sequences
+
+ +
+ + + +
SequenceLength (bp)
tig00000002160227
tig0000000477407
tig0000000895889
tig0000001360103
tig00000014129457
tig00000016129375
tig0000001859560
tig0000001980998
tig0000002166449
tig0000002351030
tig0000002791183
tig0000003580216
tig00000038124001
tig0000003961408
tig00000049105692
tig00000074a8614523
tig00000074b9386108
tig0000007418000631
tig000000782032043
tig000000857664127
tig000001033958330
tig0000015637043
tig00000176118536
tig0000021952186
tig0000025620220626
tig0000026025653
tig00000338990607
tig0000036266705
tig00000364545125
tig000004366619025
tig00000460555095
tig0000063581473
tig0000104439992
tig000010624439422
tig0000109652312
tig000012741762723
tig0000129048696
tig0000132611032741
tig000014859685813
tig0000150242553
tig0000152841571
tig0000162742479
tig00001716583222
tig0000178059238
tig000019853096471
tig0000218170085
tig0000225039330
tig0000225557758
tig0000252552182
tig000026111384223
tig0000271196339
tig0000278349553
tig0000281430305
tig00002831107271
tig00002838135671
tig0000284049261
tig0000285075194
tig0000287249272
tig0000288142016
tig00002888124878
tig0000291360471
tig00002922138091
tig0000296339610
tig00002969159510
tig0000297271339
tig0000299498894
tig0000301247742
tig00003033108768
tig0000309957824
tig0000310248934
tig00003141156148
tig0000318729262
tig0000319144748
tig00003200109170
tig00003201120889
tig00003202108079
tig0000321032922
tig00003241106751
tig00003243109049
tig0000325355148
tig0000332127869
tig0000335976960
tig0000336274092
tig0000340256343
tig0000340468614
tig0000341062368
tig0000341370157
tig0000343953383
tig0000345264794
tig0000346873959
tig0000350142264
tig0000350731909
tig0000353766623
tig0000355149086
tig0000361138512
tig0000362436072
tig0000364741240
tig0000369439939
tig0000369924055
tig0000370552001
tig0000373814779
tig0000376975738
tig0000383648272
tig0000384251348
tig0000384732086
tig0000386055533
tig0000391237510
tig000039895974
tig000041254136
tig000041517477
tig000041823972
tig0000422219603
tig00027329164847
tig0002733022269229
tig0002733121064
tig000273322338332
tig000273343029434
tig0002733723390289
tig0002733843617
tig00027339992608
tig0002734120461179
tig0002734256961
tig000273431830093
tig0002734414135645
tig0002734543822
tig0002734656356
tig000273482935044
tig0002734950773
tig00027350688067
tig000273522174261
tig000273548654799
tig0002735552001
tig00027356384091
tig0002735748150
tig0002735998992
tig0002736551546
tig0002737063554
tig0002737260324
tig00027374154539
tig0002737733742
tig000273834564581
tig0002738519062658
tig00027386594076
tig0002738745621
tig0002738883762
tig0002738913413199
tig0002739057047
tig000273916545815
tig000273928241
tig000273931591272
tig0002739544568
tig000273961019373
tig0002739739539
tig0002739810193138
tig000274009682158
tig00027402799915
tig000274032286359
tig0002740465140
tig0002740514711342
tig0002741253718
tig0002741415929712
tig00027415188104
tig00027416136877
tig0002741786576
tig0002741871976
tig0002741999582
tig000274206289440
tig000274216025335
tig00027423648608
tig0002742442781
tig0002742512880937
tig00027426206798
tig000274276237148
tig0002742844062
tig00027429148793
tig00027430193460
tig00027431113746
tig0002743211627331
tig000274339727910
tig0002743564817
tig000274369217371
tig0002743835458
tig000274393896075
tig0002744023938
tig000274412737666
tig0002744258680
tig000274433081249
tig0002744429242
tig00027447112778
tig000274485642938
tig0002744963498
tig0002745163035
tig00027452133069
tig000274531476636
tig00027456132092
tig00027458106940
tig00027459126490
tig0002746082787
tig0002746136414
tig0002746275827
tig0002746497443
tig00027467125767
tig0002746859829
tig0002747028935
tig0002747134870
tig0002747234457
tig0002747664338
tig0002747852443
tig0002748748136
tig0002748910001
+
+
chunk4148 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_carolina_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima.html new file mode 100644 index 00000000..70ac8e3e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima.html @@ -0,0 +1,109 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:347,321,046
Golden Path Length:347,321,046
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:47,886
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
59 sequences
+
+ +
+ + + +
SequenceLength (bp)
139656875
234451706
335526804
431572834
526274045
629275208
726599614
825472747
921796211
1022418184
1126393634
1225020143
UN-Ctg37241712
UN-Ctg38285771
UN-Ctg39220846
UN-Ctg40136550
UN-Ctg41104094
UN-Ctg4299044
UN-Ctg4392801
UN-Ctg4490830
UN-Ctg4589626
UN-Ctg4682446
UN-Ctg4774458
UN-Ctg4873113
UN-Ctg4970610
UN-Ctg5067074
UN-Ctg5162711
UN-Ctg5262187
UN-Ctg5360608
UN-Ctg5457716
UN-Ctg5554206
UN-Ctg5648475
UN-Ctg5747599
UN-Ctg5843218
UN-Ctg5942752
UN-Ctg6040563
UN-Ctg6137872
UN-Ctg6236687
UN-Ctg6335359
UN-Ctg6434083
UN-Ctg6533756
UN-Ctg6633214
UN-Ctg6732611
UN-Ctg6832466
UN-Ctg6932005
UN-Ctg7030676
UN-Ctg7129811
UN-Ctg7228023
UN-Ctg7327666
UN-Ctg7427637
UN-Ctg7523984
UN-Ctg7623015
UN-Ctg7721693
UN-Ctg7821053
UN-Ctg7919363
UN-Ctg8015054
UN-Ctg8113998
UN-Ctg8213471
UN-Ctg8310534
+
+
chunk3504 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_glaberrima_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula.html new file mode 100644 index 00000000..23db6486 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula.html @@ -0,0 +1,97 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:388,593,428
Golden Path Length:388,593,428
Genebuild by: CSHL
Genebuild started: Jul 2018
Genebuild version: 2018-07-CSHL
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:52,718
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
47 sequences
+
+ +
+ + + +
SequenceLength (bp)
145664349
236906571
339367850
434316930
530257704
633537877
729772470
828865088
923906556
1024753583
1131489372
1227342405
UN-Ctg53205312
UN-Ctg54160854
UN-Ctg55119319
UN-Ctg56107666
UN-Ctg57103248
UN-Ctg5888329
UN-Ctg5984894
UN-Ctg6078225
UN-Ctg6177729
UN-Ctg6275317
UN-Ctg6373669
UN-Ctg6470339
UN-Ctg6569311
UN-Ctg6662568
UN-Ctg6761938
UN-Ctg6861225
UN-Ctg6960586
UN-Ctg7060091
UN-Ctg7158435
UN-Ctg7258369
UN-Ctg7354937
UN-Ctg7453901
UN-Ctg7553452
UN-Ctg7652680
UN-Ctg7751047
UN-Ctg7849442
UN-Ctg7948922
UN-Ctg8048264
UN-Ctg8146330
UN-Ctg8246690
UN-Ctg8344485
UN-Ctg8440041
UN-Ctg8538075
UN-Ctg8628892
UN-Ctg8718091
+
+
chunk3909 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_glumaepatula_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata.html new file mode 100644 index 00000000..48fcca03 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata.html @@ -0,0 +1,40 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:454.pools.2012Oct, Oct 2012
Database version:75.02
:
:
Genebuild by: CSHL
Genebuild method: Fgenesh
Genebuild started: Mar 2013
Genebuild released: Mar 2013
Genebuild last updated/patched: Mar 2013

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
granulata_3s35245667
+
+
contig7261 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s.html new file mode 100644 index 00000000..020355d6 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s.html @@ -0,0 +1,418 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OGE.2013Sep, Aug 2013
Database version:76.03
:35,245,667
Golden Path Length:35,245,667
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + +
Protein coding gene count

Genes and/or transcript that contains an open reading frame (ORF).

:		2,751
Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:3,754
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
3s35245667
+
+
chunk
+
353 sequences
+
+ +
+ + + +
SequenceLength (bp)
3s:1..100000100000
3s:10000001..10100000100000
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+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata3s_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_granulata_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_indica.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_indica.html new file mode 100644 index 00000000..3b5f1e16 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_indica.html @@ -0,0 +1,70 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM465v1, Aug 2013
Database version:87.2
Base Pairs:374,545,499
Golden Path Length:374,545,499
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		37,411
Long Non coding genes:5,882
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:45,446
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
147283185
1022204031
1123035369
1223049917
238103930
341884883
434718618
531240961
632913967
727957088
830396518
921757032
+
+
chunk3752 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_indica_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_indica_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_indica_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8.html new file mode 100644 index 00000000..61188183 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8.html @@ -0,0 +1,155 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Rice_IR8_v1.7, Dec 2016
Database version:87.1
Base Pairs:389,082,167
Golden Path Length:389,088,367
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:56,823
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144746683
237475564
339065119
435713470
531269760
632072649
730380234
830236384
924243884
1025246678
1132337678
1225963606
+
+
supercontig
+
3 sequences
+
+ +
+ + + +
SequenceLength (bp)
IR8_Chr00_Ctg130-0006588843
IR8_Chr00_Ctg291-0006798459
IR8_Chr00_Ctg1520-00066149356
+
+
contig
+
66 sequences
+
+ +
+ + + +
SequenceLength (bp)
MPPV01000001.113957568
MPPV01000002.1772818
MPPV01000003.12829530
MPPV01000004.1599510
MPPV01000005.1493967
MPPV01000006.126092790
MPPV01000007.114714266
MPPV01000008.1850289
MPPV01000009.13255014
MPPV01000010.118655595
MPPV01000011.13811878
MPPV01000012.116902864
MPPV01000013.11058269
MPPV01000014.117121279
MPPV01000015.1170329
MPPV01000016.12251857
MPPV01000017.16057010
MPPV01000018.1831905
MPPV01000019.183630
MPPV01000020.1566450
MPPV01000021.1377629
MPPV01000022.118891260
MPPV01000023.16653029
MPPV01000024.11348859
MPPV01000025.17352252
MPPV01000026.16974593
MPPV01000027.115493534
MPPV01000028.1100022
MPPV01000029.16320144
MPPV01000030.13931259
MPPV01000031.11171307
MPPV01000032.15379507
MPPV01000033.1705275
MPPV01000034.114564657
MPPV01000035.116690981
MPPV01000036.113689053
MPPV01000037.16240730
MPPV01000038.11305531
MPPV01000039.1963550
MPPV01000040.14540254
MPPV01000041.14076855
MPPV01000042.11073145
MPPV01000043.11305338
MPPV01000044.1897330
MPPV01000045.14679785
MPPV01000046.15152866
MPPV01000047.13031427
MPPV01000048.12190648
MPPV01000049.11234270
MPPV01000050.18012759
MPPV01000051.15527597
MPPV01000052.1988256
MPPV01000053.13258227
MPPV01000054.13173925
MPPV01000055.1667642
MPPV01000056.1595836
MPPV01000057.120808775
MPPV01000058.14918926
MPPV01000059.19001889
MPPV01000060.13726225
MPPV01000061.113380425
MPPV01000062.11309713
MPPV01000063.125963406
MPPV01000064.188843
MPPV01000065.1149356
MPPV01000066.198459
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_indicair8_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata.html new file mode 100644 index 00000000..17fa31ea --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata.html @@ -0,0 +1,44 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:O_longistaminata_v1.0, May 2015
Database version:87.2
Base Pairs:326,442,508
Golden Path Length:326,442,508
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: May 2015
Genebuild version: 2015-05-OGE
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		31,686
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:31,686
+ + +

Coordinate Systems

+ + + + + + + + +
scaffold60198 sequences
chunk61414 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata_IPtop500.html new file mode 100644 index 00000000..c1f001a1 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_longistaminata_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		17251923
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		16244059
3IPR000719
Protein kinase domain		15933858
4IPR032675
Leucine-rich repeat domain, L domain-like		15845353
5IPR008271
Serine/threonine-protein kinase, active site		11261147
6IPR017441
Protein kinase, ATP binding site		10061025
7IPR013320
Concanavalin A-like lectin/glucanase domain		9041149
8IPR002182
NB-ARC		629702
9IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		616786
10IPR011990
Tetratricopeptide-like helical domain		5971822
11IPR001611
Leucine-rich repeat		5693355
12IPR002885
Pentatricopeptide repeat		50810589
13IPR013083
Zinc finger, RING/FYVE/PHD-type		463511
14IPR016040
NAD(P)-binding domain		4491047
15IPR001128
Cytochrome P450		4002248
16IPR003591
Leucine-rich repeat, typical subtype		3882677
17IPR016024
Armadillo-type fold		382826
18IPR029058
Alpha/Beta hydrolase fold		382940
19IPR001810
F-box domain		3751044
20IPR012677
Nucleotide-binding alpha-beta plait domain		321901
21IPR017853
Glycoside hydrolase superfamily		315355
22IPR009057
Homeodomain-like		307648
23IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		300307
24IPR011989
Armadillo-like helical		290539
25IPR015943
WD40/YVTN repeat-like-containing domain		282438
26IPR020846
Major facilitator superfamily domain		275496
27IPR002401
Cytochrome P450, E-class, group I		2721441
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		271702
29IPR013781
Glycoside hydrolase, catalytic domain		270340
30IPR000504
RNA recognition motif domain		2661066
31IPR017972
Cytochrome P450, conserved site		260264
32IPR017986
WD40-repeat-containing domain		256603
33IPR003593
AAA+ ATPase domain		250346
34IPR012336
Thioredoxin-like fold		241557
35IPR001841
Zinc finger, RING-type		237568
36IPR001680
WD40 repeat		2342141
37IPR011992
EF-hand domain pair		188455
38IPR020683
Ankyrin repeat-containing domain		182863
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		182385
40IPR002048
EF-hand domain		175992
41IPR001005
SANT/Myb domain		173327
42IPR023214
HAD-like domain		170477
43IPR002110
Ankyrin repeat		1701085
44IPR012337
Ribonuclease H-like domain		169313
45IPR011333
POZ domain		169181
46IPR010255
Haem peroxidase		168190
47IPR002016
Haem peroxidase, plant/fungal/bacterial		167583
48IPR011991
Winged helix-turn-helix DNA-binding domain		165306
49IPR025287
Wall-associated receptor kinase galacturonan-binding domain		160171
50IPR018247
EF-Hand 1, calcium-binding site		156337
51IPR013830
SGNH hydrolase-type esterase domain		153347
52IPR001650
Helicase, C-terminal		149424
53IPR023753
FAD/NAD(P)-binding domain		146514
54IPR014710
RmlC-like jelly roll fold		145186
55IPR029044
Nucleotide-diphospho-sugar transferases		143344
56IPR013785
Aldolase-type TIM barrel		139180
57IPR005174
Domain unknown function DUF295		139149
58IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		137545
59IPR025315
Domain of unknown function DUF4220		136143
60IPR014001
Helicase superfamily 1/2, ATP-binding domain		136262
61IPR019775
WD40 repeat, conserved site		133217
62IPR001480
Bulb-type lectin domain		133724
63IPR008974
TRAF-like		131251
64IPR003441
NAC domain		130380
65IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		129170
66IPR023213
Chloramphenicol acetyltransferase-like domain		129193
67IPR013026
Tetratricopeptide repeat-containing domain		129167
68IPR003439
ABC transporter-like		128383
69IPR007658
Protein of unknown function DUF594		126127
70IPR017930
Myb domain		124150
71IPR000210
BTB/POZ domain		123332
72IPR021109
Aspartic peptidase domain		122346
73IPR027443
Isopenicillin N synthase-like		122148
74IPR019734
Tetratricopeptide repeat		121837
75IPR008972
Cupredoxin		119418
76IPR015424
Pyridoxal phosphate-dependent transferase		119132
77IPR012340
Nucleic acid-binding, OB-fold		115171
78IPR003959
ATPase, AAA-type, core		114136
79IPR001461
Aspartic peptidase		111214
80IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		110117
81IPR005123
Oxoglutarate/iron-dependent dioxygenase		109197
82IPR000823
Plant peroxidase		109425
83IPR000858
S-locus glycoprotein domain		107113
84IPR004158
Protein of unknown function DUF247, plant		107119
85IPR011051
RmlC-like cupin domain		106137
86IPR003480
Transferase		106123
87IPR000109
Proton-dependent oligopeptide transporter family		105209
88IPR011050
Pectin lyase fold/virulence factor		105114
89IPR003609
PAN/Apple domain		104273
90IPR012334
Pectin lyase fold		104127
91IPR033121
Peptidase family A1 domain		103114
92IPR000008
C2 domain		101629
93IPR010987
Glutathione S-transferase, C-terminal-like		101294
94IPR001932
PPM-type phosphatase domain		101558
95IPR005225
Small GTP-binding protein domain		9797
96IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		97205
97IPR015500
Peptidase S8, subtilisin-related		97231
98IPR026961
PGG domain		95163
99IPR001220
Legume lectin domain		94105
100IPR011011
Zinc finger, FYVE/PHD-type		93108
101IPR001623
DnaJ domain		92594
102IPR024788
Malectin-like carbohydrate-binding domain		92103
103IPR007087
Zinc finger, C2H2		91280
104IPR032799
Xylanase inhibitor, C-terminal		9196
105IPR000742
EGF-like domain		89193
106IPR004045
Glutathione S-transferase, N-terminal		89170
107IPR015300
DNA-binding pseudobarrel domain		89250
108IPR002347
Glucose/ribitol dehydrogenase		88584
109IPR015655
Protein phosphatase 2C family		88134
110IPR005828
Major facilitator, sugar transporter-like		87121
111IPR002083
MATH/TRAF domain		87167
112IPR003657
WRKY domain		87474
113IPR001881
EGF-like calcium-binding domain		86130
114IPR016039
Thiolase-like		85304
115IPR019794
Peroxidase, active site		8586
116IPR011545
DEAD/DEAH box helicase domain		8488
117IPR018097
EGF-like calcium-binding, conserved site		8484
118IPR009072
Histone-fold		84168
119IPR031052
FHY3/FAR1 family		83112
120IPR008949
Isoprenoid synthase domain		82177
121IPR017871
ABC transporter, conserved site		82109
122IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		8189
123IPR011676
Domain of unknown function DUF1618		8087
124IPR003340
B3 DNA binding domain		77309
125IPR001563
Peptidase S10, serine carboxypeptidase		77362
126IPR000490
Glycoside hydrolase, family 17		77115
127IPR001087
GDSL lipase/esterase		7678
128IPR006447
Myb domain, plants		7575
129IPR029071
Ubiquitin-related domain		7586
130IPR006121
Heavy metal-associated domain, HMA		74207
131IPR020472
G-protein beta WD-40 repeat		74222
132IPR029052
Metallo-dependent phosphatase-like		74179
133IPR004827
Basic-leucine zipper domain		74256
134IPR000209
Peptidase S8/S53 domain		74350
135IPR032867
DYW domain		7273
136IPR001965
Zinc finger, PHD-type		72106
137IPR016177
DNA-binding domain		71103
138IPR032861
Xylanase inhibitor, N-terminal		7173
139IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		71131
140IPR013057
Amino acid transporter, transmembrane domain		7083
141IPR013766
Thioredoxin domain		69124
142IPR006566
FBD domain		6981
143IPR027640
Kinesin-like protein		68163
144IPR007117
Expansin, cellulose-binding-like domain		68267
145IPR001806
Small GTPase superfamily		6874
146IPR002100
Transcription factor, MADS-box		67471
147IPR001356
Homeobox domain		67158
148IPR013128
Peptidase C1A		6670
149IPR003960
ATPase, AAA-type, conserved site		6671
150IPR001752
Kinesin motor domain		66463
151IPR009009
RlpA-like double-psi beta-barrel domain		65179
152IPR020568
Ribosomal protein S5 domain 2-type fold		6580
153IPR026057
PC-Esterase		6470
154IPR000073
Alpha/beta hydrolase fold-1		64103
155IPR026992
Non-haem dioxygenase N-terminal domain		6467
156IPR006045
Cupin 1		64155
157IPR011993
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)		64116
158IPR024171
S-receptor-like serine/threonine-protein kinase		6363
159IPR029962
Trichome birefringence-like family		6375
160IPR002902
Gnk2-homologous domain		63164
161IPR016159
Cullin repeat-like-containing domain		6281
162IPR030184
WAT1-related protein		6269
163IPR003613
U box domain		62170
164IPR000225
Armadillo		62434
165IPR018108
Mitochondrial substrate/solute carrier		61304
166IPR023395
Mitochondrial carrier domain		61134
167IPR017907
Zinc finger, RING-type, conserved site		6162
168IPR001471
AP2/ERF domain		60348
169IPR013763
Cyclin-like		60266
170IPR019793
Peroxidases heam-ligand binding site		6060
171IPR002528
Multi antimicrobial extrusion protein		60113
172IPR000270
PB1 domain		60102
173IPR005630
Terpene synthase, metal-binding domain		5966
174IPR013525
ABC-2 type transporter		5881
175IPR011527
ABC transporter type 1, transmembrane domain		58299
176IPR000571
Zinc finger, CCCH-type		58430
177IPR008979
Galactose-binding domain-like		57137
178IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5657
179IPR029055
Nucleophile aminohydrolases, N-terminal		55103
180IPR007112
Expansin/pollen allergen, DPBB domain		5597
181IPR002035
von Willebrand factor, type A		55162
182IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5479
183IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		5457
184IPR006553
Leucine-rich repeat, cysteine-containing subtype		54334
185IPR016135
Ubiquitin-conjugating enzyme/RWD-like		54130
186IPR000668
Peptidase C1A, papain C-terminal		54172
187IPR005829
Sugar transporter, conserved site		5382
188IPR022059
Protein of unknown function DUF3615		5357
189IPR008928
Six-hairpin glycosidase-like		5367
190IPR002085
Alcohol dehydrogenase superfamily, zinc-type		5365
191IPR014756
Immunoglobulin E-set		5362
192IPR017451
F-box associated interaction domain		5256
193IPR019787
Zinc finger, PHD-finger		5298
194IPR001906
Terpene synthase, N-terminal domain		52110
195IPR011032
GroES-like		51118
196IPR000873
AMP-dependent synthetase/ligase		5167
197IPR004140
Exocyst complex protein Exo70		51115
198IPR009003
Peptidase S1, PA clan		5172
199IPR012871
Protein of unknown function DUF1677, Oryza sativa		5063
200IPR011042
Six-bladed beta-propeller, TolB-like		5055
201IPR015880
Zinc finger, C2H2-like		50150
202IPR023828
Peptidase S8, subtilisin, Ser-active site		4949
203IPR000620
EamA domain		4975
204IPR000048
IQ motif, EF-hand binding site		49263
205IPR008250
P-type ATPase, A domain		48104
206IPR023393
START-like domain		4851
207IPR000152
EGF-type aspartate/asparagine hydroxylation site		4848
208IPR005202
Transcription factor GRAS		48102
209IPR011706
Multicopper oxidase, type 2		4848
210IPR003663
Sugar/inositol transporter		48199
211IPR016181
Acyl-CoA N-acyltransferase		4796
212IPR007118
Expansin/Lol pI		47225
213IPR019786
Zinc finger, PHD-type, conserved site		4753
214IPR003245
Phytocyanin domain		47129
215IPR004046
Glutathione S-transferase, C-terminal		4747
216IPR017877
Myb-like domain		4755
217IPR013783
Immunoglobulin-like fold		4658
218IPR023299
P-type ATPase, cytoplasmic domain N		4686
219IPR013126
Heat shock protein 70 family		46245
220IPR011707
Multicopper oxidase, type 3		4647
221IPR008978
HSP20-like chaperone		4590
222IPR001360
Glycoside hydrolase, family 1		45289
223IPR009000
Translation protein, beta-barrel domain		4549
224IPR003594
Histidine kinase-like ATPase, C-terminal domain		45164
225IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		4548
226IPR001757
P-type ATPase		45157
227IPR028889
Ubiquitin specific protease domain		4545
228IPR000070
Pectinesterase, catalytic		4553
229IPR001878
Zinc finger, CCHC-type		45273
230IPR001117
Multicopper oxidase, type 1		4445
231IPR011006
CheY-like superfamily		4447
232IPR011012
Longin-like domain		4446
233IPR006671
Cyclin, N-terminal		4468
234IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4450
235IPR000743
Glycoside hydrolase, family 28		4464
236IPR000608
Ubiquitin-conjugating enzyme E2		4393
237IPR000330
SNF2-related, N-terminal domain		4347
238IPR000222
PPM-type phosphatase, divalent cation binding		4343
239IPR003653
Ulp1 protease family, C-terminal catalytic domain		4376
240IPR001789
Signal transduction response regulator, receiver domain		43113
241IPR013201
Cathepsin propeptide inhibitor domain (I29)		4284
242IPR005135
Endonuclease/exonuclease/phosphatase		42147
243IPR018253
DnaJ domain, conserved site		4243
244IPR001214
SET domain		42110
245IPR023210
NADP-dependent oxidoreductase domain		42137
246IPR001395
Aldo/keto reductase/potassium channel subunit beta		4255
247IPR002921
Fungal lipase-like domain		4142
248IPR004265
Plant disease resistance response protein		4141
249IPR029045
ClpP/crotonase-like domain		41112
250IPR006501
Pectinesterase inhibitor domain		41157
251IPR004314
Domain of unknown function DUF239		4145
252IPR012341
Six-hairpin glycosidase		4161
253IPR001229
Jacalin-like lectin domain		41231
254IPR000626
Ubiquitin domain		40114
255IPR001251
CRAL-TRIO lipid binding domain		40190
256IPR011701
Major facilitator superfamily		4043
257IPR002659
Glycosyl transferase, family 31		4069
258IPR000425
Major intrinsic protein		40242
259IPR000644
CBS domain		40225
260IPR007527
Zinc finger, SWIM-type		4068
261IPR023271
Aquaporin-like		3985
262IPR016166
FAD-binding, type 2		3968
263IPR005150
Cellulose synthase		3962
264IPR024752
Myb/SANT-like domain		3939
265IPR002487
Transcription factor, K-box		3978
266IPR033389
AUX/IAA domain		3842
267IPR001929
Germin		38108
268IPR003137
PA domain		3838
269IPR029061
Thiamin diphosphate-binding fold		38112
270IPR014014
RNA helicase, DEAD-box type, Q motif		3838
271IPR007125
Histone H2A/H2B/H3		3838
272IPR001077
O-methyltransferase, family 2		3840
273IPR019378
GDP-fucose protein O-fucosyltransferase		3842
274IPR004088
K Homology domain, type 1		38259
275IPR004330
FAR1 DNA binding domain		3845
276IPR025558
Domain of unknown function DUF4283		3838
277IPR004853
Sugar phosphate transporter domain		3741
278IPR018200
Ubiquitin specific protease, conserved site		3759
279IPR012946
X8 domain		3784
280IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		3771
281IPR004864
Late embryogenesis abundant protein, LEA-14		3742
282IPR004839
Aminotransferase, class I/classII		3738
283IPR025846
PMR5 N-terminal domain		3737
284IPR016461
O-methyltransferase COMT-type		3645
285IPR003656
Zinc finger, BED-type		3693
286IPR018303
P-type ATPase, phosphorylation site		3636
287IPR025661
Cysteine peptidase, asparagine active site		3637
288IPR000757
Glycoside hydrolase, family 16		3669
289IPR025659
Tubby C-terminal-like domain		3544
290IPR005299
SAM dependent carboxyl methyltransferase		3538
291IPR029021
Protein-tyrosine phosphatase-like		3582
292IPR018181
Heat shock protein 70, conserved site		3565
293IPR003406
Glycosyl transferase, family 14		3539
294IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		3577
295IPR015915
Kelch-type beta propeller		3541
296IPR003855
Potassium transporter		3560
297IPR001099
Chalcone/stilbene synthase, N-terminal		3537
298IPR018490
Cyclic nucleotide-binding-like		3435
299IPR032710
NTF2-like domain		3458
300IPR001478
PDZ domain		3496
301IPR011013
Galactose mutarotase-like domain		3439
302IPR003690
Mitochodrial transcription termination factor		34200
303IPR020845
AMP-binding, conserved site		3434
304IPR004813
Oligopeptide transporter, OPT superfamily		3475
305IPR000595
Cyclic nucleotide-binding domain		3481
306IPR011043
Galactose oxidase/kelch, beta-propeller		3436
307IPR002912
ACT domain		3467
308IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3484
309IPR006626
Parallel beta-helix repeat		33153
310IPR007493
Protein of unknown function DUF538		33101
311IPR001296
Glycosyl transferase, family 1		3333
312IPR004263
Exostosin-like		3335
313IPR013154
Alcohol dehydrogenase, N-terminal		3334
314IPR016072
SKP1 component, dimerisation		3364
315IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		3349
316IPR001701
Glycoside hydrolase, family 9		3343
317IPR013094
Alpha/beta hydrolase fold-3		3334
318IPR006073
GTP binding domain		3385
319IPR019821
Kinesin motor domain, conserved site		3232
320IPR013149
Alcohol dehydrogenase, C-terminal		3232
321IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3240
322IPR006564
Zinc finger, PMZ-type		3233
323IPR001969
Aspartic peptidase, active site		3247
324IPR002423
Chaperonin Cpn60/TCP-1 family		3239
325IPR004320
Protein of unknown function DUF241, plant		3233
326IPR000408
Regulator of chromosome condensation, RCC1		32451
327IPR004367
Cyclin, C-terminal domain		3259
328IPR022742
Serine aminopeptidase, S33		3232
329IPR004087
K Homology domain		3264
330IPR019780
Germin, manganese binding site		3232
331IPR008942
ENTH/VHS		3163
332IPR010402
CCT domain		3161
333IPR000182
GNAT domain		3152
334IPR025110
AMP-binding enzyme C-terminal domain		3131
335IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		3182
336IPR006016
UspA		3131
337IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		3180
338IPR031112
AP2-like ethylene-responsive transcription factor		3132
339IPR021720
Malectin		3131
340IPR027409
GroEL-like apical domain		3164
341IPR029047
Heat shock protein 70kD, peptide-binding domain		3173
342IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		3131
343IPR015947
PUA-like domain		3140
344IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3038
345IPR002403
Cytochrome P450, E-class, group IV		30133
346IPR001938
Thaumatin		30207
347IPR002495
Glycosyl transferase, family 8		3032
348IPR014720
Double-stranded RNA-binding domain		30103
349IPR023298
P-type ATPase, transmembrane domain		3062
350IPR029000
Cyclophilin-like domain		2963
351IPR009060
UBA-like		2937
352IPR012675
Beta-grasp domain		2930
353IPR000863
Sulfotransferase domain		2935
354IPR020946
Flavin monooxygenase-like		2937
355IPR005746
Thioredoxin		2935
356IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		2933
357IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2961
358IPR002937
Amine oxidase		2929
359IPR004041
NAF domain		2828
360IPR013601
FAE1/Type III polyketide synthase-like protein		2831
361IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28146
362IPR018451
NAF/FISL domain		2828
363IPR002068
Alpha crystallin/Hsp20 domain		2856
364IPR000795
Transcription factor, GTP-binding domain		28141
365IPR002293
Amino acid/polyamine transporter I		2873
366IPR020904
Short-chain dehydrogenase/reductase, conserved site		2828
367IPR002963
Expansin		28181
368IPR017970
Homeobox, conserved site		2828
369IPR033443
Pentacotripeptide-repeat region of PROPR		2830
370IPR029062
Class I glutamine amidotransferase-like		2873
371IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2840
372IPR003676
Small auxin-up RNA		2828
373IPR006689
Small GTPase superfamily, ARF/SAR type		2799
374IPR006153
Cation/H+ exchanger		2731
375IPR001279
Metallo-beta-lactamase		2792
376IPR033131
Pectinesterase, Asp active site		2728
377IPR002355
Multicopper oxidase, copper-binding site		2727
378IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2727
379IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		2727
380IPR027923
Hydrophobic seed protein		2727
381IPR005821
Ion transport domain		2729
382IPR015902
Glycoside hydrolase, family 13		2744
383IPR016161
Aldehyde/histidinol dehydrogenase		2727
384IPR018202
Peptidase S10, serine carboxypeptidase, active site		2728
385IPR006702
Domain of unknown function DUF588		2727
386IPR004141
Strictosidine synthase		2626
387IPR015940
Ubiquitin-associated domain		2682
388IPR004316
SWEET sugar transporter		2648
389IPR029466
No apical meristem-associated, C-terminal domain		2626
390IPR008991
Translation protein SH3-like domain		2627
391IPR001353
Proteasome, subunit alpha/beta		2627
392IPR022812
Dynamin superfamily		26119
393IPR001320
Ionotropic glutamate receptor		2644
394IPR020635
Tyrosine-protein kinase, catalytic domain		2626
395IPR029064
50S ribosomal protein L30e-like		2657
396IPR010525
Auxin response factor		2628
397IPR029048
Heat shock protein 70kD, C-terminal domain		2650
398IPR015916
Galactose oxidase, beta-propeller		2527
399IPR017938
Riboflavin synthase-like beta-barrel		2529
400IPR033124
Serine carboxypeptidases, histidine active site		2525
401IPR011074
CRAL/TRIO, N-terminal domain		2564
402IPR001763
Rhodanese-like domain		25104
403IPR003337
Trehalose-phosphatase		2548
404IPR003008
Tubulin/FtsZ, GTPase domain		25120
405IPR004883
Lateral organ boundaries, LOB		2546
406IPR031107
Small heat shock protein HSP20		2526
407IPR001876
Zinc finger, RanBP2-type		25176
408IPR022357
Major intrinsic protein, conserved site		2525
409IPR029993
Plant galacturonosyltransferase GAUT		2532
410IPR025486
Domain of unknown function DUF4378		2525
411IPR029006
ADF-H/Gelsolin-like domain		2550
412IPR001638
Solute-binding protein family 3/N-terminal domain of MltF		2529
413IPR025660
Cysteine peptidase, histidine active site		2526
414IPR002913
START domain		2564
415IPR015590
Aldehyde dehydrogenase domain		2528
416IPR003100
PAZ domain		2484
417IPR000727
Target SNARE coiled-coil homology domain		2458
418IPR022149
Protein of unknown function DUF3681		2425
419IPR001440
Tetratricopeptide repeat 1		2426
420IPR010920
LSM domain		2425
421IPR000717
Proteasome component (PCI) domain		2445
422IPR008422
Homeobox KN domain		2424
423IPR012416
CALMODULIN-BINDING PROTEIN60		2425
424IPR010989
t-SNARE		2425
425IPR006652
Kelch repeat type 1		24103
426IPR008266
Tyrosine-protein kinase, active site		2424
427IPR025521
Domain of unknown function DUF4409		2425
428IPR025875
Leucine rich repeat 4		2424
429IPR002067
Mitochondrial carrier protein		24116
430IPR013780
Glycosyl hydrolase, family 13, all-beta		2424
431IPR012328
Chalcone/stilbene synthase, C-terminal		2424
432IPR016162
Aldehyde dehydrogenase N-terminal domain		2427
433IPR017927
Ferredoxin reductase-type FAD-binding domain		2323
434IPR004240
Nonaspanin (TM9SF)		2359
435IPR004000
Actin family		23158
436IPR016073
SKP1 component, POZ domain		2323
437IPR013187
F-box associated domain, type 3		2326
438IPR001357
BRCT domain		23137
439IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2344
440IPR005516
Remorin, C-terminal		2324
441IPR029056
Ribokinase-like		2355
442IPR033275
E3 ubiquitin-protein ligase MARCH-like		2325
443IPR026892
Glycoside hydrolase family 3		2334
444IPR011060
Ribulose-phosphate binding barrel		2324
445IPR023313
Ubiquitin-conjugating enzyme, active site		2323
446IPR006379
HAD-superfamily hydrolase, subfamily IIB		2323
447IPR001232
S-phase kinase-associated protein 1-like		2323
448IPR029069
HotDog domain		2364
449IPR006094
FAD linked oxidase, N-terminal		2323
450IPR002109
Glutaredoxin		2347
451IPR003311
AUX/IAA protein		2328
452IPR001313
Pumilio RNA-binding repeat		23323
453IPR029033
Histidine phosphatase superfamily		2371
454IPR015797
NUDIX hydrolase domain-like		2347
455IPR006867
Domain of unknown function DUF632		2328
456IPR033133
Pumilio homology domain		2222
457IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2222
458IPR032872
Wall-associated receptor kinase, C-terminal		2224
459IPR011016
Zinc finger, RING-CH-type		2255
460IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2227
461IPR007657
Glycosyltransferase AER61, uncharacterised		2222
462IPR026960
Reverse transcriptase zinc-binding domain		2222
463IPR009030
Insulin-like growth factor binding protein, N-terminal		2223
464IPR027356
NPH3 domain		2245
465IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2222
466IPR017926
Glutamine amidotransferase		2240
467IPR020103
Pseudouridine synthase, catalytic domain		2239
468IPR004014
Cation-transporting P-type ATPase, N-terminal		2240
469IPR029057
Phosphoribosyltransferase-like		2259
470IPR004776
Auxin efflux carrier		2227
471IPR014722
Ribosomal protein L2 domain 2		2222
472IPR017937
Thioredoxin, conserved site		2227
473IPR028082
Periplasmic binding protein-like I		2240
474IPR020843
Polyketide synthase, enoylreductase domain		2222
475IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		2241
476IPR023329
Chlorophyll a/b binding protein domain		2224
477IPR018119
Strictosidine synthase, conserved region		2222
478IPR016163
Aldehyde dehydrogenase, C-terminal		2225
479IPR014718
Glycoside hydrolase-type carbohydrate-binding, subgroup		2127
480IPR001902
SLC26A/SulP transporter		2132
481IPR000782
FAS1 domain		2181
482IPR013328
6-phosphogluconate dehydrogenase, domain 2		2128
483IPR025525
hAT-like transposase, RNase-H fold		2122
484IPR033138
Multicopper oxidases, conserved site		2121
485IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		2121
486IPR003347
JmjC domain		2154
487IPR013581
Plant PDR ABC transporter associated		2122
488IPR027413
GroEL-like equatorial domain		2143
489IPR013816
ATP-grasp fold, subdomain 2		2127
490IPR006694
Fatty acid hydroxylase		2123
491IPR016021
MIF4G-like domain		2137
492IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2122
493IPR003165
Piwi domain		2159
494IPR022796
Chlorophyll A-B binding protein		2122
495IPR015679
Phospholipase D family		2142
496IPR000169
Cysteine peptidase, cysteine active site		2121
497IPR000086
NUDIX hydrolase domain		2140
498IPR006439
HAD hydrolase, subfamily IA		2153
499IPR006594
LIS1 homology motif		2041
500IPR000528
Plant lipid transfer protein/Par allergen		2075
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis.html new file mode 100644 index 00000000..194b50eb --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis.html @@ -0,0 +1,230 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:393,639,427
Golden Path Length:393,639,427
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:54,942
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
180 sequences
+
+ +
+ + + +
SequenceLength (bp)
142804815
237283348
340595595
434272791
530045131
631576741
730507914
829018812
923643651
1024084775
1129168041
1226254206
UN-Ctg401015623
UN-Ctg41473970
UN-Ctg42356539
UN-Ctg43272270
UN-Ctg44262298
UN-Ctg45260731
UN-Ctg46249267
UN-Ctg47246957
UN-Ctg48230131
UN-Ctg49214515
UN-Ctg50207031
UN-Ctg51187982
UN-Ctg52187415
UN-Ctg53162407
UN-Ctg54160638
UN-Ctg55159482
UN-Ctg56154193
UN-Ctg57150414
UN-Ctg58150036
UN-Ctg59149144
UN-Ctg60148803
UN-Ctg61142810
UN-Ctg62137183
UN-Ctg63135027
UN-Ctg64129649
UN-Ctg65128120
UN-Ctg66126628
UN-Ctg67117047
UN-Ctg68116209
UN-Ctg69115750
UN-Ctg70111134
UN-Ctg71107842
UN-Ctg72106144
UN-Ctg73103230
UN-Ctg74103100
UN-Ctg75100659
UN-Ctg7698428
UN-Ctg7797694
UN-Ctg7897224
UN-Ctg7997709
UN-Ctg8096024
UN-Ctg8191564
UN-Ctg8290991
UN-Ctg8390743
UN-Ctg8490673
UN-Ctg8589767
UN-Ctg8686802
UN-Ctg8787523
UN-Ctg8886199
UN-Ctg8984231
UN-Ctg9084032
UN-Ctg9183027
UN-Ctg9282708
UN-Ctg9381639
UN-Ctg9477053
UN-Ctg9575834
UN-Ctg9674801
UN-Ctg9774776
UN-Ctg9874692
UN-Ctg9973066
UN-Ctg10072663
UN-Ctg10172607
UN-Ctg10271982
UN-Ctg10371954
UN-Ctg10471036
UN-Ctg10570743
UN-Ctg10669934
UN-Ctg10769160
UN-Ctg10869035
UN-Ctg10969000
UN-Ctg11068128
UN-Ctg11167174
UN-Ctg11266478
UN-Ctg11365084
UN-Ctg11465038
UN-Ctg11564737
UN-Ctg11664519
UN-Ctg11763981
UN-Ctg11863261
UN-Ctg11961477
UN-Ctg12061945
UN-Ctg12161854
UN-Ctg12261411
UN-Ctg12361236
UN-Ctg12460607
UN-Ctg12560339
UN-Ctg12659739
UN-Ctg12759102
UN-Ctg12858785
UN-Ctg12958583
UN-Ctg13058153
UN-Ctg13158042
UN-Ctg13255327
UN-Ctg13355483
UN-Ctg13454709
UN-Ctg13554736
UN-Ctg13653689
UN-Ctg13753708
UN-Ctg13853262
UN-Ctg13952817
UN-Ctg14052680
UN-Ctg14150575
UN-Ctg14250569
UN-Ctg14349784
UN-Ctg14449573
UN-Ctg14549474
UN-Ctg14649473
UN-Ctg14748862
UN-Ctg14848114
UN-Ctg14948045
UN-Ctg15047776
UN-Ctg15147762
UN-Ctg15247602
UN-Ctg15347163
UN-Ctg15446957
UN-Ctg15546352
UN-Ctg15645596
UN-Ctg15745002
UN-Ctg15844872
UN-Ctg15944934
UN-Ctg16044443
UN-Ctg16144480
UN-Ctg16244203
UN-Ctg16343468
UN-Ctg16443064
UN-Ctg16543073
UN-Ctg16642861
UN-Ctg16742836
UN-Ctg16842630
UN-Ctg16942624
UN-Ctg17042479
UN-Ctg17142071
UN-Ctg17242103
UN-Ctg17341418
UN-Ctg17440817
UN-Ctg17539781
UN-Ctg17639777
UN-Ctg17737862
UN-Ctg17837838
UN-Ctg17937221
UN-Ctg18036830
UN-Ctg18136581
UN-Ctg18235654
UN-Ctg18335521
UN-Ctg18435432
UN-Ctg18534755
UN-Ctg18635009
UN-Ctg18733403
UN-Ctg18832470
UN-Ctg18932118
UN-Ctg19031626
UN-Ctg19131663
UN-Ctg19230519
UN-Ctg19330426
UN-Ctg19430113
UN-Ctg19529925
UN-Ctg19629586
UN-Ctg19728842
UN-Ctg19828516
UN-Ctg19928256
UN-Ctg20028259
UN-Ctg20126161
UN-Ctg20225339
UN-Ctg20325280
UN-Ctg20421804
UN-Ctg20518699
UN-Ctg20618362
UN-Ctg20717148
+
+
chunk4024 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_meridionalis_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta.html new file mode 100644 index 00000000..eaef9433 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta.html @@ -0,0 +1,51 @@ +

Summary

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Assembly:chr3s, Sep 2009
Database version:62.01
Base Pairs:61,615,268
Golden Path Length:45,181,754
Genebuild by:CSHL
Genebuild method:Fgenesh
Genebuild started:Nov 2010
Genebuild released:blank
Genebuild last updated/patched:blank
+ +

Gene counts

+ + + + + + + + +
Gene exons:21,837
Gene transcripts:3,966
+ \ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minuta_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb.html new file mode 100644 index 00000000..911acfaf --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb.html @@ -0,0 +1,302 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:chr3s,
Database version:75.02
:
:
Genebuild by: CSHL
Genebuild method: Fgenesh
Genebuild started: Jul 2011
Genebuild version: 2011-07-CSHL

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
minutaBB_3s19970960
+
+
contig
+
252 sequences
+
+ +
+ + + +
SequenceLength (bp)
AC213909124399
AC213910121580
AC215815214202
AC215815.1214202
AC225894130320
AC225896122876
AC225897138331
AC225898111436
AC22589998287
AC225900109997
AC225900.1109997
AC225901120543
AC225902134423
AC225903135600
AC225904134562
AC225905156787
AC225906153474
AC225906.1153474
AC225907139215
AC225907.1139215
AC225908110491
AC225909152310
AC226069124989
AC226070126782
AC226072134376
AC226073122613
AC226076146166
AC226077113516
AC226080128501
AC22608197172
AC226254143110
AC22625590947
AC226256105033
AC226257133642
AC226258103786
AC22625947898
AC226260118298
AC226261117046
AC226262175709
AC226263151319
AC226264136804
AC226265110710
AC226266146406
AC22635197684
AC22635576135
AC226355.176135
AC226356127759
AC226357131284
AC226357.1131284
AC226357.2131284
AC22635885711
AC226358.185711
AC226359137725
AC226360108263
AC226361115331
AC22636295141
AC226363110385
AC226363.1110385
AC226364111255
AC226364.1111255
AC226365124266
AC226365.1124266
AC226366127011
AC226407135713
AC226408101920
AC226409127747
AC22641099707
AC22641195645
AC226412108154
AC226413165416
AC226413.1165416
AC226415105044
AC22641799307
AC226418148630
AC226419139472
AC226420141739
AC226421126867
AC226421.1126867
AC226633118069
AC226633.1118069
AC226704126145
AC226706118096
AC226707133090
AC226708121506
AC226708.1121506
AC226710115893
AC226772155789
AC226773114429
AC226774120656
AC226775113902
AC226776130780
AC226777109756
AC226778121400
AC226778.1121400
AC226779162581
AC226780136882
AC226781139483
AC226782146940
AC226783109574
AC226784126095
AC226784.1126095
AC226785146468
AC226786133755
AC22678799836
AC226788121805
AC226789163408
AC22680597646
AC226805.197646
AC226806134350
AC226807104312
AC226808121378
AC226809118689
AC226810127251
AC226811118303
AC226812143971
AC226813128518
AC22681499342
AC226815115498
AC226816119092
AC226817110167
AC226817.1110167
AC226818125067
AC226819112925
AC22682093666
AC226821117477
AC226822187280
AC229741130811
AC22974889902
AC229750122511
AC229752129064
AC229753116434
AC229758141190
AC229764117100
AC229764.1117100
AC229766108641
AC229769137642
AC229779132912
AC229780103110
AC229780.1103110
AC229781154288
AC229781.1154288
AC229785128979
AC229792106974
AC229796132946
AC229798157116
AC229905117601
AC229906145851
AC229907117194
AC229907.1117194
AC229908114584
AC22991367127
AC229913.167127
AC229914108899
AC229915109640
AC229916100551
AC229916.1100551
AC229917121012
AC229918120708
AC229919133441
AC229920166779
AC229922186893
AC229923152242
AC229924118567
AC229925125086
AC229926131898
AC229927131310
AC22992875636
AC229929102229
AC229930116540
AC229931134231
AC229932111692
AC229933115258
AC22993485310
AC229935135994
AC229936109106
AC229936.1109106
AC229937140798
AC22993991599
AC229939.191599
AC229942120593
AC229943100698
AC229944127198
AC231124121305
AC231125120684
AC231126138753
AC231126.1138753
AC231127160703
AC231128117335
AC231129104059
AC23113089171
AC231131137454
AC231132124179
AC231132.1124179
AC231133133576
AC231134120810
AC231135107350
AC231135.1107350
AC231136146314
AC23113792051
AC231138136317
AC231140126528
AC231141120631
AC231201118622
AC231333122870
AC233030127011
AC23303198463
AC233033122408
AC233034133616
AC233035107940
AC233035.1107940
AC233036125781
AC233037115181
AC233038118837
AC23303962388
AC233040112071
AC233041113983
AC233042135810
AC233043144947
AC233044109947
AC233045124971
AC233045.1124971
AC233046117989
AC233047124674
AC233048204238
AC233049156557
AC233049.1156557
AC233050110346
AC233051127311
AC233052160718
AC233052.1160718
AC233549115300
AC236521141259
AC236522139833
AC236523115901
AC236524106798
AC236526106004
AC236527131828
AC23652962173
AC236530130466
AC23653589618
AC236537117693
AC236538127646
AC236541113819
AC236542188666
AC236543123313
AC236546117642
AC236547123925
AC236549175008
AC237796130595
AC237797141989
AC237798104559
AC23779999868
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s.html new file mode 100644 index 00000000..2ecde5f8 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s.html @@ -0,0 +1,265 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OGE.2011Aug, Aug 2013
Database version:76.03
:19,970,960
Golden Path Length:19,970,960
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + +
Protein coding gene count

Genes and/or transcript that contains an open reading frame (ORF).

:		1,928
Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:2,566
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
3s19970960
+
+
chunk
+
200 sequences
+
+ +
+ + + +
SequenceLength (bp)
3s:1..100000100000
3s:10000001..10100000100000
3s:1000001..1100000100000
3s:100001..200000100000
3s:10100001..10200000100000
3s:10200001..10300000100000
3s:10300001..10400000100000
3s:10400001..10500000100000
3s:10500001..10600000100000
3s:10600001..10700000100000
3s:10700001..10800000100000
3s:10800001..10900000100000
3s:10900001..11000000100000
3s:11000001..11100000100000
3s:1100001..1200000100000
3s:11100001..11200000100000
3s:11200001..11300000100000
3s:11300001..11400000100000
3s:11400001..11500000100000
3s:11500001..11600000100000
3s:11600001..11700000100000
3s:11700001..11800000100000
3s:11800001..11900000100000
3s:11900001..12000000100000
3s:12000001..12100000100000
3s:1200001..1300000100000
3s:12100001..12200000100000
3s:12200001..12300000100000
3s:12300001..12400000100000
3s:12400001..12500000100000
3s:12500001..12600000100000
3s:12600001..12700000100000
3s:12700001..12800000100000
3s:12800001..12900000100000
3s:12900001..13000000100000
3s:13000001..13100000100000
3s:1300001..1400000100000
3s:13100001..13200000100000
3s:13200001..13300000100000
3s:13300001..13400000100000
3s:13400001..13500000100000
3s:13500001..13600000100000
3s:13600001..13700000100000
3s:13700001..13800000100000
3s:13800001..13900000100000
3s:13900001..14000000100000
3s:14000001..14100000100000
3s:1400001..1500000100000
3s:14100001..14200000100000
3s:14200001..14300000100000
3s:14300001..14400000100000
3s:14400001..14500000100000
3s:14500001..14600000100000
3s:14600001..14700000100000
3s:14700001..14800000100000
3s:14800001..14900000100000
3s:14900001..15000000100000
3s:15000001..15100000100000
3s:1500001..1600000100000
3s:15100001..15200000100000
3s:15200001..15300000100000
3s:15300001..15400000100000
3s:15400001..15500000100000
3s:15500001..15600000100000
3s:15600001..15700000100000
3s:15700001..15800000100000
3s:15800001..15900000100000
3s:15900001..16000000100000
3s:16000001..16100000100000
3s:1600001..1700000100000
3s:16100001..16200000100000
3s:16200001..16300000100000
3s:16300001..16400000100000
3s:16400001..16500000100000
3s:16500001..16600000100000
3s:16600001..16700000100000
3s:16700001..16800000100000
3s:16800001..16900000100000
3s:16900001..17000000100000
3s:17000001..17100000100000
3s:1700001..1800000100000
3s:17100001..17200000100000
3s:17200001..17300000100000
3s:17300001..17400000100000
3s:17400001..17500000100000
3s:17500001..17600000100000
3s:17600001..17700000100000
3s:17700001..17800000100000
3s:17800001..17900000100000
3s:17900001..18000000100000
3s:18000001..18100000100000
3s:1800001..1900000100000
3s:18100001..18200000100000
3s:18200001..18300000100000
3s:18300001..18400000100000
3s:18400001..18500000100000
3s:18500001..18600000100000
3s:18600001..18700000100000
3s:18700001..18800000100000
3s:18800001..18900000100000
3s:18900001..19000000100000
3s:19000001..19100000100000
3s:1900001..2000000100000
3s:19100001..19200000100000
3s:19200001..19300000100000
3s:19300001..19400000100000
3s:19400001..19500000100000
3s:19500001..19600000100000
3s:19600001..19700000100000
3s:19700001..19800000100000
3s:19800001..19900000100000
3s:19900001..1997096070960
3s:2000001..2100000100000
3s:200001..300000100000
3s:2100001..2200000100000
3s:2200001..2300000100000
3s:2300001..2400000100000
3s:2400001..2500000100000
3s:2500001..2600000100000
3s:2600001..2700000100000
3s:2700001..2800000100000
3s:2800001..2900000100000
3s:2900001..3000000100000
3s:3000001..3100000100000
3s:300001..400000100000
3s:3100001..3200000100000
3s:3200001..3300000100000
3s:3300001..3400000100000
3s:3400001..3500000100000
3s:3500001..3600000100000
3s:3600001..3700000100000
3s:3700001..3800000100000
3s:3800001..3900000100000
3s:3900001..4000000100000
3s:4000001..4100000100000
3s:400001..500000100000
3s:4100001..4200000100000
3s:4200001..4300000100000
3s:4300001..4400000100000
3s:4400001..4500000100000
3s:4500001..4600000100000
3s:4600001..4700000100000
3s:4700001..4800000100000
3s:4800001..4900000100000
3s:4900001..5000000100000
3s:5000001..5100000100000
3s:500001..600000100000
3s:5100001..5200000100000
3s:5200001..5300000100000
3s:5300001..5400000100000
3s:5400001..5500000100000
3s:5500001..5600000100000
3s:5600001..5700000100000
3s:5700001..5800000100000
3s:5800001..5900000100000
3s:5900001..6000000100000
3s:6000001..6100000100000
3s:600001..700000100000
3s:6100001..6200000100000
3s:6200001..6300000100000
3s:6300001..6400000100000
3s:6400001..6500000100000
3s:6500001..6600000100000
3s:6600001..6700000100000
3s:6700001..6800000100000
3s:6800001..6900000100000
3s:6900001..7000000100000
3s:7000001..7100000100000
3s:700001..800000100000
3s:7100001..7200000100000
3s:7200001..7300000100000
3s:7300001..7400000100000
3s:7400001..7500000100000
3s:7500001..7600000100000
3s:7600001..7700000100000
3s:7700001..7800000100000
3s:7800001..7900000100000
3s:7900001..8000000100000
3s:8000001..8100000100000
3s:800001..900000100000
3s:8100001..8200000100000
3s:8200001..8300000100000
3s:8300001..8400000100000
3s:8400001..8500000100000
3s:8500001..8600000100000
3s:8600001..8700000100000
3s:8700001..8800000100000
3s:8800001..8900000100000
3s:8900001..9000000100000
3s:9000001..9100000100000
3s:900001..1000000100000
3s:9100001..9200000100000
3s:9200001..9300000100000
3s:9300001..9400000100000
3s:9400001..9500000100000
3s:9500001..9600000100000
3s:9600001..9700000100000
3s:9700001..9800000100000
3s:9800001..9900000100000
3s:9900001..10000000100000
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb3s_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutabb_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc.html new file mode 100644 index 00000000..3c19a75d --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc.html @@ -0,0 +1,361 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:chr3s,
Database version:75.02
:
:
Genebuild by: CSHL
Genebuild method: Fgenesh
Genebuild started: Jul 2011
Genebuild version: 2011-07-CSHL

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
minutaCC_3s25210794
+
+
contig
+
311 sequences
+
+ +
+ + + +
SequenceLength (bp)
AC213823143750
AC213911107117
AC213912106777
AC21391397955
AC21391497800
AC213915103834
AC215813111846
AC215814112197
AC216031127799
AC216032154918
AC216033136262
AC216760131972
AC217192146430
AC217193126253
AC217194131152
AC217195119701
AC226071140428
AC226074105398
AC22607591724
AC226078129845
AC226079115330
AC229738153063
AC229739104438
AC229740121094
AC229742135768
AC229743119233
AC229744156285
AC229745127105
AC229746100442
AC229747145681
AC229749138298
AC229751142837
AC229754127562
AC229755125759
AC229756118913
AC229757112960
AC229759117668
AC229760114603
AC229761124089
AC229762130783
AC229762.1130783
AC229763117066
AC229765139785
AC229765.1139785
AC229767130613
AC229768127260
AC229770105245
AC229771108042
AC229772123450
AC229773131368
AC229774105218
AC229775120669
AC229776123426
AC229777135904
AC229777.1135904
AC229778103044
AC229782112362
AC229783141989
AC229784113873
AC229786150481
AC229786.1150481
AC229787125512
AC229788132487
AC22978997949
AC229790127197
AC229793135448
AC229794160706
AC229795106826
AC229797137260
AC229909122749
AC229911123840
AC231493103358
AC231494113582
AC231495139114
AC231496126746
AC231497139213
AC231497.1139213
AC231498108610
AC231498.1108610
AC231499149524
AC231499.1149524
AC231500149980
AC231501128220
AC23150279367
AC231504149980
AC231505121314
AC231506118188
AC231507147289
AC231508107202
AC231508.1107202
AC231510119776
AC231511132139
AC231512117893
AC231513140793
AC231515124832
AC231516126184
AC231516.1126184
AC231517160565
AC231518158612
AC231519122972
AC231785109635
AC231786131545
AC231786.1131545
AC231787146617
AC231788105755
AC231789179883
AC231790132776
AC23179192719
AC231792107016
AC231793106057
AC231793.1106057
AC231794129458
AC231795126334
AC231795.1126334
AC231795.2126334
AC231796115004
AC231797108819
AC231798136102
AC23179996940
AC231799.196940
AC231800115408
AC231801103306
AC231802159212
AC231803149395
AC231804199297
AC23180598862
AC231806114408
AC231808118488
AC231809129944
AC231810100079
AC231811115162
AC231812132447
AC231813124123
AC231814137047
AC231815123914
AC231816105580
AC231816.1105580
AC231817140418
AC231818111325
AC231819106903
AC231820126900
AC231821133236
AC231822150477
AC231823114512
AC231824160120
AC231825131512
AC231826145653
AC231827159986
AC231828125575
AC231829120486
AC231830115594
AC231851161095
AC231851.1161095
AC231852108488
AC231853159785
AC231853.1159785
AC231855177453
AC231856120503
AC231857118176
AC231858111430
AC231859109936
AC231859.1109936
AC231860124497
AC231861121212
AC231861.1121212
AC231862108108
AC231863115370
AC231864129515
AC231865126548
AC231871156042
AC231872134676
AC231873113123
AC231873.1113123
AC231874134913
AC231874.1134913
AC231876125424
AC231876.1125424
AC231877160802
AC231878141245
AC231879135638
AC231880151178
AC231880.1151178
AC231881114768
AC231882123139
AC231883148404
AC231884129807
AC231885118663
AC231886132025
AC23188797902
AC231933122831
AC231934139117
AC231935118367
AC231936145731
AC231937135149
AC231938119988
AC231938.1119988
AC231939120691
AC231940115442
AC231941124918
AC231941.1124918
AC231942120762
AC232128129677
AC232129153315
AC232130119501
AC232131156313
AC232132128128
AC232133121992
AC23213471878
AC232135116925
AC232136100667
AC232137110143
AC232138161954
AC232139118096
AC232140136248
AC232141106697
AC232142114376
AC232143112825
AC23214499239
AC232145104761
AC232146120345
AC232147104350
AC232148157753
AC232149117113
AC232150107446
AC232151123582
AC232152116379
AC232153126905
AC232154120132
AC232155106409
AC232156118933
AC232157106470
AC232158106071
AC232159127119
AC232160163289
AC232161103587
AC232162133637
AC232163104808
AC232164135637
AC232165130871
AC232166106601
AC232167123903
AC232168109598
AC232324150372
AC232325143340
AC232326119788
AC232327130618
AC232328144307
AC232329136516
AC232329.1136516
AC232329.2136516
AC232330138393
AC232331143745
AC232332140276
AC232333113880
AC232334103324
AC232334.1103324
AC232334.2103324
AC232335116874
AC232335.1116874
AC232336128760
AC232337111380
AC232338102466
AC232340128891
AC232341113581
AC232342127400
AC232343105624
AC232343.1105624
AC232344114997
AC232346132344
AC232347134146
AC232349105373
AC232350121195
AC232351128969
AC232353140162
AC232581106994
AC232582156508
AC232583140770
AC232584156508
AC232585134532
AC233540146171
AC233541146082
AC233541.1146082
AC233542142873
AC233543131098
AC233544113064
AC233545112143
AC233546114239
AC233547146086
AC233548144025
AC233550104550
AC233789135540
AC233790146966
AC233790.1146966
AC233790.2146966
AC233791121874
AC233792109402
AC233793203182
AC233794152880
AC233795137729
AC233796139835
AC233797127188
AC233797.1127188
AC233797.2127188
AC236531137897
AC236532133091
AC236534109753
AC236539120835
AC236540155153
AC236544142165
AC236545119342
AC236548100349
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s.html new file mode 100644 index 00000000..ec7a14bc --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s.html @@ -0,0 +1,318 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OGE.2011Aug, Aug 2013
Database version:76.03
:25,210,794
Golden Path Length:25,210,794
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + +
Protein coding gene count

Genes and/or transcript that contains an open reading frame (ORF).

:		2,249
Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:2,993
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
3s25210794
+
+
chunk
+
253 sequences
+
+ +
+ + + +
SequenceLength (bp)
3s:1..100000100000
3s:10000001..10100000100000
3s:1000001..1100000100000
3s:100001..200000100000
3s:10100001..10200000100000
3s:10200001..10300000100000
3s:10300001..10400000100000
3s:10400001..10500000100000
3s:10500001..10600000100000
3s:10600001..10700000100000
3s:10700001..10800000100000
3s:10800001..10900000100000
3s:10900001..11000000100000
3s:11000001..11100000100000
3s:1100001..1200000100000
3s:11100001..11200000100000
3s:11200001..11300000100000
3s:11300001..11400000100000
3s:11400001..11500000100000
3s:11500001..11600000100000
3s:11600001..11700000100000
3s:11700001..11800000100000
3s:11800001..11900000100000
3s:11900001..12000000100000
3s:12000001..12100000100000
3s:1200001..1300000100000
3s:12100001..12200000100000
3s:12200001..12300000100000
3s:12300001..12400000100000
3s:12400001..12500000100000
3s:12500001..12600000100000
3s:12600001..12700000100000
3s:12700001..12800000100000
3s:12800001..12900000100000
3s:12900001..13000000100000
3s:13000001..13100000100000
3s:1300001..1400000100000
3s:13100001..13200000100000
3s:13200001..13300000100000
3s:13300001..13400000100000
3s:13400001..13500000100000
3s:13500001..13600000100000
3s:13600001..13700000100000
3s:13700001..13800000100000
3s:13800001..13900000100000
3s:13900001..14000000100000
3s:14000001..14100000100000
3s:1400001..1500000100000
3s:14100001..14200000100000
3s:14200001..14300000100000
3s:14300001..14400000100000
3s:14400001..14500000100000
3s:14500001..14600000100000
3s:14600001..14700000100000
3s:14700001..14800000100000
3s:14800001..14900000100000
3s:14900001..15000000100000
3s:15000001..15100000100000
3s:1500001..1600000100000
3s:15100001..15200000100000
3s:15200001..15300000100000
3s:15300001..15400000100000
3s:15400001..15500000100000
3s:15500001..15600000100000
3s:15600001..15700000100000
3s:15700001..15800000100000
3s:15800001..15900000100000
3s:15900001..16000000100000
3s:16000001..16100000100000
3s:1600001..1700000100000
3s:16100001..16200000100000
3s:16200001..16300000100000
3s:16300001..16400000100000
3s:16400001..16500000100000
3s:16500001..16600000100000
3s:16600001..16700000100000
3s:16700001..16800000100000
3s:16800001..16900000100000
3s:16900001..17000000100000
3s:17000001..17100000100000
3s:1700001..1800000100000
3s:17100001..17200000100000
3s:17200001..17300000100000
3s:17300001..17400000100000
3s:17400001..17500000100000
3s:17500001..17600000100000
3s:17600001..17700000100000
3s:17700001..17800000100000
3s:17800001..17900000100000
3s:17900001..18000000100000
3s:18000001..18100000100000
3s:1800001..1900000100000
3s:18100001..18200000100000
3s:18200001..18300000100000
3s:18300001..18400000100000
3s:18400001..18500000100000
3s:18500001..18600000100000
3s:18600001..18700000100000
3s:18700001..18800000100000
3s:18800001..18900000100000
3s:18900001..19000000100000
3s:19000001..19100000100000
3s:1900001..2000000100000
3s:19100001..19200000100000
3s:19200001..19300000100000
3s:19300001..19400000100000
3s:19400001..19500000100000
3s:19500001..19600000100000
3s:19600001..19700000100000
3s:19700001..19800000100000
3s:19800001..19900000100000
3s:19900001..20000000100000
3s:20000001..20100000100000
3s:2000001..2100000100000
3s:200001..300000100000
3s:20100001..20200000100000
3s:20200001..20300000100000
3s:20300001..20400000100000
3s:20400001..20500000100000
3s:20500001..20600000100000
3s:20600001..20700000100000
3s:20700001..20800000100000
3s:20800001..20900000100000
3s:20900001..21000000100000
3s:21000001..21100000100000
3s:2100001..2200000100000
3s:21100001..21200000100000
3s:21200001..21300000100000
3s:21300001..21400000100000
3s:21400001..21500000100000
3s:21500001..21600000100000
3s:21600001..21700000100000
3s:21700001..21800000100000
3s:21800001..21900000100000
3s:21900001..22000000100000
3s:22000001..22100000100000
3s:2200001..2300000100000
3s:22100001..22200000100000
3s:22200001..22300000100000
3s:22300001..22400000100000
3s:22400001..22500000100000
3s:22500001..22600000100000
3s:22600001..22700000100000
3s:22700001..22800000100000
3s:22800001..22900000100000
3s:22900001..23000000100000
3s:23000001..23100000100000
3s:2300001..2400000100000
3s:23100001..23200000100000
3s:23200001..23300000100000
3s:23300001..23400000100000
3s:23400001..23500000100000
3s:23500001..23600000100000
3s:23600001..23700000100000
3s:23700001..23800000100000
3s:23800001..23900000100000
3s:23900001..24000000100000
3s:24000001..24100000100000
3s:2400001..2500000100000
3s:24100001..24200000100000
3s:24200001..24300000100000
3s:24300001..24400000100000
3s:24400001..24500000100000
3s:24500001..24600000100000
3s:24600001..24700000100000
3s:24700001..24800000100000
3s:24800001..24900000100000
3s:24900001..25000000100000
3s:25000001..25100000100000
3s:2500001..2600000100000
3s:25100001..25200000100000
3s:25200001..2521079410794
3s:2600001..2700000100000
3s:2700001..2800000100000
3s:2800001..2900000100000
3s:2900001..3000000100000
3s:3000001..3100000100000
3s:300001..400000100000
3s:3100001..3200000100000
3s:3200001..3300000100000
3s:3300001..3400000100000
3s:3400001..3500000100000
3s:3500001..3600000100000
3s:3600001..3700000100000
3s:3700001..3800000100000
3s:3800001..3900000100000
3s:3900001..4000000100000
3s:4000001..4100000100000
3s:400001..500000100000
3s:4100001..4200000100000
3s:4200001..4300000100000
3s:4300001..4400000100000
3s:4400001..4500000100000
3s:4500001..4600000100000
3s:4600001..4700000100000
3s:4700001..4800000100000
3s:4800001..4900000100000
3s:4900001..5000000100000
3s:5000001..5100000100000
3s:500001..600000100000
3s:5100001..5200000100000
3s:5200001..5300000100000
3s:5300001..5400000100000
3s:5400001..5500000100000
3s:5500001..5600000100000
3s:5600001..5700000100000
3s:5700001..5800000100000
3s:5800001..5900000100000
3s:5900001..6000000100000
3s:6000001..6100000100000
3s:600001..700000100000
3s:6100001..6200000100000
3s:6200001..6300000100000
3s:6300001..6400000100000
3s:6400001..6500000100000
3s:6500001..6600000100000
3s:6600001..6700000100000
3s:6700001..6800000100000
3s:6800001..6900000100000
3s:6900001..7000000100000
3s:7000001..7100000100000
3s:700001..800000100000
3s:7100001..7200000100000
3s:7200001..7300000100000
3s:7300001..7400000100000
3s:7400001..7500000100000
3s:7500001..7600000100000
3s:7600001..7700000100000
3s:7700001..7800000100000
3s:7800001..7900000100000
3s:7900001..8000000100000
3s:8000001..8100000100000
3s:800001..900000100000
3s:8100001..8200000100000
3s:8200001..8300000100000
3s:8300001..8400000100000
3s:8400001..8500000100000
3s:8500001..8600000100000
3s:8600001..8700000100000
3s:8700001..8800000100000
3s:8800001..8900000100000
3s:8900001..9000000100000
3s:9000001..9100000100000
3s:900001..1000000100000
3s:9100001..9200000100000
3s:9200001..9300000100000
3s:9300001..9400000100000
3s:9400001..9500000100000
3s:9500001..9600000100000
3s:9600001..9700000100000
3s:9700001..9800000100000
3s:9800001..9900000100000
3s:9900001..10000000100000
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc3s_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_minutacc_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara.html new file mode 100644 index 00000000..3fba29f0 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara.html @@ -0,0 +1,76 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:395,534,265
Golden Path Length:395,534,265
Genebuild by: CSHL
Genebuild started: Jul 2018
Genebuild version: 2018-07-CSHL
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:53,535
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
26 sequences
+
+ +
+ + + +
SequenceLength (bp)
144777331
237617280
339444530
434895103
531081614
631959707
731328962
829944492
923930135
1029664397
1132449966
1226869529
UN-Ctg34304382
UN-Ctg35251620
UN-Ctg36186140
UN-Ctg37178580
UN-Ctg38103931
UN-Ctg3987798
UN-Ctg4075341
UN-Ctg4173934
UN-Ctg4262263
UN-Ctg4360882
UN-Ctg4456571
UN-Ctg4549831
UN-Ctg4639864
UN-Ctg4740082
+
+
chunk3967 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_nivara_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis.html new file mode 100644 index 00000000..c4f7a82a --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis.html @@ -0,0 +1,241 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:chr3s,
Database version:75.02
:
:
Genebuild by: CSHL
Genebuild method: Fgenesh
Genebuild started: Jul 2011
Genebuild version: 2011-07-CSHL

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
officinalis_3s26195419
+
+
contig
+
191 sequences
+
+ +
+ + + +
SequenceLength (bp)
AC213143140638
AC213144193602
AC213145238087
AC213146119521
AC213147122838
AC213148196402
AC213824198093
AC214379276906
AC214380119418
AC214381108292
AC215526211558
AC215527167038
AC215528237939
AC215529186836
AC215530206458
AC215531239301
AC215532183111
AC216034146649
AC216035229608
AC216667178120
AC216667_1178120
AC216668191612
AC216668_1191612
AC216925157468
AC216926209779
AC216927214519
AC216928141175
AC216928_126659
AC216929107316
AC216930147707
AC216931124985
AC216932171063
AC216933193954
AC217445198106
AC217446178369
AC217447305063
AC217448150172
AC217449178595
AC217449_1135325
AC217506194857
AC217847215697
AC217917162184
AC217918176872
AC217919238461
AC217920238727
AC217921179976
AC217922252575
AC218022161917
AC219182197798
AC219183216537
AC219184156321
AC219185114816
AC219186175412
AC219187156010
AC220919156325
AC220921206555
AC220922174276
AC220989189704
AC220990188158
AC220991144514
AC220992191317
AC223446235758
AC223447270371
AC223448197900
AC223449202410
AC223450162002
AC225066185897
AC225067210269
AC225068184780
AC225069207167
AC225069_115051
AC225070172111
AC225071176836
AC225072150984
AC225073145437
AC225074131491
AC225074_1100388
AC225075229890
AC225076150028
AC225077197985
AC225078200863
AC225079201714
AC225080141962
AC225081184578
AC225081_1111379
AC225082193658
AC225083222095
AC225084162511
AC225085130076
AC225086180597
AC225086_1180597
AC225087176936
AC225088182770
AC225089118664
AC225090209128
AC225091175004
AC225092156244
AC225101210567
AC225102189409
AC225103158838
AC225104180973
AC225105249842
AC225106109957
AC225107194842
AC225108144904
AC225109192577
AC225110256696
AC225111119698
AC225112204785
AC225113185338
AC225114143685
AC225115211107
AC225232182836
AC225233160963
AC225234106274
AC225235223589
AC225236286440
AC225237181851
AC225238148727
AC225239240318
AC225240157680
AC225241226367
AC225243153439
AC225244108824
AC225245161127
AC225246117381
AC225247245466
AC225248147987
AC225249230007
AC225250154292
AC225251114765
AC225252234234
AC225253158300
AC225254243856
AC225255228719
AC225256110820
AC225323169112
AC225396177967
AC225397135786
AC225398202829
AC225399140401
AC225400163154
AC225401206087
AC225402178773
AC225554137086
AC225917213228
AC225918192537
AC225919163133
AC225920221723
AC225921120291
AC225922183602
AC225923189390
AC225924176638
AC225925161715
AC225926133851
AC226082253594
AC226083219066
AC226084215766
AC226085112314
AC226086210406
AC226087231510
AC226088158582
AC226089285058
AC226090128306
AC226091236322
AC226092198831
AC226093226631
AC226094238240
AC226095235471
AC226096191784
AC226097128462
AC226098229844
AC232882187536
AC232883207005
AC232884184393
AC232885164731
AC232886224115
AC232887106977
AC232888194716
AC232889219472
AC232890142465
AC232891117590
AC232892133628
AC232894110128
AC232895221974
AC232897133082
AC232898138484
AC232899246593
AC232900105080
AC232901239618
AC232902163822
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s.html new file mode 100644 index 00000000..4c25be0c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s.html @@ -0,0 +1,327 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OGE.2011Aug, Aug 2013
Database version:76.03
:26,195,419
Golden Path Length:26,195,419
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + +
Protein coding gene count

Genes and/or transcript that contains an open reading frame (ORF).

:		2,178
Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:2,892
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
3s26195419
+
+
chunk
+
262 sequences
+
+ +
+ + + +
SequenceLength (bp)
3s:1..100000100000
3s:10000001..10100000100000
3s:1000001..1100000100000
3s:100001..200000100000
3s:10100001..10200000100000
3s:10200001..10300000100000
3s:10300001..10400000100000
3s:10400001..10500000100000
3s:10500001..10600000100000
3s:10600001..10700000100000
3s:10700001..10800000100000
3s:10800001..10900000100000
3s:10900001..11000000100000
3s:11000001..11100000100000
3s:1100001..1200000100000
3s:11100001..11200000100000
3s:11200001..11300000100000
3s:11300001..11400000100000
3s:11400001..11500000100000
3s:11500001..11600000100000
3s:11600001..11700000100000
3s:11700001..11800000100000
3s:11800001..11900000100000
3s:11900001..12000000100000
3s:12000001..12100000100000
3s:1200001..1300000100000
3s:12100001..12200000100000
3s:12200001..12300000100000
3s:12300001..12400000100000
3s:12400001..12500000100000
3s:12500001..12600000100000
3s:12600001..12700000100000
3s:12700001..12800000100000
3s:12800001..12900000100000
3s:12900001..13000000100000
3s:13000001..13100000100000
3s:1300001..1400000100000
3s:13100001..13200000100000
3s:13200001..13300000100000
3s:13300001..13400000100000
3s:13400001..13500000100000
3s:13500001..13600000100000
3s:13600001..13700000100000
3s:13700001..13800000100000
3s:13800001..13900000100000
3s:13900001..14000000100000
3s:14000001..14100000100000
3s:1400001..1500000100000
3s:14100001..14200000100000
3s:14200001..14300000100000
3s:14300001..14400000100000
3s:14400001..14500000100000
3s:14500001..14600000100000
3s:14600001..14700000100000
3s:14700001..14800000100000
3s:14800001..14900000100000
3s:14900001..15000000100000
3s:15000001..15100000100000
3s:1500001..1600000100000
3s:15100001..15200000100000
3s:15200001..15300000100000
3s:15300001..15400000100000
3s:15400001..15500000100000
3s:15500001..15600000100000
3s:15600001..15700000100000
3s:15700001..15800000100000
3s:15800001..15900000100000
3s:15900001..16000000100000
3s:16000001..16100000100000
3s:1600001..1700000100000
3s:16100001..16200000100000
3s:16200001..16300000100000
3s:16300001..16400000100000
3s:16400001..16500000100000
3s:16500001..16600000100000
3s:16600001..16700000100000
3s:16700001..16800000100000
3s:16800001..16900000100000
3s:16900001..17000000100000
3s:17000001..17100000100000
3s:1700001..1800000100000
3s:17100001..17200000100000
3s:17200001..17300000100000
3s:17300001..17400000100000
3s:17400001..17500000100000
3s:17500001..17600000100000
3s:17600001..17700000100000
3s:17700001..17800000100000
3s:17800001..17900000100000
3s:17900001..18000000100000
3s:18000001..18100000100000
3s:1800001..1900000100000
3s:18100001..18200000100000
3s:18200001..18300000100000
3s:18300001..18400000100000
3s:18400001..18500000100000
3s:18500001..18600000100000
3s:18600001..18700000100000
3s:18700001..18800000100000
3s:18800001..18900000100000
3s:18900001..19000000100000
3s:19000001..19100000100000
3s:1900001..2000000100000
3s:19100001..19200000100000
3s:19200001..19300000100000
3s:19300001..19400000100000
3s:19400001..19500000100000
3s:19500001..19600000100000
3s:19600001..19700000100000
3s:19700001..19800000100000
3s:19800001..19900000100000
3s:19900001..20000000100000
3s:20000001..20100000100000
3s:2000001..2100000100000
3s:200001..300000100000
3s:20100001..20200000100000
3s:20200001..20300000100000
3s:20300001..20400000100000
3s:20400001..20500000100000
3s:20500001..20600000100000
3s:20600001..20700000100000
3s:20700001..20800000100000
3s:20800001..20900000100000
3s:20900001..21000000100000
3s:21000001..21100000100000
3s:2100001..2200000100000
3s:21100001..21200000100000
3s:21200001..21300000100000
3s:21300001..21400000100000
3s:21400001..21500000100000
3s:21500001..21600000100000
3s:21600001..21700000100000
3s:21700001..21800000100000
3s:21800001..21900000100000
3s:21900001..22000000100000
3s:22000001..22100000100000
3s:2200001..2300000100000
3s:22100001..22200000100000
3s:22200001..22300000100000
3s:22300001..22400000100000
3s:22400001..22500000100000
3s:22500001..22600000100000
3s:22600001..22700000100000
3s:22700001..22800000100000
3s:22800001..22900000100000
3s:22900001..23000000100000
3s:23000001..23100000100000
3s:2300001..2400000100000
3s:23100001..23200000100000
3s:23200001..23300000100000
3s:23300001..23400000100000
3s:23400001..23500000100000
3s:23500001..23600000100000
3s:23600001..23700000100000
3s:23700001..23800000100000
3s:23800001..23900000100000
3s:23900001..24000000100000
3s:24000001..24100000100000
3s:2400001..2500000100000
3s:24100001..24200000100000
3s:24200001..24300000100000
3s:24300001..24400000100000
3s:24400001..24500000100000
3s:24500001..24600000100000
3s:24600001..24700000100000
3s:24700001..24800000100000
3s:24800001..24900000100000
3s:24900001..25000000100000
3s:25000001..25100000100000
3s:2500001..2600000100000
3s:25100001..25200000100000
3s:25200001..25300000100000
3s:25300001..25400000100000
3s:25400001..25500000100000
3s:25500001..25600000100000
3s:25600001..25700000100000
3s:25700001..25800000100000
3s:25800001..25900000100000
3s:25900001..26000000100000
3s:26000001..26100000100000
3s:2600001..2700000100000
3s:26100001..2619541995419
3s:2700001..2800000100000
3s:2800001..2900000100000
3s:2900001..3000000100000
3s:3000001..3100000100000
3s:300001..400000100000
3s:3100001..3200000100000
3s:3200001..3300000100000
3s:3300001..3400000100000
3s:3400001..3500000100000
3s:3500001..3600000100000
3s:3600001..3700000100000
3s:3700001..3800000100000
3s:3800001..3900000100000
3s:3900001..4000000100000
3s:4000001..4100000100000
3s:400001..500000100000
3s:4100001..4200000100000
3s:4200001..4300000100000
3s:4300001..4400000100000
3s:4400001..4500000100000
3s:4500001..4600000100000
3s:4600001..4700000100000
3s:4700001..4800000100000
3s:4800001..4900000100000
3s:4900001..5000000100000
3s:5000001..5100000100000
3s:500001..600000100000
3s:5100001..5200000100000
3s:5200001..5300000100000
3s:5300001..5400000100000
3s:5400001..5500000100000
3s:5500001..5600000100000
3s:5600001..5700000100000
3s:5700001..5800000100000
3s:5800001..5900000100000
3s:5900001..6000000100000
3s:6000001..6100000100000
3s:600001..700000100000
3s:6100001..6200000100000
3s:6200001..6300000100000
3s:6300001..6400000100000
3s:6400001..6500000100000
3s:6500001..6600000100000
3s:6600001..6700000100000
3s:6700001..6800000100000
3s:6800001..6900000100000
3s:6900001..7000000100000
3s:7000001..7100000100000
3s:700001..800000100000
3s:7100001..7200000100000
3s:7200001..7300000100000
3s:7300001..7400000100000
3s:7400001..7500000100000
3s:7500001..7600000100000
3s:7600001..7700000100000
3s:7700001..7800000100000
3s:7800001..7900000100000
3s:7900001..8000000100000
3s:8000001..8100000100000
3s:800001..900000100000
3s:8100001..8200000100000
3s:8200001..8300000100000
3s:8300001..8400000100000
3s:8400001..8500000100000
3s:8500001..8600000100000
3s:8600001..8700000100000
3s:8700001..8800000100000
3s:8800001..8900000100000
3s:8900001..9000000100000
3s:9000001..9100000100000
3s:900001..1000000100000
3s:9100001..9200000100000
3s:9200001..9300000100000
3s:9300001..9400000100000
3s:9400001..9500000100000
3s:9500001..9600000100000
3s:9600001..9700000100000
3s:9700001..9800000100000
3s:9800001..9900000100000
3s:9900001..10000000100000
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis3s_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_officinalis_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata.html new file mode 100644 index 00000000..e769e34b --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata.html @@ -0,0 +1,111 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGI_PacBIO,
Database version:87.4
Base Pairs:422,391,326
Golden Path Length:422,391,326
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,443
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
61 sequences
+
+ +
+ + + +
SequenceLength (bp)
148196116
242391796
340826366
434321815
532501981
637950339
733104438
831250912
928723895
1027915717
1131610942
1230283698
UN-Ctg36365518
UN-Ctg37155778
UN-Ctg38151772
UN-Ctg39131053
UN-Ctg40119123
UN-Ctg4198710
UN-Ctg4296464
UN-Ctg4395309
UN-Ctg4493966
UN-Ctg4585563
UN-Ctg4679482
UN-Ctg4774524
UN-Ctg4873832
UN-Ctg4972033
UN-Ctg5070534
UN-Ctg5166963
UN-Ctg5260476
UN-Ctg5359204
UN-Ctg5457313
UN-Ctg5557041
UN-Ctg5656574
UN-Ctg5755668
UN-Ctg5854526
UN-Ctg5953794
UN-Ctg6053363
UN-Ctg6151294
UN-Ctg6246932
UN-Ctg6348742
UN-Ctg6448628
UN-Ctg6548523
UN-Ctg6648313
UN-Ctg6748276
UN-Ctg6846791
UN-Ctg6943546
UN-Ctg7043808
UN-Ctg7142550
UN-Ctg7242019
UN-Ctg7341150
UN-Ctg7440285
UN-Ctg7539977
UN-Ctg7639429
UN-Ctg7738880
UN-Ctg7838117
UN-Ctg7938232
UN-Ctg8035275
UN-Ctg8128298
UN-Ctg8227050
UN-Ctg8325138
UN-Ctg8423475
+
+
chunk4254 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_punctata_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon.html new file mode 100644 index 00000000..27a581b1 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon.html @@ -0,0 +1,66 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OR_W1943, Aug 2013
Database version:87.11
Base Pairs:338,040,714
Golden Path Length:338,040,714
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-OGE
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		37,071
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:50,219
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
139866532
233962743
334446443
430521686
526652778
627870862
726200591
825958679
920482102
1020731201
1127785585
1223561512
+
+
chunk3386 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s.html new file mode 100644 index 00000000..417e3fc1 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s.html @@ -0,0 +1,44 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:chr3s,
Database version:75.02
:
:
Genebuild by: CSHL
Genebuild method: Fgenesh
Genebuild started: Apr 2011
Genebuild released: Apr 2011
Genebuild last updated/patched: Apr 2011
Genebuild version: 2011-04-CSHL

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
rufipogon_3s19684009
+
+
scaffold4491 sequences
contig6581 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon3s_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop40.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop40.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop40.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop500.html new file mode 100644 index 00000000..2eeb4930 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_rufipogon_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		14462425
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		13845528
3IPR000719
Protein kinase domain		13795258
4IPR032675
Leucine-rich repeat domain, L domain-like		12936271
5IPR008271
Serine/threonine-protein kinase, active site		11171683
6IPR017441
Protein kinase, ATP binding site		9601419
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		7881445
8IPR013083
Zinc finger, RING/FYVE/PHD-type		677962
9IPR001810
F-box domain		6702635
10IPR011990
Tetratricopeptide-like helical		6012609
11IPR002885
Pentatricopeptide repeat		48913926
12IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		469920
13IPR002182
NB-ARC		460708
14IPR001611
Leucine-rich repeat		4463329
15IPR001841
Zinc finger, RING-type		4261403
16IPR009057
Homeodomain-like		4011073
17IPR016040
NAD(P)-binding domain		3911370
18IPR029058
Alpha/Beta hydrolase fold		3721345
19IPR016024
Armadillo-type fold		3681373
20IPR013210
Leucine-rich repeat-containing N-terminal, type 2		319416
21IPR001128
Cytochrome P450		3172556
22IPR003591
Leucine-rich repeat, typical subtype		3132895
23IPR012677
Nucleotide-binding, alpha-beta plait		3111270
24IPR011989
Armadillo-like helical		280860
25IPR003593
AAA+ ATPase domain		276583
26IPR015943
WD40/YVTN repeat-like-containing domain		273690
27IPR000504
RNA recognition motif domain		2681637
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		265937
29IPR017853
Glycoside hydrolase, superfamily		264445
30IPR002401
Cytochrome P450, E-class, group I		2612003
31IPR001005
SANT/Myb domain		253735
32IPR020846
Major facilitator superfamily domain		251808
33IPR017972
Cytochrome P450, conserved site		248353
34IPR017986
WD40-repeat-containing domain		244956
35IPR001680
WD40 repeat		2303560
36IPR012336
Thioredoxin-like fold		227723
37IPR013781
Glycoside hydrolase, catalytic domain		223380
38IPR017930
Myb domain		202330
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		199590
40IPR011992
EF-hand domain pair		196618
41IPR011991
Winged helix-turn-helix DNA-binding domain		182416
42IPR002048
EF-hand domain		1781374
43IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		178904
44IPR016177
DNA-binding domain		176267
45IPR023214
HAD-like domain		171739
46IPR007087
Zinc finger, C2H2		165612
47IPR020683
Ankyrin repeat-containing domain		1651109
48IPR018247
EF-Hand 1, calcium-binding site		164457
49IPR001471
AP2/ERF domain		1611102
50IPR011333
BTB/POZ fold		159262
51IPR002110
Ankyrin repeat		1541648
52IPR003441
NAC domain		144478
53IPR029044
Nucleotide-diphospho-sugar transferases		142476
54IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		142358
55IPR014001
Helicase, superfamily 1/2, ATP-binding domain		141440
56IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		140243
57IPR023213
Chloramphenicol acetyltransferase-like domain		140298
58IPR001650
Helicase, C-terminal		139640
59IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		138774
60IPR019775
WD40 repeat, conserved site		133342
61IPR005174
Protein of unknown function DUF295		132174
62IPR013026
Tetratricopeptide repeat-containing domain		128230
63IPR012340
Nucleic acid-binding, OB-fold		127254
64IPR008974
TRAF-like		125337
65IPR003439
ABC transporter-like		124595
66IPR019734
Tetratricopeptide repeat		1231282
67IPR001623
DnaJ domain		121983
68IPR012337
Ribonuclease H-like domain		121365
69IPR013830
SGNH hydrolase-type esterase domain		120500
70IPR000210
BTB/POZ domain		119547
71IPR014710
RmlC-like jelly roll fold		119206
72IPR003480
Transferase		119153
73IPR029071
Ubiquitin-related domain		115149
74IPR021109
Aspartic peptidase domain		114472
75IPR003959
ATPase, AAA-type, core		114187
76IPR025315
Domain of unknown function DUF4220		114121
77IPR013785
Aldolase-type TIM barrel		113249
78IPR025287
Wall-associated receptor kinase galacturonan-binding domain		113194
79IPR001480
Bulb-type lectin domain		111906
80IPR000008
C2 domain		108924
81IPR001461
Aspartic peptidase		107376
82IPR005123
Oxoglutarate/iron-dependent dioxygenase		105282
83IPR011050
Pectin lyase fold/virulence factor		105121
84IPR012334
Pectin lyase fold		105127
85IPR011011
Zinc finger, FYVE/PHD-type		104162
86IPR033121
Peptidase family A1 domain		102150
87IPR008972
Cupredoxin		101487
88IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		101144
89IPR015424
Pyridoxal phosphate-dependent transferase		101143
90IPR005225
Small GTP-binding protein domain		99123
91IPR003657
DNA-binding WRKY		99686
92IPR032799
Xylanase inhibitor, C-terminal		97127
93IPR015300
DNA-binding pseudobarrel domain		96345
94IPR027443
Isopenicillin N synthase-like		95159
95IPR032861
Xylanase inhibitor, N-terminal		95126
96IPR032867
DYW domain		95105
97IPR001932
Protein phosphatase 2C (PP2C)-like domain		95742
98IPR001087
Lipase, GDSL		93119
99IPR007658
Protein of unknown function DUF594		9399
100IPR000109
Proton-dependent oligopeptide transporter family		90293
101IPR001356
Homeobox domain		90280
102IPR005828
General substrate transporter		88143
103IPR011051
RmlC-like cupin domain		88152
104IPR000858
S-locus glycoprotein		87138
105IPR003609
Apple-like		87369
106IPR017871
ABC transporter, conserved site		87165
107IPR017907
Zinc finger, RING-type, conserved site		87123
108IPR006447
Myb domain, plants		86103
109IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		86143
110IPR004827
Basic-leucine zipper domain		84381
111IPR015880
Zinc finger, C2H2-like		84266
112IPR000073
Alpha/beta hydrolase fold-1		83228
113IPR015655
Protein phosphatase 2C		83188
114IPR011676
Domain of unknown function DUF1618		82113
115IPR000742
Epidermal growth factor-like domain		82298
116IPR009072
Histone-fold		82182
117IPR020472
G-protein beta WD-40 repeat		81384
118IPR001220
Legume lectin domain		81102
119IPR006121
Heavy metal-associated domain, HMA		80244
120IPR002347
Glucose/ribitol dehydrogenase		80977
121IPR026992
Non-haem dioxygenase N-terminal domain		80112
122IPR001965
Zinc finger, PHD-type		80169
123IPR026961
PGG domain		79173
124IPR002083
MATH/TRAF domain		79235
125IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		79115
126IPR003340
B3 DNA binding domain		78435
127IPR017451
F-box associated interaction domain		7790
128IPR000270
Phox/Bem1p		76154
129IPR012871
Protein of unknown function DUF1677, Oryza sativa		7592
130IPR003613
U box domain		75270
131IPR000626
Ubiquitin domain		73206
132IPR013766
Thioredoxin domain		73182
133IPR002100
Transcription factor, MADS-box		73745
134IPR002902
Gnk2-homologous domain		72427
135IPR010987
Glutathione S-transferase, C-terminal-like		72344
136IPR016039
Thiolase-like		71344
137IPR018097
EGF-like calcium-binding, conserved site		70106
138IPR000571
Zinc finger, CCCH-type		70741
139IPR001881
EGF-like calcium-binding domain		69178
140IPR006501
Pectinesterase inhibitor domain		69312
141IPR011993
Pleckstrin homology-like domain		69196
142IPR006566
FBD domain		68104
143IPR004158
Protein of unknown function DUF247, plant		6878
144IPR000225
Armadillo		68662
145IPR024171
S-receptor-like serine/threonine-protein kinase		6769
146IPR015500
Peptidase S8, subtilisin-related		67346
147IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		67244
148IPR009009
RlpA-like double-psi beta-barrel domain		66220
149IPR003960
ATPase, AAA-type, conserved site		6592
150IPR013057
Amino acid transporter, transmembrane		6586
151IPR016159
Cullin repeat-like-containing domain		65105
152IPR000048
IQ motif, EF-hand binding site		65554
153IPR008949
Terpenoid synthase		64208
154IPR005829
Sugar transporter, conserved site		64131
155IPR029052
Metallo-dependent phosphatase-like		64234
156IPR020568
Ribosomal protein S5 domain 2-type fold		63102
157IPR023395
Mitochondrial carrier domain		63179
158IPR004045
Glutathione S-transferase, N-terminal		63224
159IPR000490
Glycoside hydrolase, family 17		63133
160IPR001806
Small GTPase superfamily		6386
161IPR018108
Mitochondrial substrate/solute carrier		62452
162IPR005202
Transcription factor GRAS		61135
163IPR013128
Peptidase C1A		6084
164IPR026057
PC-Esterase		6088
165IPR007117
Expansin, cellulose-binding-like domain		60267
166IPR009003
Trypsin-like cysteine/serine peptidase domain		60131
167IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5991
168IPR004864
Late embryogenesis abundant protein, LEA-14		5963
169IPR003663
Sugar/inositol transporter		59407
170IPR016135
Ubiquitin-conjugating enzyme/RWD-like		58171
171IPR029962
Trichome birefringence-like family		5797
172IPR013763
Cyclin-like		57472
173IPR019787
Zinc finger, PHD-finger		57135
174IPR008979
Galactose-binding domain-like		57186
175IPR025846
PMR5 N-terminal domain		5776
176IPR001878
Zinc finger, CCHC-type		57449
177IPR001563
Peptidase S10, serine carboxypeptidase		56453
178IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		56100
179IPR007112
Expansin/pollen allergen, DPBB domain		56119
180IPR024788
Malectin-like carbohydrate-binding domain		56108
181IPR010259
Proteinase inhibitor I9		55137
182IPR006553
Leucine-rich repeat, cysteine-containing subtype		55479
183IPR027640
Kinesin-like protein		55259
184IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		55118
185IPR019786
Zinc finger, PHD-type, conserved site		5581
186IPR003676
Auxin-induced protein, ARG7		5572
187IPR017877
Myb-like domain		5574
188IPR000209
Peptidase S8/S53 domain		55539
189IPR023393
START-like domain		5477
190IPR022059
Protein of unknown function DUF3615		5485
191IPR003245
Plastocyanin-like		54202
192IPR001752
Kinesin, motor domain		54759
193IPR016181
Acyl-CoA N-acyltransferase		53142
194IPR010255
Haem peroxidase		5391
195IPR013094
Alpha/beta hydrolase fold-3		5365
196IPR002921
Lipase, class 3		5262
197IPR011032
GroES (chaperonin 10)-like		52140
198IPR002528
Multi antimicrobial extrusion protein		52204
199IPR030184
WAT1-related protein		5286
200IPR000620
Drug/metabolite transporter		52138
201IPR013525
ABC-2 type transporter		51141
202IPR013201
Proteinase inhibitor I29, cathepsin propeptide		51146
203IPR014014
RNA helicase, DEAD-box type, Q motif		5174
204IPR004140
Exocyst complex protein Exo70		51144
205IPR002035
von Willebrand factor, type A		51277
206IPR002016
Haem peroxidase, plant/fungal/bacterial		51329
207IPR012946
X8 domain		50148
208IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		5063
209IPR004265
Plant disease resistance response protein		5052
210IPR018253
DnaJ domain, conserved site		5059
211IPR006045
Cupin 1		50178
212IPR000668
Peptidase C1A, papain C-terminal		50272
213IPR008978
HSP20-like chaperone		49104
214IPR000608
Ubiquitin-conjugating enzyme, E2		49119
215IPR007118
Expansin/Lol pI		49285
216IPR008250
P-type ATPase, A domain		49191
217IPR006016
UspA		4854
218IPR011527
ABC transporter type 1, transmembrane domain		48415
219IPR023299
P-type ATPase, cytoplasmic domain N		48139
220IPR011042
Six-bladed beta-propeller, TolB-like		4776
221IPR009060
UBA-like		4656
222IPR001509
NAD-dependent epimerase/dehydratase		4698
223IPR016166
FAD-binding, type 2		4698
224IPR008928
Six-hairpin glycosidase-like		4679
225IPR001906
Terpene synthase, N-terminal domain		46147
226IPR000070
Pectinesterase, catalytic		4655
227IPR033389
AUX/IAA domain		4561
228IPR000873
AMP-dependent synthetase/ligase		4574
229IPR005630
Terpene synthase, metal-binding domain		4572
230IPR011006
CheY-like superfamily		4568
231IPR023828
Peptidase S8, subtilisin, Ser-active site		4585
232IPR001757
Cation-transporting P-type ATPase		45251
233IPR000743
Glycoside hydrolase, family 28		4573
234IPR001789
Signal transduction response regulator, receiver domain		45172
235IPR000182
GNAT domain		4491
236IPR011701
Major facilitator superfamily		4492
237IPR018303
P-type ATPase, phosphorylation site		4466
238IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4466
239IPR029055
Nucleophile aminohydrolases, N-terminal		43109
240IPR000152
EGF-type aspartate/asparagine hydroxylation site		4371
241IPR017970
Homeobox, conserved site		4346
242IPR014756
Immunoglobulin E-set		4363
243IPR001214
SET domain		43189
244IPR004853
Triose-phosphate transporter domain		4250
245IPR000330
SNF2-related		4270
246IPR003594
Histidine kinase-like ATPase, ATP-binding domain		42259
247IPR004088
K Homology domain, type 1		42455
248IPR002109
Glutaredoxin		4286
249IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4263
250IPR009000
Translation protein, beta-barrel domain		4163
251IPR001938
Thaumatin		41400
252IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4148
253IPR011707
Multicopper oxidase, type 3		4151
254IPR001117
Multicopper oxidase, type 1		4052
255IPR015916
Galactose oxidase, beta-propeller		4051
256IPR029021
Protein-tyrosine phosphatase-like		40159
257IPR029045
ClpP/crotonase-like domain		40212
258IPR020845
AMP-binding, conserved site		4060
259IPR011706
Multicopper oxidase, type 2		4050
260IPR011043
Galactose oxidase/kelch, beta-propeller		4051
261IPR015947
PUA-like domain		4066
262IPR002068
Alpha crystallin/Hsp20 domain		3974
263IPR003137
Protease-associated domain, PA		3952
264IPR004263
Exostosin-like		3949
265IPR027356
NPH3 domain		3975
266IPR011012
Longin-like domain		3958
267IPR006671
Cyclin, N-terminal		39116
268IPR000644
CBS domain		39311
269IPR001574
Ribosome-inactivating protein		39106
270IPR008942
ENTH/VHS		38103
271IPR010402
CCT domain		3889
272IPR004041
NAF domain		3847
273IPR016461
Caffeate O-methyltransferase (COMT) family		3871
274IPR018451
NAF/FISL domain		3846
275IPR013783
Immunoglobulin-like fold		3857
276IPR001077
O-methyltransferase, family 2		3848
277IPR002495
Glycosyl transferase, family 8		3855
278IPR008889
VQ		3839
279IPR025322
Protein of unknown function DUF4228, plant		3738
280IPR025659
Tubby C-terminal-like domain		3759
281IPR001969
Aspartic peptidase, active site		3769
282IPR005135
Endonuclease/exonuclease/phosphatase		37253
283IPR020904
Short-chain dehydrogenase/reductase, conserved site		3754
284IPR004839
Aminotransferase, class I/classII		3749
285IPR004883
Lateral organ boundaries, LOB		3777
286IPR031107
Small heat shock protein HSP20		3740
287IPR019378
GDP-fucose protein O-fucosyltransferase		3750
288IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3757
289IPR004314
Domain of unknown function DUF239		3748
290IPR000823
Plant peroxidase		37264
291IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3738
292IPR006626
Parallel beta-helix repeat		36188
293IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3657
294IPR013126
Heat shock protein 70 family		36281
295IPR002487
Transcription factor, K-box		36128
296IPR013154
Alcohol dehydrogenase GroES-like		3537
297IPR006652
Kelch repeat type 1		35159
298IPR019794
Peroxidase, active site		3554
299IPR006094
FAD linked oxidase, N-terminal		3540
300IPR006458
Ovate protein family, C-terminal		3599
301IPR002912
ACT domain		35119
302IPR012967
Plant methyltransferase dimerisation		3538
303IPR011016
Zinc finger, RING-CH-type		3492
304IPR001296
Glycosyl transferase, family 1		3447
305IPR023271
Aquaporin-like		3493
306IPR008266
Tyrosine-protein kinase, active site		3452
307IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		3435
308IPR000425
Major intrinsic protein		34324
309IPR002067
Mitochondrial carrier protein		34198
310IPR023298
P-type ATPase, transmembrane domain		34114
311IPR025661
Cysteine peptidase, asparagine active site		3447
312IPR013149
Alcohol dehydrogenase, C-terminal		3344
313IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3337
314IPR022742
Putative lysophospholipase		3348
315IPR000863
Sulfotransferase domain		3348
316IPR016167
FAD-binding, type 2, subdomain 1		3338
317IPR004087
K Homology domain		33109
318IPR015915
Kelch-type beta propeller		3359
319IPR020843
Polyketide synthase, enoylreductase		3339
320IPR012341
Six-hairpin glycosidase		3350
321IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		3299
322IPR019821
Kinesin, motor region, conserved site		3253
323IPR007493
Protein of unknown function DUF538		32120
324IPR001251
CRAL-TRIO domain		32209
325IPR033131
Pectinesterase, Asp active site		3234
326IPR014720
Double-stranded RNA-binding domain		32215
327IPR001223
Glycoside hydrolase, family 18, catalytic domain		3236
328IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		32143
329IPR006073
GTP binding domain		3297
330IPR018490
Cyclic nucleotide-binding-like		3146
331IPR032710
NTF2-like domain		3170
332IPR001360
Glycoside hydrolase, family 1		31436
333IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		3182
334IPR003690
Mitochodrial transcription termination factor-related		31290
335IPR027923
Hydrophobic seed protein		3137
336IPR022357
Major intrinsic protein, conserved site		3137
337IPR000169
Cysteine peptidase, cysteine active site		3149
338IPR003311
AUX/IAA protein		3145
339IPR000595
Cyclic nucleotide-binding domain		31115
340IPR025660
Cysteine peptidase, histidine active site		3146
341IPR006311
Twin-arginine translocation pathway, signal sequence		3132
342IPR000315
Zinc finger, B-box		30126
343IPR001478
PDZ domain		30116
344IPR002423
Chaperonin Cpn60/TCP-1		3048
345IPR012675
Beta-grasp domain		3035
346IPR003406
Glycosyl transferase, family 14		3041
347IPR016072
SKP1 component, dimerisation		3063
348IPR019793
Peroxidases heam-ligand binding site		3051
349IPR027409
GroEL-like apical domain		3092
350IPR005746
Thioredoxin		3052
351IPR004046
Glutathione S-transferase, C-terminal		3056
352IPR016138
Ribosome-inactivating protein, subdomain 1		3031
353IPR001099
Chalcone/stilbene synthase, N-terminal		3036
354IPR001929
Germin		2994
355IPR005299
SAM dependent carboxyl methyltransferase		2960
356IPR008991
Translation protein SH3-like domain		2930
357IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2937
358IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2970
359IPR011013
Galactose mutarotase-like domain		2946
360IPR002963
Expansin		29249
361IPR007125
Histone core		2932
362IPR008480
Protein of unknown function DUF761, plant		2929
363IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2943
364IPR003851
Zinc finger, Dof-type		29119
365IPR018202
Peptidase S10, serine carboxypeptidase, active site		2935
366IPR000757
Glycoside hydrolase, family 16		2975
367IPR001229
Mannose-binding lectin		29283
368IPR000727
Target SNARE coiled-coil domain		28100
369IPR006153
Cation/H+ exchanger		2838
370IPR013088
Zinc finger, NHR/GATA-type		2835
371IPR002659
Glycosyl transferase, family 31		2877
372IPR000795
Elongation factor, GTP-binding domain		28210
373IPR007650
Protein of unknown function DUF581		2833
374IPR031112
AP2-like ethylene-responsive transcription factor		2847
375IPR002123
Phospholipid/glycerol acyltransferase		2857
376IPR005150
Cellulose synthase		2854
377IPR033443
Pentacotripeptide-repeat region of PROPR		2841
378IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2845
379IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2849
380IPR029047
Heat shock protein 70kD, peptide-binding domain		2879
381IPR000679
Zinc finger, GATA-type		28121
382IPR025110
AMP-binding enzyme C-terminal domain		2739
383IPR000782
FAS1 domain		27162
384IPR013601
FAE1/Type III polyketide synthase-like protein		2728
385IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2751
386IPR029000
Cyclophilin-like domain		2772
387IPR029061
Thiamin diphosphate-binding fold		27136
388IPR019557
Aminotransferase-like, plant mobile domain		2729
389IPR005333
Transcription factor, TCP		2727
390IPR009030
Insulin-like growth factor binding protein, N-terminal		2749
391IPR033124
Serine carboxypeptidases, histidine active site		2739
392IPR000408
Regulator of chromosome condensation, RCC1		27716
393IPR004367
Cyclin, C-terminal domain		2787
394IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2780
395IPR005821
Ion transport domain		2734
396IPR014044
CAP domain		27128
397IPR012328
Chalcone/stilbene synthase, C-terminal		2731
398IPR003855
K+ potassium transporter		2760
399IPR023210
NADP-dependent oxidoreductase domain		27150
400IPR005175
Domain of unknown function DUF296		2756
401IPR010525
Auxin response factor		2738
402IPR017938
Riboflavin synthase-like beta-barrel		2641
403IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		26181
404IPR013187
F-box associated domain, type 3		2628
405IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2689
406IPR001357
BRCT domain		26360
407IPR010920
Like-Sm (LSM) domain		2631
408IPR027725
Heat shock transcription factor family		2642
409IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		2688
410IPR002355
Multicopper oxidase, copper-binding site		2633
411IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2628
412IPR004014
Cation-transporting P-type ATPase, N-terminal		2657
413IPR001849
Pleckstrin homology domain		2690
414IPR001232
SKP1 component		2630
415IPR029062
Class I glutamine amidotransferase-like		2697
416IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2633
417IPR031127
E3 ubiquitin ligase RBR family		2644
418IPR002913
START domain		26101
419IPR001395
Aldo/keto reductase		2652
420IPR017927
Ferredoxin reductase-type FAD-binding domain		2533
421IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2526
422IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2591
423IPR007657
Glycosyltransferase AER61, uncharacterised		2530
424IPR001279
Beta-lactamase-like		25205
425IPR006379
HAD-superfamily hydrolase, subfamily IIB		2535
426IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		25126
427IPR001876
Zinc finger, RanBP2-type		25291
428IPR004813
Oligopeptide transporter, OPT superfamily		2589
429IPR029069
HotDog domain		25103
430IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2550
431IPR001701
Glycoside hydrolase, family 9		2531
432IPR025486
Domain of unknown function DUF4378		2535
433IPR000232
Heat shock factor (HSF)-type, DNA-binding		25152
434IPR003100
Argonaute/Dicer protein, PAZ domain		24223
435IPR000528
Plant lipid transfer protein/Par allergen		24115
436IPR003954
RNA recognition motif domain, eukaryote		2462
437IPR004162
E3 ubiquitin-protein ligase SINA like		2430
438IPR008422
Homeobox KN domain		2432
439IPR013216
Methyltransferase type 11		2428
440IPR012416
Calmodulin binding protein-like		2429
441IPR018181
Heat shock protein 70, conserved site		2478
442IPR011074
CRAL/TRIO, N-terminal domain		2494
443IPR001763
Rhodanese-like domain		24131
444IPR003337
Trehalose-phosphatase		2460
445IPR025875
Leucine rich repeat 4		2427
446IPR017937
Thioredoxin, conserved site		2439
447IPR019780
Germin, manganese binding site		2434
448IPR013780
Glycosyl hydrolase, family 13, all-beta		2436
449IPR013323
SIAH-type domain		2434
450IPR006439
HAD hydrolase, subfamily IA		24113
451IPR001487
Bromodomain		24269
452IPR015797
NUDIX hydrolase domain-like		2455
453IPR006867
Domain of unknown function DUF632		2426
454IPR017884
SANT domain		2337
455IPR010666
Zinc finger, GRF-type		2329
456IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		23101
457IPR016073
SKP1 component, POZ domain		2327
458IPR003106
Leucine zipper, homeobox-associated		2334
459IPR002867
Zinc finger, C6HC-type		23123
460IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		2325
461IPR004316
SWEET sugar transporter		2347
462IPR001024
PLAT/LH2 domain		23109
463IPR025753
AAA-type ATPase, N-terminal domain		2326
464IPR017887
Transcription factor TCP subgroup		2323
465IPR033275
E3 ubiquitin-protein ligase MARCH-like		2329
466IPR001041
2Fe-2S ferredoxin-type domain		2367
467IPR008971
HSP40/DnaJ peptide-binding		2268
468IPR006593
Cytochrome b561/ferric reductase transmembrane		2266
469IPR033138
Multicopper oxidases, conserved site		2225
470IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		2230
471IPR021790
Protein of unknown function DUF3355		2224
472IPR020103
Pseudouridine synthase, catalytic domain		2259
473IPR023313
Ubiquitin-conjugating enzyme, active site		2226
474IPR004776
Auxin efflux carrier		2235
475IPR014722
Ribosomal protein L2 domain 2		2222
476IPR002939
Chaperone DnaJ, C-terminal		2234
477IPR000086
NUDIX hydrolase domain		2248
478IPR029006
ADF-H/Gelsolin-like domain		22103
479IPR002937
Amine oxidase		2229
480IPR029033
Histidine phosphatase superfamily		22117
481IPR023329
Chlorophyll a/b binding protein domain		2226
482IPR006689
Small GTPase superfamily, ARF/SAR type		21110
483IPR013328
Dehydrogenase, multihelical		2135
484IPR008962
PapD-like		2163
485IPR002403
Cytochrome P450, E-class, group IV		21102
486IPR007612
LURP1-like domain		2133
487IPR001107
Band 7 protein		2171
488IPR013581
Plant PDR ABC transporter associated		2143
489IPR000253
Forkhead-associated (FHA) domain		21104
490IPR000340
Dual specificity phosphatase, catalytic domain		2128
491IPR008914
Phosphatidylethanolamine-binding protein PEBP		2172
492IPR005516
Remorin, C-terminal		2121
493IPR014977
WRC domain		2148
494IPR001353
Proteasome, subunit alpha/beta		2126
495IPR027413
GroEL-like equatorial domain		2159
496IPR025422
Transcription factor TGA like domain		2143
497IPR010989
t-SNARE		2127
498IPR002293
Amino acid/polyamine transporter I		2182
499IPR003008
Tubulin/FtsZ, GTPase domain		21101
500IPR000300
Inositol polyphosphate-related phosphatase		2131
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa.html new file mode 100644 index 00000000..5aa31497 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa.html @@ -0,0 +1,70 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:IRGSP-1.0, Aug 2013
Database version:87.7
Base Pairs:373,245,519
Golden Path Length:373,245,519
Genebuild by: Maker
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09-Maker
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		38,550
Long Non coding genes:6,811
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:57,378
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
143270923
235937250
336413819
435502694
529958434
631248787
729697621
828443022
923012720
1023207287
1129021106
1227531856
+
+
chunk3740 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa_IPtop500.html new file mode 100644 index 00000000..6ddb91dd --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Oryza_sativa_IPtop500.html @@ -0,0 +1,6 @@ + + + + + +
No InterPro data
diff --git a/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus.html b/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus.html new file mode 100644 index 00000000..e1f5151a --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus.html @@ -0,0 +1,110 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM9206v1, Jan 2011
Database version:86.1
Base Pairs:13,204,888
Golden Path Length:13,204,888
Genebuild by: EnsemblPlants
Genebuild method: Generated from ENA annotation
Genebuild started: Apr 2007
Genebuild released: Apr 2007
Genebuild last updated/patched: Jan 2011
Genebuild version: 2011-01-EnsemblPlants
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		7,603
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		37
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:7,640
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
21 sequences
+
+ +
+ + + +
SequenceLength (bp)
11152508
2895087
3982987
4930724
5847696
6818664
7783246
8701771
9670853
10613585
11593542
12538963
13528469
14708927
15468366
16428333
17366173
18149386
19154676
20549133
21321799
+
+
contig
+
21 sequences
+
+ +
+ + + +
SequenceLength (bp)
CP000581.11152508
CP000582.1895087
CP000583.1982987
CP000584.1930724
CP000585.1847696
CP000586.1818664
CP000587.1783246
CP000588.1701771
CP000589.1670853
CP000590.1613585
CP000591.1593542
CP000592.1538963
CP000593.1528469
CP000594.1708927
CP000595.1468366
CP000596.1428333
CP000597.1366173
CP000598.1149386
CP000599.1154676
CP000600.1549133
CP000601.1321799
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus_IPtop500.html new file mode 100644 index 00000000..5cd89390 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Ostreococcus_lucimarinus_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		4631419
2IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		169402
3IPR011009
Protein kinase-like domain		148180
4IPR015943
WD40/YVTN repeat-like-containing domain		146235
5IPR016040
NAD(P)-binding domain		145364
6IPR011990
Tetratricopeptide-like helical		137421
7IPR016024
Armadillo-type fold		133339
8IPR017986
WD40-repeat-containing domain		132312
9IPR003593
AAA+ ATPase domain		127165
10IPR000719
Protein kinase domain		121319
11IPR001680
WD40 repeat		1171193
12IPR014001
Helicase, superfamily 1/2, ATP-binding domain		103202
13IPR013083
Zinc finger, RING/FYVE/PHD-type		100112
14IPR001650
Helicase, C-terminal		99297
15IPR011989
Armadillo-like helical		91207
16IPR008271
Serine/threonine-protein kinase, active site		8888
17IPR012336
Thioredoxin-like fold		82181
18IPR029058
Alpha/Beta hydrolase fold		82208
19IPR020683
Ankyrin repeat-containing domain		77281
20IPR012677
Nucleotide-binding, alpha-beta plait		76208
21IPR019775
WD40 repeat, conserved site		75138
22IPR013026
Tetratricopeptide repeat-containing domain		7595
23IPR019734
Tetratricopeptide repeat		72409
24IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		7072
25IPR012340
Nucleic acid-binding, OB-fold		69105
26IPR000504
RNA recognition motif domain		67262
27IPR017441
Protein kinase, ATP binding site		6565
28IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		64269
29IPR001623
DnaJ domain		64402
30IPR023214
HAD-like domain		63183
31IPR013785
Aldolase-type TIM barrel		6167
32IPR011991
Winged helix-turn-helix DNA-binding domain		58108
33IPR003959
ATPase, AAA-type, core		5567
34IPR009057
Homeodomain-like		54127
35IPR002110
Ankyrin repeat		54299
36IPR001841
Zinc finger, RING-type		53125
37IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		5072
38IPR020846
Major facilitator superfamily domain		50100
39IPR003439
ABC transporter-like		46131
40IPR005225
Small GTP-binding protein domain		4546
41IPR018108
Mitochondrial substrate/solute carrier		43243
42IPR023395
Mitochondrial carrier domain		4389
43IPR002048
EF-hand domain		41206
44IPR020472
G-protein beta WD-40 repeat		41123
45IPR011992
EF-hand domain pair		41111
46IPR020568
Ribosomal protein S5 domain 2-type fold		4049
47IPR029044
Nucleotide-diphospho-sugar transferases		3879
48IPR013766
Thioredoxin domain		3867
49IPR018247
EF-Hand 1, calcium-binding site		3868
50IPR017871
ABC transporter, conserved site		3852
51IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		3739
52IPR015424
Pyridoxal phosphate-dependent transferase		3642
53IPR016181
Acyl-CoA N-acyltransferase		3573
54IPR001005
SANT/Myb domain		3575
55IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		3237
56IPR009000
Translation protein, beta-barrel domain		3137
57IPR013783
Immunoglobulin-like fold		3168
58IPR014014
RNA helicase, DEAD-box type, Q motif		3131
59IPR001214
SET domain		3168
60IPR032675
Leucine-rich repeat domain, L domain-like		3069
61IPR029071
Ubiquitin-related domain		3034
62IPR014756
Immunoglobulin E-set		3072
63IPR000182
GNAT domain		2853
64IPR005123
Oxoglutarate/iron-dependent dioxygenase		2846
65IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2828
66IPR006073
GTP binding domain		2877
67IPR011701
Major facilitator superfamily		2729
68IPR017853
Glycoside hydrolase, superfamily		2734
69IPR020103
Pseudouridine synthase, catalytic domain		2736
70IPR000571
Zinc finger, CCCH-type		27132
71IPR003347
JmjC domain		2653
72IPR002347
Glucose/ribitol dehydrogenase		26170
73IPR012337
Ribonuclease H-like domain		2651
74IPR029052
Metallo-dependent phosphatase-like		2665
75IPR014710
RmlC-like jelly roll fold		2535
76IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		2526
77IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		24136
78IPR029000
Cyclophilin-like domain		2449
79IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2445
80IPR029055
Nucleophile aminohydrolases, N-terminal		2449
81IPR003960
ATPase, AAA-type, conserved site		2426
82IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2433
83IPR002067
Mitochondrial carrier protein		24113
84IPR009072
Histone-fold		2448
85IPR004843
Calcineurin-like phosphoesterase domain, apaH type		2323
86IPR000330
SNF2-related		2325
87IPR022796
Chlorophyll A-B binding protein		2323
88IPR004088
K Homology domain, type 1		23157
89IPR001611
Leucine-rich repeat		23121
90IPR010920
Like-Sm (LSM) domain		2222
91IPR000795
Elongation factor, GTP-binding domain		22111
92IPR001763
Rhodanese-like domain		2299
93IPR000073
Alpha/beta hydrolase fold-1		2237
94IPR013781
Glycoside hydrolase, catalytic domain		2225
95IPR018253
DnaJ domain, conserved site		2222
96IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2239
97IPR017930
Myb domain		2236
98IPR001199
Cytochrome b5-like heme/steroid binding domain		21123
99IPR011011
Zinc finger, FYVE/PHD-type		2124
100IPR015797
NUDIX hydrolase domain-like		2139
101IPR007197
Radical SAM		2021
102IPR019787
Zinc finger, PHD-finger		2036
103IPR029045
ClpP/crotonase-like domain		2054
104IPR001965
Zinc finger, PHD-type		2028
105IPR008978
HSP20-like chaperone		1943
106IPR002885
Pentatricopeptide repeat		19268
107IPR013816
ATP-grasp fold, subdomain 2		1921
108IPR004147
UbiB domain		1919
109IPR017907
Zinc finger, RING-type, conserved site		1919
110IPR029033
Histidine phosphatase superfamily		1953
111IPR006620
Prolyl 4-hydroxylase, alpha subunit		1818
112IPR006195
Aminoacyl-tRNA synthetase, class II		1818
113IPR001163
Ribonucleoprotein LSM domain		1834
114IPR013216
Methyltransferase type 11		1818
115IPR016135
Ubiquitin-conjugating enzyme/RWD-like		1836
116IPR004087
K Homology domain		1838
117IPR032710
NTF2-like domain		1730
118IPR015353
Rubisco LSMT, substrate-binding domain		1749
119IPR001478
PDZ domain		1758
120IPR006145
Pseudouridine synthase, RsuA/RluB/C/D/E/F		1717
121IPR011993
Pleckstrin homology-like domain		1729
122IPR000626
Ubiquitin domain		1644
123IPR016123
Mog1/PsbP, alpha/beta/alpha sandwich		1631
124IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1616
125IPR008250
P-type ATPase, A domain		1634
126IPR001279
Beta-lactamase-like		1658
127IPR005135
Endonuclease/exonuclease/phosphatase		1666
128IPR013078
Histidine phosphatase superfamily, clade-1		1627
129IPR011012
Longin-like domain		1616
130IPR004045
Glutathione S-transferase, N-terminal		1632
131IPR018303
P-type ATPase, phosphorylation site		1616
132IPR023299
P-type ATPase, cytoplasmic domain N		1630
133IPR001757
Cation-transporting P-type ATPase		1645
134IPR019410
Nicotinamide N-methyltransferase-like		1616
135IPR017937
Thioredoxin, conserved site		1616
136IPR000086
NUDIX hydrolase domain		1631
137IPR023329
Chlorophyll a/b binding protein domain		1617
138IPR001932
Protein phosphatase 2C (PP2C)-like domain		16101
139IPR007502
Helicase-associated domain		1530
140IPR004853
Triose-phosphate transporter domain		1515
141IPR009060
UBA-like		1517
142IPR000608
Ubiquitin-conjugating enzyme, E2		1529
143IPR000008
C2 domain		15120
144IPR000717
Proteasome component (PCI) domain		1527
145IPR012675
Beta-grasp domain		1515
146IPR001353
Proteasome, subunit alpha/beta		1515
147IPR027640
Kinesin-like protein		1526
148IPR019786
Zinc finger, PHD-type, conserved site		1515
149IPR013815
ATP-grasp fold, subdomain 1		1520
150IPR005746
Thioredoxin		1524
151IPR010987
Glutathione S-transferase, C-terminal-like		1541
152IPR000644
CBS domain		1573
153IPR001752
Kinesin, motor domain		15119
154IPR015947
PUA-like domain		1525
155IPR003029
Ribosomal protein S1, RNA-binding domain		1550
156IPR011032
GroES (chaperonin 10)-like		1427
157IPR018490
Cyclic nucleotide-binding-like		1420
158IPR002909
IPT domain		1465
159IPR008991
Translation protein SH3-like domain		1415
160IPR001344
Chlorophyll A-B binding protein, plant		1415
161IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		1428
162IPR013763
Cyclin-like		1475
163IPR007087
Zinc finger, C2H2		1428
164IPR000408
Regulator of chromosome condensation, RCC1		14187
165IPR005821
Ion transport domain		1426
166IPR029028
Alpha/beta knot methyltransferases		1414
167IPR001202
WW domain		1469
168IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		1434
169IPR005069
Nucleotide-diphospho-sugar transferase		1414
170IPR000727
Target SNARE coiled-coil domain		1328
171IPR001251
CRAL-TRIO domain		1354
172IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1313
173IPR013320
Concanavalin A-like lectin/glucanase, subgroup		1331
174IPR000873
AMP-dependent synthetase/ligase		1313
175IPR001296
Glycosyl transferase, family 1		1313
176IPR002423
Chaperonin Cpn60/TCP-1		1313
177IPR027413
GroEL-like equatorial domain		1326
178IPR004839
Aminotransferase, class I/classII		1313
179IPR027409
GroEL-like apical domain		1326
180IPR002035
von Willebrand factor, type A		1337
181IPR029026
tRNA (guanine-N1-)-methyltransferase, N-terminal		1314
182IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		1314
183IPR031157
Tr-type G domain, conserved site		1313
184IPR006439
HAD hydrolase, subfamily IA		1325
185IPR001806
Small GTPase superfamily		1313
186IPR002683
Photosystem II PsbP, oxygen evolving complex		1313
187IPR005804
Fatty acid desaturase, type 1		1313
188IPR006638
Elongator protein 3/MiaB/NifB		1212
189IPR017938
Riboflavin synthase-like beta-barrel		1213
190IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		1237
191IPR008775
Phytanoyl-CoA dioxygenase		1212
192IPR003034
SAP domain		1231
193IPR001357
BRCT domain		1267
194IPR009071
High mobility group box domain		1263
195IPR000253
Forkhead-associated (FHA) domain		1238
196IPR023393
START-like domain		1213
197IPR029056
Ribokinase-like		1226
198IPR003594
Histidine kinase-like ATPase, ATP-binding domain		1242
199IPR002528
Multi antimicrobial extrusion protein		1228
200IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		1217
201IPR015655
Protein phosphatase 2C		1219
202IPR011051
RmlC-like cupin domain		1212
203IPR015915
Kelch-type beta propeller		1218
204IPR011709
Domain of unknown function DUF1605		1212
205IPR001487
Bromodomain		1293
206IPR002937
Amine oxidase		1212
207IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		1222
208IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		1212
209IPR025714
Methyltransferase domain		1111
210IPR009022
Elongation factor G, III-V domain		1126
211IPR008984
SMAD/FHA domain		1111
212IPR002942
RNA-binding S4 domain		1134
213IPR029021
Protein-tyrosine phosphatase-like		1121
214IPR017941
Rieske [2Fe-2S] iron-sulphur domain		1141
215IPR016177
DNA-binding domain		1115
216IPR032466
Metal-dependent hydrolase		1114
217IPR000640
Translation elongation factor EFG, V domain		1127
218IPR016021
MIF4-like, type 1/2/3		1115
219IPR007052
CS domain		1120
220IPR005829
Sugar transporter, conserved site		1115
221IPR008979
Galactose-binding domain-like		1116
222IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		1111
223IPR000742
Epidermal growth factor-like domain		1177
224IPR014722
Ribosomal protein L2 domain 2		1111
225IPR029069
HotDog domain		1127
226IPR029062
Class I glutamine amidotransferase-like		1122
227IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		1145
228IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		1111
229IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		1121
230IPR000595
Cyclic nucleotide-binding domain		1143
231IPR001128
Cytochrome P450		1170
232IPR002912
ACT domain		1118
233IPR000679
Zinc finger, GATA-type		1135
234IPR017927
Ferredoxin reductase-type FAD-binding domain		1010
235IPR001433
Oxidoreductase FAD/NAD(P)-binding		1010
236IPR032781
ABC-transporter extension domain		1010
237IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		1017
238IPR013088
Zinc finger, NHR/GATA-type		1010
239IPR002553
Clathrin/coatomer adaptor, adaptin-like, N-terminal		1010
240IPR029061
Thiamin diphosphate-binding fold		1034
241IPR001471
AP2/ERF domain		1059
242IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		1020
243IPR005828
General substrate transporter		1011
244IPR003323
Ovarian tumour, otubain		1018
245IPR011060
Ribulose-phosphate binding barrel		1010
246IPR001537
tRNA/rRNA methyltransferase, SpoU type		1011
247IPR023313
Ubiquitin-conjugating enzyme, active site		1010
248IPR000286
Histone deacetylase superfamily		1035
249IPR011006
CheY-like superfamily		1010
250IPR013032
EGF-like, conserved site		1054
251IPR007125
Histone core		1010
252IPR029039
Flavoprotein-like		1019
253IPR020892
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site		1010
254IPR000994
Peptidase M24, structural domain		1034
255IPR004154
Anticodon-binding		1024
256IPR015902
Glycoside hydrolase, family 13		1017
257IPR011004
Trimeric LpxA-like		1012
258IPR002194
Chaperonin TCP-1, conserved site		1027
259IPR002085
Alcohol dehydrogenase superfamily, zinc-type		1013
260IPR000642
Peptidase M41		1010
261IPR000305
GIY-YIG nuclease superfamily		1011
262IPR017998
Chaperone tailless complex polypeptide 1 (TCP-1)		1050
263IPR023210
NADP-dependent oxidoreductase domain		1032
264IPR027410
TCP-1-like chaperonin intermediate domain		1020
265IPR000594
UBA/THIF-type NAD/FAD binding fold		1022
266IPR001395
Aldo/keto reductase		1013
267IPR029064
50S ribosomal protein L30e-like		1020
268IPR001789
Signal transduction response regulator, receiver domain		1028
269IPR029060
PIN domain-like		920
270IPR008254
Flavodoxin/nitric oxide synthase		916
271IPR021133
HEAT, type 2		920
272IPR013525
ABC-2 type transporter		910
273IPR000387
Protein-tyrosine/Dual specificity phosphatase		99
274IPR019821
Kinesin, motor region, conserved site		99
275IPR013128
Peptidase C1A		913
276IPR011889
Bacterial surface protein 26-residue repeat		959
277IPR016039
Thiolase-like		998
278IPR000340
Dual specificity phosphatase, catalytic domain		99
279IPR001509
NAD-dependent epimerase/dehydratase		99
280IPR023801
Histone deacetylase domain		919
281IPR003495
CobW/HypB/UreG domain		99
282IPR011611
Carbohydrate kinase PfkB		910
283IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		99
284IPR006447
Myb domain, plants		99
285IPR005046
Protein of unknown function DUF285		933
286IPR011332
Zinc-binding ribosomal protein		99
287IPR003008
Tubulin/FtsZ, GTPase domain		940
288IPR003107
RNA-processing protein, HAT helix		972
289IPR011053
Single hybrid motif		910
290IPR029057
Phosphoribosyltransferase-like		926
291IPR006843
Plastid lipid-associated protein/fibrillin conserved domain		910
292IPR006634
TRAM/LAG1/CLN8 homology domain		921
293IPR020845
AMP-binding, conserved site		99
294IPR016193
Cytidine deaminase-like		911
295IPR031167
OBG-type guanine nucleotide-binding (G) domain		99
296IPR000668
Peptidase C1A, papain C-terminal		939
297IPR033443
Pentacotripeptide-repeat region of PROPR		99
298IPR013780
Glycosyl hydrolase, family 13, all-beta		99
299IPR003613
U box domain		921
300IPR009081
Acyl carrier protein-like		9111
301IPR020843
Polyketide synthase, enoylreductase domain		99
302IPR002641
Patatin/Phospholipase A2-related		99
303IPR004827
Basic-leucine zipper domain		929
304IPR000048
IQ motif, EF-hand binding site		954
305IPR004274
NLI interacting factor		927
306IPR002921
Lipase, class 3		88
307IPR023267
RNA (C5-cytosine) methyltransferase		832
308IPR033762
MCM OB domain		88
309IPR008949
Terpenoid synthase		816
310IPR008971
HSP40/DnaJ peptide-binding		817
311IPR013328
Dehydrogenase, multihelical		89
312IPR006153
Cation/H+ exchanger		88
313IPR016064
ATP-NAD kinase-like domain		810
314IPR002575
Aminoglycoside phosphotransferase		88
315IPR003954
RNA recognition motif domain, eukaryote		814
316IPR001305
Heat shock protein DnaJ, cysteine-rich domain		817
317IPR003607
HD/PDEase domain		810
318IPR011237
Peptidase M16 domain		823
319IPR009078
Ferritin-like superfamily		88
320IPR000089
Biotin/lipoyl attachment		815
321IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		88
322IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		820
323IPR001810
F-box domain		816
324IPR002938
Monooxygenase, FAD-binding		810
325IPR011257
DNA glycosylase		816
326IPR011761
ATP-grasp fold		89
327IPR001269
tRNA-dihydrouridine synthase		818
328IPR013154
Alcohol dehydrogenase GroES-like		88
329IPR001678
Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p		816
330IPR017932
Glutamine amidotransferase type 2 domain		811
331IPR004365
OB-fold nucleic acid binding domain, AA-tRNA synthetase-type		88
332IPR022742
Putative lysophospholipase		88
333IPR002123
Phospholipid/glycerol acyltransferase		813
334IPR009001
Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal		88
335IPR000569
HECT domain		832
336IPR011013
Galactose mutarotase-like domain		89
337IPR002192
Pyruvate phosphate dikinase, PEP/pyruvate-binding		811
338IPR001208
Mini-chromosome maintenance, DNA-dependent ATPase		856
339IPR022967
RNA-binding domain, S1		825
340IPR011527
ABC transporter type 1, transmembrane domain		828
341IPR003689
Zinc/iron permease		88
342IPR001709
Flavoprotein pyridine nucleotide cytochrome reductase		849
343IPR006671
Cyclin, N-terminal		89
344IPR016161
Aldehyde/histidinol dehydrogenase		88
345IPR016185
Pre-ATP-grasp domain		817
346IPR002939
Chaperone DnaJ, C-terminal		88
347IPR020588
DNA recombination and repair protein RecA-like, ATP-binding domain		88
348IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		837
349IPR011249
Metalloenzyme, LuxS/M16 peptidase-like		826
350IPR000195
Rab-GTPase-TBC domain		840
351IPR000760
Inositol monophosphatase		839
352IPR031327
Mini-chromosome maintenance protein		88
353IPR001048
Aspartate/glutamate/uridylate kinase		827
354IPR014720
Double-stranded RNA-binding domain		813
355IPR016197
Chromo domain-like		810
356IPR006047
Glycosyl hydrolase, family 13, catalytic domain		816
357IPR015946
K homology domain-like, alpha/beta		89
358IPR000620
Drug/metabolite transporter		814
359IPR000555
JAB1/MPN/MOV34 metalloenzyme domain		813
360IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		89
361IPR001878
Zinc finger, CCHC-type		899
362IPR007863
Peptidase M16, C-terminal domain		813
363IPR000432
DNA mismatch repair protein MutS, C-terminal		820
364IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		867
365IPR001041
2Fe-2S ferredoxin-type domain		820
366IPR017877
Myb-like domain		89
367IPR008942
ENTH/VHS		713
368IPR006689
Small GTPase superfamily, ARF/SAR type		731
369IPR025110
AMP-binding enzyme C-terminal domain		77
370IPR000467
G-patch domain		719
371IPR000433
Zinc finger, ZZ-type		725
372IPR018506
Cytochrome b5, heme-binding site		77
373IPR000782
FAS1 domain		742
374IPR014030
Beta-ketoacyl synthase, N-terminal		726
375IPR013149
Alcohol dehydrogenase, C-terminal		77
376IPR001606
ARID/BRIGHT DNA-binding domain		729
377IPR017975
Tubulin, conserved site		77
378IPR011008
Dimeric alpha-beta barrel		710
379IPR023333
Proteasome B-type subunit		77
380IPR011016
Zinc finger, RING-CH-type		717
381IPR011629
Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal		725
382IPR002314
Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain		77
383IPR009053
Prefoldin		714
384IPR018150
Aminoacyl-tRNA synthetase, class II (D/K/N)-like		711
385IPR021109
Aspartic peptidase domain		719
386IPR012676
TGS-like		77
387IPR008280
Tubulin/FtsZ, C-terminal		77
388IPR018962
Domain of unknown function DUF1995		77
389IPR001907
ATP-dependent Clp protease proteolytic subunit		738
390IPR009030
Insulin-like growth factor binding protein, N-terminal		712
391IPR020084
NUDIX hydrolase, conserved site		77
392IPR005101
DNA photolyase, FAD-binding/Cryptochrome, C-terminal		710
393IPR018181
Heat shock protein 70, conserved site		716
394IPR002562
3'-5' exonuclease domain		711
395IPR013520
Exonuclease, RNase T/DNA polymerase III		714
396IPR010989
t-SNARE		77
397IPR017926
Glutamine amidotransferase		713
398IPR031112
AP2-like ethylene-responsive transcription factor		77
399IPR015847
Exoribonuclease, phosphorolytic domain 2		714
400IPR012171
Fatty acid/sphingolipid desaturase		77
401IPR027443
Isopenicillin N synthase-like		78
402IPR004160
Translation elongation factor EFTu/EF1A, C-terminal		77
403IPR005331
Sulfotransferase		77
404IPR014031
Beta-ketoacyl synthase, C-terminal		726
405IPR004014
Cation-transporting P-type ATPase, N-terminal		711
406IPR002478
PUA domain		716
407IPR019489
Clp ATPase, C-terminal		714
408IPR007696
DNA mismatch repair protein MutS, core		717
409IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		717
410IPR003591
Leucine-rich repeat, typical subtype		734
411IPR001683
Phox homologous domain		733
412IPR001164
Arf GTPase activating protein		741
413IPR000169
Cysteine peptidase, cysteine active site		77
414IPR005936
Peptidase, FtsH		712
415IPR000426
Proteasome alpha-subunit, N-terminal domain		719
416IPR002109
Glutaredoxin		714
417IPR001356
Homeobox domain		718
418IPR011335
Restriction endonuclease type II-like		77
419IPR013126
Heat shock protein 70 family		759
420IPR018525
Mini-chromosome maintenance, conserved site		77
421IPR029006
ADF-H/Gelsolin-like domain		77
422IPR009003
Trypsin-like cysteine/serine peptidase domain		78
423IPR023298
P-type ATPase, transmembrane domain		714
424IPR004364
Aminoacyl-tRNA synthetase, class II (D/K/N)		78
425IPR011765
Peptidase M16, N-terminal		77
426IPR000836
Phosphoribosyltransferase domain		77
427IPR001173
Glycosyltransferase 2-like		77
428IPR013657
UAA transporter		77
429IPR023332
Proteasome A-type subunit		77
430IPR020841
Polyketide synthase, beta-ketoacyl synthase domain		724
431IPR016162
Aldehyde dehydrogenase, N-terminal		78
432IPR001247
Exoribonuclease, phosphorolytic domain 1		79
433IPR023562
Clp protease proteolytic subunit /Translocation-enhancing protein TepA		714
434IPR008974
TRAF-like		711
435IPR015590
Aldehyde dehydrogenase domain		77
436IPR017972
Cytochrome P450, conserved site		77
437IPR016163
Aldehyde dehydrogenase, C-terminal		77
438IPR017896
4Fe-4S ferredoxin-type, iron-sulphur binding domain		714
439IPR000225
Armadillo		739
440IPR018201
Beta-ketoacyl synthase, active site		614
441IPR014718
Glycoside hydrolase-type carbohydrate-binding, subgroup		66
442IPR004294
Carotenoid oxygenase		615
443IPR017884
SANT domain		67
444IPR006091
Acyl-CoA oxidase/dehydrogenase, central domain		66
445IPR013632
DNA recombination and repair protein Rad51, C-terminal		66
446IPR022764
Peptidase S54, rhomboid domain		611
447IPR006171
Toprim domain		618
448IPR023404
Radical SAM, alpha/beta horseshoe		66
449IPR004000
Actin-related protein		645
450IPR000537
UbiA prenyltransferase family		66
451IPR027408
PNPase/RNase PH domain		68
452IPR004193
Glycoside hydrolase, family 13, N-terminal		66
453IPR013784
Carbohydrate-binding-like fold		66
454IPR010280
(Uracil-5)-methyltransferase family		612
455IPR014352
FERM/acyl-CoA-binding protein, 3-helical bundle		66
456IPR018957
Zinc finger, C3HC4 RING-type		66
457IPR009008
Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain		613
458IPR002125
CMP/dCMP deaminase, zinc-binding		611
459IPR006204
GHMP kinase N-terminal domain		66
460IPR000313
PWWP domain		69
461IPR020094
Pseudouridine synthase I, TruA, N-terminal		66
462IPR020045
5'-3' exonuclease, C-terminal domain		68
463IPR000961
AGC-kinase, C-terminal		68
464IPR013155
Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding		66
465IPR027359
Voltage-dependent channel, four helix bundle domain		619
466IPR002401
Cytochrome P450, E-class, group I		636
467IPR002300
Aminoacyl-tRNA synthetase, class Ia		68
468IPR018392
LysM domain		622
469IPR010994
RuvA domain 2-like		68
470IPR020095
Pseudouridine synthase I, TruA, C-terminal		68
471IPR027450
Alpha-ketoglutarate-dependent dioxygenase AlkB-like		612
472IPR003358
tRNA (guanine-N-7) methyltransferase		612
473IPR011050
Pectin lyase fold/virulence factor		612
474IPR002569
Peptide methionine sulphoxide reductase MsrA		622
475IPR016166
FAD-binding, type 2		611
476IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		69
477IPR013534
Starch synthase, catalytic domain		66
478IPR003958
Transcription factor CBF/NF-Y/archaeal histone		66
479IPR000850
Adenylate kinase/UMP-CMP kinase		636
480IPR006050
DNA photolyase, N-terminal		618
481IPR004039
Rubredoxin-type fold		66
482IPR021134
Bestrophin/UPF0187		67
483IPR027256
Cation-transporting P-type ATPase, subfamily IB		66
484IPR013057
Amino acid transporter, transmembrane		67
485IPR011835
Glycogen/starch synthase, ADP-glucose type		69
486IPR006076
FAD dependent oxidoreductase		66
487IPR006598
Lipopolysaccharide-modifying protein		611
488IPR001494
Importin-beta, N-terminal domain		614
489IPR011641
Tyrosine-protein kinase ephrin type A/B receptor-like		647
490IPR003435
Chaperonin-like RbcX		66
491IPR005937
26S proteasome subunit P45		66
492IPR003890
MIF4G-like, type 3		614
493IPR018517
tRNA-dihydrouridine synthase, conserved site		66
494IPR004046
Glutathione S-transferase, C-terminal		66
495IPR009075
Acyl-CoA dehydrogenase/oxidase C-terminal		611
496IPR001849
Pleckstrin homology domain		616
497IPR004038
Ribosomal protein L7Ae/L30e/S12e/Gadd45		66
498IPR005475
Transketolase-like, pyrimidine-binding domain		612
499IPR013830
SGNH hydrolase superfamily		617
500IPR001406
Pseudouridine synthase I, TruA		618
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens.html b/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens.html new file mode 100644 index 00000000..83944c44 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens.html @@ -0,0 +1,44 @@ + +

Summary

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Assembly:ASM242v1, Jul 2006
Database version:86.11
Base Pairs:479,985,347
Golden Path Length:479,985,347
Genebuild by: JGI
Genebuild method: Imported from JGI-Phytozome
Genebuild started: Mar 2011
Genebuild released: Mar 2011
Genebuild last updated/patched: Mar 2011
Genebuild version: 2011-03-Phypa1.6
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		32,273
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:38,354
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Coordinate Systems

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scaffold2106 sequences
chunk6482 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens_IPtop500.html new file mode 100644 index 00000000..1ee78295 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Physcomitrella_patens_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		11213253
2IPR011009
Protein kinase-like domain		8761049
3IPR000719
Protein kinase, catalytic domain		7972009
4IPR008271
Serine/threonine-protein kinase, active site		522549
5IPR032675
Leucine-rich repeat domain, L domain-like		5111577
6IPR013083
Zinc finger, RING/FYVE/PHD-type		454542
7IPR017441
Protein kinase, ATP binding site		416443
8IPR016024
Armadillo-type fold		4071051
9IPR016040
NAD(P)-binding domain		3981077
10IPR015943
WD40/YVTN repeat-like-containing domain		341614
11IPR011990
Tetratricopeptide-like helical		3301274
12IPR011989
Armadillo-like helical		316706
13IPR017986
WD40-repeat-containing domain		315850
14IPR029058
Alpha/Beta hydrolase fold		311913
15IPR009057
Homeodomain-like		298733
16IPR013320
Concanavalin A-like lectin/glucanase, subgroup		295407
17IPR001680
WD40 repeat		2833281
18IPR003593
AAA+ ATPase domain		272380
19IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		260415
20IPR001841
Zinc finger, RING-type		255591
21IPR001611
Leucine-rich repeat		2471171
22IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		243679
23IPR012677
Nucleotide-binding, alpha-beta plait		240800
24IPR001810
F-box domain, cyclin-like		228647
25IPR000504
RNA recognition motif domain		2101068
26IPR012336
Thioredoxin-like fold		205580
27IPR001005
SANT/Myb domain		183445
28IPR011992
EF-hand-like domain		175486
29IPR019775
WD40 repeat, conserved site		174328
30IPR016177
DNA-binding, integrase-type		173193
31IPR011991
Winged helix-turn-helix DNA-binding domain		169317
32IPR001471
AP2/ERF domain		165923
33IPR017853
Glycoside hydrolase, superfamily		162213
34IPR014001
Helicase, superfamily 1/2, ATP-binding domain		159324
35IPR001650
Helicase, C-terminal		155470
36IPR023214
HAD-like domain		148505
37IPR020846
Major facilitator superfamily domain		144335
38IPR002048
Calcium-binding EF-hand		143990
39IPR013785
Aldolase-type TIM barrel		140189
40IPR029044
Nucleotide-diphospho-sugar transferases		136347
41IPR003439
ABC transporter-like		136386
42IPR013026
Tetratricopeptide repeat-containing domain		136202
43IPR017930
Myb domain		134201
44IPR019734
Tetratricopeptide repeat		1301184
45IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		130555
46IPR013210
Leucine-rich repeat-containing N-terminal, type 2		129137
47IPR003959
ATPase, AAA-type, core		125166
48IPR005225
Small GTP-binding protein domain		124140
49IPR013781
Glycoside hydrolase, catalytic domain		118145
50IPR003591
Leucine-rich repeat, typical subtype		116861
51IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		114600
52IPR020472
G-protein beta WD-40 repeat		113378
53IPR003594
Histidine kinase-like ATPase, ATP-binding domain		111540
54IPR001623
DnaJ domain		110876
55IPR012340
Nucleic acid-binding, OB-fold		110162
56IPR018247
EF-Hand 1, calcium-binding site		109291
57IPR011011
Zinc finger, FYVE/PHD-type		109135
58IPR002885
Pentatricopeptide repeat		1082569
59IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		108152
60IPR015424
Pyridoxal phosphate-dependent transferase		104130
61IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		103122
62IPR029071
Ubiquitin-related domain		103186
63IPR015916
Galactose oxidase, beta-propeller		101115
64IPR023395
Mitochondrial carrier domain		98231
65IPR001128
Cytochrome P450		98626
66IPR000008
C2 calcium-dependent membrane targeting		97661
67IPR007087
Zinc finger, C2H2		97303
68IPR018108
Mitochondrial substrate/solute carrier		97588
69IPR017871
ABC transporter, conserved site		97125
70IPR011333
BTB/POZ fold		97105
71IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		95102
72IPR012334
Pectin lyase fold		93117
73IPR011050
Pectin lyase fold/virulence factor		92116
74IPR001965
Zinc finger, PHD-type		92139
75IPR006121
Heavy metal-associated domain, HMA		91255
76IPR020683
Ankyrin repeat-containing domain		91436
77IPR011006
CheY-like superfamily		89114
78IPR001789
Signal transduction response regulator, receiver domain		88285
79IPR002182
NB-ARC		8788
80IPR000073
Alpha/beta hydrolase fold-1		86226
81IPR017907
Zinc finger, RING-type, conserved site		8594
82IPR014756
Immunoglobulin E-set		8593
83IPR027640
Kinesin-like protein		83285
84IPR001752
Kinesin, motor domain		83649
85IPR011993
Pleckstrin homology-like domain		83163
86IPR013766
Thioredoxin domain		82197
87IPR002110
Ankyrin repeat		82612
88IPR009072
Histone-fold		82176
89IPR000225
Armadillo		82766
90IPR014710
RmlC-like jelly roll fold		80113
91IPR019787
Zinc finger, PHD-finger		80147
92IPR002401
Cytochrome P450, E-class, group I		79602
93IPR020568
Ribosomal protein S5 domain 2-type fold		79104
94IPR013783
Immunoglobulin-like fold		76106
95IPR000210
BTB/POZ domain		76199
96IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		7697
97IPR000626
Ubiquitin domain		74419
98IPR029052
Metallo-dependent phosphatase-like		74198
99IPR013830
SGNH hydrolase-type esterase domain		73173
100IPR003960
ATPase, AAA-type, conserved site		7290
101IPR012337
Ribonuclease H-like domain		72161
102IPR023393
START-like domain		6987
103IPR006447
Myb domain, plants		6975
104IPR019786
Zinc finger, PHD-type, conserved site		6979
105IPR001806
Small GTPase superfamily		6981
106IPR019821
Kinesin, motor region, conserved site		6869
107IPR005467
Signal transduction histidine kinase, core		6872
108IPR010255
Haem peroxidase		6877
109IPR005123
Oxoglutarate/iron-dependent dioxygenase		67142
110IPR002016
Haem peroxidase, plant/fungal/bacterial		67432
111IPR017972
Cytochrome P450, conserved site		6672
112IPR016181
Acyl-CoA N-acyltransferase		65157
113IPR003661
Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain		64256
114IPR029055
Nucleophile aminohydrolases, N-terminal		64140
115IPR027443
Isopenicillin N synthase-like		6480
116IPR015915
Kelch-type beta propeller		6484
117IPR001878
Zinc finger, CCHC-type		64479
118IPR004843
Metallophosphoesterase domain		6266
119IPR002347
Glucose/ribitol dehydrogenase		62513
120IPR006553
Leucine-rich repeat, cysteine-containing subtype		62505
121IPR004263
Exostosin-like		6164
122IPR011043
Galactose oxidase/kelch, beta-propeller		5970
123IPR023329
Chlorophyll a/b binding protein domain		5972
124IPR016039
Thiolase-like		58266
125IPR022796
Chlorophyll A-B binding protein		5869
126IPR000571
Zinc finger, CCCH-type		58451
127IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		5764
128IPR014014
RNA helicase, DEAD-box type, Q motif		5760
129IPR004358
Signal transduction histidine kinase-related protein, C-terminal		57219
130IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		5666
131IPR015300
DNA-binding pseudobarrel domain		56157
132IPR000182
GNAT domain		55108
133IPR003340
B3 DNA binding domain		55222
134IPR010920
Like-Sm (LSM) domain		5560
135IPR010987
Glutathione S-transferase, C-terminal-like		55191
136IPR001356
Homeobox domain		55164
137IPR001214
SET domain		55141
138IPR000823
Plant peroxidase		55451
139IPR008928
Six-hairpin glycosidase-like		5464
140IPR011051
RmlC-like cupin domain		5464
141IPR001932
Protein phosphatase 2C (PP2C)-like		54398
142IPR029045
ClpP/crotonase-like domain		53154
143IPR002035
von Willebrand factor, type A		53164
144IPR015880
Zinc finger, C2H2-like		53168
145IPR016135
Ubiquitin-conjugating enzyme/RWD-like		52109
146IPR002067
Mitochondrial carrier protein		52279
147IPR018253
DnaJ domain, conserved site		5156
148IPR011032
GroES-like		50112
149IPR008250
P-type ATPase, A domain		50133
150IPR011527
ABC transporter, transmembrane domain, type 1		50245
151IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		50129
152IPR002912
ACT domain		50118
153IPR000048
IQ motif, EF-hand binding site		50288
154IPR002921
Lipase, class 3		4950
155IPR008972
Cupredoxin		49163
156IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4982
157IPR026992
Non-haem dioxygenase N-terminal domain		4953
158IPR003613
U box domain		49128
159IPR023299
P-type ATPase, cytoplasmic domain N		48100
160IPR000330
SNF2-related		4750
161IPR019793
Peroxidases heam-ligand binding site		4750
162IPR001757
Cation-transporting P-type ATPase		47149
163IPR000644
Cystathionine beta-synthase, core		47284
164IPR029000
Cyclophilin-like domain		46102
165IPR001305
Heat shock protein DnaJ, cysteine-rich domain		46113
166IPR001344
Chlorophyll A-B binding protein, plant		4661
167IPR000070
Pectinesterase, catalytic		4660
168IPR017877
Myb-like domain		4659
169IPR032710
NTF2-like domain		4588
170IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		45265
171IPR008978
HSP20-like chaperone		4589
172IPR009060
UBA-like		4560
173IPR021109
Aspartic peptidase		45140
174IPR009009
Barwin-related endoglucanase		45129
175IPR015655
Protein phosphatase 2C		4588
176IPR001087
Lipase, GDSL		4450
177IPR013525
ABC-2 type transporter		4462
178IPR011012
Longin-like domain		4449
179IPR004827
Basic-leucine zipper domain		44180
180IPR011701
Major facilitator superfamily		4350
181IPR029021
Protein-tyrosine phosphatase-like		43140
182IPR019794
Peroxidase, active site		4345
183IPR005202
Transcription factor GRAS		4385
184IPR018303
P-type ATPase, phosphorylation site		4347
185IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		4368
186IPR002085
Alcohol dehydrogenase superfamily, zinc-type		4360
187IPR013763
Cyclin-like		41208
188IPR007112
Expansin/pollen allergen, DPBB domain		4176
189IPR004045
Glutathione S-transferase, N-terminal		4198
190IPR011042
Six-bladed beta-propeller, TolB-like		4163
191IPR000608
Ubiquitin-conjugating enzyme, E2		4086
192IPR008991
Translation protein SH3-like domain		4045
193IPR013057
Amino acid transporter, transmembrane		4052
194IPR013126
Heat shock protein 70 family		40238
195IPR007117
Expansin, cellulose-binding-like domain		40160
196IPR001353
Proteasome, subunit alpha/beta		3943
197IPR027356
NPH3 domain		3987
198IPR015813
Pyruvate/Phosphoenolpyruvate kinase		39128
199IPR009880
Glyoxal oxidase, N-terminal		3943
200IPR007118
Expansin/Lol pI		38216
201IPR000873
AMP-dependent synthetase/ligase		3852
202IPR015202
Domain of unknown function DUF1929		3839
203IPR008979
Galactose-binding domain-like		3898
204IPR000315
Zinc finger, B-box		37134
205IPR007125
Histone core		3737
206IPR001849
Pleckstrin homology domain		3791
207IPR000757
Glycoside hydrolase, family 16		3784
208IPR006073
GTP binding domain		3796
209IPR000014
PAS domain		36225
210IPR004853
Domain of unknown function DUF250		3640
211IPR001163
Ribonucleoprotein LSM domain		3672
212IPR029061
Thiamin diphosphate-binding fold		36125
213IPR005828
General substrate transporter		3652
214IPR003008
Tubulin/FtsZ, GTPase domain		36174
215IPR003657
DNA-binding WRKY		36196
216IPR001296
Glycosyl transferase, family 1		3535
217IPR013154
Alcohol dehydrogenase GroES-like		3537
218IPR006652
Kelch repeat type 1		35141
219IPR011332
Ribosomal protein, zinc-binding domain		3537
220IPR011013
Galactose mutarotase-like domain		3544
221IPR020845
AMP-binding, conserved site		3546
222IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3543
223IPR001461
Peptidase A1		35146
224IPR016159
Cullin repeat-like-containing domain		3549
225IPR022812
Dynamin superfamily		34260
226IPR029056
Ribokinase-like		3486
227IPR000490
Glycoside hydrolase, family 17		3470
228IPR029033
Histidine phosphatase superfamily		34111
229IPR000727
Target SNARE coiled-coil domain		3381
230IPR006689
Small GTPase superfamily, ARF/SAR type		33176
231IPR019956
Ubiquitin subgroup		33125
232IPR003441
No apical meristem (NAM) protein		33102
233IPR000717
Proteasome component (PCI) domain		3369
234IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		3395
235IPR001279
Beta-lactamase-like		33132
236IPR000795
Elongation factor, GTP-binding domain		33190
237IPR012675
Beta-grasp domain		3334
238IPR004883
Lateral organ boundaries, LOB		3371
239IPR033121
Peptidase family A1 domain		3344
240IPR014720
Double-stranded RNA-binding domain		33135
241IPR000270
Phox/Bem1p		3364
242IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		32106
243IPR004161
Translation elongation factor EFTu/EF1A, domain 2		3232
244IPR008280
Tubulin/FtsZ, C-terminal		3236
245IPR033131
Pectinesterase, Asp active site		3241
246IPR016166
FAD-binding, type 2		3264
247IPR002963
Expansin		32229
248IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		3234
249IPR019378
GDP-fucose protein O-fucosyltransferase		3232
250IPR014722
Ribosomal protein L2 domain 2		3237
251IPR017937
Thioredoxin, conserved site		3248
252IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		3235
253IPR012341
Six-hairpin glycosidase		3234
254IPR006594
LisH dimerisation motif		3171
255IPR013216
Methyltransferase type 11		3137
256IPR032861
Xylanase inhibitor, N-terminal		3135
257IPR001202
WW domain		31136
258IPR024788
Malectin-like carbohydrate-binding domain		3136
259IPR029060
PIN domain-like		3064
260IPR010402
CCT domain		3068
261IPR030381
Dynamin-type guanine nucleotide-binding (G) domain		3035
262IPR005135
Endonuclease/exonuclease/phosphatase		30121
263IPR002423
Chaperonin Cpn60/TCP-1		3031
264IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		3060
265IPR001763
Rhodanese-like domain		30210
266IPR003406
Glycosyl transferase, family 14		3033
267IPR027409
GroEL-like apical domain		3062
268IPR023210
NADP-dependent oxidoreductase domain		3095
269IPR015947
PUA-like domain		3046
270IPR001395
Aldo/keto reductase		3044
271IPR008942
ENTH/VHS		2961
272IPR000217
Tubulin		29256
273IPR001251
CRAL-TRIO domain		29173
274IPR001478
PDZ domain		29111
275IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		2980
276IPR013816
ATP-grasp fold, subdomain 2		2937
277IPR008266
Tyrosine-protein kinase, active site		2930
278IPR004839
Aminotransferase, class I/classII		2936
279IPR003245
Plastocyanin-like		2994
280IPR017970
Homeobox, conserved site		2934
281IPR004088
K Homology domain, type 1		29198
282IPR029062
Class I glutamine amidotransferase-like		2976
283IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		2932
284IPR020843
Polyketide synthase, enoylreductase		2933
285IPR017975
Tubulin, conserved site		2830
286IPR002068
Alpha crystallin/Hsp20 domain		2854
287IPR001401
Dynamin, GTPase domain		2833
288IPR002123
Phospholipid/glycerol acyltransferase		2857
289IPR032799
Xylanase inhibitor, C-terminal		2833
290IPR015712
DNA-directed RNA polymerase, subunit 2		2843
291IPR028033
Domain of unknown function DUF4462		28118
292IPR023313
Ubiquitin-conjugating enzyme, active site		2831
293IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		2831
294IPR000894
Ribulose bisphosphate carboxylase small chain, domain		28116
295IPR005746
Thioredoxin		2847
296IPR029069
HotDog domain		28129
297IPR004087
K Homology domain		2853
298IPR006671
Cyclin, N-terminal		2842
299IPR000595
Cyclic nucleotide-binding domain		2896
300IPR008948
L-Aspartase-like		2828
301IPR024156
Small GTPase superfamily, ARF type		2835
302IPR017938
Riboflavin synthase-like beta-barrel		2729
303IPR013149
Alcohol dehydrogenase, C-terminal		2729
304IPR011611
Carbohydrate kinase PfkB		2733
305IPR013078
Histidine phosphatase superfamily, clade-1		2776
306IPR016161
Aldehyde/histidinol dehydrogenase		2731
307IPR004147
UbiB domain		2728
308IPR009003
Trypsin-like cysteine/serine peptidase domain		2734
309IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		27106
310IPR029064
50S ribosomal protein L30e-like		2764
311IPR015797
NUDIX hydrolase domain-like		2776
312IPR021133
HEAT, type 2		2661
313IPR018490
Cyclic nucleotide-binding-like		2640
314IPR001357
BRCT domain		26172
315IPR018392
Peptidoglycan-binding lysin domain		26141
316IPR032466
Metal-dependent hydrolase		2635
317IPR027413
GroEL-like equatorial domain		2654
318IPR000408
Regulator of chromosome condensation, RCC1		26480
319IPR004864
Late embryogenesis abundant protein, LEA-14		2630
320IPR002100
Transcription factor, MADS-box		26201
321IPR007081
RNA polymerase Rpb1, domain 5		2626
322IPR011004
Trimeric LpxA-like		2629
323IPR033443
Pentacotripeptide-repeat region of PROPR		2636
324IPR031157
Tr-type G domain, conserved site		2627
325IPR029047
Heat shock protein 70kD, peptide-binding domain		2657
326IPR002937
Amine oxidase		2634
327IPR008889
VQ		2626
328IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		26199
329IPR002913
START domain		2672
330IPR017927
Ferredoxin reductase-type FAD-binding domain		2525
331IPR000326
Phosphatidic acid phosphatase type 2/haloperoxidase		2593
332IPR013328
Dehydrogenase, multihelical		2532
333IPR019954
Ubiquitin conserved site		2580
334IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		2548
335IPR003137
Protease-associated domain, PA		2527
336IPR016455
Xyloglucan endotransglucosylase/hydrolase		2526
337IPR023271
Aquaporin-like		2559
338IPR010989
t-SNARE		2527
339IPR001199
Cytochrome b5-like heme/steroid binding domain		25193
340IPR022742
Alpha/beta hydrolase, N-terminal		2530
341IPR005829
Sugar transporter, conserved site		2548
342IPR023213
Chloramphenicol acetyltransferase-like domain		2547
343IPR013815
ATP-grasp fold, subdomain 1		2532
344IPR031107
Small heat shock protein HSP20		2525
345IPR000425
Major intrinsic protein		25224
346IPR004046
Glutathione S-transferase, C-terminal		2535
347IPR002495
Glycosyl transferase, family 8		2527
348IPR023123
Tubulin, C-terminal		2527
349IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2527
350IPR023298
P-type ATPase, transmembrane domain		2563
351IPR015500
Peptidase S8, subtilisin-related		25106
352IPR006595
CTLH, C-terminal LisH motif		2554
353IPR018082
AmbAllergen		25168
354IPR015590
Aldehyde dehydrogenase domain		2529
355IPR003029
Ribosomal protein S1, RNA-binding domain		2579
356IPR008630
Galactosyl transferase		2427
357IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2493
358IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2429
359IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2450
360IPR014977
WRC domain		2447
361IPR012946
X8 domain		2454
362IPR004014
Cation-transporting P-type ATPase, N-terminal		2452
363IPR006461
Uncharacterised protein family Cys-rich		2452
364IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		2468
365IPR012328
Chalcone/stilbene synthase, C-terminal		2428
366IPR003851
Zinc finger, Dof-type		2497
367IPR000722
RNA polymerase, alpha subunit		2428
368IPR016163
Aldehyde dehydrogenase, C-terminal		2426
369IPR029048
Heat shock protein 70kD, C-terminal domain		2454
370IPR000209
Peptidase S8/S53 domain		24123
371IPR006195
Aminoacyl-tRNA synthetase, class II		2325
372IPR006134
DNA-directed DNA polymerase, family B, multifunctional domain		2325
373IPR002553
Clathrin/coatomer adaptor, adaptin-like, N-terminal		2325
374IPR000109
Proton-dependent oligopeptide transporter family		2357
375IPR002022
Pectate lyase/Amb allergen		2352
376IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2326
377IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		2328
378IPR000047
Helix-turn-helix motif		2356
379IPR022967
RNA-binding domain, S1		2347
380IPR001494
Importin-beta, N-terminal		2360
381IPR006094
FAD linked oxidase, N-terminal		2323
382IPR002109
Glutaredoxin		2352
383IPR000086
NUDIX hydrolase domain		2360
384IPR024681
Ribulose bisphosphate carboxylase, small chain		23126
385IPR000375
Dynamin central domain		2332
386IPR016162
Aldehyde dehydrogenase, N-terminal		2327
387IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		2324
388IPR025610
Transcription factor MYC/MYB N-terminal		2324
389IPR008949
Terpenoid synthase		2251
390IPR008971
HSP40/DnaJ peptide-binding		2263
391IPR000387
Protein-tyrosine/Dual specificity phosphatase		2223
392IPR009022
Elongation factor G, III-V domain		2252
393IPR002173
Carbohydrate/puine kinase, PfkB, conserved site		2232
394IPR001969
Peptidase aspartic, active site		2233
395IPR011761
ATP-grasp fold		2227
396IPR011074
CRAL/TRIO, N-terminal domain		2254
397IPR020103
Pseudouridine synthase, catalytic domain		2237
398IPR003130
Dynamin GTPase effector		2241
399IPR001876
Zinc finger, RanBP2-type		22154
400IPR003616
Post-SET domain		2235
401IPR002939
Chaperone DnaJ, C-terminal		2224
402IPR000642
Peptidase M41		2224
403IPR016130
Protein-tyrosine phosphatase, active site		2224
404IPR003663
Sugar/inositol transporter		22127
405IPR001041
2Fe-2S ferredoxin-type domain		2260
406IPR001099
Chalcone/stilbene synthase, N-terminal		2226
407IPR025110
Domain of unknown function DUF4009		2127
408IPR000433
Zinc finger, ZZ-type		2171
409IPR001929
Germin		2164
410IPR029035
DHS-like NAD/FAD-binding domain		2162
411IPR006153
Cation/H+ exchanger		2125
412IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		2124
413IPR004331
SPX, N-terminal		2152
414IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2164
415IPR001697
Pyruvate kinase		21167
416IPR002942
RNA-binding S4 domain		2180
417IPR000340
Dual specificity phosphatase, catalytic domain		2123
418IPR001509
NAD-dependent epimerase/dehydratase		2124
419IPR007120
DNA-directed RNA polymerase, subunit 2, domain 6		2158
420IPR015793
Pyruvate kinase, barrel		2125
421IPR018060
DNA binding HTH domain, AraC-type		2158
422IPR016021
MIF4-like, type 1/2/3		2146
423IPR001375
Peptidase S9, prolyl oligopeptidase, catalytic domain		2124
424IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2128
425IPR020892
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site		2122
426IPR005821
Ion transport domain		2133
427IPR006045
Cupin 1		2145
428IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2135
429IPR000426
Proteasome, alpha-subunit, N-terminal domain		2167
430IPR000322
Glycoside hydrolase, family 31		2123
431IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		2153
432IPR011037
Pyruvate kinase-like, insert domain		2124
433IPR006502
Protein of unknown function DUF506, plant		2162
434IPR023332
Proteasome A-type subunit		2124
435IPR001487
Bromodomain		21144
436IPR022764
Peptidase S54, rhomboid domain		2057
437IPR001563
Peptidase S10, serine carboxypeptidase		20131
438IPR000782
FAS1 domain		20109
439IPR003106
Leucine zipper, homeobox-associated		2029
440IPR005024
Snf7 family		2023
441IPR008984
SMAD/FHA domain		2021
442IPR003347
JmjC domain		2051
443IPR015806
Pyruvate kinase, beta-barrel insert domain		2022
444IPR018181
Heat shock protein 70, conserved site		2057
445IPR020904
Short-chain dehydrogenase/reductase, conserved site		2023
446IPR005150
Cellulose synthase		2022
447IPR011053
Single hybrid motif		2024
448IPR023296
Glycosyl hydrolase, five-bladed beta-propellor domain		2047
449IPR002528
Multi antimicrobial extrusion protein		2060
450IPR004038
Ribosomal protein L7Ae/L30e/S12e/Gadd45		2021
451IPR013780
Glycosyl hydrolase, family 13, all-beta		2021
452IPR001701
Glycoside hydrolase, family 9		2020
453IPR029006
ADF-H/Gelsolin-like domain		2036
454IPR017850
Alkaline-phosphatase-like, core domain		2034
455IPR024083
Fumarase/histidase, N-terminal		2022
456IPR005804
Fatty acid desaturase, type 1		2022
457IPR025659
Tubby C-terminal-like domain		1929
458IPR016123
Mog1/PsbP, alpha/beta/alpha sandwich		1948
459IPR003954
RNA recognition motif domain, eukaryote		1937
460IPR009078
Ferritin/ribonucleotide reductase-like		1921
461IPR000089
Biotin/lipoyl attachment		1939
462IPR000253
Forkhead-associated (FHA) domain		1975
463IPR001907
ATP-dependent Clp protease proteolytic subunit		19141
464IPR001345
Phosphoglycerate/bisphosphoglycerate mutase, active site		1920
465IPR006694
Fatty acid hydroxylase		1921
466IPR000640
Translation elongation factor EFG, V domain		1957
467IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		1934
468IPR017849
Alkaline phosphatase-like, alpha/beta/alpha		1930
469IPR006379
HAD-superfamily hydrolase, subfamily IIB		1920
470IPR030458
Glycosyl hydrolases family 31, active site		1920
471IPR029057
Phosphoribosyltransferase-like		1964
472IPR008166
Domain of unknown function DUF23		1920
473IPR023828
Peptidase S8, subtilisin, Ser-active site		1920
474IPR022357
Major intrinsic protein, conserved site		1922
475IPR005835
Nucleotidyl transferase		1921
476IPR025486
Domain of unknown function DUF4378		1919
477IPR016197
Chromo domain-like		1934
478IPR000620
Drug/metabolite transporter		1934
479IPR023562
Clp protease proteolytic subunit /Translocation-enhancing protein TepA		1952
480IPR008974
TRAF-like		1945
481IPR017884
SANT domain		1828
482IPR010730
Heterokaryon incompatibility		1818
483IPR016064
ATP-NAD kinase-like domain		1840
484IPR024041
Ammonium transporter AmtB-like domain		1837
485IPR020850
GTPase effector domain, GED		1821
486IPR006592
RNA polymerase, N-terminal		1818
487IPR017941
Rieske [2Fe-2S] iron-sulphur domain		1873
488IPR017451
F-box associated interaction domain		1819
489IPR015794
Pyruvate kinase, alpha/beta		1819
490IPR001451
Bacterial transferase hexapeptide repeat		1830
491IPR004367
Cyclin, C-terminal domain		1836
492IPR002293
Amino acid/polyamine transporter I		1865
493IPR011060
Ribulose-phosphate binding barrel		1821
494IPR001025
Bromo adjacent homology (BAH) domain		1857
495IPR023631
Amidase signature domain		1879
496IPR013761
Sterile alpha motif/pointed domain		1835
497IPR015902
Glycoside hydrolase, family 13		1833
498IPR029020
Ammonium/urea transporter		1820
499IPR005475
Transketolase-like, pyrimidine-binding domain		1838
500IPR000120
Amidase		1825
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa.html b/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa.html new file mode 100644 index 00000000..b496480a --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa.html @@ -0,0 +1,77 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:JGI2.0, Jan 2010
Database version:86.20
Base Pairs:417,137,944
Golden Path Length:417,137,944
Genebuild by: JGI
Genebuild method: Imported from JGI-Phytozome
Genebuild started: Jan 2010
Genebuild version: 2010-01-JGI
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		41,377
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:45,778
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
19 sequences
+
+ +
+ + + +
SequenceLength (bp)
148367220
223562801
320216605
423188140
525802683
626894541
715101417
818835763
912942059
1021538349
1118885544
1214929429
1315658869
1417716633
1515134944
1614134809
1714661173
1814966190
1916008726
+
+
scaffold2518 sequences
chunk6393 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa_IPtop500.html new file mode 100644 index 00000000..20f1f61f --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Populus_trichocarpa_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		20032329
2IPR000719
Protein kinase, catalytic domain		18764816
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		18314962
4IPR032675
Leucine-rich repeat domain, L domain-like		14755162
5IPR008271
Serine/threonine-protein kinase, active site		13601472
6IPR017441
Protein kinase, ATP binding site		11171215
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		10051267
8IPR013083
Zinc finger, RING/FYVE/PHD-type		846960
9IPR001611
Leucine-rich repeat		7985007
10IPR001245
Serine-threonine/tyrosine-protein kinase		7731132
11IPR011990
Tetratricopeptide-like helical		7052390
12IPR016040
NAD(P)-binding domain		6111540
13IPR009057
Homeodomain-like		6051530
14IPR002885
Pentatricopeptide repeat		59513284
15IPR001841
Zinc finger, RING-type		5321323
16IPR016024
Armadillo-type fold		5021113
17IPR029058
Alpha/Beta hydrolase fold		5011284
18IPR002182
NB-ARC		492537
19IPR003591
Leucine-rich repeat, typical subtype		4703333
20IPR001128
Cytochrome P450		4372653
21IPR001005
SANT domain, DNA binding		4041170
22IPR011989
Armadillo-like helical		403805
23IPR012677
Nucleotide-binding, alpha-beta plait		3991354
24IPR003593
ATPase, AAA+ type, core		392550
25IPR015943
WD40/YVTN repeat-like-containing domain		392704
26IPR013210
Leucine-rich repeat-containing N-terminal, type 2		385416
27IPR017986
WD40-repeat-containing domain		3731022
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		357939
29IPR002401
Cytochrome P450, E-class, group I		3562375
30IPR000504
RNA recognition motif domain		3511789
31IPR001810
F-box domain, cyclin-like		345978
32IPR001680
WD40 repeat		3343739
33IPR017853
Glycoside hydrolase, superfamily		328430
34IPR012336
Thioredoxin-like fold		324853
35IPR017972
Cytochrome P450, conserved site		320332
36IPR017930
Transcription regulator HTH, Myb-type, DNA-binding		317552
37IPR011991
Winged helix-turn-helix transcription repressor DNA-binding		306541
38IPR020846
Major facilitator superfamily		304631
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		291682
40IPR013781
Glycoside hydrolase, subgroup, catalytic core		267327
41IPR011992
EF-hand-like domain		262679
42IPR012337
Ribonuclease H-like		248444
43IPR001480
Bulb-type lectin domain		2461380
44IPR016177
DNA-binding, integrase-type		227263
45IPR002048
Calcium-binding EF-hand		2251491
46IPR020683
Ankyrin repeat-containing domain		2251128
47IPR023214
HAD-like domain		220684
48IPR018247
EF-Hand 1, calcium-binding site		218497
49IPR011598
Helix-loop-helix DNA-binding		2171086
50IPR000477
Reverse transcriptase		216329
51IPR011050
Pectin lyase fold/virulence factor		214221
52IPR012334
Pectin lyase fold		212227
53IPR001471
Pathogenesis-related transcriptional factor/ERF, DNA-binding		2111344
54IPR002110
Ankyrin repeat		2081519
55IPR019775
WD40 repeat, conserved site		199348
56IPR007087
Zinc finger, C2H2-type		198680
57IPR005135
Endonuclease/exonuclease/phosphatase		187423
58IPR029044
Nucleotide-diphospho-sugar transferases		184492
59IPR003439
ABC transporter-like		182560
60IPR000858
S-locus glycoprotein		180189
61IPR013830
Esterase, SGNH hydrolase-type		179493
62IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		177742
63IPR001650
Helicase, C-terminal		176583
64IPR015300
DNA-binding pseudobarrel domain		175419
65IPR027443
Isopenicillin N synthase-like		174194
66IPR014001
DEAD-like helicase		173378
67IPR003441
No apical meristem (NAM) protein		169545
68IPR003959
ATPase, AAA-type, core		169211
69IPR029071
Ubiquitin-related domain		168265
70IPR008972
Cupredoxin		167675
71IPR005123
Oxoglutarate/iron-dependent oxygenase		165319
72IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		165211
73IPR003609
Apple-like		161466
74IPR025558
Domain of unknown function DUF4283		161164
75IPR023213
Chloramphenicol acetyltransferase-like domain		160300
76IPR013026
Tetratricopeptide repeat-containing		160242
77IPR026960
Reverse transcriptase zinc-binding domain		159160
78IPR000157
Toll-Interleukin receptor		158781
79IPR019734
Tetratricopeptide repeat		1551380
80IPR001623
Heat shock protein DnaJ, N-terminal		1531193
81IPR005225
Small GTP-binding protein		151162
82IPR004158
Protein of unknown function DUF247, plant		146172
83IPR014710
RmlC-like jelly roll fold		144171
84IPR012340
Nucleic acid-binding, OB-fold		144207
85IPR013785
Aldolase-type TIM barrel		143199
86IPR003340
Transcriptional factor B3		141484
87IPR011011
Zinc finger, FYVE/PHD-type		141176
88IPR000008
C2 calcium-dependent membrane targeting		1401120
89IPR003480
Transferase		139151
90IPR026992
Non-haem dioxygenase N-terminal domain		138144
91IPR015424
Pyridoxal phosphate-dependent transferase, major domain		138174
92IPR001356
Homeobox domain		135380
93IPR001087
Lipase, GDSL		132138
94IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		130156
95IPR010255
Haem peroxidase		130139
96IPR002347
Glucose/ribitol dehydrogenase		1281248
97IPR002016
Haem peroxidase, plant/fungal/bacterial		126811
98IPR001932
Protein phosphatase 2C-like		126836
99IPR017871
ABC transporter, conserved site		124165
100IPR001878
Zinc finger, CCHC-type		123598
101IPR006121
Heavy metal transport/detoxification protein		120429
102IPR020472
G-protein beta WD-40 repeat		120390
103IPR017907
Zinc finger, RING-type, conserved site		120137
104IPR000270
Phox/Bem1p		120237
105IPR025287
Wall-associated receptor kinase galacturonan-binding domain		119120
106IPR006501
Pectinesterase inhibitor		118580
107IPR000073
Alpha/beta hydrolase fold-1		117274
108IPR021820
S-locus receptor kinase, C-terminal		115124
109IPR032867
DYW domain		115116
110IPR000225
Armadillo		1151027
111IPR021109
Peptidase aspartic		113339
112IPR015880
Zinc finger, C2H2-like		112357
113IPR000626
Ubiquitin domain		111524
114IPR006447
Myb-like DNA-binding domain, SHAQKYF class		111128
115IPR015655
Protein phosphatase 2C		111203
116IPR001965
Zinc finger, PHD-type		111192
117IPR026961
PGG domain		110116
118IPR000823
Plant peroxidase		110890
119IPR011333
BTB/POZ fold		108129
120IPR003657
DNA-binding WRKY		108706
121IPR023393
START-like domain		107113
122IPR005828
General substrate transporter		107128
123IPR009072
Histone-fold		107218
124IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		106133
125IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		105117
126IPR010987
Glutathione S-transferase, C-terminal-like		104301
127IPR011051
Cupin, RmlC-type		104117
128IPR005202
Transcription factor GRAS		102206
129IPR003676
Auxin responsive SAUR protein		102104
130IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage		101261
131IPR001806
Ras GTPase		100109
132IPR013766
Thioredoxin domain		99209
133IPR000571
Zinc finger, CCCH-type		99802
134IPR002902
Gnk2-homologous domain		98388
135IPR001461
Peptidase A1		98287
136IPR019793
Peroxidases heam-ligand binding site		97101
137IPR015500
Peptidase S8, subtilisin-related		97348
138IPR000070
Pectinesterase, catalytic		9599
139IPR003960
ATPase, AAA-type, conserved site		94110
140IPR016166
FAD-binding, type 2		94191
141IPR027640
Kinesin-like protein		94262
142IPR004045
Glutathione S-transferase, N-terminal		94194
143IPR003613
U box domain		94282
144IPR011993
Pleckstrin homology-type		94215
145IPR033121
Peptidase family A1 domain		93107
146IPR023395
Mitochondrial carrier domain		93225
147IPR029052
Metallo-dependent phosphatase-like		93255
148IPR004827
Basic-leucine zipper (bZIP) transcription factor		93351
149IPR018108
Mitochondrial substrate/solute carrier		92564
150IPR008978
HSP20-like chaperone		91192
151IPR024171
S-receptor-like serine/threonine-protein kinase		9193
152IPR000048
IQ motif, EF-hand binding site		91490
153IPR011032
GroES-like		90213
154IPR008949
Terpenoid synthase		90213
155IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		9096
156IPR000209
Peptidase S8/S53, subtilisin/kexin/sedolisin		90459
157IPR001752
Kinesin, motor domain		89752
158IPR002100
Transcription factor, MADS-box		88606
159IPR000109
Oligopeptide transporter		87178
160IPR019794
Peroxidase, active site		8791
161IPR000210
BTB/POZ domain		86243
162IPR032861
Xylanase inhibitor, N-terminal		8694
163IPR017451
F-box associated interaction domain		8591
164IPR013057
Amino acid transporter, transmembrane		8596
165IPR020568
Ribosomal protein S5 domain 2-type fold		85114
166IPR006094
FAD linked oxidase, N-terminal		8588
167IPR002085
Alcohol dehydrogenase superfamily, zinc-containing		85120
168IPR000490
Glycoside hydrolase, family 17		85136
169IPR019786
Zinc finger, PHD-type, conserved site		84104
170IPR016135
Ubiquitin-conjugating enzyme/RWD-like		84198
171IPR018253
Heat shock protein DnaJ, conserved site		8389
172IPR008906
HAT dimerisation		8285
173IPR019787
Zinc finger, PHD-finger		82149
174IPR013087
Zinc finger, C2H2-type/integrase, DNA-binding		82154
175IPR001117
Multicopper oxidase, type 1		8183
176IPR013763
Cyclin-like		81401
177IPR032799
Xylanase inhibitor, C-terminal		8188
178IPR002528
Multi antimicrobial extrusion protein		81243
179IPR011706
Multicopper oxidase, type 2		8183
180IPR000743
Glycoside hydrolase, family 28		81132
181IPR004843
Metallo-dependent phosphatase		8094
182IPR008250
ATPase, P-type, ATPase-associated domain		80194
183IPR008930
Terpenoid cylases/protein prenyltransferase alpha-alpha toroid		80162
184IPR003245
Plastocyanin-like		79232
185IPR011707
Multicopper oxidase, type 3		7980
186IPR016181
Acyl-CoA N-acyltransferase		78178
187IPR016039
Thiolase-like		78324
188IPR011527
ABC transporter, transmembrane domain, type 1		78427
189IPR001757
ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter		78293
190IPR000873
AMP-dependent synthetase/ligase		7782
191IPR023299
ATPase, P-type, cytoplasmic domain N		77173
192IPR013525
ABC-2 type transporter		76112
193IPR023828
Peptidase S8, subtilisin, Ser-active site		7577
194IPR016167
FAD-binding, type 2, subdomain 1		7577
195IPR006045
Cupin 1		75169
196IPR002068
Heat shock protein Hsp20		73145
197IPR012946
X8 domain		73152
198IPR025836
Zinc knuckle CX2CX4HX4C		7377
199IPR005829
Sugar transporter, conserved site		73131
200IPR024752
Myb/SANT-like domain		7284
201IPR013149
Alcohol dehydrogenase, C-terminal		7175
202IPR000608
Ubiquitin-conjugating enzyme, E2		71167
203IPR033131
Pectinesterase, Asp active site		7173
204IPR021720
Malectin		7182
205IPR011006
CheY-like superfamily		7198
206IPR000742
Epidermal growth factor-like, type 3		70124
207IPR024788
Malectin-like carbohydrate-binding domain		7077
208IPR010259
Proteinase inhibitor I9, subtilisin propeptide		69112
209IPR004263
Exostosin-like		6972
210IPR008928
Six-hairpin glycosidase-like		6985
211IPR018303
ATPase, P-type phosphorylation site		6982
212IPR003663
Sugar/inositol transporter		69376
213IPR001789
Signal transduction response regulator, receiver domain		69239
214IPR026057
PC-Esterase		6873
215IPR001509
NAD-dependent epimerase/dehydratase		6883
216IPR009009
Barwin-related endoglucanase		68185
217IPR008979
Galactose-binding domain-like		68183
218IPR006626
Parallel beta-helix repeat		67340
219IPR008266
Tyrosine-protein kinase, active site		6774
220IPR013094
Alpha/beta hydrolase fold-3		6769
221IPR027806
Harbinger transposase-derived nuclease domain		6667
222IPR012951
Berberine/berberine-like		6667
223IPR031107
Small heat shock protein HSP20		6667
224IPR029055
Nucleophile aminohydrolases, N-terminal		65142
225IPR017970
Homeobox, conserved site		6569
226IPR028082
Periplasmic binding protein-like I		65107
227IPR017877
Myb-like domain		6589
228IPR001563
Peptidase S10, serine carboxypeptidase		64355
229IPR029962
Trichome birefringence-like family		6482
230IPR002912
Amino acid-binding ACT		63174
231IPR019821
Kinesin, motor region, conserved site		6269
232IPR009060
UBA-like		6290
233IPR005630
Terpene synthase, metal-binding domain		6274
234IPR003656
Zinc finger, BED-type predicted		62139
235IPR014756
Immunoglobulin E-set		6274
236IPR020845
AMP-binding, conserved site		6163
237IPR025846
PMR5 N-terminal domain		6161
238IPR002109
Glutaredoxin		61129
239IPR000182
GCN5-related N-acetyltransferase (GNAT) domain		60119
240IPR006016
UspA		6066
241IPR014014
RNA helicase, DEAD-box type, Q motif		6067
242IPR004864
Late embryogenesis abundant protein, group 2		6061
243IPR029045
ClpP/crotonase-like domain		60190
244IPR019378
GDP-fucose protein O-fucosyltransferase		6065
245IPR004088
K Homology, type 1		60679
246IPR001220
Legume lectin, beta chain		6061
247IPR001828
Extracellular ligand-binding receptor		6063
248IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		5974
249IPR002355
Multicopper oxidase, copper-binding site		5961
250IPR031052
FHY3/FAR1 family		5984
251IPR003594
ATPase-like, ATP-binding domain		59262
252IPR001320
Ionotropic glutamate receptor		59119
253IPR000425
Major intrinsic protein		59486
254IPR001214
SET domain		59176
255IPR015916
Galactose oxidase, beta-propeller		5866
256IPR025322
Protein of unknown function DUF4228		5861
257IPR000782
FAS1 domain		58318
258IPR011016
Zinc finger, RING-CH-type		57149
259IPR023271
Aquaporin-like		57121
260IPR003690
Mitochodrial transcription termination factor-related		57434
261IPR004883
Lateral organ boundaries, LOB		57118
262IPR002921
Lipase, class 3		5658
263IPR003137
Protease-associated domain, PA		5659
264IPR013154
Alcohol dehydrogenase GroES-like		5660
265IPR001906
Terpene synthase-like		56123
266IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		5670
267IPR000330
SNF2-related		5564
268IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		5565
269IPR006553
Leucine-rich repeat, cysteine-containing subtype		55448
270IPR008974
TRAF-like		55170
271IPR033389
AUX/IAA domain		5474
272IPR030184
WAT1-related protein		5456
273IPR001929
Germin		53154
274IPR004839
Aminotransferase, class I/classII		5356
275IPR004087
K Homology		53172
276IPR002067
Mitochondrial carrier protein		53300
277IPR023298
ATPase, P-type, transmembrane domain		53118
278IPR001638
Extracellular solute-binding protein, family 3		5353
279IPR004853
Domain of unknown function DUF250		5255
280IPR006671
Cyclin, N-terminal		5294
281IPR016159
Cullin repeat-like-containing domain		5277
282IPR025398
Domain of unknown function DUF4371		5263
283IPR015797
NUDIX hydrolase domain-like		52125
284IPR033138
Multicopper oxidases, conserved site		5151
285IPR001251
Cellular retinaldehyde-binding/triple function, C-terminal		51273
286IPR013783
Immunoglobulin-like fold		5168
287IPR022742
Alpha/beta hydrolase, N-terminal		5154
288IPR011012
Longin-like domain		5152
289IPR002495
Glycosyl transferase, family 8		5154
290IPR015915
Kelch-type beta propeller		5168
291IPR020843
Polyketide synthase, enoylreductase		5152
292IPR025110
Domain of unknown function DUF4009		5051
293IPR032872
Wall-associated receptor kinase, C-terminal		5051
294IPR004159
Protein of unknown function DUF248, methyltransferase putative		5053
295IPR018289
MULE transposase, conserved domain		5054
296IPR007112
Expansin/pollen allergen, DPBB domain		5089
297IPR014720
Double-stranded RNA-binding-like		50203
298IPR000620
Drug/metabolite transporter		5092
299IPR008889
VQ		5050
300IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		5050
301IPR008942
ENTH/VHS		49113
302IPR001938
Thaumatin, pathogenesis-related		49581
303IPR023313
Ubiquitin-conjugating enzyme, active site		4957
304IPR000668
Peptidase C1A, papain C-terminal		49222
305IPR017761
Laccase		4950
306IPR029000
Cyclophilin-like domain		48101
307IPR010920
Like-Sm ribonucleoprotein (LSM)-related domain		4850
308IPR013128
Peptidase C1A, papain		4852
309IPR029021
Protein-tyrosine phosphatase-like		48147
310IPR006652
Kelch repeat type 1		48184
311IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		4863
312IPR000644
Cystathionine beta-synthase, core		48282
313IPR007527
Zinc finger, SWIM-type		4895
314IPR002130
Peptidyl-prolyl cis-trans isomerase, cyclophilin-type		47265
315IPR025525
Domain of unknown function DUF4413		4750
316IPR001360
Glycoside hydrolase, family 1		47292
317IPR019557
Aminotransferase-like, plant mobile domain		4750
318IPR005150
Cellulose synthase		4766
319IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		4773
320IPR000086
NUDIX hydrolase domain		47112
321IPR025315
Domain of unknown function DUF4220		4754
322IPR002487
Transcription factor, K-box		47104
323IPR010402
CCT domain		46103
324IPR000315
Zinc finger, B-box		46205
325IPR001296
Glycosyl transferase, group 1		4651
326IPR001969
Peptidase aspartic, active site		4673
327IPR011013
Glycoside hydrolase-type carbohydrate-binding		4664
328IPR025875
Leucine rich repeat 4		4654
329IPR017937
Thioredoxin, conserved site		4659
330IPR004330
Transcription factor, FAR1-related		4657
331IPR032710
NTF2-like domain		4598
332IPR011701
Major facilitator superfamily MFS-1		4550
333IPR013216
Methyltransferase type 11		4551
334IPR003406
Glycosyl transferase, family 14		4546
335IPR002035
von Willebrand factor, type A		45172
336IPR025659
Tubby C-terminal-like domain		4453
337IPR006153
Cation/H+ exchanger		4452
338IPR027356
NPH3 domain		44102
339IPR004265
Plant disease resistance response protein		4445
340IPR004367
Cyclin, C-terminal		4495
341IPR007125
Histone core		4444
342IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		4448
343IPR008480
Protein of unknown function DUF761, plant		4445
344IPR003851
Zinc finger, Dof-type		44191
345IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		4448
346IPR001395
Aldo/keto reductase		4455
347IPR011074
Phosphatidylinositol transfer protein-like, N-terminal		43130
348IPR020904
Short-chain dehydrogenase/reductase, conserved site		4349
349IPR000863
Sulfotransferase domain		4347
350IPR002641
Patatin/Phospholipase A2-related		4346
351IPR023210
NADP-dependent oxidoreductase domain		43130
352IPR000727
Target SNARE coiled-coil domain		42113
353IPR002423
Chaperonin Cpn60/TCP-1		4244
354IPR007658
Protein of unknown function DUF594		4243
355IPR005746
Thioredoxin		4279
356IPR022357
Major intrinsic protein, conserved site		4243
357IPR000757
Glycoside hydrolase, family 16		4289
358IPR015947
Pseudouridine synthase/archaeosine transglycosylase-like		4264
359IPR033275
E3 ubiquitin-protein ligase MARCH-like		4153
360IPR001849
Pleckstrin homology domain		41107
361IPR000916
Bet v I allergen		4167
362IPR000169
Peptidase, cysteine peptidase active site		4142
363IPR011043
Galactose oxidase/kelch, beta-propeller		4147
364IPR009091
Regulator of chromosome condensation/beta-lactamase-inhibitor protein II		41105
365IPR001487
Bromodomain		41335
366IPR012341
Six-hairpin glycosidase		4145
367IPR005175
Domain of unknown function DUF296		4186
368IPR002913
Lipid-binding START		41123
369IPR006594
LisH dimerisation motif		4090
370IPR019956
Ubiquitin subgroup		40138
371IPR006564
Zinc finger, PMZ-type		4043
372IPR004146
DC1		40145
373IPR018202
Peptidase S10, serine carboxypeptidase, active site		4045
374IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		39169
375IPR016461
O-methyltransferase, COMT, eukaryota		3969
376IPR013088
Zinc finger, NHR/GATA-type		3945
377IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		3988
378IPR033124
Serine carboxypeptidases, histidine active site		3943
379IPR027409
GroEL-like apical domain		3980
380IPR001077
O-methyltransferase, family 2		3940
381IPR019780
Germin, manganese binding site		3939
382IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3942
383IPR025660
Cysteine peptidase, histidine active site		3941
384IPR000679
Zinc finger, GATA-type		39169
385IPR018490
Cyclic nucleotide-binding-like		3840
386IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		3866
387IPR013201
Proteinase inhibitor I29, cathepsin propeptide		3876
388IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		38106
389IPR029061
Thiamin diphosphate-binding fold		38148
390IPR012675
Beta-grasp fold, ferredoxin-type		3844
391IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3845
392IPR007117
Pollen allergen/expansin, C-terminal		38152
393IPR025661
Cysteine peptidase, asparagine active site		3838
394IPR000595
Cyclic nucleotide-binding domain		38100
395IPR011042
Six-bladed beta-propeller, TolB-like		3844
396IPR006073
GTP1/OBG		38112
397IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3765
398IPR018957
Zinc finger, C3HC4 RING-type		3742
399IPR007118
Expansin/Lol pI		37207
400IPR008991
Translation protein SH3-like		3739
401IPR000717
Proteasome component (PCI) domain		3778
402IPR002328
Alcohol dehydrogenase, zinc-containing, conserved site		3740
403IPR000795
Protein synthesis factor, GTP-binding		37208
404IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3739
405IPR003008
Tubulin/FtsZ, GTPase domain		37171
406IPR013695
Wall-associated kinase		3738
407IPR004046
Glutathione S-transferase, C-terminal		3738
408IPR018097
EGF-like calcium-binding, conserved site		3737
409IPR003855
K+ potassium transporter		3764
410IPR010525
Auxin response factor		3749
411IPR017884
SANT, eukarya		3646
412IPR017103
Ionotropic glutamate receptor, plant		3636
413IPR000528
Plant lipid transfer protein/Par allergen		36162
414IPR013601
FAE1/Type III polyketide synthase-like protein		3639
415IPR006593
Cytochrome b561/ferric reductase transmembrane		36104
416IPR001024
Lipoxygenase, LH2		36152
417IPR018392
Peptidoglycan-binding lysin domain		36134
418IPR008280
Tubulin/FtsZ, C-terminal		3637
419IPR016455
Xyloglucan endotransglucosylase/hydrolase		3638
420IPR010989
t-SNARE		3642
421IPR002293
Amino acid/polyamine transporter I		36111
422IPR033443
Pentacotripeptide-repeat region of PROPR		3640
423IPR002939
Chaperone DnaJ, C-terminal		3638
424IPR013126
Heat shock protein 70		36267
425IPR017927
Ferredoxin reductase-type FAD-binding domain		3544
426IPR008971
HSP40/DnaJ peptide-binding		3587
427IPR001279
Beta-lactamase-like		35138
428IPR001353
Proteasome, subunit alpha/beta		3538
429IPR027413
GroEL-like equatorial domain		3566
430IPR022796
Chlorophyll A-B binding protein		3544
431IPR001876
Zinc finger, RanBP2-type		35394
432IPR001701
Glycoside hydrolase, family 9		3536
433IPR003311
AUX/IAA protein		3550
434IPR017938
Riboflavin synthase-like beta-barrel		3446
435IPR013328
Dehydrogenase, multihelical		3446
436IPR008422
Homeobox KN domain		3436
437IPR001881
EGF-like calcium-binding		3442
438IPR004320
Protein of unknown function DUF241, plant		3435
439IPR000639
Epoxide hydrolase-like		34152
440IPR004014
ATPase, P-type cation-transporter, N-terminal		3471
441IPR015813
Pyruvate/Phosphoenolpyruvate kinase		34105
442IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		3435
443IPR005821
Ion transport		3435
444IPR029006
ADF-H/Gelsolin-like domain		3477
445IPR012967
Plant methyltransferase dimerisation		3435
446IPR017949
Thaumatin, conserved site		3338
447IPR006689
ARF/SAR superfamily		33164
448IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		33106
449IPR000217
Tubulin		33302
450IPR000253
Forkhead-associated (FHA) domain		33112
451IPR027725
Heat shock transcription factor family		3339
452IPR005333
Transcription factor, TCP		3333
453IPR017887
Transcription factor TCP subgroup		3333
454IPR031112
AP2-like ethylene-responsive transcription factor		3335
455IPR004776
Auxin efflux carrier		3345
456IPR008502
Protein of unknown function DUF784, Arabidopsis thaliana		3333
457IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		3361
458IPR022251
Protein of unknown function wound-induced		3333
459IPR004294
Carotenoid oxygenase		3269
460IPR003106
Leucine zipper, homeobox-associated		3250
461IPR004331
SPX, N-terminal		3278
462IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3234
463IPR001305
Heat shock protein DnaJ, cysteine-rich domain		3296
464IPR002659
Glycosyl transferase, family 31		3273
465IPR011047
Quinonprotein alcohol dehydrogenase-like		3257
466IPR022812
Dynamin superfamily		32201
467IPR000408
Regulator of chromosome condensation, RCC1		32571
468IPR001905
Ammonium transporter		3256
469IPR016161
Aldehyde/histidinol dehydrogenase		3237
470IPR029047
Heat shock protein 70kD, peptide-binding domain		3272
471IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		32297
472IPR007612
Protein of unknown function DUF567		3131
473IPR024041
Ammonium transporter AmtB-like		3163
474IPR007493
Protein of unknown function DUF538		31100
475IPR003954
RNA recognition motif domain, eukaryote		3165
476IPR017975
Tubulin, conserved site		3131
477IPR025886
Phloem protein 2-like		3135
478IPR029056
Ribokinase-like		3179
479IPR002083
MATH/TRAF domain		31172
480IPR006580
Zinc finger, TTF-type		3131
481IPR004333
Transcription factor, SBP-box		31123
482IPR004813
Oligopeptide transporter OPT superfamily		3171
483IPR029069
HotDog domain		31111
484IPR029062
Class I glutamine amidotransferase-like		3186
485IPR023123
Tubulin, C-terminal		3131
486IPR000195
Rab-GAP/TBC domain		31169
487IPR016162
Aldehyde dehydrogenase, N-terminal		3138
488IPR002937
Amine oxidase		3142
489IPR023329
Chlorophyll a/b binding protein domain		3142
490IPR011065
Kunitz inhibitor ST1-like		3030
491IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		3078
492IPR025753
AAA-type ATPase, N-terminal domain		3032
493IPR001440
Tetratricopeptide TPR-1		3046
494IPR008984
SMAD/FHA domain		3034
495IPR005299
SAM dependent carboxyl methyltransferase		3034
496IPR009071
High mobility group, superfamily		30141
497IPR006068
ATPase, P-type cation-transporter, C-terminal		3031
498IPR014977
WRC domain		3062
499IPR008263
Glycoside hydrolase, family 16, active site		3032
500IPR029020
Ammonium/urea transporter		3033
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Prunus_persica.html b/gramene/htdocs/ssi/species.weix/stats_Prunus_persica.html new file mode 100644 index 00000000..8922ff51 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Prunus_persica.html @@ -0,0 +1,274 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Prupe1_0, Mar 2013
Database version:86.1
Base Pairs:224,608,292
Golden Path Length:227,251,827
Genebuild by: IPGI
Genebuild method: Generated by the IPGI
Genebuild started: Mar 2013
Genebuild released: Mar 2013
Genebuild last updated/patched: Mar 2013
Genebuild version: 2013-03
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		28,087
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		21
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:30,339
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
8 sequences
+
+ +
+ + + +
SequenceLength (bp)
146877626
226807724
322025550
430528727
518502877
628902582
722790193
821829753
+
+
supercontig
+
194 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaffold_92126789
scaffold_10851981
scaffold_11736058
scaffold_12675284
scaffold_13670721
scaffold_14575512
scaffold_15516056
scaffold_16390024
scaffold_17370749
scaffold_18333953
scaffold_22167479
scaffold_2369963
scaffold_2572028
scaffold_2638727
scaffold_2832503
scaffold_2932043
scaffold_3030119
scaffold_3128663
scaffold_3327846
scaffold_3425707
scaffold_3623381
scaffold_3723004
scaffold_3921452
scaffold_4118507
scaffold_4322324
scaffold_4417159
scaffold_4518055
scaffold_4616788
scaffold_4816633
scaffold_4918477
scaffold_5015657
scaffold_5118614
scaffold_5314945
scaffold_6212576
scaffold_6412283
scaffold_6512174
scaffold_6612005
scaffold_6813972
scaffold_6914802
scaffold_7111897
scaffold_7211986
scaffold_7312137
scaffold_7711014
scaffold_7811828
scaffold_7911057
scaffold_8012322
scaffold_8110689
scaffold_8210576
scaffold_8310595
scaffold_8411032
scaffold_8810450
scaffold_8910992
scaffold_919725
scaffold_959539
scaffold_1018670
scaffold_1038950
scaffold_1088262
scaffold_11215118
scaffold_11510646
scaffold_1197602
scaffold_1227938
scaffold_1237332
scaffold_1277027
scaffold_1328362
scaffold_1347505
scaffold_1366961
scaffold_1387029
scaffold_1408426
scaffold_1417301
scaffold_1456400
scaffold_1468639
scaffold_1478239
scaffold_1486550
scaffold_1496232
scaffold_1506164
scaffold_1516128
scaffold_1526087
scaffold_1547028
scaffold_1557971
scaffold_1576143
scaffold_1586001
scaffold_1606780
scaffold_1625646
scaffold_1645581
scaffold_1666743
scaffold_1675507
scaffold_1686895
scaffold_1697410
scaffold_1725491
scaffold_1735735
scaffold_1745263
scaffold_1755625
scaffold_1765579
scaffold_1776011
scaffold_1787275
scaffold_1795300
scaffold_1805261
scaffold_1826000
scaffold_1855192
scaffold_1865047
scaffold_1925029
scaffold_1934817
scaffold_1945295
scaffold_1985301
scaffold_1994608
scaffold_2005090
scaffold_2024575
scaffold_2034533
scaffold_2056379
scaffold_20710371
scaffold_21013173
scaffold_2116207
scaffold_2135496
scaffold_2144346
scaffold_2194817
scaffold_2225602
scaffold_2245334
scaffold_2264100
scaffold_2304624
scaffold_2314478
scaffold_2324499
scaffold_2367279
scaffold_2394116
scaffold_2424391
scaffold_2436198
scaffold_2454914
scaffold_2474257
scaffold_2484247
scaffold_2503699
scaffold_2536946
scaffold_2554017
scaffold_2574016
scaffold_2584525
scaffold_2593541
scaffold_2605131
scaffold_2613536
scaffold_2653576
scaffold_2663476
scaffold_2674999
scaffold_2694446
scaffold_2703708
scaffold_2717959
scaffold_2773415
scaffold_2813362
scaffold_2823153
scaffold_2834837
scaffold_2873789
scaffold_2903424
scaffold_2913885
scaffold_2924092
scaffold_2952907
scaffold_2963892
scaffold_2973789
scaffold_2994251
scaffold_3023320
scaffold_30612535
scaffold_3073020
scaffold_3088994
scaffold_3093815
scaffold_3136282
scaffold_3172957
scaffold_3182997
scaffold_3192380
scaffold_3222890
scaffold_3232068
scaffold_3242374
scaffold_3304850
scaffold_3322536
scaffold_3353154
scaffold_3365815
scaffold_3375022
scaffold_3381589
scaffold_3396504
scaffold_3413429
scaffold_3421501
scaffold_3434969
scaffold_3441452
scaffold_3451821
scaffold_3466007
scaffold_3473708
scaffold_3483411
scaffold_3491306
scaffold_3505997
scaffold_3515575
scaffold_3541164
scaffold_3551163
scaffold_3561145
scaffold_3572995
scaffold_3582805
scaffold_3601099
scaffold_3611092
scaffold_3621071
scaffold_3631061
scaffold_3646571
+
+
contig2740 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Prunus_persica_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Prunus_persica_IPtop500.html new file mode 100644 index 00000000..96b1568e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Prunus_persica_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		12903422
2IPR011009
Protein kinase-like domain		11871301
3IPR032675
Leucine-rich repeat domain, L domain-like		11113854
4IPR000719
Protein kinase domain		11052672
5IPR008271
Serine/threonine-protein kinase, active site		809822
6IPR017441
Protein kinase, ATP binding site		655668
7IPR011990
Tetratricopeptide-like helical domain		6112065
8IPR013320
Concanavalin A-like lectin/glucanase, subgroup		610758
9IPR001611
Leucine-rich repeat		5693405
10IPR013083
Zinc finger, RING/FYVE/PHD-type		555610
11IPR002885
Pentatricopeptide repeat		55313029
12IPR012337
Ribonuclease H-like domain		461729
13IPR016040
NAD(P)-binding domain		4541073
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		421595
15IPR004252
Probable transposase, Ptta/En/Spm, plant		416416
16IPR002182
NB-ARC		406424
17IPR001810
F-box domain		4051089
18IPR001841
Zinc finger, RING-type		376906
19IPR003591
Leucine-rich repeat, typical subtype		3672524
20IPR009057
Homeodomain-like		346843
21IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		340661
22IPR029058
Alpha/Beta hydrolase fold		324799
23IPR016024
Armadillo-type fold		315758
24IPR001128
Cytochrome P450		3141915
25IPR003593
AAA+ ATPase domain		302411
26IPR013210
Leucine-rich repeat-containing N-terminal, type 2		281288
27IPR002401
Cytochrome P450, E-class, group I		2651754
28IPR017853
Glycoside hydrolase, superfamily		264304
29IPR015943
WD40/YVTN repeat-like-containing domain		262431
30IPR012677
Nucleotide-binding, alpha-beta plait		257775
31IPR017986
WD40-repeat-containing domain		251656
32IPR011989
Armadillo-like helical		250528
33IPR017972
Cytochrome P450, conserved site		241241
34IPR001005
SANT/Myb domain		238665
35IPR012336
Thioredoxin-like fold		235563
36IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		234641
37IPR000504
RNA recognition motif domain		2321053
38IPR011991
Winged helix-turn-helix DNA-binding domain		227369
39IPR001680
WD40 repeat		2262693
40IPR013781
Glycoside hydrolase, catalytic domain		219249
41IPR018289
MULE transposase domain		217218
42IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		217509
43IPR020846
Major facilitator superfamily domain		216454
44IPR017930
Myb domain		187312
45IPR020683
Ankyrin repeat-containing domain		178900
46IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		175846
47IPR025312
Domain of unknown function DUF4216		173173
48IPR001878
Zinc finger, CCHC-type		169673
49IPR011992
EF-hand domain pair		168405
50IPR011050
Pectin lyase fold/virulence factor		164170
51IPR002110
Ankyrin repeat		1641199
52IPR012334
Pectin lyase fold		162173
53IPR005123
Oxoglutarate/iron-dependent dioxygenase		156285
54IPR027443
Isopenicillin N synthase-like		154164
55IPR023214
HAD-like domain		153447
56IPR008906
HAT dimerisation domain, C-terminal		150152
57IPR000477
Reverse transcriptase domain		147212
58IPR018247
EF-Hand 1, calcium-binding site		146306
59IPR002048
EF-hand domain		145909
60IPR019775
WD40 repeat, conserved site		143255
61IPR014001
Helicase, superfamily 1/2, ATP-binding domain		142285
62IPR017451
F-box associated interaction domain		139139
63IPR003439
ABC transporter-like		139434
64IPR001650
Helicase, C-terminal		138419
65IPR016177
DNA-binding domain		138156
66IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		137618
67IPR031052
FHY3/FAR1 family		133141
68IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		131159
69IPR014710
RmlC-like jelly roll fold		130157
70IPR026960
Reverse transcriptase zinc-binding domain		129129
71IPR032867
DYW domain		129131
72IPR001471
AP2/ERF domain		128807
73IPR008972
Cupredoxin		127464
74IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		126528
75IPR026992
Non-haem dioxygenase N-terminal domain		126126
76IPR006564
Zinc finger, PMZ-type		124124
77IPR007527
Zinc finger, SWIM-type		122223
78IPR029044
Nucleotide-diphospho-sugar transferases		120294
79IPR013830
SGNH hydrolase superfamily		120310
80IPR007087
Zinc finger, C2H2		117399
81IPR003441
NAC domain		115346
82IPR012340
Nucleic acid-binding, OB-fold		115166
83IPR021109
Aspartic peptidase domain		114291
84IPR029071
Ubiquitin-related domain		114179
85IPR015300
DNA-binding pseudobarrel domain		112285
86IPR003959
ATPase, AAA-type, core		110135
87IPR013026
Tetratricopeptide repeat-containing domain		109154
88IPR002085
Alcohol dehydrogenase superfamily, zinc-type		106129
89IPR004332
Transposase, MuDR, plant		104104
90IPR026961
PGG domain		103103
91IPR019734
Tetratricopeptide repeat		102797
92IPR001480
Bulb-type lectin domain		102524
93IPR011032
GroES (chaperonin 10)-like		101223
94IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		101110
95IPR004158
Protein of unknown function DUF247, plant		101118
96IPR015424
Pyridoxal phosphate-dependent transferase		98111
97IPR013785
Aldolase-type TIM barrel		97118
98IPR002347
Glucose/ribitol dehydrogenase		97958
99IPR020472
G-protein beta WD-40 repeat		97306
100IPR000008
C2 domain		96768
101IPR005225
Small GTP-binding protein domain		96100
102IPR001087
Lipase, GDSL		9393
103IPR001623
DnaJ domain		93669
104IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		9399
105IPR003340
B3 DNA binding domain		90320
106IPR005135
Endonuclease/exonuclease/phosphatase		90211
107IPR017871
ABC transporter, conserved site		90124
108IPR011011
Zinc finger, FYVE/PHD-type		88106
109IPR025525
Domain of unknown function DUF4413		8586
110IPR017907
Zinc finger, RING-type, conserved site		8589
111IPR023213
Chloramphenicol acetyltransferase-like domain		83166
112IPR001461
Aspartic peptidase		83233
113IPR023393
START-like domain		8186
114IPR011333
BTB/POZ fold		8187
115IPR003609
Apple-like		80212
116IPR005828
General substrate transporter		8088
117IPR000073
Alpha/beta hydrolase fold-1		80180
118IPR002100
Transcription factor, MADS-box		80560
119IPR010987
Glutathione S-transferase, C-terminal-like		80235
120IPR033121
Peptidase family A1 domain		7985
121IPR011051
RmlC-like cupin domain		7995
122IPR010255
Haem peroxidase		7982
123IPR004330
FAR1 DNA binding domain		7980
124IPR002016
Haem peroxidase, plant/fungal/bacterial		78526
125IPR001360
Glycoside hydrolase, family 1		77464
126IPR004045
Glutathione S-transferase, N-terminal		77154
127IPR003676
Auxin-induced protein, ARG7		7777
128IPR013154
Alcohol dehydrogenase GroES-like		7680
129IPR032861
Xylanase inhibitor, N-terminal		7678
130IPR001932
Protein phosphatase 2C (PP2C)-like domain		76469
131IPR003480
Transferase		7684
132IPR000626
Ubiquitin domain		75345
133IPR013149
Alcohol dehydrogenase, C-terminal		7579
134IPR032799
Xylanase inhibitor, C-terminal		7475
135IPR003245
Plastocyanin-like		74215
136IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		7483
137IPR001356
Homeobox domain		73198
138IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		72166
139IPR000070
Pectinesterase, catalytic		7272
140IPR027806
Harbinger transposase-derived nuclease domain		7172
141IPR013766
Thioredoxin domain		71137
142IPR006501
Pectinesterase inhibitor domain		71340
143IPR000571
Zinc finger, CCCH-type		71592
144IPR025287
Wall-associated receptor kinase galacturonan-binding domain		7071
145IPR000858
S-locus glycoprotein		7071
146IPR000225
Armadillo		70583
147IPR000270
Phox/Bem1p		69120
148IPR025452
Domain of unknown function DUF4218		6872
149IPR006447
Myb domain, plants		6871
150IPR019793
Peroxidases heam-ligand binding site		6869
151IPR015500
Peptidase S8, subtilisin-related		68258
152IPR000823
Plant peroxidase		68589
153IPR004864
Late embryogenesis abundant protein, LEA-14		6768
154IPR001965
Zinc finger, PHD-type		67102
155IPR006121
Heavy metal-associated domain, HMA		66201
156IPR002902
Gnk2-homologous domain		66219
157IPR000209
Peptidase S8/S53 domain		66340
158IPR000210
BTB/POZ domain		65170
159IPR005162
Retrotransposon gag domain		6565
160IPR029052
Metallo-dependent phosphatase-like		65166
161IPR015880
Zinc finger, C2H2-like		65198
162IPR003656
Zinc finger, BED-type predicted		64158
163IPR015655
Protein phosphatase 2C		64111
164IPR000109
Proton-dependent oligopeptide transporter family		63129
165IPR003960
ATPase, AAA-type, conserved site		6369
166IPR016135
Ubiquitin-conjugating enzyme/RWD-like		63140
167IPR002528
Multi antimicrobial extrusion protein		63170
168IPR000743
Glycoside hydrolase, family 28		6395
169IPR010259
Proteinase inhibitor I9		6288
170IPR009072
Histone-fold		62126
171IPR004843
Phosphoesterase domain		6164
172IPR005829
Sugar transporter, conserved site		61106
173IPR003657
DNA-binding WRKY		61354
174IPR025398
Domain of unknown function DUF4371		6174
175IPR020843
Polyketide synthase, enoylreductase domain		6164
176IPR019557
Aminotransferase-like, plant mobile domain		6065
177IPR013057
Amino acid transporter, transmembrane		6063
178IPR024788
Malectin-like carbohydrate-binding domain		6061
179IPR003663
Sugar/inositol transporter		59318
180IPR029480
Transposase-associated domain		5858
181IPR018108
Mitochondrial substrate/solute carrier		58345
182IPR023395
Mitochondrial carrier domain		58133
183IPR011993
Pleckstrin homology-like domain		57114
184IPR013525
ABC-2 type transporter		5683
185IPR008979
Galactose-binding domain-like		56152
186IPR020568
Ribosomal protein S5 domain 2-type fold		5674
187IPR001806
Small GTPase superfamily		5659
188IPR016166
FAD-binding, type 2		55109
189IPR018253
DnaJ domain, conserved site		5555
190IPR011527
ABC transporter type 1, transmembrane domain		55294
191IPR003613
U box domain		55163
192IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5555
193IPR025558
Domain of unknown function DUF4283		5556
194IPR033131
Pectinesterase, Asp active site		5454
195IPR019787
Zinc finger, PHD-finger		54105
196IPR027640
Kinesin-like protein		54149
197IPR024752
Myb/SANT-like domain		5465
198IPR010264
Plant self-incompatibility S1		5454
199IPR018490
Cyclic nucleotide-binding-like		5358
200IPR019786
Zinc finger, PHD-type, conserved site		5365
201IPR019794
Peroxidase, active site		5354
202IPR001752
Kinesin, motor domain		53419
203IPR000608
Ubiquitin-conjugating enzyme, E2		52117
204IPR026057
PC-Esterase		5254
205IPR004263
Exostosin-like		5252
206IPR006045
Cupin 1		52128
207IPR006094
FAD linked oxidase, N-terminal		5253
208IPR030184
WAT1-related protein		5257
209IPR006527
F-box associated domain, type 1		5252
210IPR001117
Multicopper oxidase, type 1		5153
211IPR008978
HSP20-like chaperone		51106
212IPR009009
RlpA-like double-psi beta-barrel domain		51137
213IPR013763
Cyclin-like		51236
214IPR000595
Cyclic nucleotide-binding domain		51119
215IPR016181
Acyl-CoA N-acyltransferase		50108
216IPR029962
Trichome birefringence-like family		5064
217IPR014014
RNA helicase, DEAD-box type, Q motif		5055
218IPR023828
Peptidase S8, subtilisin, Ser-active site		4949
219IPR011706
Multicopper oxidase, type 2		4950
220IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		4950
221IPR013128
Peptidase C1A, papain		4849
222IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4893
223IPR005174
Protein of unknown function DUF295		4848
224IPR005202
Transcription factor GRAS		4896
225IPR000490
Glycoside hydrolase, family 17		4884
226IPR004827
Basic-leucine zipper domain		48175
227IPR000048
IQ motif, EF-hand binding site		48315
228IPR011707
Multicopper oxidase, type 3		4849
229IPR000873
AMP-dependent synthetase/ligase		4748
230IPR008250
P-type ATPase, A domain		4799
231IPR003594
Histidine kinase-like ATPase, ATP-binding domain		47176
232IPR008266
Tyrosine-protein kinase, active site		4747
233IPR000668
Peptidase C1A, papain C-terminal		47165
234IPR000620
Drug/metabolite transporter		4784
235IPR008974
TRAF-like		47113
236IPR012946
X8 domain		4692
237IPR023299
P-type ATPase, cytoplasmic domain N		4692
238IPR001757
Cation-transporting P-type ATPase		46177
239IPR001509
NAD-dependent epimerase/dehydratase		4547
240IPR001214
SET domain		45122
241IPR023210
NADP-dependent oxidoreductase domain		45143
242IPR001395
Aldo/keto reductase		4558
243IPR006904
Protein of unknown function DUF716, TMEM45		4469
244IPR002068
Alpha crystallin/Hsp20 domain		4484
245IPR018303
P-type ATPase, phosphorylation site		4446
246IPR001220
Legume lectin domain		4447
247IPR014756
Immunoglobulin E-set		4449
248IPR015916
Galactose oxidase, beta-propeller		4347
249IPR001929
Germin		43127
250IPR020904
Short-chain dehydrogenase/reductase, conserved site		4344
251IPR008928
Six-hairpin glycosidase-like		4354
252IPR001320
Ionotropic glutamate receptor		4385
253IPR016167
FAD-binding, type 2, subdomain 1		4343
254IPR025846
PMR5 N-terminal domain		4344
255IPR001563
Peptidase S10, serine carboxypeptidase		42261
256IPR006016
UspA		4244
257IPR006553
Leucine-rich repeat, cysteine-containing subtype		42346
258IPR004883
Lateral organ boundaries, LOB		4284
259IPR028082
Periplasmic binding protein-like I		4270
260IPR001828
Extracellular ligand-binding receptor		4243
261IPR013094
Alpha/beta hydrolase fold-3		4245
262IPR016039
Thiolase-like		41189
263IPR003137
Protease-associated domain, PA		4141
264IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		4142
265IPR029055
Nucleophile aminohydrolases, N-terminal		4183
266IPR003690
Mitochodrial transcription termination factor-related		41316
267IPR014044
CAP domain		41161
268IPR002921
Lipase, class 3		4040
269IPR019821
Kinesin, motor region, conserved site		4040
270IPR013783
Immunoglobulin-like fold		4047
271IPR000916
Bet v I domain		4061
272IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		4099
273IPR006153
Cation/H+ exchanger		3940
274IPR024171
S-receptor-like serine/threonine-protein kinase		3939
275IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		39181
276IPR011043
Galactose oxidase/kelch, beta-propeller		3948
277IPR024553
Domain of unknown function DUF2828		3970
278IPR000182
GNAT domain		3868
279IPR008949
Terpenoid synthase		3879
280IPR013187
F-box associated domain, type 3		3838
281IPR001969
Aspartic peptidase, active site		3857
282IPR001938
Thaumatin		38429
283IPR000742
Epidermal growth factor-like domain		3874
284IPR005821
Ion transport domain		3840
285IPR031107
Small heat shock protein HSP20		3840
286IPR002067
Mitochondrial carrier protein		38198
287IPR001638
Extracellular solute-binding protein, family 3		3839
288IPR001584
Integrase, catalytic core		3763
289IPR006626
Parallel beta-helix repeat		37184
290IPR004853
Triose-phosphate transporter domain		3739
291IPR012951
Berberine/berberine-like		3737
292IPR004046
Glutathione S-transferase, C-terminal		3739
293IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3739
294IPR009000
Translation protein, beta-barrel domain		3642
295IPR006580
Zinc finger, TTF-type		3636
296IPR020845
AMP-binding, conserved site		3637
297IPR013126
Heat shock protein 70 family		36315
298IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3638
299IPR015797
NUDIX hydrolase domain-like		3676
300IPR017877
Myb-like domain		3651
301IPR000330
SNF2-related		3535
302IPR018181
Heat shock protein 70, conserved site		3582
303IPR002083
MATH/TRAF domain		35122
304IPR011012
Longin-like domain		3536
305IPR029045
ClpP/crotonase-like domain		35102
306IPR016159
Cullin repeat-like-containing domain		3547
307IPR006073
GTP binding domain		3597
308IPR033389
AUX/IAA domain		3442
309IPR010920
Like-Sm (LSM) domain		3439
310IPR029021
Protein-tyrosine phosphatase-like		3485
311IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		3436
312IPR002355
Multicopper oxidase, copper-binding site		3434
313IPR007112
Expansin/pollen allergen, DPBB domain		3465
314IPR017970
Homeobox, conserved site		3435
315IPR002035
von Willebrand factor, type A		3497
316IPR002109
Glutaredoxin		3473
317IPR029047
Heat shock protein 70kD, peptide-binding domain		3471
318IPR001487
Bromodomain		34269
319IPR015947
PUA-like domain		3448
320IPR008942
ENTH/VHS		3366
321IPR032710
NTF2-like domain		3358
322IPR001251
CRAL-TRIO domain		33170
323IPR011701
Major facilitator superfamily		3334
324IPR013201
Proteinase inhibitor I29, cathepsin propeptide		3363
325IPR006652
Kelch repeat type 1		33124
326IPR004839
Aminotransferase, class I/classII		3335
327IPR011006
CheY-like superfamily		3340
328IPR019378
GDP-fucose protein O-fucosyltransferase		3334
329IPR002495
Glycosyl transferase, family 8		3333
330IPR006671
Cyclin, N-terminal		3350
331IPR000086
NUDIX hydrolase domain		3367
332IPR001789
Signal transduction response regulator, receiver domain		33104
333IPR009060
UBA-like		3240
334IPR004088
K Homology domain, type 1		32268
335IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		3153
336IPR004265
Plant disease resistance response protein		3131
337IPR008502
Prolamin-like domain		3135
338IPR000644
CBS domain		31192
339IPR015915
Kelch-type beta propeller		3138
340IPR023298
P-type ATPase, transmembrane domain		3173
341IPR002487
Transcription factor, K-box		3166
342IPR025110
AMP-binding enzyme C-terminal domain		3031
343IPR025659
Tubby C-terminal-like domain		3034
344IPR033138
Multicopper oxidases, conserved site		3030
345IPR008991
Translation protein SH3-like domain		3032
346IPR011016
Zinc finger, RING-CH-type		3068
347IPR001296
Glycosyl transferase, family 1		3030
348IPR023271
Aquaporin-like		3061
349IPR011013
Galactose mutarotase-like domain		3038
350IPR003406
Glycosyl transferase, family 14		3030
351IPR023313
Ubiquitin-conjugating enzyme, active site		3035
352IPR005746
Thioredoxin		3039
353IPR000425
Major intrinsic protein		30247
354IPR029069
HotDog domain		3084
355IPR006566
FBD domain		3043
356IPR014720
Double-stranded RNA-binding domain		30115
357IPR002912
ACT domain		3075
358IPR025660
Cysteine peptidase, histidine active site		3030
359IPR005804
Fatty acid desaturase, type 1		3030
360IPR004873
BURP domain		2996
361IPR025836
Zinc knuckle CX2CX4HX4C		2931
362IPR019780
Germin, manganese binding site		2929
363IPR013242
Retroviral aspartyl protease		2929
364IPR017761
Laccase		2929
365IPR000757
Glycoside hydrolase, family 16		2958
366IPR000727
Target SNARE coiled-coil domain		2875
367IPR025322
Protein of unknown function DUF4228, plant		2828
368IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2832
369IPR005150
Cellulose synthase		2845
370IPR022796
Chlorophyll A-B binding protein		2831
371IPR004087
K Homology domain		2868
372IPR000169
Cysteine peptidase, cysteine active site		2829
373IPR025661
Cysteine peptidase, asparagine active site		2828
374IPR011042
Six-bladed beta-propeller, TolB-like		2836
375IPR017949
Thaumatin, conserved site		2727
376IPR000782
FAS1 domain		27159
377IPR003954
RNA recognition motif domain, eukaryote		2751
378IPR007118
Expansin/Lol pI		27153
379IPR013581
Plant PDR ABC transporter associated		2727
380IPR013216
Methyltransferase type 11		2732
381IPR021820
S-locus receptor kinase, C-terminal		2727
382IPR012675
Beta-grasp domain		2728
383IPR022742
Putative lysophospholipase		2729
384IPR021720
Malectin		2727
385IPR004014
Cation-transporting P-type ATPase, N-terminal		2753
386IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		2728
387IPR001849
Pleckstrin homology domain		2761
388IPR017937
Thioredoxin, conserved site		2732
389IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2727
390IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		2728
391IPR016197
Chromo domain-like		2734
392IPR010402
CCT domain		2654
393IPR000528
Plant lipid transfer protein/Par allergen		26117
394IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		26152
395IPR029000
Cyclophilin-like domain		2658
396IPR025753
AAA-type ATPase, N-terminal domain		2626
397IPR000795
Elongation factor, GTP-binding domain		26152
398IPR016455
Xyloglucan endotransglucosylase/hydrolase		2626
399IPR011074
CRAL/TRIO, N-terminal domain		2676
400IPR008480
Protein of unknown function DUF761, plant		2626
401IPR029481
ABC-transporter extracellular N-terminal domain		2626
402IPR003851
Zinc finger, Dof-type		26103
403IPR007117
Expansin, cellulose-binding-like domain		26104
404IPR011709
Domain of unknown function DUF1605		2626
405IPR008889
VQ		2626
406IPR006594
LisH dimerisation motif		2558
407IPR007502
Helicase-associated domain		2550
408IPR006195
Aminoacyl-tRNA synthetase, class II		2526
409IPR005299
SAM dependent carboxyl methyltransferase		2528
410IPR018392
LysM domain		2587
411IPR004367
Cyclin, C-terminal domain		2547
412IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2528
413IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2528
414IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2529
415IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2568
416IPR023329
Chlorophyll a/b binding protein domain		2527
417IPR002913
START domain		2568
418IPR025610
Transcription factor MYC/MYB N-terminal		2529
419IPR017884
SANT domain		2426
420IPR002156
Ribonuclease H domain		2424
421IPR001357
BRCT domain		24171
422IPR000315
Zinc finger, B-box		2496
423IPR027356
NPH3 domain		2448
424IPR010989
t-SNARE		2427
425IPR007125
Histone core		2425
426IPR022357
Major intrinsic protein, conserved site		2424
427IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2442
428IPR006439
HAD hydrolase, subfamily IA		2461
429IPR001223
Glycoside hydrolase, family 18, catalytic domain		2425
430IPR012341
Six-hairpin glycosidase		2425
431IPR024949
Bet v I type allergen		24170
432IPR017103
Ionotropic glutamate receptor, plant		2323
433IPR032872
Wall-associated receptor kinase, C-terminal		2324
434IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2356
435IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		2342
436IPR001163
Ribonucleoprotein LSM domain		2353
437IPR029472
Gag-polypeptide of LTR copia-type		2323
438IPR029061
Thiamin diphosphate-binding fold		2382
439IPR033124
Serine carboxypeptidases, histidine active site		2325
440IPR003008
Tubulin/FtsZ, GTPase domain		23100
441IPR020103
Pseudouridine synthase, catalytic domain		2336
442IPR014722
Ribosomal protein L2 domain 2		2324
443IPR029062
Class I glutamine amidotransferase-like		2360
444IPR003311
AUX/IAA protein		2337
445IPR031127
E3 ubiquitin ligase RBR family		2326
446IPR018202
Peptidase S10, serine carboxypeptidase, active site		2325
447IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		23189
448IPR018082
AmbAllergen		23141
449IPR017927
Ferredoxin reductase-type FAD-binding domain		2223
450IPR003347
JmjC domain		2259
451IPR007750
Protein of unknown function DUF674		2228
452IPR005630
Terpene synthase, metal-binding domain		2222
453IPR004320
Protein of unknown function DUF241, plant		2223
454IPR022812
Dynamin superfamily		22143
455IPR031112
AP2-like ethylene-responsive transcription factor		2225
456IPR026892
Glycoside hydrolase family 3		2235
457IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2223
458IPR006461
Uncharacterised protein family Cys-rich		2243
459IPR024079
Metallopeptidase, catalytic domain		2222
460IPR013780
Glycosyl hydrolase, family 13, all-beta		2222
461IPR016130
Protein-tyrosine phosphatase, active site		2222
462IPR002641
Patatin/Phospholipase A2-related		2222
463IPR006689
Small GTPase superfamily, ARF/SAR type		21100
464IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2180
465IPR013601
FAE1/Type III polyketide synthase-like protein		2123
466IPR019956
Ubiquitin		2176
467IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2139
468IPR016461
Caffeate O-methyltransferase (COMT) family		2140
469IPR030381
Dynamin-type guanine nucleotide-binding (G) domain		2121
470IPR001024
PLAT/LH2 domain		2195
471IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2121
472IPR013088
Zinc finger, NHR/GATA-type		2122
473IPR006068
Cation-transporting P-type ATPase, C-terminal		2122
474IPR020471
Aldo/keto reductase subgroup		2194
475IPR001279
Beta-lactamase-like		2180
476IPR020084
NUDIX hydrolase, conserved site		2123
477IPR001353
Proteasome, subunit alpha/beta		2123
478IPR029056
Ribokinase-like		2151
479IPR025314
Domain of unknown function DUF4219		2121
480IPR000408
Regulator of chromosome condensation, RCC1		21396
481IPR002293
Amino acid/polyamine transporter I		2171
482IPR003107
RNA-processing protein, HAT helix		21158
483IPR004326
Mlo-related protein		2124
484IPR025875
Leucine rich repeat 4		2121
485IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2131
486IPR001906
Terpene synthase, N-terminal domain		2144
487IPR029006
ADF-H/Gelsolin-like domain		2142
488IPR000232
Heat shock factor (HSF)-type, DNA-binding		21108
489IPR000679
Zinc finger, GATA-type		2182
490IPR005175
Domain of unknown function DUF296		2142
491IPR001764
Glycoside hydrolase, family 3, N-terminal		21115
492IPR017938
Riboflavin synthase-like beta-barrel		2022
493IPR002772
Glycoside hydrolase family 3 C-terminal domain		2059
494IPR002867
Zinc finger, C6HC-type		2069
495IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2058
496IPR008422
Homeobox KN domain		2022
497IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2022
498IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		2056
499IPR002659
Glycosyl transferase, family 31		2041
500IPR008280
Tubulin/FtsZ, C-terminal		2020
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii.html b/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii.html new file mode 100644 index 00000000..07dc7557 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii.html @@ -0,0 +1,1586 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:v1.0, May 2011
Database version:86.1
Base Pairs:212,645,483
Golden Path Length:212,645,483
Genebuild by: ENA
Genebuild method: Generated from ENA and UniProtKB annotation
Genebuild started: Jul 2010
Genebuild released: Jul 2010
Genebuild last updated/patched: May 2011
Genebuild version: 2011-05-ENA
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		34,799
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		66
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:34,914
+ + +

Coordinate Systems

+ + + + + + + + +
supercontig
+
759 sequences
+
+ +
+ + + +
SequenceLength (bp)
GL3775656951972
GL3775666181961
GL3775674463058
GL3775684340499
GL3775694143896
GL3775704135178
GL3775713967200
GL3775723908038
GL3775733666672
GL3775743149477
GL3775753093912
GL3775762904818
GL3775772902290
GL3775782863689
GL3775792757670
GL3775802676847
GL3775812470656
GL3775822450372
GL3775832350400
GL3775842302610
GL3775852305360
GL3775862100764
GL3775872094916
GL3775882034879
GL3775891997012
GL3775902002060
GL3775911973895
GL3775921968041
GL3775931968525
GL3775941886115
GL3775951905289
GL3775961846953
GL3775971840579
GL3775981846321
GL3775991796630
GL3776001770965
GL3776011749879
GL3776021705930
GL3776031751465
GL3776041708524
GL3776051743703
GL3776061675513
GL3776071658784
GL3776081658729
GL3776091630749
GL3776101506775
GL3776111511927
GL3776121463349
GL3776131464571
GL3776141480447
GL3776151473132
GL3776161441712
GL3776171451693
GL3776181419048
GL3776191387680
GL3776201343795
GL3776211299822
GL3776221296709
GL3776231263218
GL3776241266795
GL3776251246421
GL3776261275566
GL3776271161766
GL3776281151164
GL3776291143871
GL3776301132267
GL3776311098469
GL3776321081329
GL3776331049549
GL3776341032227
GL377635997799
GL377636987446
GL377637981669
GL377638970821
GL377639993844
GL377640967469
GL377641914710
GL377642903794
GL377643880892
GL377644882469
GL377645928904
GL377646890268
GL377647853333
GL377648859278
GL377649832636
GL377650845143
GL377651830751
GL377652828699
GL377653814213
GL377654797443
GL377655799544
GL377656751281
GL377657765235
GL377658741856
GL377659749943
GL377660719092
GL377661694339
GL377662669108
GL377663682814
GL377664658485
GL377665648882
GL377666641370
GL377667621399
GL377668677250
GL377669609495
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HM173080143775
+
+
contig
+
759 sequences
+
+ +
+ + + +
SequenceLength (bp)
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GL377933.18488
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GL377961.17788
GL377962.17671
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GL377964.18998
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GL377966.17683
GL377967.17581
GL377968.17511
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GL377971.17838
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GL377973.17446
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GL377975.17277
GL377976.17095
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GL377979.17363
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GL377983.16817
GL377984.16746
GL377985.16742
GL377986.16660
GL377987.16570
GL377988.16722
GL377989.16491
GL377990.16488
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GL378020.16904
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GL378047.15502
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GL378050.15127
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GL378202.13746
GL378203.13856
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GL378205.13621
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GL378207.13752
GL378208.13595
GL378209.13581
GL378210.13764
GL378211.13642
GL378212.13525
GL378213.13514
GL378214.14107
GL378215.13594
GL378216.15053
GL378217.13752
GL378218.13704
GL378219.13659
GL378220.13828
GL378221.13440
GL378222.13435
GL378223.13632
GL378224.14044
GL378225.13730
GL378226.13393
GL378227.13833
GL378228.13488
GL378229.13727
GL378230.14022
GL378231.13294
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GL378233.13492
GL378234.13198
GL378235.13187
GL378236.13436
GL378237.13830
GL378238.13702
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GL378240.13476
GL378241.13582
GL378242.13602
GL378243.13910
GL378244.13344
GL378245.13592
GL378246.13305
GL378247.13488
GL378248.13726
GL378249.13102
GL378250.13559
GL378251.13446
GL378252.12963
GL378253.13302
GL378254.13404
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GL378256.13630
GL378257.13198
GL378258.13549
GL378259.13450
GL378260.13065
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GL378263.13330
GL378264.13400
GL378265.13193
GL378266.13658
GL378267.12645
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GL378270.12627
GL378271.12819
GL378272.13170
GL378273.13247
GL378274.12386
GL378275.12291
GL378276.12983
GL378277.12254
GL378278.13138
GL378279.13086
GL378280.12909
GL378281.12862
GL378282.13060
GL378283.12048
GL378284.12038
GL378285.12019
GL378286.12843
GL378287.12681
GL378288.12747
GL378289.12401
GL378290.11669
GL378291.11608
GL378292.11592
GL378293.11583
GL378294.11555
GL378295.11534
GL378296.11365
GL378297.11325
GL378298.11290
GL378299.11287
GL378300.11285
GL378301.11264
GL378302.13456
GL378303.11168
GL378304.11137
GL378305.11093
GL378306.11046
GL378307.1977
GL378308.1923
GL378309.1892
GL378310.1862
GL378311.1852
GL378312.1827
GL378313.1813
GL378314.1806
GL378315.1790
GL378316.1773
GL378317.1759
GL378318.1647
GL378319.1464
GL378320.1455
GL378321.1437
GL378322.1399
HM173080.1143775
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii_IPtop500.html new file mode 100644 index 00000000..563740dc --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Selaginella_moellendorffii_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR002885
Pentatricopeptide repeat		184631161
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		16284544
3IPR011990
Tetratricopeptide-like helical		15835153
4IPR011009
Protein kinase-like domain		13711499
5IPR000719
Protein kinase, catalytic domain		11662880
6IPR008271
Serine/threonine-protein kinase, active site		793797
7IPR013083
Zinc finger, RING/FYVE/PHD-type		651701
8IPR016040
NAD(P)-binding domain		6141333
9IPR032675
Leucine-rich repeat domain, L domain-like		5711631
10IPR017441
Protein kinase, ATP binding site		562566
11IPR016024
Armadillo-type fold		5251258
12IPR029058
Alpha/Beta hydrolase fold		4751152
13IPR001128
Cytochrome P450		4412528
14IPR015943
WD40/YVTN repeat-like-containing domain		428669
15IPR003593
AAA+ ATPase domain		424606
16IPR013320
Concanavalin A-like lectin/glucanase, subgroup		420575
17IPR011989
Armadillo-like helical		417924
18IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		406992
19IPR017986
WD40-repeat-containing domain		398946
20IPR001611
Leucine-rich repeat		3972256
21IPR001680
WD40 repeat		3683979
22IPR001841
Zinc finger, RING-type		360812
23IPR002401
Cytochrome P450, E-class, group I		3582182
24IPR012336
Thioredoxin-like fold		320737
25IPR001810
F-box domain, cyclin-like		317795
26IPR009057
Homeodomain-like		317711
27IPR012677
Nucleotide-binding, alpha-beta plait		316962
28IPR017853
Glycoside hydrolase, superfamily		309353
29IPR023214
HAD-like domain		295807
30IPR017972
Cytochrome P450, conserved site		286286
31IPR000504
RNA recognition motif domain		2771279
32IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		277446
33IPR020846
Major facilitator superfamily domain		274530
34IPR013781
Glycoside hydrolase, catalytic domain		259302
35IPR001650
Helicase, C-terminal		258742
36IPR014001
Helicase, superfamily 1/2, ATP-binding domain		243474
37IPR003439
ABC transporter-like		242734
38IPR003591
Leucine-rich repeat, typical subtype		2341566
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		230599
40IPR001480
Bulb-type lectin domain		228974
41IPR011992
EF-hand-like domain		221556
42IPR019775
WD40 repeat, conserved site		220383
43IPR013210
Leucine-rich repeat-containing N-terminal, type 2		219227
44IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		210904
45IPR013830
SGNH hydrolase-type esterase domain		210626
46IPR013026
Tetratricopeptide repeat-containing domain		203290
47IPR005123
Oxoglutarate/iron-dependent dioxygenase		198362
48IPR012340
Nucleic acid-binding, OB-fold		198299
49IPR019734
Tetratricopeptide repeat		1961453
50IPR011991
Winged helix-turn-helix DNA-binding domain		196368
51IPR001005
SANT/Myb domain		195404
52IPR002048
Calcium-binding EF-hand		1871075
53IPR010255
Haem peroxidase		180181
54IPR002016
Haem peroxidase, plant/fungal/bacterial		1761151
55IPR001087
Lipase, GDSL		174174
56IPR027443
Isopenicillin N synthase-like		174177
57IPR032867
DYW domain		173173
58IPR003959
ATPase, AAA-type, core		171208
59IPR017871
ABC transporter, conserved site		170215
60IPR013785
Aldolase-type TIM barrel		165186
61IPR018247
EF-Hand 1, calcium-binding site		163357
62IPR000823
Plant peroxidase		1611328
63IPR014710
RmlC-like jelly roll fold		160199
64IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		158196
65IPR023213
Chloramphenicol acetyltransferase-like domain		154282
66IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		151156
67IPR015915
Kelch-type beta propeller		151198
68IPR011011
Zinc finger, FYVE/PHD-type		146158
69IPR015424
Pyridoxal phosphate-dependent transferase		144162
70IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		143149
71IPR011051
RmlC-like cupin domain		143148
72IPR017930
Myb domain		143192
73IPR029044
Nucleotide-diphospho-sugar transferases		142341
74IPR003480
Transferase		141149
75IPR020472
G-protein beta WD-40 repeat		136408
76IPR015500
Peptidase S8, subtilisin-related		136468
77IPR001623
DnaJ domain		129925
78IPR026992
Non-haem dioxygenase N-terminal domain		129129
79IPR019793
Peroxidases heam-ligand binding site		128128
80IPR000209
Peptidase S8/S53 domain		128644
81IPR000008
C2 calcium-dependent membrane targeting		123701
82IPR005225
Small GTP-binding protein domain		123127
83IPR029052
Metallo-dependent phosphatase-like		121302
84IPR016177
DNA-binding, integrase-type		120137
85IPR000073
Alpha/beta hydrolase fold-1		117219
86IPR008949
Terpenoid synthase		116252
87IPR001471
AP2/ERF domain		114695
88IPR020683
Ankyrin repeat-containing domain		114454
89IPR002347
Glucose/ribitol dehydrogenase		111978
90IPR017907
Zinc finger, RING-type, conserved site		111114
91IPR001214
SET domain		110251
92IPR020568
Ribosomal protein S5 domain 2-type fold		109141
93IPR011527
ABC transporter, transmembrane domain, type 1		109553
94IPR000225
Armadillo		109880
95IPR011050
Pectin lyase fold/virulence factor		108117
96IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		108133
97IPR018108
Mitochondrial substrate/solute carrier		107608
98IPR023395
Mitochondrial carrier domain		107221
99IPR012334
Pectin lyase fold		107111
100IPR013766
Thioredoxin domain		105194
101IPR007087
Zinc finger, C2H2		104309
102IPR027640
Kinesin-like protein		104185
103IPR016161
Aldehyde/histidinol dehydrogenase		104104
104IPR001752
Kinesin, motor domain		104750
105IPR001965
Zinc finger, PHD-type		103129
106IPR004045
Glutathione S-transferase, N-terminal		102198
107IPR001932
Protein phosphatase 2C (PP2C)-like		101553
108IPR003960
ATPase, AAA-type, conserved site		100112
109IPR019794
Peroxidase, active site		100100
110IPR010987
Glutathione S-transferase, C-terminal-like		99282
111IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		99449
112IPR002110
Ankyrin repeat		99540
113IPR011032
GroES-like		98197
114IPR015590
Aldehyde dehydrogenase domain		9499
115IPR013057
Amino acid transporter, transmembrane		9395
116IPR004274
NLI interacting factor		93274
117IPR010259
Proteinase inhibitor I9		92129
118IPR006045
Cupin 1		92213
119IPR019787
Zinc finger, PHD-finger		91139
120IPR016163
Aldehyde dehydrogenase, C-terminal		9191
121IPR004843
Metallophosphoesterase domain		9090
122IPR003594
Histidine kinase-like ATPase, ATP-binding domain		90329
123IPR012337
Ribonuclease H-like domain		90196
124IPR015655
Protein phosphatase 2C		90130
125IPR000873
AMP-dependent synthetase/ligase		8989
126IPR023828
Peptidase S8, subtilisin, Ser-active site		8989
127IPR029071
Ubiquitin-related domain		89136
128IPR013525
ABC-2 type transporter		88129
129IPR019786
Zinc finger, PHD-type, conserved site		8890
130IPR016166
FAD-binding, type 2		86166
131IPR005202
Transcription factor GRAS		85169
132IPR014014
RNA helicase, DEAD-box type, Q motif		8484
133IPR011333
BTB/POZ fold		8496
134IPR023393
START-like domain		8386
135IPR002085
Alcohol dehydrogenase superfamily, zinc-type		83106
136IPR029021
Protein-tyrosine phosphatase-like		81201
137IPR008979
Galactose-binding domain-like		80172
138IPR000571
Zinc finger, CCCH-type		80498
139IPR011993
Pleckstrin homology-like domain		80148
140IPR006652
Kelch repeat type 1		79275
141IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		7979
142IPR016135
Ubiquitin-conjugating enzyme/RWD-like		78151
143IPR000109
Proton-dependent oligopeptide transporter family		76163
144IPR021109
Aspartic peptidase		76230
145IPR009009
Barwin-related endoglucanase		76203
146IPR005828
General substrate transporter		7692
147IPR009072
Histone-fold		76159
148IPR019821
Kinesin, motor region, conserved site		7575
149IPR029055
Nucleophile aminohydrolases, N-terminal		75146
150IPR002921
Lipase, class 3		7474
151IPR016181
Acyl-CoA N-acyltransferase		74162
152IPR008972
Cupredoxin		74272
153IPR008280
Tubulin/FtsZ, C-terminal		7474
154IPR013154
Alcohol dehydrogenase GroES-like		7475
155IPR003008
Tubulin/FtsZ, GTPase domain		74316
156IPR014756
Immunoglobulin E-set		74100
157IPR008978
HSP20-like chaperone		73155
158IPR000330
SNF2-related		7373
159IPR001279
Beta-lactamase-like		73252
160IPR003613
U box domain		73212
161IPR006094
FAD linked oxidase, N-terminal		7272
162IPR000217
Tubulin		71594
163IPR001461
Peptidase A1		71193
164IPR001356
Homeobox domain		71200
165IPR015916
Galactose oxidase, beta-propeller		7087
166IPR001509
NAD-dependent epimerase/dehydratase		7073
167IPR000490
Glycoside hydrolase, family 17		70114
168IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		7076
169IPR017877
Myb-like domain		6984
170IPR032799
Xylanase inhibitor, C-terminal		6869
171IPR029045
ClpP/crotonase-like domain		68179
172IPR001757
Cation-transporting P-type ATPase		68151
173IPR000210
BTB/POZ domain		67158
174IPR005135
Endonuclease/exonuclease/phosphatase		66207
175IPR023299
P-type ATPase, cytoplasmic domain N		66131
176IPR013149
Alcohol dehydrogenase, C-terminal		6566
177IPR017975
Tubulin, conserved site		6565
178IPR008250
P-type ATPase, A domain		65140
179IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		65184
180IPR033121
Peptidase family A1 domain		6572
181IPR023210
NADP-dependent oxidoreductase domain		65200
182IPR001395
Aldo/keto reductase		6596
183IPR013783
Immunoglobulin-like fold		64100
184IPR018253
DnaJ domain, conserved site		6464
185IPR023123
Tubulin, C-terminal		6464
186IPR001878
Zinc finger, CCHC-type		64244
187IPR000626
Ubiquitin domain		63292
188IPR001929
Germin		62178
189IPR000608
Ubiquitin-conjugating enzyme, E2		62124
190IPR011701
Major facilitator superfamily		6263
191IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		6268
192IPR012946
X8 domain		62124
193IPR006447
Myb domain, plants		6262
194IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		62143
195IPR003137
Protease-associated domain, PA		6161
196IPR018303
P-type ATPase, phosphorylation site		6161
197IPR011043
Galactose oxidase/kelch, beta-propeller		6180
198IPR000182
GNAT domain		60105
199IPR006553
Leucine-rich repeat, cysteine-containing subtype		60472
200IPR002067
Mitochondrial carrier protein		60294
201IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		59154
202IPR008928
Six-hairpin glycosidase-like		5872
203IPR020845
AMP-binding, conserved site		5858
204IPR000668
Peptidase C1A, papain C-terminal		58194
205IPR019780
Germin, manganese binding site		5860
206IPR020843
Polyketide synthase, enoylreductase		5757
207IPR003663
Sugar/inositol transporter		57309
208IPR016162
Aldehyde dehydrogenase, N-terminal		5759
209IPR025110
Domain of unknown function DUF4009		5656
210IPR032710
NTF2-like domain		5695
211IPR013128
Peptidase C1A, papain		5658
212IPR012675
Beta-grasp domain		5656
213IPR005829
Sugar transporter, conserved site		5695
214IPR015300
DNA-binding pseudobarrel domain		56123
215IPR006121
Heavy metal-associated domain, HMA		55186
216IPR029061
Thiamin diphosphate-binding fold		55171
217IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		55109
218IPR017938
Riboflavin synthase-like beta-barrel		5461
219IPR013216
Methyltransferase type 11		5455
220IPR011006
CheY-like superfamily		5468
221IPR000644
Cystathionine beta-synthase, core		54317
222IPR029033
Histidine phosphatase superfamily		54150
223IPR001789
Signal transduction response regulator, receiver domain		54177
224IPR016039
Thiolase-like		53234
225IPR004263
Exostosin-like		5355
226IPR007112
Expansin/pollen allergen, DPBB domain		53102
227IPR001806
Small GTPase superfamily		5353
228IPR000387
Protein-tyrosine/Dual specificity phosphatase		5252
229IPR011012
Longin-like domain		5252
230IPR002035
von Willebrand factor, type A		52154
231IPR029062
Class I glutamine amidotransferase-like		52113
232IPR015880
Zinc finger, C2H2-like		52156
233IPR017927
Ferredoxin reductase-type FAD-binding domain		5151
234IPR006073
GTP binding domain		51141
235IPR013763
Cyclin-like		50220
236IPR000270
Phox/Bem1p		5088
237IPR003340
B3 DNA binding domain		49164
238IPR004853
Domain of unknown function DUF250		4949
239IPR002068
Alpha crystallin/Hsp20 domain		49103
240IPR004265
Plant disease resistance response protein		4949
241IPR002123
Phospholipid/glycerol acyltransferase		4992
242IPR032861
Xylanase inhibitor, N-terminal		4951
243IPR011042
Six-bladed beta-propeller, TolB-like		4959
244IPR000048
IQ motif, EF-hand binding site		49419
245IPR000340
Dual specificity phosphatase, catalytic domain		4848
246IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		4848
247IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		4848
248IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		47264
249IPR029000
Cyclophilin-like domain		4797
250IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		4747
251IPR013780
Glycosyl hydrolase, family 13, all-beta		4747
252IPR003851
Zinc finger, Dof-type		47134
253IPR010920
Like-Sm (LSM) domain		4646
254IPR005467
Signal transduction histidine kinase, core		4545
255IPR033443
Pentacotripeptide-repeat region of PROPR		4550
256IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		4576
257IPR029510
Aldehyde dehydrogenase, glutamic acid active site		4444
258IPR000795
Elongation factor, GTP-binding domain		44234
259IPR019378
GDP-fucose protein O-fucosyltransferase		4444
260IPR016130
Protein-tyrosine phosphatase, active site		4444
261IPR000070
Pectinesterase, catalytic		4446
262IPR000727
Target SNARE coiled-coil domain		43113
263IPR001024
Lipoxygenase, LH2		43169
264IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		4382
265IPR013078
Histidine phosphatase superfamily, clade-1		4391
266IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		4361
267IPR001360
Glycoside hydrolase, family 1		42284
268IPR003661
Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain		42159
269IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		4271
270IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		4276
271IPR023346
Lysozyme-like domain		4245
272IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4242
273IPR002912
ACT domain		4299
274IPR024880
COPII coat assembly protein, Sec16		4171
275IPR000408
Regulator of chromosome condensation, RCC1		41622
276IPR002528
Multi antimicrobial extrusion protein		41108
277IPR029069
HotDog domain		41131
278IPR002109
Glutaredoxin		4180
279IPR013094
Alpha/beta hydrolase fold-3		4142
280IPR004827
Basic-leucine zipper domain		41143
281IPR015947
PUA-like domain		4158
282IPR003441
No apical meristem (NAM) protein		40121
283IPR024298
Ancestral coatomer element 1, Sec16/Sec31		4046
284IPR020103
Pseudouridine synthase, catalytic domain		4067
285IPR004088
K Homology domain, type 1		40260
286IPR017937
Thioredoxin, conserved site		4048
287IPR002937
Amine oxidase		4041
288IPR001041
2Fe-2S ferredoxin-type domain		40104
289IPR003029
Ribosomal protein S1, RNA-binding domain		40134
290IPR006195
Aminoacyl-tRNA synthetase, class II		3939
291IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		39109
292IPR013581
Plant PDR ABC transporter associated		3939
293IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		3939
294IPR020471
Aldo/keto reductase subgroup		39177
295IPR008914
Phosphatidylethanolamine-binding protein PEBP		39102
296IPR001478
PDZ domain		39148
297IPR024950
Dual specificity phosphatase		3951
298IPR002100
Transcription factor, MADS-box		39259
299IPR005746
Thioredoxin		3955
300IPR002589
Appr-1-p processing		39100
301IPR001563
Peptidase S10, serine carboxypeptidase		38199
302IPR001305
Heat shock protein DnaJ, cysteine-rich domain		38100
303IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		3838
304IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		3838
305IPR023271
Aquaporin-like		3876
306IPR004839
Aminotransferase, class I/classII		3839
307IPR022967
RNA-binding domain, S1		3893
308IPR022796
Chlorophyll A-B binding protein		3838
309IPR000425
Major intrinsic protein		38304
310IPR004993
GH3 auxin-responsive promoter		3876
311IPR004147
UbiB domain		3838
312IPR014720
Double-stranded RNA-binding domain		38119
313IPR025661
Cysteine peptidase, asparagine active site		3838
314IPR000757
Glycoside hydrolase, family 16		3878
315IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3739
316IPR011016
Zinc finger, RING-CH-type		3799
317IPR005630
Terpene synthase, metal-binding domain		3738
318IPR000172
Glucose-methanol-choline oxidoreductase, N-terminal		3776
319IPR003245
Plastocyanin-like		37112
320IPR011058
Cyanovirin-N		37141
321IPR008942
ENTH/VHS		3669
322IPR028992
Hedgehog/Intein (Hint) domain		3670
323IPR023313
Ubiquitin-conjugating enzyme, active site		3636
324IPR015813
Pyruvate/Phosphoenolpyruvate kinase		3695
325IPR013121
Ferric reductase, NAD binding		3636
326IPR003657
DNA-binding WRKY		36211
327IPR007117
Expansin, cellulose-binding-like domain		36144
328IPR000620
Drug/metabolite transporter		3669
329IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		36110
330IPR000726
Glycoside hydrolase, family 19, catalytic		3545
331IPR001251
CRAL-TRIO domain		35170
332IPR001357
BRCT domain		35199
333IPR007118
Expansin/Lol pI		35203
334IPR008991
Translation protein SH3-like domain		3539
335IPR029056
Ribokinase-like		3571
336IPR002902
Gnk2-homologous domain		3578
337IPR008266
Tyrosine-protein kinase, active site		3535
338IPR025875
Leucine rich repeat 4		3536
339IPR029481
ABC-transporter extracellular N-terminal domain		3535
340IPR001876
Zinc finger, RanBP2-type		35266
341IPR029060
PIN domain-like		3460
342IPR013112
FAD-binding 8		3434
343IPR002423
Chaperonin Cpn60/TCP-1		3434
344IPR001353
Proteasome, subunit alpha/beta		3435
345IPR001763
Rhodanese-like domain		34155
346IPR002293
Amino acid/polyamine transporter I		34103
347IPR007867
Glucose-methanol-choline oxidoreductase, C-terminal		3434
348IPR004358
Signal transduction histidine kinase-related protein, C-terminal		34120
349IPR007125
Histone core		3434
350IPR027409
GroEL-like apical domain		3468
351IPR004087
K Homology domain		3464
352IPR030184
WAT1-related protein		3434
353IPR009003
Trypsin-like cysteine/serine peptidase domain		3440
354IPR000743
Glycoside hydrolase, family 28		3454
355IPR015797
NUDIX hydrolase domain-like		3472
356IPR004316
SWEET sugar transporter		3362
357IPR003954
RNA recognition motif domain, eukaryote		3362
358IPR009060
UBA-like		3340
359IPR004161
Translation elongation factor EFTu/EF1A, domain 2		3333
360IPR032466
Metal-dependent hydrolase		3340
361IPR010989
t-SNARE		3333
362IPR011013
Galactose mutarotase-like domain		3335
363IPR020904
Short-chain dehydrogenase/reductase, conserved site		3335
364IPR001077
O-methyltransferase, family 2		3334
365IPR001715
Calponin homology domain		33166
366IPR013126
Heat shock protein 70 family		33241
367IPR003676
Auxin responsive SAUR protein		3333
368IPR004331
SPX, N-terminal		3285
369IPR024709
O-fucosyltransferase, plant		3232
370IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		3232
371IPR003347
JmjC domain		3276
372IPR027413
GroEL-like equatorial domain		3264
373IPR027356
NPH3 domain		3264
374IPR022742
Alpha/beta hydrolase, N-terminal		3232
375IPR011059
Metal-dependent hydrolase, composite domain		3272
376IPR016160
Aldehyde dehydrogenase, conserved site		3232
377IPR012341
Six-hairpin glycosidase		3233
378IPR023329
Chlorophyll a/b binding protein domain		3234
379IPR001767
Hint domain		3232
380IPR016461
Caffeate O-methyltransferase (COMT) family		3151
381IPR012951
Berberine/berberine-like		3131
382IPR026057
PC-Esterase		3131
383IPR013838
Beta tubulin, autoregulation binding site		3131
384IPR013130
Ferric reductase transmembrane component-like domain		3131
385IPR007817
Pyoverdine biosynthesis		3132
386IPR018170
Aldo/keto reductase, conserved site		3167
387IPR013816
ATP-grasp fold, subdomain 2		3141
388IPR008963
Purple acid phosphatase-like, N-terminal		3131
389IPR000086
NUDIX hydrolase domain		3159
390IPR004294
Carotenoid oxygenase		3067
391IPR021133
HEAT, type 2		3086
392IPR000717
Proteasome component (PCI) domain		3058
393IPR018392
Peptidoglycan-binding lysin domain		30164
394IPR002963
Expansin		30243
395IPR025846
PMR5 N-terminal domain		3030
396IPR001849
Pleckstrin homology domain		3069
397IPR000169
Cysteine peptidase, cysteine active site		3030
398IPR006671
Cyclin, N-terminal		3040
399IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		30115
400IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		3062
401IPR000192
Aminotransferase, class V/Cysteine desulfurase		3030
402IPR015914
Purple acid phosphatase, N-terminal		3056
403IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		3030
404IPR011707
Multicopper oxidase, type 3		3030
405IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		2929
406IPR001163
Ribonucleoprotein LSM domain		2957
407IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2958
408IPR006734
Protein of unknown function DUF597		2929
409IPR016455
Xyloglucan endotransglucosylase/hydrolase		2929
410IPR022812
Dynamin superfamily		29164
411IPR006694
Fatty acid hydroxylase		2929
412IPR004883
Lateral organ boundaries, LOB		2958
413IPR014722
Ribosomal protein L2 domain 2		2931
414IPR022357
Major intrinsic protein, conserved site		2929
415IPR002452
Alpha tubulin		29329
416IPR002495
Glycosyl transferase, family 8		2931
417IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2929
418IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		2971
419IPR008974
TRAF-like		2963
420IPR006016
UspA		2830
421IPR009078
Ferritin/ribonucleotide reductase-like		2828
422IPR029962
Trichome birefringence-like family		2828
423IPR007173
D-arabinono-1,4-lactone oxidase		2828
424IPR001938
Thaumatin		28296
425IPR033131
Pectinesterase, Asp active site		2828
426IPR011074
CRAL/TRIO, N-terminal domain		2867
427IPR001199
Cytochrome b5-like heme/steroid binding domain		28178
428IPR007696
DNA mismatch repair protein MutS, core		2874
429IPR016167
FAD-binding, type 2, subdomain 1		2828
430IPR011706
Multicopper oxidase, type 2		2828
431IPR031157
Tr-type G domain, conserved site		2828
432IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		2851
433IPR003812
Fido domain		2868
434IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		28227
435IPR001117
Multicopper oxidase, type 1		2727
436IPR006594
LisH dimerisation motif		2752
437IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2785
438IPR008971
HSP40/DnaJ peptide-binding		2771
439IPR011237
Peptidase M16 domain		2760
440IPR000315
Zinc finger, B-box		2790
441IPR000933
Glycoside hydrolase, family 29		2758
442IPR003609
Apple-like		2742
443IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2754
444IPR017926
Glutamine amidotransferase type 1		2748
445IPR004864
Late embryogenesis abundant protein, LEA-14		2729
446IPR002453
Beta tubulin		27331
447IPR001494
Importin-beta, N-terminal		2768
448IPR000994
Peptidase M24, structural domain		2790
449IPR013815
ATP-grasp fold, subdomain 1		2734
450IPR015902
Glycoside hydrolase, family 13		2743
451IPR011948
Dullard phosphatase domain, eukaryotic		2727
452IPR002939
Chaperone DnaJ, C-terminal		2727
453IPR001223
Glycoside hydrolase, family 18, catalytic domain		2728
454IPR000432
DNA mismatch repair protein MutS, C-terminal		2767
455IPR002913
START domain		2770
456IPR006689
Small GTPase superfamily, ARF/SAR type		26124
457IPR029035
DHS-like NAD/FAD-binding domain		2665
458IPR025659
Tubby C-terminal-like domain		2633
459IPR006153
Cation/H+ exchanger		2626
460IPR030381
Dynamin-type guanine nucleotide-binding (G) domain		2626
461IPR015353
Rubisco LS methyltransferase, substrate-binding domain		2668
462IPR009022
Elongation factor G, III-V domain		2658
463IPR007197
Radical SAM		2626
464IPR000907
Lipoxygenase		2649
465IPR001969
Peptidase aspartic, active site		2639
466IPR011060
Ribulose-phosphate binding barrel		2626
467IPR020892
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site		2626
468IPR011004
Trimeric LpxA-like		2628
469IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2636
470IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2632
471IPR001202
WW domain		26128
472IPR016185
Pre-ATP-grasp domain		2659
473IPR001701
Glycoside hydrolase, family 9		2626
474IPR004314
Domain of unknown function DUF239		2628
475IPR000595
Cyclic nucleotide-binding domain		2675
476IPR001148
Alpha carbonic anhydrase		26126
477IPR019587
Polyketide cyclase/dehydrase		2626
478IPR018490
Cyclic nucleotide-binding-like		2532
479IPR016064
ATP-NAD kinase-like domain		2538
480IPR016123
Mog1/PsbP, alpha/beta/alpha sandwich		2552
481IPR008265
Lipase, GDSL, active site		2525
482IPR013819
Lipoxygenase, C-terminal		25150
483IPR023561
Carbonic anhydrase, alpha-class		2525
484IPR023298
P-type ATPase, transmembrane domain		2557
485IPR010658
Nodulin-like		2525
486IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		2525
487IPR012317
Poly(ADP-ribose) polymerase, catalytic domain		2546
488IPR007502
Helicase-associated domain		2448
489IPR010030
Plant-specific FAD-dependent oxidoreductase		2424
490IPR002182
NB-ARC		2425
491IPR011611
Carbohydrate kinase PfkB		2424
492IPR018181
Heat shock protein 70, conserved site		2459
493IPR031112
AP2-like ethylene-responsive transcription factor		2426
494IPR033275
E3 ubiquitin-protein ligase MARCH-like		2424
495IPR000640
Translation elongation factor EFG, V domain		2463
496IPR016021
MIF4-like, type 1/2/3		2448
497IPR000639
Epoxide hydrolase-like		24107
498IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2428
499IPR003587
Hint domain N-terminal		2424
500IPR003107
RNA-processing protein, HAT helix		24219
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Setaria_italica.html b/gramene/htdocs/ssi/species.weix/stats_Setaria_italica.html new file mode 100644 index 00000000..0e595ace --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Setaria_italica.html @@ -0,0 +1,417 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:JGIv2.0, Jan 2012
Database version:86.21
Base Pairs:405,737,341
Golden Path Length:405,737,341
Genebuild by: JGI
Genebuild method: Imported from JGI
Genebuild started: Jan 2012
Genebuild version: JGIv2.1
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		35,471
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:40,599
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
9 sequences
+
+ +
+ + + +
SequenceLength (bp)
142145699
249200776
350652576
440408058
547253416
636015257
735964515
840690061
958970518
+
+
scaffold
+
336 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaffold_142145699
scaffold_249200776
scaffold_350652576
scaffold_440408058
scaffold_547253416
scaffold_636015257
scaffold_735964515
scaffold_840690061
scaffold_958970518
scaffold_10423243
scaffold_11408550
scaffold_12360304
scaffold_13279254
scaffold_14147140
scaffold_1678252
scaffold_1777904
scaffold_1879790
scaffold_2057724
scaffold_2250389
scaffold_2346235
scaffold_2445277
scaffold_2539684
scaffold_2644270
scaffold_2756494
scaffold_2829974
scaffold_2928733
scaffold_3028486
scaffold_3127688
scaffold_3227884
scaffold_3326352
scaffold_3429946
scaffold_3525944
scaffold_3628912
scaffold_3725793
scaffold_3825255
scaffold_4219846
scaffold_4318880
scaffold_4420609
scaffold_4618744
scaffold_4718210
scaffold_4817096
scaffold_4917009
scaffold_5216191
scaffold_5316026
scaffold_5416010
scaffold_5517033
scaffold_5715281
scaffold_5815042
scaffold_6014994
scaffold_6114873
scaffold_6214866
scaffold_6314953
scaffold_6415137
scaffold_6514645
scaffold_6614186
scaffold_6814027
scaffold_6915228
scaffold_7113873
scaffold_7213923
scaffold_7313667
scaffold_7413538
scaffold_7513748
scaffold_7612945
scaffold_7812662
scaffold_7912567
scaffold_8012411
scaffold_8112385
scaffold_8212359
scaffold_8312212
scaffold_8512172
scaffold_9011772
scaffold_9211685
scaffold_9611541
scaffold_9811652
scaffold_9911906
scaffold_10214106
scaffold_10310668
scaffold_10510337
scaffold_10712949
scaffold_1109960
scaffold_1119955
scaffold_1129921
scaffold_1139913
scaffold_1149831
scaffold_1159823
scaffold_1169736
scaffold_1189770
scaffold_1199771
scaffold_1209575
scaffold_12214708
scaffold_1239737
scaffold_1249584
scaffold_12710483
scaffold_1299287
scaffold_1309460
scaffold_1329188
scaffold_13411146
scaffold_13510290
scaffold_1378975
scaffold_1388940
scaffold_1398851
scaffold_1408751
scaffold_1418732
scaffold_1428704
scaffold_14310815
scaffold_14412534
scaffold_1468401
scaffold_1478464
scaffold_1488433
scaffold_1498288
scaffold_1518897
scaffold_1528193
scaffold_1548350
scaffold_1558113
scaffold_1578090
scaffold_1607940
scaffold_1667715
scaffold_1687577
scaffold_1747470
scaffold_1757346
scaffold_1767465
scaffold_1777351
scaffold_1787310
scaffold_1807103
scaffold_1828111
scaffold_1836984
scaffold_1846966
scaffold_1856961
scaffold_1876828
scaffold_1886779
scaffold_1896959
scaffold_1927619
scaffold_1936572
scaffold_1946569
scaffold_1956534
scaffold_1968263
scaffold_1988693
scaffold_1997500
scaffold_2006450
scaffold_2016541
scaffold_2026421
scaffold_2036723
scaffold_2046363
scaffold_2066318
scaffold_2096233
scaffold_2117760
scaffold_2126303
scaffold_2139283
scaffold_2156825
scaffold_2169342
scaffold_2186372
scaffold_2206011
scaffold_2216093
scaffold_2235949
scaffold_2256038
scaffold_2266007
scaffold_2295777
scaffold_2325693
scaffold_2335684
scaffold_2355632
scaffold_2365622
scaffold_2375620
scaffold_2385603
scaffold_2397933
scaffold_2405558
scaffold_2425439
scaffold_2435415
scaffold_2445364
scaffold_2455619
scaffold_2475497
scaffold_2487489
scaffold_2495313
scaffold_2507366
scaffold_2525257
scaffold_2535256
scaffold_2555216
scaffold_2565202
scaffold_2595790
scaffold_2605148
scaffold_2615095
scaffold_2625063
scaffold_2635049
scaffold_2645048
scaffold_2664986
scaffold_2674971
scaffold_2685160
scaffold_2726080
scaffold_2734889
scaffold_2744871
scaffold_2754869
scaffold_2765143
scaffold_2774932
scaffold_2784825
scaffold_2794817
scaffold_2805017
scaffold_2834689
scaffold_2857618
scaffold_2864641
scaffold_2884590
scaffold_2894586
scaffold_2904585
scaffold_2944494
scaffold_2984436
scaffold_3015446
scaffold_3024779
scaffold_3044295
scaffold_3064267
scaffold_3074265
scaffold_3084537
scaffold_3094246
scaffold_3104244
scaffold_3134207
scaffold_3164564
scaffold_3184119
scaffold_3194110
scaffold_3225256
scaffold_3234096
scaffold_3254052
scaffold_3264629
scaffold_3274375
scaffold_3295009
scaffold_3304027
scaffold_3314011
scaffold_3334002
scaffold_3343986
scaffold_3364215
scaffold_3384050
scaffold_3393943
scaffold_3404024
scaffold_3413921
scaffold_3423921
scaffold_3434010
scaffold_3483838
scaffold_3494005
scaffold_3508265
scaffold_3534373
scaffold_3544167
scaffold_3563846
scaffold_3583710
scaffold_3593900
scaffold_3623666
scaffold_3633664
scaffold_3643733
scaffold_3663584
scaffold_3693534
scaffold_3703528
scaffold_3713478
scaffold_3733429
scaffold_3743508
scaffold_3783353
scaffold_3793337
scaffold_3803434
scaffold_3813982
scaffold_3823330
scaffold_3833314
scaffold_3853285
scaffold_3863431
scaffold_3873493
scaffold_3883369
scaffold_3893251
scaffold_3923578
scaffold_3933113
scaffold_3943112
scaffold_3983065
scaffold_3993678
scaffold_4003043
scaffold_4023250
scaffold_4033323
scaffold_4043464
scaffold_4083177
scaffold_4092879
scaffold_4113516
scaffold_4123346
scaffold_4143225
scaffold_4162773
scaffold_4204776
scaffold_4215034
scaffold_4222720
scaffold_4243200
scaffold_4292560
scaffold_4302511
scaffold_4322504
scaffold_4333061
scaffold_4352401
scaffold_4363171
scaffold_4412850
scaffold_4422281
scaffold_4432805
scaffold_4442253
scaffold_4462213
scaffold_4472770
scaffold_4482197
scaffold_4493204
scaffold_4515660
scaffold_4522168
scaffold_4621987
scaffold_4631964
scaffold_4651906
scaffold_4661879
scaffold_4683036
scaffold_4691852
scaffold_4711817
scaffold_4722774
scaffold_4731744
scaffold_4745585
scaffold_4752787
scaffold_4761709
scaffold_4775952
scaffold_4781677
scaffold_4791675
scaffold_4801673
scaffold_4821617
scaffold_4842164
scaffold_4852566
scaffold_4861522
scaffold_4871451
scaffold_4881358
scaffold_4891350
scaffold_4901331
scaffold_4911318
scaffold_4921306
scaffold_4931254
scaffold_4941213
scaffold_4951190
scaffold_4961175
scaffold_4971753
scaffold_4981140
scaffold_4991140
scaffold_5001134
scaffold_5015217
scaffold_5021110
scaffold_5031051
scaffold_5041047
scaffold_5051031
scaffold_5061007
scaffold_5071005
+
+
+ +

Other

+ + + + + +
FGENESH gene predictions:52,980
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/stats_Setaria_italica_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Setaria_italica_IPtop500.html new file mode 100644 index 00000000..f9a1ecfa --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Setaria_italica_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		14464306
2IPR011009
Protein kinase-like domain		14021749
3IPR000719
Protein kinase, catalytic domain		13373854
4IPR032675
Leucine-rich repeat domain, L domain-like		11984191
5IPR008271
Serine/threonine-protein kinase, active site		10471183
6IPR017441
Protein kinase, ATP binding site		9311049
7IPR001810
F-box domain, cyclin-like		7171631
8IPR013083
Zinc finger, RING/FYVE/PHD-type		697853
9IPR013320
Concanavalin A-like lectin/glucanase, subgroup		696941
10IPR011990
Tetratricopeptide-like helical		5912062
11IPR001611
Leucine-rich repeat		4912648
12IPR002885
Pentatricopeptide repeat		48811348
13IPR016040
NAD(P)-binding domain		4581297
14IPR001841
Zinc finger, RING-type		4401201
15IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		432692
16IPR029058
Alpha/Beta hydrolase fold		4151171
17IPR002182
NB-ARC		404458
18IPR009057
Homeodomain-like		3941002
19IPR016024
Armadillo-type fold		356949
20IPR001128
Cytochrome P450		3522240
21IPR003591
Leucine-rich repeat, typical subtype		3272337
22IPR002401
Cytochrome P450, E-class, group I		3122095
23IPR013210
Leucine-rich repeat-containing N-terminal, type 2		309326
24IPR020846
Major facilitator superfamily domain		302724
25IPR003593
AAA+ ATPase domain		301446
26IPR017972
Cytochrome P450, conserved site		296297
27IPR012677
Nucleotide-binding, alpha-beta plait		2791003
28IPR015943
WD40/YVTN repeat-like-containing domain		275547
29IPR011989
Armadillo-like helical		270645
30IPR012336
Thioredoxin-like fold		261698
31IPR017853
Glycoside hydrolase, superfamily		261356
32IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		259771
33IPR001005
SANT/Myb domain		256746
34IPR017986
WD40-repeat-containing domain		253740
35IPR000504
RNA recognition motif domain		2461335
36IPR001680
WD40 repeat		2393007
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		232619
38IPR017930
Myb domain		216354
39IPR013781
Glycoside hydrolase, catalytic domain		215278
40IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		193921
41IPR011991
Winged helix-turn-helix DNA-binding domain		190401
42IPR016177
DNA-binding, integrase-type		185223
43IPR011333
BTB/POZ fold		179209
44IPR001471
AP2/ERF domain		1741121
45IPR023214
HAD-like domain		171569
46IPR011992
EF-hand-like domain		171478
47IPR002016
Haem peroxidase, plant/fungal/bacterial		1651145
48IPR010255
Haem peroxidase		164172
49IPR007087
Zinc finger, C2H2		163559
50IPR018289
MULE transposase domain		160162
51IPR013830
SGNH hydrolase-type esterase domain		159540
52IPR002048
Calcium-binding EF-hand		1581152
53IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		152741
54IPR000210
BTB/POZ domain		152449
55IPR000823
Plant peroxidase		1521297
56IPR008974
TRAF-like		151287
57IPR029044
Nucleotide-diphospho-sugar transferases		147375
58IPR012337
Ribonuclease H-like domain		146290
59IPR019793
Peroxidases heam-ligand binding site		144152
60IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		144344
61IPR003441
No apical meristem (NAM) protein		142447
62IPR001650
Helicase, C-terminal		142506
63IPR007527
Zinc finger, SWIM-type		142192
64IPR019557
Aminotransferase-like, plant mobile domain		141188
65IPR023213
Chloramphenicol acetyltransferase-like domain		141271
66IPR014001
Helicase, superfamily 1/2, ATP-binding domain		141330
67IPR019775
WD40 repeat, conserved site		139271
68IPR005123
Oxoglutarate/iron-dependent dioxygenase		138289
69IPR018247
EF-Hand 1, calcium-binding site		138368
70IPR020683
Ankyrin repeat-containing domain		137796
71IPR003439
ABC transporter-like		137449
72IPR027443
Isopenicillin N synthase-like		133158
73IPR012340
Nucleic acid-binding, OB-fold		133209
74IPR002110
Ankyrin repeat		1331190
75IPR008972
Cupredoxin		131627
76IPR001878
Zinc finger, CCHC-type		131651
77IPR013785
Aldolase-type TIM barrel		128202
78IPR001087
Lipase, GDSL		126132
79IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		125184
80IPR003959
ATPase, AAA-type, core		125179
81IPR006564
Zinc finger, PMZ-type		123125
82IPR003480
Transferase		123139
83IPR011676
Domain of unknown function DUF1618		121124
84IPR013026
Tetratricopeptide repeat-containing domain		121183
85IPR019794
Peroxidase, active site		120125
86IPR019734
Tetratricopeptide repeat		1191031
87IPR001623
DnaJ domain		119928
88IPR021109
Aspartic peptidase		118407
89IPR001461
Peptidase A1		117375
90IPR025287
Wall-associated receptor kinase galacturonan-binding domain		114131
91IPR029071
Ubiquitin-related domain		113223
92IPR011011
Zinc finger, FYVE/PHD-type		113162
93IPR002347
Glucose/ribitol dehydrogenase		1111166
94IPR014710
RmlC-like jelly roll fold		110137
95IPR032799
Xylanase inhibitor, C-terminal		110120
96IPR003657
DNA-binding WRKY		110629
97IPR025315
Domain of unknown function DUF4220		110118
98IPR005828
General substrate transporter		108136
99IPR007658
Protein of unknown function DUF594		107107
100IPR005225
Small GTP-binding protein domain		107129
101IPR032861
Xylanase inhibitor, N-terminal		106116
102IPR033121
Peptidase family A1 domain		106127
103IPR004332
Transposase, MuDR, plant		105106
104IPR009009
Barwin-related endoglucanase		104290
105IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		103140
106IPR026992
Non-haem dioxygenase N-terminal domain		103119
107IPR005174
Protein of unknown function DUF295		102104
108IPR015424
Pyridoxal phosphate-dependent transferase		102140
109IPR000008
C2 calcium-dependent membrane targeting		100805
110IPR017871
ABC transporter, conserved site		98139
111IPR015300
DNA-binding pseudobarrel domain		98302
112IPR012334
Pectin lyase fold		98103
113IPR002083
MATH/TRAF domain		97180
114IPR000073
Alpha/beta hydrolase fold-1		97249
115IPR011050
Pectin lyase fold/virulence factor		96102
116IPR010987
Glutathione S-transferase, C-terminal-like		96317
117IPR000109
Proton-dependent oligopeptide transporter family		95222
118IPR031052
FHY3/FAR1 family		94117
119IPR015880
Zinc finger, C2H2-like		93256
120IPR001356
Homeobox domain		92273
121IPR001932
Protein phosphatase 2C (PP2C)-like		92655
122IPR024752
Myb/SANT-like domain		9192
123IPR000742
Epidermal growth factor-like domain		90217
124IPR032867
DYW domain		9090
125IPR017907
Zinc finger, RING-type, conserved site		90115
126IPR009072
Histone-fold		90188
127IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		88111
128IPR006447
Myb domain, plants		87102
129IPR004045
Glutathione S-transferase, N-terminal		87192
130IPR001965
Zinc finger, PHD-type		87169
131IPR000626
Ubiquitin domain		86497
132IPR012871
Protein of unknown function DUF1677, Oryza sativa		8692
133IPR003340
B3 DNA binding domain		85388
134IPR001480
Bulb-type lectin domain		85466
135IPR020472
G-protein beta WD-40 repeat		83291
136IPR005829
Sugar transporter, conserved site		83162
137IPR011051
RmlC-like cupin domain		8398
138IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		83118
139IPR000270
Phox/Bem1p		82168
140IPR003960
ATPase, AAA-type, conserved site		8197
141IPR013128
Peptidase C1A, papain		80100
142IPR002100
Transcription factor, MADS-box		80535
143IPR015655
Protein phosphatase 2C		80163
144IPR004827
Basic-leucine zipper domain		80352
145IPR007117
Expansin, cellulose-binding-like domain		79331
146IPR003663
Sugar/inositol transporter		76447
147IPR029052
Metallo-dependent phosphatase-like		75218
148IPR018097
EGF-like calcium-binding, conserved site		7577
149IPR006121
Heavy metal-associated domain, HMA		74241
150IPR015500
Peptidase S8, subtilisin-related		74285
151IPR007112
Expansin/pollen allergen, DPBB domain		73146
152IPR003613
U box domain		73224
153IPR003676
Auxin responsive SAUR protein		7373
154IPR011993
Pleckstrin homology-like domain		73150
155IPR016039
Thiolase-like		72363
156IPR003609
Apple-like		72190
157IPR013057
Amino acid transporter, transmembrane		7279
158IPR007118
Expansin/Lol pI		71423
159IPR001881
EGF-like calcium-binding		71118
160IPR013766
Thioredoxin domain		71169
161IPR002528
Multi antimicrobial extrusion protein		71221
162IPR009003
Trypsin-like cysteine/serine peptidase domain		71114
163IPR011706
Multicopper oxidase, type 2		7074
164IPR001117
Multicopper oxidase, type 1		6974
165IPR013201
Proteinase inhibitor I29, cathepsin propeptide		69144
166IPR006501
Pectinesterase inhibitor		69271
167IPR011707
Multicopper oxidase, type 3		6972
168IPR004843
Metallophosphoesterase domain		6882
169IPR000858
S-locus glycoprotein		6871
170IPR026057
PC-Esterase		6872
171IPR019787
Zinc finger, PHD-finger		68155
172IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		68119
173IPR030184
WAT1-related protein		6874
174IPR013094
Alpha/beta hydrolase fold-3		6868
175IPR000209
Peptidase S8/S53 domain		68392
176IPR010259
Proteinase inhibitor I9		6796
177IPR010285
DNA helicase PIF1, ATP-dependent		6783
178IPR001509
NAD-dependent epimerase/dehydratase		6776
179IPR000668
Peptidase C1A, papain C-terminal		67341
180IPR000048
IQ motif, EF-hand binding site		67433
181IPR019786
Zinc finger, PHD-type, conserved site		66101
182IPR006566
FBD domain		6674
183IPR029962
Trichome birefringence-like family		6587
184IPR000571
Zinc finger, CCCH-type		65666
185IPR000225
Armadillo		65555
186IPR020568
Ribosomal protein S5 domain 2-type fold		6484
187IPR016135
Ubiquitin-conjugating enzyme/RWD-like		63171
188IPR025846
PMR5 N-terminal domain		6365
189IPR001806
Small GTPase superfamily		6375
190IPR002902
Gnk2-homologous domain		62236
191IPR018108
Mitochondrial substrate/solute carrier		62404
192IPR023395
Mitochondrial carrier domain		62155
193IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		62143
194IPR000620
Drug/metabolite transporter		61111
195IPR013763
Cyclin-like		60294
196IPR026961
PGG domain		60135
197IPR004330
FAR1 DNA binding domain		6064
198IPR017451
F-box associated interaction domain		5963
199IPR011527
ABC transporter, transmembrane domain, type 1		59334
200IPR001563
Peptidase S10, serine carboxypeptidase		58424
201IPR011701
Major facilitator superfamily		5873
202IPR008979
Galactose-binding domain-like		58160
203IPR001220
Legume lectin domain		5861
204IPR000490
Glycoside hydrolase, family 17		58105
205IPR016181
Acyl-CoA N-acyltransferase		57127
206IPR027640
Kinesin-like protein		57152
207IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		57103
208IPR003245
Plastocyanin-like		57168
209IPR005202
Transcription factor GRAS		57119
210IPR016159
Cullin repeat-like-containing domain		5778
211IPR001752
Kinesin, motor domain		57438
212IPR011042
Six-bladed beta-propeller, TolB-like		5774
213IPR011032
GroES-like		56149
214IPR008949
Terpenoid synthase		56137
215IPR025659
Tubby C-terminal-like domain		5666
216IPR004864
Late embryogenesis abundant protein, LEA-14		5560
217IPR003690
Mitochodrial transcription termination factor-related		55330
218IPR002035
von Willebrand factor, type A		55217
219IPR011043
Galactose oxidase/kelch, beta-propeller		5559
220IPR025476
Helitron helicase-like domain		5560
221IPR024171
S-receptor-like serine/threonine-protein kinase		5455
222IPR000873
AMP-dependent synthetase/ligase		5466
223IPR025660
Cysteine peptidase, histidine active site		5459
224IPR000152
EGF-type aspartate/asparagine hydroxylation site		5356
225IPR008250
P-type ATPase, A domain		52135
226IPR025661
Cysteine peptidase, asparagine active site		5256
227IPR002921
Lipase, class 3		5156
228IPR008978
HSP20-like chaperone		51123
229IPR000608
Ubiquitin-conjugating enzyme, E2		51136
230IPR014014
RNA helicase, DEAD-box type, Q motif		5162
231IPR002355
Multicopper oxidase, copper-binding site		5154
232IPR023828
Peptidase S8, subtilisin, Ser-active site		5153
233IPR018303
P-type ATPase, phosphorylation site		5160
234IPR001757
Cation-transporting P-type ATPase		51234
235IPR002085
Alcohol dehydrogenase superfamily, zinc-type		5175
236IPR007493
Protein of unknown function DUF538		50151
237IPR003137
Protease-associated domain, PA		5059
238IPR023393
START-like domain		5055
239IPR012946
X8 domain		50116
240IPR023299
P-type ATPase, cytoplasmic domain N		50108
241IPR000169
Cysteine peptidase, cysteine active site		5057
242IPR016166
FAD-binding, type 2		49110
243IPR008928
Six-hairpin glycosidase-like		4975
244IPR018253
DnaJ domain, conserved site		4954
245IPR004158
Protein of unknown function DUF247, plant		4955
246IPR001214
SET domain		49146
247IPR015916
Galactose oxidase, beta-propeller		4856
248IPR001969
Peptidase aspartic, active site		4783
249IPR001938
Thaumatin		47467
250IPR011006
CheY-like superfamily		4756
251IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4755
252IPR000182
GNAT domain		4684
253IPR013525
ABC-2 type transporter		4672
254IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4658
255IPR004265
Plant disease resistance response protein		4646
256IPR006045
Cupin 1		46106
257IPR004046
Glutathione S-transferase, C-terminal		4649
258IPR014756
Immunoglobulin E-set		4660
259IPR017970
Homeobox, conserved site		4549
260IPR020845
AMP-binding, conserved site		4554
261IPR001789
Signal transduction response regulator, receiver domain		45147
262IPR033389
AUX/IAA domain		4458
263IPR033138
Multicopper oxidases, conserved site		4447
264IPR009060
UBA-like		4464
265IPR029055
Nucleophile aminohydrolases, N-terminal		44116
266IPR006553
Leucine-rich repeat, cysteine-containing subtype		44353
267IPR003594
Histidine kinase-like ATPase, ATP-binding domain		44201
268IPR002109
Glutaredoxin		4498
269IPR015947
PUA-like domain		4466
270IPR023271
Aquaporin-like		43103
271IPR000425
Major intrinsic protein		43406
272IPR024788
Malectin-like carbohydrate-binding domain		4347
273IPR000743
Glycoside hydrolase, family 28		4368
274IPR013149
Alcohol dehydrogenase, C-terminal		4249
275IPR002068
Alpha crystallin/Hsp20 domain		4291
276IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4249
277IPR005135
Endonuclease/exonuclease/phosphatase		42184
278IPR013154
Alcohol dehydrogenase GroES-like		4249
279IPR006671
Cyclin, N-terminal		4268
280IPR023210
NADP-dependent oxidoreductase domain		42149
281IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4248
282IPR001395
Aldo/keto reductase		4266
283IPR017877
Myb-like domain		4261
284IPR006016
UspA		4147
285IPR000330
SNF2-related		4152
286IPR004263
Exostosin-like		4145
287IPR031107
Small heat shock protein HSP20		4148
288IPR000070
Pectinesterase, catalytic		4144
289IPR018202
Peptidase S10, serine carboxypeptidase, active site		4148
290IPR007657
Glycosyltransferase AER61, uncharacterised		4045
291IPR004140
Exocyst complex protein Exo70		40106
292IPR011012
Longin-like domain		4053
293IPR007125
Histone core		4043
294IPR029045
ClpP/crotonase-like domain		40182
295IPR001906
Terpene synthase, N-terminal domain		4088
296IPR002912
ACT domain		40120
297IPR001929
Germin		39116
298IPR029021
Protein-tyrosine phosphatase-like		39106
299IPR013783
Immunoglobulin-like fold		3954
300IPR001077
O-methyltransferase, family 2		3944
301IPR000644
Cystathionine beta-synthase, core		39301
302IPR007612
LURP1-like domain		3838
303IPR006626
Parallel beta-helix repeat		38197
304IPR004853
Domain of unknown function DUF250		3849
305IPR001251
CRAL-TRIO domain		38225
306IPR004088
K Homology domain, type 1		38349
307IPR006094
FAD linked oxidase, N-terminal		3845
308IPR025322
Protein of unknown function DUF4228		3739
309IPR032710
NTF2-like domain		3772
310IPR016461
Caffeate O-methyltransferase (COMT) family		3769
311IPR005630
Terpene synthase, metal-binding domain		3744
312IPR004320
Protein of unknown function DUF241, plant		3741
313IPR019378
GDP-fucose protein O-fucosyltransferase		3737
314IPR002067
Mitochondrial carrier protein		37201
315IPR008942
ENTH/VHS		3676
316IPR010402
CCT domain		3682
317IPR001296
Glycosyl transferase, family 1		3640
318IPR003406
Glycosyl transferase, family 14		3637
319IPR002963
Expansin		36301
320IPR022357
Major intrinsic protein, conserved site		3644
321IPR000757
Glycoside hydrolase, family 16		3672
322IPR025110
Domain of unknown function DUF4009		3539
323IPR013216
Methyltransferase type 11		3550
324IPR012675
Beta-grasp domain		3540
325IPR020904
Short-chain dehydrogenase/reductase, conserved site		3538
326IPR004839
Aminotransferase, class I/classII		3544
327IPR002495
Glycosyl transferase, family 8		3536
328IPR019780
Germin, manganese binding site		3535
329IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3535
330IPR020843
Polyketide synthase, enoylreductase		3540
331IPR029033
Histidine phosphatase superfamily		3595
332IPR004041
NAF domain		3446
333IPR011013
Galactose mutarotase-like domain		3445
334IPR004813
Oligopeptide transporter OPT superfamily		3469
335IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3436
336IPR012341
Six-hairpin glycosidase		3445
337IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3436
338IPR019956
Ubiquitin subgroup		33118
339IPR001360
Glycoside hydrolase, family 1		33269
340IPR019821
Kinesin, motor region, conserved site		3335
341IPR018451
NAF/FISL domain		3345
342IPR008991
Translation protein SH3-like domain		3337
343IPR006652
Kelch repeat type 1		33144
344IPR005150
Cellulose synthase		3351
345IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		3335
346IPR016167
FAD-binding, type 2, subdomain 1		3339
347IPR012967
Plant methyltransferase dimerisation		3336
348IPR006073
GTP binding domain		33102
349IPR013181
Protein of unknown function DUF1719, Oryza sativa		3368
350IPR004141
Strictosidine synthase		3233
351IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3263
352IPR013187
F-box associated domain, type 3		3232
353IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		3232
354IPR011016
Zinc finger, RING-CH-type		32114
355IPR033124
Serine carboxypeptidases, histidine active site		3237
356IPR022059
Protein of unknown function DUF3615		3233
357IPR004883
Lateral organ boundaries, LOB		3264
358IPR004087
K Homology domain		3288
359IPR013780
Glycosyl hydrolase, family 13, all-beta		3235
360IPR023298
P-type ATPase, transmembrane domain		3289
361IPR002487
Transcription factor, K-box		3288
362IPR008889
VQ		3232
363IPR002913
START domain		3295
364IPR013601
FAE1/Type III polyketide synthase-like protein		3132
365IPR010920
Like-Sm (LSM) domain		3136
366IPR001279
Beta-lactamase-like		31124
367IPR004367
Cyclin, C-terminal domain		3163
368IPR022742
Alpha/beta hydrolase, N-terminal		3139
369IPR013078
Histidine phosphatase superfamily, clade-1		3160
370IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3143
371IPR015915
Kelch-type beta propeller		3145
372IPR014720
Double-stranded RNA-binding domain		31138
373IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3188
374IPR018119
Strictosidine synthase, conserved region		3132
375IPR000727
Target SNARE coiled-coil domain		3086
376IPR005795
Major pollen allergen Lol pI		30223
377IPR018490
Cyclic nucleotide-binding-like		3034
378IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		3052
379IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		3074
380IPR001478
PDZ domain		30141
381IPR000795
Elongation factor, GTP-binding domain		30159
382IPR016455
Xyloglucan endotransglucosylase/hydrolase		3030
383IPR002123
Phospholipid/glycerol acyltransferase		3071
384IPR008266
Tyrosine-protein kinase, active site		3034
385IPR008480
Protein of unknown function DUF761, plant		3030
386IPR005746
Thioredoxin		3049
387IPR000595
Cyclic nucleotide-binding domain		3089
388IPR003855
K+ potassium transporter		3064
389IPR006153
Cation/H+ exchanger		2938
390IPR002423
Chaperonin Cpn60/TCP-1		2932
391IPR007650
Protein of unknown function DUF581		2929
392IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		2963
393IPR027356
NPH3 domain		2970
394IPR011074
CRAL/TRIO, N-terminal domain		29101
395IPR029480
Transposase-associated domain		2929
396IPR002293
Amino acid/polyamine transporter I		29106
397IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2929
398IPR015813
Pyruvate/Phosphoenolpyruvate kinase		29107
399IPR027409
GroEL-like apical domain		2963
400IPR006458
Ovate protein family, C-terminal		2981
401IPR003311
AUX/IAA protein		2944
402IPR010666
Zinc finger, GRF-type		2829
403IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		28195
404IPR029000
Cyclophilin-like domain		2867
405IPR013088
Zinc finger, NHR/GATA-type		2834
406IPR002659
Glycosyl transferase, family 31		2866
407IPR033131
Pectinesterase, Asp active site		2828
408IPR031112
AP2-like ethylene-responsive transcription factor		2832
409IPR000863
Sulfotransferase domain		2828
410IPR023313
Ubiquitin-conjugating enzyme, active site		2837
411IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2833
412IPR020946
Flavin monooxygenase-like		2846
413IPR001849
Pleckstrin homology domain		2879
414IPR029069
HotDog domain		2895
415IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2854
416IPR003851
Zinc finger, Dof-type		28112
417IPR001487
Bromodomain		28249
418IPR000679
Zinc finger, GATA-type		28127
419IPR017938
Riboflavin synthase-like beta-barrel		2740
420IPR002867
Zinc finger, C6HC-type		27105
421IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2732
422IPR004014
Cation-transporting P-type ATPase, N-terminal		2766
423IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2734
424IPR005821
Ion transport domain		2729
425IPR015902
Glycoside hydrolase, family 13		2744
426IPR033443
Pentacotripeptide-repeat region of PROPR		2730
427IPR029062
Class I glutamine amidotransferase-like		2786
428IPR013126
Heat shock protein 70 family		27244
429IPR029006
ADF-H/Gelsolin-like domain		2755
430IPR031127
E3 ubiquitin ligase RBR family		2736
431IPR017761
Laccase		2728
432IPR015797
NUDIX hydrolase domain-like		2763
433IPR017927
Ferredoxin reductase-type FAD-binding domain		2632
434IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		26108
435IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		26104
436IPR019954
Ubiquitin conserved site		2693
437IPR025753
AAA-type ATPase, N-terminal domain		2627
438IPR001357
BRCT domain		26165
439IPR001763
Rhodanese-like domain		26169
440IPR000408
Regulator of chromosome condensation, RCC1		26573
441IPR014722
Ribosomal protein L2 domain 2		2631
442IPR017937
Thioredoxin, conserved site		2643
443IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2650
444IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		2674
445IPR005069
Nucleotide-diphospho-sugar transferase		2626
446IPR000782
FAS1 domain		25149
447IPR013328
Dehydrogenase, multihelical		2536
448IPR006195
Aminoacyl-tRNA synthetase, class II		2529
449IPR003397
Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24		2527
450IPR001440
Tetratricopeptide TPR-1		2543
451IPR004162
E3 ubiquitin-protein ligase SINA like		2527
452IPR003347
JmjC domain		2571
453IPR029061
Thiamin diphosphate-binding fold		25113
454IPR000639
Epoxide hydrolase-like		25113
455IPR006379
HAD-superfamily hydrolase, subfamily IIB		2525
456IPR003616
Post-SET domain		2535
457IPR001701
Glycoside hydrolase, family 9		2526
458IPR013323
SIAH-type domain		2526
459IPR002641
Patatin/Phospholipase A2-related		2526
460IPR001041
2Fe-2S ferredoxin-type domain		2568
461IPR004316
SWEET sugar transporter		2459
462IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2489
463IPR003954
RNA recognition motif domain, eukaryote		2446
464IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2466
465IPR029466
No apical meristem-associated, C-terminal domain		2424
466IPR008422
Homeobox KN domain		2428
467IPR018170
Aldo/keto reductase, conserved site		2462
468IPR004314
Domain of unknown function DUF239		2428
469IPR001223
Glycoside hydrolase, family 18, catalytic domain		2424
470IPR029047
Heat shock protein 70kD, peptide-binding domain		2455
471IPR005175
Domain of unknown function DUF296		2448
472IPR001099
Chalcone/stilbene synthase, N-terminal		2425
473IPR010525
Auxin response factor		2435
474IPR006689
Small GTPase superfamily, ARF/SAR type		23144
475IPR009606
Protein of unknown function DUF1218		2323
476IPR003106
Leucine zipper, homeobox-associated		2337
477IPR024709
O-fucosyltransferase, plant		2323
478IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		2324
479IPR000315
Zinc finger, B-box		23108
480IPR001163
Ribonucleoprotein LSM domain		2351
481IPR020471
Aldo/keto reductase subgroup		23136
482IPR027725
Heat shock transcription factor family		2332
483IPR018181
Heat shock protein 70, conserved site		2357
484IPR013010
Zinc finger, SIAH-type		2323
485IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2323
486IPR008963
Purple acid phosphatase-like, N-terminal		2325
487IPR012328
Chalcone/stilbene synthase, C-terminal		2323
488IPR025486
Domain of unknown function DUF4378		2323
489IPR002937
Amine oxidase		2326
490IPR001229
Mannose-binding lectin		23152
491IPR003614
Knottin		2351
492IPR017884
SANT domain		2227
493IPR000864
Proteinase inhibitor I13, potato inhibitor I		22125
494IPR032872
Wall-associated receptor kinase, C-terminal		2223
495IPR000717
Proteasome component (PCI) domain		2255
496IPR018392
Peptidoglycan-binding lysin domain		2282
497IPR009030
Growth factor, receptor		2222
498IPR001353
Proteasome, subunit alpha/beta		2223
499IPR011257
DNA glycosylase		2260
500IPR029056
Ribokinase-like		2266
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Solanum_lycopersicum.html b/gramene/htdocs/ssi/species.weix/stats_Solanum_lycopersicum.html new file mode 100644 index 00000000..1f8a3468 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Solanum_lycopersicum.html @@ -0,0 +1,82 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:SL2.50, Oct 2014
Database version:86.250
Base Pairs:737,636,465
Golden Path Length:823,630,941
Genebuild by: SolTub_3.0
Genebuild method: Generated from ENA annotation
Genebuild started: May 2011
Genebuild released: May 2011
Genebuild last updated/patched: Oct 2014
Genebuild version: 2014-10-EnsemblPlants
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		33,837
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		76
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:38,735
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
198543444
255340444
370787664
466470942
565875088
649751636
768045021
865866657
972482091
1065527505
1156302525
1267145203
+
+
supercontig3223 sequences
contig26877 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):71,156,260
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		14133555
2IPR011009
Protein kinase-like domain		12171325
3IPR000719
Protein kinase domain		11362741
4IPR008271
Serine/threonine-protein kinase, active site		836838
5IPR032675
Leucine-rich repeat domain, L domain-like		8362539
6IPR013083
Zinc finger, RING/FYVE/PHD-type		674718
7IPR017441
Protein kinase, ATP binding site		670671
8IPR011990
Tetratricopeptide-like helical domain		5781941
9IPR013320
Concanavalin A-like lectin/glucanase domain		524649
10IPR009057
Homeodomain-like		4721087
11IPR002885
Pentatricopeptide repeat		47110932
12IPR016040
NAD(P)-binding domain		4361000
13IPR001841
Zinc finger, RING-type		428994
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		408617
15IPR001611
Leucine-rich repeat		4052448
16IPR029058
Alpha/Beta hydrolase fold		395958
17IPR016024
Armadillo-type fold		365817
18IPR001810
F-box domain		328858
19IPR012677
Nucleotide-binding alpha-beta plait domain		312902
20IPR015943
WD40/YVTN repeat-like-containing domain		305491
21IPR001005
SANT/Myb domain		293785
22IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		287710
23IPR003593
AAA+ ATPase domain		286370
24IPR017986
WD40-repeat-containing domain		284683
25IPR011989
Armadillo-like helical		280542
26IPR000504
RNA recognition motif domain		2741176
27IPR013210
Leucine-rich repeat-containing N-terminal, type 2		267278
28IPR001680
WD40 repeat		2622811
29IPR012336
Thioredoxin-like fold		261593
30IPR020846
Major facilitator superfamily domain		257511
31IPR001128
Cytochrome P450		2551660
32IPR002182
NB-ARC		248262
33IPR017930
Myb domain		245380
34IPR002401
Cytochrome P450, E-class, group I		2351716
35IPR003591
Leucine-rich repeat, typical subtype		2321713
36IPR012337
Ribonuclease H-like domain		230373
37IPR017972
Cytochrome P450, conserved site		227227
38IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		218512
39IPR017853
Glycoside hydrolase superfamily		209239
40IPR011992
EF-hand domain pair		200487
41IPR027443
Isopenicillin N synthase-like		196202
42IPR011991
Winged helix-turn-helix DNA-binding domain		188351
43IPR016177
DNA-binding domain		186222
44IPR005123
Oxoglutarate/iron-dependent dioxygenase		182333
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		179784
46IPR001471
AP2/ERF domain		1731081
47IPR002048
EF-hand domain		1721181
48IPR013781
Glycoside hydrolase, catalytic domain		170187
49IPR014001
Helicase superfamily 1/2, ATP-binding domain		160313
50IPR018247
EF-Hand 1, calcium-binding site		158382
51IPR001650
Helicase, C-terminal		157465
52IPR007087
Zinc finger, C2H2		157495
53IPR023214
HAD-like domain		157437
54IPR012334
Pectin lyase fold		156166
55IPR011050
Pectin lyase fold/virulence factor		155161
56IPR012340
Nucleic acid-binding, OB-fold		155209
57IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		152251
58IPR019775
WD40 repeat, conserved site		148253
59IPR029044
Nucleotide-diphospho-sugar transferases		141328
60IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		141537
61IPR007527
Zinc finger, SWIM-type		141247
62IPR003439
ABC transporter-like		141389
63IPR026992
Non-haem dioxygenase N-terminal domain		140140
64IPR015424
Pyridoxal phosphate-dependent transferase		129138
65IPR013026
Tetratricopeptide repeat-containing domain		126167
66IPR009072
Histone-fold		126253
67IPR000008
C2 domain		125833
68IPR006564
Zinc finger, PMZ-type		125125
69IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		125132
70IPR020683
Ankyrin repeat-containing domain		125567
71IPR003959
ATPase, AAA-type, core		125143
72IPR010255
Haem peroxidase		124131
73IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		122142
74IPR013830
SGNH hydrolase-type esterase domain		122350
75IPR008972
Cupredoxin		121443
76IPR019734
Tetratricopeptide repeat		119830
77IPR029071
Ubiquitin-related domain		119152
78IPR005225
Small GTP-binding protein domain		119120
79IPR002016
Haem peroxidase, plant/fungal/bacterial		118791
80IPR014710
RmlC-like jelly roll fold		117150
81IPR011011
Zinc finger, FYVE/PHD-type		115134
82IPR002110
Ankyrin repeat		114792
83IPR001878
Zinc finger, CCHC-type		114481
84IPR001623
DnaJ domain		113802
85IPR018289
MULE transposase domain		113114
86IPR013785
Aldolase-type TIM barrel		110127
87IPR006447
Myb domain, plants		108109
88IPR023213
Chloramphenicol acetyltransferase-like domain		108186
89IPR001356
Homeobox domain		108294
90IPR015300
DNA-binding pseudobarrel domain		108313
91IPR001932
Protein phosphatase 2C (PP2C)-like domain		107580
92IPR023393
START-like domain		106108
93IPR003676
Auxin-induced protein, ARG7		106107
94IPR000823
Plant peroxidase		106896
95IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		105264
96IPR021109
Aspartic peptidase domain		103309
97IPR002100
Transcription factor, MADS-box		103686
98IPR001461
Aspartic peptidase		103274
99IPR015500
Peptidase S8, subtilisin-related		103357
100IPR003441
NAC domain		101294
101IPR002347
Glucose/ribitol dehydrogenase		101958
102IPR019557
Aminotransferase-like, plant mobile domain		99124
103IPR020472
G-protein beta WD-40 repeat		99297
104IPR019793
Peroxidases heam-ligand binding site		9999
105IPR003340
B3 DNA binding domain		98409
106IPR015410
Domain of unknown function DUF1985		9898
107IPR032867
DYW domain		9797
108IPR003480
Transferase		97101
109IPR017451
F-box associated interaction domain		9697
110IPR000073
Alpha/beta hydrolase fold-1		96193
111IPR033121
Peptidase family A1 domain		95101
112IPR001480
Bulb-type lectin domain		95501
113IPR015655
Protein phosphatase 2C		93145
114IPR001965
Zinc finger, PHD-type		93139
115IPR000209
Peptidase S8/S53 domain		93472
116IPR001087
GDSL lipase/esterase		9292
117IPR010987
Glutathione S-transferase, C-terminal-like		92256
118IPR011545
DEAD/DEAH box helicase domain		9295
119IPR017907
Zinc finger, RING-type, conserved site		9292
120IPR017871
ABC transporter, conserved site		91116
121IPR000109
Proton-dependent oligopeptide transporter family		90187
122IPR032799
Xylanase inhibitor, C-terminal		9091
123IPR011333
BTB/POZ fold		9099
124IPR006501
Pectinesterase inhibitor domain		87417
125IPR000626
Ubiquitin domain		86300
126IPR032861
Xylanase inhibitor, N-terminal		8586
127IPR015880
Zinc finger, C2H2-like		84224
128IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		8396
129IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		82108
130IPR003657
DNA-binding WRKY		82481
131IPR011051
RmlC-like cupin domain		82102
132IPR011993
Pleckstrin homology-like domain		79151
133IPR019794
Peroxidase, active site		7878
134IPR001806
Small GTPase superfamily		7879
135IPR013766
Thioredoxin domain		77156
136IPR000571
Zinc finger, CCCH-type		77616
137IPR019786
Zinc finger, PHD-type, conserved site		7685
138IPR002528
Multi antimicrobial extrusion protein		76208
139IPR000270
Phox/Bem1p		76131
140IPR000070
Pectinesterase, catalytic		7679
141IPR008543
Uncharacterised protein family Ycf2		7592
142IPR000225
Armadillo		75618
143IPR026057
PC-Esterase		7474
144IPR029962
Trichome birefringence-like family		7491
145IPR019787
Zinc finger, PHD-finger		74134
146IPR004045
Glutathione S-transferase, N-terminal		73143
147IPR004827
Basic-leucine zipper domain		71252
148IPR005828
General substrate transporter		7082
149IPR003960
ATPase, AAA-type, conserved site		6975
150IPR016135
Ubiquitin-conjugating enzyme/RWD-like		69140
151IPR025846
PMR5 N-terminal domain		6969
152IPR008949
Isoprenoid synthase domain		68141
153IPR016181
Acyl-CoA N-acyltransferase		67162
154IPR004332
Transposase, MuDR, plant		6767
155IPR006904
Protein of unknown function DUF716 (TMEM45)		6679
156IPR000210
BTB/POZ domain		66167
157IPR008978
HSP20-like chaperone		65128
158IPR018108
Mitochondrial substrate/solute carrier		65354
159IPR023395
Mitochondrial carrier domain		65142
160IPR000858
S-locus glycoprotein		6466
161IPR006121
Heavy metal-associated domain, HMA		64221
162IPR027640
Kinesin-like protein		64183
163IPR008979
Galactose-binding domain-like		64167
164IPR029052
Metallo-dependent phosphatase-like		64150
165IPR003613
U box domain		64188
166IPR002085
Alcohol dehydrogenase superfamily, zinc-type		6376
167IPR001752
Kinesin motor domain		63473
168IPR000330
SNF2-related		6264
169IPR013763
Cyclin-like		62290
170IPR004843
Calcineurin-like phosphoesterase domain, apaH type		6161
171IPR031052
FHY3/FAR1 family		6166
172IPR014756
Immunoglobulin E-set		6166
173IPR003137
Protease-associated domain, PA		6061
174IPR001563
Peptidase S10, serine carboxypeptidase		59327
175IPR013525
ABC-2 type transporter		5981
176IPR000608
Ubiquitin-conjugating enzyme E2		59119
177IPR000048
IQ motif, EF-hand binding site		59402
178IPR011032
GroES (chaperonin 10)-like		58127
179IPR000873
AMP-dependent synthetase/ligase		5861
180IPR003609
Apple-like		58161
181IPR013057
Amino acid transporter, transmembrane domain		5859
182IPR002109
Glutaredoxin		58113
183IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		5792
184IPR010285
DNA helicase Pif1 like		5660
185IPR020568
Ribosomal protein S5 domain 2-type fold		5667
186IPR002913
START domain		56150
187IPR009009
RlpA-like double-psi beta-barrel domain		55153
188IPR011006
CheY-like superfamily		5558
189IPR002921
Fungal lipase-like domain		5454
190IPR018253
DnaJ domain, conserved site		5454
191IPR006045
Cupin 1		54146
192IPR005202
Transcription factor GRAS		54108
193IPR016166
FAD-binding, type 2		53104
194IPR001214
SET domain		53144
195IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5353
196IPR011707
Multicopper oxidase, type 3		5353
197IPR025558
Domain of unknown function DUF4283		5354
198IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		5393
199IPR001789
Signal transduction response regulator, receiver domain		53150
200IPR011701
Major facilitator superfamily		5254
201IPR029045
ClpP/crotonase-like domain		52136
202IPR000743
Glycoside hydrolase, family 28		5289
203IPR001117
Multicopper oxidase, type 1		5151
204IPR000999
Ribonuclease III domain		51247
205IPR004088
K Homology domain, type 1		51365
206IPR011706
Multicopper oxidase, type 2		5151
207IPR016039
Thiolase-like		50210
208IPR014014
RNA helicase, DEAD-box type, Q motif		5050
209IPR007125
Histone core		5051
210IPR011527
ABC transporter type 1, transmembrane domain		50244
211IPR030184
WAT1-related protein		5052
212IPR000620
EamA domain		5087
213IPR002068
Alpha crystallin/Hsp20 domain		4991
214IPR003245
Plastocyanin-like		49140
215IPR000490
Glycoside hydrolase, family 17		4981
216IPR000182
GNAT domain		4893
217IPR023271
Aquaporin-like		4895
218IPR005829
Sugar transporter, conserved site		4891
219IPR006671
Cyclin, N-terminal		4875
220IPR016159
Cullin repeat-like-containing domain		4868
221IPR006626
Parallel beta-helix repeat		47245
222IPR004263
Exostosin-like		4748
223IPR003594
Histidine kinase-like ATPase, C-terminal domain		47172
224IPR004883
Lateral organ boundaries, LOB		4794
225IPR017970
Homeobox, conserved site		4747
226IPR003663
Sugar/inositol transporter		47263
227IPR024171
S-receptor-like serine/threonine-protein kinase		4646
228IPR012946
X8 domain		4692
229IPR023828
Peptidase S8, subtilisin, Ser-active site		4646
230IPR020845
AMP-binding, conserved site		4646
231IPR000425
Major intrinsic protein		46383
232IPR019821
Kinesin motor domain, conserved site		4545
233IPR009060
UBA-like		4552
234IPR008250
P-type ATPase, A domain		4596
235IPR005630
Terpene synthase, metal-binding domain		4546
236IPR013783
Immunoglobulin-like fold		4550
237IPR003958
Transcription factor CBF/NF-Y/archaeal histone		4545
238IPR004839
Aminotransferase, class I/classII		4547
239IPR006702
Domain of unknown function DUF588		4545
240IPR015916
Galactose oxidase, beta-propeller		4447
241IPR006553
Leucine-rich repeat, cysteine-containing subtype		44310
242IPR033131
Pectinesterase, Asp active site		4444
243IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4445
244IPR023299
P-type ATPase, cytoplasmic domain N		4488
245IPR006016
UspA		4343
246IPR013149
Alcohol dehydrogenase, C-terminal		4343
247IPR029055
Nucleophile aminohydrolases, N-terminal		4387
248IPR009000
Translation protein, beta-barrel domain		4346
249IPR023313
Ubiquitin-conjugating enzyme, active site		4343
250IPR008928
Six-hairpin glycosidase-like		4351
251IPR001757
P-type ATPase		43140
252IPR000916
Bet v I domain		4372
253IPR006094
FAD linked oxidase, N-terminal		4343
254IPR007021
Domain of unknown function DUF659		4345
255IPR032710
NTF2-like domain		4275
256IPR025312
Domain of unknown function DUF4216		4242
257IPR000315
Zinc finger, B-box		42144
258IPR001280
Photosystem I PsaA/PsaB		42155
259IPR019378
GDP-fucose protein O-fucosyltransferase		4242
260IPR004046
Glutathione S-transferase, C-terminal		4242
261IPR004087
K Homology domain		4291
262IPR002495
Glycosyl transferase, family 8		4243
263IPR017877
Myb-like domain		4256
264IPR011016
Zinc finger, RING-CH-type		4194
265IPR005135
Endonuclease/exonuclease/phosphatase		41140
266IPR007112
Expansin/pollen allergen, DPBB domain		4178
267IPR011013
Galactose mutarotase-like domain		4153
268IPR011012
Longin-like domain		4141
269IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		4141
270IPR000644
CBS domain		41233
271IPR028889
Ubiquitin specific protease domain		4141
272IPR004853
Triose-phosphate transporter domain		4040
273IPR010920
Like-Sm (LSM) domain		4040
274IPR029021
Protein-tyrosine phosphatase-like		4092
275IPR016167
FAD-binding, type 2, subdomain 1		4040
276IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		4055
277IPR002487
Transcription factor, K-box		4080
278IPR008942
ENTH/VHS		3976
279IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		3941
280IPR007118
Expansin/Lol pI		39213
281IPR029061
Thiamin diphosphate-binding fold		39117
282IPR013154
Alcohol dehydrogenase GroES-like		3939
283IPR000863
Sulfotransferase domain		3942
284IPR031107
Small heat shock protein HSP20		3939
285IPR018303
P-type ATPase, phosphorylation site		3939
286IPR007117
Expansin, cellulose-binding-like domain		39155
287IPR033389
AUX/IAA domain		3845
288IPR025110
AMP-binding enzyme C-terminal domain		3838
289IPR018490
Cyclic nucleotide-binding-like		3839
290IPR025287
Wall-associated receptor kinase galacturonan-binding domain		3839
291IPR001251
CRAL-TRIO domain		38182
292IPR001969
Aspartic peptidase, active site		3855
293IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		38189
294IPR013094
Alpha/beta hydrolase fold-3		3839
295IPR011042
Six-bladed beta-propeller, TolB-like		3848
296IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3842
297IPR000757
Glycoside hydrolase, family 16		3877
298IPR008974
TRAF-like		3872
299IPR008991
Translation protein SH3-like domain		3737
300IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		3737
301IPR012675
Beta-grasp domain		3737
302IPR006652
Kelch repeat type 1		37153
303IPR002902
Gnk2-homologous domain		37132
304IPR004864
Late embryogenesis abundant protein, LEA-14		3738
305IPR001906
Terpene synthase, N-terminal domain		3779
306IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3737
307IPR006594
LIS1 homology motif		3668
308IPR000528
Plant lipid transfer protein/Par allergen		36166
309IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		3639
310IPR013128
Peptidase C1A		3638
311IPR020904
Short-chain dehydrogenase/reductase, conserved site		3636
312IPR002035
von Willebrand factor, type A		36102
313IPR000668
Peptidase C1A, papain C-terminal		36160
314IPR002067
Mitochondrial carrier protein		36182
315IPR001584
Integrase, catalytic core		3568
316IPR029000
Cyclophilin-like domain		3576
317IPR022357
Major intrinsic protein, conserved site		3535
318IPR000595
Cyclic nucleotide-binding domain		3591
319IPR005333
Transcription factor, TCP		3434
320IPR017887
Transcription factor TCP subgroup		3434
321IPR016455
Xyloglucan endotransglucosylase/hydrolase		3434
322IPR001938
Thaumatin		34388
323IPR022742
Putative lysophospholipase		3434
324IPR032308
Jas TPL-binding domain		3436
325IPR005150
Cellulose synthase		3445
326IPR005746
Thioredoxin		3446
327IPR023298
P-type ATPase, transmembrane domain		3463
328IPR002937
Amine oxidase		3439
329IPR018202
Peptidase S10, serine carboxypeptidase, active site		3435
330IPR006073
GTP binding domain		3490
331IPR015797
NUDIX hydrolase domain-like		3466
332IPR000727
Target SNARE coiled-coil domain		3389
333IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		33171
334IPR018200
Ubiquitin specific protease, conserved site		3357
335IPR008906
HAT dimerisation domain, C-terminal		3333
336IPR004367
Cyclin, C-terminal domain		3364
337IPR022796
Chlorophyll A-B binding protein		3334
338IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		3344
339IPR002912
ACT domain		3378
340IPR011905
Glutaredoxin-like, plant II		3333
341IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		3333
342IPR015947
PUA-like domain		3343
343IPR006153
Cation/H+ exchanger		3233
344IPR004316
SWEET sugar transporter		3263
345IPR026961
PGG domain		3233
346IPR003406
Glycosyl transferase, family 14		3232
347IPR005821
Ion transport domain		3233
348IPR014722
Ribosomal protein L2 domain 2		3232
349IPR001849
Pleckstrin homology domain		3265
350IPR000169
Cysteine peptidase, cysteine active site		3232
351IPR003851
Zinc finger, Dof-type		32126
352IPR015915
Kelch-type beta propeller		3240
353IPR011043
Galactose oxidase/kelch, beta-propeller		3235
354IPR024788
Malectin-like carbohydrate-binding domain		3233
355IPR012341
Six-hairpin glycosidase		3233
356IPR005175
Domain of unknown function DUF296		3263
357IPR023329
Chlorophyll a/b binding protein domain		3233
358IPR003614
Knottin, scorpion toxin-like		3273
359IPR027356
NPH3 domain		3161
360IPR011332
Zinc-binding ribosomal protein		3131
361IPR002129
Pyridoxal phosphate-dependent decarboxylase		3131
362IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		3138
363IPR020843
Polyketide synthase, enoylreductase domain		3131
364IPR006527
F-box associated domain, type 1		3132
365IPR010402
CCT domain		3062
366IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		3085
367IPR001929
Germin		3087
368IPR013088
Zinc finger, NHR/GATA-type		3031
369IPR013216
Methyltransferase type 11		3030
370IPR001296
Glycosyl transferase, family 1		3030
371IPR025886
Phloem protein 2-like		3030
372IPR003690
Mitochodrial transcription termination factor		30220
373IPR008896
Uncharacterised protein family Ycf1		3033
374IPR017937
Thioredoxin, conserved site		3037
375IPR000086
NUDIX hydrolase domain		3058
376IPR014720
Double-stranded RNA-binding domain		30117
377IPR023827
Peptidase S8, subtilisin, Asp-active site		3031
378IPR025660
Cysteine peptidase, histidine active site		3030
379IPR000679
Zinc finger, GATA-type		30123
380IPR025322
Protein of unknown function DUF4228, plant		2929
381IPR004041
NAF domain		2929
382IPR025659
Tubby C-terminal-like domain		2935
383IPR001344
Chlorophyll A-B binding protein, plant		2930
384IPR000907
Lipoxygenase		2945
385IPR000795
Elongation factor, GTP-binding domain		29160
386IPR011074
CRAL/TRIO, N-terminal domain		2969
387IPR004265
Plant disease resistance response protein		2930
388IPR013819
Lipoxygenase, C-terminal		29145
389IPR031307
Ninja family		2933
390IPR004000
Actin family		28163
391IPR001440
Tetratricopeptide TPR1		2835
392IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2856
393IPR033275
E3 ubiquitin-protein ligase MARCH-like		2830
394IPR002355
Multicopper oxidase, copper-binding site		2828
395IPR002935
O-methyltransferase, family 3		2851
396IPR008480
Protein of unknown function DUF761, plant		2828
397IPR029006
ADF-H/Gelsolin-like domain		2851
398IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2868
399IPR023210
NADP-dependent oxidoreductase domain		2891
400IPR001395
Aldo/keto reductase		2839
401IPR030182
Purine permease, plant		2828
402IPR003106
Leucine zipper, homeobox-associated		2738
403IPR001163
Ribonucleoprotein LSM domain		2750
404IPR002423
Chaperonin Cpn60/TCP-1 family		2728
405IPR025422
Transcription factor TGA like domain		2727
406IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		2727
407IPR027409
GroEL-like apical domain		2752
408IPR027923
Hydrophobic seed protein		2727
409IPR004910
Yippee/Mis18		2727
410IPR029062
Class I glutamine amidotransferase-like		2767
411IPR006458
Ovate protein family, C-terminal		2773
412IPR025661
Cysteine peptidase, asparagine active site		2727
413IPR001041
2Fe-2S ferredoxin-type domain		2766
414IPR017884
SANT domain		2627
415IPR000782
FAS1 domain		26153
416IPR033138
Multicopper oxidases, conserved site		2626
417IPR007493
Protein of unknown function DUF538		2678
418IPR001357
BRCT domain		26200
419IPR018957
Zinc finger, C3HC4 RING-type		2626
420IPR027725
Heat shock transcription factor family		2630
421IPR032881
Oberon, PHD finger domain		2626
422IPR022812
Dynamin superfamily		26128
423IPR002119
Histone H2A		26133
424IPR000047
Helix-turn-helix motif		2652
425IPR008266
Tyrosine-protein kinase, active site		2626
426IPR008263
Glycoside hydrolase, family 16, active site		2626
427IPR002963
Expansin		26212
428IPR001220
Legume lectin domain		2626
429IPR004993
GH3 auxin-responsive promoter		2655
430IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2653
431IPR004330
FAR1 DNA binding domain		2627
432IPR008889
VQ		2626
433IPR013328
6-phosphogluconate dehydrogenase, domain 2		2532
434IPR001024
PLAT/LH2 domain		25103
435IPR001360
Glycoside hydrolase, family 1		25154
436IPR013187
F-box associated domain, type 3		2525
437IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2563
438IPR012951
Berberine/berberine-like		2525
439IPR014025
Glutaredoxin subgroup		2575
440IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2550
441IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		2539
442IPR033124
Serine carboxypeptidases, histidine active site		2526
443IPR010989
t-SNARE		2527
444IPR031112
AP2-like ethylene-responsive transcription factor		2527
445IPR000408
Regulator of chromosome condensation, RCC1		25398
446IPR003008
Tubulin/FtsZ, GTPase domain		25106
447IPR029069
HotDog domain		2570
448IPR013126
Heat shock protein 70 family		25202
449IPR004314
Domain of unknown function DUF239		2526
450IPR000232
Heat shock factor (HSF)-type, DNA-binding		25143
451IPR031127
E3 ubiquitin ligase RBR family		2529
452IPR001487
Bromodomain		25171
453IPR013809
ENTH domain		2552
454IPR006689
Small GTPase superfamily, ARF/SAR type		24104
455IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2446
456IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2424
457IPR024709
O-fucosyltransferase, plant		2424
458IPR018451
NAF/FISL domain		2424
459IPR003347
JmjC domain		2463
460IPR002648
Isopentenyl transferase		2424
461IPR004252
Probable transposase, Ptta/En/Spm, plant		2424
462IPR001246
Lipoxygenase, plant		24150
463IPR001876
Zinc finger, RanBP2-type		24204
464IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2435
465IPR004838
Aminotransferases, class-I, pyridoxal-phosphate-binding site		2424
466IPR001701
Glycoside hydrolase, family 9		2424
467IPR004158
Protein of unknown function DUF247, plant		2427
468IPR003311
AUX/IAA protein		2428
469IPR017927
Ferredoxin reductase-type FAD-binding domain		2323
470IPR029060
PIN domain-like		2340
471IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2364
472IPR008971
HSP40/DnaJ peptide-binding		2355
473IPR006593
Cytochrome b561/ferric reductase transmembrane		2364
474IPR002867
Zinc finger, C6HC-type		2375
475IPR006195
Aminoacyl-tRNA synthetase, class II		2323
476IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2368
477IPR003661
Signal transduction histidine kinase EnvZ-like, dimerisation/phosphoacceptor domain		2360
478IPR003954
RNA recognition motif domain, eukaryote		2334
479IPR013581
Plant PDR ABC transporter associated		2323
480IPR000717
Proteasome component (PCI) domain		2344
481IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2323
482IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		2323
483IPR018392
LysM domain		2379
484IPR021115
Pyridoxal-phosphate binding site		2323
485IPR002022
Pectate lyase/Amb allergen		2348
486IPR011257
DNA glycosylase		2355
487IPR001763
Rhodanese-like domain		23103
488IPR008176
Gamma thionin		2344
489IPR029481
ABC-transporter extracellular N-terminal domain		2323
490IPR004146
DC1		2357
491IPR004813
Oligopeptide transporter, OPT superfamily		2342
492IPR016161
Aldehyde/histidinol dehydrogenase		2323
493IPR003616
Post-SET domain		2332
494IPR016130
Protein-tyrosine phosphatase, active site		2323
495IPR003855
Potassium transporter		2344
496IPR029047
Heat shock protein 70kD, peptide-binding domain		2350
497IPR012317
Poly(ADP-ribose) polymerase, catalytic domain		2352
498IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		23191
499IPR018082
AmbAllergen		23168
500IPR029064
50S ribosomal protein L30e-like		2346
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum.html b/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum.html new file mode 100644 index 00000000..5c059705 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum.html @@ -0,0 +1,71 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:SolTub_3.0, May 2011
Database version:86.4
Base Pairs:727,424,546
Golden Path Length:810,654,046
Genebuild by: SolTub_3.0
Genebuild method: Import
Genebuild started: May 2011
Genebuild version: SolTub_3.0
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,021
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		332
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:60,163
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
13 sequences
+
+ +
+ + + +
SequenceLength (bp)
0085736662
188663952
248614681
362190286
472208621
552070158
659532096
756760843
856938457
961540751
1059756223
1145475667
1261165649
+
+
superscaffold66254 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum_IPtop500.html new file mode 100644 index 00000000..6106ca53 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Solanum_tuberosum_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		13314203
2IPR011009
Protein kinase-like domain		12492017
3IPR032675
Leucine-rich repeat domain, L domain-like		12194417
4IPR000719
Protein kinase, catalytic domain		11734166
5IPR008271
Serine/threonine-protein kinase, active site		8461194
6IPR017441
Protein kinase, ATP binding site		7141001
7IPR013083
Zinc finger, RING/FYVE/PHD-type		648910
8IPR013320
Concanavalin A-like lectin/glucanase, subgroup		577977
9IPR001611
Leucine-rich repeat		5743740
10IPR011990
Tetratricopeptide-like helical		5622327
11IPR001810
F-box domain, cyclin-like		5361590
12IPR002885
Pentatricopeptide repeat		49913924
13IPR001128
Cytochrome P450		4813822
14IPR002182
NB-ARC		445548
15IPR016040
NAD(P)-binding domain		4411484
16IPR009057
Homeodomain-like		4311269
17IPR001841
Zinc finger, RING-type		4311266
18IPR002401
Cytochrome P450, E-class, group I		4113248
19IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		396807
20IPR029058
Alpha/Beta hydrolase fold		3781421
21IPR017972
Cytochrome P450, conserved site		370481
22IPR003591
Leucine-rich repeat, typical subtype		3392726
23IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		320912
24IPR013210
Leucine-rich repeat-containing N-terminal, type 2		283325
25IPR012677
Nucleotide-binding, alpha-beta plait		2771310
26IPR020846
Major facilitator superfamily domain		274806
27IPR016024
Armadillo-type fold		272585
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		2681009
29IPR001005
SANT/Myb domain		266842
30IPR012336
Thioredoxin-like fold		263746
31IPR017451
F-box associated interaction domain		256272
32IPR000504
RNA recognition motif domain		2471748
33IPR003593
AAA+ ATPase domain		245398
34IPR015943
WD40/YVTN repeat-like-containing domain		243599
35IPR016177
DNA-binding, integrase-type		230295
36IPR011989
Armadillo-like helical		224461
37IPR017986
WD40-repeat-containing domain		220803
38IPR001471
AP2/ERF domain		2191419
39IPR017930
Myb domain		219410
40IPR027443
Isopenicillin N synthase-like		215353
41IPR011991
Winged helix-turn-helix transcription repressor DNA-binding		212530
42IPR017853
Glycoside hydrolase, superfamily		206342
43IPR001680
WD40 repeat		2033164
44IPR012337
Ribonuclease H-like domain		195420
45IPR005123
Oxoglutarate/iron-dependent dioxygenase		194516
46IPR011992
EF-hand-like domain		180587
47IPR001878
Zinc finger, CCHC-type		177933
48IPR013781
Glycoside hydrolase, catalytic domain		168270
49IPR007087
Zinc finger, C2H2		163639
50IPR011598
Helix-loop-helix domain		163999
51IPR002048
Calcium-binding EF-hand		1591356
52IPR002100
Transcription factor, MADS-box		1581154
53IPR023213
Chloramphenicol acetyltransferase-like domain		156312
54IPR026992
Non-haem dioxygenase N-terminal domain		155220
55IPR011050
Pectin lyase fold/virulence factor		154213
56IPR012334
Pectin lyase fold		154218
57IPR003480
Transferase		150179
58IPR018247
EF-Hand 1, calcium-binding site		148443
59IPR023214
HAD-like domain		146605
60IPR012340
Nucleic acid-binding, OB-fold		145246
61IPR003676
Auxin responsive SAUR protein		143152
62IPR015424
Pyridoxal phosphate-dependent transferase, major domain		139203
63IPR025558
Domain of unknown function DUF4283		139145
64IPR023393
START-like domain		131183
65IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		130181
66IPR010255
Haem peroxidase		129176
67IPR014710
RmlC-like jelly roll fold		128213
68IPR029044
Nucleotide-diphospho-sugar transferases		125449
69IPR002016
Haem peroxidase, plant/fungal/bacterial		123907
70IPR019775
WD40 repeat, conserved site		120294
71IPR003439
ABC transporter-like		118433
72IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		117741
73IPR020683
Ankyrin repeat-containing domain		117809
74IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		117350
75IPR003441
No apical meristem (NAM) protein		116413
76IPR008972
Cupredoxin		116581
77IPR013830
Esterase, SGNH hydrolase-type		114407
78IPR009072
Histone-fold		113254
79IPR002347
Glucose/ribitol dehydrogenase		1121338
80IPR013026
Tetratricopeptide repeat-containing domain		112203
81IPR029071
Ubiquitin-related domain		111190
82IPR015300
DNA-binding pseudobarrel domain		111413
83IPR021109
Peptidase aspartic		110445
84IPR005225
Small GTP-binding protein domain		109133
85IPR011333
BTB/POZ fold		109158
86IPR001623
Heat shock protein DnaJ, N-terminal		108966
87IPR000823
Plant peroxidase		108996
88IPR001650
Helicase, C-terminal		107431
89IPR015500
Peptidase S8, subtilisin-related		106385
90IPR014001
Helicase, superfamily 1/2, ATP-binding domain		106266
91IPR002110
Ankyrin repeat		1051076
92IPR000008
C2 calcium-dependent membrane targeting		103991
93IPR006501
Pectinesterase inhibitor		103537
94IPR003959
ATPase, AAA-type, core		103167
95IPR019734
Tetratricopeptide repeat		1011029
96IPR001356
Homeobox domain		101365
97IPR013785
Aldolase-type TIM barrel		100185
98IPR000073
Alpha/beta hydrolase fold-1		100257
99IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		100169
100IPR001461
Peptidase A1		100349
101IPR006447
Myb domain, plants		98144
102IPR003340
B3 DNA binding domain		97498
103IPR019793
Peroxidases heam-ligand binding site		97112
104IPR032867
DYW domain		97114
105IPR011051
RmlC-like cupin domain		96148
106IPR000209
Peptidase S8/S53, subtilisin/kexin/sedolisin		96534
107IPR015880
Zinc finger, C2H2-like		95295
108IPR001932
Protein phosphatase 2C-like		95871
109IPR008949
Terpenoid synthase		93267
110IPR033121
Peptidase family A1 domain		93147
111IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		93137
112IPR017907
Zinc finger, RING-type, conserved site		92123
113IPR005828
General substrate transporter		90149
114IPR032799
Xylanase inhibitor, C-terminal		88121
115IPR011011
Zinc finger, FYVE/PHD-type		88132
116IPR000109
Proton-dependent oligopeptide transporter family		87274
117IPR001480
Bulb-type lectin domain		87653
118IPR003657
DNA-binding WRKY		86740
119IPR032861
Xylanase inhibitor, N-terminal		85120
120IPR001087
Lipase, GDSL		82108
121IPR015655
Protein phosphatase 2C		82238
122IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		81452
123IPR020472
G-protein beta WD-40 repeat		80318
124IPR010987
Glutathione S-transferase, C-terminal-like		80307
125IPR000626
Ubiquitin domain		79373
126IPR017871
ABC transporter, conserved site		79128
127IPR001806
Small GTPase superfamily		7997
128IPR019794
Peroxidase, active site		7887
129IPR000270
Phox/Bem1p		78199
130IPR006527
F-box associated domain, type 1		7781
131IPR002528
Multi antimicrobial extrusion protein		75277
132IPR000225
Armadillo		75740
133IPR000916
Bet v I domain		74169
134IPR008978
HSP20-like chaperone		73161
135IPR000571
Zinc finger, CCCH-type		73863
136IPR010259
Proteinase inhibitor I9		71102
137IPR013766
Thioredoxin domain		71178
138IPR004045
Glutathione S-transferase, N-terminal		71180
139IPR000210
BTB/POZ domain		70257
140IPR006045
Cupin 1		70189
141IPR000070
Pectinesterase, catalytic		7088
142IPR005630
Terpene synthase, metal-binding domain		6999
143IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		69181
144IPR004827
Basic-leucine zipper domain		68318
145IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		67133
146IPR005174
Protein of unknown function DUF295		6778
147IPR016181
Acyl-CoA N-acyltransferase		66201
148IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		6695
149IPR011043
Galactose oxidase/kelch, beta-propeller		6680
150IPR013763
Cyclin-like		65432
151IPR016135
Ubiquitin-conjugating enzyme/RWD-like		65195
152IPR003613
U box domain		65260
153IPR026057
PC-Esterase		64103
154IPR002085
Alcohol dehydrogenase superfamily, zinc-type		64123
155IPR002109
Glutaredoxin		64150
156IPR001965
Zinc finger, PHD-type		63125
157IPR011032
GroES-like		61192
158IPR000858
S-locus glycoprotein		6196
159IPR029962
Trichome birefringence-like family		61118
160IPR005135
Endonuclease/exonuclease/phosphatase		61239
161IPR003960
ATPase, AAA-type, conserved site		6188
162IPR018022
tRNA delta(2)-isopentenylpyrophosphate transferase		61108
163IPR003137
Protease-associated domain, PA		6069
164IPR023395
Mitochondrial carrier domain		60242
165IPR029052
Metallo-dependent phosphatase-like		60242
166IPR003609
Apple-like		59257
167IPR018108
Mitochondrial substrate/solute carrier		59507
168IPR002068
Alpha crystallin/Hsp20 domain		58120
169IPR003245
Plastocyanin-like		58184
170IPR006121
Heavy metal-associated domain, HMA		57228
171IPR000608
Ubiquitin-conjugating enzyme, E2		57165
172IPR009009
Barwin-related endoglucanase		57204
173IPR001906
Terpene synthase-like		57157
174IPR005829
Sugar transporter, conserved site		56146
175IPR013057
Amino acid transporter, transmembrane		56102
176IPR024171
S-receptor-like serine/threonine-protein kinase		5563
177IPR006553
Leucine-rich repeat, cysteine-containing subtype		55466
178IPR019786
Zinc finger, PHD-type, conserved site		5582
179IPR005202
Transcription factor GRAS		55121
180IPR000490
Glycoside hydrolase, family 17		55123
181IPR003663
Sugar/inositol transporter		55386
182IPR002921
Lipase, class 3		5484
183IPR004843
Metallophosphoesterase domain		5484
184IPR007125
Histone core		5457
185IPR018253
Heat shock protein DnaJ, conserved site		5468
186IPR000743
Glycoside hydrolase, family 28		54129
187IPR000182
GNAT domain		53126
188IPR013525
ABC-2 type transporter		5389
189IPR013187
F-box associated domain, type 3		5354
190IPR016039
Thiolase-like		53304
191IPR020568
Ribosomal protein S5 domain 2-type fold		5389
192IPR011993
Pleckstrin homology-like domain		53152
193IPR001117
Multicopper oxidase, type 1		5178
194IPR000528
Plant lipid transfer protein/Par allergen		51322
195IPR027640
Kinesin-like protein		51166
196IPR017970
Homeobox, conserved site		5166
197IPR017877
Myb-like domain		5171
198IPR015916
Galactose oxidase, beta-propeller		5060
199IPR026960
Reverse transcriptase zinc-binding domain		5051
200IPR004864
Late embryogenesis abundant protein, LEA-14		5056
201IPR011006
CheY-like superfamily		5073
202IPR029045
ClpP/crotonase-like domain		50214
203IPR025846
PMR5 N-terminal domain		5068
204IPR013242
Retroviral aspartyl protease		5050
205IPR011701
Major facilitator superfamily		4971
206IPR001563
Peptidase S10, serine carboxypeptidase		48405
207IPR016166
FAD-binding, type 2		48107
208IPR031107
Small heat shock protein HSP20		4853
209IPR000048
IQ motif, EF-hand binding site		48394
210IPR001789
Signal transduction response regulator, receiver domain		48196
211IPR006904
Protein of unknown function DUF716, TMEM45		4769
212IPR002156
Ribonuclease H domain		4753
213IPR029055
Nucleophile aminohydrolases, N-terminal		47124
214IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		4779
215IPR000425
Major intrinsic protein		47474
216IPR004088
K Homology domain, type 1		47618
217IPR011706
Multicopper oxidase, type 2		4772
218IPR006671
Cyclin, N-terminal		47109
219IPR013094
Alpha/beta hydrolase fold-3		4754
220IPR011707
Multicopper oxidase, type 3		4763
221IPR000873
AMP-dependent synthetase/ligase		4678
222IPR019557
Aminotransferase-like, plant mobile domain		4655
223IPR023271
Aquaporin-like		46133
224IPR008979
Galactose-binding domain-like		46215
225IPR023828
Peptidase S8, subtilisin, Ser-active site		4652
226IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4654
227IPR019787
Zinc finger, PHD-finger		45120
228IPR020904
Short-chain dehydrogenase/reductase, conserved site		4558
229IPR014756
Immunoglobulin E-set		4560
230IPR002913
Lipid-binding START		45175
231IPR025287
Wall-associated receptor kinase galacturonan-binding domain		4455
232IPR001929
Germin		44148
233IPR033131
Pectinesterase, Asp active site		4451
234IPR011527
ABC transporter, transmembrane domain, type 1		44323
235IPR004263
Exostosin-like		4366
236IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		4370
237IPR004839
Aminotransferase, class I/classII		4359
238IPR004883
Lateral organ boundaries, LOB		4392
239IPR006566
FBD domain		4384
240IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		4359
241IPR011016
Zinc finger, RING-CH-type		42166
242IPR001969
Peptidase aspartic, active site		4287
243IPR023313
Ubiquitin-conjugating enzyme, active site		4255
244IPR006094
FAD linked oxidase, N-terminal		4248
245IPR016159
Cullin repeat-like-containing domain		4268
246IPR030184
WAT1-related protein		4266
247IPR004158
Protein of unknown function DUF247, plant		4251
248IPR001752
Kinesin, motor domain		42441
249IPR006016
UspA		4155
250IPR006626
Parallel beta-helix repeat		41271
251IPR013149
Alcohol dehydrogenase, C-terminal		4158
252IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		4165
253IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4160
254IPR004046
Glutathione S-transferase, C-terminal		4158
255IPR015915
Kelch-type beta propeller		4164
256IPR008974
TRAF-like		41132
257IPR016461
O-methyltransferase, caffeic acid-type		4079
258IPR014014
RNA helicase, DEAD-box type, Q motif		4057
259IPR026961
PGG domain		4050
260IPR013154
Alcohol dehydrogenase GroES-like		4056
261IPR022796
Chlorophyll A-B binding protein		4052
262IPR001757
ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter		40184
263IPR002495
Glycosyl transferase, family 8		4057
264IPR001214
SET domain		40151
265IPR023329
Chlorophyll a/b binding protein domain		4053
266IPR001509
NAD-dependent epimerase/dehydratase		3951
267IPR012946
X8 domain		39118
268IPR025886
Phloem protein 2-like		3962
269IPR001077
O-methyltransferase, family 2		3954
270IPR023299
ATPase, P-type, cytoplasmic domain N		39110
271IPR000477
Reverse transcriptase		3968
272IPR003594
ATPase-like, ATP-binding domain		38210
273IPR007112
Expansin/pollen allergen, DPBB domain		3893
274IPR008928
Six-hairpin glycosidase-like		3877
275IPR019378
GDP-fucose protein O-fucosyltransferase		3876
276IPR000620
Drug/metabolite transporter		3886
277IPR011905
Glutaredoxin-like, plant II		3840
278IPR016073
SKP1 component, POZ		3739
279IPR009060
UBA-like		3758
280IPR001344
Chlorophyll A-B binding protein, plant		3751
281IPR004367
Cyclin, C-terminal		3784
282IPR020845
AMP-binding, conserved site		3752
283IPR001232
SKP1 component		3740
284IPR008889
VQ		3741
285IPR015797
NUDIX hydrolase domain-like		37125
286IPR033389
AUX/IAA domain		3656
287IPR011065
Kunitz inhibitor ST1-like		3636
288IPR001251
CRAL-TRIO domain		36324
289IPR007118
Expansin/Lol pI		36230
290IPR016072
SKP1 component, dimerisation		3675
291IPR011012
Longin-like domain		3651
292IPR008480
Protein of unknown function DUF761, plant		3639
293IPR022357
Major intrinsic protein, conserved site		3641
294IPR007117
Pollen allergen/expansin, C-terminal		36190
295IPR024788
Malectin-like carbohydrate-binding domain		3648
296IPR002160
Proteinase inhibitor I3, Kunitz legume		36155
297IPR011042
Six-bladed beta-propeller, TolB-like		3654
298IPR000757
Glycoside hydrolase, family 16		3699
299IPR000727
Target SNARE coiled-coil domain		35117
300IPR032710
NTF2-like domain		3597
301IPR004853
Domain of unknown function DUF250		3560
302IPR000330
SNF2-related		3542
303IPR008250
ATPase, P-type, ATPase-associated domain		35105
304IPR000668
Peptidase C1A, papain C-terminal		35188
305IPR004087
K Homology domain		35151
306IPR000644
Cystathionine beta-synthase, core		35286
307IPR003851
Zinc finger, Dof-type		35174
308IPR023210
NADP-dependent oxidoreductase domain		35161
309IPR001395
Aldo/keto reductase		3568
310IPR010920
Like-Sm (LSM) domain		3445
311IPR013128
Peptidase C1A, papain		3444
312IPR000315
Zinc finger, B-box		34196
313IPR006652
Kelch repeat type 1		34137
314IPR003690
Mitochodrial transcription termination factor-related		34322
315IPR002067
Mitochondrial carrier protein		34198
316IPR002487
Transcription factor, K-box		34121
317IPR005175
Domain of unknown function DUF296		3487
318IPR024593
Domain of unknown function DUF3444		3342
319IPR001938
Thaumatin, pathogenesis-related		33430
320IPR027356
NPH3 domain		33111
321IPR003958
Transcription factor CBF/NF-Y/archaeal histone		3338
322IPR008266
Tyrosine-protein kinase, active site		3346
323IPR005746
Thioredoxin		3358
324IPR023827
Peptidase S8, subtilisin, Asp-active site		3337
325IPR025660
Cysteine peptidase, histidine active site		3338
326IPR010402
CCT domain		32108
327IPR025110
Domain of unknown function DUF4009		3244
328IPR003406
Glycosyl transferase, family 14		3254
329IPR000863
Sulfotransferase domain		3233
330IPR018303
ATPase, P-type phosphorylation site		3244
331IPR033443
Pentacotripeptide-repeat region of PROPR		3247
332IPR031127
E3 ubiquitin ligase RBR family		3250
333IPR002912
ACT domain		32110
334IPR025322
Protein of unknown function DUF4228		3134
335IPR018490
Cyclic nucleotide-binding-like		3149
336IPR002403
Cytochrome P450, E-class, group IV		31147
337IPR007493
Protein of unknown function DUF538		31108
338IPR032872
Wall-associated receptor kinase, C-terminal		3140
339IPR013088
Zinc finger, NHR/GATA-type		3148
340IPR008991
Translation protein SH3-like		3136
341IPR013216
Methyltransferase type 11		3141
342IPR027725
Heat shock transcription factor family		3149
343IPR005333
Transcription factor, TCP		3139
344IPR017887
Transcription factor TCP subgroup		3139
345IPR013783
Immunoglobulin-like fold		3138
346IPR017392
Pathogenesis-related genes transcriptional activator PTI6		3136
347IPR004265
Plant disease resistance response protein		3138
348IPR022742
Alpha/beta hydrolase, N-terminal		3146
349IPR004146
DC1		3189
350IPR000169
Cysteine peptidase, cysteine active site		3136
351IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3150
352IPR000595
Cyclic nucleotide-binding domain		31134
353IPR020843
Polyketide synthase, enoylreductase		3136
354IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3146
355IPR000679
Zinc finger, GATA-type		31176
356IPR025659
Tubby C-terminal-like domain		3056
357IPR001296
Glycosyl transferase, family 1		3042
358IPR002129
Pyridoxal phosphate-dependent decarboxylase		3041
359IPR016167
FAD-binding, type 2, subdomain 1		3032
360IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3066
361IPR004314
Domain of unknown function DUF239		3041
362IPR023298
ATPase, P-type, transmembrane domain		3074
363IPR000232
Heat shock factor (HSF)-type, DNA-binding		30201
364IPR012341
Six-hairpin glycosidase		3052
365IPR008942
ENTH/VHS		2966
366IPR004000
Actin family		29245
367IPR000782
FAS1 domain		29201
368IPR004316
SWEET sugar transporter		2960
369IPR029000
Cyclophilin-like domain		2986
370IPR018957
Zinc finger, C3HC4 RING-type		2938
371IPR029021
Protein-tyrosine phosphatase-like		2996
372IPR014025
Glutaredoxin subgroup		2987
373IPR029061
Thiamin diphosphate-binding fold		29124
374IPR012675
Beta-grasp domain		2934
375IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		2938
376IPR016897
E3 ubiquitin ligase, SCF complex, Skp subunit		2929
377IPR004813
Oligopeptide transporter OPT superfamily		2981
378IPR000086
NUDIX hydrolase domain		29100
379IPR010264
Plant self-incompatibility S1		2931
380IPR018202
Peptidase S10, serine carboxypeptidase, active site		2944
381IPR004041
NAF domain		2836
382IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		28194
383IPR015410
Domain of unknown function DUF1985		2829
384IPR019821
Kinesin, motor region, conserved site		2837
385IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2866
386IPR011074
CRAL/TRIO, N-terminal domain		28118
387IPR033275
E3 ubiquitin-protein ligase MARCH-like		2864
388IPR002902
Gnk2-homologous domain		28148
389IPR000742
Epidermal growth factor-like domain		2888
390IPR014722
Translation protein SH3-like, subgroup		2830
391IPR001220
Legume lectin domain		2831
392IPR006458
Ovate protein family, C-terminal		2882
393IPR012967
Plant methyltransferase dimerisation		2834
394IPR015947
PUA-like domain		2844
395IPR005299
SAM dependent carboxyl methyltransferase		2734
396IPR021820
S-locus receptor kinase, C-terminal		2738
397IPR002423
Chaperonin Cpn60/TCP-1		2738
398IPR001353
Proteasome, subunit alpha/beta		2734
399IPR031112
AP2-like ethylene-responsive transcription factor		2757
400IPR000047
Helix-turn-helix motif		2772
401IPR027409
GroEL-like apical domain		2770
402IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2743
403IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2750
404IPR029033
Histidine phosphatase superfamily		27146
405IPR005804
Fatty acid desaturase, type 1		2730
406IPR003106
Leucine zipper, homeobox-associated		2648
407IPR012951
Berberine/berberine-like		2628
408IPR000717
Proteasome component (PCI) domain		2666
409IPR000795
Protein synthesis factor, GTP-binding		26164
410IPR016455
Xyloglucan endotransglucosylase/hydrolase		2630
411IPR004140
Exo70 exocyst complex subunit		2659
412IPR025422
DOG1 domain		2635
413IPR010989
t-SNARE		2644
414IPR006694
Fatty acid hydroxylase		2635
415IPR005150
Cellulose synthase		2665
416IPR019780
Germin, manganese binding site		2633
417IPR020635
Tyrosine-protein kinase, catalytic domain		2632
418IPR013126
Heat shock protein 70 family		26261
419IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		2674
420IPR029006
ADF-H/Gelsolin-like domain		2644
421IPR025661
Cysteine peptidase, asparagine active site		2627
422IPR010658
Nodulin-like		2632
423IPR002937
Amine oxidase		2647
424IPR006073
GTP binding domain		2686
425IPR019956
Ubiquitin subgroup		2595
426IPR006153
Cation/H+ exchanger		2536
427IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2534
428IPR025753
AAA-type ATPase, N-terminal domain		2526
429IPR024709
O-fucosyltransferase, plant		2539
430IPR018451
NAF/FISL domain		2533
431IPR001163
Ribonucleoprotein LSM domain		2554
432IPR018392
Peptidoglycan-binding lysin domain		25115
433IPR001881
EGF-like calcium-binding		2562
434IPR002022
Pectate lyase/Amb allergen		2562
435IPR002355
Multicopper oxidase, copper-binding site		2537
436IPR003008
Tubulin/FtsZ, GTPase domain		25152
437IPR011013
Glycoside hydrolase-type carbohydrate-binding		2546
438IPR029069
HotDog domain		2583
439IPR017937
Thioredoxin, conserved site		2535
440IPR003604
Zinc finger, U1-type		2556
441IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		2534
442IPR003311
AUX/IAA protein		2537
443IPR018097
EGF-like calcium-binding, conserved site		2527
444IPR018082
AmbAllergen		25218
445IPR030182
Purine permease, plant		2529
446IPR017884
SANT domain		2431
447IPR000467
G-patch domain		2480
448IPR013601
FAE1/Type III polyketide synthase-like protein		2433
449IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		24120
450IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2457
451IPR001024
Lipoxygenase, LH2		24109
452IPR033138
Multicopper oxidases, conserved site		2435
453IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		2488
454IPR008280
Tubulin/FtsZ, C-terminal		2432
455IPR032454
Histone H2A, C-terminal domain		2424
456IPR002119
Histone H2A		24143
457IPR011332
Ribosomal protein, zinc-binding domain		2430
458IPR014002
Tudor-like, plant		24108
459IPR005821
Ion transport domain		2433
460IPR002035
von Willebrand factor, type A		24128
461IPR029062
Class I glutamine amidotransferase-like		2499
462IPR004993
GH3 auxin-responsive promoter		2476
463IPR014720
Double-stranded RNA-binding-like		24123
464IPR009091
Regulator of chromosome condensation/beta-lactamase-inhibitor protein II		24108
465IPR000010
Proteinase inhibitor I25, cystatin		2486
466IPR004240
Nonaspanin (TM9SF)		2382
467IPR006689
Small GTPase superfamily, ARF/SAR type		23138
468IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2383
469IPR002867
Zinc finger, C6HC-type		23107
470IPR003954
RNA recognition motif domain, eukaryote		2342
471IPR009071
High mobility group, superfamily		23178
472IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		2327
473IPR002659
Glycosyl transferase, family 31		2392
474IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		2332
475IPR033124
Serine carboxypeptidases, histidine active site		2338
476IPR027413
GroEL-like equatorial domain		2350
477IPR022812
Dynamin superfamily		23127
478IPR015813
Pyruvate/Phosphoenolpyruvate kinase		2385
479IPR002963
Expansin		23222
480IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2331
481IPR016161
Aldehyde/histidinol dehydrogenase		2338
482IPR015425
Actin-binding FH2		2384
483IPR004838
Aminotransferases, class-I, pyridoxal-phosphate-binding site		2324
484IPR001701
Glycoside hydrolase, family 9		2339
485IPR025486
Domain of unknown function DUF4378		2335
486IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		23263
487IPR001041
2Fe-2S ferredoxin-type domain		2364
488IPR025610
Transcription factor MYC/MYB N-terminal		2341
489IPR017949
Thaumatin, conserved site		2225
490IPR029060
PIN domain-like		2251
491IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		22132
492IPR008422
Homeobox KN domain		2234
493IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2265
494IPR018170
Aldo/keto reductase, conserved site		2254
495IPR029056
Ribokinase-like		2292
496IPR001199
Cytochrome b5		22178
497IPR000569
HECT domain		2285
498IPR006459
Uncharacterised protein family UPF0497, trans-membrane plant subgroup		2225
499IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2229
500IPR027923
Hydrophobic seed protein		2222
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Theobroma_cacao.html b/gramene/htdocs/ssi/species.weix/stats_Theobroma_cacao.html new file mode 100644 index 00000000..df64fc89 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Theobroma_cacao.html @@ -0,0 +1,892 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Theobroma_cacao_20110822, May 2014
Database version:86.1
Base Pairs:330,821,260
Golden Path Length:345,993,675
Genebuild by: EnsemblPlants
Genebuild method: Generated from ENA annotation
Genebuild started: Jun 2013
Genebuild released: Jun 2013
Genebuild last updated/patched: May 2014
Genebuild version: 2014-05-EnsemblPlants
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		29,188
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,186
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
10 sequences
+
+ +
+ + + +
SequenceLength (bp)
138988864
242436413
334397752
433492547
540442896
627290986
724379470
821543242
942035188
1025448839
+
+
supercontig
+
814 sequences
+
+ +
+ + + +
SequenceLength (bp)
KE1328793810378
KE132880539985
KE1328819113421
KE1328828369677
KE1328831367713
KE1328847436102
KE1328851833507
KE132886471973
KE1328871093710
KE132888713974
KE1328891434333
KE1328902472171
KE13289117340
KE132892184580
KE1328933482064
KE1328949595
KE1328952928279
KE1328964527862
KE1328979988651
KE1328983000966
KE1328996664682
KE1329001680558
KE1329012783764
KE1329026464358
KE132903805634
KE1329047866812
KE1329053114749
KE1329061958886
KE1329073038825
KE1329081404811
KE1329093633588
KE1329105794409
KE132911392544
KE1329124163526
KE1329132939602
KE13291410380066
KE1329151693468
KE1329162473143
KE1329178976342
KE13291817282
KE1329194727229
KE1329205165017
KE1329214588264
KE1329223581162
KE132923777823
KE1329246612708
KE1329253276251
KE13292610022412
KE1329273030375
KE1329282813591
KE1329292812053
KE1329302838257
KE1329312204196
KE1329321664003
KE1329337571419
KE1329346338705
KE1329355897174
KE1329361880634
KE132937303335
KE1329381361520
KE132939912091
KE1329401106772
KE1329411067128
KE1329424950232
KE132943460293
KE1329443328211
KE132945835194
KE1329461015987
KE1329473103962
KE1329481300747
KE1329494345749
KE1329501843104
KE1329514426218
KE1329521277569
KE1329534486862
KE1329543786505
KE1329553565994
KE1329562763331
KE132957397084
KE132958769679
KE1329591041492
KE1329602921908
KE1329611357253
KE13296244777
KE1329633136747
KE1329641062788
KE1329653379153
KE1329661839807
KE1329671372880
KE132968989563
KE132969322304
KE1329706320791
KE132971232175
KE1329723028908
KE132973728356
KE1329741398756
KE132975198252
KE1329761264175
KE1329776698745
KE1329781078814
KE1329793417544
KE1329806700353
KE1329812083360
KE1329821486694
KE1329832427738
KE1329841855733
KE132985277240
KE132986343371
KE1329872706696
KE1329881907951
KE1329891977024
KE1329901360196
KE1329912212483
scaffold_111723764
scaffold_12944446
scaffold_13760943
scaffold_15426896
scaffold_16244831
scaffold_17217361
scaffold_18203745
scaffold_19198416
scaffold_20207352
scaffold_21186582
scaffold_22174665
scaffold_23195249
scaffold_24175184
scaffold_25160365
scaffold_26125162
scaffold_28156112
scaffold_29160914
scaffold_30114666
scaffold_3189769
scaffold_3286689
scaffold_33104694
scaffold_34149823
scaffold_3587099
scaffold_3670775
scaffold_3768023
scaffold_3882138
scaffold_3965447
scaffold_4088323
scaffold_4191650
scaffold_42106909
scaffold_4362851
scaffold_44108710
scaffold_45102092
scaffold_4699878
scaffold_47114767
scaffold_4888910
scaffold_4974925
scaffold_5068208
scaffold_5157704
scaffold_5255636
scaffold_5374452
scaffold_5463953
scaffold_5563971
scaffold_5658393
scaffold_5766202
scaffold_5857527
scaffold_5949466
scaffold_6067577
scaffold_61102493
scaffold_6268957
scaffold_6359779
scaffold_6467466
scaffold_6545821
scaffold_66111039
scaffold_6748522
scaffold_6837195
scaffold_6954082
scaffold_7068217
scaffold_7240699
scaffold_7337939
scaffold_7458298
scaffold_7587458
scaffold_7650089
scaffold_7747184
scaffold_7841609
scaffold_7944616
scaffold_8039408
scaffold_8169466
scaffold_8230270
scaffold_8357459
scaffold_8433211
scaffold_8531749
scaffold_8658382
scaffold_8765195
scaffold_8827103
scaffold_8926671
scaffold_9030129
scaffold_9136891
scaffold_9234448
scaffold_9324153
scaffold_9426351
scaffold_9626889
scaffold_9725785
scaffold_9831435
scaffold_9933501
scaffold_10024831
scaffold_10125094
scaffold_10221391
scaffold_10345664
scaffold_10655277
scaffold_10720468
scaffold_10821691
scaffold_10954430
scaffold_11022090
scaffold_11126169
scaffold_11217532
scaffold_11342716
scaffold_11435239
scaffold_11517120
scaffold_11618635
scaffold_11716592
scaffold_11822983
scaffold_11925815
scaffold_12017948
scaffold_12330096
scaffold_12442237
scaffold_12520772
scaffold_12615491
scaffold_12727148
scaffold_12922148
scaffold_13018796
scaffold_13226075
scaffold_13314057
scaffold_13617558
scaffold_13722902
scaffold_13813665
scaffold_13919975
scaffold_14019666
scaffold_14233070
scaffold_14330622
scaffold_14524513
scaffold_14713021
scaffold_14813082
scaffold_14920622
scaffold_15013504
scaffold_15216805
scaffold_15414169
scaffold_15521775
scaffold_15621219
scaffold_15718963
scaffold_15815686
scaffold_15923777
scaffold_16011861
scaffold_16120399
scaffold_16335233
scaffold_16511531
scaffold_16912086
scaffold_17027215
scaffold_17111662
scaffold_17223639
scaffold_17310581
scaffold_17410577
scaffold_17611042
scaffold_17810266
scaffold_17917721
scaffold_18010855
scaffold_18218329
scaffold_18410884
scaffold_18510587
scaffold_1869936
scaffold_18710635
scaffold_18817651
scaffold_19010021
scaffold_19115577
scaffold_19419639
scaffold_1959566
scaffold_19611139
scaffold_19712536
scaffold_1989125
scaffold_1998962
scaffold_2009011
scaffold_20114324
scaffold_2029051
scaffold_20311111
scaffold_20512124
scaffold_2078411
scaffold_20820550
scaffold_20919225
scaffold_21019403
scaffold_2118293
scaffold_2128148
scaffold_2138998
scaffold_2148261
scaffold_2158150
scaffold_21612693
scaffold_2178098
scaffold_2189752
scaffold_2199202
scaffold_22022781
scaffold_2217789
scaffold_2257609
scaffold_22621290
scaffold_22718960
scaffold_22823631
scaffold_2297504
scaffold_2308485
scaffold_2317484
scaffold_2327466
scaffold_23311401
scaffold_2347429
scaffold_2357473
scaffold_2367462
scaffold_2377359
scaffold_23820901
scaffold_24010020
scaffold_24121271
scaffold_24221748
scaffold_2439417
scaffold_24410856
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		11681892
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		11214950
3IPR000719
Protein kinase domain		11153827
4IPR032675
Leucine-rich repeat domain, L domain-like		10114190
5IPR008271
Serine/threonine-protein kinase, active site		8191145
6IPR017441
Protein kinase, ATP binding site		692951
7IPR012337
Ribonuclease H-like domain		6451320
8IPR013320
Concanavalin A-like lectin/glucanase, subgroup		6321007
9IPR011990
Tetratricopeptide-like helical		6042891
10IPR013083
Zinc finger, RING/FYVE/PHD-type		5981015
11IPR001611
Leucine-rich repeat		5724537
12IPR002885
Pentatricopeptide repeat		51515132
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		430888
14IPR016040
NAD(P)-binding domain		3831376
15IPR001841
Zinc finger, RING-type		3741242
16IPR003591
Leucine-rich repeat, typical subtype		3692940
17IPR009057
Homeodomain-like		3631191
18IPR013210
Leucine-rich repeat-containing N-terminal, type 2		340388
19IPR029058
Alpha/Beta hydrolase fold		3271209
20IPR016024
Armadillo-type fold		3111558
21IPR001128
Cytochrome P450		3102192
22IPR001810
F-box domain		2991018
23IPR003593
AAA+ ATPase domain		288576
24IPR002182
NB-ARC		282325
25IPR015943
WD40/YVTN repeat-like-containing domain		271919
26IPR012677
Nucleotide-binding, alpha-beta plait		2701398
27IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		2661104
28IPR002401
Cytochrome P450, E-class, group I		2571935
29IPR017986
WD40-repeat-containing domain		2571307
30IPR011989
Armadillo-like helical		2511087
31IPR001005
SANT/Myb domain		249872
32IPR000504
RNA recognition motif domain		2381897
33IPR017972
Cytochrome P450, conserved site		237269
34IPR001680
WD40 repeat		2324947
35IPR017853
Glycoside hydrolase, superfamily		230442
36IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		230255
37IPR012336
Thioredoxin-like fold		217742
38IPR020846
Major facilitator superfamily domain		213675
39IPR020683
Ankyrin repeat-containing domain		2061298
40IPR017930
Myb domain		198393
41IPR001878
Zinc finger, CCHC-type		1871021
42IPR002110
Ankyrin repeat		1861591
43IPR013781
Glycoside hydrolase, catalytic domain		180329
44IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		174464
45IPR011992
EF-hand domain pair		170575
46IPR001584
Integrase, catalytic core		163290
47IPR000477
Reverse transcriptase domain		157223
48IPR011991
Winged helix-turn-helix DNA-binding domain		150414
49IPR019775
WD40 repeat, conserved site		147478
50IPR005135
Endonuclease/exonuclease/phosphatase		145427
51IPR002156
Ribonuclease H domain		142151
52IPR002048
EF-hand domain		1411192
53IPR023214
HAD-like domain		141739
54IPR005162
Retrotransposon gag domain		140141
55IPR005123
Oxoglutarate/iron-dependent dioxygenase		136318
56IPR016177
DNA-binding domain		135178
57IPR007087
Zinc finger, C2H2		135494
58IPR018247
EF-Hand 1, calcium-binding site		134377
59IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		134943
60IPR027443
Isopenicillin N synthase-like		133187
61IPR029044
Nucleotide-diphospho-sugar transferases		127495
62IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		126782
63IPR001471
AP2/ERF domain		124838
64IPR014001
Helicase, superfamily 1/2, ATP-binding domain		124549
65IPR003439
ABC transporter-like		123532
66IPR015300
DNA-binding pseudobarrel domain		123416
67IPR001650
Helicase, C-terminal		120799
68IPR021109
Aspartic peptidase domain		117375
69IPR026992
Non-haem dioxygenase N-terminal domain		116142
70IPR032867
DYW domain		116125
71IPR012340
Nucleic acid-binding, OB-fold		114319
72IPR001480
Bulb-type lectin domain		114780
73IPR001965
Zinc finger, PHD-type		114415
74IPR003959
ATPase, AAA-type, core		113221
75IPR013026
Tetratricopeptide repeat-containing domain		111292
76IPR003441
NAC domain		110386
77IPR008972
Cupredoxin		109524
78IPR019734
Tetratricopeptide repeat		1071660
79IPR011050
Pectin lyase fold/virulence factor		107139
80IPR001623
DnaJ domain		1071030
81IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		107227
82IPR012334
Pectin lyase fold		107144
83IPR003340
B3 DNA binding domain		104521
84IPR026961
PGG domain		104121
85IPR023213
Chloramphenicol acetyltransferase-like domain		104217
86IPR013830
SGNH hydrolase superfamily		103361
87IPR013785
Aldolase-type TIM barrel		101223
88IPR029071
Ubiquitin-related domain		98181
89IPR011011
Zinc finger, FYVE/PHD-type		98246
90IPR025558
Domain of unknown function DUF4283		98100
91IPR003480
Transferase		97110
92IPR026960
Reverse transcriptase zinc-binding domain		9697
93IPR014710
RmlC-like jelly roll fold		96164
94IPR005225
Small GTP-binding protein domain		95142
95IPR000858
S-locus glycoprotein		92116
96IPR000008
C2 domain		90996
97IPR020472
G-protein beta WD-40 repeat		90519
98IPR010255
Haem peroxidase		89112
99IPR001087
Lipase, GDSL		88106
100IPR002347
Glucose/ribitol dehydrogenase		881074
101IPR015424
Pyridoxal phosphate-dependent transferase		87146
102IPR003609
Apple-like		86293
103IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		86139
104IPR002016
Haem peroxidase, plant/fungal/bacterial		86659
105IPR003676
Auxin-induced protein, ARG7		8390
106IPR010987
Glutathione S-transferase, C-terminal-like		82310
107IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		82218
108IPR023393
START-like domain		80121
109IPR000073
Alpha/beta hydrolase fold-1		80290
110IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		80180
111IPR000823
Plant peroxidase		78699
112IPR017451
F-box associated interaction domain		7786
113IPR017871
ABC transporter, conserved site		77151
114IPR017907
Zinc finger, RING-type, conserved site		77134
115IPR000225
Armadillo		771059
116IPR004146
DC1		76376
117IPR006501
Pectinesterase inhibitor domain		74357
118IPR019786
Zinc finger, PHD-type, conserved site		73170
119IPR004045
Glutathione S-transferase, N-terminal		73201
120IPR011051
RmlC-like cupin domain		73103
121IPR001356
Homeobox domain		72306
122IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		71117
123IPR001932
Protein phosphatase 2C (PP2C)-like domain		71779
124IPR006447
Myb domain, plants		70105
125IPR000109
Proton-dependent oligopeptide transporter family		69195
126IPR002100
Transcription factor, MADS-box		69695
127IPR011333
BTB/POZ fold		69130
128IPR000270
Phox/Bem1p		69192
129IPR000571
Zinc finger, CCCH-type		69931
130IPR003960
ATPase, AAA-type, conserved site		68114
131IPR005828
General substrate transporter		68118
132IPR019793
Peroxidases heam-ligand binding site		6882
133IPR009072
Histone-fold		68179
134IPR015880
Zinc finger, C2H2-like		68244
135IPR024171
S-receptor-like serine/threonine-protein kinase		6770
136IPR001461
Aspartic peptidase		67293
137IPR019787
Zinc finger, PHD-finger		66226
138IPR033121
Peptidase family A1 domain		66115
139IPR000626
Ubiquitin domain		65324
140IPR025287
Wall-associated receptor kinase galacturonan-binding domain		6374
141IPR018108
Mitochondrial substrate/solute carrier		63524
142IPR023395
Mitochondrial carrier domain		63215
143IPR029052
Metallo-dependent phosphatase-like		63273
144IPR006121
Heavy metal-associated domain, HMA		62252
145IPR013766
Thioredoxin domain		62184
146IPR015500
Peptidase S8, subtilisin-related		62356
147IPR008949
Terpenoid synthase		61170
148IPR008978
HSP20-like chaperone		61159
149IPR002528
Multi antimicrobial extrusion protein		61219
150IPR015655
Protein phosphatase 2C		61195
151IPR004158
Protein of unknown function DUF247, plant		6174
152IPR024788
Malectin-like carbohydrate-binding domain		6178
153IPR000209
Peptidase S8/S53 domain		61484
154IPR019794
Peroxidase, active site		6067
155IPR032799
Xylanase inhibitor, C-terminal		5982
156IPR032861
Xylanase inhibitor, N-terminal		5985
157IPR003657
DNA-binding WRKY		59434
158IPR021820
S-locus receptor kinase, C-terminal		5863
159IPR010259
Proteinase inhibitor I9		57119
160IPR013242
Retroviral aspartyl protease		5757
161IPR003613
U box domain		57215
162IPR000620
Drug/metabolite transporter		57140
163IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5695
164IPR000210
BTB/POZ domain		56256
165IPR001806
Small GTPase superfamily		5688
166IPR003245
Plastocyanin-like		55173
167IPR020568
Ribosomal protein S5 domain 2-type fold		55132
168IPR030184
WAT1-related protein		5584
169IPR016197
Chromo domain-like		5588
170IPR004827
Basic-leucine zipper domain		55310
171IPR011993
Pleckstrin homology-like domain		55255
172IPR013525
ABC-2 type transporter		54107
173IPR009009
RlpA-like double-psi beta-barrel domain		54160
174IPR002902
Gnk2-homologous domain		54280
175IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		54118
176IPR023828
Peptidase S8, subtilisin, Ser-active site		5475
177IPR001752
Kinesin, motor domain		54897
178IPR011032
GroES (chaperonin 10)-like		53207
179IPR016166
FAD-binding, type 2		53124
180IPR008979
Galactose-binding domain-like		53234
181IPR027640
Kinesin-like protein		52334
182IPR016135
Ubiquitin-conjugating enzyme/RWD-like		52162
183IPR001563
Peptidase S10, serine carboxypeptidase		51421
184IPR013763
Cyclin-like		51418
185IPR025314
Domain of unknown function DUF4219		5151
186IPR005829
Sugar transporter, conserved site		51119
187IPR002085
Alcohol dehydrogenase superfamily, zinc-type		51122
188IPR003663
Sugar/inositol transporter		51392
189IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		5163
190IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		51130
191IPR016181
Acyl-CoA N-acyltransferase		50165
192IPR002068
Alpha crystallin/Hsp20 domain		50104
193IPR001969
Aspartic peptidase, active site		5097
194IPR004864
Late embryogenesis abundant protein, LEA-14		5059
195IPR018253
DnaJ domain, conserved site		5070
196IPR002219
Protein kinase C-like, phorbol ester/diacylglycerol binding		50318
197IPR023780
Chromo domain		4964
198IPR026057
PC-Esterase		4869
199IPR013057
Amino acid transporter, transmembrane		4879
200IPR025846
PMR5 N-terminal domain		4864
201IPR011706
Multicopper oxidase, type 2		4866
202IPR014756
Immunoglobulin E-set		4886
203IPR000048
IQ motif, EF-hand binding site		48577
204IPR004263
Exostosin-like		4764
205IPR018289
MULE transposase domain		4780
206IPR006045
Cupin 1		47111
207IPR011707
Multicopper oxidase, type 3		4762
208IPR001117
Multicopper oxidase, type 1		4666
209IPR011527
ABC transporter type 1, transmembrane domain		46400
210IPR005202
Transcription factor GRAS		46115
211IPR001757
Cation-transporting P-type ATPase		46279
212IPR006094
FAD linked oxidase, N-terminal		4650
213IPR007527
Zinc finger, SWIM-type		46146
214IPR015916
Galactose oxidase, beta-propeller		4565
215IPR008250
P-type ATPase, A domain		45182
216IPR023299
P-type ATPase, cytoplasmic domain N		45168
217IPR000070
Pectinesterase, catalytic		4559
218IPR000608
Ubiquitin-conjugating enzyme, E2		44135
219IPR014014
RNA helicase, DEAD-box type, Q motif		4494
220IPR018303
P-type ATPase, phosphorylation site		4480
221IPR000490
Glycoside hydrolase, family 17		44109
222IPR001214
SET domain		44204
223IPR002921
Lipase, class 3		4349
224IPR029962
Trichome birefringence-like family		4376
225IPR000873
AMP-dependent synthetase/ligase		4376
226IPR008502
Prolamin-like domain		4244
227IPR019821
Kinesin, motor region, conserved site		4187
228IPR013149
Alcohol dehydrogenase, C-terminal		4176
229IPR016039
Thiolase-like		41269
230IPR006564
Zinc finger, PMZ-type		4170
231IPR001509
NAD-dependent epimerase/dehydratase		4151
232IPR012946
X8 domain		41128
233IPR006553
Leucine-rich repeat, cysteine-containing subtype		41540
234IPR016167
FAD-binding, type 2, subdomain 1		4147
235IPR031107
Small heat shock protein HSP20		4146
236IPR001220
Legume lectin domain		4145
237IPR025724
GAG-pre-integrase domain		4141
238IPR029055
Nucleophile aminohydrolases, N-terminal		40112
239IPR005630
Terpene synthase, metal-binding domain		4050
240IPR013783
Immunoglobulin-like fold		4072
241IPR003594
Histidine kinase-like ATPase, ATP-binding domain		40264
242IPR008928
Six-hairpin glycosidase-like		4084
243IPR000743
Glycoside hydrolase, family 28		4082
244IPR004332
Transposase, MuDR, plant		3943
245IPR009000
Translation protein, beta-barrel domain		3984
246IPR011006
CheY-like superfamily		3976
247IPR001789
Signal transduction response regulator, receiver domain		39193
248IPR000182
GNAT domain		3886
249IPR009060
UBA-like		3868
250IPR013154
Alcohol dehydrogenase GroES-like		3869
251IPR031052
FHY3/FAR1 family		3893
252IPR007112
Expansin/pollen allergen, DPBB domain		3873
253IPR005150
Cellulose synthase		3891
254IPR003690
Mitochodrial transcription termination factor-related		38357
255IPR004046
Glutathione S-transferase, C-terminal		3846
256IPR000916
Bet v I domain		3868
257IPR002067
Mitochondrial carrier protein		38248
258IPR023210
NADP-dependent oxidoreductase domain		38178
259IPR001395
Aldo/keto reductase		3874
260IPR032710
NTF2-like domain		37110
261IPR006016
UspA		3756
262IPR004853
Triose-phosphate transporter domain		3755
263IPR011016
Zinc finger, RING-CH-type		37130
264IPR011012
Longin-like domain		3756
265IPR029045
ClpP/crotonase-like domain		37190
266IPR020845
AMP-binding, conserved site		3762
267IPR019378
GDP-fucose protein O-fucosyltransferase		3754
268IPR001906
Terpene synthase, N-terminal domain		3785
269IPR013094
Alpha/beta hydrolase fold-3		3738
270IPR004330
FAR1 DNA binding domain		3773
271IPR010920
Like-Sm (LSM) domain		3658
272IPR005299
SAM dependent carboxyl methyltransferase		3645
273IPR004265
Plant disease resistance response protein		3637
274IPR008266
Tyrosine-protein kinase, active site		3647
275IPR006671
Cyclin, N-terminal		36109
276IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3667
277IPR000757
Glycoside hydrolase, family 16		3678
278IPR001929
Germin		35105
279IPR006153
Cation/H+ exchanger		3543
280IPR011701
Major facilitator superfamily		3562
281IPR008906
HAT dimerisation domain, C-terminal		3544
282IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		3562
283IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		3569
284IPR004839
Aminotransferase, class I/classII		3553
285IPR004883
Lateral organ boundaries, LOB		3572
286IPR015915
Kelch-type beta propeller		3566
287IPR002109
Glutaredoxin		3579
288IPR033389
AUX/IAA domain		3464
289IPR006626
Parallel beta-helix repeat		34206
290IPR012951
Berberine/berberine-like		3434
291IPR033131
Pectinesterase, Asp active site		3443
292IPR006652
Kelch repeat type 1		34164
293IPR020904
Short-chain dehydrogenase/reductase, conserved site		3441
294IPR025875
Leucine rich repeat 4		3443
295IPR002035
von Willebrand factor, type A		34169
296IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		3444
297IPR000330
SNF2-related		3375
298IPR002355
Multicopper oxidase, copper-binding site		3338
299IPR017970
Homeobox, conserved site		3347
300IPR011043
Galactose oxidase/kelch, beta-propeller		3350
301IPR002487
Transcription factor, K-box		33112
302IPR008974
TRAF-like		33125
303IPR008942
ENTH/VHS		3281
304IPR025110
AMP-binding enzyme C-terminal domain		3240
305IPR029021
Protein-tyrosine phosphatase-like		32140
306IPR004088
K Homology domain, type 1		32799
307IPR002495
Glycosyl transferase, family 8		3247
308IPR016159
Cullin repeat-like-containing domain		3274
309IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3235
310IPR014720
Double-stranded RNA-binding domain		32201
311IPR023298
P-type ATPase, transmembrane domain		32109
312IPR011042
Six-bladed beta-propeller, TolB-like		3272
313IPR006073
GTP binding domain		32163
314IPR017877
Myb-like domain		3256
315IPR010402
CCT domain		31100
316IPR001251
CRAL-TRIO domain		31248
317IPR003137
Protease-associated domain, PA		3147
318IPR023271
Aquaporin-like		3172
319IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		3183
320IPR022742
Putative lysophospholipase		3148
321IPR011013
Galactose mutarotase-like domain		3157
322IPR000863
Sulfotransferase domain		3135
323IPR023313
Ubiquitin-conjugating enzyme, active site		3145
324IPR005174
Protein of unknown function DUF295		3134
325IPR000425
Major intrinsic protein		31296
326IPR001223
Glycoside hydrolase, family 18, catalytic domain		3137
327IPR002912
ACT domain		31123
328IPR015797
NUDIX hydrolase domain-like		3192
329IPR000727
Target SNARE coiled-coil domain		30104
330IPR000528
Plant lipid transfer protein/Par allergen		30147
331IPR025322
Protein of unknown function DUF4228, plant		3031
332IPR013216
Methyltransferase type 11		3040
333IPR006461
Uncharacterised protein family Cys-rich		3061
334IPR000644
CBS domain		30278
335IPR001360
Glycoside hydrolase, family 1		29279
336IPR004367
Cyclin, C-terminal domain		29104
337IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2963
338IPR000086
NUDIX hydrolase domain		2975
339IPR007117
Expansin, cellulose-binding-like domain		29123
340IPR020843
Polyketide synthase, enoylreductase		2946
341IPR018202
Peptidase S10, serine carboxypeptidase, active site		2944
342IPR015947
PUA-like domain		2969
343IPR006594
LisH dimerisation motif		28131
344IPR000467
G-patch domain		2894
345IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28314
346IPR029000
Cyclophilin-like domain		28120
347IPR007118
Expansin/Lol pI		28167
348IPR029061
Thiamin diphosphate-binding fold		28170
349IPR016455
Xyloglucan endotransglucosylase/hydrolase		2828
350IPR000742
Epidermal growth factor-like domain		2863
351IPR005746
Thioredoxin		2847
352IPR017884
SANT domain		2753
353IPR000782
FAS1 domain		27134
354IPR025659
Tubby C-terminal-like domain		2742
355IPR025753
AAA-type ATPase, N-terminal domain		2731
356IPR001296
Glycosyl transferase, family 1		2753
357IPR001938
Thaumatin		27364
358IPR025886
Phloem protein 2-like		2732
359IPR001320
Ionotropic glutamate receptor		2777
360IPR001849
Pleckstrin homology domain		27160
361IPR004087
K Homology domain		27196
362IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2781
363IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		27134
364IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2637
365IPR008991
Translation protein SH3-like domain		2634
366IPR000315
Zinc finger, B-box		26148
367IPR029472
Gag-polypeptide of LTR copia-type		2626
368IPR006694
Fatty acid hydroxylase		2640
369IPR003008
Tubulin/FtsZ, GTPase domain		26195
370IPR007125
Histone core		2627
371IPR008480
Protein of unknown function DUF761, plant		2627
372IPR000169
Cysteine peptidase, cysteine active site		2630
373IPR000595
Cyclic nucleotide-binding domain		26119
374IPR001638
Extracellular solute-binding protein, family 3		2639
375IPR001487
Bromodomain		26397
376IPR012341
Six-hairpin glycosidase		2642
377IPR033138
Multicopper oxidases, conserved site		2529
378IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2583
379IPR013581
Plant PDR ABC transporter associated		2534
380IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		2595
381IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2580
382IPR000795
Elongation factor, GTP-binding domain		25247
383IPR027356
NPH3 domain		2579
384IPR011074
CRAL/TRIO, N-terminal domain		25114
385IPR002123
Phospholipid/glycerol acyltransferase		2570
386IPR003406
Glycosyl transferase, family 14		2541
387IPR004014
Cation-transporting P-type ATPase, N-terminal		2574
388IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		25125
389IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		2555
390IPR029481
ABC-transporter extracellular N-terminal domain		2529
391IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		25121
392IPR000668
Peptidase C1A, papain C-terminal		25134
393IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		2555
394IPR008889
VQ		2525
395IPR018490
Cyclic nucleotide-binding-like		2448
396IPR013328
Dehydrogenase, multihelical		2456
397IPR016461
Caffeate O-methyltransferase (COMT) family		2447
398IPR001357
BRCT domain		24365
399IPR013088
Zinc finger, NHR/GATA-type		2433
400IPR009071
High mobility group box domain		24165
401IPR013128
Peptidase C1A		2428
402IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2451
403IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		2446
404IPR018392
LysM domain		24110
405IPR008280
Tubulin/FtsZ, C-terminal		2434
406IPR012675
Beta-grasp domain		2442
407IPR001077
O-methyltransferase, family 2		2431
408IPR004993
GH3 auxin-responsive promoter		2461
409IPR013780
Glycosyl hydrolase, family 13, all-beta		2441
410IPR003851
Zinc finger, Dof-type		24131
411IPR029006
ADF-H/Gelsolin-like domain		2475
412IPR025660
Cysteine peptidase, histidine active site		2427
413IPR000679
Zinc finger, GATA-type		24122
414IPR002913
START domain		24153
415IPR017927
Ferredoxin reductase-type FAD-binding domain		2339
416IPR017938
Riboflavin synthase-like beta-barrel		2344
417IPR000953
Chromo domain/shadow		2379
418IPR001024
PLAT/LH2 domain		23114
419IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		2385
420IPR024709
O-fucosyltransferase, plant		2333
421IPR003347
JmjC domain		23177
422IPR001279
Beta-lactamase-like		23173
423IPR002423
Chaperonin Cpn60/TCP-1		2353
424IPR003656
Zinc finger, BED-type predicted		2385
425IPR010989
t-SNARE		2343
426IPR000639
Epoxide hydrolase-like		23132
427IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2336
428IPR021720
Malectin		2335
429IPR008263
Glycoside hydrolase, family 16, active site		2324
430IPR022357
Major intrinsic protein, conserved site		2328
431IPR029069
HotDog domain		2397
432IPR029062
Class I glutamine amidotransferase-like		2390
433IPR001944
Glycoside hydrolase, family 35		23331
434IPR019780
Germin, manganese binding site		2326
435IPR006566
FBD domain		2347
436IPR016161
Aldehyde/histidinol dehydrogenase		2346
437IPR025661
Cysteine peptidase, asparagine active site		2325
438IPR006527
F-box associated domain, type 1		2328
439IPR006195
Aminoacyl-tRNA synthetase, class II		2241
440IPR025525
Domain of unknown function DUF4413		2227
441IPR018957
Zinc finger, C3HC4 RING-type		2233
442IPR004320
Protein of unknown function DUF241, plant		2222
443IPR002083
MATH/TRAF domain		22115
444IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2243
445IPR005821
Ion transport domain		2236
446IPR004776
Auxin efflux carrier		2244
447IPR014722
Ribosomal protein L2 domain 2		2226
448IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2262
449IPR017761
Laccase		2227
450IPR016162
Aldehyde dehydrogenase, N-terminal		2249
451IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		21111
452IPR004316
SWEET sugar transporter		2159
453IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		21114
454IPR007493
Protein of unknown function DUF538		2178
455IPR003954
RNA recognition motif domain, eukaryote		2171
456IPR005333
Transcription factor, TCP		2125
457IPR017887
Transcription factor TCP subgroup		2125
458IPR031112
AP2-like ethylene-responsive transcription factor		2128
459IPR000408
Regulator of chromosome condensation, RCC1		21898
460IPR026892
Glycoside hydrolase family 3		2143
461IPR020103
Pseudouridine synthase, catalytic domain		2171
462IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2145
463IPR027409
GroEL-like apical domain		21100
464IPR020946
Flavin monooxygenase-like		2127
465IPR017937
Thioredoxin, conserved site		2141
466IPR028082
Periplasmic binding protein-like I		2172
467IPR001828
Extracellular ligand-binding receptor		2136
468IPR003311
AUX/IAA protein		2157
469IPR012967
Plant methyltransferase dimerisation		2125
470IPR029033
Histidine phosphatase superfamily		2186
471IPR005175
Domain of unknown function DUF296		2152
472IPR001764
Glycoside hydrolase, family 3, N-terminal		21162
473IPR015590
Aldehyde dehydrogenase domain		2142
474IPR016163
Aldehyde dehydrogenase, C-terminal		2141
475IPR019956
Ubiquitin		2081
476IPR002772
Glycoside hydrolase family 3 C-terminal domain		2099
477IPR008971
HSP40/DnaJ peptide-binding		2065
478IPR002403
Cytochrome P450, E-class, group IV		20124
479IPR000217
Tubulin		20238
480IPR001440
Tetratricopeptide TPR1		2059
481IPR032872
Wall-associated receptor kinase, C-terminal		2026
482IPR027806
Harbinger transposase-derived nuclease domain		2023
483IPR020471
Aldo/keto reductase subgroup		20114
484IPR000907
Lipoxygenase		2051
485IPR001478
PDZ domain		20156
486IPR001353
Proteasome, subunit alpha/beta		2027
487IPR029056
Ribokinase-like		2072
488IPR013819
Lipoxygenase, C-terminal		20169
489IPR031330
Glycoside hydrolase 35, catalytic domain		2034
490IPR002963
Expansin		20174
491IPR021099
Plant organelle RNA recognition domain		2022
492IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2034
493IPR023123
Tubulin, C-terminal		2024
494IPR002641
Patatin/Phospholipase A2-related		2026
495IPR024752
Myb/SANT-like domain		2061
496IPR002937
Amine oxidase		2034
497IPR023329
Chlorophyll a/b binding protein domain		2026
498IPR010525
Auxin response factor		2046
499IPR024949
Bet v I type allergen		20150
500IPR004294
Carotenoid oxygenase		1960
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense.html b/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense.html new file mode 100644 index 00000000..7f73e4f9 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense.html @@ -0,0 +1,61 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Trpr, Apr 2016
Database version:86.1
Base Pairs:296,217,290
Golden Path Length:304,842,038
Genebuild by: TGAC
Genebuild method: Imported from TGAC
Genebuild started: Apr 2016
Genebuild version: 2016-04-TGAC
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,948
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:41,302
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
7 sequences
+
+ +
+ + + +
SequenceLength (bp)
LG128142018
LG232560536
LG331061273
LG428907061
LG515272566
LG622682783
LG730551617
+
+
contig9457 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense_IPtop500.html new file mode 100644 index 00000000..461ceaea --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Trifolium_pratense_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		17874764
2IPR011009
Protein kinase-like domain		15281764
3IPR032675
Leucine-rich repeat domain, L domain-like		14934489
4IPR000719
Protein kinase domain		13163104
5IPR008271
Serine/threonine-protein kinase, active site		838859
6IPR017441
Protein kinase, ATP binding site		739760
7IPR013320
Concanavalin A-like lectin/glucanase domain		728984
8IPR013083
Zinc finger, RING/FYVE/PHD-type		704786
9IPR011990
Tetratricopeptide-like helical domain		6242094
10IPR002885
Pentatricopeptide repeat		61212491
11IPR001611
Leucine-rich repeat		5933752
12IPR016040
NAD(P)-binding domain		5261237
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		525729
14IPR009057
Homeodomain-like		5001179
15IPR001841
Zinc finger, RING-type		4631085
16IPR001128
Cytochrome P450		4582450
17IPR029058
Alpha/Beta hydrolase fold		4411083
18IPR016024
Armadillo-type fold		425908
19IPR001810
F-box domain		4151157
20IPR002182
NB-ARC		414446
21IPR012337
Ribonuclease H-like domain		373619
22IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		361890
23IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		354371
24IPR015943
WD40/YVTN repeat-like-containing domain		340537
25IPR017853
Glycoside hydrolase superfamily		339401
26IPR011989
Armadillo-like helical		335616
27IPR002401
Cytochrome P450, E-class, group I		3341906
28IPR003593
AAA+ ATPase domain		329426
29IPR017986
WD40-repeat-containing domain		326782
30IPR020846
Major facilitator superfamily domain		325660
31IPR001005
SANT/Myb domain		312801
32IPR012677
Nucleotide-binding alpha-beta plait domain		309952
33IPR003591
Leucine-rich repeat, typical subtype		3082136
34IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		299317
35IPR011991
Winged helix-turn-helix DNA-binding domain		296514
36IPR001680
WD40 repeat		2922815
37IPR017972
Cytochrome P450, conserved site		278282
38IPR013781
Glycoside hydrolase, catalytic domain		274324
39IPR000504
RNA recognition motif domain		2551185
40IPR017930
Myb domain		255385
41IPR012336
Thioredoxin-like fold		254584
42IPR012334
Pectin lyase fold		249284
43IPR011050
Pectin lyase fold/virulence factor		248276
44IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		234563
45IPR012340
Nucleic acid-binding, OB-fold		232325
46IPR015300
DNA-binding pseudobarrel domain		227589
47IPR027443
Isopenicillin N synthase-like		222262
48IPR011992
EF-hand domain pair		216537
49IPR023214
HAD-like domain		196543
50IPR007087
Zinc finger, C2H2		187585
51IPR002048
EF-hand domain		1861155
52IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		186980
53IPR014001
Helicase superfamily 1/2, ATP-binding domain		186348
54IPR021109
Aspartic peptidase domain		184428
55IPR016177
DNA-binding domain		181207
56IPR001650
Helicase, C-terminal		177530
57IPR003439
ABC transporter-like		175421
58IPR001471
AP2/ERF domain		1741069
59IPR031052
FHY3/FAR1 family		171189
60IPR019775
WD40 repeat, conserved site		170283
61IPR018247
EF-Hand 1, calcium-binding site		167371
62IPR023753
FAD/NAD(P)-binding domain		165601
63IPR013830
SGNH hydrolase-type esterase domain		165354
64IPR010255
Haem peroxidase		164179
65IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		162731
66IPR000477
Reverse transcriptase domain		159272
67IPR002016
Haem peroxidase, plant/fungal/bacterial		158776
68IPR005123
Oxoglutarate/iron-dependent dioxygenase		156276
69IPR020683
Ankyrin repeat-containing domain		154729
70IPR003959
ATPase, AAA-type, core		153185
71IPR014710
RmlC-like jelly roll fold		146178
72IPR026992
Non-haem dioxygenase N-terminal domain		145150
73IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		143174
74IPR000823
Plant peroxidase		141854
75IPR015500
Peptidase S8, subtilisin-related		138388
76IPR029044
Nucleotide-diphospho-sugar transferases		137322
77IPR002110
Ankyrin repeat		137868
78IPR013785
Aldolase-type TIM barrel		132161
79IPR002100
Transcription factor, MADS-box		130812
80IPR003340
B3 DNA binding domain		129480
81IPR000008
C2 domain		129839
82IPR000109
Proton-dependent oligopeptide transporter family		128280
83IPR023213
Chloramphenicol acetyltransferase-like domain		128226
84IPR008972
Cupredoxin		124409
85IPR029071
Ubiquitin-related domain		124167
86IPR011011
Zinc finger, FYVE/PHD-type		124151
87IPR006501
Pectinesterase inhibitor domain		124548
88IPR011545
DEAD/DEAH box helicase domain		121124
89IPR009072
Histone-fold		121244
90IPR003480
Transferase		121137
91IPR002347
Short-chain dehydrogenase/reductase SDR		120970
92IPR001878
Zinc finger, CCHC-type		120516
93IPR000209
Peptidase S8/S53 domain		119561
94IPR005135
Endonuclease/exonuclease/phosphatase		118292
95IPR005828
Major facilitator, sugar transporter-like		118138
96IPR001480
Bulb-type lectin domain		118632
97IPR015424
Pyridoxal phosphate-dependent transferase		117128
98IPR019734
Tetratricopeptide repeat		116927
99IPR013026
Tetratricopeptide repeat-containing domain		116158
100IPR005225
Small GTP-binding protein domain		115118
101IPR001932
PPM-type phosphatase domain		114612
102IPR018289
MULE transposase domain		111111
103IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		111266
104IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		110117
105IPR032867
DYW domain		110110
106IPR017871
ABC transporter, conserved site		109132
107IPR006553
Leucine-rich repeat, cysteine-containing subtype		108691
108IPR011051
RmlC-like cupin domain		108131
109IPR030184
WAT1-related protein		108125
110IPR001623
DnaJ domain		107790
111IPR004330
FAR1 DNA binding domain		105108
112IPR010285
DNA helicase Pif1-like		104117
113IPR000070
Pectinesterase, catalytic		103119
114IPR015655
Protein phosphatase 2C family		102171
115IPR001461
Aspartic peptidase A1 family		102248
116IPR003657
WRKY domain		101551
117IPR017907
Zinc finger, RING-type, conserved site		101104
118IPR005162
Retrotransposon gag domain		100100
119IPR001087
GDSL lipase/esterase		98103
120IPR003441
NAC domain		98300
121IPR011527
ABC transporter type 1, transmembrane domain		98417
122IPR007527
Zinc finger, SWIM-type		98174
123IPR000743
Glycoside hydrolase, family 28		97148
124IPR002085
Alcohol dehydrogenase superfamily, zinc-type		96115
125IPR015880
Zinc finger, C2H2-like		96252
126IPR033121
Peptidase family A1 domain		95108
127IPR025558
Domain of unknown function DUF4283		95100
128IPR001965
Zinc finger, PHD-type		94146
129IPR006121
Heavy metal-associated domain, HMA		93279
130IPR006447
Myb domain, plants		9399
131IPR013057
Amino acid transporter, transmembrane domain		93101
132IPR011333
SKP1/BTB/POZ domain		93100
133IPR006564
Zinc finger, PMZ-type		9191
134IPR020472
G-protein beta WD-40 repeat		90276
135IPR026960
Reverse transcriptase zinc-binding domain		8990
136IPR011032
GroES-like		88193
137IPR001563
Peptidase S10, serine carboxypeptidase		88404
138IPR023395
Mitochondrial carrier domain		88192
139IPR006566
FBD domain		88146
140IPR000626
Ubiquitin domain		87315
141IPR001360
Glycoside hydrolase family 1		87414
142IPR008906
HAT, C-terminal dimerisation domain		8790
143IPR027640
Kinesin-like protein		87219
144IPR018108
Mitochondrial substrate/solute carrier		87434
145IPR000225
Armadillo		87616
146IPR000858
S-locus glycoprotein domain		8592
147IPR001356
Homeobox domain		85251
148IPR001806
Small GTPase superfamily		8591
149IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		8494
150IPR032861
Xylanase inhibitor, N-terminal		8386
151IPR013763
Cyclin-like		82345
152IPR011993
PH domain-like		81168
153IPR007750
Protein of unknown function DUF674		80100
154IPR003960
ATPase, AAA-type, conserved site		8092
155IPR032799
Xylanase inhibitor, C-terminal		8083
156IPR000270
PB1 domain		80138
157IPR001752
Kinesin motor domain		80535
158IPR019787
Zinc finger, PHD-finger		79152
159IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		79128
160IPR000073
Alpha/beta hydrolase fold-1		79155
161IPR010987
Glutathione S-transferase, C-terminal-like		79225
162IPR000571
Zinc finger, CCCH-type		79636
163IPR017451
F-box associated interaction domain		7878
164IPR023393
START-like domain		7884
165IPR000620
EamA domain		78114
166IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		77114
167IPR013766
Thioredoxin domain		77143
168IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		7575
169IPR029962
Trichome birefringence-like family		7597
170IPR009009
RlpA-like protein, double-psi beta-barrel domain		75195
171IPR002902
Gnk2-homologous domain		75291
172IPR000048
IQ motif, EF-hand binding site		75436
173IPR006045
Cupin 1		74167
174IPR026057
PC-Esterase		7377
175IPR023828
Peptidase S8, subtilisin, Ser-active site		7373
176IPR003609
PAN/Apple domain		72212
177IPR019786
Zinc finger, PHD-type, conserved site		7188
178IPR019793
Peroxidases heam-ligand binding site		7172
179IPR001220
Legume lectin domain		7073
180IPR011006
CheY-like superfamily		6977
181IPR000668
Peptidase C1A, papain C-terminal		69212
182IPR004827
Basic-leucine zipper domain		69266
183IPR008974
TRAF-like		69141
184IPR016181
Acyl-CoA N-acyltransferase		68143
185IPR013128
Peptidase C1A		6874
186IPR003676
Small auxin-up RNA		6869
187IPR001789
Signal transduction response regulator, receiver domain		68198
188IPR016039
Thiolase-like		67264
189IPR000873
AMP-dependent synthetase/ligase		6783
190IPR008979
Galactose-binding domain-like		67185
191IPR020568
Ribosomal protein S5 domain 2-type fold		6784
192IPR002528
Multi antimicrobial extrusion protein		67140
193IPR019794
Peroxidase, active site		6768
194IPR029052
Metallo-dependent phosphatase-like		66158
195IPR003613
U box domain		66199
196IPR003663
Sugar/inositol transporter		66310
197IPR010264
Plant self-incompatibility S1		6666
198IPR008978
HSP20-like chaperone		65132
199IPR026961
PGG domain		6569
200IPR016461
O-methyltransferase COMT-type		6477
201IPR023271
Aquaporin-like		64135
202IPR000425
Major intrinsic protein		64405
203IPR009000
Translation protein, beta-barrel domain		6368
204IPR005829
Sugar transporter, conserved site		6396
205IPR008928
Six-hairpin glycosidase-like		6378
206IPR004045
Glutathione S-transferase, N-terminal		63126
207IPR016159
Cullin repeat-like-containing domain		6384
208IPR014756
Immunoglobulin E-set		6369
209IPR017877
Myb-like domain		6376
210IPR014014
RNA helicase, DEAD-box type, Q motif		6262
211IPR025846
PMR5 N-terminal domain		6262
212IPR016135
Ubiquitin-conjugating enzyme/RWD-like		61131
213IPR003245
Phytocyanin domain		61173
214IPR004883
Lateral organ boundaries, LOB		61119
215IPR013154
Alcohol dehydrogenase, N-terminal		6064
216IPR004158
Protein of unknown function DUF247, plant		6062
217IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5961
218IPR033131
Pectinesterase, Asp active site		5960
219IPR005202
Transcription factor GRAS		59124
220IPR029055
Nucleophile aminohydrolases, N-terminal		58110
221IPR004864
Late embryogenesis abundant protein, LEA-14		5860
222IPR000757
Glycoside hydrolase family 16		58115
223IPR001969
Aspartic peptidase, active site		5776
224IPR013525
ABC-2 type transporter		5670
225IPR001077
O-methyltransferase, family 2		5658
226IPR013126
Heat shock protein 70 family		56309
227IPR004314
Domain of unknown function DUF239		5660
228IPR008949
Isoprenoid synthase domain		55117
229IPR008250
P-type ATPase, A domain		55119
230IPR000210
BTB/POZ domain		55142
231IPR006626
Parallel beta-helix repeat		54267
232IPR029472
Gag-polypeptide of LTR copia-type		5454
233IPR003594
Histidine kinase-like ATPase, C-terminal domain		54199
234IPR005150
Cellulose synthase		5471
235IPR018253
DnaJ domain, conserved site		5456
236IPR006671
Cyclin, N-terminal		5481
237IPR000608
Ubiquitin-conjugating enzyme E2		53112
238IPR001214
SET domain		53143
239IPR006153
Cation/H+ exchanger		5254
240IPR002109
Glutaredoxin		52107
241IPR000742
EGF-like domain		5187
242IPR023299
P-type ATPase, cytoplasmic domain N		51109
243IPR004853
Sugar phosphate transporter domain		5051
244IPR023210
NADP-dependent oxidoreductase domain		50158
245IPR000182
GNAT domain		4987
246IPR027806
Harbinger transposase-derived nuclease domain		4950
247IPR012946
X8 domain		4998
248IPR025836
Zinc knuckle CX2CX4HX4C		4952
249IPR020904
Short-chain dehydrogenase/reductase, conserved site		4954
250IPR004813
Oligopeptide transporter, OPT superfamily		4996
251IPR016197
Chromo domain-like		4956
252IPR024788
Malectin-like carbohydrate-binding domain		4951
253IPR013149
Alcohol dehydrogenase, C-terminal		4848
254IPR007118
Expansin/Lol pI		48216
255IPR002068
Alpha crystallin/Hsp20 domain		4893
256IPR004263
Exostosin-like		4852
257IPR001757
P-type ATPase		48132
258IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		48109
259IPR000528
Plant lipid transfer protein/Par allergen		47210
260IPR001024
PLAT/LH2 domain		47167
261IPR000330
SNF2-related, N-terminal domain		4750
262IPR007112
Expansin/pollen allergen, DPBB domain		4786
263IPR004088
K Homology domain, type 1		47349
264IPR025724
GAG-pre-integrase domain		4747
265IPR013094
Alpha/beta hydrolase fold-3		4747
266IPR012967
Plant methyltransferase dimerisation		4748
267IPR001584
Integrase, catalytic core		4682
268IPR015916
Galactose oxidase, beta-propeller		4651
269IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		4647
270IPR000490
Glycoside hydrolase family 17		4673
271IPR011042
Six-bladed beta-propeller, TolB-like		4653
272IPR011707
Multicopper oxidase, type 3		4647
273IPR001395
Aldo/keto reductase/potassium channel subunit beta		4667
274IPR000782
FAS1 domain		45229
275IPR013783
Immunoglobulin-like fold		4554
276IPR004265
Plant disease resistance response protein		4546
277IPR004367
Cyclin, C-terminal domain		4580
278IPR020845
AMP-binding, conserved site		4548
279IPR031107
Small heat shock protein HSP20		4546
280IPR012341
Six-hairpin glycosidase		4551
281IPR006702
Domain of unknown function DUF588		4547
282IPR004316
SWEET sugar transporter		4469
283IPR006652
Kelch repeat type 1		44155
284IPR011013
Galactose mutarotase-like domain		4450
285IPR003690
Transcription termination factor, mitochondrial/chloroplastic		44297
286IPR007117
Expansin, cellulose-binding-like domain		44174
287IPR025398
Domain of unknown function DUF4371		4447
288IPR013955
Replication factor A, C-terminal		4447
289IPR018202
Serine carboxypeptidase, serine active site		4445
290IPR011701
Major facilitator superfamily		4345
291IPR022812
Dynamin superfamily		43165
292IPR004252
Probable transposase, Ptta/En/Spm, plant		4344
293IPR011012
Longin-like domain		4345
294IPR007125
Histone H2A/H2B/H3		4344
295IPR011706
Multicopper oxidase, type 2		4344
296IPR023298
P-type ATPase, transmembrane domain		4374
297IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		4348
298IPR001117
Multicopper oxidase, type 1		4242
299IPR017884
SANT domain		4250
300IPR018490
Cyclic nucleotide-binding-like		4244
301IPR019821
Kinesin motor domain, conserved site		4242
302IPR001251
CRAL-TRIO lipid binding domain		42201
303IPR010920
LSM domain		4243
304IPR003137
PA domain		4242
305IPR018061
Retropepsins		4242
306IPR019378
GDP-fucose protein O-fucosyltransferase		4248
307IPR002067
Mitochondrial carrier protein		42203
308IPR015915
Kelch-type beta propeller		4251
309IPR011692
Stress up-regulated Nod 19		4251
310IPR005175
PPC domain		4283
311IPR001929
Germin		41120
312IPR025525
hAT-like transposase, RNase-H fold		4144
313IPR000222
PPM-type phosphatase, divalent cation binding		4142
314IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		4142
315IPR018303
P-type ATPase, phosphorylation site		4143
316IPR002035
von Willebrand factor, type A		41121
317IPR014720
Double-stranded RNA-binding domain		41174
318IPR000595
Cyclic nucleotide-binding domain		4195
319IPR029047
Heat shock protein 70kD, peptide-binding domain		4192
320IPR033389
AUX/IAA domain		4045
321IPR008942
ENTH/VHS		4083
322IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		4041
323IPR029045
ClpP/crotonase-like domain		40115
324IPR001944
Glycoside hydrolase, family 35		40213
325IPR001701
Glycoside hydrolase family 9		4041
326IPR031127
E3 ubiquitin ligase RBR family		4047
327IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		40100
328IPR015947
PUA-like domain		4059
329IPR005299
SAM dependent carboxyl methyltransferase		3943
330IPR013201
Cathepsin propeptide inhibitor domain (I29)		3980
331IPR000795
Transcription factor, GTP-binding domain		39199
332IPR022742
Serine aminopeptidase, S33		3942
333IPR008266
Tyrosine-protein kinase, active site		3940
334IPR025521
Domain of unknown function DUF4409		3939
335IPR008480
Protein of unknown function DUF761, plant		3939
336IPR002912
ACT domain		3986
337IPR002487
Transcription factor, K-box		3975
338IPR032710
NTF2-like domain		3865
339IPR029021
Protein-tyrosine phosphatase-like		3891
340IPR005630
Terpene synthase, metal-binding domain		3840
341IPR001938
Thaumatin		38364
342IPR002083
MATH/TRAF domain		38124
343IPR017970
Homeobox, conserved site		3841
344IPR022357
Major intrinsic protein, conserved site		3838
345IPR002495
Glycosyl transferase, family 8		3840
346IPR028919
Viral movement protein		3838
347IPR000644
CBS domain		38188
348IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3838
349IPR004242
Transposon, En/Spm-like		3840
350IPR006594
LIS1 homology motif		3793
351IPR004873
BURP domain		37113
352IPR006016
UspA		3737
353IPR002867
IBR domain		37114
354IPR029000
Cyclophilin-like domain		3782
355IPR003656
Zinc finger, BED-type		3780
356IPR027356
NPH3 domain		3777
357IPR016166
FAD-binding, type 2		3771
358IPR003406
Glycosyl transferase, family 14		3741
359IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		3796
360IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3739
361IPR004046
Glutathione S-transferase, C-terminal		3739
362IPR028889
Ubiquitin specific protease domain		3738
363IPR024752
Myb/SANT-like domain		3744
364IPR002921
Fungal lipase-like domain		3636
365IPR002156
Ribonuclease H domain		3636
366IPR003871
Domain of unknown function DUF223		3638
367IPR009060
UBA-like		3640
368IPR008991
Translation protein SH3-like domain		3637
369IPR029061
Thiamin diphosphate-binding fold		36122
370IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		3637
371IPR000907
Lipoxygenase		3670
372IPR023780
Chromo domain		3638
373IPR004839
Aminotransferase, class I/classII		3637
374IPR033443
Pentacotripeptide-repeat region of PROPR		3641
375IPR016161
Aldehyde/histidinol dehydrogenase		3638
376IPR003851
Zinc finger, Dof-type		36139
377IPR025476
Helitron helicase-like domain		3641
378IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		35195
379IPR024171
S-receptor-like serine/threonine-protein kinase		3535
380IPR005746
Thioredoxin		3549
381IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		3551
382IPR011043
Galactose oxidase/kelch, beta-propeller		3539
383IPR020843
Polyketide synthase, enoylreductase domain		3535
384IPR025110
AMP-binding enzyme C-terminal domain		3435
385IPR025322
Protein of unknown function DUF4228, plant		3434
386IPR019956
Ubiquitin		3498
387IPR013101
Leucine-rich repeat 2		3437
388IPR004320
Protein of unknown function DUF241, plant		3434
389IPR031112
AP2-like ethylene-responsive transcription factor		3445
390IPR025875
Leucine rich repeat 4		3435
391IPR005821
Ion transport domain		3436
392IPR004087
K Homology domain		3482
393IPR008889
VQ		3434
394IPR000010
Cystatin domain		3459
395IPR006073
GTP binding domain		3496
396IPR015797
NUDIX hydrolase domain-like		3467
397IPR018200
Ubiquitin specific protease, conserved site		3351
398IPR011016
Zinc finger, RING-CH-type		3387
399IPR011074
CRAL/TRIO, N-terminal domain		3385
400IPR002963
Expansin		33251
401IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		3333
402IPR025660
Cysteine peptidase, histidine active site		3335
403IPR002913
START domain		3392
404IPR000727
Target SNARE coiled-coil homology domain		3285
405IPR013216
Methyltransferase type 11		3233
406IPR025452
Domain of unknown function DUF4218		3232
407IPR014722
Ribosomal protein L2 domain 2		3233
408IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		3266
409IPR016162
Aldehyde dehydrogenase N-terminal domain		3240
410IPR015590
Aldehyde dehydrogenase domain		3234
411IPR025659
Tubby C-terminal-like domain		3136
412IPR013088
Zinc finger, NHR/GATA-type		3133
413IPR001373
Cullin, N-terminal		3142
414IPR000408
Regulator of chromosome condensation, RCC1		31493
415IPR002293
Amino acid/polyamine transporter I		3191
416IPR004326
Mlo-related protein		3138
417IPR000916
Bet v I/Major latex protein		3148
418IPR017937
Thioredoxin, conserved site		3138
419IPR019780
Germin, manganese binding site		3131
420IPR025661
Cysteine peptidase, asparagine active site		3132
421IPR001487
Bromodomain		31250
422IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		3133
423IPR000679
Zinc finger, GATA-type		31125
424IPR018082
AmbAllergen		31187
425IPR003840
DNA helicase		3032
426IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		3081
427IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		3085
428IPR006043
Xanthine/uracil/vitamin C permease		3078
429IPR003347
JmjC domain		3087
430IPR000315
B-box-type zinc finger		30121
431IPR019557
Aminotransferase-like, plant mobile domain		3030
432IPR003822
Paired amphipathic helix		30180
433IPR029068
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase		3077
434IPR025886
Phloem protein 2-like		3030
435IPR013819
Lipoxygenase, C-terminal		30171
436IPR003653
Ulp1 protease family, C-terminal catalytic domain		3044
437IPR005174
Domain unknown function DUF295		3032
438IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		3035
439IPR001849
Pleckstrin homology domain		3078
440IPR001995
Peptidase A2A, retrovirus, catalytic		3030
441IPR006094
FAD linked oxidase, N-terminal		3031
442IPR012474
Frigida-like		3033
443IPR011065
Kunitz inhibitor ST1-like		2929
444IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2951
445IPR001163
LSM domain, eukaryotic/archaea-type		2954
446IPR001296
Glycosyl transferase, family 1		2930
447IPR000086
NUDIX hydrolase domain		2956
448IPR020966
Aluminum-activated malate transporter		2933
449IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		2930
450IPR002160
Proteinase inhibitor I3, Kunitz legume		2992
451IPR011713
Leucine-rich repeat 3		2929
452IPR029033
Histidine phosphatase superfamily		2989
453IPR006527
F-box associated domain, type 1		2929
454IPR010402
CCT domain		2862
455IPR004141
Strictosidine synthase		2829
456IPR013601
FAE1/Type III polyketide synthase-like protein		2828
457IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		2872
458IPR029030
Caspase-like domain		2842
459IPR002423
Chaperonin Cpn60/TCP-1 family		2830
460IPR001025
Bromo adjacent homology (BAH) domain		2886
461IPR016072
SKP1 component, dimerisation		2850
462IPR010525
Auxin response factor		2828
463IPR026055
Fatty acyl-CoA reductase		2845
464IPR004041
NAF domain		2728
465IPR003106
Leucine zipper, homeobox-associated		2742
466IPR025312
Domain of unknown function DUF4216		2727
467IPR018451
NAF/FISL domain		2728
468IPR008280
Tubulin/FtsZ, C-terminal		2727
469IPR002022
Pectate lyase/Amb allergen		2754
470IPR004140
Exocyst complex protein Exo70		2762
471IPR029056
Ribokinase-like		2766
472IPR010989
t-SNARE		2728
473IPR016021
MIF4G-like domain		2742
474IPR003008
Tubulin/FtsZ, GTPase domain		27124
475IPR031330
Glycoside hydrolase 35, catalytic domain		2731
476IPR001246
Lipoxygenase, plant		27184
477IPR001232
S-phase kinase-associated protein 1-like		2728
478IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		2733
479IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2740
480IPR003311
AUX/IAA protein		2735
481IPR003855
Potassium transporter		2748
482IPR016163
Aldehyde dehydrogenase, C-terminal		2728
483IPR029048
Heat shock protein 70kD, C-terminal domain		2757
484IPR002710
Dilute domain		2652
485IPR032872
Wall-associated receptor kinase, C-terminal		2626
486IPR000717
Proteasome component (PCI) domain		2648
487IPR004161
Translation elongation factor EFTu-like, domain 2		2628
488IPR012675
Beta-grasp domain		2626
489IPR018170
Aldo/keto reductase, conserved site		2656
490IPR033124
Serine carboxypeptidases, histidine active site		2626
491IPR021720
Malectin		2629
492IPR016167
FAD-binding, type 2, subdomain 1		2626
493IPR027409
GroEL-like apical domain		2653
494IPR029069
HotDog domain		2679
495IPR001906
Terpene synthase, N-terminal domain		2653
496IPR001609
Myosin head, motor domain		26143
497IPR004274
FCP1 homology domain		2673
498IPR017927
Ferredoxin reductase-type FAD-binding domain		2526
499IPR017938
Riboflavin synthase-like beta-barrel		2530
500IPR015940
Ubiquitin-associated domain		2569
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Triticum_aestivum.html b/gramene/htdocs/ssi/species.weix/stats_Triticum_aestivum.html new file mode 100644 index 00000000..d78a992c --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Triticum_aestivum.html @@ -0,0 +1,48 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:TGACv1, Dec 2015
Database version:86.3
Base Pairs:13,427,354,022
Golden Path Length:13,427,354,022
Genebuild by: TGACv1
Genebuild method: Imported from TGAC
Genebuild started: Dec 2015
Genebuild version: 2016-05-TGAC
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		103,539
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:166,589
+ + +

Coordinate Systems

+ + + + +
scaffold735943 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):504,092
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR032675
Leucine-rich repeat domain, L domain-like		527124853
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		507821684
3IPR011009
Protein kinase-like domain		50129150
4IPR000719
Protein kinase domain		485520648
5IPR001810
F-box domain		398412838
6IPR008271
Serine/threonine-protein kinase, active site		39076395
7IPR017441
Protein kinase, ATP binding site		35255719
8IPR013320
Concanavalin A-like lectin/glucanase domain		30095351
9IPR013083
Zinc finger, RING/FYVE/PHD-type		21723976
10IPR002182
NB-ARC		20623824
11IPR011990
Tetratricopeptide-like helical domain		18378674
12IPR001611
Leucine-rich repeat		161413341
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		15783774
14IPR002885
Pentatricopeptide repeat		143246551
15IPR001841
Zinc finger, RING-type		13985110
16IPR016040
NAD(P)-binding domain		13585279
17IPR001128
Cytochrome P450		13149907
18IPR009057
Homeodomain-like		12864769
19IPR029058
Alpha/Beta hydrolase fold		12644687
20IPR002401
Cytochrome P450, E-class, group I		11618988
21IPR017972
Cytochrome P450, conserved site		10961284
22IPR012337
Ribonuclease H-like domain		10752658
23IPR003591
Leucine-rich repeat, typical subtype		106110487
24IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		10341415
25IPR016024
Armadillo-type fold		9944013
26IPR003593
AAA+ ATPase domain		9752175
27IPR020846
Major facilitator superfamily domain		9043066
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		8913780
29IPR015943
WD40/YVTN repeat-like-containing domain		8702611
30IPR012677
Nucleotide-binding alpha-beta plait domain		8695486
31IPR012336
Thioredoxin-like fold		8542675
32IPR001005
SANT/Myb domain		8443209
33IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		8212407
34IPR017853
Glycoside hydrolase superfamily		8031586
35IPR011989
Armadillo-like helical		7862834
36IPR008974
TRAF-like		7811799
37IPR011333
SKP1/BTB/POZ domain		7671161
38IPR017986
WD40-repeat-containing domain		7603494
39IPR000504
RNA recognition motif domain		7607478
40IPR001680
WD40 repeat		73514899
41IPR000477
Reverse transcriptase domain		7021270
42IPR001878
Zinc finger, CCHC-type		6885093
43IPR017930
Myb domain		6731525
44IPR000210
BTB/POZ domain		6563124
45IPR013781
Glycoside hydrolase, catalytic domain		6561263
46IPR010255
Haem peroxidase		647825
47IPR002016
Haem peroxidase, plant/fungal/bacterial		6465131
48IPR009072
Histone-fold		6361557
49IPR011991
Winged helix-turn-helix DNA-binding domain		6141827
50IPR000823
Plant peroxidase		6135744
51IPR016177
DNA-binding domain		602883
52IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		5723968
53IPR001471
AP2/ERF domain		5683982
54IPR019793
Peroxidases heam-ligand binding site		566686
55IPR026960
Reverse transcriptase zinc-binding domain		563588
56IPR007087
Zinc finger, C2H2		5632364
57IPR020683
Ankyrin repeat-containing domain		5524697
58IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		5501449
59IPR011992
EF-hand domain pair		5482123
60IPR005174
Domain unknown function DUF295		540655
61IPR002110
Ankyrin repeat		5326777
62IPR023213
Chloramphenicol acetyltransferase-like domain		5291107
63IPR013830
SGNH hydrolase-type esterase domain		5242058
64IPR002048
EF-hand domain		5105004
65IPR005135
Endonuclease/exonuclease/phosphatase		5062099
66IPR015300
DNA-binding pseudobarrel domain		5002297
67IPR021109
Aspartic peptidase domain		4941621
68IPR031052
FHY3/FAR1 family		493972
69IPR002083
MATH/TRAF domain		4931235
70IPR003480
Transferase		488572
71IPR017451
F-box associated interaction domain		483628
72IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		482710
73IPR019794
Peroxidase, active site		481573
74IPR005123
Oxoglutarate/iron-dependent dioxygenase		4671260
75IPR018247
EF-Hand 1, calcium-binding site		4611656
76IPR001087
GDSL lipase/esterase		4591127
77IPR023214
HAD-like domain		4582778
78IPR003441
NAC domain		4571860
79IPR029071
Ubiquitin-related domain		4521139
80IPR001480
Bulb-type lectin domain		4503206
81IPR023753
FAD/NAD(P)-binding domain		4482969
82IPR003959
ATPase, AAA-type, core		4471631
83IPR025315
Domain of unknown function DUF4220		446619
84IPR027443
Isopenicillin N synthase-like		445663
85IPR006566
FBD domain		441676
86IPR029044
Nucleotide-diphospho-sugar transferases		4261755
87IPR019775
WD40 repeat, conserved site		4231305
88IPR003340
B3 DNA binding domain		4182938
89IPR003439
ABC transporter-like		4162186
90IPR001650
Helicase, C-terminal		4072841
91IPR014001
Helicase superfamily 1/2, ATP-binding domain		4061454
92IPR019734
Tetratricopeptide repeat		4044874
93IPR003609
PAN/Apple domain		4011486
94IPR012340
Nucleic acid-binding, OB-fold		400879
95IPR007658
Protein of unknown function DUF594		399511
96IPR013026
Tetratricopeptide repeat-containing domain		395905
97IPR014710
RmlC-like jelly roll fold		391720
98IPR008972
Cupredoxin		3901781
99IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		390760
100IPR026992
Non-haem dioxygenase N-terminal domain		385526
101IPR018289
MULE transposase domain		383597
102IPR000858
S-locus glycoprotein domain		379517
103IPR011676
Domain of unknown function DUF1618		376514
104IPR001461
Aspartic peptidase A1 family		3731208
105IPR007527
Zinc finger, SWIM-type		370933
106IPR025558
Domain of unknown function DUF4283		369432
107IPR007125
Histone H2A/H2B/H3		365426
108IPR001623
DnaJ domain		3553733
109IPR033121
Peptidase family A1 domain		354493
110IPR010987
Glutathione S-transferase, C-terminal-like		3501269
111IPR000626
Ubiquitin domain		3482549
112IPR013785
Aldolase-type TIM barrel		346660
113IPR032799
Xylanase inhibitor, C-terminal		343397
114IPR032861
Xylanase inhibitor, N-terminal		343402
115IPR006501
Pectinesterase inhibitor domain		3351474
116IPR000008
C2 domain		3284281
117IPR004045
Glutathione S-transferase, N-terminal		328796
118IPR000109
Proton-dependent oligopeptide transporter family		3271129
119IPR002347
Short-chain dehydrogenase/reductase SDR		3254137
120IPR011011
Zinc finger, FYVE/PHD-type		322835
121IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		320567
122IPR015424
Pyridoxal phosphate-dependent transferase		317577
123IPR001881
EGF-like calcium-binding domain		311649
124IPR024171
S-receptor-like serine/threonine-protein kinase		309391
125IPR000742
EGF-like domain		3091184
126IPR017871
ABC transporter, conserved site		302688
127IPR011051
RmlC-like cupin domain		302473
128IPR017907
Zinc finger, RING-type, conserved site		302569
129IPR015880
Zinc finger, C2H2-like		3001091
130IPR003657
WRKY domain		2972358
131IPR026961
PGG domain		292909
132IPR001356
Homeobox domain		2921405
133IPR004330
FAR1 DNA binding domain		291529
134IPR009009
RlpA-like protein, double-psi beta-barrel domain		290890
135IPR006447
Myb domain, plants		290485
136IPR018097
EGF-like calcium-binding, conserved site		288396
137IPR003960
ATPase, AAA-type, conserved site		285479
138IPR002902
Gnk2-homologous domain		2821239
139IPR005225
Small GTP-binding protein domain		279423
140IPR003676
Small auxin-up RNA		279291
141IPR006564
Zinc finger, PMZ-type		277440
142IPR020472
G-protein beta WD-40 repeat		2731530
143IPR000073
Alpha/beta hydrolase fold-1		269957
144IPR011050
Pectin lyase fold/virulence factor		266364
145IPR012334
Pectin lyase fold		266365
146IPR001220
Legume lectin domain		264294
147IPR011545
DEAD/DEAH box helicase domain		262504
148IPR001932
PPM-type phosphatase domain		2622746
149IPR005828
Major facilitator, sugar transporter-like		261504
150IPR003690
Transcription termination factor, mitochondrial/chloroplastic		2612144
151IPR006121
Heavy metal-associated domain, HMA		258993
152IPR016039
Thiolase-like		2571393
153IPR004827
Basic-leucine zipper domain		2571783
154IPR001965
Zinc finger, PHD-type		254889
155IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		246425
156IPR000270
PB1 domain		242958
157IPR004265
Plant disease resistance response protein		241262
158IPR022059
Protein of unknown function DUF3615		241336
159IPR015500
Peptidase S8, subtilisin-related		2401137
160IPR032867
DYW domain		239313
161IPR001584
Integrase, catalytic core		238487
162IPR013128
Peptidase C1A		236308
163IPR007117
Expansin, cellulose-binding-like domain		2351020
164IPR003245
Phytocyanin domain		234746
165IPR015655
Protein phosphatase 2C family		233722
166IPR009003
Peptidase S1, PA clan		229634
167IPR005829
Sugar transporter, conserved site		227630
168IPR007112
Expansin/pollen allergen, DPBB domain		225474
169IPR000209
Peptidase S8/S53 domain		2241528
170IPR006045
Cupin 1		223666
171IPR002100
Transcription factor, MADS-box		2211903
172IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		221281
173IPR029052
Metallo-dependent phosphatase-like		219903
174IPR007118
Expansin/Lol pI		2161318
175IPR016166
FAD-binding, type 2		214611
176IPR016135
Ubiquitin-conjugating enzyme/RWD-like		213758
177IPR012871
Protein of unknown function DUF1677, Oryza sativa		212287
178IPR001509
NAD-dependent epimerase/dehydratase		212337
179IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		209302
180IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		207669
181IPR006553
Leucine-rich repeat, cysteine-containing subtype		2052312
182IPR002528
Multi antimicrobial extrusion protein		205978
183IPR011993
PH domain-like		204733
184IPR000668
Peptidase C1A, papain C-terminal		2031014
185IPR019956
Ubiquitin		201878
186IPR000571
Zinc finger, CCCH-type		2013620
187IPR004162
E3 ubiquitin-protein ligase SIN-like		200269
188IPR013766
Thioredoxin domain		200599
189IPR008978
HSP20-like chaperone		198528
190IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		198365
191IPR019787
Zinc finger, PHD-finger		198770
192IPR013763
Cyclin-like		1961368
193IPR000490
Glycoside hydrolase family 17		195489
194IPR013323
SIAH-type domain		195260
195IPR001563
Peptidase S10, serine carboxypeptidase		1931724
196IPR025836
Zinc knuckle CX2CX4HX4C		193216
197IPR013057
Amino acid transporter, transmembrane domain		193266
198IPR030184
WAT1-related protein		193260
199IPR024788
Malectin-like carbohydrate-binding domain		192268
200IPR004864
Late embryogenesis abundant protein, LEA-14		190236
201IPR000152
EGF-type aspartate/asparagine hydroxylation site		190268
202IPR013094
Alpha/beta hydrolase fold-3		190216
203IPR003663
Sugar/inositol transporter		1901589
204IPR023828
Peptidase S8, subtilisin, Ser-active site		188249
205IPR013187
F-box associated domain, type 3		187233
206IPR002035
von Willebrand factor, type A		187989
207IPR008949
Isoprenoid synthase domain		186526
208IPR000620
EamA domain		185439
209IPR013201
Cathepsin propeptide inhibitor domain (I29)		184438
210IPR020568
Ribosomal protein S5 domain 2-type fold		184377
211IPR003613
U box domain		184777
212IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		184574
213IPR008979
Galactose-binding domain-like		183789
214IPR011527
ABC transporter type 1, transmembrane domain		1831951
215IPR013010
Zinc finger, SIAH-type		181229
216IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		181424
217IPR006094
FAD linked oxidase, N-terminal		181234
218IPR019786
Zinc finger, PHD-type, conserved site		180396
219IPR011701
Major facilitator superfamily		179306
220IPR011006
CheY-like superfamily		179295
221IPR000048
IQ motif, EF-hand binding site		1792104
222IPR001929
Germin		178571
223IPR004046
Glutathione S-transferase, C-terminal		177217
224IPR001789
Signal transduction response regulator, receiver domain		177807
225IPR004158
Protein of unknown function DUF247, plant		176222
226IPR005202
Transcription factor GRAS		175572
227IPR000608
Ubiquitin-conjugating enzyme E2		174614
228IPR023395
Mitochondrial carrier domain		174640
229IPR001806
Small GTPase superfamily		174252
230IPR018108
Mitochondrial substrate/solute carrier		1731590
231IPR017877
Myb-like domain		170357
232IPR000873
AMP-dependent synthetase/ligase		169593
233IPR016167
FAD-binding, type 2, subdomain 1		169203
234IPR011032
GroES-like		167562
235IPR011043
Galactose oxidase/kelch, beta-propeller		166221
236IPR001969
Aspartic peptidase, active site		165352
237IPR000225
Armadillo		1652347
238IPR002068
Alpha crystallin/Hsp20 domain		163384
239IPR016159
Cullin repeat-like-containing domain		163290
240IPR023393
START-like domain		162265
241IPR027640
Kinesin-like protein		161894
242IPR018253
DnaJ domain, conserved site		161247
243IPR031107
Small heat shock protein HSP20		161188
244IPR002109
Glutaredoxin		160360
245IPR026057
PC-Esterase		159244
246IPR003614
Knottin, scorpion toxin-like		159384
247IPR001214
SET domain		1571011
248IPR003653
Ulp1 protease family, C-terminal catalytic domain		156330
249IPR025846
PMR5 N-terminal domain		156224
250IPR001752
Kinesin motor domain		1552711
251IPR019780
Germin, manganese binding site		154168
252IPR002085
Alcohol dehydrogenase superfamily, zinc-type		152302
253IPR029962
Trichome birefringence-like family		150279
254IPR006702
Domain of unknown function DUF588		150177
255IPR029055
Nucleophile aminohydrolases, N-terminal		149487
256IPR014014
RNA helicase, DEAD-box type, Q motif		149289
257IPR011707
Multicopper oxidase, type 3		149196
258IPR013525
ABC-2 type transporter		147327
259IPR008906
HAT, C-terminal dimerisation domain		147196
260IPR008962
PapD-like		146768
261IPR003137
PA domain		146362
262IPR008266
Tyrosine-protein kinase, active site		145223
263IPR020845
AMP-binding, conserved site		145256
264IPR002921
Fungal lipase-like domain		144223
265IPR001117
Multicopper oxidase, type 1		144196
266IPR016461
O-methyltransferase COMT-type		144306
267IPR001938
Thaumatin		1441451
268IPR008928
Six-hairpin glycosidase-like		144279
269IPR004320
Protein of unknown function DUF241, plant		143146
270IPR016181
Acyl-CoA N-acyltransferase		142464
271IPR027806
Harbinger transposase-derived nuclease domain		142262
272IPR004332
Transposase, MuDR, plant		141174
273IPR012946
X8 domain		141502
274IPR001077
O-methyltransferase, family 2		141174
275IPR011706
Multicopper oxidase, type 2		141190
276IPR013601
FAE1/Type III polyketide synthase-like protein		138149
277IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		138264
278IPR005630
Terpene synthase, metal-binding domain		138187
279IPR001906
Terpene synthase, N-terminal domain		137363
280IPR011042
Six-bladed beta-propeller, TolB-like		137294
281IPR000535
Major sperm protein (MSP) domain		136643
282IPR009000
Translation protein, beta-barrel domain		136284
283IPR025322
Protein of unknown function DUF4228, plant		135146
284IPR001360
Glycoside hydrolase family 1		1341522
285IPR000757
Glycoside hydrolase family 16		134324
286IPR000222
PPM-type phosphatase, divalent cation binding		133248
287IPR025659
Tubby C-terminal-like domain		132313
288IPR019954
Ubiquitin conserved site		132424
289IPR008480
Protein of unknown function DUF761, plant		132138
290IPR027923
Hydrophobic seed protein		132137
291IPR007321
Transposase (putative), gypsy type		132154
292IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		132216
293IPR012967
Plant methyltransferase dimerisation		131163
294IPR002119
Histone H2A		130971
295IPR024752
Myb/SANT-like domain		130226
296IPR000743
Glycoside hydrolase, family 28		130271
297IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		129138
298IPR025660
Cysteine peptidase, histidine active site		129152
299IPR002487
Transcription factor, K-box		129365
300IPR006016
UspA		128198
301IPR000164
Histone H3/CENP-A		1281364
302IPR001951
Histone H4		128887
303IPR018121
Seven-in-absentia protein, TRAF-like domain		128162
304IPR032454
Histone H2A, C-terminal domain		127166
305IPR001478
PDZ domain		127685
306IPR014756
Immunoglobulin E-set		127257
307IPR019809
Histone H4, conserved site		126129
308IPR023299
P-type ATPase, cytoplasmic domain N		126519
309IPR013149
Alcohol dehydrogenase, C-terminal		125195
310IPR008999
Actin cross-linking		125232
311IPR001757
P-type ATPase		1251001
312IPR004314
Neprosin		125155
313IPR004140
Exocyst complex component Exo70		124519
314IPR013154
Alcohol dehydrogenase, N-terminal		124193
315IPR020904
Short-chain dehydrogenase/reductase, conserved site		124154
316IPR000863
Sulfotransferase domain		124147
317IPR017970
Homeobox, conserved site		124198
318IPR022796
Chlorophyll A-B binding protein		124352
319IPR015916
Galactose oxidase, beta-propeller		123219
320IPR023271
Aquaporin-like		123350
321IPR000425
Major intrinsic protein		1231327
322IPR000169
Cysteine peptidase, cysteine active site		123152
323IPR006671
Cyclin, N-terminal		123264
324IPR000644
CBS domain		1231294
325IPR025661
Cysteine peptidase, asparagine active site		123147
326IPR001229
Jacalin-like lectin domain		123924
327IPR033389
AUX/IAA domain		122272
328IPR010402
CCT domain		122378
329IPR008250
P-type ATPase, A domain		122606
330IPR003594
Histidine kinase-like ATPase, C-terminal domain		1221086
331IPR004263
Exostosin-like		121170
332IPR007650
Zf-FLZ domain		121148
333IPR004088
K Homology domain, type 1		1212560
334IPR007657
Glycosyltransferase AER61, uncharacterised		120215
335IPR023210
NADP-dependent oxidoreductase domain		120554
336IPR000182
GNAT domain		119398
337IPR023296
Glycosyl hydrolase, five-bladed beta-propellor domain		119432
338IPR018303
P-type ATPase, phosphorylation site		119277
339IPR001395
Aldo/keto reductase/potassium channel subunit beta		119215
340IPR008942
ENTH/VHS		118479
341IPR007493
Protein of unknown function DUF538		118419
342IPR013783
Immunoglobulin-like fold		118278
343IPR003656
Zinc finger, BED-type		118443
344IPR020946
Flavin monooxygenase-like		117220
345IPR005162
Retrotransposon gag domain		116120
346IPR010713
Xyloglucan endo-transglycosylase, C-terminal		115139
347IPR013126
Heat shock protein 70 family		1151676
348IPR032458
Histone H2A conserved site		115149
349IPR025110
AMP-binding enzyme C-terminal domain		114341
350IPR006652
Kelch repeat type 1		114839
351IPR015915
Kelch-type beta propeller		113267
352IPR018202
Serine carboxypeptidase, serine active site		113167
353IPR000558
Histone H2B		112950
354IPR011016
Zinc finger, RING-CH-type		112551
355IPR022357
Major intrinsic protein, conserved site		112155
356IPR020843
Polyketide synthase, enoylreductase domain		112158
357IPR029466
No apical meristem-associated, C-terminal domain		111131
358IPR029045
ClpP/crotonase-like domain		111505
359IPR007679
Domain of unknown function DUF569		111122
360IPR010285
DNA helicase Pif1-like		110125
361IPR000330
SNF2-related, N-terminal domain		110207
362IPR016455
Xyloglucan endotransglucosylase/hydrolase		110125
363IPR011013
Galactose mutarotase-like domain		110193
364IPR023796
Serpin domain		110395
365IPR009060
UBA-like		109260
366IPR033124
Serine carboxypeptidases, histidine active site		109132
367IPR000215
Serpin family		109135
368IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		109254
369IPR028889
Ubiquitin specific protease domain		109254
370IPR001574
Ribosome-inactivating protein		109288
371IPR001251
CRAL-TRIO lipid binding domain		1081112
372IPR002963
Expansin		108894
373IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		108116
374IPR031127
E3 ubiquitin ligase RBR family		108178
375IPR002867
IBR domain		106527
376IPR019557
Aminotransferase-like, plant mobile domain		106161
377IPR000070
Pectinesterase, catalytic		106132
378IPR015947
PUA-like domain		106252
379IPR004316
SWEET sugar transporter		105264
380IPR006626
Parallel beta-helix repeat		105718
381IPR004839
Aminotransferase, class I/classII		105194
382IPR004813
Oligopeptide transporter, OPT superfamily		104486
383IPR013189
Glycosyl hydrolase family 32, C-terminal		104516
384IPR013148
Glycosyl hydrolase family 32, N-terminal		103186
385IPR032710
NTF2-like domain		103287
386IPR002355
Multicopper oxidase, copper-binding site		103132
387IPR001362
Glycoside hydrolase, family 32		103186
388IPR019378
GDP-fucose protein O-fucosyltransferase		103177
389IPR012341
Six-hairpin glycosidase		103171
390IPR002495
Glycosyl transferase, family 8		102171
391IPR002156
Ribonuclease H domain		101109
392IPR004853
Sugar phosphate transporter domain		101221
393IPR011332
Zinc-binding ribosomal protein		101113
394IPR003406
Glycosyl transferase, family 14		101160
395IPR008889
VQ		101102
396IPR006073
GTP binding domain		101574
397IPR022742
Serine aminopeptidase, S33		100154
398IPR006458
Ovate protein family, C-terminal		100287
399IPR029021
Protein-tyrosine phosphatase-like		99354
400IPR000315
B-box-type zinc finger		99480
401IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		99359
402IPR012675
Beta-grasp domain		98177
403IPR000782
FAS1 domain		97559
404IPR018490
Cyclic nucleotide-binding-like		97197
405IPR009030
Growth factor receptor cysteine-rich domain		97130
406IPR025875
Leucine rich repeat 4		97153
407IPR004087
K Homology domain		97537
408IPR004041
NAF domain		96162
409IPR018200
Ubiquitin specific protease, conserved site		96360
410IPR000595
Cyclic nucleotide-binding domain		96504
411IPR002912
ACT domain		96422
412IPR029047
Heat shock protein 70kD, peptide-binding domain		96351
413IPR018451
NAF/FISL domain		95160
414IPR013216
Methyltransferase type 11		95150
415IPR000528
Plant lipid transfer protein/Par allergen		94499
416IPR005150
Cellulose synthase		94251
417IPR011012
Longin-like domain		94161
418IPR014720
Double-stranded RNA-binding domain		941137
419IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		94166
420IPR023329
Chlorophyll a/b binding protein domain		94157
421IPR005795
Major pollen allergen Lol pI		93757
422IPR017938
Riboflavin synthase-like beta-barrel		93213
423IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		93197
424IPR010920
LSM domain		92151
425IPR001296
Glycosyl transferase, family 1		92220
426IPR029062
Class I glutamine amidotransferase-like		92433
427IPR002067
Mitochondrial carrier protein		92789
428IPR003851
Zinc finger, Dof-type		92449
429IPR017927
Ferredoxin reductase-type FAD-binding domain		90151
430IPR008991
Translation protein SH3-like domain		90134
431IPR002659
Glycosyl transferase, family 31		90285
432IPR018181
Heat shock protein 70, conserved site		90359
433IPR023313
Ubiquitin-conjugating enzyme, active site		90156
434IPR001232
S-phase kinase-associated protein 1-like		9097
435IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		90212
436IPR007612
LURP1-related protein domain		89102
437IPR033138
Multicopper oxidases, conserved site		89117
438IPR002403
Cytochrome P450, E-class, group IV		88640
439IPR011074
CRAL/TRIO, N-terminal domain		88497
440IPR001849
Pleckstrin homology domain		88489
441IPR019821
Kinesin motor domain, conserved site		87198
442IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		87147
443IPR004883
Lateral organ boundaries, LOB		86202
444IPR016197
Chromo domain-like		86158
445IPR005175
PPC domain		86225
446IPR027214
Cystatin		85101
447IPR001357
BRCT domain		85992
448IPR013088
Zinc finger, NHR/GATA-type		85157
449IPR001344
Chlorophyll A-B binding protein, plant		85133
450IPR027725
Heat shock transcription factor family		85171
451IPR002423
Chaperonin Cpn60/TCP-1 family		85136
452IPR025886
Phloem protein 2-like		85205
453IPR025314
Domain of unknown function DUF4219		8597
454IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		85116
455IPR005821
Ion transport domain		85312
456IPR005746
Thioredoxin		85141
457IPR003311
AUX/IAA protein		85190
458IPR000679
Zinc finger, GATA-type		85552
459IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		84327
460IPR001763
Rhodanese-like domain		84722
461IPR006694
Fatty acid hydroxylase		84138
462IPR029069
HotDog domain		84407
463IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		84161
464IPR025724
GAG-pre-integrase domain		8493
465IPR003100
PAZ domain		83911
466IPR006153
Cation/H+ exchanger		83127
467IPR000795
Transcription factor, GTP-binding domain		83827
468IPR027409
GroEL-like apical domain		83261
469IPR000232
Heat shock factor (HSF)-type, DNA-binding		83785
470IPR016072
SKP1 component, dimerisation		82172
471IPR001320
Ionotropic glutamate receptor		82230
472IPR000010
Cystatin domain		82162
473IPR012951
Berberine/berberine-like		8186
474IPR033131
Pectinesterase, Asp active site		81101
475IPR006461
PLAC8 motif-containing protein		81215
476IPR013780
Glycosyl hydrolase, all-beta		81118
477IPR025398
Domain of unknown function DUF4371		81105
478IPR003855
Potassium transporter		81289
479IPR016073
SKP1 component, POZ domain		8085
480IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		80188
481IPR004367
Cyclin, C-terminal domain		80298
482IPR002129
Pyridoxal phosphate-dependent decarboxylase		80116
483IPR000727
Target SNARE coiled-coil homology domain		79276
484IPR015940
Ubiquitin-associated domain		79426
485IPR006195
Aminoacyl-tRNA synthetase, class II		79114
486IPR025753
AAA-type ATPase, N-terminal domain		79180
487IPR013771
Bifunctional trypsin/alpha-amylase inhibitor helical domain		79111
488IPR002641
Patatin/Phospholipase A2-related		79124
489IPR001487
Bromodomain		791165
490IPR002937
Amine oxidase		79130
491IPR027356
NPH3 domain		78356
492IPR008963
Purple acid phosphatase-like, N-terminal		78119
493IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		78186
494IPR012328
Chalcone/stilbene synthase, C-terminal		78110
495IPR001638
Solute-binding protein family 3/N-terminal domain of MltF		78139
496IPR015914
Purple acid phosphatase, N-terminal		78233
497IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		77116
498IPR001701
Glycoside hydrolase family 9		77109
499IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		77334
500IPR017761
Laccase		7797
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu.html b/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu.html new file mode 100644 index 00000000..0574bcbf --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu.html @@ -0,0 +1,63 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ASM34745v1, Apr 2013
Database version:86.1
Base Pairs:3,008,981,354
Golden Path Length:3,747,163,292
Genebuild by: BGI
Genebuild method: Generated from ENA annotation
Genebuild started: May 2014
Genebuild released: Dec 2012
Genebuild last updated/patched: Apr 2013
Genebuild version: 2013-04-BGI
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		34,903
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		74
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:37,604
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
1 sequence
+
+ +
+ + + +
SequenceLength (bp)
Pt115773
+
+
supercontig499221 sequences
contig1455437 sequences
diff --git a/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu_IPtop500.html new file mode 100644 index 00000000..81778cf8 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Triticum_urartu_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		15191672
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		15043851
3IPR032675
Leucine-rich repeat domain, L domain-like		14444527
4IPR000719
Protein kinase domain		14353630
5IPR008271
Serine/threonine-protein kinase, active site		10661082
6IPR017441
Protein kinase, ATP binding site		926940
7IPR001810
F-box domain		8591999
8IPR013320
Concanavalin A-like lectin/glucanase, subgroup		8341086
9IPR002182
NB-ARC		531592
10IPR011990
Tetratricopeptide-like helical		5211614
11IPR016040
NAD(P)-binding domain		4661126
12IPR013083
Zinc finger, RING/FYVE/PHD-type		459506
13IPR001611
Leucine-rich repeat		4572746
14IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		445602
15IPR002885
Pentatricopeptide repeat		4349339
16IPR001128
Cytochrome P450		4262519
17IPR029058
Alpha/Beta hydrolase fold		351870
18IPR009057
Homeodomain-like		328744
19IPR002401
Cytochrome P450, E-class, group I		3151795
20IPR003591
Leucine-rich repeat, typical subtype		3112356
21IPR017972
Cytochrome P450, conserved site		304306
22IPR016024
Armadillo-type fold		299636
23IPR020846
Major facilitator superfamily domain		283518
24IPR013210
Leucine-rich repeat-containing N-terminal, type 2		281283
25IPR012677
Nucleotide-binding, alpha-beta plait		270779
26IPR003593
AAA+ ATPase domain		269367
27IPR017853
Glycoside hydrolase, superfamily		263312
28IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		255672
29IPR015943
WD40/YVTN repeat-like-containing domain		251412
30IPR012336
Thioredoxin-like fold		234514
31IPR001841
Zinc finger, RING-type		234551
32IPR017986
WD40-repeat-containing domain		226554
33IPR000504
RNA recognition motif domain		221947
34IPR011989
Armadillo-like helical		219409
35IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		219511
36IPR013781
Glycoside hydrolase, catalytic domain		217275
37IPR001680
WD40 repeat		2112018
38IPR001005
SANT/Myb domain		211517
39IPR010255
Haem peroxidase		201224
40IPR002016
Haem peroxidase, plant/fungal/bacterial		2001153
41IPR000823
Plant peroxidase		1831215
42IPR011333
BTB/POZ fold		174211
43IPR011991
Winged helix-turn-helix DNA-binding domain		171327
44IPR012337
Ribonuclease H-like domain		168308
45IPR013830
SGNH hydrolase-type esterase domain		167449
46IPR009072
Histone-fold		167344
47IPR011992
EF-hand domain pair		160410
48IPR017930
Myb domain		159233
49IPR020683
Ankyrin repeat-containing domain		156755
50IPR008974
TRAF-like		155295
51IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		153600
52IPR017451
F-box associated interaction domain		152155
53IPR000210
BTB/POZ domain		150474
54IPR002048
EF-hand domain		148915
55IPR023213
Chloramphenicol acetyltransferase-like domain		148247
56IPR023214
HAD-like domain		146401
57IPR019793
Peroxidases heam-ligand binding site		146148
58IPR027443
Isopenicillin N synthase-like		144168
59IPR002110
Ankyrin repeat		1411014
60IPR012340
Nucleic acid-binding, OB-fold		138196
61IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		138316
62IPR001480
Bulb-type lectin domain		137751
63IPR018247
EF-Hand 1, calcium-binding site		135312
64IPR025315
Domain of unknown function DUF4220		135140
65IPR014001
Helicase, superfamily 1/2, ATP-binding domain		135259
66IPR001650
Helicase, C-terminal		134392
67IPR005123
Oxoglutarate/iron-dependent dioxygenase		134242
68IPR005174
Protein of unknown function DUF295		134138
69IPR003480
Transferase		133155
70IPR003439
ABC transporter-like		132383
71IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		131170
72IPR019794
Peroxidase, active site		130131
73IPR029044
Nucleotide-diphospho-sugar transferases		128319
74IPR019775
WD40 repeat, conserved site		126206
75IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		126532
76IPR003959
ATPase, AAA-type, core		125157
77IPR007658
Protein of unknown function DUF594		124125
78IPR001087
Lipase, GDSL		122122
79IPR014710
RmlC-like jelly roll fold		122145
80IPR015424
Pyridoxal phosphate-dependent transferase		121138
81IPR019734
Tetratricopeptide repeat		120756
82IPR008972
Cupredoxin		120439
83IPR003609
Apple-like		120332
84IPR015300
DNA-binding pseudobarrel domain		120368
85IPR025287
Wall-associated receptor kinase galacturonan-binding domain		117133
86IPR013785
Aldolase-type TIM barrel		116146
87IPR007087
Zinc finger, C2H2		116344
88IPR013026
Tetratricopeptide repeat-containing domain		116150
89IPR021109
Aspartic peptidase domain		114336
90IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		114127
91IPR006566
FBD domain		114134
92IPR000858
S-locus glycoprotein		112117
93IPR001461
Aspartic peptidase		110221
94IPR000109
Proton-dependent oligopeptide transporter family		107239
95IPR010987
Glutathione S-transferase, C-terminal-like		107321
96IPR003441
NAC domain		105314
97IPR004045
Glutathione S-transferase, N-terminal		104211
98IPR002083
MATH/TRAF domain		103220
99IPR003340
B3 DNA binding domain		100444
100IPR016039
Thiolase-like		99405
101IPR009009
RlpA-like double-psi beta-barrel domain		99256
102IPR032799
Xylanase inhibitor, C-terminal		9999
103IPR029071
Ubiquitin-related domain		98141
104IPR002347
Glucose/ribitol dehydrogenase		96707
105IPR033121
Peptidase family A1 domain		9498
106IPR011051
RmlC-like cupin domain		92101
107IPR000008
C2 domain		90603
108IPR005828
General substrate transporter		90110
109IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		9095
110IPR001623
DnaJ domain		88588
111IPR031052
FHY3/FAR1 family		8898
112IPR006501
Pectinesterase inhibitor domain		87342
113IPR011011
Zinc finger, FYVE/PHD-type		8699
114IPR003657
DNA-binding WRKY		86485
115IPR001878
Zinc finger, CCHC-type		86480
116IPR007125
Histone core		8587
117IPR012334
Pectin lyase fold		8598
118IPR011050
Pectin lyase fold/virulence factor		8492
119IPR026992
Non-haem dioxygenase N-terminal domain		8486
120IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		8489
121IPR032861
Xylanase inhibitor, N-terminal		8385
122IPR001932
Protein phosphatase 2C (PP2C)-like domain		83454
123IPR005225
Small GTP-binding protein domain		8285
124IPR032867
DYW domain		8284
125IPR024171
S-receptor-like serine/threonine-protein kinase		8080
126IPR017871
ABC transporter, conserved site		80105
127IPR003690
Mitochodrial transcription termination factor-related		78444
128IPR016177
DNA-binding domain		7798
129IPR001220
Legume lectin domain		7790
130IPR015500
Peptidase S8, subtilisin-related		77219
131IPR003960
ATPase, AAA-type, conserved site		7687
132IPR015655
Protein phosphatase 2C		76125
133IPR000742
Epidermal growth factor-like domain		74176
134IPR024752
Myb/SANT-like domain		7475
135IPR000209
Peptidase S8/S53 domain		74370
136IPR001471
AP2/ERF domain		73409
137IPR007117
Expansin, cellulose-binding-like domain		73294
138IPR012871
Protein of unknown function DUF1677, Oryza sativa		7276
139IPR001509
NAD-dependent epimerase/dehydratase		7173
140IPR000626
Ubiquitin domain		70272
141IPR026961
PGG domain		70198
142IPR017907
Zinc finger, RING-type, conserved site		7071
143IPR002528
Multi antimicrobial extrusion protein		69171
144IPR002100
Transcription factor, MADS-box		69474
145IPR013187
F-box associated domain, type 3		6868
146IPR000073
Alpha/beta hydrolase fold-1		68120
147IPR013128
Peptidase C1A		6777
148IPR001881
EGF-like calcium-binding domain		6795
149IPR004827
Basic-leucine zipper domain		67222
150IPR011032
GroES (chaperonin 10)-like		66151
151IPR006121
Heavy metal-associated domain, HMA		66183
152IPR005829
Sugar transporter, conserved site		66105
153IPR003245
Plastocyanin-like		66185
154IPR029052
Metallo-dependent phosphatase-like		66150
155IPR007112
Expansin/pollen allergen, DPBB domain		65114
156IPR013057
Amino acid transporter, transmembrane		6575
157IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		65128
158IPR006045
Cupin 1		64143
159IPR001356
Homeobox domain		64161
160IPR004158
Protein of unknown function DUF247, plant		6477
161IPR001563
Peptidase S10, serine carboxypeptidase		63337
162IPR020472
G-protein beta WD-40 repeat		63189
163IPR002085
Alcohol dehydrogenase superfamily, zinc-type		6382
164IPR001965
Zinc finger, PHD-type		6396
165IPR007118
Expansin/Lol pI		62266
166IPR006447
Myb domain, plants		6263
167IPR018097
EGF-like calcium-binding, conserved site		6262
168IPR003676
Auxin-induced protein, ARG7		6263
169IPR000668
Peptidase C1A, papain C-terminal		61219
170IPR000490
Glycoside hydrolase, family 17		61112
171IPR024788
Malectin-like carbohydrate-binding domain		6163
172IPR008949
Terpenoid synthase		60125
173IPR002902
Gnk2-homologous domain		60193
174IPR004046
Glutathione S-transferase, C-terminal		6061
175IPR000270
Phox/Bem1p		6091
176IPR004265
Plant disease resistance response protein		5959
177IPR022059
Protein of unknown function DUF3615		5959
178IPR011676
Domain of unknown function DUF1618		5960
179IPR003663
Sugar/inositol transporter		59272
180IPR020568
Ribosomal protein S5 domain 2-type fold		5873
181IPR006553
Leucine-rich repeat, cysteine-containing subtype		57316
182IPR016135
Ubiquitin-conjugating enzyme/RWD-like		57127
183IPR030184
WAT1-related protein		5768
184IPR018289
MULE transposase domain		5656
185IPR011527
ABC transporter type 1, transmembrane domain		56309
186IPR016159
Cullin repeat-like-containing domain		5666
187IPR027640
Kinesin-like protein		55145
188IPR023395
Mitochondrial carrier domain		54128
189IPR011993
Pleckstrin homology-like domain		5495
190IPR001806
Small GTPase superfamily		5463
191IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5353
192IPR006912
Harbinger transposase-derived protein, plant		5357
193IPR018108
Mitochondrial substrate/solute carrier		53262
194IPR002035
von Willebrand factor, type A		53137
195IPR001752
Kinesin, motor domain		53392
196IPR026057
PC-Esterase		5257
197IPR000873
AMP-dependent synthetase/ligase		5266
198IPR001938
Thaumatin		52363
199IPR013763
Cyclin-like		52197
200IPR013766
Thioredoxin domain		5293
201IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		5275
202IPR003613
U box domain		52154
203IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		5180
204IPR001929
Germin		51148
205IPR013525
ABC-2 type transporter		5174
206IPR001360
Glycoside hydrolase, family 1		51343
207IPR000620
Drug/metabolite transporter		5179
208IPR017877
Myb-like domain		5159
209IPR013601
FAE1/Type III polyketide synthase-like protein		5061
210IPR010259
Proteinase inhibitor I9		5072
211IPR029962
Trichome birefringence-like family		5056
212IPR005135
Endonuclease/exonuclease/phosphatase		50152
213IPR016166
FAD-binding, type 2		5090
214IPR003594
Histidine kinase-like ATPase, ATP-binding domain		50166
215IPR008979
Galactose-binding domain-like		50112
216IPR000864
Proteinase inhibitor I13, potato inhibitor I		49255
217IPR008978
HSP20-like chaperone		49102
218IPR011701
Major facilitator superfamily		4950
219IPR013201
Proteinase inhibitor I29, cathepsin propeptide		4999
220IPR029055
Nucleophile aminohydrolases, N-terminal		4997
221IPR009000
Translation protein, beta-barrel domain		4952
222IPR008266
Tyrosine-protein kinase, active site		4949
223IPR023828
Peptidase S8, subtilisin, Ser-active site		4949
224IPR011043
Galactose oxidase/kelch, beta-propeller		4852
225IPR000477
Reverse transcriptase domain		4868
226IPR002403
Cytochrome P450, E-class, group IV		47229
227IPR013149
Alcohol dehydrogenase, C-terminal		4747
228IPR008250
P-type ATPase, A domain		4795
229IPR013154
Alcohol dehydrogenase GroES-like		4748
230IPR023210
NADP-dependent oxidoreductase domain		47154
231IPR005630
Terpene synthase, metal-binding domain		4647
232IPR019787
Zinc finger, PHD-finger		4680
233IPR011006
CheY-like superfamily		4647
234IPR001906
Terpene synthase, N-terminal domain		4693
235IPR009003
Trypsin-like cysteine/serine peptidase domain		4661
236IPR000571
Zinc finger, CCCH-type		46387
237IPR015880
Zinc finger, C2H2-like		46139
238IPR001789
Signal transduction response regulator, receiver domain		46133
239IPR000608
Ubiquitin-conjugating enzyme, E2		4591
240IPR001395
Aldo/keto reductase		4557
241IPR001117
Multicopper oxidase, type 1		4444
242IPR004140
Exocyst complex protein Exo70		4497
243IPR000863
Sulfotransferase domain		4447
244IPR007527
Zinc finger, SWIM-type		4474
245IPR000757
Glycoside hydrolase, family 16		4489
246IPR000225
Armadillo		44318
247IPR023393
START-like domain		4345
248IPR014014
RNA helicase, DEAD-box type, Q motif		4343
249IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4374
250IPR004839
Aminotransferase, class I/classII		4347
251IPR005202
Transcription factor GRAS		4392
252IPR023299
P-type ATPase, cytoplasmic domain N		4379
253IPR011706
Multicopper oxidase, type 2		4344
254IPR001757
Cation-transporting P-type ATPase		43136
255IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4343
256IPR025659
Tubby C-terminal-like domain		4251
257IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		4242
258IPR020843
Polyketide synthase, enoylreductase		4242
259IPR004330
FAR1 DNA binding domain		4246
260IPR002921
Lipase, class 3		4141
261IPR022796
Chlorophyll A-B binding protein		4143
262IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		4142
263IPR003614
Knottin, scorpion toxin-like		4191
264IPR016461
Caffeate O-methyltransferase (COMT) family		4065
265IPR004162
E3 ubiquitin-protein ligase SINA like		4044
266IPR000330
SNF2-related		4041
267IPR008928
Six-hairpin glycosidase-like		4051
268IPR019780
Germin, manganese binding site		4041
269IPR013126
Heat shock protein 70 family		40297
270IPR025661
Cysteine peptidase, asparagine active site		4040
271IPR011707
Multicopper oxidase, type 3		4042
272IPR026960
Reverse transcriptase zinc-binding domain		3939
273IPR023271
Aquaporin-like		3988
274IPR000152
EGF-type aspartate/asparagine hydroxylation site		3939
275IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3940
276IPR031107
Small heat shock protein HSP20		3942
277IPR004813
Oligopeptide transporter, OPT superfamily		3995
278IPR000425
Major intrinsic protein		39260
279IPR004088
K Homology domain, type 1		39246
280IPR004314
Domain of unknown function DUF239		3941
281IPR002068
Alpha crystallin/Hsp20 domain		3875
282IPR012946
X8 domain		3884
283IPR029045
ClpP/crotonase-like domain		38109
284IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3838
285IPR001214
SET domain		38103
286IPR000048
IQ motif, EF-hand binding site		38170
287IPR000743
Glycoside hydrolase, family 28		3855
288IPR033389
AUX/IAA domain		3740
289IPR007493
Protein of unknown function DUF538		37114
290IPR019786
Zinc finger, PHD-type, conserved site		3740
291IPR018303
P-type ATPase, phosphorylation site		3737
292IPR029047
Heat shock protein 70kD, peptide-binding domain		3780
293IPR016181
Acyl-CoA N-acyltransferase		3676
294IPR001077
O-methyltransferase, family 2		3637
295IPR013323
SIAH-type domain		3636
296IPR002487
Transcription factor, K-box		3673
297IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3640
298IPR001750
NADH:ubiquinone/plastoquinone oxidoreductase		3535
299IPR001251
CRAL-TRIO domain		35166
300IPR002119
Histone H2A		35174
301IPR020845
AMP-binding, conserved site		3536
302IPR019378
GDP-fucose protein O-fucosyltransferase		3538
303IPR015915
Kelch-type beta propeller		3544
304IPR025660
Cysteine peptidase, histidine active site		3535
305IPR032710
NTF2-like domain		3461
306IPR003137
Protease-associated domain, PA		3434
307IPR006564
Zinc finger, PMZ-type		3434
308IPR004263
Exostosin-like		3435
309IPR027923
Hydrophobic seed protein		3436
310IPR006094
FAD linked oxidase, N-terminal		3435
311IPR014756
Immunoglobulin E-set		3438
312IPR000070
Pectinesterase, catalytic		3441
313IPR011042
Six-bladed beta-propeller, TolB-like		3445
314IPR004316
SWEET sugar transporter		3360
315IPR032454
Histone H2A, C-terminal domain		3334
316IPR004320
Protein of unknown function DUF241, plant		3336
317IPR018181
Heat shock protein 70, conserved site		3380
318IPR011012
Longin-like domain		3333
319IPR020946
Flavin monooxygenase-like		3341
320IPR031127
E3 ubiquitin ligase RBR family		3343
321IPR012967
Plant methyltransferase dimerisation		3333
322IPR023796
Serpin domain		33108
323IPR010402
CCT domain		3262
324IPR025110
AMP-binding enzyme C-terminal domain		3232
325IPR019956
Ubiquitin		3289
326IPR002423
Chaperonin Cpn60/TCP-1		3240
327IPR012675
Beta-grasp domain		3232
328IPR000215
Serpin family		3242
329IPR013010
Zinc finger, SIAH-type		3232
330IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		3232
331IPR027409
GroEL-like apical domain		3265
332IPR018253
DnaJ domain, conserved site		3232
333IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		3239
334IPR028082
Periplasmic binding protein-like I		3248
335IPR006671
Cyclin, N-terminal		3243
336IPR016161
Aldehyde/histidinol dehydrogenase		3235
337IPR023298
P-type ATPase, transmembrane domain		3262
338IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		3237
339IPR023329
Chlorophyll a/b binding protein domain		3237
340IPR000558
Histone H2B		31228
341IPR005795
Major pollen allergen Lol pI		31177
342IPR015916
Galactose oxidase, beta-propeller		3134
343IPR004853
Triose-phosphate transporter domain		3132
344IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site		3143
345IPR008991
Translation protein SH3-like domain		3131
346IPR013783
Immunoglobulin-like fold		3137
347IPR025875
Leucine rich repeat 4		3134
348IPR000644
CBS domain		31172
349IPR016162
Aldehyde dehydrogenase, N-terminal		3136
350IPR018202
Peptidase S10, serine carboxypeptidase, active site		3133
351IPR017938
Riboflavin synthase-like beta-barrel		3039
352IPR008962
PapD-like		3068
353IPR019821
Kinesin, motor region, conserved site		3030
354IPR029021
Protein-tyrosine phosphatase-like		3071
355IPR007750
Protein of unknown function DUF674		3042
356IPR000795
Elongation factor, GTP-binding domain		30163
357IPR000164
Histone H3		30234
358IPR001951
Histone H4		30188
359IPR006694
Fatty acid hydroxylase		3030
360IPR004864
Late embryogenesis abundant protein, LEA-14		3032
361IPR020904
Short-chain dehydrogenase/reductase, conserved site		3030
362IPR023296
Glycosyl hydrolase, five-bladed beta-propellor domain		3056
363IPR001320
Ionotropic glutamate receptor		3058
364IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3030
365IPR002912
ACT domain		3062
366IPR006073
GTP binding domain		3085
367IPR015590
Aldehyde dehydrogenase domain		3036
368IPR001229
Mannose-binding lectin		30159
369IPR017927
Ferredoxin reductase-type FAD-binding domain		2929
370IPR018490
Cyclic nucleotide-binding-like		2929
371IPR002867
Zinc finger, C6HC-type		2998
372IPR007612
LURP1-like domain		2931
373IPR006626
Parallel beta-helix repeat		29142
374IPR009060
UBA-like		2933
375IPR001279
Beta-lactamase-like		2992
376IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		2929
377IPR001478
PDZ domain		29101
378IPR011332
Zinc-binding ribosomal protein		2929
379IPR011013
Galactose mutarotase-like domain		2934
380IPR002129
Pyridoxal phosphate-dependent decarboxylase		2931
381IPR019825
Legume lectin, beta chain, Mn/Ca-binding site		2930
382IPR029062
Class I glutamine amidotransferase-like		2977
383IPR004087
K Homology domain		2958
384IPR000169
Cysteine peptidase, cysteine active site		2929
385IPR000595
Cyclic nucleotide-binding domain		2968
386IPR003855
K+ potassium transporter		2959
387IPR016163
Aldehyde dehydrogenase, C-terminal		2931
388IPR008942
ENTH/VHS		2856
389IPR006016
UspA		2829
390IPR010920
Like-Sm (LSM) domain		2828
391IPR002659
Glycosyl transferase, family 31		2857
392IPR001296
Glycosyl transferase, family 1		2828
393IPR001969
Aspartic peptidase, active site		2842
394IPR007650
Protein of unknown function DUF581		2828
395IPR011074
CRAL/TRIO, N-terminal domain		2868
396IPR002355
Multicopper oxidase, copper-binding site		2828
397IPR005150
Cellulose synthase		2846
398IPR003406
Glycosyl transferase, family 14		2831
399IPR025846
PMR5 N-terminal domain		2828
400IPR029069
HotDog domain		2864
401IPR002495
Glycosyl transferase, family 8		2828
402IPR001638
Extracellular solute-binding protein, family 3		2829
403IPR015947
PUA-like domain		2836
404IPR004041
NAF domain		2727
405IPR001344
Chlorophyll A-B binding protein, plant		2731
406IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		2755
407IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2772
408IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2731
409IPR018121
Seven-in-absentia protein, TRAF-like domain		2727
410IPR012341
Six-hairpin glycosidase		2732
411IPR000727
Target SNARE coiled-coil domain		2669
412IPR013148
Glycosyl hydrolase family 32, N-terminal		2628
413IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		2626
414IPR001440
Tetratricopeptide TPR1		2630
415IPR001357
BRCT domain		26153
416IPR018451
NAF/FISL domain		2626
417IPR004161
Translation elongation factor EFTu/EF1A, domain 2		2626
418IPR019557
Aminotransferase-like, plant mobile domain		2628
419IPR027413
GroEL-like equatorial domain		2652
420IPR025886
Phloem protein 2-like		2627
421IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		2627
422IPR029039
Flavoprotein-like		2651
423IPR014722
Ribosomal protein L2 domain 2		2626
424IPR013780
Glycosyl hydrolase, family 13, all-beta		2626
425IPR002109
Glutaredoxin		2651
426IPR014720
Double-stranded RNA-binding domain		26103
427IPR000528
Plant lipid transfer protein/Par allergen		25103
428IPR013328
Dehydrogenase, multihelical		2532
429IPR006153
Cation/H+ exchanger		2530
430IPR033138
Multicopper oxidases, conserved site		2525
431IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2529
432IPR003656
Zinc finger, BED-type predicted		2557
433IPR033131
Pectinesterase, Asp active site		2525
434IPR019809
Histone H4, conserved site		2525
435IPR008263
Glycoside hydrolase, family 16, active site		2525
436IPR002963
Expansin		25152
437IPR016167
FAD-binding, type 2, subdomain 1		2525
438IPR012328
Chalcone/stilbene synthase, C-terminal		2525
439IPR013189
Glycosyl hydrolase family 32, C-terminal		2564
440IPR003311
AUX/IAA protein		2531
441IPR013094
Alpha/beta hydrolase fold-3		2526
442IPR015797
NUDIX hydrolase domain-like		2552
443IPR001574
Ribosome-inactivating protein		2545
444IPR000535
MSP domain		2449
445IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2464
446IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2461
447IPR032872
Wall-associated receptor kinase, C-terminal		2424
448IPR027806
Harbinger transposase-derived nuclease domain		2426
449IPR029061
Thiamin diphosphate-binding fold		2478
450IPR033124
Serine carboxypeptidases, histidine active site		2425
451IPR001763
Rhodanese-like domain		24112
452IPR001362
Glycoside hydrolase, family 32		2424
453IPR015712
DNA-directed RNA polymerase, subunit 2		2432
454IPR022357
Major intrinsic protein, conserved site		2424
455IPR033443
Pentacotripeptide-repeat region of PROPR		2424
456IPR001828
Extracellular ligand-binding receptor		2425
457IPR029006
ADF-H/Gelsolin-like domain		2456
458IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2466
459IPR003100
Argonaute/Dicer protein, PAZ domain		2390
460IPR029466
No apical meristem-associated, C-terminal domain		2324
461IPR013581
Plant PDR ABC transporter associated		2323
462IPR011016
Zinc finger, RING-CH-type		2356
463IPR020471
Aldo/keto reductase subgroup		2397
464IPR023346
Lysozyme-like domain		2324
465IPR010989
t-SNARE		2324
466IPR023313
Ubiquitin-conjugating enzyme, active site		2323
467IPR008480
Protein of unknown function DUF761, plant		2324
468IPR017970
Homeobox, conserved site		2323
469IPR005821
Ion transport domain		2323
470IPR013120
Male sterility, NAD-binding		2326
471IPR020635
Tyrosine-protein kinase, catalytic domain		2323
472IPR002641
Patatin/Phospholipase A2-related		2323
473IPR001487
Bromodomain		23156
474IPR008948
L-Aspartase-like		2324
475IPR026055
Fatty acyl-CoA reductase		2343
476IPR000182
GNAT domain		2236
477IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		22117
478IPR000726
Glycoside hydrolase, family 19, catalytic		2245
479IPR006195
Aminoacyl-tRNA synthetase, class II		2222
480IPR029000
Cyclophilin-like domain		2247
481IPR005299
SAM dependent carboxyl methyltransferase		2225
482IPR004100
ATPase, F1 complex alpha/beta subunit, N-terminal domain		2242
483IPR018170
Aldo/keto reductase, conserved site		2250
484IPR001133
NADH-ubiquinone oxidoreductase chain 4L/K		2249
485IPR000408
Regulator of chromosome condensation, RCC1		22353
486IPR002293
Amino acid/polyamine transporter I		2256
487IPR004252
Probable transposase, Ptta/En/Spm, plant		2222
488IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2224
489IPR013771
Bifunctional trypsin/alpha-amylase inhibitor helical domain		2236
490IPR015902
Glycoside hydrolase, family 13		2236
491IPR017937
Thioredoxin, conserved site		2224
492IPR020003
ATPase, alpha/beta subunit, nucleotide-binding domain, active site		2222
493IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		2222
494IPR005069
Nucleotide-diphospho-sugar transferase		2223
495IPR001041
2Fe-2S ferredoxin-type domain		2240
496IPR001099
Chalcone/stilbene synthase, N-terminal		2226
497IPR029048
Heat shock protein 70kD, C-terminal domain		2243
498IPR005379
Uncharacterised domain XH		2121
499IPR019954
Ubiquitin conserved site		2149
500IPR012951
Berberine/berberine-like		2121
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera.html b/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera.html new file mode 100644 index 00000000..dd2ab90b --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera.html @@ -0,0 +1,749 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:IGGP_12x, Jun 2011
Database version:86.3
Base Pairs:486,175,922
Golden Path Length:486,265,422
Genebuild by: CRIBI
Genebuild method: Imported from CRIBI V1 Grape Genome
Genebuild started: Nov 2012
Genebuild version: 2012-07-CRIBI
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		29,971
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:29,971
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
33 sequences
+
+ +
+ + + +
SequenceLength (bp)
1_random568933
3_random1220746
4_random76237
5_random421237
7_random1447032
9_random487831
10_random789605
11_random282498
12_random1566225
13_random3268264
16_random740079
17_random829735
18_random5170003
Un43220988
123037639
218779844
319341862
423867706
525021643
621508407
721026613
822385789
923006712
1018140952
1119818926
1222702307
1324396255
1430274277
1520304914
1622053297
1717126926
1829360087
1924021853
+
+
scaffold
+
644 sequences
+
+ +
+ + + +
SequenceLength (bp)
FN594950.113101952
FN594951.19552000
FN594952.14844358
FN594953.1440532
FN594954.1780110
FN594955.11774200
FN594956.11712984
FN594957.12437385
FN594958.14029473
FN594959.14659288
FN594960.1752143
FN594962.1213862
FN594963.1701338
FN594964.12910913
FN594965.1715717
FN594966.1811682
FN594967.12680158
FN594968.12066584
FN594969.1217586
FN594970.11925037
FN594971.11639675
FN594972.12843967
FN594973.11161519
FN594974.11918470
FN594976.1651257
FN594978.1242490
FN594984.198336
FN594985.1241907
FN594986.1263020
FN594991.1144944
FN594992.180994
FN595003.160018
FN595011.138731
FN595014.137006
FN595227.112878483
FN595228.12802053
FN595229.15830166
FN595231.17849088
FN595232.12206237
FN595233.13837240
FN595234.14235575
FN595235.14220673
FN595237.1793319
FN595238.1176784
FN595239.11435681
FN595240.11254285
FN595241.13618370
FN595242.11686736
FN595243.12981817
FN595244.1506955
FN595245.11471607
FN595246.11912363
FN595247.11581850
FN595248.11180538
FN595250.11378641
FN595251.1262544
FN595253.1488362
FN595257.1186110
FN595265.1108164
FN595294.124732
FN595496.13109742
FN595497.13720581
FN595498.1385931
FN595500.12183187
FN595502.12319817
FN595503.11758815
FN595504.17659439
FN595506.14739470
FN595507.11639895
FN595509.12332751
FN595510.11949161
FN595512.11730034
FN595513.15191286
FN595514.12215503
FN595515.11146539
FN595516.1636875
FN595518.11187480
FN595528.1187084
FN595533.1212746
FN595540.155158
FN595549.139180
FN595749.15111369
FN595750.13498497
FN595751.11703147
FN595752.16551432
FN595753.11906469
FN595754.17291438
FN595755.1909381
FN595756.15539103
FN595757.11858083
FN595759.12751913
FN595761.11031042
FN595762.1503721
FN595763.13290913
FN595764.1611545
FN595765.12584205
FN595766.13337837
FN595767.13166202
FN595769.11748875
FN595770.1630796
FN595771.11312920
FN595772.11033657
FN595773.1883960
FN595785.1384407
FN595787.1112709
FN595990.13620423
FN595991.18015839
FN595992.19678648
FN595995.12793448
FN595996.11790842
FN595997.1462794
FN595998.15112644
FN595999.1710388
FN596000.11557079
FN596001.1571376
FN596002.14313178
FN596003.1548849
FN596004.11548057
FN596005.11506749
FN596006.12412620
FN596008.13439364
FN596009.11670891
FN596010.11321583
FN596011.11566225
FN596012.1186189
FN596013.1326739
FN596014.1717240
FN596018.1122672
FN596026.1254686
FN596027.1301635
FN596054.127630
FN596241.12959756
FN596243.11637615
FN596245.18916299
FN596246.1973691
FN596247.16287576
FN596248.15389857
FN596249.13990021
FN596251.14456262
FN596252.12301139
FN596253.1351176
FN596254.11761938
FN596255.1721504
FN596256.11829172
FN596257.11441328
FN596258.12897252
FN596259.1487324
FN596260.12138748
FN596261.11593492
FN596263.11126722
FN596264.1447185
FN596265.1596857
FN596267.1433727
FN596268.1441593
FN596269.1646900
FN596270.1232563
FN596271.1105370
FN596274.1182601
FN596275.1210496
FN596277.1175758
FN596493.1421237
FN596494.111167083
FN596495.1487831
FN596497.1503537
FN596498.1568933
FN596499.13567730
FN596500.11545769
FN596501.1980435
FN596502.19409903
FN596505.13743456
FN596506.13239241
FN596508.13513447
FN596510.13203665
FN596511.11753748
FN596512.1386469
FN596513.1653924
FN596514.11437984
FN596515.11220746
FN596517.1829735
FN596531.1232483
FN596550.120724
FN596633.15859
FN596738.15856704
FN596739.13157216
FN596740.12164761
FN596741.11680211
FN596742.13764787
FN596743.11042043
FN596744.13426264
FN596745.12414522
FN596746.12577670
FN596747.15783157
FN596748.14459287
FN596749.1425691
FN596751.11544587
FN596752.11052295
FN596753.11926089
FN596754.1364040
FN596755.13199904
FN596756.11300385
FN596757.11907455
FN596758.11091482
FN596759.11070034
FN596762.1788917
FN596766.1411915
FN596770.1225645
FN596776.1160132
FN596790.156353
FN596793.131424
FN596802.133822
FN596834.120189
Un:1..100000100000
Un:10000001..10100000100000
Un:1000001..1100000100000
Un:100001..200000100000
Un:10100001..10200000100000
Un:10200001..10300000100000
Un:10300001..10400000100000
Un:10400001..10500000100000
Un:10500001..10600000100000
Un:10600001..10700000100000
Un:10700001..10800000100000
Un:10800001..10900000100000
Un:10900001..11000000100000
Un:11000001..11100000100000
Un:1100001..1200000100000
Un:11100001..11200000100000
Un:11200001..11300000100000
Un:11300001..11400000100000
Un:11400001..11500000100000
Un:11500001..11600000100000
Un:11600001..11700000100000
Un:11700001..11800000100000
Un:11800001..11900000100000
Un:11900001..12000000100000
Un:12000001..12100000100000
Un:1200001..1300000100000
Un:12100001..12200000100000
Un:12200001..12300000100000
Un:12300001..12400000100000
Un:12400001..12500000100000
Un:12500001..12600000100000
Un:12600001..12700000100000
Un:12700001..12800000100000
Un:12800001..12900000100000
Un:12900001..13000000100000
Un:13000001..13100000100000
Un:1300001..1400000100000
Un:13100001..13200000100000
Un:13200001..13300000100000
Un:13300001..13400000100000
Un:13400001..13500000100000
Un:13500001..13600000100000
Un:13600001..13700000100000
Un:13700001..13800000100000
Un:13800001..13900000100000
Un:13900001..14000000100000
Un:14000001..14100000100000
Un:1400001..1500000100000
Un:14100001..14200000100000
Un:14200001..14300000100000
Un:14300001..14400000100000
Un:14400001..14500000100000
Un:14500001..14600000100000
Un:14600001..14700000100000
Un:14700001..14800000100000
Un:14800001..14900000100000
Un:14900001..15000000100000
Un:15000001..15100000100000
Un:1500001..1600000100000
Un:15100001..15200000100000
Un:15200001..15300000100000
Un:15300001..15400000100000
Un:15400001..15500000100000
Un:15500001..15600000100000
Un:15600001..15700000100000
Un:15700001..15800000100000
Un:15800001..15900000100000
Un:15900001..16000000100000
Un:16000001..16100000100000
Un:1600001..1700000100000
Un:16100001..16200000100000
Un:16200001..16300000100000
Un:16300001..16400000100000
Un:16400001..16500000100000
Un:16500001..16600000100000
Un:16600001..16700000100000
Un:16700001..16800000100000
Un:16800001..16900000100000
Un:16900001..17000000100000
Un:17000001..17100000100000
Un:1700001..1800000100000
Un:17100001..17200000100000
Un:17200001..17300000100000
Un:17300001..17400000100000
Un:17400001..17500000100000
Un:17500001..17600000100000
Un:17600001..17700000100000
Un:17700001..17800000100000
Un:17800001..17900000100000
Un:17900001..18000000100000
Un:18000001..18100000100000
Un:1800001..1900000100000
Un:18100001..18200000100000
Un:18200001..18300000100000
Un:18300001..18400000100000
Un:18400001..18500000100000
Un:18500001..18600000100000
Un:18600001..18700000100000
Un:18700001..18800000100000
Un:18800001..18900000100000
Un:18900001..19000000100000
Un:19000001..19100000100000
Un:1900001..2000000100000
Un:19100001..19200000100000
Un:19200001..19300000100000
Un:19300001..19400000100000
Un:19400001..19500000100000
Un:19500001..19600000100000
Un:19600001..19700000100000
Un:19700001..19800000100000
Un:19800001..19900000100000
Un:19900001..20000000100000
Un:20000001..20100000100000
Un:2000001..2100000100000
Un:200001..300000100000
Un:20100001..20200000100000
Un:20200001..20300000100000
Un:20300001..20400000100000
Un:20400001..20500000100000
Un:20500001..20600000100000
Un:20600001..20700000100000
Un:20700001..20800000100000
Un:20800001..20900000100000
Un:20900001..21000000100000
Un:21000001..21100000100000
Un:2100001..2200000100000
Un:21100001..21200000100000
Un:21200001..21300000100000
Un:21300001..21400000100000
Un:21400001..21500000100000
Un:21500001..21600000100000
Un:21600001..21700000100000
Un:21700001..21800000100000
Un:21800001..21900000100000
Un:21900001..22000000100000
Un:22000001..22100000100000
Un:2200001..2300000100000
Un:22100001..22200000100000
Un:22200001..22300000100000
Un:22300001..22400000100000
Un:22400001..22500000100000
Un:22500001..22600000100000
Un:22600001..22700000100000
Un:22700001..22800000100000
Un:22800001..22900000100000
Un:22900001..23000000100000
Un:23000001..23100000100000
Un:2300001..2400000100000
Un:23100001..23200000100000
Un:23200001..23300000100000
Un:23300001..23400000100000
Un:23400001..23500000100000
Un:23500001..23600000100000
Un:23600001..23700000100000
Un:23700001..23800000100000
Un:23800001..23900000100000
Un:23900001..24000000100000
Un:24000001..24100000100000
Un:2400001..2500000100000
Un:24100001..24200000100000
Un:24200001..24300000100000
Un:24300001..24400000100000
Un:24400001..24500000100000
Un:24500001..24600000100000
Un:24600001..24700000100000
Un:24700001..24800000100000
Un:24800001..24900000100000
Un:24900001..25000000100000
Un:25000001..25100000100000
Un:2500001..2600000100000
Un:25100001..25200000100000
Un:25200001..25300000100000
Un:25300001..25400000100000
Un:25400001..25500000100000
Un:25500001..25600000100000
Un:25600001..25700000100000
Un:25700001..25800000100000
Un:25800001..25900000100000
Un:25900001..26000000100000
Un:26000001..26100000100000
Un:2600001..2700000100000
Un:26100001..26200000100000
Un:26200001..26300000100000
Un:26300001..26400000100000
Un:26400001..26500000100000
Un:26500001..26600000100000
Un:26600001..26700000100000
Un:26700001..26800000100000
Un:26800001..26900000100000
Un:26900001..27000000100000
Un:27000001..27100000100000
Un:2700001..2800000100000
Un:27100001..27200000100000
Un:27200001..27300000100000
Un:27300001..27400000100000
Un:27400001..27500000100000
Un:27500001..27600000100000
Un:27600001..27700000100000
Un:27700001..27800000100000
Un:27800001..27900000100000
Un:27900001..28000000100000
Un:28000001..28100000100000
Un:2800001..2900000100000
Un:28100001..28200000100000
Un:28200001..28300000100000
Un:28300001..28400000100000
Un:28400001..28500000100000
Un:28500001..28600000100000
Un:28600001..28700000100000
Un:28700001..28800000100000
Un:28800001..28900000100000
Un:28900001..29000000100000
Un:29000001..29100000100000
Un:2900001..3000000100000
Un:29100001..29200000100000
Un:29200001..29300000100000
Un:29300001..29400000100000
Un:29400001..29500000100000
Un:29500001..29600000100000
Un:29600001..29700000100000
Un:29700001..29800000100000
Un:29800001..29900000100000
Un:29900001..30000000100000
Un:30000001..30100000100000
Un:3000001..3100000100000
Un:300001..400000100000
Un:30100001..30200000100000
Un:30200001..30300000100000
Un:30300001..30400000100000
Un:30400001..30500000100000
Un:30500001..30600000100000
Un:30600001..30700000100000
Un:30700001..30800000100000
Un:30800001..30900000100000
Un:30900001..31000000100000
Un:31000001..31100000100000
Un:3100001..3200000100000
Un:31100001..31200000100000
Un:31200001..31300000100000
Un:31300001..31400000100000
Un:31400001..31500000100000
Un:31500001..31600000100000
Un:31600001..31700000100000
Un:31700001..31800000100000
Un:31800001..31900000100000
Un:31900001..32000000100000
Un:32000001..32100000100000
Un:3200001..3300000100000
Un:32100001..32200000100000
Un:32200001..32300000100000
Un:32300001..32400000100000
Un:32400001..32500000100000
Un:32500001..32600000100000
Un:32600001..32700000100000
Un:32700001..32800000100000
Un:32800001..32900000100000
Un:32900001..33000000100000
Un:33000001..33100000100000
Un:3300001..3400000100000
Un:33100001..33200000100000
Un:33200001..33300000100000
Un:33300001..33400000100000
Un:33400001..33500000100000
Un:33500001..33600000100000
Un:33600001..33700000100000
Un:33700001..33800000100000
Un:33800001..33900000100000
Un:33900001..34000000100000
Un:34000001..34100000100000
Un:3400001..3500000100000
Un:34100001..34200000100000
Un:34200001..34300000100000
Un:34300001..34400000100000
Un:34400001..34500000100000
Un:34500001..34600000100000
Un:34600001..34700000100000
Un:34700001..34800000100000
Un:34800001..34900000100000
Un:34900001..35000000100000
Un:35000001..35100000100000
Un:3500001..3600000100000
Un:35100001..35200000100000
Un:35200001..35300000100000
Un:35300001..35400000100000
Un:35400001..35500000100000
Un:35500001..35600000100000
Un:35600001..35700000100000
Un:35700001..35800000100000
Un:35800001..35900000100000
Un:35900001..36000000100000
Un:36000001..36100000100000
Un:3600001..3700000100000
Un:36100001..36200000100000
Un:36200001..36300000100000
Un:36300001..36400000100000
Un:36400001..36500000100000
Un:36500001..36600000100000
Un:36600001..36700000100000
Un:36700001..36800000100000
Un:36800001..36900000100000
Un:36900001..37000000100000
Un:37000001..37100000100000
Un:3700001..3800000100000
Un:37100001..37200000100000
Un:37200001..37300000100000
Un:37300001..37400000100000
Un:37400001..37500000100000
Un:37500001..37600000100000
Un:37600001..37700000100000
Un:37700001..37800000100000
Un:37800001..37900000100000
Un:37900001..38000000100000
Un:38000001..38100000100000
Un:3800001..3900000100000
Un:38100001..38200000100000
Un:38200001..38300000100000
Un:38300001..38400000100000
Un:38400001..38500000100000
Un:38500001..38600000100000
Un:38600001..38700000100000
Un:38700001..38800000100000
Un:38800001..38900000100000
Un:38900001..39000000100000
Un:39000001..39100000100000
Un:3900001..4000000100000
Un:39100001..39200000100000
Un:39200001..39300000100000
Un:39300001..39400000100000
Un:39400001..39500000100000
Un:39500001..39600000100000
Un:39600001..39700000100000
Un:39700001..39800000100000
Un:39800001..39900000100000
Un:39900001..40000000100000
Un:40000001..40100000100000
Un:4000001..4100000100000
Un:400001..500000100000
Un:40100001..40200000100000
Un:40200001..40300000100000
Un:40300001..40400000100000
Un:40400001..40500000100000
Un:40500001..40600000100000
Un:40600001..40700000100000
Un:40700001..40800000100000
Un:40800001..40900000100000
Un:40900001..41000000100000
Un:41000001..41100000100000
Un:4100001..4200000100000
Un:41100001..41200000100000
Un:41200001..41300000100000
Un:41300001..41400000100000
Un:41400001..41500000100000
Un:41500001..41600000100000
Un:41600001..41700000100000
Un:41700001..41800000100000
Un:41800001..41900000100000
Un:41900001..42000000100000
Un:42000001..42100000100000
Un:4200001..4300000100000
Un:42100001..42200000100000
Un:42200001..42300000100000
Un:42300001..42400000100000
Un:42400001..42500000100000
Un:42500001..42600000100000
Un:42600001..42700000100000
Un:42700001..42800000100000
Un:42800001..42900000100000
Un:42900001..43000000100000
Un:43000001..43100000100000
Un:4300001..4400000100000
Un:43100001..43200000100000
Un:43200001..4322098820988
Un:4400001..4500000100000
Un:4500001..4600000100000
Un:4600001..4700000100000
Un:4700001..4800000100000
Un:4800001..4900000100000
Un:4900001..5000000100000
Un:5000001..5100000100000
Un:500001..600000100000
Un:5100001..5200000100000
Un:5200001..5300000100000
Un:5300001..5400000100000
Un:5400001..5500000100000
Un:5500001..5600000100000
Un:5600001..5700000100000
Un:5700001..5800000100000
Un:5800001..5900000100000
Un:5900001..6000000100000
Un:6000001..6100000100000
Un:600001..700000100000
Un:6100001..6200000100000
Un:6200001..6300000100000
Un:6300001..6400000100000
Un:6400001..6500000100000
Un:6500001..6600000100000
Un:6600001..6700000100000
Un:6700001..6800000100000
Un:6800001..6900000100000
Un:6900001..7000000100000
Un:7000001..7100000100000
Un:700001..800000100000
Un:7100001..7200000100000
Un:7200001..7300000100000
Un:7300001..7400000100000
Un:7400001..7500000100000
Un:7500001..7600000100000
Un:7600001..7700000100000
Un:7700001..7800000100000
Un:7800001..7900000100000
Un:7900001..8000000100000
Un:8000001..8100000100000
Un:800001..900000100000
Un:8100001..8200000100000
Un:8200001..8300000100000
Un:8300001..8400000100000
Un:8400001..8500000100000
Un:8500001..8600000100000
Un:8600001..8700000100000
Un:8700001..8800000100000
Un:8800001..8900000100000
Un:8900001..9000000100000
Un:9000001..9100000100000
Un:900001..1000000100000
Un:9100001..9200000100000
Un:9200001..9300000100000
Un:9300001..9400000100000
Un:9400001..9500000100000
Un:9500001..9600000100000
Un:9600001..9700000100000
Un:9700001..9800000100000
Un:9800001..9900000100000
Un:9900001..10000000100000
+
+
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):457,245
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera_IPtop500.html new file mode 100644 index 00000000..eefc055e --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Vitis_vinifera_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		14111531
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		13613466
3IPR000719
Protein kinase, catalytic domain		13023196
4IPR032675
Leucine-rich repeat domain, L domain-like		10373597
5IPR008271
Serine/threonine-protein kinase, active site		963985
6IPR017441
Protein kinase, ATP binding site		789800
7IPR013320
Concanavalin A-like lectin/glucanase, subgroup		745919
8IPR011990
Tetratricopeptide-like helical		6482163
9IPR002885
Pentatricopeptide repeat		56713367
10IPR001611
Leucine-rich repeat		5513505
11IPR013083
Zinc finger, RING/FYVE/PHD-type		519560
12IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		493649
13IPR016040
NAD(P)-binding domain		4891084
14IPR001128
Cytochrome P450		3932346
15IPR009057
Homeodomain-like		392924
16IPR029058
Alpha/Beta hydrolase fold		382921
17IPR002182
NB-ARC		356375
18IPR016024
Armadillo-type fold		353726
19IPR003591
Leucine-rich repeat, typical subtype		3482406
20IPR002401
Cytochrome P450, E-class, group I		3352169
21IPR001841
Zinc finger, RING-type		323755
22IPR003593
AAA+ ATPase domain		317422
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like		310786
24IPR011989
Armadillo-like helical		294555
25IPR017972
Cytochrome P450, conserved site		290301
26IPR015943
WD40/YVTN repeat-like-containing domain		287454
27IPR017986
WD40-repeat-containing domain		276671
28IPR001005
SANT/Myb domain		271755
29IPR017853
Glycoside hydrolase, superfamily		270315
30IPR012336
Thioredoxin-like fold		266612
31IPR012677
Nucleotide-binding, alpha-beta plait		258764
32IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		253641
33IPR001680
WD40 repeat		2492710
34IPR013210
Leucine-rich repeat-containing N-terminal, type 2		233244
35IPR020683
Ankyrin repeat-containing domain		2251076
36IPR000504
RNA recognition motif domain		2241012
37IPR013781
Glycoside hydrolase, catalytic domain		221253
38IPR017930
Myb domain		216354
39IPR020846
Major facilitator superfamily domain		210438
40IPR001810
F-box domain, cyclin-like		193473
41IPR011991
Winged helix-turn-helix DNA-binding domain		192352
42IPR011992
EF-hand-like domain		185453
43IPR002110
Ankyrin repeat		1801326
44IPR032867
DYW domain		173173
45IPR003439
ABC transporter-like		168470
46IPR005123
Oxoglutarate/iron-dependent dioxygenase		167323
47IPR023214
HAD-like domain		166452
48IPR027443
Isopenicillin N synthase-like		165174
49IPR002048
Calcium-binding EF-hand		1611009
50IPR008972
Cupredoxin		161697
51IPR029044
Nucleotide-diphospho-sugar transferases		158386
52IPR019775
WD40 repeat, conserved site		154253
53IPR018247
EF-Hand 1, calcium-binding site		151344
54IPR016177
DNA-binding, integrase-type		146165
55IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		145590
56IPR011050
Pectin lyase fold/virulence factor		143153
57IPR012334
Pectin lyase fold		143157
58IPR014710
RmlC-like jelly roll fold		142165
59IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		139620
60IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		139270
61IPR026992
Non-haem dioxygenase N-terminal domain		138140
62IPR026961
PGG domain		137140
63IPR001471
AP2/ERF domain		135849
64IPR014001
Helicase, superfamily 1/2, ATP-binding domain		133254
65IPR001650
Helicase, C-terminal		128378
66IPR012340
Nucleic acid-binding, OB-fold		124170
67IPR015424
Pyridoxal phosphate-dependent transferase		121132
68IPR003959
ATPase, AAA-type, core		121138
69IPR019734
Tetratricopeptide repeat		120830
70IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		120143
71IPR013026
Tetratricopeptide repeat-containing domain		120150
72IPR001480
Bulb-type lectin domain		119607
73IPR011051
RmlC-like cupin domain		116126
74IPR008949
Terpenoid synthase		114238
75IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		114118
76IPR007087
Zinc finger, C2H2		114347
77IPR010987
Glutathione S-transferase, C-terminal-like		113317
78IPR016039
Thiolase-like		105405
79IPR013785
Aldolase-type TIM barrel		104125
80IPR004045
Glutathione S-transferase, N-terminal		104206
81IPR002347
Glucose/ribitol dehydrogenase		103937
82IPR005225
Small GTP-binding protein domain		102104
83IPR000008
C2 calcium-dependent membrane targeting		101712
84IPR015500
Peptidase S8, subtilisin-related		101352
85IPR020472
G-protein beta WD-40 repeat		100300
86IPR013830
SGNH hydrolase-type esterase domain		100289
87IPR003609
Apple-like		99255
88IPR000209
Peptidase S8/S53 domain		98539
89IPR001623
DnaJ domain		97666
90IPR011706
Multicopper oxidase, type 2		9798
91IPR010255
Haem peroxidase		96100
92IPR001117
Multicopper oxidase, type 1		9597
93IPR000858
S-locus glycoprotein		9498
94IPR005630
Terpene synthase, metal-binding domain		9498
95IPR017871
ABC transporter, conserved site		94120
96IPR029071
Ubiquitin-related domain		94134
97IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		93104
98IPR002085
Alcohol dehydrogenase superfamily, zinc-type		92110
99IPR023213
Chloramphenicol acetyltransferase-like domain		91157
100IPR002016
Haem peroxidase, plant/fungal/bacterial		91607
101IPR011032
GroES-like		90203
102IPR000073
Alpha/beta hydrolase fold-1		90202
103IPR011011
Zinc finger, FYVE/PHD-type		89104
104IPR006045
Cupin 1		88202
105IPR011707
Multicopper oxidase, type 3		8890
106IPR001087
Lipase, GDSL		8791
107IPR001932
Protein phosphatase 2C (PP2C)-like		87477
108IPR012337
Ribonuclease H-like domain		84156
109IPR011545
DNA/RNA helicase, DEAD/DEAH box type, N-terminal		8485
110IPR001356
Homeobox domain		83218
111IPR003480
Transferase		8286
112IPR019793
Peroxidases heam-ligand binding site		8184
113IPR001906
Terpene synthase, N-terminal domain		81166
114IPR000823
Plant peroxidase		81673
115IPR000225
Armadillo		81650
116IPR009072
Histone-fold		80158
117IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		79363
118IPR023393
START-like domain		7779
119IPR015655
Protein phosphatase 2C		77122
120IPR003676
Auxin responsive SAUR protein		7780
121IPR021109
Aspartic peptidase		76218
122IPR023828
Peptidase S8, subtilisin, Ser-active site		7582
123IPR000571
Zinc finger, CCCH-type		75599
124IPR001806
Small GTPase superfamily		7577
125IPR025287
Wall-associated receptor kinase galacturonan-binding domain		7476
126IPR013525
ABC-2 type transporter		74104
127IPR008978
HSP20-like chaperone		74147
128IPR003441
No apical meristem (NAM) protein		74222
129IPR013766
Thioredoxin domain		74134
130IPR011333
BTB/POZ fold		7480
131IPR005150
Cellulose synthase		73118
132IPR010259
Proteinase inhibitor I9		72110
133IPR002355
Multicopper oxidase, copper-binding site		7273
134IPR027640
Kinesin-like protein		72177
135IPR001461
Peptidase A1		72182
136IPR006447
Myb domain, plants		7171
137IPR023395
Mitochondrial carrier domain		71151
138IPR003960
ATPase, AAA-type, conserved site		7074
139IPR017907
Zinc finger, RING-type, conserved site		7070
140IPR015880
Zinc finger, C2H2-like		70193
141IPR005828
General substrate transporter		6977
142IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		69162
143IPR000270
Phox/Bem1p		69108
144IPR001752
Kinesin, motor domain		69476
145IPR013149
Alcohol dehydrogenase, C-terminal		6869
146IPR001509
NAD-dependent epimerase/dehydratase		6869
147IPR013057
Amino acid transporter, transmembrane		6871
148IPR002528
Multi antimicrobial extrusion protein		68186
149IPR033121
Peptidase family A1 domain		6876
150IPR029052
Metallo-dependent phosphatase-like		68165
151IPR001965
Zinc finger, PHD-type		68101
152IPR001929
Germin		67200
153IPR001878
Zinc finger, CCHC-type		67460
154IPR000109
Proton-dependent oligopeptide transporter family		66138
155IPR019794
Peroxidase, active site		6668
156IPR011993
Pleckstrin homology-like domain		66126
157IPR006121
Heavy metal-associated domain, HMA		65205
158IPR033138
Multicopper oxidases, conserved site		6465
159IPR018108
Mitochondrial substrate/solute carrier		64352
160IPR004046
Glutathione S-transferase, C-terminal		6465
161IPR002068
Alpha crystallin/Hsp20 domain		63121
162IPR023299
P-type ATPase, cytoplasmic domain N		62126
163IPR008250
P-type ATPase, A domain		61129
164IPR002100
Transcription factor, MADS-box		61456
165IPR000626
Ubiquitin domain		60254
166IPR032799
Xylanase inhibitor, C-terminal		6061
167IPR011527
ABC transporter, transmembrane domain, type 1		60314
168IPR019780
Germin, manganese binding site		6060
169IPR000743
Glycoside hydrolase, family 28		60100
170IPR004843
Metallophosphoesterase domain		5961
171IPR001563
Peptidase S10, serine carboxypeptidase		59345
172IPR000210
BTB/POZ domain		59152
173IPR019787
Zinc finger, PHD-finger		59107
174IPR020568
Ribosomal protein S5 domain 2-type fold		5972
175IPR003657
DNA-binding WRKY		59352
176IPR001757
Cation-transporting P-type ATPase		58240
177IPR003613
U box domain		58169
178IPR009009
Barwin-related endoglucanase		57157
179IPR013154
Alcohol dehydrogenase GroES-like		5760
180IPR031107
Small heat shock protein HSP20		5657
181IPR000070
Pectinesterase, catalytic		5659
182IPR017761
Laccase		5656
183IPR013763
Cyclin-like		55247
184IPR020843
Polyketide synthase, enoylreductase		5555
185IPR011042
Six-bladed beta-propeller, TolB-like		5571
186IPR019786
Zinc finger, PHD-type, conserved site		5463
187IPR032861
Xylanase inhibitor, N-terminal		5455
188IPR013094
Alpha/beta hydrolase fold-3		5454
189IPR024788
Malectin-like carbohydrate-binding domain		5457
190IPR004827
Basic-leucine zipper domain		54199
191IPR016181
Acyl-CoA N-acyltransferase		53116
192IPR024171
S-receptor-like serine/threonine-protein kinase		5353
193IPR002902
Gnk2-homologous domain		53201
194IPR016135
Ubiquitin-conjugating enzyme/RWD-like		53109
195IPR005829
Sugar transporter, conserved site		5380
196IPR029045
ClpP/crotonase-like domain		53129
197IPR006501
Pectinesterase inhibitor		53258
198IPR015300
DNA-binding pseudobarrel domain		53128
199IPR008266
Tyrosine-protein kinase, active site		5254
200IPR018303
P-type ATPase, phosphorylation site		5256
201IPR030184
WAT1-related protein		5252
202IPR003663
Sugar/inositol transporter		52263
203IPR023210
NADP-dependent oxidoreductase domain		52156
204IPR001099
Chalcone/stilbene synthase, N-terminal		5253
205IPR003340
B3 DNA binding domain		51178
206IPR003594
Histidine kinase-like ATPase, ATP-binding domain		51175
207IPR000620
Drug/metabolite transporter		5189
208IPR018253
DnaJ domain, conserved site		5050
209IPR000048
IQ motif, EF-hand binding site		50337
210IPR001395
Aldo/keto reductase		5070
211IPR014014
RNA helicase, DEAD-box type, Q motif		4949
212IPR023298
P-type ATPase, transmembrane domain		4998
213IPR016461
Caffeate O-methyltransferase (COMT) family		4884
214IPR029061
Thiamin diphosphate-binding fold		48143
215IPR001077
O-methyltransferase, family 2		4850
216IPR005202
Transcription factor GRAS		4897
217IPR012328
Chalcone/stilbene synthase, C-terminal		4850
218IPR000490
Glycoside hydrolase, family 17		4875
219IPR003137
Protease-associated domain, PA		4750
220IPR029055
Nucleophile aminohydrolases, N-terminal		4792
221IPR020904
Short-chain dehydrogenase/reductase, conserved site		4747
222IPR004839
Aminotransferase, class I/classII		4749
223IPR008979
Galactose-binding domain-like		47118
224IPR004883
Lateral organ boundaries, LOB		4794
225IPR002921
Lipase, class 3		4648
226IPR000608
Ubiquitin-conjugating enzyme, E2		4691
227IPR026057
PC-Esterase		4647
228IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		4679
229IPR008928
Six-hairpin glycosidase-like		4657
230IPR033131
Pectinesterase, Asp active site		4546
231IPR003653
Peptidase C48, SUMO/Sentrin/Ubl1		4574
232IPR011006
CheY-like superfamily		4552
233IPR001214
SET domain		45119
234IPR016166
FAD-binding, type 2		4485
235IPR003245
Plastocyanin-like		44129
236IPR000742
Epidermal growth factor-like domain		44104
237IPR001220
Legume lectin domain		4445
238IPR014756
Immunoglobulin E-set		4446
239IPR001789
Signal transduction response regulator, receiver domain		44132
240IPR019821
Kinesin, motor region, conserved site		4343
241IPR029962
Trichome birefringence-like family		4352
242IPR009000
Translation elongation/initiation factor/Ribosomal, beta-barrel		4346
243IPR004088
K Homology domain, type 1		43315
244IPR002912
ACT domain		4392
245IPR017877
Myb-like domain		4352
246IPR000873
AMP-dependent synthetase/ligase		4244
247IPR031052
FHY3/FAR1 family		4247
248IPR000182
GNAT domain		4177
249IPR021820
S-locus receptor kinase, C-terminal		4141
250IPR006652
Kelch repeat type 1		41153
251IPR007112
Expansin/pollen allergen, DPBB domain		4171
252IPR021720
Malectin		4144
253IPR009060
UBA-like		4046
254IPR000330
SNF2-related		4041
255IPR002328
Alcohol dehydrogenase, zinc-type, conserved site		4042
256IPR006553
Leucine-rich repeat, cysteine-containing subtype		40309
257IPR025846
PMR5 N-terminal domain		4041
258IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		4041
259IPR000757
Glycoside hydrolase, family 16		4078
260IPR015916
Galactose oxidase, beta-propeller		3943
261IPR018088
Chalcone/stilbene synthase, active site		3939
262IPR002035
von Willebrand factor, type A		39113
263IPR002495
Glycosyl transferase, family 8		3940
264IPR015915
Kelch-type beta propeller		3947
265IPR033389
AUX/IAA domain		3842
266IPR001360
Glycoside hydrolase, family 1		38220
267IPR004263
Exostosin-like		3839
268IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site		3838
269IPR004864
Late embryogenesis abundant protein, LEA-14		3839
270IPR018202
Peptidase S10, serine carboxypeptidase, active site		3840
271IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		3840
272IPR004853
Domain of unknown function DUF250		3737
273IPR010920
Like-Sm (LSM) domain		3737
274IPR005299
SAM dependent carboxyl methyltransferase		3740
275IPR011016
Zinc finger, RING-CH-type		3785
276IPR002067
Mitochondrial carrier protein		37179
277IPR006671
Cyclin, N-terminal		3758
278IPR004330
FAR1 DNA binding domain		3738
279IPR008974
TRAF-like		3788
280IPR023271
Aquaporin-like		3671
281IPR011012
Longin-like domain		3636
282IPR000425
Major intrinsic protein		36270
283IPR006094
FAD linked oxidase, N-terminal		3638
284IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3637
285IPR011141
Polyketide synthase, type III		3636
286IPR012967
Plant methyltransferase dimerisation		3638
287IPR015797
NUDIX hydrolase domain-like		3672
288IPR006626
Parallel beta-helix repeat		35167
289IPR000217
Tubulin		35200
290IPR011701
Major facilitator superfamily		3535
291IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		3583
292IPR013783
Immunoglobulin-like fold		3541
293IPR012946
X8 domain		3570
294IPR004014
Cation-transporting P-type ATPase, N-terminal		3571
295IPR001849
Pleckstrin homology domain		3567
296IPR002109
Glutaredoxin		3570
297IPR004141
Strictosidine synthase		3434
298IPR006016
UspA		3435
299IPR013216
Methyltransferase type 11		3435
300IPR008280
Tubulin/FtsZ, C-terminal		3434
301IPR033124
Serine carboxypeptidases, histidine active site		3435
302IPR017970
Homeobox, conserved site		3434
303IPR020845
AMP-binding, conserved site		3434
304IPR019378
GDP-fucose protein O-fucosyltransferase		3435
305IPR000916
Bet v I domain		3460
306IPR004087
K Homology domain		3476
307IPR002487
Transcription factor, K-box		3467
308IPR001251
CRAL-TRIO domain		33161
309IPR005135
Endonuclease/exonuclease/phosphatase		33117
310IPR004265
Plant disease resistance response protein		3333
311IPR003690
Mitochodrial transcription termination factor-related		33307
312IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2		3333
313IPR001320
Ionotropic glutamate receptor		3364
314IPR025875
Leucine rich repeat 4		3333
315IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		3338
316IPR020946
Flavin monooxygenase-like		3345
317IPR016161
Aldehyde/histidinol dehydrogenase		3334
318IPR012341
Six-hairpin glycosidase		3334
319IPR008942
ENTH/VHS		3264
320IPR032710
NTF2-like domain		3256
321IPR011047
Quinonprotein alcohol dehydrogenase-like-superfamily		3249
322IPR005746
Thioredoxin		3241
323IPR016159
Cullin repeat-like-containing domain		3247
324IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain		3232
325IPR000727
Target SNARE coiled-coil domain		3182
326IPR029021
Protein-tyrosine phosphatase-like		3176
327IPR013581
Plant PDR ABC transporter associated		3131
328IPR001296
Glycosyl transferase, family 1		3131
329IPR001969
Peptidase aspartic, active site		3144
330IPR003008
Tubulin/FtsZ, GTPase domain		31120
331IPR007125
Histone core		3131
332IPR018502
Annexin repeat		31223
333IPR000644
Cystathionine beta-synthase, core		31166
334IPR013126
Heat shock protein 70 family		31183
335IPR002130
Cyclophilin-like peptidyl-prolyl cis-trans isomerase domain		30165
336IPR029000
Cyclophilin-like domain		3062
337IPR000315
Zinc finger, B-box		30113
338IPR026892
Glycoside hydrolase family 3		3038
339IPR011013
Galactose mutarotase-like domain		3032
340IPR023313
Ubiquitin-conjugating enzyme, active site		3030
341IPR029481
ABC-transporter extracellular N-terminal domain		3030
342IPR007527
Zinc finger, SWIM-type		3057
343IPR007117
Expansin, cellulose-binding-like domain		30120
344IPR001638
Extracellular solute-binding protein, family 3		3033
345IPR006073
GTP binding domain		3083
346IPR015947
PUA-like domain		3044
347IPR018119
Strictosidine synthase, conserved region		3032
348IPR025110
Domain of unknown function DUF4009		2929
349IPR006153
Cation/H+ exchanger		2929
350IPR007493
Protein of unknown function DUF538		2986
351IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2929
352IPR007118
Expansin/Lol pI		29166
353IPR013128
Peptidase C1A, papain		2931
354IPR008991
Translation protein SH3-like domain		2930
355IPR006068
Cation-transporting P-type ATPase, C-terminal		2931
356IPR003101
Coactivator CBP, KIX domain		2944
357IPR004182
GRAM domain		2957
358IPR016455
Xyloglucan endotransglucosylase/hydrolase		2929
359IPR001938
Thaumatin		29338
360IPR000668
Peptidase C1A, papain C-terminal		29125
361IPR028082
Periplasmic binding protein-like I		2948
362IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		2943
363IPR001223
Glycoside hydrolase, family 18, catalytic domain		2931
364IPR002641
Patatin/Phospholipase A2-related		2931
365IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2973
366IPR016162
Aldehyde dehydrogenase, N-terminal		2937
367IPR015590
Aldehyde dehydrogenase domain		2932
368IPR010402
CCT domain		2856
369IPR006689
Small GTPase superfamily, ARF/SAR type		28105
370IPR021133
HEAT, type 2		2864
371IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site		2844
372IPR009078
Ferritin/ribonucleotide reductase-like		2828
373IPR022742
Alpha/beta hydrolase, N-terminal		2828
374IPR018289
MULE transposase domain		2828
375IPR003958
Transcription factor CBF/NF-Y/archaeal histone		2828
376IPR016167
FAD-binding, type 2, subdomain 1		2829
377IPR001944
Glycoside hydrolase, family 35		28178
378IPR000086
NUDIX hydrolase domain		2857
379IPR016163
Aldehyde dehydrogenase, C-terminal		2829
380IPR006702
Uncharacterised protein family UPF0497, trans-membrane plant		2828
381IPR013601
FAE1/Type III polyketide synthase-like protein		2727
382IPR018490
Cyclic nucleotide-binding-like		2729
383IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2750
384IPR025659
Tubby C-terminal-like domain		2731
385IPR001547
Glycoside hydrolase, family 5		2727
386IPR002659
Glycosyl transferase, family 31		2748
387IPR020471
Aldo/keto reductase subgroup		27127
388IPR012675
Beta-grasp domain		2727
389IPR027356
NPH3 domain		2753
390IPR029056
Ribokinase-like		2757
391IPR004813
Oligopeptide transporter OPT superfamily		2755
392IPR029069
HotDog domain		2777
393IPR001701
Glycoside hydrolase, family 9		2727
394IPR001828
Extracellular ligand-binding receptor		2732
395IPR014720
Double-stranded RNA-binding domain		27108
396IPR032697
Squalene cyclase, N-terminal		2727
397IPR003855
K+ potassium transporter		2745
398IPR025660
Cysteine peptidase, histidine active site		2727
399IPR001764
Glycoside hydrolase, family 3, N-terminal		27126
400IPR017884
SANT domain		2627
401IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2626
402IPR006564
Zinc finger, PMZ-type		2626
403IPR000795
Elongation factor, GTP-binding domain		26136
404IPR004367
Cyclin, C-terminal domain		2649
405IPR003406
Glycosyl transferase, family 14		2627
406IPR008263
Glycoside hydrolase, family 16, active site		2626
407IPR027409
GroEL-like apical domain		2651
408IPR005821
Ion transport domain		2627
409IPR008927
6-phosphogluconate dehydrogenase, C-terminal-like		2629
410IPR000169
Cysteine peptidase, cysteine active site		2626
411IPR000595
Cyclic nucleotide-binding domain		2677
412IPR011043
Galactose oxidase/kelch, beta-propeller		2628
413IPR029047
Heat shock protein 70kD, peptide-binding domain		2656
414IPR017927
Ferredoxin reductase-type FAD-binding domain		2525
415IPR025322
Protein of unknown function DUF4228		2525
416IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		2580
417IPR002772
Glycoside hydrolase family 3 C-terminal domain		2576
418IPR025753
AAA-type ATPase, N-terminal domain		2525
419IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2550
420IPR002423
Chaperonin Cpn60/TCP-1		2527
421IPR011074
CRAL/TRIO, N-terminal domain		2571
422IPR010989
t-SNARE		2528
423IPR000408
Regulator of chromosome condensation, RCC1		25413
424IPR015813
Pyruvate/Phosphoenolpyruvate kinase		2575
425IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site		2525
426IPR017937
Thioredoxin, conserved site		2529
427IPR003851
Zinc finger, Dof-type		25100
428IPR003311
AUX/IAA protein		2533
429IPR006439
HAD-superfamily hydrolase, subfamily IA, variant 1		2564
430IPR032696
Squalene cyclase, C-terminal		2526
431IPR001487
Bromodomain		25176
432IPR008948
L-Aspartase-like		2526
433IPR006594
LisH dimerisation motif		2450
434IPR000782
FAS1 domain		24146
435IPR001305
Heat shock protein DnaJ, cysteine-rich domain		2457
436IPR001163
Ribonucleoprotein LSM domain		2446
437IPR001279
Beta-lactamase-like		2486
438IPR018170
Aldo/keto reductase, conserved site		2456
439IPR000639
Epoxide hydrolase-like		24112
440IPR022796
Chlorophyll A-B binding protein		2424
441IPR014722
Ribosomal protein L2 domain 2		2424
442IPR033443
Pentacotripeptide-repeat region of PROPR		2425
443IPR002937
Amine oxidase		2424
444IPR023329
Chlorophyll a/b binding protein domain		2425
445IPR017938
Riboflavin synthase-like beta-barrel		2325
446IPR001179
Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain		2362
447IPR003347
JmjC domain		2360
448IPR013201
Proteinase inhibitor I29, cathepsin propeptide		2346
449IPR022812
Dynamin superfamily		23117
450IPR029039
Flavoprotein-like		2344
451IPR022357
Major intrinsic protein, conserved site		2323
452IPR029062
Class I glutamine amidotransferase-like		2358
453IPR018456
PTR2 family proton/oligopeptide symporter, conserved site		2328
454IPR003604
Zinc finger, U1-type		2349
455IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		2332
456IPR013780
Glycosyl hydrolase, family 13, all-beta		2323
457IPR004158
Protein of unknown function DUF247, plant		2323
458IPR004314
Domain of unknown function DUF239		2326
459IPR025315
Domain of unknown function DUF4220		2328
460IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site		2327
461IPR013328
Dehydrogenase, multihelical		2225
462IPR006408
Calcium-transporting P-type ATPase, subfamily IIB		2225
463IPR023346
Lysozyme-like domain		2225
464IPR033275
E3 ubiquitin-protein ligase MARCH-like		2228
465IPR001025
Bromo adjacent homology (BAH) domain		2266
466IPR031330
Glycoside hydrolase 35, catalytic domain		2222
467IPR004776
Auxin efflux carrier		2224
468IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily		2248
469IPR029006
ADF-H/Gelsolin-like domain		2239
470IPR025661
Cysteine peptidase, asparagine active site		2222
471IPR024083
Fumarase/histidase, N-terminal		2222
472IPR005175
Domain of unknown function DUF296		2244
473IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		22178
474IPR024949
Bet v I type allergen		22137
475IPR017949
Thaumatin, conserved site		2121
476IPR004041
NAF domain		2121
477IPR001024
Lipoxygenase, LH2		2184
478IPR003954
RNA recognition motif domain, eukaryote		2141
479IPR018451
NAF/FISL domain		2121
480IPR013088
Zinc finger, NHR/GATA-type		2122
481IPR008422
Homeobox KN domain		2121
482IPR018392
Peptidoglycan-binding lysin domain		2187
483IPR004320
Protein of unknown function DUF241, plant		2121
484IPR007658
Protein of unknown function DUF594		2121
485IPR025886
Phloem protein 2-like		2121
486IPR031112
AP2-like ethylene-responsive transcription factor		2122
487IPR002293
Amino acid/polyamine transporter I		2169
488IPR006694
Fatty acid hydroxylase		2122
489IPR008030
NmrA-like		2121
490IPR002963
Expansin		21180
491IPR008480
Protein of unknown function DUF761, plant		2121
492IPR003616
Post-SET domain		2128
493IPR032846
Protein accelerated cell death 6		2127
494IPR010658
Nodulin-like		2122
495IPR002913
START domain		2159
496IPR029064
50S ribosomal protein L30e-like		2143
497IPR003100
Argonaute/Dicer protein, PAZ		2074
498IPR004873
BURP domain		2058
499IPR006593
Cytochrome b561/ferric reductase transmembrane		2056
500IPR000726
Glycoside hydrolase, family 19, catalytic		2066
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html new file mode 100644 index 00000000..abeed339 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html @@ -0,0 +1,74 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Zm-B73-REFERENCE-GRAMENE-4.0
Database version:86.7
Base Pairs:2,104,350,183
Golden Path Length:2,135,083,061
Genebuild by: CSHL
Genebuild method: MAKER-P
Genebuild started: Dec 2015
Genebuild released: Mar 2016
Genebuild last updated/patched: Mar 2016
Genebuild version: Zm0001d.1
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,498
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:139,122
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
1307041717
2244442276
3235667834
4246994605
5223902240
6174033170
7182381542
8181122637
9159769782
10150982314
Pt140384
Mt569630
+
+
contig3132 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):50,114,708
diff --git a/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.auto b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.auto new file mode 100644 index 00000000..1ccb0da6 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.auto @@ -0,0 +1,349 @@ + +

Summary

+ + + + + + + + + + + + + + + + + + + + + +
Assembly:AGPv4, Dec 2015
Database version:85.7
Base Pairs:2,103,640,169
Golden Path Length:2,134,373,047
Data source:
Genebuild by: CSHL
Genebuild method: MAKER by Campbell
Genebuild started: Dec 2015
Genebuild released: Dec 2015
Genebuild last updated/patched: Dec 2015
Genebuild version: CampbellMaker2015Dec
+

Gene counts

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		49,203
Non coding genes:58,905
    Short non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

:		2,290
    Long non coding genes

Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.

:		2,561
    :54,054
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:166,705
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
10 sequences
+
+ +
+ + + +
SequenceLength (bp)
1307,041,717
2244,442,276
3235,667,834
4246,994,605
5223,902,240
6174,033,170
7182,381,542
8181,122,637
9159,769,782
10150,982,314
+
+
contig
+
255 sequences
+
+ +
+ + + +
SequenceLength (bp)
B73V4_ctg150,531
B73V4_ctg260,109
B73V4_ctg359,657
B73V4_ctg466,261
B73V4_ctg583,265
B73V4_ctg6255,484
B73V4_ctg771,433
B73V4_ctg864,470
B73V4_ctg9110,418
B73V4_ctg10992,858
B73V4_ctg11100,537
B73V4_ctg1234,930
B73V4_ctg1370,946
B73V4_ctg1484,781
B73V4_ctg1555,297
B73V4_ctg1694,873
B73V4_ctg1770,750
B73V4_ctg1870,926
B73V4_ctg1976,840
B73V4_ctg2089,036
B73V4_ctg2165,749
B73V4_ctg2224,080
B73V4_ctg2377,423
B73V4_ctg2470,597
B73V4_ctg2541,524
B73V4_ctg26215,635
B73V4_ctg2711,339
B73V4_ctg2865,819
B73V4_ctg2966,393
B73V4_ctg30110,255
B73V4_ctg31846,561
B73V4_ctg3254,684
B73V4_ctg33108,212
B73V4_ctg3439,815
B73V4_ctg3574,491
B73V4_ctg3670,486
B73V4_ctg3748,545
B73V4_ctg3891,381
B73V4_ctg3929,460
B73V4_ctg4084,148
B73V4_ctg4166,656
B73V4_ctg4267,687
B73V4_ctg4345,711
B73V4_ctg44101,180
B73V4_ctg4557,348
B73V4_ctg4665,659
B73V4_ctg4733,120
B73V4_ctg4872,581
B73V4_ctg49100,579
B73V4_ctg50381,258
B73V4_ctg5183,120
B73V4_ctg52756,422
B73V4_ctg53458,256
B73V4_ctg5482,446
B73V4_ctg56695,048
B73V4_ctg5762,662
B73V4_ctg5865,407
B73V4_ctg5953,907
B73V4_ctg60117,437
B73V4_ctg6176,354
B73V4_ctg6292,234
B73V4_ctg6363,530
B73V4_ctg6451,910
B73V4_ctg65666,287
B73V4_ctg6669,959
B73V4_ctg6760,926
B73V4_ctg6860,205
B73V4_ctg6965,268
B73V4_ctg7054,868
B73V4_ctg7177,242
B73V4_ctg72342,161
B73V4_ctg7383,778
B73V4_ctg7481,536
B73V4_ctg75516,616
B73V4_ctg765,568
B73V4_ctg7787,707
B73V4_ctg7893,364
B73V4_ctg7973,283
B73V4_ctg8065,470
B73V4_ctg8180,451
B73V4_ctg8283,476
B73V4_ctg8367,579
B73V4_ctg8498,601
B73V4_ctg85109,991
B73V4_ctg8647,381
B73V4_ctg8757,632
B73V4_ctg8858,721
B73V4_ctg8982,793
B73V4_ctg9052,427
B73V4_ctg91795,190
B73V4_ctg9294,431
B73V4_ctg9358,809
B73V4_ctg9455,397
B73V4_ctg9576,262
B73V4_ctg9644,176
B73V4_ctg9790,109
B73V4_ctg98103,641
B73V4_ctg9936,676
B73V4_ctg10087,733
B73V4_ctg10176,596
B73V4_ctg102101,603
B73V4_ctg10383,681
B73V4_ctg10485,134
B73V4_ctg10561,773
B73V4_ctg10657,130
B73V4_ctg10783,503
B73V4_ctg10857,822
B73V4_ctg109134,067
B73V4_ctg11057,973
B73V4_ctg111107,933
B73V4_ctg112139,473
B73V4_ctg11362,853
B73V4_ctg11467,958
B73V4_ctg11571,809
B73V4_ctg1169,476
B73V4_ctg11779,679
B73V4_ctg11862,538
B73V4_ctg11943,926
B73V4_ctg12055,817
B73V4_ctg12163,567
B73V4_ctg12290,796
B73V4_ctg12395,420
B73V4_ctg12444,508
B73V4_ctg12579,882
B73V4_ctg1269,160
B73V4_ctg12746,935
B73V4_ctg12886,301
B73V4_ctg129254,428
B73V4_ctg13073,561
B73V4_ctg13140,576
B73V4_ctg13283,845
B73V4_ctg13383,688
B73V4_ctg13486,441
B73V4_ctg13557,064
B73V4_ctg13660,070
B73V4_ctg13778,370
B73V4_ctg13840,594
B73V4_ctg13956,161
B73V4_ctg140344,981
B73V4_ctg14163,556
B73V4_ctg142739,442
B73V4_ctg14351,967
B73V4_ctg14453,538
B73V4_ctg14566,893
B73V4_ctg14669,976
B73V4_ctg14770,601
B73V4_ctg14873,006
B73V4_ctg14958,809
B73V4_ctg1501,738,914
B73V4_ctg15163,917
B73V4_ctg15269,060
B73V4_ctg15365,477
B73V4_ctg15458,645
B73V4_ctg155128,268
B73V4_ctg15660,365
B73V4_ctg15755,665
B73V4_ctg15848,311
B73V4_ctg15977,382
B73V4_ctg16031,799
B73V4_ctg16150,526
B73V4_ctg16240,634
B73V4_ctg16350,620
B73V4_ctg16466,428
B73V4_ctg16567,904
B73V4_ctg16659,352
B73V4_ctg16753,643
B73V4_ctg16854,946
B73V4_ctg16947,089
B73V4_ctg170105,189
B73V4_ctg17172,536
B73V4_ctg17243,047
B73V4_ctg17366,538
B73V4_ctg17466,228
B73V4_ctg17569,465
B73V4_ctg17659,418
B73V4_ctg17741,679
B73V4_ctg178340,736
B73V4_ctg17985,784
B73V4_ctg18080,324
B73V4_ctg181351,693
B73V4_ctg1821,278,389
B73V4_ctg18396,695
B73V4_ctg18452,129
B73V4_ctg18556,966
B73V4_ctg18664,245
B73V4_ctg1876,454
B73V4_ctg18882,080
B73V4_ctg18971,282
B73V4_ctg19059,524
B73V4_ctg19172,401
B73V4_ctg19266,116
B73V4_ctg193526,805
B73V4_ctg19441,461
B73V4_ctg19558,299
B73V4_ctg196138,544
B73V4_ctg19745,447
B73V4_ctg19846,041
B73V4_ctg19960,303
B73V4_ctg20054,466
B73V4_ctg20173,251
B73V4_ctg20253,313
B73V4_ctg20382,450
B73V4_ctg20428,410
B73V4_ctg20555,164
B73V4_ctg20673,968
B73V4_ctg20746,344
B73V4_ctg20867,134
B73V4_ctg20958,608
B73V4_ctg21060,995
B73V4_ctg21155,641
B73V4_ctg21243,787
B73V4_ctg21374,799
B73V4_ctg21474,080
B73V4_ctg21555,962
B73V4_ctg21661,539
B73V4_ctg21758,830
B73V4_ctg21853,522
B73V4_ctg21961,449
B73V4_ctg22062,284
B73V4_ctg22144,889
B73V4_ctg22280,070
B73V4_ctg22363,290
B73V4_ctg22455,301
B73V4_ctg22564,997
B73V4_ctg22653,614
B73V4_ctg22741,417
B73V4_ctg22817,651
B73V4_ctg22985,258
B73V4_ctg23065,674
B73V4_ctg23173,141
B73V4_ctg23252,477
B73V4_ctg23394,458
B73V4_ctg23436,081
B73V4_ctg23570,135
B73V4_ctg23654,117
B73V4_ctg2377,104
B73V4_ctg23861,153
B73V4_ctg23995,256
B73V4_ctg24045,166
B73V4_ctg24152,360
B73V4_ctg24256,713
B73V4_ctg24351,365
B73V4_ctg24448,860
B73V4_ctg24576,559
B73V4_ctg24647,028
B73V4_ctg24781,363
B73V4_ctg24866,018
B73V4_ctg24930,460
B73V4_ctg25063,031
B73V4_ctg25151,883
B73V4_ctg25252,549
B73V4_ctg25382,972
B73V4_ctg25469,595
B73V4_ctg25546,945
B73V4_ctg2729124,116
+
+
diff --git a/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.grm b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.grm new file mode 100644 index 00000000..abeed339 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Zea_mays.html.grm @@ -0,0 +1,74 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Zm-B73-REFERENCE-GRAMENE-4.0
Database version:86.7
Base Pairs:2,104,350,183
Golden Path Length:2,135,083,061
Genebuild by: CSHL
Genebuild method: MAKER-P
Genebuild started: Dec 2015
Genebuild released: Mar 2016
Genebuild last updated/patched: Mar 2016
Genebuild version: Zm0001d.1
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,498
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:139,122
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
1307041717
2244442276
3235667834
4246994605
5223902240
6174033170
7182381542
8181122637
9159769782
10150982314
Pt140384
Mt569630
+
+
contig3132 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):50,114,708
diff --git a/gramene/htdocs/ssi/species.weix/stats_Zea_mays_IPtop500.html b/gramene/htdocs/ssi/species.weix/stats_Zea_mays_IPtop500.html new file mode 100644 index 00000000..3cc58784 --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_Zea_mays_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		171718053
2IPR011009
Protein kinase-like domain		16775148
3IPR000719
Protein kinase domain		151710251
4IPR008271
Serine/threonine-protein kinase, active site		10902778
5IPR017441
Protein kinase, ATP binding site		9762336
6IPR013083
Zinc finger, RING/FYVE/PHD-type		9372907
7IPR032675
Leucine-rich repeat domain, L domain-like		7134554
8IPR013320
Concanavalin A-like lectin/glucanase domain		6911652
9IPR011990
Tetratricopeptide-like helical domain		6745847
10IPR009057
Homeodomain-like		5912818
11IPR001841
Zinc finger, RING-type		5782538
12IPR002885
Pentatricopeptide repeat		54816112
13IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		5302059
14IPR016024
Armadillo-type fold		5238844
15IPR016040
NAD(P)-binding domain		5122879
16IPR029058
Alpha/Beta hydrolase fold		5022533
17IPR012677
Nucleotide-binding alpha-beta plait domain		4514292
18IPR011989
Armadillo-like helical		4395447
19IPR001611
Leucine-rich repeat		3953061
20IPR015943
WD40/YVTN repeat-like-containing domain		3853020
21IPR000504
RNA recognition motif domain		3765439
22IPR001005
SANT/Myb domain		3721574
23IPR017986
WD40-repeat-containing domain		3614042
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		3582436
25IPR025476
Helitron helicase-like domain		354412
26IPR012336
Thioredoxin-like fold		3431517
27IPR001128
Cytochrome P450		3302439
28IPR001680
WD40 repeat		32513273
29IPR012337
Ribonuclease H-like domain		3201108
30IPR001810
F-box domain		3191070
31IPR012340
Nucleic acid-binding, OB-fold		3191257
32IPR020846
Major facilitator superfamily domain		3171205
33IPR003593
AAA+ ATPase domain		3031706
34IPR010285
DNA helicase Pif1-like		298358
35IPR017930
Myb domain		295644
36IPR017853
Glycoside hydrolase superfamily		276983
37IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		269461
38IPR002401
Cytochrome P450, E-class, group I		2591909
39IPR011992
EF-hand domain pair		2561916
40IPR011991
Winged helix-turn-helix DNA-binding domain		2521200
41IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		2451638
42IPR016177
DNA-binding domain		244406
43IPR017972
Cytochrome P450, conserved site		244285
44IPR007087
Zinc finger, C2H2		2331247
45IPR001471
AP2/ERF domain		2321763
46IPR003591
Leucine-rich repeat, typical subtype		2272242
47IPR002048
EF-hand domain		2263638
48IPR013781
Glycoside hydrolase, catalytic domain		220747
49IPR001932
PPM-type phosphatase domain		2191811
50IPR023214
HAD-like domain		2122184
51IPR029044
Nucleotide-diphospho-sugar transferases		2081622
52IPR018247
EF-Hand 1, calcium-binding site		2061172
53IPR003653
Ulp1 protease family, C-terminal catalytic domain		205555
54IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		201602
55IPR019775
WD40 repeat, conserved site		1981131
56IPR015655
Protein phosphatase 2C family		190498
57IPR023753
FAD/NAD(P)-binding domain		1891789
58IPR010255
Haem peroxidase		175280
59IPR014001
Helicase superfamily 1/2, ATP-binding domain		1722230
60IPR013785
Aldolase-type TIM barrel		171754
61IPR005135
Endonuclease/exonuclease/phosphatase		170907
62IPR001650
Helicase, C-terminal		1673294
63IPR002016
Haem peroxidase, plant/fungal/bacterial		1671476
64IPR003441
NAC domain		166668
65IPR011011
Zinc finger, FYVE/PHD-type		1641130
66IPR015424
Pyridoxal phosphate-dependent transferase		162379
67IPR001623
DnaJ domain		1612393
68IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		161702
69IPR003959
ATPase, AAA-type, core		153840
70IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		150339
71IPR020683
Ankyrin repeat-containing domain		1471863
72IPR003439
ABC transporter-like		1471764
73IPR019793
Peroxidases heam-ligand binding site		143195
74IPR013026
Tetratricopeptide repeat-containing domain		142765
75IPR000823
Plant peroxidase		1421391
76IPR002182
NB-ARC		141323
77IPR021109
Aspartic peptidase domain		141664
78IPR013830
SGNH hydrolase-type esterase domain		140556
79IPR009072
Histone-fold		140377
80IPR001356
Homeobox domain		1361030
81IPR004827
Basic-leucine zipper domain		136926
82IPR014710
RmlC-like jelly roll fold		135348
83IPR019734
Tetratricopeptide repeat		1334570
84IPR001461
Aspartic peptidase A1 family		133625
85IPR002110
Ankyrin repeat		1332349
86IPR033121
Peptidase family A1 domain		132260
87IPR003657
WRKY domain		130909
88IPR015880
Zinc finger, C2H2-like		130611
89IPR000477
Reverse transcriptase domain		129250
90IPR023213
Chloramphenicol acetyltransferase-like domain		128267
91IPR020472
G-protein beta WD-40 repeat		1271183
92IPR000008
C2 domain		1252212
93IPR011333
SKP1/BTB/POZ domain		125297
94IPR005225
Small GTP-binding protein domain		124276
95IPR011545
DEAD/DEAH box helicase domain		124567
96IPR012334
Pectin lyase fold		124399
97IPR011050
Pectin lyase fold/virulence factor		123363
98IPR006447
Myb domain, plants		119179
99IPR001965
Zinc finger, PHD-type		1191312
100IPR009009
RlpA-like protein, double-psi beta-barrel domain		117434
101IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		116280
102IPR005123
Oxoglutarate/iron-dependent dioxygenase		115336
103IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		115309
104IPR000270
PB1 domain		114510
105IPR008972
Cupredoxin		111640
106IPR029052
Metallo-dependent phosphatase-like		111679
107IPR001087
GDSL lipase/esterase		110139
108IPR017907
Zinc finger, RING-type, conserved site		110287
109IPR011993
PH domain-like		110825
110IPR003480
Transferase		110121
111IPR005828
Major facilitator, sugar transporter-like		109251
112IPR029071
Ubiquitin-related domain		109306
113IPR013766
Thioredoxin domain		108409
114IPR007117
Expansin, cellulose-binding-like domain		108589
115IPR013763
Cyclin-like		1071117
116IPR008906
HAT, C-terminal dimerisation domain		106177
117IPR019794
Peroxidase, active site		106141
118IPR015300
DNA-binding pseudobarrel domain		106686
119IPR027443
Isopenicillin N synthase-like		103177
120IPR011051
RmlC-like cupin domain		103215
121IPR032799
Xylanase inhibitor, C-terminal		101137
122IPR032861
Xylanase inhibitor, N-terminal		99131
123IPR000048
IQ motif, EF-hand binding site		993637
124IPR007112
Expansin/pollen allergen, DPBB domain		98228
125IPR001806
Small GTPase superfamily		98252
126IPR003340
B3 DNA binding domain		97927
127IPR000225
Armadillo		972465
128IPR017871
ABC transporter, conserved site		96463
129IPR007118
Expansin/Lol pI		95633
130IPR019787
Zinc finger, PHD-finger		95905
131IPR019786
Zinc finger, PHD-type, conserved site		95720
132IPR001752
Kinesin motor domain		954140
133IPR027640
Kinesin-like protein		941379
134IPR000073
Alpha/beta hydrolase fold-1		93412
135IPR000571
Zinc finger, CCCH-type		932934
136IPR003960
ATPase, AAA-type, conserved site		92397
137IPR023395
Mitochondrial carrier domain		92431
138IPR002347
Short-chain dehydrogenase/reductase SDR		911386
139IPR016135
Ubiquitin-conjugating enzyme/RWD-like		91507
140IPR005202
Transcription factor GRAS		91187
141IPR032867
DYW domain		91117
142IPR006121
Heavy metal-associated domain, HMA		90515
143IPR000210
BTB/POZ domain		90437
144IPR003656
Zinc finger, BED-type		90261
145IPR003676
Small auxin-up RNA		9096
146IPR018108
Mitochondrial substrate/solute carrier		89905
147IPR017877
Myb-like domain		88196
148IPR000109
Proton-dependent oligopeptide transporter family		86234
149IPR029055
Nucleophile aminohydrolases, N-terminal		86505
150IPR027124
SWR1-complex protein 5/Craniofacial development protein		8693
151IPR003613
U box domain		86458
152IPR024752
Myb/SANT-like domain		86110
153IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		85223
154IPR001251
CRAL-TRIO lipid binding domain		851055
155IPR004045
Glutathione S-transferase, N-terminal		85292
156IPR007021
Domain of unknown function DUF659		85129
157IPR020568
Ribosomal protein S5 domain 2-type fold		84333
158IPR010987
Glutathione S-transferase, C-terminal-like		84398
159IPR016181
Acyl-CoA N-acyltransferase		83407
160IPR001878
Zinc finger, CCHC-type		831058
161IPR004864
Late embryogenesis abundant protein, LEA-14		8296
162IPR005829
Sugar transporter, conserved site		82207
163IPR001480
Bulb-type lectin domain		82553
164IPR016039
Thiolase-like		81602
165IPR003594
Histidine kinase-like ATPase, C-terminal domain		811021
166IPR026992
Non-haem dioxygenase N-terminal domain		81105
167IPR000608
Ubiquitin-conjugating enzyme E2		80419
168IPR002100
Transcription factor, MADS-box		791146
169IPR013057
Amino acid transporter, transmembrane domain		77160
170IPR033389
AUX/IAA domain		75218
171IPR008949
Isoprenoid synthase domain		75274
172IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		75265
173IPR029962
Trichome birefringence-like family		74121
174IPR003609
PAN/Apple domain		74251
175IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		73103
176IPR000626
Ubiquitin domain		72507
177IPR023299
P-type ATPase, cytoplasmic domain N		72771
178IPR006501
Pectinesterase inhibitor domain		72490
179IPR006671
Cyclin, N-terminal		72191
180IPR018253
DnaJ domain, conserved site		71135
181IPR026057
PC-Esterase		70108
182IPR025846
PMR5 N-terminal domain		7090
183IPR004088
K Homology domain, type 1		701602
184IPR002109
Glutaredoxin		70174
185IPR008974
TRAF-like		70407
186IPR001509
NAD-dependent epimerase/dehydratase		69113
187IPR001757
P-type ATPase		691146
188IPR015500
Peptidase S8, subtilisin-related		69506
189IPR008979
Galactose-binding domain-like		68747
190IPR014756
Immunoglobulin E-set		68275
191IPR000209
Peptidase S8/S53 domain		68694
192IPR013845
Ribosomal protein S4e, central region		67159
193IPR023393
START-like domain		66182
194IPR017970
Homeobox, conserved site		66116
195IPR025398
Domain of unknown function DUF4371		6668
196IPR013094
Alpha/beta hydrolase fold-3		6672
197IPR002921
Fungal lipase-like domain		65103
198IPR008942
ENTH/VHS		65346
199IPR000858
S-locus glycoprotein domain		6584
200IPR008978
HSP20-like chaperone		65208
201IPR004853
Sugar phosphate transporter domain		65164
202IPR011701
Major facilitator superfamily		65122
203IPR008250
P-type ATPase, A domain		65723
204IPR014014
RNA helicase, DEAD-box type, Q motif		65210
205IPR011006
CheY-like superfamily		65174
206IPR000876
Ribosomal protein S4e		6590
207IPR003663
Sugar/inositol transporter		65579
208IPR001789
Signal transduction response regulator, receiver domain		65406
209IPR003245
Phytocyanin domain		64191
210IPR007125
Histone H2A/H2B/H3		6473
211IPR002035
von Willebrand factor, type A		64731
212IPR001563
Peptidase S10, serine carboxypeptidase		63677
213IPR001969
Aspartic peptidase, active site		63139
214IPR000668
Peptidase C1A, papain C-terminal		63329
215IPR016159
Cullin repeat-like-containing domain		63183
216IPR009060
UBA-like		62255
217IPR011527
ABC transporter type 1, transmembrane domain		621278
218IPR023298
P-type ATPase, transmembrane domain		62405
219IPR008889
VQ		6262
220IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		62386
221IPR013128
Peptidase C1A		6194
222IPR003008
Tubulin/FtsZ, GTPase domain		61421
223IPR029045
ClpP/crotonase-like domain		61977
224IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		59342
225IPR000222
PPM-type phosphatase, divalent cation binding		59113
226IPR002528
Multi antimicrobial extrusion protein		59286
227IPR010402
CCT domain		58230
228IPR000182
GNAT domain		58212
229IPR011012
Longin-like domain		58148
230IPR018303
P-type ATPase, phosphorylation site		58312
231IPR000490
Glycoside hydrolase family 17		58119
232IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		57130
233IPR012946
X8 domain		57195
234IPR015915
Kelch-type beta propeller		57177
235IPR001214
SET domain		57749
236IPR002487
Transcription factor, K-box		57219
237IPR011032
GroES-like		56224
238IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		56169
239IPR009000
Translation protein, beta-barrel domain		56204
240IPR006045
Cupin 1		56235
241IPR019378
GDP-fucose protein O-fucosyltransferase		56186
242IPR004087
K Homology domain		56389
243IPR005795
Major pollen allergen Lol pI		55466
244IPR025322
Protein of unknown function DUF4228, plant		5557
245IPR000873
AMP-dependent synthetase/ligase		55191
246IPR013783
Immunoglobulin-like fold		55254
247IPR012675
Beta-grasp domain		55131
248IPR008928
Six-hairpin glycosidase-like		55195
249IPR005824
KOW		55331
250IPR000743
Glycoside hydrolase, family 28		55244
251IPR024171
S-receptor-like serine/threonine-protein kinase		5460
252IPR001296
Glycosyl transferase, family 1		54190
253IPR011074
CRAL/TRIO, N-terminal domain		54414
254IPR003137
PA domain		53115
255IPR011042
Six-bladed beta-propeller, TolB-like		53112
256IPR011016
Zinc finger, RING-CH-type		52245
257IPR006553
Leucine-rich repeat, cysteine-containing subtype		521331
258IPR004367
Cyclin, C-terminal domain		52132
259IPR002902
Gnk2-homologous domain		52250
260IPR004839
Aminotransferase, class I/classII		52132
261IPR030184
WAT1-related protein		5287
262IPR002068
Alpha crystallin/Hsp20 domain		51131
263IPR003165
Piwi domain		51507
264IPR002912
ACT domain		51254
265IPR000620
EamA domain		51137
266IPR013525
ABC-2 type transporter		50428
267IPR006652
Kelch repeat type 1		50399
268IPR023828
Peptidase S8, subtilisin, Ser-active site		50109
269IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		50203
270IPR002067
Mitochondrial carrier protein		50382
271IPR000644
CBS domain		50727
272IPR013126
Heat shock protein 70 family		50966
273IPR014720
Double-stranded RNA-binding domain		50876
274IPR015916
Galactose oxidase, beta-propeller		4980
275IPR004000
Actin family		49577
276IPR031657
Replication protein A, OB domain		4982
277IPR025659
Tubby C-terminal-like domain		4991
278IPR029000
Cyclophilin-like domain		49277
279IPR010920
LSM domain		4983
280IPR008991
Translation protein SH3-like domain		49104
281IPR004263
Exostosin-like		4985
282IPR023271
Aquaporin-like		49259
283IPR005150
Cellulose synthase		49257
284IPR005174
Domain unknown function DUF295		4949
285IPR000425
Major intrinsic protein		49710
286IPR003851
Zinc finger, Dof-type		49211
287IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		49193
288IPR022742
Serine aminopeptidase, S33		4887
289IPR003406
Glycosyl transferase, family 14		4885
290IPR004883
Lateral organ boundaries, LOB		48106
291IPR029069
HotDog domain		48246
292IPR001220
Legume lectin domain		4852
293IPR011043
Galactose oxidase/kelch, beta-propeller		4864
294IPR025315
Domain of unknown function DUF4220		4866
295IPR025660
Cysteine peptidase, histidine active site		4866
296IPR004041
NAF domain		4783
297IPR019821
Kinesin motor domain, conserved site		47294
298IPR018451
NAF/FISL domain		4783
299IPR000330
SNF2-related, N-terminal domain		47554
300IPR001938
Thaumatin		47480
301IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		47315
302IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		47202
303IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		47406
304IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		46696
305IPR029021
Protein-tyrosine phosphatase-like		46394
306IPR000315
B-box-type zinc finger		46266
307IPR013216
Methyltransferase type 11		4683
308IPR005333
Transcription factor, TCP		4647
309IPR001353
Proteasome, subunit alpha/beta		46107
310IPR023313
Ubiquitin-conjugating enzyme, active site		46108
311IPR027409
GroEL-like apical domain		46291
312IPR020845
AMP-binding, conserved site		46124
313IPR001849
Pleckstrin homology domain		46478
314IPR002495
Glycosyl transferase, family 8		46143
315IPR028889
Ubiquitin specific protease domain		46309
316IPR003311
AUX/IAA protein		4696
317IPR000070
Pectinesterase, catalytic		46113
318IPR008971
HSP40/DnaJ peptide-binding		45214
319IPR001929
Germin		45140
320IPR006626
Parallel beta-helix repeat		45382
321IPR017887
Transcription factor TCP subgroup		4546
322IPR007650
Zf-FLZ domain		4549
323IPR007658
Protein of unknown function DUF594		4555
324IPR004252
Probable transposase, Ptta/En/Spm, plant		4578
325IPR002963
Expansin		45366
326IPR031107
Small heat shock protein HSP20		4549
327IPR006458
Ovate protein family, C-terminal		45133
328IPR015947
PUA-like domain		45184
329IPR006016
UspA		44157
330IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase		4484
331IPR013201
Cathepsin propeptide inhibitor domain (I29)		44122
332IPR004265
Plant disease resistance response protein		4466
333IPR020635
Tyrosine-protein kinase, catalytic domain		4460
334IPR029006
ADF-H/Gelsolin-like domain		44711
335IPR018202
Serine carboxypeptidase, serine active site		4478
336IPR006702
Domain of unknown function DUF588		4448
337IPR000217
Tubulin		43529
338IPR002423
Chaperonin Cpn60/TCP-1 family		43163
339IPR002083
MATH/TRAF domain		43439
340IPR016166
FAD-binding, type 2		43219
341IPR014722
Ribosomal protein L2 domain 2		4360
342IPR005746
Thioredoxin		4374
343IPR000169
Cysteine peptidase, cysteine active site		4375
344IPR002085
Alcohol dehydrogenase superfamily, zinc-type		43123
345IPR025661
Cysteine peptidase, asparagine active site		4358
346IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2		43109
347IPR006073
GTP binding domain		43282
348IPR001305
Heat shock protein DnaJ, cysteine-rich domain		42283
349IPR029062
Class I glutamine amidotransferase-like		42260
350IPR019780
Germin, manganese binding site		4243
351IPR002939
Chaperone DnaJ, C-terminal		4289
352IPR010658
Nodulin-like		4254
353IPR010399
Tify domain		42199
354IPR001117
Multicopper oxidase, type 1		4174
355IPR017938
Riboflavin synthase-like beta-barrel		41133
356IPR002659
Glycosyl transferase, family 31		41202
357IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		41259
358IPR027934
Cellulose synthase, RING-type zinc finger		41103
359IPR011706
Multicopper oxidase, type 2		4184
360IPR003855
Potassium transporter		41201
361IPR007493
Protein of unknown function DUF538		40168
362IPR013088
Zinc finger, NHR/GATA-type		4069
363IPR005630
Terpene synthase, metal-binding domain		4085
364IPR004140
Exocyst complex component Exo70		40103
365IPR027356
NPH3 domain		40153
366IPR000742
EGF-like domain		40142
367IPR016161
Aldehyde/histidinol dehydrogenase		40159
368IPR012341
Six-hairpin glycosidase		4095
369IPR000679
Zinc finger, GATA-type		40246
370IPR015797
NUDIX hydrolase domain-like		40148
371IPR010525
Auxin response factor		40185
372IPR006153
Cation/H+ exchanger		39206
373IPR029061
Thiamin diphosphate-binding fold		39355
374IPR018467
CO/COL/TOC1, conserved site		3954
375IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		39371
376IPR008480
Protein of unknown function DUF761, plant		3939
377IPR001906
Terpene synthase, N-terminal domain		39177
378IPR011707
Multicopper oxidase, type 3		3971
379IPR005175
PPC domain		39113
380IPR002913
START domain		39418
381IPR000727
Target SNARE coiled-coil homology domain		38159
382IPR032710
NTF2-like domain		38144
383IPR018200
Ubiquitin specific protease, conserved site		38371
384IPR029466
No apical meristem-associated, C-terminal domain		3843
385IPR026961
PGG domain		3895
386IPR004333
Transcription factor, SBP-box		38288
387IPR022357
Major intrinsic protein, conserved site		3874
388IPR001164
Arf GTPase activating protein		38583
389IPR001487
Bromodomain		381230
390IPR003106
Leucine zipper, homeobox-associated		3761
391IPR007657
Glycosyltransferase AER61, uncharacterised		3752
392IPR033124
Serine carboxypeptidases, histidine active site		3770
393IPR002119
Histone H2A		37209
394IPR011013
Galactose mutarotase-like domain		37151
395IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		37787
396IPR006867
Domain of unknown function DUF632		3791
397IPR001433
Oxidoreductase FAD/NAD(P)-binding		3658
398IPR001163
LSM domain, eukaryotic/archaea-type		3692
399IPR026960
Reverse transcriptase zinc-binding domain		3642
400IPR000795
Transcription factor, GTP-binding domain		36738
401IPR010989
t-SNARE		3674
402IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		3652
403IPR013780
Glycosyl hydrolase, all-beta		36118
404IPR023210
NADP-dependent oxidoreductase domain		36261
405IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		36210
406IPR001395
Aldo/keto reductase/potassium channel subunit beta		36101
407IPR015590
Aldehyde dehydrogenase domain		36138
408IPR025110
AMP-binding enzyme C-terminal domain		3565
409IPR015940
Ubiquitin-associated domain		35443
410IPR018490
Cyclic nucleotide-binding-like		35113
411IPR001279
Metallo-beta-lactamase		35339
412IPR005516
Remorin, C-terminal		3567
413IPR004014
Cation-transporting P-type ATPase, N-terminal		35252
414IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		35100
415IPR001876
Zinc finger, RanBP2-type		351208
416IPR004813
Oligopeptide transporter, OPT superfamily		35163
417IPR002775
DNA/RNA-binding protein Alba-like		35131
418IPR006094
FAD linked oxidase, N-terminal		3552
419IPR000595
Cyclic nucleotide-binding domain		35247
420IPR013955
Replication factor A, C-terminal		3555
421IPR029047
Heat shock protein 70kD, peptide-binding domain		35344
422IPR016162
Aldehyde dehydrogenase N-terminal domain		35164
423IPR000757
Glycoside hydrolase family 16		3593
424IPR023329
Chlorophyll a/b binding protein domain		3542
425IPR006689
Small GTPase superfamily, ARF/SAR type		34242
426IPR000782
FAS1 domain		34195
427IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3462
428IPR000023
Phosphofructokinase domain		34169
429IPR013149
Alcohol dehydrogenase, C-terminal		3475
430IPR032454
Histone H2A, C-terminal domain		3438
431IPR014977
WRC domain		34135
432IPR022796
Chlorophyll A-B binding protein		3438
433IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		34133
434IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3442
435IPR002937
Amine oxidase		3497
436IPR008948
L-Aspartase-like		3472
437IPR017927
Ferredoxin reductase-type FAD-binding domain		3396
438IPR017884
SANT domain		33161
439IPR001360
Glycoside hydrolase family 1		33712
440IPR000717
Proteasome component (PCI) domain		33186
441IPR013154
Alcohol dehydrogenase, N-terminal		3369
442IPR000408
Regulator of chromosome condensation, RCC1		332296
443IPR006580
Zinc finger, TTF-type		3333
444IPR004264
Transposase, Tnp1/En/Spm-like		3346
445IPR023410
14-3-3 domain		33168
446IPR005821
Ion transport domain		33126
447IPR000095
CRIB domain		33133
448IPR013601
FAE1/Type III polyketide synthase-like protein		3234
449IPR016461
O-methyltransferase COMT-type		3273
450IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		3240
451IPR003347
JmjC domain		32472
452IPR027725
Heat shock transcription factor family		3259
453IPR008280
Tubulin/FtsZ, C-terminal		3280
454IPR004182
GRAM domain		32120
455IPR003121
SWIB/MDM2 domain		32406
456IPR025422
Transcription factor TGA like domain		3299
457IPR013816
ATP-grasp fold, subdomain 2		32228
458IPR031112
AP2-like ethylene-responsive transcription factor		3297
459IPR016167
FAD-binding, type 2, subdomain 1		3248
460IPR001077
O-methyltransferase, family 2		3243
461IPR004046
Glutathione S-transferase, C-terminal		3255
462IPR017937
Thioredoxin, conserved site		32100
463IPR020843
Polyketide synthase, enoylreductase domain		3253
464IPR024788
Malectin-like carbohydrate-binding domain		3257
465IPR003954
RNA recognition motif domain, eukaryote		31223
466IPR009071
High mobility group box domain		31270
467IPR005467
Histidine kinase domain		31100
468IPR017926
Glutamine amidotransferase		31163
469IPR002123
Phospholipid/glycerol acyltransferase		31121
470IPR020904
Short-chain dehydrogenase/reductase, conserved site		3163
471IPR002498
Phosphatidylinositol-4-phosphate 5-kinase, core		31355
472IPR000300
Inositol polyphosphate-related phosphatase		3191
473IPR029057
Phosphoribosyltransferase-like		31255
474IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type		31100
475IPR029993
Plant galacturonosyltransferase GAUT		31110
476IPR001701
Glycoside hydrolase family 9		3153
477IPR000232
Heat shock factor (HSF)-type, DNA-binding		31219
478IPR018097
EGF-like calcium-binding, conserved site		3144
479IPR003100
PAZ domain		301186
480IPR006195
Aminoacyl-tRNA synthetase, class II		3096
481IPR008984
SMAD/FHA domain		30149
482IPR008422
Homeobox KN domain		3061
483IPR001344
Chlorophyll A-B binding protein, plant		3039
484IPR016455
Xyloglucan endotransglucosylase/hydrolase		3033
485IPR003337
Trehalose-phosphatase		30155
486IPR002293
Amino acid/polyamine transporter I		30182
487IPR011004
Trimeric LpxA-like		30100
488IPR001926
Tryptophan synthase beta subunit-like PLP-dependent enzyme		30146
489IPR027484
Phosphatidylinositol-4-phosphate 5-kinase, N-terminal domain		30102
490IPR002641
Patatin/Phospholipase A2-related		3062
491IPR029064
50S ribosomal protein L30e-like		3094
492IPR029048
Heat shock protein 70kD, C-terminal domain		30267
493IPR004294
Carotenoid oxygenase		2970
494IPR006594
LIS1 homology motif		29391
495IPR004141
Strictosidine synthase		2933
496IPR000308
14-3-3 protein		29301
497IPR012678
Ribosomal protein L23/L15e core domain		2939
498IPR001440
Tetratricopeptide repeat 1		29104
499IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		29110
500IPR006068
Cation-transporting P-type ATPase, C-terminal		29105
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diff --git a/gramene/htdocs/ssi/species.weix/stats_pan_compara_species.html b/gramene/htdocs/ssi/species.weix/stats_pan_compara_species.html new file mode 100644 index 00000000..8dba41ad --- /dev/null +++ b/gramene/htdocs/ssi/species.weix/stats_pan_compara_species.html @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
Arabidopsis thalianaSorghum bicolorBrachypodium distachyon
Oryza barthiiOryza glumaepatulaOryza granulata
Oryza longistaminataOryza meridionalisOryza minutabb
Oryza minutaccOryza nivaraOryza officinalis
Oryza punctataOryza rufipogonLeersia perrieri
Oryza sativaOryza indicaOryza brachyantha
Oryza glaberrima
diff --git a/gramene/htdocs/ssi/species/about_Aegilops_tauschii.html b/gramene/htdocs/ssi/species/about_Aegilops_tauschii.html new file mode 100644 index 00000000..7a8a0487 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Aegilops_tauschii.html @@ -0,0 +1,72 @@ + +

Wheat genomics resources are developed as part of our involvement in the consortium Triticeae Genomics For Sustainable Agriculture, funded by the BBSRC, and led by TGAC.

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BBSRC logo

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About Aegilops tauschii

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Aegilops tauschii (goatgrass) is the diploid progenitor of the bread wheat D-genome, providing important evolutionary information for wheat. The bread wheat genome is a hexaploid, resulting from the hybridization of the wild A. tauschii with a cultivated tetraploid wheat, Triticum turgidum. This spontaneous event occured about 8,000 years ago in the Fertile Crescent.

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Assembly

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The genome of Aegilops tauschii accession AL8/78 was sequenced by the BGI using a whole-genome shotgum strategy, and assembled using SOAPdenovo software. The genome assembly achieved contigs with a N50 size of 4.51 kbp. Using paired-end information, and additional Roche/454 long-read sequences, the draft assembly was 4.23 Gbp, with a scaffold N50 length of 57.6 kbp.

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The chloroplast genome component and its gene annotation are also present. This was imported from ENA entry, JQ754651.

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Annotation

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34,498 protein-coding genes were predicted, using FGENESH and GeneID, supplemented with evidence-based information using RNA-Seq and ESTs sequences. For more details about genome sequencing and gene prediction see [1].

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Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

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Triticeae Repeats from TREP were aligned to the A. tauschii genome using RepeatMasker.

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Regulation and sequence alignments

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RNA-Seq data, ESTs and UniGene datasets have also been aligned to the Aegilops tauschii genome:

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Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. [5]

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The wheat genome assemblies previously generated by Brenchley et al. (PMID:23192148) have been aligned to the bread wheat survey sequence, Brachypodium, barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii). Homoeologous variants inferred between the three wheat genomes (A, B, and D) are displayed in the context of the gene models of these five genomes.

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Sequences of diploid progenitor and ancestral species permitted homoeologous variants to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

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The wheat gene alignments and the projected wheat SNPs are available on the Location view, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

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Links

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Links (Aegilops tauschii)

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  • GigaDB
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  • ENA study: SRP002455: Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors
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  • ENA study: DRP000562: RNASeq from seedling leaves of Aegilops tauschii
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  • TREP, the Triticeae Repeat Sequence Database
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Links (Triticum aestivum)

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  • MIPS Wheat Genome Database
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  • ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
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  • Triticum aestivum UniGene cluster sequences at NCBI
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  • Triticum aestivum ESTs at ENA
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References

  1. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.
    Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X et al. 2013. Nature. 496:91-95.
    2. +
  2. Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor.
    Iehisa JC, Shimizu A, Sato K, Nasuda S, Takumi S. 2012. DNA Res.. 19:487-497.
    3. +
  3. Image credit: Mark Nesbitt [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
    4. +
  4. Homoeolog-specific transcriptional bias in allopolyploid wheat.
    Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Amborella_trichopoda.html b/gramene/htdocs/ssi/species/about_Amborella_trichopoda.html new file mode 100644 index 00000000..ceb98780 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Amborella_trichopoda.html @@ -0,0 +1,22 @@ + +

About Amborella trichopoda

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Amborella trichopoda is a small, tropical shrub endemic to New Caledonia. It is the only species in the genus Amborella, which is the only member of the family Amborellaceae. As the only living species on the sister lineage to all other flowering plants, it is an important reference for studying plant evolution. Individual Amborella trichopoda are usually sprawling understory shrubs, although occasionally they grow up to eight meters high. They have evergreen leaves and small, white to yellow flowers. The species is dioecious; female plants producing carpals and males producing stamens, and individual plants can change sex between flowerings. Unlike nearly all other flowering plants, they do not posses vessel elements for water conduction. Amborella's genome is a relatively compact 870Mb, arranged into 13 chromosome pairs.

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Assembly

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Amborella's draft genome sequence was published in December, 2013, by the Amborella Genome Project [1,2]. Initial sequencing and contig assembly was performed using a whole-genome shotgun (WGS) strategy. Contigs and scaffold assignments were refined, and superscaffolds constructed from them using evidence from end-sequenced BACs, single-molecule restriction digest (OpGen) experiments, and fluorescent in-situ hybridization (FISH) experiments.

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Annotation

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Ab initio annotation of genes and repetitive elements was performed using the DAWGPAWS [3] and EVidenceModeler [4] software packages. These annotations were refined through manual comparison with assembled Amborella cDNA transcripts, gene family analyses, and homology studies.

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References

  1. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
    Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC et al. 2013. Science. 342:1516-1517.
    2. +
  2. The Amborella genome and the evolution of flowering plants.
    2013. Science. 342:1241089.
    3. +
  3. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.
    Estill JC, Bennetzen JL. 2009. Plant Methods. 5:8.
    4. +
  4. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Genome Biol.. 9:R7.

Picture credit: Scott Zona via Wikimedia Commons: http://commons.wikimedia.org/wiki/File:Amborella_trichopoda_%283173820625%29.jpg

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Arabidopsis_lyrata.html b/gramene/htdocs/ssi/species/about_Arabidopsis_lyrata.html new file mode 100644 index 00000000..c4918d23 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Arabidopsis_lyrata.html @@ -0,0 +1,27 @@ + +

About Arabidopsis lyrata

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Arabidopsis lyrata is a small perennial outcrossing brassica that is distributed within Eastern Asia, Europe and Northwestern America. A close relative of the dicot model, Arabidopsis thaliana, Arabidopsis lyrata has a genome size that is 1.5x larger with a haploid chromosome number of 8.

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Assembly

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The genome was assembled by the Stanford Human Genome Center with assistance from the A. lyrata community. Sequencing followed a whole genome shotgun strategy and achieved an average genome coverage of 8x. The 206.7 Mbp Araly1 assembly contains 695 nuclear scaffolds.

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Annotation

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The genome was annotated by the U.S. Department of Energy Joint Genome Institute (JGI) using collaborator-submitted data, custom JGI analyses, and the automated JGI Annotation Pipeline and is predicted to have approximately 32,670 genes.

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Links

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References

  1. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
    Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H et al. 2011. Nat. Genet.. 43:476-481.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Arabidopsis_thaliana.html b/gramene/htdocs/ssi/species/about_Arabidopsis_thaliana.html new file mode 100644 index 00000000..c74f62a7 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Arabidopsis_thaliana.html @@ -0,0 +1,54 @@ + +

About Arabidopsis thaliana

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Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish. Arabidopsis is not of major agronomic significance, but it offers important advantages for basic research in genetics and molecular biology. Arabidopsis thaliana has a genome size of ~135 Mbp, and a haploid chromosome number of 5.

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Assembly

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The complete genome sequence of Arabidopsis thaliana was first published by the Arabidopsis Genome Initiative in 2000 [1] and was determined by a BAC-by-BAC sequencing strategy anchored to chromosomes using a variety of genetic and physical maps.

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Annotation

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This browser is based on data from Araport11 gene annotation, a comprehensive reannotation of the Col-0 genome released June, 2016. This annotation annotation was constructed using 113 public RNA-seq data sets along with annotation contributions from NCBI, UniProt, and laboratories conducting Arabidopsis thaliana research. Details of the structural and functional annotation steps to generate the Araport11 protein-coding gene set as well as consolidation and annotation of non-coding RNAs are described in this draft manuscript on bioRxiv

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Regulation

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Mappings for probes from the following expression arrays have been added:

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Variation

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The Arabidopsis variation database was updated in release 36 (June 2017) to the latest 1001 variation data set, covering more than 10 million variant loci across 1,135 samples (Cell 2016). The phenotypic data from a GWAS study of 107 phenotypes in 95 inbred lines carried out by Atwell et al. [5] has been retained.

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In this major update, the following arabidopsis variation datasets were obsoleted (but are still available in the Ensembl Plants Archive site):

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Links

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References

  1. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
    CHIA-YI Cheng, Vivek Krishnakumar, Agnes Chan, Seth Schobel, Christopher D. Town. 2016. bioRxiv.
    2. +
  2. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Arabidopsis Genome Initiative. 2000. Nature. 408:796-815.
    3. +
  3. The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
    Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L et al. 2008. Nucleic Acids Res.. 36:D1009-14.
    4. +
  4. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.
    Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjlmsson BJ et al. 2012. Nat. Genet.. 44:212-216.
    5. +
  5. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
    Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA et al. 2007. Science. 317:338-342.
    6. +
  6. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
    Atwell S, Huang YS, Vilhjlmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT et al. 2010. Nature. 465:627-631.

Picture credit: By Emmanuel Boutet (Own work) [GFDL, CC-BY-SA-3.0 or CC BY-SA 2.5-2.0-1.0], via Wikimedia Commons

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Beta_vulgaris.html b/gramene/htdocs/ssi/species/about_Beta_vulgaris.html new file mode 100644 index 00000000..947c996f --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Beta_vulgaris.html @@ -0,0 +1,19 @@ + +

About Beta vulgaris

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Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates providing nearly 30% of the world's annual sugar production and a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n=18 chromosomes, has an estimated genome size of 714-758 Mbp and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops [1].

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Assembly

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The double haploid sugar beet line KWS2320 was sequenced using the Roche/454, Illumina and Sanger sequencing platforms. The initial assembly was integrated with genome-wide genetic and physical map information, resulting in 225 genetically anchored scaffolds (394.6 Mb), assigned to nine chromosomes. The final assembly comprised 566.6 Mbp in 2,171 scaffolds and 38,337 unscaffolded contigs. The N50 size was 2.01 Mb (the 72nd scaffold) and the chromosomally assigned fraction 84.7%. A total of 94% of the publicly available isogenic expressed sequence tags (ESTs) were located in the assembly, suggesting that gene-containing regions are comprehensively covered [1]

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Annotation

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A total of 27,421 protein-coding genes supported by mRNA evidence were predicted; 91% included start and stop codons [1].

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References

  1. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
    Dohm JC, Minoche AE, Holtgrwe D, Capella-Gutirrez S, Zakrzewski F, Tafer H, Rupp O, Srensen TR, Stracke R, Reinhardt R et al. 2014. Nature. 505:546-549.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Betula_pendula.html b/gramene/htdocs/ssi/species/about_Betula_pendula.html new file mode 100644 index 00000000..e2d6783e --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Betula_pendula.html @@ -0,0 +1,10 @@ + +

About Betula pendula

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About the assembly.

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About the annotation.

+ diff --git a/gramene/htdocs/ssi/species/about_Brachypodium_distachyon.html b/gramene/htdocs/ssi/species/about_Brachypodium_distachyon.html new file mode 100644 index 00000000..71076f9f --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Brachypodium_distachyon.html @@ -0,0 +1,73 @@ + +

About Brachypodium distachyon

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Brachypodium distachyon, like Arabidopsis thaliana, has several features that recommend it as a model plant for functional genomic studies, especially in the grasses. It has a small, diploid genome (~355 Mbp), small physical size, a short life-cycle and few growth requirements. Brachypodium is related to the major cereal grain species but is understood to be more closely related to the Triticeae (wheat and barley) than to the other cereals.

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Assembly

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This release represents the second improved Brachypodium distachyon (Bd21) genome including ~270 Mb of improved Brachypodium sequence. These regions were improved by dividing the gene space into ~2Mb overlapping pieces. Each region was manually inspected and then finished using a variety of technologies including Sanger (primer walks on subclones and fosmid templates, transposon sequencing on subclone templates), Illumina (small insert shatter libraries) and clone-based shotgun sequencing using both Sanger and Illumina libraries. 1,496 gaps were closed, and a total of 1.43 MB of base pairs was added to the assembly. Overall contiguity (contig N50) increased by a factor of 63 from 347.8Kb to 22 Mb.[1]

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Annotation

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74,756 transcript assemblies were constructed from 160M paired-end Illumina RNA-seq reads, 17,647 transcript assemblies from ~1.9M 454 reads. The transcript assemblies from RNA-seq reads were made using PERTRAN. 76,209 transcript assemblies were constructed using PASA from 314,866 sequences in total, consisting of the RNA-seq transcript assemblies above, as well as Sanger ESTs. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabidopsis (Arabidopsis thaliana), rice, sorghum, foxtail, grape, soybean and Swiss-Prot eukaryote proteins to soft-repeatmasked Brachypodium distachyon Bd21 genome using RepeatMasker with up to 2K BP extension on both ends unless extending into another locus on the same strand. Gene models were predicted by homology-based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan.

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The end result was 34,310 loci containing protein-coding transcripts and 52,972 protein-coding transcripts

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Sequence alignments

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Brachypodium sylvaticum transcriptome

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De novo gene models from the RNA-Seq analysis of three Brachypodium sylvaticum populations [2] were mapped to the B. distachyon reference genome. Click here for example. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC project PRJNA182761.

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Triticum aestivum transcriptome

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Wheat RNA-Seq, EST and UniGene datasets have been aligned to the Brachypodium distachyon genome:

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Variation

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Brachypodium variation data

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Approximately 394,000 genetic variations have been identified by the alignment of transcriptome assemblies from three slender false brome (Brachypodium sylvaticum) populations [2]. Two populations come from B. sylvaticum's native range (Greece and Spain) and one comes from its invasive range (Oregon). Both the transciptome alignments and variation data are available in Ensembl Plants. Click here for example.

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Wheat inter-homoeologous variants

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As part of the wheat genome analysis, we have aligned a set of Triticum aestivum (bread wheat) homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon genome. SNPs have been classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B [3].

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The wheat sequence alignments and the projected homoeologous SNPs are available as tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

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Links

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Links (Brachypodium distachyon)

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Links (Triticum aestivum)

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  • MIPS Wheat Genome Database
    • +
  • ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
    • +
  • ENA study ERP001415: 454 sequencing of Triticum aestivum (bread wheat) cv. Chinese spring cDNA samples from a pool of tissues, from plants under drought stress and from circadian-sampled leaves
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  • Triticum aestivum ESTs at ENA
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  • Triticum aestivum UniGene cluster sequences at NCBI
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References

  1. Genome sequencing and analysis of the model grass Brachypodium distachyon.
    The International Brachypodium Initiative. 2010. Nature. 463:763-768.
    2. +
  2. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae).
    Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, and Pankaj Jaiswal. 2013. Applications in Plant Sciences. 1(3):1200011.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Brassica_napus.html b/gramene/htdocs/ssi/species/about_Brassica_napus.html new file mode 100644 index 00000000..2cb12e1c --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Brassica_napus.html @@ -0,0 +1,19 @@ + +

About Brassica napus

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Oilseed rape (Brassica napus) was formed ~7,500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72-fold genome multiplication since the origin of angiosperms and high gene content. Cultivation began in Europe during the Middle Ages and spread worldwide. Diversifying selection gave rise to oilseed rape (canola), rutabaga, fodder rape, and kale morphotypes grown for oil, fodder, and food.

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Assembly

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The homozygous B. napus genome of European winter oilseed cultivar ‘Darmor-bzh’ was assembled with long-read 454 GS-FLX+ Titanium and Sanger sequence. Correction and gap filling used 79 Gbp of Illumina HiSeq sequence. The final assembly of 849.7 Mbp was obtained using SOAP and Newbler, with 89% nongapped sequence. The assembly covers ~79% of the 1,130 Mbp genome and includes 95.6% of Brassica expressed sequence tags (ESTs) [1].

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Annotation

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A total of 101,040 gene models were estimated from 35.5 Gbp of RNA-Seq data in combination with ab initio gene prediction, protein and EST alignments, and transposon masking. Of these, 91,167 were confirmed by matches with B. rapa and/or B. oleracea predicted proteomes [1].

+ + +

References

  1. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B et al. 2014. Science. 345:950-953.
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About Brassica oleracea

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Brassica oleracea L. (n=9, C genome) is a widely cultivated vegetable species integral to human diets, with a classification of cultivar groups based on the specialized morphology of their edible structures (kales, cabbages, Brussels sprouts, broccoli, kohl rabi and cauliflower).

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Assembly

+

The genomic sequence within this version of Ensembl includes 33,459 scaffolds (>200 bp) with an N50 of 850 kb that was assembled at NRC-Saskatoon using a hybrid approach from Illumina, Roche 454 and Sanger sequence data [1]. The assembly has been orientated and assigned to the nine pseudochromosomes using dense genotype-by-sequencing genetic maps.

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Annotation

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Gene prediction of the assembled genomic scaffolds was conducted by JCVI and NRC-Saskatoon using MAKER and PASA [1]. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes.

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Links

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  • http://brassica.info
    This site collates and exchanges open source information relating to Brassica genomics and genetics.
    • +
  • http://brassicadb.org
    The Brassica database (BRAD) is a web-based database of genetic data at the whole genome scale for important Brassica crops.
    • +
+ +

References

  1. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
    Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL et al. 2014. Genome Biol.. 15:R77.

Picture credit: "Fractal Broccoli" by Jon Sullivan. Licensed under Public domain via Wikimedia Commons.

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BrassicaInfoThe Brassica rapa genome browser has been developed through a joint effort by the Ensembl Genomes group and Rothamsted Research. From release 13 of Ensembl Genomes, the EBI will be maintaining the genome browser for B. rapa in the context of Ensembl Plants.

+ +

Rothamsted Research Acknowledges:

+ +
  • BBSRC for funding (grant number BB/E017797/1)
    • +
  • Ian Bancroft and Martin Trick at the John Innes Centre for providing the gene annotation.
    • +
  • Nick James and Sean May (NASC) for their assistance in establishing BrassEnsembl.
    • +
+ + +

About Brassica rapa

+ +

Brassica rapa (Chinese cabbage) is a widely cultivated leaf and root vegetable. The genome was sequenced as a contribution to the Multinational Brassica Genome Sequencing Project and was published in August 2011 (Wang X, et. al. Nature 2011).

+ + + +

Assembly

+ +

The genomic sequence within this version of Ensembl includes 193 large scaffolds assembled by CAAS-IVF, which have been orientated and assigned to pseudochromosomes using publicly available genetic markers.

+ + + +

Annotation

+ +

Gene prediction of the assembled genomic scaffolds has been conducted by CAAS-IVF using GLEAN and BLAT. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes (E=1E-5) and Gene Ontology terms are provided through significant similarity to UniProtKB proteins (E=1E-5).

+ + + +

Sequence alignments

+ +

Further annotations generated by RRes are displayed as additional tracks:

+ +
  • Arabidopsis coding sequences aligned using BLAT: +
    • Alignment parameters: minmatch(2), minscore(30), min identity(80), maxGap(2), evalue threshold(1e-5).
      • +
    • Dataset: 33,410 Arabidopsis TAIR v9 coding sequences.
      • +
    • External links: AtEnsembl transcripts.
      • +
    • +
  • A 95k Brassica UniGene set generated by JCVI aligned using BLAT: +
    • Alignment parameters: default BLAT (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
      • +
    • Dataset: 94,558 Brassica UniGenes.
      • +
    • +
  • A 135k Brassica UniGene set generated by RRes aligned using BLAT: +
    • Alignment parameters: default BLAT (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
      • +
    • Dataset: 135 201 Brassica UniGenes.
      • +
    • +
  • B. rapa BAC end sequences aligned using Decypher tera-blastn: +
    • Alignment parameters: match_score(1), mismatch_score(-3), open_penalty(-5), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-50), word_size (9), query_increment(3), extension_threshold(20), percent identity(95).
      • +
    • Dataset: 196,837 B. rapa BAC end sequences obtained from GenBank 5-Aug-2010.
      • +
    • External links: GenBank.
      • +
    • +
  • B. rapa ESTs aligned using Decypher tera-blastn: +
    • Alignment parameters: match_score(1), mismatch_score(-1), open_penalty(-1), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-20), word_size(9), query_increment(3), extension_threshold(20), percent identity(90).
      • +
    • Dataset: 902,700 Brassica ESTs obtained from GenBank 13-Aug-2010.
      • +
    • External links: GenBank.
      • +
    • +
+ +

References

  1. The genome of the mesopolyploid crop species Brassica rapa.
    Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F et al. 2011. Nat. Genet.. 43:1035-1039.

Picture credit: School Division, Houghton Mifflin Company

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About Cajunus cajan

+ +

Pigeonpea (Cajunus cajan) is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world[1]. Pigeonpea is grown on ∼5 million hectares, making it the sixth most important legume food crop globally. Domesticated >3,500 years ago in India, it is the main protein source for more than a billion people in the developing world and a cash crop that supports the livelihoods of millions of resource-poor farmers in Asia, Africa, South America, Central America and the Caribbean.

+ + + +

Assembly

+ +

Illumina GA and HiSeq 2000 Sequencing system were used to sequence 11 small-insert (180–800 bp) and 11 large-insert (2–20 kb) libraries [1]. This generated a total of 237.2 Gb of paired-end reads, ranging from 50–100 bp. Filtering and correction of the sequence data for very small and/or bad-quality sequences yielded 130.7 Gb of high-quality sequence, ∼163.4× coverage of the pigeonpea genome. Analysis of sequence data for GC content indicated a similar GC content distribution in the genomes of pigeonpea and soybean. Additionally, a set of 88,860 bacterial artificial chromosome (BAC) end sequences were generated using Sanger sequencing from two BAC libraries (69,120 clones) by using the HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes.

+ +

SOAPdenovo was used to assemble 605.78 Mb of the pigeonpea genome de novo, generating a sequence with a contig N50 of 21.95 kb, and longest contig length of 185.39 kb. This was then improved by using both the paired-BAC end sequences (41,302) that passed after filtering through RepeatMasker, and a genetic map comprising 833 marker loci. This increased N50 to 516.06 kb (longest scaffold in chromosome level of 48.97 Mb) . The draft genome assembly has <5.69% (∼34 Mb) unclosed gaps. These analyses showed that mapped genetic loci provide additional information for assembling superscaffolds, especially in regions in which scaffolds were not large enough to cross the repeat rich regions. The generated chromosome-scale scaffolds can be considered as 'pseudomolecules'. The estimated pigeonpea genome size, based on K-mer statistics, is 833.07 Mb, suggesting that the assembly captures 72.7% of the genome in the genome scaffolds. If only the 6,534 scaffolds >2 kb are considered, the assembly spans 578 Mb with an N50 of 0.58 Mb.

+ + + +

Annotation

+ +

A combination of de novo gene prediction programs and homology-based methods were used to predict gene models in the pigeonpea genome. These were combined using the GLEAN algorithm, resulting in the identification of 48,680 genes with an average transcript length of 2,348.70 bp, coding sequence size of 959.35 bp and 3.59 exons per gene. The majority of these predicted genes (99.6%) were supported either by de novo gene prediction, expressed sequence tags (EST)/unigenes or homology-based searching, or a combination of these approaches[1]. Of these genes Ensembl Plants display 2212 genes which were imported from ENA (European Nucleotide Archive).

+ + +

References

  1. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.
    Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena, Jessica A Schlueter, Mark T A Donoghue, Sarwar Azam, Guangyi Fan, Adam M Whaley et al. 2012. Nature Biotechnology. 30:83-89.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Chlamydomonas_reinhardtii.html b/gramene/htdocs/ssi/species/about_Chlamydomonas_reinhardtii.html new file mode 100644 index 00000000..80b375f9 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Chlamydomonas_reinhardtii.html @@ -0,0 +1,20 @@ + +

About Chlamydomonas reinhardtii

+ +

Chlamydomonas reinhardtii is a unicellular green alga from the phylum Chlorophyta, which diverged from land plants over a billion years ago. C. reinhardtii is a model species for studying a broad range of fundamental biological processes including the evolution of chloroplast-based photosynthesis and the structure of eukaryotic flagella. It is haploid, and has a nuclear genome comprising 17 chromosomes with a total size of ~120 Mbp.

+ + +

Assembly

+ +The 121 Mbp draft sequence of the Chlamydomonas nuclear genome was generated at 13x coverage by whole-genome, shotgun sequencing of plasmid and fosmid libraries, followed +by assembly into ~1500 contigs [1]. Assembly into chromosomes was done on the basis of genetic mapping. + + +

Annotation

+ +The set of gene predictions in version 5.5 incorporates new JGI gene expression data from 1M reads generated from nitrogen-starved cells on the 454 Titatnium platform as well as 239M 2x150 stranded Illumina reads and other smaller RNA-Seq datasets. The underlying gene prediction was performed by Mario Stanke using Augustus (annotation version u11.6) + +

The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).

+ + +

References

  1. The Chlamydomonas genome reveals the evolution of key animal and plant functions.
    Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marchal-Drouard L et al. 2007. Science. 318:245-250.

Picture credit: By Ninghui Shi [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0)], from Wikimedia Commons

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Chondrus_crispus.html b/gramene/htdocs/ssi/species/about_Chondrus_crispus.html new file mode 100644 index 00000000..e83c91e7 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Chondrus_crispus.html @@ -0,0 +1,25 @@ + +

About Chondrus crispus

+ +

Wikipedia

+ +

Chondrus crispus - commonly called Irish moss or carrageen moss (Irish carraigín, "little rock") - is a species of red algae which grows abundantly along the rocky parts of the Atlantic coast of Europe and North America. In its fresh condition this protist is soft and cartilaginous, varying in color from a greenish-yellow, through red, to a dark purple or purplish-brown. The principal constituent is a mucilaginous body, made of the polysaccharide carrageenan, which constitutes 55% of its weight. The organism also consists of nearly 10% protein and about 15% mineral matter, and is rich in iodine and sulfur. When softened in water it has a sea-like odour and because of the abundant cell wall polysaccharides it will form a jelly when boiled, containing from 20 to 100 times its weight of water.

+ +

(Text and image from Wikipedia, the free encyclopaedia.)

+ + + +

Assembly

+ +

The assembly presented is the ASM35022v2 assembly submitted to INSDC with the assembly accession GCA_000350225.2.

+ + + +

Annotation

+ +

The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_000350225.2, with additional non-coding genes derived from Rfam. For more details, please visit INSDC annotation import.

+ +

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 59,047 Low complexity (Dust) features, covering 3 Mb (2.4% of the genome); 1,027 RepeatMasker features (annotated with the RepBase library), covering 0 Mb (0.1% of the genome); 19,602 RepeatMasker features (annotated with the PGSB-REdat library), covering 6 Mb (5.7% of the genome); 28,669 Tandem repeats (TRF) features, covering 3 Mb (2.7% of the genome).

+ + +

References

  1. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.
    Janoukovec J, Liu SL, Martone PT, Carr W, Leblanc C, Colln J, Keeling PJ. 2013. PLoS ONE. 8:e59001.

Picture credit: Wikipedia, the free encyclopedia

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About Corcorus capsularis

+ +

Corcorus capsularis (white jute) is one of the most important sources of natural fibre, along with Corcorus olitorius, covering ∼80% of global bast fibre production. The genome size is approximately 400 Mbp (n = 7). The assembly presented here is at the scaffold level, comprising 6,125 scaffolds with a scaffold N50 of 4.1 Mbp.

+ + + +

Assembly

+ +

Whole-genome shotgun sequencing was performed using Roche/454 GS FLX and was assembled using CABOG (version 7). A total of 13.69 Gbp of sequence data was generated (~30x), consisting of 7.87 Gbp of shotgun sequences (~20x), 2.04 Gbp of 3-kbp paired-end sequences (14x physical coverage), 2.26 Gbp of 8-kbp paired-end sequences (15x physical coverage), and 1.51 Gbp of 20-kbp paired-end sequences (11x physical coverage). The resulting assembly was 338 Mbp in 6,125 scaffolds with a scaffold N50 of 4.1 Mbp. Eighty per cent of the assembly was covered with 231 scaffolds (minimum length 120 kbp) and is estimated to cover about 82% of the genome [1].

+ +

More than 97% of the isotigs generated from transcriptome sequencing of seedlings aligned to the genome indicating comprehensive coverage of the gene-rich regions. In addition, more than 97% of the conserved core eukaryotic genes [2] were present in the genome.

+ + + +

Annotation

+ +

A total of 30,096 protein-coding genes were predicted by a combination of de novo, homology and transcriptome-based approaches [1].

+ + +

References

  1. Comparative genomics of two jute species and insight into fibre biogenesis.
    Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QM, Hossain MZ, Ahmed R, Hossain MS et al. 2017. Nature plants. 3:16223.
    2. +
  2. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
    Parra G, Bradnam K, Korf I. 2007. Bioinformatics. 23:1061.

Picture credit: By Luigi Chiesa (Scan by Luigi Chiesa) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.0 it (http://creativecommons.org/licenses/by-sa/2.0/it/deed.en)], via Wikimedia Commons

\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Cucumis_sativus.html b/gramene/htdocs/ssi/species/about_Cucumis_sativus.html new file mode 100644 index 00000000..3d5c83da --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Cucumis_sativus.html @@ -0,0 +1,23 @@ + +

About Cucumis sativus

+ +

Cucumber (Cucumis sativus) is a widely cultivated plant in the gourd family, Cucurbitaceae. It is a creeping vine that bears cucumiform fruits that are used as vegetables. There are three main varieties of cucumber: slicing, pickling, and seedless. Within these varieties, several cultivars have been created. In North America, the term "wild cucumber" refers to plants in the genera Echinocystis and Marah, but these are not closely related. The cucumber is originally from South Asia, but now grows on most continents. Many different types of cucumber are traded on the global market. [1]

+ + + +

Assembly

+ +

The 'Chinese long' inbred line 9930 was selected for the genome sequencing project. A total of 26.5 billion high-quality base pairs were generated, or 72.2-fold genome coverage, of which the Sanger reads provided 3.9-fold coverage and the Illumina GA reads provided 68.3-fold coverage The GA reads ranged in length from 42 to 53 bp. [2]

+ +

The final assembly is of length 195,669,205 bp consisting of 190 scaffolds (N50 = 29,076,228) and 11,366 contigs (N50 = 42,349) [3].

+ + + +

Annotation

+ +

Protein coding gene prediction was done using three methods (cDNA-EST, homology based and ab initio) and a consensus gene set was built by merging all of the results. A total of 26,682 genes were predicted, with a mean coding sequence size of 1,046 bp and an average of 4.39 exons per gene. Under an 80% sequence overlap threshold, 26.7% of the genes were supported by all three gene prediction methods, 25% had both ab initio prediction and homology-based evidence, and 7.4% had ab initio prediction and cDNA-EST expression evidence; the remaining genes were primarily derived from pure ab initio prediction, but the majority of these were supported by multiple gene finders. About 81% of the genes have homologs in the TrEMBL protein database, and 66% can be classified by InterPro. In total, 82% of the genes have either known homologs or can be functionally classified [2].

+ + +

References

  1. Cucumber.
    Wikipedia.
    2. +
  2. The genome of the cucumber, Cucumis sativus L.
    Sanwen Huang, Ruiqiang Li[]Songgang Li. 2009. Nature Genetics. 41:12751281.
    3. +
  3. NCBI page for Cucumis sativus (cucumber) assembly.
    NCBI.

Picture credit: By Francisco Manuel Blanco (O.S.A.) [Public domain], via Wikimedia Commons

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About Cyanidioschyzon merolae

+ +

Cyanidioschyzon merolae is a unicellular red alga from the phylum Rhodophyta and is one of the most primitive red algae. Rhodophyta is an evolutionarily interesting group that falls in Archaeplastida along with green plants but has also given rise to highly diverse groups of protists, including the photosynthetic and non-photosynthetic Chromalveolata. C. merolae can live in acidic hot springs, with pH below 2 and at 45°C.

+ + + +

Assembly

+ +

The nuclear genome is compact (16 Mbp), comprising 20 chromosomes with 5,331 predicted genes. Interestingly, only 26 of the predicted genes have introns.

+ + + +

Annotation

+ +

The genome annotation for Cyanidioschyzon merolae has been imported from Cyanidioschyzon merolae Genome project.

+ +

The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

+ + + +

Links

+ + + +

References

  1. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.
    Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K et al. 2004. Nature. 428:653-657.
    2. +
  2. Image credit: NEON (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Daucus_carota.html b/gramene/htdocs/ssi/species/about_Daucus_carota.html new file mode 100644 index 00000000..f5a5d8dd --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Daucus_carota.html @@ -0,0 +1,21 @@ + +

About Daucus carota subsp. sativus

+ +

Carrot is a globally important root crop whose production has quadrupled between 1976 and 2013, outpacing the overall rate of increase in vegetable production and world population growth through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions[1]

+ + + +

Assembly

+ +

An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. BAC end sequences was used and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions.

+ +

The resulting v2.0 assembly spans 421.5 Mbp and contains 4,907 scaffolds (N50 of 12.7 Mbp), accounting for approximately 90% of the estimated genome size. The scaftig N50 of 31.2 kbp is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mbp) of the assembled genome is included in only 60 super-scaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4 [1].

+ + + +

Annotation

+ +

In assembly v1.0 gene annotation, 32,113 genes were predicted, of which 79% had substantial homology with known genes. The majority (98.7%) of gene predictions had supporting cDNA and/or EST evidence, demonstrating the high accuracy of gene prediction. Relative to five other closely related genomes, carrot was enriched for genes involved in a wide range of molecular functions. 564 tRNAs, 31 rRNA fragments, 532 small nuclear RNA (snRNA) genes, and 248 microRNAs (miRNAs) were also identified, distributed among 46 families.[1]

+ + +

References

  1. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.
    Massimo Iorizzo, Shelby Ellison, Douglas Senalik, Peng Zeng, Pimchanok Satapoomin, Jiaying Huang, Megan Bowman, Marina Iovene, Walter Sanseverino, Pablo Cavagnaro et al. 2016. Nature Genetics. 48:657666.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Dioscorea_rotundata.html b/gramene/htdocs/ssi/species/about_Dioscorea_rotundata.html new file mode 100644 index 00000000..ce20d128 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Dioscorea_rotundata.html @@ -0,0 +1,23 @@ + +

About Dioscorea rotundata

+ +

White Guinea yam (Dioscorea rotundata Poir.) is a common staple food that has contributed enormously to the subsistence and socio-cultural life of millions of people principally in West and Central Africa. Belonging to the monocotyledon the Dioscorea genus, under the family Dioscoreaceae, there are about 450 known species mainly distributed in tropical and subtropical regions of the world. The entire genus is characterised by the occurrence of separate male and female plants (dioecy), a rare trait in angiosperms that has limited efficient breeding. The reference for D. rotundata comes from a diploid individual with an assembled genome size of 594 Mb.

+ + + +

Assembly

+ +

The TDr96_F1 line used for whole genome sequencing was selected from F1 progeny obtained from an open-pollinated D. rotundata breeding line (TDr96/00629) grown under field conditions on the experimental fields of the International Institute of Tropical Agriculture (IITA) in Nigeria. Total DNA from leaf tissue was used for construction of paired-end and mate-pair libraries (2, 3, 4, 5, 6, 8, 20, and 40 Kb insert). These were sequenced using the Illumina MiSeq and HiSeq2500 platforms. In addition, 30,750 BAC clones corresponding to 3,072 Mb of sequence and 5.4× genome coverage were constructed. Of these, 9984 clones were used for BAC-end sequencing, with paired-end reads. A total of 85.14 Gb of sequence data was generated, representing ~149.4x coverage of the 570 Mb genome size estimated by flow cytometry [1].

+ +

Reads were assembled following the ALLPATHS-LG pipeline, using paired-end and mate-pair data, with additional scaffolding carried out using SSPACE and the BAC-end reads. Scaffolds were anchored and ordered into 21 pseudo-chromosomes using a genetic map generated from 150 F1 individuals, obtained from a cross between TDr97/02627 (P1:Female) and TDr99/02627 (P2:Male) breeding lines using RAD-tags as linkage markers. The 21 pseudo-chromosomes represent 76.5 % of the total scaffolds, with a size of ~454 Mb [1].

+ + + +

Annotation

+ +

Gene models were generated using MAKER, with publicly available homologous EST and protein sequences from related species, and assembled transcripts generated using RNA-seq from 18 different D. rotundata tissues. An initial MAKER set of gene models was combined with a legacy AUGUSTUS annotation using JIGSAW to produce 26,198 gene models. These were functionally annotated using BLAST2GO and InterProSCAN [1].

+ +

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 8,371 RepeatMasker features (with the RepBase library), covering 1 Mb (0.2% of the genome); 918,128 Low complexity (Dust) features, covering 83 Mb (18.2% of the genome); 193,894 RepeatMasker features (with the reDAT library), covering 58 Mb (12.8% of the genome); 281,939 Tandem repeats (TRF) features, covering 22 Mb (4.9% of the genome).

+ + +

References

  1. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.
    Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A et al. 2017. BMC Biol.. 15:86.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Galdieria_sulphuraria.html b/gramene/htdocs/ssi/species/about_Galdieria_sulphuraria.html new file mode 100644 index 00000000..9323bdde --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Galdieria_sulphuraria.html @@ -0,0 +1,21 @@ + +

About Galdieria sulphuraria

+ +

Galdieria sulphuraria is an extremophilic unicellular species of red algae. It is the type species of the genus Galdieria. It is known for its broad metabolic capacities, including photosynthesis and heterotrophic growth on over 50 different extracellular carbon sources. The members of the Cyanidiophyceae family are among the most acidophilic known photosynthetic organisms, and the growth conditions of G. sulphuraria, pH between 0 and 4, and temperatures up to 56°C, are among the most extreme known for eukaryotes. Analysis of its genome suggests that its thermoacidophilic adaptations derive from horizontal gene transfer from archaea and bacteria, another rarity among eukaryotes.

+ + + +

Assembly

+ +

The assembly presented is the ASM34128v1 assembly submitted to INSDC with the assembly accession GCA_000341285.1.

+ + + +

Annotation

+ +

The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_000341285.1, with additional non-coding genes derived from Rfam. For more details, please visit INSDC annotation import.

+ +

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 9,272 Low complexity (Dust) features, covering 0 Mb (3.6% of the genome); 251 RepeatMasker features (annotated with the RepBase library), covering 0 Mb (0.3% of the genome); 1,654 RepeatMasker features (annotated with the PGSB-REdat library), covering 0 Mb (1.5% of the genome); 1,406 Tandem repeats (TRF) features, covering 0 Mb (1.0% of the genome).

+ + +

References

  1. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.
    Schnknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Brutigam A, Baker BJ, Banfield JF, Garavito RM et al. 2013. Science. 339:1207-1210.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Glycine_max.html b/gramene/htdocs/ssi/species/about_Glycine_max.html new file mode 100644 index 00000000..d1c14bc8 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Glycine_max.html @@ -0,0 +1,27 @@ + +

About Glycine max

+ +

Glycine max (soybean) is a crop legume that globally constitutes one of the most important sources of animal feed protein and cooking oil. Having originated in East Asia soy is now cultivated world-wide with greatest production in the U.S. Though only a minor proportion of the crop is eaten directly by humans, soybean is a valuable source of protein, containing all essential amino acids, and frequently used as a dietary substitute for meat. Like other legumes, soybean is able to fix atmospheric nitrogen by engaging in a symbiotic relationship with microbial organisms. The complete sequence of the soybean genome not only impacts research and breeding of this crop, but also serves as a reference for genomics research in other legumes. Representing the order Fabales within the eudicot taxonomy, the sequence will also advance research in comparative phylogenomics. As a paleopolyploid, the soybean genome shows evidence of two ancient whole genome duplications, one early in the legume lineage and a second more recent event specific to the soybean lineage. The soybean genome has 20 chromosomes and an estimated size of 1,115 Mbp.

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Assembly

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Glycine max var. Williams 82 was sequenced, assembled, and annotated by the U.S. Department of Energy Joint Genome Institute (JGI) in collaboration with a consortium of research labs and published in 2010. About 13 million shotgun Sanger reads were assembled into 20 chromosomes totalling 975 Mbp with an additional amount in unmapped scaffolds.

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Annotation

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The v1.1 gene set integrates ~1.6 M ESTs and 1.5 billion paired-end Illumina RNA-seq reads with homology- and ab initio-based gene predictions. A total of 54,175 protein-coding loci were predicted and classified into six levels of support (see JGI Phytozome for additional details).

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Links

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References

  1. Genome sequence of the palaeopolyploid soybean.
    Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J et al. 2010. Nature. 463:178-183.
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  2. Image credit: USDA.
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About Gossypium raimondii

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Gossypium raimondii is a species of cotton plant endemic to northern Peru. The Gossypium genus is ideal for investigating emergent consequences of polyploidy. A-genome diploids native to Africa and Mexican D-genome diploids diverged ∼5–10 Myr ago. They were reunited ∼1–2 Myr ago by trans-oceanic dispersal of a maternal A-genome propagule resembling G. herbaceum to the New World, hybridization with a native D-genome species resembling G. raimondii, and chromosome doubling. The nascent AtDt allopolyploid spread throughout the American tropics and subtropics, diverging into at least five species; two of these species (G. hirsutum and G. barbadense) were independently domesticated to spawn one of the world’s largest industries (textiles) and become a major oilseed.[1]

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Assembly

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Assembly of 80,765,952 sequence reads used a modified version of Arachne, integrating linear (15x genome coverage) and paired (3.1x genome coverage) Roche 454 libraries corrected using 41.9 Gbp Illumina sequence, with 1.54x paired-end Sanger sequences from two subclone, six fosmid and two BAC libraries. Cotton genetic and physical maps, and Vitis vinifera and Theobroma cacao synteny were used to identify 51 joins across 64 scaffolds to form the 13 chromosomes. The remaining scaffolds were screened for contamination to produce a final assembly of 1,033 scaffolds (19,735 contigs) and 761.4 Mbp [1][2].

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Annotation

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85,746 transcript assemblies were made from about 1 billion pairs of D5 paired-end Illumina RNA-Seq reads, 55,294 transcript assemblies about 0.25B D5 single end Illumina RNAseq reads, 62,526 transcript assemblies from 0.15B TET single end Illumina RNAseq reads. All these transcript assemblies from RNAseq reads were made using PERTRAN. 120,929 transcript assemblies were constructed using PASA from 56,638 D5 Sanger ESTs, 2.5M D5 454 RNAseq reads and all RNA-Seq transcript assemblies above. 133,073 transcript assemblies were constructed using PASA from 296,214 TET Sanger ESTs and about 2.9M TET 454 reads. The larger number of transcript assemblies from fewer TET sequences is due to fragment nature of the assemblies. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabi (Arabidopsis thaliana), cacao, rice, soybean, grape and poplar proteins to repeat-soft-masked G. raimondii genome using RepeatMasker with up to 2 kbp extension on both ends unless extending into another locus on the same strand.

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Gene models were predicted by homology-based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan. The best scored predictions for each locus are selected using multiple positive factors including EST and protein support, and one negative factor: overlap with repeats. The selected gene predictions were improved by PASA. Improvement includes adding UTRs, splicing correction, and adding alternative transcripts. PASA-improved gene model proteins were subject to protein homology analysis to above mentioned proteomes to obtain Cscore and protein coverage. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score and protein coverage is highest percentage of protein aligned to the best of homologs. PASA-improved transcripts were selected based on Cscore, protein coverage, EST coverage, and its CDS overlapping with repeats. The transcripts were selected if its Cscore is larger than or equal to 0.5 and protein coverage larger than or equal to 0.5, or it has EST coverage, but its CDS overlapping with repeats is less than 20%. For gene models whose CDS overlaps with repeats for more that 20%, its Cscore must be at least 0.9 and homology coverage at least 70% to be selected. The selected gene models were subject to Pfam analysis and gene models whose protein is more than 30% in Pfam TE domains were removed. Final gene set has 37,505 protein coding genes and 77,267 protein coding transcripts[1][2].

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References

  1. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Andrew H. Paterson, Jonathan F. Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C. Showmaker, Shengqiang Shu, Joshua Udall et al. 2012. Nature. 492:423427.
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  2. Gossypium raimondii (D5) genome JGI assembly v2.0 (annot v2.1).
    COTTONGEN.
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About Helianthus annuus

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The domesticated sunflower, Helianthus annuus, is a globally important oil crop that has promise for climate change adaptation, maintaining stable yields across a wide variety of environmental conditions, including drought. The large genome (3.6 gigabases) consists of long and highly similar repeats, making the assembly very challenging.

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Assembly

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The assembly of Helianthus annuus inbred line XRQ was performed using 102-fold coverage of single-molecule real-time (SMRT) cells on the PacBio RS II platform. In total 32.8 million subreads were generated with a read N50 of 13.7 kb and a mean read length of 10.3 kb. The 367 Gbp of raw sequence (340 Gbp of subread data) was assembled into 3 Gbp (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content [1].

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The assembly was performed using WGS 8.3. Reads were first corrected using the PBcR wgs8.3rc1 assembly pipeline and the assembly was polished with quiver after the construction of the pseudomolecules. To overcome challenges associated with the sunflower genome assembly, substantial parameter tuning, code modification and software development were required [1].

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Annotation

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Gene models were predicted using EuGene 4.2. The plant early release of BUSCO (release July 2015) was run on the set of predicted transcripts, and it detected 92% of complete gene models (590 complete single copy and 291 duplicated, respectively) plus 10 additional fragmented gene models.

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References

  1. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.
    Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brire C, Owens GL, Carrre S, Mayjonade B et al. 2017. Nature. 546:148-152.

Picture credit: By i_am_jim (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

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About Hordeum vulgare

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Hordeum vulgare (barley) is the world's fourth most important cereal crop and an important model for ecological adaptation, having been cultivated in all temperate regions from the Arctic Circle to the tropics. It was one of the first domesticated cereal grains originating in the Fertile Crescent over 10,000 years ago. About two-thirds of the global barley crop is used for animal feed, while the remaining third underpins the malting, brewing, and distilling industries. Although the human diet is not a primary use, barley offers potential health benefits, and is still the major calorie source in several parts of the world. Barley is a diploid member of the grass family, making it a natural model for the genetics and genomics of the Triticeae tribe, including polyploid wheat and rye. With a haploid genome size of ~5.3 Gbp in 7 chromosomes, it is one of the largest diploid genomes sequenced to date.

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Assembly

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The barley genome assembly presented here was produced by the International Barley Genome Sequencing Consortium (IBSC) [1] using a hierarchical approach. Initially multiplexed short read BAC by BAC contig assemblies (N50: 79 kbp) were scaffolded using physical, genetic and optical maps (N50: 1.9 Mbp) and were assigned to chromosomes using a POPSEQ genetic map. Finally, the linear order and orientation of scaffold sequences was determined using chromosome-conformation capture sequencing (Hi-C) [2].

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The final chromosome-scale assembly consisted of 6,347 ordered super-scaffolds composed of merged assemblies of individual BACs, representing 4.79 Gbp (~95%) of the genomic sequence content, of which 4.54 Gbp have been assigned to precise chromosomal locations in the Hi-C map.

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The chloroplast genome component and its gene annotation are also present (KC912687).

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Annotation

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Mapping of transcriptome data and reference protein sequences from other plant species identified 83,105 putative gene loci including protein coding genes, non-coding RNAs, pseudogenes and transcribed transposons. These loci were filtered and divided into 39,734 high-confidence and 41,949 low-confidence genes based on sequence homology. Additionally 19,908 long non-coding RNAs and 792 microRNA precursor loci were predicted. Using a set of conserved eukaryotic core genes (BUSCO), it was estimated that the predicted gene models represent 98% of the cv. Morex barley gene complement.

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Regulation

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Mappings for probes from the Barley1 GeneChip array, the Agilent barley full-length cDNA array, and the barley PGRC1 10k A and B array set can be viewed in the browser. For example, see the results for Contig2083_s_at.

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Variation

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Five sources of barley variation data are shown:

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  1. Variation data from WGS survey sequencing of four cultivars, Barke, Bowman, Igri, Haruna Nijo and a wild barley (H. spontaneum). The data was collected as described in [3].
    2. +
  2. SNPs discovered from RNA-Seq performed on the embryo tissues of 9 spring barley varieties (Barke, Betzes, Bowman, Derkado, Intro, Optic, Quench, Sergeant and Tocada) and Morex using Illumina HiSeq 2000 [3].
    3. +
  3. Approximately five million variations from population sequencing of 90 Morex x Barke individuals [4].
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  4. Approximately six million variations from population sequencing of 84 Oregon Wolfe barley individuals [4].
    5. +
  5. SNPs from the Illumina iSelect 9k barley SNP chip[6]. ~2,600 mapped genetic markers associated with these SNPs [5] are also displayed.
    6. +
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References

  1. A chromosome conformation capture ordered sequence of the barley genome.
    Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J et al. 2017. Nature. 544:427-433.
    2. +
  2. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. 2009. Science. 326:289-93.
    3. +
  3. A physical, genetic and functional sequence assembly of the barley genome.
    International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K et al. 2012. Nature. 491:711-716.
    4. +
  4. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.
    Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S et al. 2014. Plant Physiol.. 164
    5. +
  5. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
    Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muoz-Amatrian M, Close TJ, Wise RP, Schulman AH et al. 2013. Plant J.. 76:718-727.

Picture credit: Lucash (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons

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About Leersia perrieri

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Leersia perrieri comes from Madagascar. It was the nearest outgroup of the genus Oryza included in the OMAP project. It has 12 chromosomes with a nuclear genome size of 323Mb (flow cytometry). The sequencing and assembly of this genome was carried out as part of the Oryza Genome Evolution project funded by NSF Award #1026200.

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Assembly

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The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession IRGC105164. Illumina reads of different library sizes were assembled with Allpaths-LG and gaps were closed with GapFiller. The estimated coverage from the WGS was 150x. Total sequence length is 266,687,832 bp; Number of contigs is 10,288; Contig N50: 48,151bp.

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Annotation

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Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

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Gramene/Ensembl Genomes Annotation

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Additional annotations generated by the Gramene and Ensembl Plants project include:

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  • Gene phylogenetic trees with other other Gramene species, see example.
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  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
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  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
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Links

+ + + diff --git a/gramene/htdocs/ssi/species/about_Lupinus_angustifolius.html b/gramene/htdocs/ssi/species/about_Lupinus_angustifolius.html new file mode 100644 index 00000000..87af8f61 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Lupinus_angustifolius.html @@ -0,0 +1,19 @@ + +

About Lupinus angustifolius

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Lupins are grain legumes that form an integral part of sustainable farming systems and have been an important part of the human diet for thousands of years. Planted in rotation with cereal crops, lupins reduce the need for nitrogenous fertilizer, provide valuable disease breaks and boost cereal yields. Lupins thrive on low-nutrient soils due to their ability to fix atmospheric nitrogen in symbiosis with beneficial bacteria and efficiently take up phosphorus from soils. Consequently, they are effective ecological pioneers and able to colonize extremely impoverished soils such as coastal sand dunes and new lava soils set down by recently erupted volcanoes. Narrow-leafed lupin (Lupinus angustifolius) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free [1].

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Assembly

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The haploid genome size for NLL was previously estimated by flow cytometry to be 924 Mbp. K-mer-based estimation of genome size predicted a similar value of 951 Mb. Initial assembly of the Tanjil genome using only paired-end Illumina data produced 191 701 scaffolds in 521 Mbp, with an N50 of 10,137 and N50 length of 13.8 kbp. The assembly was improved via scaffolding with additional paired-end, mate-pairs and BAC-end data totalling an average coverage of 162.8x. This resulted in a contig assembly with 1,068,669 contigs, totalling 810 Mbp or 85% of the k-mer-based estimated genome size. The final scaffold assembly after removing scaffolds less than 200 bp comprised 14,379 scaffolds totalling 609 Mbp with a contig N50 length of 45,646 bp and scaffold N50 of 232 and scaffold N50 length of 703 Kb [1].

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Annotation

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A total of 33,076 protein-coding genes were annotated after combining evidence from transcriptome alignments derived from five different tissue types (leaf, stem, root, flower and seed), protein homology, and in silico gene prediction. Additionally, peptide data from proteomics analysis of leaf, seed, stem and root samples were mapped to both the translated gene annotations and the 6-frame translation of the whole-genome assembly. Proteogenomic comparison of peptide-mapping versus gene annotation supported between 94 and 1134 annotations per tissue type, and provided valuable information on tissue localization for the products of these genes. InterPro terms were the most informative functional annotation assigned to NLL proteins with 26,580 (80.4%) proteins annotated [1].

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References

  1. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plantmicrobe interactions and legume evolution.
    James K. Hane, Yao Ming, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven Cannon et al. 2016. Plant Biotechnology Journal. 15:318-330.
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About Manihot esculenta

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Cassava (Manihot esculenta Crantz) is grown throughout tropical Africa, Asia and the Americas for its starchy storage roots, and feeds an estimated 750 million people each day. Farmers choose it for its high productivity and its ability to withstand a variety of environmental conditions (including significant water stress) in which other crops fail. However, it has low protein content, and is susceptible to a range of biotic stresses. Despite these problems, the crop production potential for cassava is enormous, and its capacity to grow in a variety of environmental conditions makes it a plant of the future for emerging tropical nations. Cassava is also an excellent energy source - its roots contain 20-40% starch that costs 15-30% less to produce per hectare than starch from corn, making it an attractive and strategic source of renewable energy [2].

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Assembly

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This assembly was created by the DOE-Joint Genome Institute and was obtained by a whole genome shotgun (WGS) strategy, using 454 Life Sciences technology. The cassava genome assembled into 12,977 scaffolds span a total of 532.5 Mbp [1].

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Annotation

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To produce the current "Cassava V6.1" gene set, the homology-based gene prediction programs FgenesH and GenomeScan were used, along with the PASA program to integrate expression information from cassava ESTs and RNA-Seq.

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Transcript data from three sources were integrated. First, RNA-Seq root and shoot tissues from Albert and Namikonga varieties, with and without challenge by CBSV 1x50 (1,055,722,008 initial reads, 895,271,180 reads after quality trimming) and 2x100 (340,899,946 initial reads; 282,586,400 reads after quality trimming) reads were aligned to the genome and assembled with phytozome in-house software Pertran. This yielded 51,588 and 62,488 transcript assemblies from PE and SE reads respectively. These were aligned to the genome with PASA (90 % identity and 60% coverage cutoffs) to make 69,624 aligned assemblies. In addition, ESTs from previous 454 sequencing were assembled with Pertran and added to 80,459 ESTs from GenBank and aligned to the genome with PASA (95% identity, 60% coverage) to generate 27,470 aligned assembles [2].

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References

  1. The Cassava Genome: Current Progress, Future Directions.
    Simon Prochnik, Pradeep Reddy Marri, Brian Desany, Pablo D. Rabinowicz, Chinnappa Kodira, Mohammed Mohiuddin, Fausto Rodriguez, Claude Fauquet, Joseph Tohme, Timothy Harkins et al. 2012. Tropical Plant Biology. 5:88-94.
    2. +
  2. Phytozome: a comparative platform for green plant genomics.
    David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam and Daniel S. Rokhsar. 2012. Nucleic Acids Research. 40
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About Medicago truncatula

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Medicago truncatula (Barrel Medic) is a small annual legume native to the Mediterranean region. As other legumes, it forms symbioses with nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi.
+This species has been chosen as a model organism for legume biology because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production, and is amenable to genetic transformation.
M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox. The complete reference sequence displayed here is the 4.0 assembly update published in 2014 [2]. The nuclear genome has 8 chromosomes.

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Assembly

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Medicago truncatula cultivar A17 was sequenced and assembled by the Medicago truncatula Sequencing Consortium in 2011 [1]. The draft sequence is based on a BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes.

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In 2014, the assembly was updated (Mt 4.0) [2] and replaces the previous assembly (Mt3.5). Whereas the Mt3.5 release consisted of ~250 Mb in pseudomolecules and ~100 Mb of unanchored sequence, the Mt4.0 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~330 Mb aligns accurately with the Optical Map. Most of the sequences and genes that were previously in the unanchored portion of Mt3.5 have now been incorporated into Mt4.0 pseudomolecules, with the exception of only ~20Mb of unplaced sequence.

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Annotation

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Genome annotation (Mt3.5) was carried out by the International Medicago Genome Annotation Group (IMGAG) [1]. JCVI has continued to curate and improve the M. truncatula genome sequence and annotation, and published in 2014 a new gene set (Mt4.0) [2]. Altogether, Pseudomolecules and unassigned BACs (Mt4.0) contain a total of 50,444 protein-coding gene loci (~31,500 high confidence genes and ~19,000 low confidence genes).

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The new pseudomolecules were annotated by combining Mt3.5 gene models, with predictions from Augustus and FGENESH as well as expression data and protein matches primarily using Evidence Modeler (EVM). Whenever possible, gene identifiers have been preserved between Mt3.5 and Mt4.0.

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Non coding RNA genes have also been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).

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Regulation

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269,501 EST sequences have been aligned to the genome with STAR.

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Links

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References

  1. The Medicago genome provides insight into the evolution of rhizobial symbioses.
    Young N,Debell F,Oldroyd GED,Geurts R, Cannon ED,Udvardi MK,Benedito VA,Mayer KFX,Gouzy J,Schoof H et al. 2011. Nature. 480:520-524.
    2. +
  2. An improved genome release (version Mt4.0) for the model legume Medicago truncatula.
    Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H et al. 2014. BMC Genomics. 15:312.
    3. +
  3. Image from WikiCommons.
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About Musa acuminata

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Musa acuminata (banana) is native to tropical South and Southeast Asia and is cultivated throughout the tropics. Grown primarily for its fruit, rich in starch, banana is the most popular fruit in industrialized countries. Cultivars mainly involve Musa acuminata (A-genome) and Musa balbisiana (B-genome) and are sometimes diploid but generally triploid. Banana is the first non-grass monocotyledon to be sequenced, making it an important genome for the comparative analysis of plants.

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Assembly

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The genome sequence, assembly and protein coding genes annotation of the Musa acuminata ssp. malaccensis doubled-haploid genome have been generated by the Global Musa Genomics Consortium, led jointly by the CIRAD and the Genoscope.

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Its genome was released in July 2012 consisting of 24,425 contigs and 7,513 scaffolds with a total length of 472.2 Mbp, which represented 90% of the estimated DH-Pahang genome size. 70% of the assembly (332 Mbp) were anchored along the 11 Musa linkage groups of the Pahang genetic map.

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Annotation

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About 36,500 protein-coding genes were identified, as well as 235 microRNAs from 37 families.

+ + +

References

  1. The Genetic Diversity of Banana in Figures.
    Lescot T.. 2011. FruiTrop..
    2. +
  2. Image credit: Telrnya (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
    3. +
  3. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
    D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M et al. 2012. Nature. 488:213-217.
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About Nicotiana attenuata

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The pyridine alkaloid nicotine, whose addictive properties are well known to humans, is the signature compound of the genus Nicotiana (Solanaceae). In nature, nicotine is arguably one of the most broadly effective plant defense metabolites, in that it poisons acetylcholine receptors and is thereby toxic to all heterotrophs with neuromuscular junctions. Field studies using genetically modified Nicotiana attenuata(coyote tobacco) plants, an annual wild diploid native to western North America, have revealed that this toxin fulfills multifaceted ecological functions that contribute to plant fitness [1].

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Assembly

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The sequencing of the genome of N. attenuata was done using 30× Illumina short reads, 4.5x 454 reads, and 10x PacBio single-molecule long reads. It was then assembled into 2.37 Gbp of sequences representing 92% of the expected genome size. From this was generated a 50x optical map and a high-density linkage map for super-scaffolding, which anchored 825.8 Mbp to 12 linkage groups and resulted in a final assembly with a N50 contig equal to 90.4 kbp and a scaffold size of 524.5 kb [1].

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Annotation

+ +

Using approximately 50x Illumina short reads, the Nicotiana obtusifolia genome was assembled with a 59.5 kbp and 134.1 kbp N50 contig and scaffold N50 size, respectively. The combined annotation pipeline integrating both hint-guided AUGUSTUS and MAKER2 gene prediction pipelines predicted 33,449 gene models in the N. attenuata genome. More than 71% of these gene models were fully supported by RNA-sequencing (RNA-seq) reads and 12,617 and 18,176 of these genes are orthologous to Arabidopsis and tomato genes, respectively [1].

+ + +

References

  1. Wild tobacco genomes reveal the evolution of nicotine biosynthesis.
    Shuqing Xu, Thomas Brockmoller,a, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke et al. 2017. PNAS. 114(23):61336138.
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Oryza_aus.html b/gramene/htdocs/ssi/species/about_Oryza_aus.html new file mode 100644 index 00000000..6c36a51a --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_aus.html @@ -0,0 +1,76 @@ +

About Oryza sativa aus (cA1) subgroup OsN22

+ + +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. N22 (collected from: India) is selected as the representative of cA1 subpopulation, in which the accessions are mostly collected from India, Bangladesh and Nepal.

+ +

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

+ + +

Images

+ +

N22 from Rod Wing's group +

Image provided by Yong Zhou

+

+ + + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. N22 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA1 subpopulation. The whole DNA was sequenced by 65 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+

For more detailed information please refer to below:

+ + +

OsN22RS2

+

Organism name: Oryza sativa aus subgroup (rice)

+

Infraspecific name: Cultivar: N 22::IRGC 19379-1 (IRGC 117534)

+

BioSample: SAMN04568482

+

BioProject: PRJNA315689

+

Submitter: University of Arizona

+

Date: 2020/01/06

+

Assembly level: Chromosome

+

Genome representation: full

+

GenBank assembly accession: GCA_001952365.3 (latest)

+

RefSeq assembly accession: n/a

+

RefSeq assembly and GenBank assembly identical: n/a

+

WGS Project: LWDA02

+

Assembly method: CANU v. v1.5; MECAT v. v1.3; FALCON v. 2017.06.28-18.01-py2.7-ucs4

+

Expected final version: no

+

Genome coverage: 65.0x

+

Sequencing technology: PacBio

+

IDs: 8130841 [UID] 22230838 [GenBank]

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Regulation

+ +

N/A

+ + +

Variation

+ +

19,343,353 SNPs called for this Magic16 genome that is part of the 3000 rice genome project by Dr. Rod Wing's group from resequencing reads using GATK4 software.

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
+ + +

References

+ +

Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

+ +

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K et al. 2018. “Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation across the Genus Oryza.” Nature Genetics 50 (2): 285–96.

+ +

Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M et al. 2018. “Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice.” Nature 557 (7703): 43–49.

+ + +

Links

+ +

GenBank: GCA_001952365.3

+

Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

USDA repo for germplasm: N22

+

IRRI repo: IRGC 135996, N 22

diff --git a/gramene/htdocs/ssi/species/about_Oryza_barthii.html b/gramene/htdocs/ssi/species/about_Oryza_barthii.html new file mode 100644 index 00000000..0b5989d1 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_barthii.html @@ -0,0 +1,29 @@ + + +

About Oryza barthii

+

Oryza barthii is the AA genome progenitor of the West African cultivated rice, O. glaberrima. It belongs to the AA genome group and has 12 chromosomes and a nuclear genome size of 411Mb (flow cytometry). It is found in mopane or savanna woodland, savanna or fadama. Grows in deep water, seasonally flooded land, stagnant water, and slowly flowing water or pools; prefers clay or black cotton soils. Found in open habitats. This work was part of the OGE project funded by NSF Award #1026200.

+ + +

Assembly

+

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using project accession ABRL03000000. The sequence data were generated by PacBio technology. The estimated coverage from the WGS was xxx. Total sequence length 344,913,874bp; Number of contigs 28; Contig N50 14,688,426bp.

+ + +

Annotation

+

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline at CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene and Ensembl Plants project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1) and other Oryza AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
    • +

Links

+ + diff --git a/gramene/htdocs/ssi/species/about_Oryza_brachyantha.html b/gramene/htdocs/ssi/species/about_Oryza_brachyantha.html new file mode 100644 index 00000000..13a56a32 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_brachyantha.html @@ -0,0 +1,37 @@ + +

About Oryza brachyantha

+ +

Oryza brachyantha (wild rice) is a distant relative of cultivated rice (O. satia Japonica and O. sativa Indica). It is placed on the basal lineage of Oryza and is the only member of the genus assigned to the F-genome type. An annual or weekly perennial tufted grass, it is distributed in west and central Africa, and grows in open wetland habitats. It has potentially useful traits for rice breeding, including resistance/tolerance to yellow stem borer, leaffolder, whorl maggot and bacterial blight. The O. brachyantha genome provides an important resource for functional and evolutionary studies in the genus Oryza. Its nuclear genome is diploid (2n = 24) and ~362 Mbp.

+ + + +

Assembly

+ +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accessionAGAT0200000. The estimated coverage from the WGS was ?. Total sequence length 258,902,551 bp; Number of contigs 26; Contig N50 11,392,507 bp. +

+ + + +

Annotation

+ +

Protein-coding genes were annotated using an evidence-based MAKER-P pipeline in CSHL. +

+ + +

Gramene/Ensembl Genomes Annotation

+ +

Additional annotations generated by the Gramene project include:

+ +
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), Arabidopsis thaliana and a few other AA genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +

+ +

Links

+ + + +

References

  1. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
    Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C et al. 2013. Nat Commun. 4:1595.
diff --git a/gramene/htdocs/ssi/species/about_Oryza_carolina.html b/gramene/htdocs/ssi/species/about_Oryza_carolina.html new file mode 100644 index 00000000..f1cc7506 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_carolina.html @@ -0,0 +1,51 @@ +

About Oryza carolina rice

+ + +

Carolina rice typically refers to the type of Oryza sativa, or Asian rice, that was grown in the Carolina Lowcountry during the colonial and antebellum periods. There were two different varietals, Carolina White rice and Carolina Gold rice, distinguishable by the color of their husks.

+ + +

Images

+ +

+

+ + +

Assembly

+ +

Sequencing was performed using PacBio technology as deascribed in Vaughn et al (2021). Raw PacBio reads (n = 3,765,107; ~70x coverage) were assembled into 209 contigs, using Canu (v1.5)(Koren et al, 2017), and polished with Quiver (smrtlink v5.0.1 suite, now at github.com/PacificBiosciences/GenomicConsensus). PacBio raw reads were further polished with pilon v1.22 (Walker et al, 2017) using "10X Genomics" linked-reads aligned by Longranger v2.1.6 (github.com/10XGenomics/longranger). Repeat masking was performed as part of the MAKER-P pipeline (Campbell et al, 2014) using custom repeat libraries, PReDa_121015_short.fasta (DNA) and TE_protein_db_121015_short_header.fasta (protein)(Stein et al, 2018; Copetti et al, 2015). + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

+

Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

+

Copetti, Dario, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, et al. 2015. “RiTE Database: A Resource Database for Genus-Wide Rice Genomics and Evolutionary Biology.” BMC Genomics 16 (July): 538.

+

Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

+

Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

+

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018;50:285–296.

+

Vaughn, Justin N., Walid Korani, Joshua C. Stein, Jeremy D. Edwards, Daniel G. Peterson, Sheron A. Simpson, Ramey C. Youngblood, et al. 2021. “Gene Disruption by Structural Mutations Drives Selection in US Rice Breeding over the Last Century.” PLoS Genetics 17 (3): e1009389.

+

Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

+ + +

Links

+ +

Useful links to other resources

+

GenBank: GCA_004007595.1 +

Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

+

USDA repo for germplasm: N/A

+

IRRI repo: N/A

diff --git a/gramene/htdocs/ssi/species/about_Oryza_glaberrima.html b/gramene/htdocs/ssi/species/about_Oryza_glaberrima.html new file mode 100644 index 00000000..3f5b35b0 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_glaberrima.html @@ -0,0 +1,39 @@ + +

Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012).

+ + +

About Oryza glaberrima

+

Oryza glaberrima (African rice) is a cultivated grain distinct from its better known cousin Oryza sativa (Asian rice). African rice was independently domesticated ~3000 years ago in the Niger River Delta from its still extant progenitor, Oryza barthii. While lacking many of the agronomic and quality traits found in Asian rice, O. glaberrima is significant for its resistance to many pests and diseases and for its tolerance of drought and infertile soils. Interspecific crosses between African and Asian rice have produced cultivars with improved yield and quality traits, that have been adopted by many African countries to meet the growing need for rice as a staple food. From a scientific perspective the genome of O. glaberrima provides insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 Mbp.

+ + +

Assembly

+

The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000. The estimated coverage from the WGS was xxx. Total sequence length 344,456,705bp; Number of contigs 25; Contig N50 15,266,279bp.

+ + +

Annotation

+

Protein-coding genes were annotated with MAKER-P software in CSHL.

+ + +

Gramene/Ensembl Genomes Annotation

+

Additional annotations generated by the Gramene project include:

+
  • Gene phylogenetic trees with other Gramene species, see example.
    • +
  • Lastz Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1), and a few AA oryza genomes, see example.
    • +
  • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
    • +
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
    • +
  • Identification of various repeat features from MIPS and AGI repeat libraries.
    • +
  • Variation effect prediction with sequence ontology, for example.
    • +

Links

+ + +

References

  1. Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences.
    Li ZM, Zheng XM, Ge S. 2011. Theor. Appl. Genet.. 123:21-31.
    2. +
  2. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.
    Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. 2010. Plant J.. 63:990-1003.
    3. +
  3. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.
    Guyot R, Garavito A, Gavory F, Samain S, Tohme J, Ghesquire A, Lorieux M. 2011. PLoS ONE. 6:e17726.
    4. +
  4. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.
    Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA. 2011. BMC Genomics. 12:142.
    5. +
  5. Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
    Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M et al. 2011. Plant J.. 66:796-805.
    6. +
  6. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum.
    Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J et al. 2010. Mol. Biol. Evol.. 27:2487-2506.
    7. +
  7. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices.
    Roulin A, Chaparro C, Pigu B, Jackson S, Panaud O. 2010. Genome Biol Evol. 2:132-139.
diff --git a/gramene/htdocs/ssi/species/about_Oryza_glumaepatula.html b/gramene/htdocs/ssi/species/about_Oryza_glumaepatula.html index eca0a0ff..2f020e01 100644 --- a/gramene/htdocs/ssi/species/about_Oryza_glumaepatula.html +++ b/gramene/htdocs/ssi/species/about_Oryza_glumaepatula.html @@ -1,29 +1,15 @@ - -

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. glumaepatula in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

- -

About Oryza glumaepatula

Oryza glumaepatula is a wild rice from South America, one of the rice species included in the OMAP project. It belongs to the AA genome group and has 12 chromosomes with a nuclear genome size of 464Mb (flow cytometry). It is found in deep and sometimes flowing water. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Antonio Oliveira (Brazil).

-

Assembly

-

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession GEN1233_2. Illumina reads of different library sizes were assembled with Allpaths-LG, scaffolds were constructed with SSPACE, and gaps were closed with GapFiller. The estimated coverage from the WGS was 135x. Total sequence length 372,860,283 bp; Number of contigs 17,912; Contig N50: 31,921bp.

- +

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession ALNU03000000. The estimated coverage from the WGS was ?. Total sequence length 386,178,655 bp; Number of contigs 33; Contig N50: 18,238,801bp.

Annotation

-

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

- +

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

- -

Variation

- -

This data comes from the Oryza Genome Evolution (OGE) project, it includes 4.9M SNPs called from 7 accessions of species Oryza glumaepatulai

- - -

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene project include:

diff --git a/gramene/htdocs/ssi/species/about_Oryza_granulata.html b/gramene/htdocs/ssi/species/about_Oryza_granulata.html index a91d27dc..1f938cb8 100644 --- a/gramene/htdocs/ssi/species/about_Oryza_granulata.html +++ b/gramene/htdocs/ssi/species/about_Oryza_granulata.html @@ -15,9 +15,6 @@

The assembly was submitted into Genbank with accession ALNT00000000.

-

Data Usage

- -

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

diff --git a/gramene/htdocs/ssi/species/about_Oryza_indica.html b/gramene/htdocs/ssi/species/about_Oryza_indica.html new file mode 100644 index 00000000..e8107b78 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_indica.html @@ -0,0 +1,31 @@ + +

About Oryza sativa Indica

+ +

Oryza sativa Indica is one of the two most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely grown in the hot climates of Southern Asia. The genome of Indica is very similar to that of Japonica, which is generally restricted to temperate climes such as Japan.

+ + + +

Assembly

+ +

The genome of Oryza sativa Indica Group cultivar 93-11 was sequenced by the Chinese Academy of Agricultural Sciences (CAAS) with PacBio technology and assembled using Canu v.1.5.

+ + + + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + + + + + + + +

Links

+ + diff --git a/gramene/htdocs/ssi/species/about_Oryza_indicair8.html b/gramene/htdocs/ssi/species/about_Oryza_indicair8.html new file mode 100644 index 00000000..fd1fd3cb --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_indicair8.html @@ -0,0 +1,49 @@ +

About Oryza sativa subgroup IR8

+ +

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations. Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa IRGC 127652 (aus variety cv. NATEL BORO::IRGC 34749-1) is selected as the representative of cA2 subpopulation.

+ + +

Images

+ +

IR 8 +

Multiple images in GRIN

+ + +

Assembly

+ +

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127652 (aus variety cv. NATEL BORO::IRGC 34749-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA2 subpopulation.

+

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

+ + +

Annotation

+ +

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

+ + +

Variation

+ +

Variation Data mapped to the assembly including SNP, SV, QTL, markers

+ +

Large structural variation of 16 PSRefSeqs are available (including map to N22):

+
  1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
    2. +
  2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
+ + +

References

+ +

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

+

Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

+

Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

+

Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

+

Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

+

Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

+ + +

Links

+ +

Useful links to other resources

+

GenBank: GCA_001889745.1

+

Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

+

USDA repo for germplasm: Multiple hits

+

IRRI repo: IR 8

+ diff --git a/gramene/htdocs/ssi/species/about_Oryza_longistaminata.html b/gramene/htdocs/ssi/species/about_Oryza_longistaminata.html index 8c09b42a..5ef7b690 100644 --- a/gramene/htdocs/ssi/species/about_Oryza_longistaminata.html +++ b/gramene/htdocs/ssi/species/about_Oryza_longistaminata.html @@ -1,70 +1,32 @@ - -

- About Oryza longistaminata -

+ +

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. glumaepatula in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Rod Wing.

+
+ + +

About Oryza longistaminata

-

Oryza longistaminata (AA genome type) is a wild rice, Perennial, tall (2 m or more), erect, and rhizomatous grass; ligule of lower leaves >15 mm, acute or 2-cleft; panicles open to intermediately open; spikelets 4.5-11.4 mm long and 2-3 mm wide, awned (2-5 cm long); anther 1.5-8.2 mm long. -

+

Oryza longistaminata (AA genome type) is a wild rice, Perennial, tall (2 m or more), erect, and rhizomatous grass; ligule of lower leaves >15 mm, acute or 2-cleft; panicles open to intermediately open; spikelets 4.5-11.4 mm long and 2-3 mm wide, awned (2-5 cm long); anther 1.5-8.2 mm long.

+ +

Assembly

+ +

A whole genome shotgun assembly (i.e. Illumina sequence, SOAP de novo assembly) of O. longistaminata was generated by Professor Wen Wang (Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China) in collaboration with BGI-Shenzhen, China. The genome assembly was composed of 135,973 scaffolds spanning 344.6Mb with a N50 scaffold size of 62.4kb. Using this assembly, the Arizona Genomics Institute (AGI) selected scaffolds and contigs that were syntenic to the short arm of chromosome 3 of O. sativa ssp.japonica, and the order and orientation of each scaffold/contig was confirmed using Genome Puzzle Mater software (GPM, unpublished) to produce a Chr3S pseudomoleclue. The final O. longistaminata chromosome 3 short arm resulted in a single scaffold of 14,404,039bp composed of 4,724 contigs.

-

- Assembly -

+ +

Annotation

-

This assembly is obtained from NCBI Genbank, O_longistaminata_v1.0. It was submitted by BGI on 2014/12/09, accession GCA_000789195.1, including 60,198 scaffolds assembled from 52.5x coverage Illumina HiSeq reads by SOAPdenovo v. 2.2. The total sequence length is 326,442,508. -

+

Protein-coding genes, annotation of repeats and transposable elements were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. MAKER-P was used as evidence-based genome annotation pipeline. RepeatMasker was used to annotate repeats and transposable elements using species-specific de novo repeat libraries. Non coding RNA genes were predicted by AGI with Infernal, tRNA genes with tRNAScan.

- - -

- Annotation -

-

Ab initio gene prediction with program fgenesh from Gramene

+ +

Links

- -

- Gramene/Ensembl Genomes Annotation -

-

Additional annotations generated by the Gramene project include:

- -
    -
  • Gene phylogenetic trees with other Oryza speices and outgroup species: Leersia perrieri, Brachypodium distachyon, Arabidopsis thaliana and Arabidopsis thaliana, see example . -
    • -
  • - Blastz Whole Genome Alignment to Oryza sativa Japonica (MSU6), see example. -
    • -
  • - Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example. -
    • -
  • - Identification of various repeat features from MIPS and AGI repeat libraries -
    • + - - -

    - References and Links -

    -

    References

    -
      - -
    • "Hierarchical scaffolding with Bambus." Pop M, Kosack DS, Salzberg SL, Genome Research, 2004. 14(1):149-59.
      • -
    - -

    - Links -

    - - - - +

    References

    1. Hierarchical scaffolding with Bambus.
      Pop M, Kosack DS, Salzberg SL. 2004. Genome Res.. 14:149-159.

    Picture credit: Paul Sanchez, Arizona Genomics Institute.

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Oryza_meridionalis.html b/gramene/htdocs/ssi/species/about_Oryza_meridionalis.html new file mode 100644 index 00000000..badfdcff --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_meridionalis.html @@ -0,0 +1,37 @@ + + +

    About Oryza meridionalis

    + +

    Oryza meridionalis is a wild rice found in Australia, one of the wild rice species included in the OMAP project. It belongs to the AA genome group. It has 12 chromosomes with a nuclear genome size of 435Mb (flow cytometry). It is found at edges of freshwater lagoons, temporary pools, and swamps in 15-20 cm of water and grows in black, clay soil in open habitats. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Olivier Panaud (France) and Robert Henry (Australia).

    + + + +

    Assembly

    + +

    The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession ALNW03000000. The estimated coverage from the WGS was ?. Total sequence length 379,254,020 bp; Number of contigs 30; Contig N50: 16,096,529 bp.

    + + + +

    Annotation

    + +

    Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

    + + +

    Gramene/Ensembl Genomes Annotation

    + +

    Additional annotations generated by the Gramene project include:

    + +
    • Gene phylogenetic trees with other Gramene species: see example.
      • +
    • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1), see example.
      • +
    • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
      • +
    • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
      • +
    • Identification of various repeat features from MIPS and AGI repeat libraries.
      • +

    Links

    + + + diff --git a/gramene/htdocs/ssi/species/about_Oryza_nivara.html b/gramene/htdocs/ssi/species/about_Oryza_nivara.html new file mode 100644 index 00000000..0a36afc6 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_nivara.html @@ -0,0 +1,36 @@ + + +

    About Oryza nivara

    + +

    Oryza nivara is a wild rice from India; one of rice species being used in the OMAP project. It belongs to the AA genome group. Breeders are interested in this organism because it exhibits resistance to grassy stunt virus. It is found in swampy areas, at edges of ponds and tanks, beside streams, in ditches, in or around rice fields. It usually grows in shallow water up to 0.3 m. seasonally dry; in open habitats. It has 12 chromosomes and a nuclear genome size of 448Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Y. Hsing (Taiwan).

    + + + +

    Assembly

    + +

    The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited to Genbank under project accession AWHD02000000. The estimated coverage from the WGS was ?. Total sequence length 393,961,846bp; Number of contigs 24; Contig N50: 18,986,252bp.

    + + + +

    Annotation

    + +

    Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

    + + +

    Gramene/Ensembl Genomes Annotation

    + +

    Additional annotations generated by the Gramene project include:

    + +
    • Gene phylogenetic trees with other Gramene species: see example.
      • +
    • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), see example.
      • +
    • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
      • +
    • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
      • +
    • Identification of various repeat features from MIPS and AGI repeat libraries.
      • +

    Links

    + + + diff --git a/gramene/htdocs/ssi/species/about_Oryza_officinalis.html b/gramene/htdocs/ssi/species/about_Oryza_officinalis.html index ca9e1cd9..ad8f6e56 100644 --- a/gramene/htdocs/ssi/species/about_Oryza_officinalis.html +++ b/gramene/htdocs/ssi/species/about_Oryza_officinalis.html @@ -15,9 +15,6 @@

    A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of Oryza officinalis using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually.

    -

    Data Usage

    - -

    These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. For inquiries and information on how to cite these data please contact Dr. Rod Wing.

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_punctata.html b/gramene/htdocs/ssi/species/about_Oryza_punctata.html new file mode 100644 index 00000000..7cfd087e --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_punctata.html @@ -0,0 +1,36 @@ + + +

    About Oryza punctata

    + +

    Oryza punctata is a wild rice species native to Africa. Breeders are interested because of demonstrated resistance to bacterial blight and brown plant hoppers. O. punctata, a diploid, belongs to the O. officinalis complex within the Oryzeae genome groups, and belongs to the BB genome type. It can be found in open or semi-open habitats such as forest margins, grassland and thickets, scrub lands, open bush or shifting cultivation fields, and rice fields. It has 12 chromosomes and a nuclear genome size of 423Mb (flow cytometry). This work was part of the OGE project funded by NSF Award #1026200.

    + + + +

    Assembly

    + +

    The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) with PacBio technology and deposited into Genbank under accession AVCL0200000. The estimated coverage from the WGS was ?. Total sequence length 419,076,415 bp; Number of contigs 28; Contig N50 18,594,736bp.

    + + + +

    Annotation

    + +

    Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline in CSHL.

    + + +

    Gramene/Ensembl Genomes Annotation

    + +

    Additional annotations generated by the Gramene project include:

    + +
    • Gene phylogenetic trees with other Gramene species: see example.
      • +
    • Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSPv1) and other AA genomes, see example.
      • +
    • Ortholog based DAGchainer synteny detection against other AA genomes, see example.
      • +
    • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
      • +
    • Identification of various repeat features from MIPS and AGI repeat libraries.
      • +

    Links

    + + + diff --git a/gramene/htdocs/ssi/species/about_Oryza_rufipogon.html b/gramene/htdocs/ssi/species/about_Oryza_rufipogon.html new file mode 100644 index 00000000..0e90264d --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_rufipogon.html @@ -0,0 +1,42 @@ + + +

    About Oryza rufipogon

    + +

    Oryza rufipogon (AA genome type) is a wild rice, perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-10 cm long; anthers >3 mm reaching 7.4 mm long.

    + +

    Chromosome number: 2n=2x=24

    + +

    Genome: AA

    +Distribution: Australia, Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Sri Lanka, Thailand, and Vietnam.

    +Habitat: Found in swamps and marshes, in open ditches, swampy grassland, ponds, along river banks, at the edges of lakes, and in or at the margins of rice fields, commonly found in deep water areas (0.2-4m). Grows in clay/loam soil and black soil, in full sun.

    + + + +

    Assembly

    + +

    The sequencing and assembly was done by Dr. Bin Han's group in Shanghai Institutes for Biological Sciences, CAS.

    + + + +

    Annotation

    + +

    Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

    + + + +

    Gramene/Ensembl Genomes Annotation

    + +

    Additional annotations generated by the Gramene and Ensembl Plants project include:

    + +
    • Gene phylogenetic trees with other other Gramene species, see example.
      • +
    • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
      • +
    • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.
      • +

    Links

    + + + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa.html b/gramene/htdocs/ssi/species/about_Oryza_sativa.html new file mode 100644 index 00000000..73654d5b --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa.html @@ -0,0 +1,76 @@ + +

    About Oryza sativa Japonica Nipponbare

    + +

    Oryza sativa Japonica (rice) is the staple food for 2.5 billion people. It is the grain with the second highest worldwide production after Zea mays. In addition to its agronomic importance, rice is an important model species for monocot plants and cereals such as maize, wheat, barley and sorghum. O. sativa has a compact diploid genome of approximately 500 Mbp (n=12) compared with the multi-gigabase genomes of maize, wheat and barley.

    + + +

    Images

    + +

    Nipponbare + + + + +

    Assembly

    + +

    Scientists from the MSU Rice Genome Annotation Project (MSU) and the International Rice Genome Sequencing Project (IRGSP) / Rice Annotation Project Database (RAP-DB) generated a unified assembly of the 12 rice pseudomolecules of Oryza sativa Japonica Group cv. Nipponbare [1,2].

    + +

    The pseudomolecule for each chromosome was constructed by joining the nucleotide sequences of each PAC/BAC clone based on the order of the clones on the physical map. Overlapping sequences were removed and physical gaps were replaced with Ns. Updated pseudomolecules were constructed based on the original IRGSP sequence data [1] in combination with a BAC-optical map and error correction using 44-fold coverage next generation sequencing reads [2]. The nucleotide sequences of 7 new clones mapped on the euchromatin/telomere junctions were added in the new genome assembly. In addition, several clones in the centromere region of chromosome 5 were improved and one gap on chromosome 11 was closed [2].

    + +

    Kawahara et al. (2013) describe the integrated Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules, also known as MSU7. Gene loci, gene models and associated annotations were independently created by each group, but can be easily compared using the common reference.

    + +

    Read more about the assembly at MSU or on rap-db.

    + + +

    Annotation

    + +

    The IRGSP gene models were imported from rap-db [3]. The most recent update was from its's Aug 4, 2017 release. This version corrected numerous protein coding gene models with manual curation, also deprecated some bad models. In total, 35,667 protein-coding genes were included in this release. Compared with last release of 37,830 genes, 35,340 stayed the same, 2,173 got deprecated, 317 updated, 10 new genes added. Feature annotation and comparative analysis pipelines have been run and variations have been projected from the old annotation to the new one. In addition, 2,387 nonCoding genes and 8,115 predicted genes were added as seperate data sets.

    + +

    The MSU-7 gene models [4] have been added into the rice genome browser for visual comparison to the IRGSP set. Gene models were generated, refined and updated for the estimated 40,000 to 60,000 rice genes, provided standardized automatic annotation pipeline described in detail here. Briefly, a number of ab initio methods have been combined with homology based evidence and refined with EST alignments.

    + +

    Cross references between the two gene sets provided by rap-db allow searching and querying using either identifier space, but only the IRGSP gene models are used in our gene trees.

    + + +

    Regulation

    + +
    • Probes from the Rice Genome Array for two rice cultivars were aligned to the genome [5].
      • +
    + + +

    Variation

    + +

    Variation data from six different large scale studies are available:

    + +
    1. The 3000 Rice Genome Project (2015, [6]), an international effort to sequence the genomes of 3,024 rice varieties from 89 countries providing 365,710 variant loci (SNPs and InDels).
      2. +
    2. Whole genome sequencing of 104 elite rice cultivars (Duitama et al. 2015, [7]), described as, "a comprehensive information resource for marker assisted selection" providing 25,769,548 variant loci.
      3. +
    3. Chip based analysis of 1,310 SNPs across 395 samples (Zhao et al. 2010, [8]), described as, "revealing the impact of domestication and breeding on the rice genome".
      4. +
    4. Chip based analysis of approximately 160k SNPs across 20 diversity rice accessions (OryzaSNP, McNally et al. 2009 [9]), described as, "revealing relationships among landraces and modern varieties of rice".
      5. +
    5. The Oryza Map Alignment Project (OMAP 2007): approximately 1.6M variant loci detected by comparing BAC End Sequences from four rice varieties to Japonica. [dbSNP]
      6. +
    6. Adaptive loss-of-function in domesticated rice (BGI 2004, [10]): A collection of approximately 3M variant loci from the comparison of the Indica (93-11) and Japonica (Nipponbare) genomes. [dbSNP]
      7. +

    The following genetic markers were remapped to the IRGSP-1.0 assembly by industry collaborator KeyGene:

    + + + + +

    Links

    + + + +

    References

    1. The map-based sequence of the rice genome.
      2005. Nature. 436:793-800.
      2. +
    2. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
      Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S et al. 2013. Rice (N Y). 6:4.
      3. +
    3. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
      Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T et al. 2013. Plant Cell Physiol.. 54:e6.
      4. +
    4. The TIGR Rice Genome Annotation Resource: improvements and new features.
      Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L et al. 2007. Nucleic Acids Res.. 35:D883-7.
      5. +
    5. Global analysis of gene expression using GeneChip microarrays.
      Zhu T. 2003. Curr. Opin. Plant Biol.. 6:418-425.
      6. +
    6. The 3,000 rice genomes project.
      2014. Gigascience. 3:7.
      7. +
    7. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.
      Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E et al. 2015. PLoS ONE. 10:e0124617.
      8. +
    8. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.
      Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A et al. 2010. PLoS ONE. 5:e10780.
      9. +
    9. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
      McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE et al. 2009. Proc. Natl. Acad. Sci. U.S.A.. 106:12273-12278.
      10. +
    10. The Genomes of Oryza sativa: a history of duplications.
      Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al. 2005. PLoS Biol.. 3:e38.
    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa117425.html b/gramene/htdocs/ssi/species/about_Oryza_sativa117425.html new file mode 100644 index 00000000..a42e19bc --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa117425.html @@ -0,0 +1,80 @@ +

    About Oryza sativa cB subgroup Os117425

    +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) (collected from: India) is selected as the representative of cB subpopulation, in which the accessions are mostly collected from India, Bangladesh, Nepal and Pakistan.

    + +

    Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    Basmati ARC 10497 from Rod Wing's group +

    Image provided by Yong Zhou

    + +

    +

    Images in GRIN

    +

    Images at IRRI

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 117425 (variety cv. ARC_10497::IRGC_12485-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cB subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os117425RS1

    + +

    Organism name: Oryza sativa aromatic subgroup (rice)

    +

    BioSample: SAMN12748569

    +

    BioProject: PRJNA565479

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831255.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYID01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 112.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433821 [UID] 15732448 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    19,010,064 SNPs called for this Magic16 genome that is part of the 3000 rice genome project by Dr. Rod Wing's group from resequencing reads using GATK4 software.

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831255.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: GSOR 301509, ARC 10497

    +

    IRRI repo: IRGC 117425, ARC 10497::IRGC 12485-1

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa125619.html b/gramene/htdocs/ssi/species/about_Oryza_sativa125619.html new file mode 100644 index 00000000..baf2b0fa --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa125619.html @@ -0,0 +1,77 @@ +

    About Oryza sativa XI-2B subgroup Os125619

    + + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) (collected from India) is selected as the representative of XI-2B subpopulation, in which the accessions are mostly collected from India and Madagascar.

    + +

    Notes for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    Larha Mugad from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 125619 (variety cv. LARHA_MUGAD::IRGC_52339-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-2B subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    + +

    For more detailed information please see below:

    + +

    Os125619RS1

    + +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    BioSample: SAMN12748589

    +

    BioProject: PRJNA565480

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831355.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIE01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 113.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433761 [UID] 15732328 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC 125619):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +h2>References + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831355.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: IRGC 125619, LARHA MUGAD::IRGC 52339-1

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa125827.html b/gramene/htdocs/ssi/species/about_Oryza_sativa125827.html new file mode 100644 index 00000000..13b46927 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa125827.html @@ -0,0 +1,79 @@ +

    About Oryza sativa XI-3B2 subgroup Os125827

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 125827 (variety cv. LIU_XU::IRGC_109232-1) (collected from: China) is selected as the representative of XI-3B2 subpopulation, in which the accessions are mostly collected from China, and the Philippines.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + + +

    Images

    + +

    Chao Meo from Rod Wing's group +

    Image provided by Yong Zhou

    +

    +

    Images at IRRI

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 125827 (variety cv. LIU_XU::IRGC_109232-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3B2 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os125827RS1

    +

    Organism name: Oryza sativa (rice)

    +

    Infraspecific name: Cultivar: LIU XU::IRGC 109232-1

    +

    BioSample: SAMN13021815

    +

    BioProject: PRJNA577228

    +

    Submitter: University of ArizonaDate: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009829375.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: WGGU01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 138.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433841 [UID] 15732488 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    19,435,202 SNPs called for this Magic16 genome that is part of the 3000 rice genome project by Dr. Rod Wing's group from resequencing reads using GATK4 software.

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + + +

    Links

    + +

    GenBank: GCA_009829375.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: GSOR 301762, LIU XU

    +

    IRRI repo: IRGC 121040, LIU XU::IRGC 74099-1

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa127518.html b/gramene/htdocs/ssi/species/about_Oryza_sativa127518.html new file mode 100644 index 00000000..4aabe2c4 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa127518.html @@ -0,0 +1,73 @@ +

    About Oryza sativa XI-3B1 subgroup Os127518

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127518 (variety cv. KHAO_YAI_GUANG::IRGC_65972-1) (collected from: Thailand) is selected as the representative of XI-3B1 subpopulation, in which the accessions are mostly collected from Thailand, Lao_People_s_Democratic_Republic, and Cambodia.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + + +

    Images

    + +

    Khao Yai Guang from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127518 (variety cv. KHAO_YAI_GUANG::IRGC_65972-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3B1 subpopulation. The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os127518RS1

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    BioSample: SAMN12748590

    +

    BioProject: PRJNA565481

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831295.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIF01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 106.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433781 [UID] 15732368 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    GenBank: GCA_009831295.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: IRGC 127518, KHAO YAI GUANG::IRGC 65972-1

    + + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa127564.html b/gramene/htdocs/ssi/species/about_Oryza_sativa127564.html new file mode 100644 index 00000000..9241b633 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa127564.html @@ -0,0 +1,76 @@ +

    About Oryza sativa XI-3A subgroup Os127564

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127564 (variety cv. LIMA::IRGC_81487-1) (collected from: Indonesia) is selected as the representative of XI-3A subpopulation, in which the accessions are mostly collected from Indonesia, Thailand, and Malaysia.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + + +

    Images

    + +

    Lima from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Brief summary of the current assembly, please provide us with assembly accession, descriptions including data generator, sequencing technology, assembly strategy, quality, statistics and biosample

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127564 (variety cv. LIMA::IRGC_81487-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-3A subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os127564RS1

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    BioSample: SAMN12715984

    +

    BioProject: PRJNA564572

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009829395.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VXJH01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 103.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433861 [UID] 15732528 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009829395.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: N/A

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa127652.html b/gramene/htdocs/ssi/species/about_Oryza_sativa127652.html new file mode 100644 index 00000000..0c028fc0 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa127652.html @@ -0,0 +1,68 @@ +

    About Oryza sativa aus (cA2) subgroup Os127652

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127652 (variety cv. NATEL_BORO::IRGC_34749-1) (collected from: Bangladesh) is selected as the representative of cA2 subpopulation, in which the accessions are mostly collected from India, and Bangladesh.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + +

    Images

    + +

    Natel Boro, aus Os127652

    +

    Images in GRIN

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127652 (variety cv. NATEL_BORO::IRGC_34749-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents cA2 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os127652RS1

    +

    Organism name: Oryza sativa aus subgroup (rice)

    +

    BioSample: SAMN12748600

    +

    BioProject: PRJNA565483

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831335.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIG01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 111.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433771 [UID] 15732348 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC 127652):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    + + +

    References

    + +

    Campbell, Michael S., Meiyee Law, Carson Holt, Joshua C. Stein, Gaurav D. Moghe, David E. Hufnagel, Jikai Lei, et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164 (2): 513–24.

    +

    Chen, Mei-Ju May, Han Lin, Li-Mei Chiang, Christopher P. Childers, and Monica F. Poelchau. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858: 75–87.

    +

    Korf, Ian. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5 (May): 59.

    +

    Solovyev, Victor, Peter Kosarev, Igor Seledsov, and Denis Vorobyev. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1 (August): S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24 (5): 637–44.

    +

    Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831335.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: PI 575205, Natel Boro

    +

    IRRI repo: IRGC 34749, NATEL BORO

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa127742.html b/gramene/htdocs/ssi/species/about_Oryza_sativa127742.html new file mode 100644 index 00000000..9626d448 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa127742.html @@ -0,0 +1,76 @@ +

    About Oryza sativa XI-1B2 subgroup Os127742

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 127742 (variety cv. PR_106::IRGC_53418-1) (collected from: India) is selected as the representative of XI-1B2 subpopulation, in which the accessions are mostly collected from India, and Philippines.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + + +

    Images

    + +

    Os127742 from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 127742 (variety cv. PR_106::IRGC_53418-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1B2 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os127742RS1

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    BioSample: SAMN12672924

    +

    BioProject: PRJNA563359

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831045.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIB01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 105.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433811 [UID] 15732428 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831045.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: N/A

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa128077.html b/gramene/htdocs/ssi/species/about_Oryza_sativa128077.html new file mode 100644 index 00000000..60d8460f --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa128077.html @@ -0,0 +1,74 @@ +

    About Oryza sativa GJ-trop2 subgroup Os128077

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 128077 (variety cv. KETAN_NANGKA::IRGC_19961-2) (collected from: Indonesia) is selected as the representative of GJ-trop2 subpopulation, in which the accessions are mostly collected from Indonesia.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + +

    Images

    + +

    Ketan Nangka from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 128077 (variety cv. KETAN_NANGKA::IRGC_19961-2) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-trop2 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    OS128077RS1

    +

    Organism name: Oryza sativa tropical japonica subgroup (rice)

    +

    BioSample: SAMN12718029

    +

    BioProject: PRJNA564615

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831275.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIC01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 125.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433801 [UID] 15732408 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC117425):

    + +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”.
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31).
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831275.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: CIor 2379, Ketan Nangka

    +

    IRRI repo: N/A

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa132278.html b/gramene/htdocs/ssi/species/about_Oryza_sativa132278.html new file mode 100644 index 00000000..b695e4f3 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa132278.html @@ -0,0 +1,70 @@ +

    About Oryza sativa GJ-subtrp subgroup Os132278

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 132278 (variety cv. CHAO_MEO::IRGC_80273-1) (collected from: Lao People's Democratic Republic) is selected as the representative of GJ-subtrp subpopulation, in which the accessions are mostly collected from India, Thailand, and Lao People’s Democratic Republic.

    + +

    Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    Chao Meo from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 132278 (variety cv. CHAO_MEO::IRGC_80273-1) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-subtrp subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os132278RS1

    +

    Organism name: Oryza sativa tropical japonica subgroup (rice)

    +

    BioSample: SAMN12748601

    +

    BioProject: PRJNA565484

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831315.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VYIH01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 123.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433791 [UID] 15732388 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC 132278):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831315.1 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: IRGC 132278, CHAO MEO::IRGC 80273-1

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativa132424.html b/gramene/htdocs/ssi/species/about_Oryza_sativa132424.html new file mode 100644 index 00000000..67da98cd --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativa132424.html @@ -0,0 +1,70 @@ +

    About Oryza sativa XI-2A subgroup Os132424

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 132424 (variety cv. GOBOL_SAIL_(BALAM)::IRGC_26624-2) (collected from: Bangladesh) is selected as the representative of XI-2A subpopulation, in which the accessions are mostly collected from India, and Bangladesh.

    + +

    Notes for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    Os132424 from Rod Wing's group +

    Image provided by Yong Zhou

    +

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 132424 (variety cv. GOBOL_SAIL_(BALAM)::IRGC_26624-2) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-2A subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    Os132424RS1

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    BioSample: SAMN12721963

    +

    BioProject: PRJNA564763

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009831025.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: VXJI01

    +

    Assembly method: FALCON v. 2017.06.28-18.01-py2.7-ucs4; MECAT v. 2-20190314; CANU v. 1.5

    +

    Expected final version: no

    +

    Genome coverage: 105.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5433871 [UID] 15732538 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IRGC 132424):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009831025.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: N/A

    +

    IRRI repo: IRGC 132424, GOBOL SAIL (BALAM)::IRGC 26624-2

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativaazucena.html b/gramene/htdocs/ssi/species/about_Oryza_sativaazucena.html new file mode 100644 index 00000000..4d64a327 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativaazucena.html @@ -0,0 +1,80 @@ +

    About Oryza sativa GJ-trop1 subgroup OsAzucena

    + + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 135833 (variety cv. Azucena) (collected from: Philippines) is selected as the representative of GJ-trop1 subpopulation, in which the accessions are mostly collected from Indonesia, Philippines, United_States_of_America, Cote_d_Ivoire, and Brazil.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    Azucena from Rod Wing's group +

    Image provided by Yong Zhou

    +

    +

    Multiple azucena images in GRIN

    +

    Multiple azucena images at IRRI

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 135833 (variety cv. Azucena) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-trop1 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    AzucenaRS1

    +

    Organism name: Oryza sativa Japonica Group (Japanese rice)

    +

    Infraspecific name: Cultivar: Azucena

    +

    BioSample: SAMN08217222

    +

    BioProject: PRJNA424001

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/06

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009830595.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: PKQC01

    +

    Assembly method: CANU v. 1.5; FALCON v. 1.8

    +

    Expected final version: no

    +

    Genome coverage: 130.0x

    +

    Sequencing technology: PacBio; Illumina

    +

    IDs: 5433851 [UID] 15732498 [GenBank]

    + + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to Azecena):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009830595.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm (multiple): +

    +

    IRRI repo: Multiple hits at IRRI

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativair64.html b/gramene/htdocs/ssi/species/about_Oryza_sativair64.html new file mode 100644 index 00000000..751726e6 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativair64.html @@ -0,0 +1,77 @@ +

    About Oryza sativa XI-1B1subgroup OsIR64

    + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 135929 (variety cv. IR64) (collected from: Philippines) is selected as the representative of XI-1B1 subpopulation, in which the accessions are mostly collected from the Philippines.

    + +

    Note for subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica.

    + + +

    Images

    + +

    IR64 from Rod Wing's group +

    Image provided by Yong Zhou

    +

    +

    Images in GRIN

    + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 135929 (variety cv. IR64) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1B1 subpopulation.

    +

    The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

    +

    For more detailed information please refer to below:

    + +

    OsIR64RS1

    +

    Organism name: Oryza sativa (rice)

    +

    Infraspecific name: Cultivar: IR64 (IRRI)

    +

    BioSample: SAMN10564385

    +

    BioProject: PRJNA509165

    +

    Submitter: University of Arizona

    +

    Date: 2020/01/22

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_009914875.1 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: RWKJ01

    +

    Assembly method: MECAT v. 1.3; CANU v. 1.5; FALCON v. 2017.06.28-18.01-py2.7-ucs4

    +

    Expected final version: no

    +

    Genome coverage: 150.0x

    +

    Sequencing technology: PacBio Sequel; Illumina

    +

    IDs: 5488871 [UID] 15884438 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Regulation

    + + +

    N/A

    + + +

    Variation

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to IR64):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al, 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke, Mario, Mark Diekhans, Robert Baertsch, and David Haussler. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_009914875.1

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: GSOR 301401, IR64

    +

    IRRI repo: IRGC 135929, IR 64-IL

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativakitaake.html b/gramene/htdocs/ssi/species/about_Oryza_sativakitaake.html new file mode 100644 index 00000000..503292dc --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativakitaake.html @@ -0,0 +1,61 @@ +

    About Oryza sativa Kitaake v3.1

    +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In addition, rice is used as a model when studying monocotyledonous species such as switchgrass, which is being investigated as a potential biofuel. Kitaake is a Japonica variety of rice and is particularly useful for research because it is neutral to photoperiod changes and has a life cycle of only 10 weeks, which allows for more rapid breeding and genetic studies.

    + +

    Image

    +

    Image provided by Rashmi Jain

    +

    Image provided by Rashmi Jain

    + + +

    Assembly

    + +

    Scientists from the University of California, Davis generated Oryza sativa kitaakeX, which carries the XA21 gene under control of the maize ubiquitin promoter (Li et al., 2017). MECAT was used to carry out the main assembly and the subsequent assembly was polished using ARROW and scaffolded with SSPACE (Jain et al., 2019). Syntenic markers from the O. sativa var japonica v7.0 release were compared with the assembly to identify misjoins (Jain et al., 2019). A total of 68 scaffold breaks were made and then oriented, ordered, and joined together and assembled into 12 chromosomes, with a total of 394 joins and 99.67% of bases anchored to chromosomes (Jain et al., 2019). In addition, the researchers used 24mers from the FALCON assembly to mask the existing Kitaake v0.50 ALLPATHS and then extracted the regions of the ALLPATHS assembly that were >1.0KB (Jain et al., 2019). These were included in the new release. Lastly, ~60x of illumina reads (2x250, 800 bp insert) were used to correct the homozygous SNPs and INDELs (Jain et al., 2019).

    + +

    For more detailed information, please see below:

    + + +

    Assembly Source: JGI

    +

    Assembly Version: v3.0

    +

    Annotation Source: JGI

    +

    Annotation Version: v3.1

    +

    Total Scaffold Length (bp): 381570803

    +

    Number of Scaffolds: 33

    +

    Min. Number of Scaffolds containing half of assembly (L50): 6

    +

    Shortest Scaffold from L50 set (N50): 30273398

    +

    Total Contig Length (bp): 377569588

    +

    Number of Contigs: 507

    +

    Min. Number of Contigs containing half of assembly (L50): 77

    +

    Shortest Contig from L50 set (N50): 1383918

    +

    Number of Protein-coding Transcripts: 48494

    +

    Number of Protein-coding Genes: 35594

    +

    Percentage of Eukaryote BUSCO Genes: 98.3

    +

    Percentage of Embroyphyte BUSCO Genes: 99.1

    + + + +

    Annotation

    + +

    The genome annotation was conducted as described in Jain et al (2019).

    + + + +

    Variation

    + +

    Genetic variation for this species will be made available in release 5.

    + +

    Funding

    + +

    NSF 2027795

    +

    JBEI US DOE (DE-AC02-05CH11231)

    +

    JGI US DOE (DE-AC02-05CH11231)

    + + +

    References

    +

    Jain R, Jenkins J, Shu S, Chern M, Martin JA et al. 2019 “Genome sequence of the model rice variety KitaakeX.” BMC Genomics 20(1).

    +

    Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS et al. 2017. “The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.” The Plant Cell 29(6): 1218–1231.

    + + +

    Links

    + +

    Phytozome: Oryza sativa Kitaake v3.1

    +

    KitBase, the KitaakeX Mutant Database

    + diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativamh63.html b/gramene/htdocs/ssi/species/about_Oryza_sativamh63.html new file mode 100644 index 00000000..0877cf5d --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativamh63.html @@ -0,0 +1,84 @@ +

    About Oryza sativa XI-adm subgroup MH63

    + + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. Minghui 63 (collected from: China) is selected as the representative of XI-adm subpopulation, in which the accessions are mostly collected from China, India, Indonesia, Philippines, Bangladesh, Thailand, Lao_People_s_Democratic_Republic, Malaysia, Myanmar, Madagascar, abd Colombia.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    from Rod Wing's group +

    Image provided by Yong Zhou

    + +

    Rice Information GateWay (RIGW)

    +

    Image source: Rice Information Gateway

    + +

    Multiple images in GRIN

    + + + +

    Assembly

    + + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. Minghui 63 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-adm subpopulation.

    + +

    The genome was sequenced from 209 pools of BAC clones using PacBio SMRT technology, and ~74 Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. For more details, see here + + + + + + +

    MH63RS2

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    Infraspecific name: Cultivar: Minghui 63

    +

    BioSample: SAMN04274565

    +

    BioProject: PRJNA302543

    +

    Submitter: Huazhong Agricultural University

    +

    Date: 2018/10/25

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_001623365.2 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: LNNK02

    +

    Assembly method: HGAP v. 3; FALCON v. 1.8; CANU v. 1.3; Miniasm v. 0.2

    +

    Expected final version: no

    +

    Genome coverage: 120.0x

    +

    Sequencing technology: PacBio

    +

    IDs: 2033571 [UID] 7637248 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to Minghui 63):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020)(https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
      3. +
    3. The syntenic region and variation could be identified between MH63 and ZS97 in Rice Information GateWay (RIGW)
    + + +

    References

    + +

    Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J et al. 2014. “MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations.” Plant Physiology 164(2):513–24.

    +

    Chen, M-J M, Lin H, Chiang LM, Childers CP, and Poelchau MF. 2019. “The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.” Methods in Molecular Biology 1858:75–87.

    +

    Korf I. 2004. “Gene Finding in Novel Genomes.” BMC Bioinformatics 5:59.

    +

    Solovyev V, Kosarev P, Seledsov I, and Vorobyev D. 2006. “Automatic Annotation of Eukaryotic Genes, Pseudogenes and Promoters.” Genome Biology 7 Suppl 1:S10.1–12.

    +

    Stanke M, Diekhans M, Baertsch R and Haussler D. 2008. “Using Native and Syntenically Mapped cDNA Alignments to Improve de Novo Gene Finding.” Bioinformatics 24(5):637–44.

    +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7(1):113.

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_001623365.2 +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/)

    +

    USDA repo for germplasm: Multiple hits

    +

    IRRI repo: N/A

    diff --git a/gramene/htdocs/ssi/species/about_Oryza_sativazs97.html b/gramene/htdocs/ssi/species/about_Oryza_sativazs97.html new file mode 100644 index 00000000..53758f85 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Oryza_sativazs97.html @@ -0,0 +1,83 @@ +

    About Oryza sativa XI-1A subgroup OsZS97

    + + +

    Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. Zhengshan 97 (collected from China) is selected as the representative of XI-1A subpopulation, in which the accessions are mostly collected from China.

    + +

    Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

    + + +

    Images

    + +

    from Rod Wing's group +

    Image provided by Yong Zhou

    + +

    Rice Information GateWay (RIGW)

    +

    Image source: Rice Information Gateway

    + +

    Multiple images in GRIN

    + + + +

    Assembly

    + +

    Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. Zhengshan 97 genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents XI-1A subpopulation.

    +

    The genome was sequenced from 166 pools of BAC clones using PacBio SMRT technology, and ~97 Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. For more details, see here + + + + +

    ZS97RS2

    +

    Organism name: Oryza sativa Indica Group (long-grained rice)

    +

    Infraspecific name: Cultivar: Zhenshan 97

    +

    BioSample: SAMN04274564

    +

    BioProject: PRJNA302542

    +

    Submitter: Huazhong Agricultural University

    +

    Date: 2018/10/23

    +

    Assembly level: Chromosome

    +

    Genome representation: full

    +

    GenBank assembly accession: GCA_001623345.2 (latest)

    +

    RefSeq assembly accession: n/a

    +

    RefSeq assembly and GenBank assembly identical: n/a

    +

    WGS Project: LNNJ02

    +

    Assembly method: HGAP v. 3; FALCON v. 1.8; CANU v. 1.3; Miniasm v. 0.2

    +

    Expected final version: no

    +

    Genome coverage: 120.0x

    +

    Sequencing technology: PacBio

    +

    IDs: 2027271 [UID] 7620918 [GenBank]

    + + +

    Annotation

    + +

    Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

    + + +

    Variation

    + +

    Variation Data mapped to the assembly including SNP, SV, QTL, markers

    + +

    19,304,992 SNPs called for this Magic16 genome that is part of the 3000 rice genome project by Dr. Rod Wing's group from resequencing reads using GATK4 software.

    + +

    Large structural variation of 16 PSRefSeqs are available (including map to Zhengshan 97):

    +
    1. A platinum standard pan-genome resource that represents the population structure of Asian rice (Zhou et al., 2020) (https://www.nature.com/articles/s41597-020-0438-2), as described as “natural variation that exists in the pan-genome of cultivated Asian rice”
      2. +
    2. Structural variations are available in the figshare link (https://figshare.com/s/dcdaea3adae5c44e2e31)
      3. +
    3. The syntenic region and variation could be identified between MH63 and ZS97 with the following link: http://rice.hzau.edu.cn/rice_rs2/
    + + +

    References

    + +

    Zhang J, Chen L-L, Sun S, Kudrna D, Copetti D, Li W, Mu T et al. 2016. “Building Two Indica Rice Reference Genomes with PacBio Long-Read and Illumina Paired-End Sequencing Data.” Scientific Data.doi: 10.1038/sdata.2016.76

    + +

    Zhang J, Chen L-L, Xing F, Kudrna DA, Yao W, Copetti D, Mu T et al. 2016. “Extensive Sequence Divergence between the Reference Genomes of Two Elite Indica Rice Varieties Zhenshan 97 and Minghui 63.” Proceedings of the National Academy of Sciences of the United States of America 113 (35): E5163–71. doi: 10.1073/pnas.1611012113

    + +

    Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.doi: 10.1038/s41597-020-0438-2

    + + +

    Links

    + +

    Useful links to other resources

    +

    GenBank: GCA_001623345.2

    +

    Persephone page for the 16 PSRefSeqs: https://web.persephonesoft.com/

    +

    USDA repo for germplasm: GSOR 80, Zhen Shan 97A

    +

    IRRI repo: NA

    + diff --git a/gramene/htdocs/ssi/species/about_Ostreococcus_lucimarinus.html b/gramene/htdocs/ssi/species/about_Ostreococcus_lucimarinus.html new file mode 100644 index 00000000..8850d5f7 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Ostreococcus_lucimarinus.html @@ -0,0 +1,42 @@ + +

    This project is a collaborative effort involving:

    + +
    + + +

    About Ostreococcus lucimarinus

    + +

    Ostreococcus lucimarinus is a unicellular green alga and an important member of the picoplankton community, which plays a central role in the oceanic carbon cycle. It is one of the smallest known free-living eukaryotic species, with an average size of 0.8 µm. Its cellular structure is characterised by remarkable simplicity, lacking a cell wall and containing a single chloroplast, a single mitochondrion, and a single Golgi body as well as its nucleus.

    + + + +

    Assembly

    + +

    The genome of Ostreococcus lucimarinus CCE9901 was sequenced by JGI and finished at the Stanford Genome Center. The v2.0 release has 13.204,894 Mbp of finished sequence. The sequences have been deposited in GenBank under accession numbers CP000581-CP000601. Detailed information about the project is availabe at the JGI website.

    + +

    The assembly release v.2.0 contains 13,204,894 bp of finished quality sequence in 21 chromosomes.

    + +

    In detail [1], whole genome shotgun Sanger sequences were assembled using the Phred, Phrap, Consed pipeline. Manual inspection and finishing was performed by targeted resequencing. Because of the high GC content, primer walks failed to resolve a large number of the gaps; these were resolved by generating pooled small insert shatter libraries from 3-kb plasmid clones. Repeats were resolved by transposon-hopping 8-kb plasmid clones. Fosmid clones were shotgun-sequenced and finished to fill large gaps, resolve large repeats, or resolve chromosome duplications and extend into chromosome telomere regions. Finished chromosomes have no gaps, and the sequence has less than one error in 100,000 bp.

    + + + +

    Annotation

    + +

    This release includes a total of 7,651 predicted gene models produced through the collaboration of JGI, Ghent University (Belgium) and UCSD annotation teams.

    + +

    In detail [1], gene prediction methods included ab initio Fgenesh, Fgenesh+, Genewise, MAGPIE, estExt, and EuGene. All predicted models were clustered and the best model per locus was selected based on homology to other proteins and EST support. The predicted set of gene models has been validated by using available experimental data and computational analysis.

    + + + +

    Links

    + + + +

    References

    1. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
      Palenik B, Grimwood J, Aerts A, Rouz P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S et al. 2007. Proc. Natl. Acad. Sci. U.S.A.. 104:7705-7710.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Phaseolus_vulgaris.html b/gramene/htdocs/ssi/species/about_Phaseolus_vulgaris.html new file mode 100644 index 00000000..883f6edd --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Phaseolus_vulgaris.html @@ -0,0 +1,22 @@ + +

    About Phaseolus vulgaris

    + +

    Legumes are the third largest family of angiosperms and include many populous species. The majority of legumes contain symbiotic bacteria within nodules in their roots that mediate nitrogen fixation and provide an advantage towards competing plants. Legume seeds are rich in protein content and thus many species have been used for human or animal consumption over the years. Legumes as a whole constitute the second largest class of crops, including peas, soybeans, peanuts, and beans. Common bean (Phaseolus vulgaris.), a major source of protein that complements carbohydrate-rich rice, maize, and cassava, is fundamental for the nutrition of more than 500 million people in developing countries [1].

    + + + +

    Assembly

    + +

    The P. vulgaris Mesoamerican common bean BAT93 genome was assembled using a hybrid sequencing strategy involving 454 single reads and 8, 10, and 20 kb mate pair libraries; 3 and 5 kb SOLiD mate pair libraries; and Sanger bacterial artificial chromosome (BAC)-end and genomic read pairs. Data free of redundancies were used as input for a Newbler assembly, and Illumina reads (45x coverage) were used to correct homopolymer errors and close or reduce gaps within scaffolds. Illumina genotyping-by-sequencing (GBS), data from a set of 60 F5 lines of a BAT93 x Jalo EEP558 advanced intercross (6.7x coverage per line on average), together with 827 public marker sequences, were used for assembly correction and scaffold anchoring. Discontinuous genotype profiles observed in 48 cases were manually corrected by breaking scaffolds at the mis-assembly points. Markers were aligned to the assembly and GBS profiles of these scaffolds were used as seeds to place other scaffolds with this or similar profiles onto chromosomes, followed by genetic map calculation. The final BAT93 genome sequence encompassed 549.6 Mbp, close to previous size estimates, with 81% of the assembly anchored to eleven linkage groups. The assembly included 97% of the conserved core eukaryotic genes, thus reflecting its completeness [1].

    + +

    These assembly includes 68,335 scaffolds (N50=433,759 bp) and 111,805 contigs (N50=10,795 bp) [2].

    + + + +

    Annotation

    + +

    Transposable elements were identified by combining de novo and homology-based approaches, finding 35% of the P. vulgaris BAT93 genome assembly to be covered by repeats, mostly long terminal repeats. To aid in gene prediction and to obtain a global view of the transcriptome during development, sequencing was done with Illumina 61 RNA samples from 34 different organs and/or developmental stages from healthy plants. In addition, two normalized libraries derived from 162 RNA samples from plants grown under optimal and stress conditions were used for 454 pyrosequencing. Illumina and 454 RNA-Seq reads, as well as public expressed sequence tags (EST) and cDNA sequences, were combined with ab initio predictions to produce an initial gene set. This was filtered to remove genes lacking both similarity to other plant proteins and any evidence of expression, resulting in 30,491 protein coding genes (PCGs), whose 66,634 transcripts encode 53,904 unique proteins. Using protein signatures and phylogeny-based transference of functional annotations it was possible to associate functions with 94% of the bean transcripts, with 76 % of them specifically associated with Gene Ontology (GO) terms [2].

    + + +

    References

    1. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
      Vlasova A, Capella-Gutirrez S, Rendn-Anaya M, Hernndez-Oate M, Minoche AE, Erb I, Cmara F, Prieto-Barja P, Corvelo A, Sanseverino W et al. 2016. Genome Biology. 17
      2. +
    2. Phaseolus vulgaris assembly in NCBI.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Physcomitrella_patens.html b/gramene/htdocs/ssi/species/about_Physcomitrella_patens.html new file mode 100644 index 00000000..1bfd22ec --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Physcomitrella_patens.html @@ -0,0 +1,29 @@ + +

    About Physcomitrella patens

    + +

    The mosses (Bryophytes) are non-vascular plants that appeared very early in the fossil record, soon after the transition of plants to terrestrial environments. The Physcomitrella patens genome is therefore valuable in understanding early evolution and adaptation of land plants. Physcomitrella also serves as a model organism for studies of physiology and development. Unlike in higher plants, targeted gene-knockouts can be made efficiently in the laboratory, thereby facilitating reverse-genetics approaches to studying gene function. The annotated genome hosted here thereby represents an important resource to the plant research community.

    + + + +

    Assembly

    + +

    Information from JGI: The haploid genome of Physcomitrella patens ssp. patens ecotype Gransden 2004 is estimated to be ~480 Mbp contained in 27 pairs of chromosomes, and was sequenced to approximately 8.1x depth.

    + +

    The genome assembly has remained unchanged since release v.1.1 (March 2007). Approximately 5.5 million shotgun reads were initially assembled using JAZZ. There are a total of 2,106 scaffolds, composed of 19,136 contigs, with a total length of ~480 Mbp. Half of the assembly is contained in 111 scaffolds, all at least 1.3 Mbp in length. The length-weighted mean contig size is 72.5 kbp.

    + + + +

    Annotation

    + +

    Gene annotations are now updated to v1.6 from Cosmoss - The Physcomitrella patens resource. Annotations were originally made by JGI using a pipeline to predict and map gene models and associated transcripts/proteins using a variety of tools based on cDNA, protein homology and ab initio methods. The release v1.6 contains 32,272 gene models and 38,354 protein-coding transcripts. Scaffold and their associated gene models that were identified as contaminants in 2009 have been removed.

    + + + +

    Links

    + + + +

    References

    1. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
      Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y et al. 2008. Science. 319:64-69.
      2. +
    2. Image credit: Pirex at en.wikipedia [Public domain], from Wikimedia Commons.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Populus_trichocarpa.html b/gramene/htdocs/ssi/species/about_Populus_trichocarpa.html new file mode 100644 index 00000000..73e01860 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Populus_trichocarpa.html @@ -0,0 +1,35 @@ + +

    About Populus trichocarpa

    + +

    Populus trichocarpa (poplar) is a deciduous broadleaf tree that is native to Western North America. It is an economically important source of timber. Its rapid growth and compact genome size (~500 Mbp, n=18) has lead to its use as a model organism for tree species.[1]

    + + + +

    Assembly

    + +

    The v3 Populus genome assembly was constructed with Arachne version 20071016HA with an attempt to merge the outbred haplotypes and an extensive attempt to remove contaminating sequence. 81 Mb of finished clone sequence was also integrated, and the latest genetic map information to construct the 19 chromosome size scaffolds which contain 388 Mb of sequence, a majority of the assembled poplar sequence. Care was taken to minimize alternative haplotypes within the assembly. The first 19 scaffolds from the assembly correspond to the poplar chromosomes. The full release covers 423 Mb pairs of sequence with an average read depth of 9.44x assembled sequence. [3]

    + + + +

    Annotation

    + +

    75,566 RNAseq transcript assemblies were constructed from about 0.6B pairs of tremulas paired-end Illumina RNAseq reads using PERTRAN (Shu et. al., manuscript in preparation). Transcript assemblies (86,677 from Populus trichocarpa and 151,316 from related poplar ESTs/mRNA) were constructed using PASA from Populus trichocarpa RNAseq transcript assemblies, ESTs/mRNAs, and ESTs/mRNAs of other Poplar species including >2.6M 454-sequenced Populus deltoides EST reads generated at JGI. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabi ( Arabidopsis thaliana), rice, soybean or grape genomes to repeat-soft-masked P. trichocarpa genome using RepeatMasker . Gene models were predicated by homology-based predictors, mainly FGENESH+ , FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan . The best scored predictions for each locus are selected using multiple positive factors including EST and protein support, and one negative factor: overlap with repeats. The selected gene predictions were improved by PASA. Improvement includes adding UTRs, splicing correction, and adding alternative transcripts. PASA-improved gene model proteins were subject to protein homology analysis to above mentioned proteomes to obtain Cscore and protein coverage. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score and protein coverage is highest percentage of protein aligned to the best of homologs. PASA-improved transcripts were selected based on Cscore, protein coverage, EST coverage, and its CDS overlapping with repeats. The transcripts were selected if its Cscore is larger than or equal to 0.5 and protein coverage larger than or equal to 0.5, or it has EST coverage, but its CDS overlapping with repeats is less than 20%. For gene models whose CDS overlaps with repeats for more that 20%, its Cscore must be at least 0.9 and homology coverage at least 70% to be selected. The selected gene models were subject to Pfam analysis and gene models whose protein is more than 30% in Pfam TE domains were removed. The final result was 41,335 loci containing protein-coding transcripts and 73,013 protein-coding transcripts.[3]

    + +
    + + + +

    Regulation

    + + + + +

    Links

    + + + +

    References

    1. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
      Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. Science. 313:1596-1604.
      2. +
    2. Image credit: Cherubino (Own work) [Public domain], via Wikimedia Commons.
      3. +
    3. Phytozome: a comparative platform for green plant genomics.
      David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam et al. 2012. Nucleic Acids Res. . 40 (D1) : D1178-D1186.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Prunus_persica.html b/gramene/htdocs/ssi/species/about_Prunus_persica.html new file mode 100644 index 00000000..c4df53d6 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Prunus_persica.html @@ -0,0 +1,37 @@ + +

    About Prunus persica

    + +

    Prunus persica (peach) is an economically important deciduous tree in the Rosaceae family that produces 20 million tons of fruit per year. The rosaceae family contains herbs, shrubs and trees with a wide variety of fruit types and habits and includes several species grown for their fruits (peaches, apples and strawberries), lumber (black cherry) and ornamental value (roses).

    + +

    Peach was first domesticated and cultivated in North-West China and has a compact diploid genome (265 Mb, 2n =16).

    + + + +

    Assembly

    + +

    The initial assembly was performed using Sanger sequence reads representing 8.5-fold coverage of a double haploid genotype of cv. Lovell using Arachne. The resulting contigs and scaffolds were filtered to give 234 scaffolds covering 224.6 Mb of the peach genome (Peach v1.0) with scaffold and contig N50/L50 values of 4 Mb/26.8 Mb and 294 kb/214.2 kb, respectively with good QC statistics [1].

    + +

    Five DNA libraries were end-sequenced, giving a total of 8.47-fold sequence coverage: 536,032 reads from the 2.8 kb sized library, 606,680 reads from the 4.4 kb sized library, 2,106,103 reads from the 7.8 kb sized library, 419,424 reads from the 35.3 kb fosmid library, and 61,440 reads from the 69.5 kb BAC library.

    + + + +

    Annotation

    + +

    A total of 27,852 protein-coding genes and 28,689 protein-coding transcripts were predicted [1].

    + +

    Predictions began with PASA transcript assemblies based on ESTs from peach and related species. Transcript assemblies and a collection of plant peptide sequences were blasted against the assembly and gene models were predicted using by homology-based predictors FGENESH+ and GenomeScan. Predicted gene models were improved and refined by PASA.

    + + + +

    Sequence alignment

    + +

    Approximately 80,000 EST sequences have been aligned to the genome with STAR [View data]

    + + + +

    Links

    + +
    • Prunus persica ESTs at ENA
      • +
    + +

    References

    1. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
      Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F et al. 2013. Nat. Genet.. 45:487-494.

    Picture credit: Image created by skyseeker and released under a Creative Commons Attribution License.

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Selaginella_moellendorffii.html b/gramene/htdocs/ssi/species/about_Selaginella_moellendorffii.html new file mode 100644 index 00000000..ba196947 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Selaginella_moellendorffii.html @@ -0,0 +1,19 @@ + +

    About Selaginella moellendorffii

    + +

    Selaginella moellendorffii is a spikemoss. They belong to the subdivsion of higher vascular plant called lycophytes, an ancient group of plants appeared around 410 million years ago. Selaginella moellendorffii is the first non-seeded plant genome reported, making it a key species for plant evolution studies.

    + + + +

    Assembly

    + +

    The nuclear genome size is ~100 Mbp, the smallest genome size of any plant yet reported.

    + + + +

    Annotation

    + +

    The genome annotation for Selaginella moellendorffii has been derived from annotation submitted to the EMBL/Genbank/DDBJ databases; and enhanced by importing data from additional sources, principally UniProtKB and GOA.

    + + +

    References

    1. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
      Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA et al. 2011. Science. 332:960-963.

    Picture credit: Emmanuel Boutet

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Setaria_italica.html b/gramene/htdocs/ssi/species/about_Setaria_italica.html new file mode 100644 index 00000000..489a31e2 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Setaria_italica.html @@ -0,0 +1,21 @@ + +

    About Setaria italica

    + +

    Setaria italica (foxtail millet) is a grain crop widely grown in Asia with particular significance in semi-arid regions of Northern China. It is also grown on a moderate scale in other parts of the world as a forage crop. It is one of the oldest domesticated crops with archeological remains from 7,500 to 7,900 years BP in northern China. Motivation for sequencing foxtail millet includes its close relationship, both genetically and physiologically, to the biofuel crop switchgrass (Panicum virgatum). Direct study of switchgrass is complicated by its large genome size and polyploidy. Data from the foxtail millet genome assists in study and improvement of switchgrass and related biofuel crops. The nuclear genome (~490 Mbp) is diploid with 9 chromosomes (2n=18).

    + + + +

    Assembly

    + +

    Setaria italica cv. Yugu1 was sequenced and assembled by the Joint Genome Institute (JGI) in collaboration with community researchers. Sanger sequencing was performed on whole-genome shotgun clone libraries having different insert sizes. Reads totalling 8.29x coverage were assembled with Arachne giving scaffolds that were arranged predominantly into 9 pseudomolecules.

    + + + +

    Annotation

    + +

    Protein-coding genes were predicted using evidence-based approaches.

    + + +

    References

    1. Reference genome sequence of the model plant Setaria.
      Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J et al. 2012. Nat. Biotechnol.. 30:555-561.
      2. +
    2. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.
      Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W et al. 2012. Nat. Biotechnol.. 30:549-554.
      3. +
    3. Image credit: Markus Hagenlocher, via WikiCommons.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Solanum_lycopersicum.html b/gramene/htdocs/ssi/species/about_Solanum_lycopersicum.html new file mode 100644 index 00000000..79de2aa7 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Solanum_lycopersicum.html @@ -0,0 +1,23 @@ + +

    About Solanum lycopersicum

    +

    Solanum lycopersicum (tomato) is a member of the nightshade family, Solanaceae, which includes a variety of agricultural crop plants (e.g. potato, pepper, eggplant, and tobacco). The tomato originated in the Andean region of South America, was grown by Aztecs in Mesoamerica, and spread to Europe by early Spanish explorers. Today, hundreds of varieties are grown throughout the world, with the largest producers being China and the United States. In addition to its value as a food, the tomato has served as an important model system for the study of fruit ripening, plant-pathogen interactions, and molecular genetic mapping. The nuclear genome contains 12 chromosomes and is ~950 Mbp in size.

    + + +

    Assembly

    +

    Solanum lycopersicum cv. Heinz 1706 was sequenced and assembled by the International Tomato Genome Sequencing Consortium. Assembly version SL2.40 combines a 22X whole genome shotgun sequence (Roche 454) with Sanger sequence data from BAC-ends, fosmid-ends and Selected BAC Mixture sequences, and additional data from Solexa and SOLiD technologies (total genome coverage 27X). The assembly is deposited into DDBJ/EMBL/GenBank under the accession AEKE00000000.2.

    + + +

    Annotation

    +

    Annotation was carried out by the International Tomato Annotation Group (ITAG) using a combination of evidence-based and ab initio methods.

    + + +

    Variation

    +

    The variation data for Solanum lycopersicum is from the study of genetic variation by whole-genome sequencing of 84 tomato accessions, including cultivated wild relatives representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group [2]. In detail, the study expored genetic variation in the tomato clade by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups. The variation data has been submitted to the ENA with accession ERP004618, and has been locus-level accessioned using the transPLANT variation archive.

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    Links

    + + +

    References

    1. The tomato genome sequence provides insights into fleshy fruit evolution.
      Tomato Genome Consortium. 2012. Nature. 485:635-641.
      2. +
    2. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
      Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L et al. 2014. Plant J.. 80:136-148.

    Picture credit: David Besa from Sonoma, USA (Flickr) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons.

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Solanum_tuberosum.html b/gramene/htdocs/ssi/species/about_Solanum_tuberosum.html new file mode 100644 index 00000000..da87a74e --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Solanum_tuberosum.html @@ -0,0 +1,24 @@ + +

    About Solanum tuberosum

    +

    Solanum tuberosum (potato) is the worlds fourth most important food crop after rice, wheat and maize. Potatoes were first introduced outside the Andes four centuries ago, and it is estimated that by the year 2020 over two billion people will depend on it for food, feed, or income. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 Mbp, making it a medium-sized plant genome. Potato is the first Solanaceae genome to be sequenced and as such, is the first asterid genome, representing a major clade of eudicots. The Solanaceae are a diverse family of agriculturally important plant species, including tomato, eggplant, pepper, tobacco, and petunia.

    + + +

    Assembly

    +

    Genome sequencing and gene prediction were performed as described in [2].

    + + +

    Annotation

    +

    Genome sequencing and gene prediction were performed as described in [2].

    +

    Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

    + + +

    Regulation

    +
    • Mapping using GSNAP of transcriptomics sequences from 16 samples from different tissues submitted to the ENA SRA as part of study ERP000527. [View data]
      • +
    • ~194,000 EST sequences have been aligned to the genome with Exonerate [View data]
      • +
    + +

    References

    1. Genome sequence and analysis of the tuber crop potato.
      The Potato Genome Sequencing Consortium. 2011. Nature. 475:189-195.
      2. +
    2. Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the Worlds Third Most Important Food Crop.
      Visser RichardGF, Bachem ChristianWB, Boer JanMde, Bryan GlennJ, Chakrabati SwarupK, Feingold Sergio, Gromadka Robert, Ham RoelandCHJvan, Huang Sanwen, Jacobs JeanneME et al. 2009. Am. J. Potato Res.. 86:417-429.
      3. +
    3. Analyzing the potato abiotic stress transcriptome using expressed sequence tags.
      Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR. 2005. Genome. 48:598-605.
      4. +
    4. Gene expression profiling of potato responses to cold, heat, and salt stress.
      Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR. 2005. Funct. Integr. Genomics. 5:201-207.
      5. +
    5. Image credit: Scott Bauer, USDA ARS [Public domain], via Wikimedia Commons.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Sorghum_bicolor.html b/gramene/htdocs/ssi/species/about_Sorghum_bicolor.html new file mode 100644 index 00000000..ed56abf6 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Sorghum_bicolor.html @@ -0,0 +1,54 @@ + +

    About Sorghum bicolor

    + +

    Sorghum bicolor is a widely grown cereal crop, particularly in Africa, ranking 5th in global cereal production. It is also used as biofuel crop and potential cellulosic feedstock. The diploid genome (~730 Mbp) has a haploid chromosome number of 10. Although highly repetitive, the genome is more tractable for sequencing than its close relative, Zea mays.

    + + + +

    Assembly

    + +

    The first genome assembly of Sorghum bicolor cv. Moench was published in 2009 [1]. Sequencing by the US department of Energy Joint Genome Institute (JGI) Community Sequencing Program in collaboration with the Plant Genome Mapping Laboratory followed a whole genome shotgun strategy reaching 8x coverage with scaffolds, where possible, being assigned to the genetic map. Since then JGI made two rounds of improvements. The most recent update of release v3.0 includes ~351 Mb of finished sorghum sequence. A total of 349 clones were manually inspected, then finished and validated using a variety of technologies. They were integrated into chromosomes by aligning to v1.0 assembly. As a result, 4,426 gaps were closed, and a total of 4.96 MB of sequence was added to the assembly. Overall contiguity (contig N50) increased by a factor of 5.8x from 204.5 KB to 1.2 MB. For more details, see phytozome.

    + + + +

    Annotation

    + +

    This browser presents data from the v3.0.1 assembly and v3.1.1 gene set (March 2007). Gene prediction is an improved process based upon resources used in original v1.0 release (Sbi1 assembly and Sbi1.4 gene set) with new geneAtlas RNA-seq data. Read more at Phytozome.

    + +

    Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 6 repeats loaded from (ENA); 685,783 Low complexity (Dust) features, covering 29 Mb (4.0% of the genome); 455,749 RepeatMasker features (with the RepBase library), covering 451 Mb (62.1% of the genome); 392,778 RepeatMasker features (with the REdat library), covering 409 Mb (56.2% of the genome); and 245,654 Tandem repeats (TRF) features, covering 41 Mb (5.7% of the genome).

    + + + +

    Variation

    + +

    Morris et al. SNPs set [2]

    + +

    The Morris et al. set is from a 2013 study of agroclimatic traits in Sorghum [2]. In this study, approximately 265,000 single nucleotide polymorphisms (SNPs) were characterized from 971 worldwide accessions, combining three previously defined sorghum diversity panels. They are: the US sorghum association panel (SAP), the sorghum mini core collection (MCC) and the Generation Challenge Program sorghum reference set (RS). GWAS studies were subsequently performed on plant height components and inflorescence architecture using 336 SAP lines. The data presented here represents the genotype information of the 378 SAP lines provided by the author.

    + +

    Mace et al. SNPs set [3]

    + +

    This Sorghum variation data set corresponds to 6,578,420 SNPs (SNPs mapping to supercontigs were removed) genotyped in 45 Sorghum bicolor lines including the BTx623 reference genome plus 2 S. propinquum lines reported by Mace et al (2013). The data was obtained by resequencing the genomes of the 44 Sorghum bicolor lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group (i.e., major races of cultivated S. bicolor, landraces, improved inbreds, progenitors, wild and weedy), and the first resequenced genome of S. propinquum, all of which were mapped to the BTx623 S. bicolor reference genome.

    + +

    Jiao et al. EMS SNPs set [5]

    + +

    The Jiao EMS dataset includes ~1.8 millions ethyl methane sulfonate (EMS)-induced G/C to A/T transition mutations annotated from 252 M3 families selected from the 6,400 sorghum mutant library in BTx623 background [1]. Genomic DNA used for sequencing was pooled from 20 M3 plants per M2 family.

    + +

    Structural Variation

    + +

    Data for structural variation in sorghum has been imported from the Database of Genomic Variants archive (dGVA) from a single study containing around 32 thousand structural variations [4]. Click here for example.

    + + + +

    Links

    + + + +

    References

    1. The Sorghum bicolor genome and the diversification of grasses.
      Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. Nature. 457:551-556.
      2. +
    2. Population genomic and genome-wide association studies of agroclimatic traits in sorghum.
      Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE et al. 2013. Proc. Natl. Acad. Sci. U.S.A.. 110:453-458.
      3. +
    3. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum.
      Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X et al. 2013. Nat Commun. 4:2320.
      4. +
    4. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).
      Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM et al. 2011. Genome Biol.. 12:R114.
      5. +
    5. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses.
      Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. 2016. Plant Cell. 28:1551-1562.

    Picture credit: By Sahaquiel9102 (Own work) [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Theobroma_cacao.html b/gramene/htdocs/ssi/species/about_Theobroma_cacao.html new file mode 100644 index 00000000..3bd15a89 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Theobroma_cacao.html @@ -0,0 +1,67 @@ + +

    This Cacao Genome Project is a collaboration among MARS, USDA-ARS, IBM, NCGR, Clemson University, HudsonAlpha Institute for Biotechnology, Indiana University and Washington State University with funding from MARS, USDA-ARS, and NSF, and contributions in effort from cacao breeders around the world.

    +
    + + +

    About Theobroma cacao

    + +

    Theobroma cacao (cacao or chocolate tree) is a neotropical plant native to Amazonian rainforests. It is now cultivated in over 50 countries. A member of Malvaceae family, its beans are harvested from pods for use as the food chocolate, in confections and cosmetics. This is the genome assembly and annotation of the Matina 1-6 cultivar, which belongs to the most cultivated cacao type worldwide.

    + + + +

    Assembly

    + +

    The 445 Mbp chromosome-level assembly of this cacao genome has scaffolds anchored and oriented to 10 chromosomes with BAC end sequencing and FISH karyotyping-based chromosome assignment, for 94.6% of total assembly, with 4.4% gap sequence, and the remainder in unlinked scaffolds. This assembly is primarily composed of Roche 454 Titanium STD reads, augmented by 6 recombination paired Titanium libraries, 3 fosmid packaged Sanger sequenced libraries, and 3 Sanger sequenced BAC Ends libraries. This genome assembly is produced by Jeremy Schmutz (Hudson Alpha, 2011-08-01).

    + +

    The genome sequence of the most widely cultivated cacao type and

    + +

    its use to identify candidate genes regulating pod color.

    + +

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053823/

    + +

    http://www.ncbi.nlm.nih.gov/nuccore/CM001879.1

    + + + +

    Annotation

    + +

    Illumina and 454 RNA-Seq reads totaling 62 Gigabases were collected from leaf, pistil and bean tissues, assembled with de-novo RNA assemblers Velvet/Oases [VELO], SOAPdenovo-Trans [SOAP], Roche Newbler, and genome-guided assembler Cufflinks [CUFF]. From this over-assembly of 1.2 million transcripts, the 48,404 most accurate cacao gene assemblies are selected with homology and genome map evidence scoring.

    + +

    Proteins from 297,061 genes of 8 plants, arabidopsis, poplar, castorbean, grape, strawberry, potato, soybean, and sorhgum are used for homology evidence. Transposons are annotated as class I retrotransposon and II DNA transposon with subcategories, totaling 8,542 intact transposons with 122,552 copies, covering 137 Mbases or 42% of genome assembly.

    + +

    Gene evidence from RNA mapped introns, plant species protein homology, expressed RNA alignments, transposons, is mapped to genome with GMAP/GSNAP [GMAP], tBLASTn, and exonerate [EXNR]. Several genome gene prediction sets were produced with AUGUSTUS [AUG], following HMM training of this predictor on cacao transcripts, by varying proportions of this gene evidence and parameters.

    + +

    EvidentialGene software [EVG] is used to annotate, score and classify gene assemblies and models with weighted evidence scores. This includes hueristics to identify and reduce gene-joins and fragment models.

    + +

    Highest evidence-scored models or assemblies are selected per locus for a primary transcript. Alternate transcripts are selected from remaining transcript assemblies (but not predictions) that vary from primary transcript in exon-intron structure. The resulting gene set is annotated with recripocal best blastp to several plant gene sets, clustered to gene families with OrthoMCL [OMCL], and annotated with family consensus function names, homology scores and references, and other gene quality scores.

    + +

    This gene annotation includes 29,408 protein coding loci, with 14,806 alternate transcripts. Gene evidence recovered in this cacao gene set includes 91% of 161333 RNA-introns, 67% of 48404 RNA assemblies, and 76% of 36Mb of plant protein alignments. This gene set construction and annotation is produced by Don Gilbert (Indiana Univ., 2012-03-08) [EVG]

    + +

    Annotation refs

    + +

    [EVG] EvidentialGene: Perfect Genes Constructed from Gigabases of RNA http://arthropods.eugenes.org/EvidentialGene/

    + +

    [AUG] Stanke M, Schoffmann O, Morgenstern B, Waack S: Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006, 7:62.

    + +

    [OMCL] Li L, Stoeckert CJ, Jr., Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189.

    + +

    [GMAP] Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.

    + +

    [EXNR] Slater GSC, Birney E: Automated generation of heuristics for biological sequence comparison. Bmc Bioinformatics 2005, 6:31.

    + +

    [VELO] Schulz, M.H., et al. (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels, Bioinformatics, 28, 1086-1092.

    + +

    [SOAP] Y. Xie, et al. (2014) SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, Epub ahead of print.

    + +

    [CUFF] Trapnell, C., et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, 28, 511-515.

    + + + +

    Links

    + + + diff --git a/gramene/htdocs/ssi/species/about_Trifolium_pratense.html b/gramene/htdocs/ssi/species/about_Trifolium_pratense.html new file mode 100644 index 00000000..b5eb856c --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Trifolium_pratense.html @@ -0,0 +1,31 @@ + +

    The red clover genome is a joint effort of TGAC and IBERS. This work was funded by an Institute Programme Grant to IBERS (BB/J004405/1) from the Biotechnology and Biological Sciences Research Council (BBSRC), by the ERANET Plant Genomics programme (ERAPG038A-TRANSLEG) and by a Capacity, Capability Challenge Programme from TGAC.

    + +

    +
    + + +

    About Trifolium pratense

    + +

    Red clover (Trifolium pratense) is one of the most important forage legume crops in temperate agriculture, and a key component of sustainable intensification of livestock farming systems. Red clover is a highly heterozygous diploid (2n = 2x = 14) species due to its gametophytic self-incompatibility system. This assembly provides a chromosome-scale reference draft genome for a red clover genotype of the variety Milvus (Milvus B). It was published in De Vega, J. J. et al. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement [1].

    + + + +

    Assembly

    + +

    This assembly provides a chromosome-scale reference draft genome for a red clover genotype of the variety Milvus (Milvus B) by integration of Whole Genome Sequencing (WGS) of short-length reads, Sanger-based bacterial artificial chromosome (BAC) end sequences, a physical and two genetic maps. WGS was assembled from paired-end and mate-pair libraries using the Platanus assembler. Three BAC libraries were created using high molecular weight DNA from a specific genotype of the Milvus variety (Milvus B). The mapping population used in this work consisted of 188 genotypes of F1 progeny from a cross between a genotype of the variety Milvus and a genotype of the variety Britta. We aligned 1,031 of the 1,388 markers from the two maps to place 532 of the longest scaffolds and used the BAC-end sequences as markers to further link unplaced scaffolds with already placed scaffolds from the same physical contig. The physical map contained 29,730 BACs, of which almost 23,000 were in contigs (77.3%).

    + + + +

    Annotation

    + + + +

    ​Links

    + + + +

    References

    1. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.
      De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon , Rognli OA, Jones C, Swain M, Geurts R et al. 2015. Sci Rep. 5:17394.

    Picture credit: By Masaki Ikeda - Own work, CC BY-SA 3.0

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Triticum_aestivum.html b/gramene/htdocs/ssi/species/about_Triticum_aestivum.html new file mode 100644 index 00000000..18c7b0bf --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_aestivum.html @@ -0,0 +1,68 @@ + +

    For information about the assembly and annotation please view the IWGSC announcement.

    + +

    The previous wheat assembly (TGACv1) and every other plant from release 31 is available in the new Ensembl Plants archive site.

    + +

    +
    + + +

    About Triticum aestivum

    + +

    Triticum aestivum (bread wheat) is a major global cereal grain essential to human nutrition. Wheat was one of the first cereals to be domesticated, originating in the fertile crescent around 7000 years ago. Bread wheat is hexaploid, with a genome size estimated at ~17 Gbp, composed of three closely-related and independently maintained genomes that are the result of a series of naturally occurring hybridization events. The ancestral progenitor genomes are considered to be Triticum urartu (the A-genome donor) and an unknown grass thought to be related to Aegilops speltoides (the B-genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides) which hybridized again with Aegilops tauschii (the D-genome donor) to produce modern bread wheat.

    + + + +

    Assembly

    + +

    The IWGSC RefSeq v1.0 is an integration of the IWGSC WGA v0.4 (comprised of Illumina short sequence reads assembled with NRGene’s DeNovoMAGICTM software) with IWGSC chromosome-based and other resources (physical maps, MTP BAC WGPTM sequence tags; and for some chromosomes: sequenced BACs, BioNano optical maps, Alignment to RH maps & GBS map of the SynOp RIL population CsxRn genetic map) Scaffolds/superscaffold have been assigned to chromosomal locations using POPSEQ data and a HiC map. Chromosomal scaffold/ superscaffold N50 is 22.8 Mb.

    + + + +

    Annotation

    + +

    The IWGSC RefSeq v1.0 annotation includes gene models generated by integrating predictions made by INRA-GDEC using Triannot and PGSB using their customised pipeline (previously MIPS pipeline). The integration was undertaken by the Earlham institute (EI), who have also added UTRs to the gene models where supporting data are available. Gene models have been assigned to high confidence (HC) or low confidence (LC) classes based on completeness, similarity to genes represented in protein and DNA databases and repeat content. The automated assignment of functional annotation to genes has been generated by PGSB based on AHRD parameters.
    +The annotation includes 110,790 high confidence genes, 158,793 low confidence genes and 13,044 long coding RNAs.
    +98,270 high confidence genes from the TGACv1 annotation [3] were aligned to the assembly using Exonerate. For each gene up to 3 alignments are displayed, compromising 196,243 alignments of which 90,686 are protein coding.

    + +

    + + + +

    + +

    + + + +

    Variation

    + +

    Data from CerealsDB [1]

    + +

    768664 markers from the 820K Axiom SNP array from CerealsDB were aligned to the assembly.
    +This was done by CerealsDB[1] using Blast with a cutoff of 1e-05. The top three hits were parsed and compared to CerealsDB genetic map data. In cases where two or more of the top three hits had an identical score, the hit agreed with the genetic map was selected. In cases of no genetic map information for a particular SNP then the top hit was selected.

    + +

    EMS Mutation data [2]

    + +

    EMS-type variants from sequenced tetraploid (cv ‘Kronos’) and hexaploid (cv ‘Cadenza’) TILLING populations. Mutations were called on the IWGSC RefSeq V1.0 assembly using the Dragen system[4]

    + +
    • 4.4 million Kronos mutations
      • +
    • 9.0 million Cadenza mutations
      • +

    Researchers and breeders can search this database online, identify mutations in the different copies of their target gene, and request seeds to study gene function or improve wheat varieties. Seeds can be requested from the UK SeedStor (https://www.seedstor.ac.uk/shopping-cart-tilling.php) or from the US based Dubcovsky lab (http://dubcovskylab.ucdavis.edu/wheat-tilling).

    + +

    This resource was generated as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and the John Innes Centre.

    + +

    + +

    + + + +

    + +
    + +

    References

    1. CerealsDB 3.0: expansion of resources and data integration.
      Wilkinson PA, Winfield MO, Barker GL,Tyrrell S, Bian X, Allen AM, Burridge A, Coghill JA, Waterfall C, Caccamo M et al. 2016. BMC Bioinformatics. 17:256.
      2. +
    2. Uncovering hidden variation in polyploid wheat.
      Ksenia V. Krasileva, Hans A. Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H. Ramirez-Gonzalez et al. . 2016. PNAS. 114:E913E921.
      3. +
    3. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
      Bernardo J. Clavijo, Luca Venturini,Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman et al. 2017. Genome Research.
      4. +
    4. Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGENTM Bio-IT Processor for Precision Medicine.
      Goyal, A., Kwon, H.J., Lee, K., Garg, R., Yun, S.Y. et al. 2017. Open Journal of Genetics. 7:9-19.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Triticum_aestivum_a.html b/gramene/htdocs/ssi/species/about_Triticum_aestivum_a.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_aestivum_a.html @@ -0,0 +1,40 @@ + +

    Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

    +

    Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

    + + +

    IWGSC Chromosome survey sequence

    +

    Assemblies

    +

    Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

    +

    The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

    + + +

    Annotations

    +

    The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
    The program findorf was used to predict the CDS within these transcripts as described in [2].

    + + +

    Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

    +

    As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
    Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

    +

    The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

    +

    Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

    +

    These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

    +

    Wheat sequence search

    +

    The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

    +

    Search is performed via the ENA search service, and currently includes:

    +

    Links

    + + diff --git a/gramene/htdocs/ssi/species/about_Triticum_aestivum_b.html b/gramene/htdocs/ssi/species/about_Triticum_aestivum_b.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_aestivum_b.html @@ -0,0 +1,40 @@ + +

    Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

    +

    Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

    + + +

    IWGSC Chromosome survey sequence

    +

    Assemblies

    +

    Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

    +

    The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

    + + +

    Annotations

    +

    The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
    The program findorf was used to predict the CDS within these transcripts as described in [2].

    + + +

    Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

    +

    As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
    Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

    +

    The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

    +

    Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

    +

    These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

    +

    Wheat sequence search

    +

    The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

    +

    Search is performed via the ENA search service, and currently includes:

    +

    Links

    + + diff --git a/gramene/htdocs/ssi/species/about_Triticum_aestivum_d.html b/gramene/htdocs/ssi/species/about_Triticum_aestivum_d.html new file mode 100644 index 00000000..cf241dfb --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_aestivum_d.html @@ -0,0 +1,40 @@ + +

    Bread wheat or common wheat (Triticum aestivum) is a major worldwide cereal grain which is essential to human food. Wheat was one of the first cereals to be domesticated, and is thought to have originated in the fertile crescent around 9000 years B.C.

    +

    Bread wheat species is hexaploid, and its genome size is estimated at 17Gbp. It is composed of three closely-related and independently maintained genomes. Bread wheat is the result of a series of hybridization events that are thought to have occurred naturally. The ancestral progenitor genomes are considered to be Triticum urartu (the A genome donor), and an unknown grass, but thought to be closely related to Aegilops speltoides (the B genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides), which then hybridized with a diploid goat grass (DD, Aegilops tauschii).

    + + +

    IWGSC Chromosome survey sequence

    +

    Assemblies

    +

    Chromosome survey sequences for bread wheat cv Chinese Spring have been generated by the International Wheat Genome Sequencing Consortium. The Genome Analysis Centre has provided an assembly of these survey sequences, which is now available through Ensembl Plants. ~11 millions contigs and ~10 millions scaffolds were generated with a contig N50 of 2.4kb. Due to the large number of scaffolds, we have only loaded a subset, comprising all scaffolds equal or greater than 3kb and additionnally, all scaffolds to which wheat cDNA alignments have been made (leading to a total of ~710,000 scaffolds loaded in the database). The set of scaffolds that was loaded has been included in the Ensembl Plants BLAST and ENA search facilities.

    +

    The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and can be searched using the TGAC blast server. The data will be available shortly in the archives of the International Nucleotide Sequence Database Consortium.

    + + +

    Annotations

    +

    The predicted gene annotations come from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. See Triticeae-CAP project page for more information.
    The program findorf was used to predict the CDS within these transcripts as described in [2].

    + + +

    Analysis of the bread wheat genome using comparative whole genome shotgun sequencing

    +

    As part of the wheat genome analysis, we have aligned a set of identified Triticum aestivum gene sequences and homoeologous SNPs (SNPs between the component A, B, and D genomes of wheat) against the Brachypodium distachyon and barley (Hordeum vulgare) genomes [1].
    Currently, the size and complexity of the wheat genome precludes a chromosome-scale assembly. However, significant sequences resources have been used to produce a gene-space assembly, included here in the syntenic context of brachypodium distachyon, a model cereal and pooid relative of wheat, as well as of barley. Sequences of diploid progenitor and ancestral species permitted homoeologous SNPs to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

    +

    The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a Brachypodium example. Click here for a barley example.

    +

    Wheat RNA-Seq, EST and Unigene datasets have also been aligned:

    +

    These data will also be aligned to the IWGSC chromosome survey sequences in the next release (release 21).

    +

    Wheat sequence search

    +

    The wheat sequence search allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. Wherever possible the results are placed in the syntenic context of Hordeum vulgare and Brachypodium distachyon.

    +

    Search is performed via the ENA search service, and currently includes:

    +

    Links

    + + diff --git a/gramene/htdocs/ssi/species/about_Triticum_aestivum_pre.html b/gramene/htdocs/ssi/species/about_Triticum_aestivum_pre.html new file mode 100644 index 00000000..225225a2 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_aestivum_pre.html @@ -0,0 +1,45 @@ + +

    This pre-site offers immediate public access to a new assembly of the wheat genome. For access to the main Ensembl Plants site, please click here.

    +
    + + +

    About Triticum aestivum

    + +

    This Ensembl Plants pre-site contains the first release of the IWGSC RefSeq v1.0 genome assembly of Triticum aestivum cv. Chinese Spring, generated by IWGSC. The assembly has a chromosomal scaffold/ superscaffold N50 of 22.8 MBb.

    + +

    Triticum aestivum (bread wheat) is a major global cereal grain essential to human nutrition. Wheat was one of the first cereals to be domesticated, originating in the fertile crescent around 7000 years ago. Bread wheat is hexaploid, with a genome size estimated at ~17 Gbp, composed of three closely-related and independently maintained genomes that are the result of a series of naturally occurring hybridization events. The ancestral progenitor genomes are considered to be Triticum urartu (the A-genome donor) and an unknown grass thought to be related to Aegilops speltoides (the B-genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides) which hybridized again with Aegilops tauschii (the D-genome donor) to produce modern bread wheat.

    + +

    + +

    The main Ensembl Plants site (http://plants.ensembl.org/Triticum_aestivum/Info/Index) contains the TGACv1 assembly and will be replaced by IWGSCv1 in the next release (July).

    + +

    The TGACv1 assembly will continue to be availble via the Ensmble Archive site.

    + + + +

    Assembly

    + +

    The IWGSC RefSeq v1.0, comprised of Illumina short sequence reads assembled with NRGene’s DeNovoMAGIC software, produced scaffolds totaling 14.5Gb with a chromosomal scaffold/superscaffold N50 of 22.8 Mb.
    +Scaffolds have been assigned to chromosomal locations using POPSEQ data and a HiC map. Over 99% of chromosome survey contigs map to the new assembly.

    + + + +

    Annotation

    + +

    The IWGSC RefSeq v1.0 annotation includes gene models generated by integrating predictions made by INRA-GDEC using Triannot and PGSB using their customised pipeline (previously MIPS pipeline). The integration was undertaken by the Earlham institute (EI), who have also added UTRs to the gene models where supporting data are available. Gene models have been assigned to high confidence (HC) or low confidence (LC) classes based on completeness, similarity to genes represented in protein and DNA databases and repeat content. The automated assignment of functional annotation to genes has been generated by PGSB based on AHRD parameters.
    +The annotation includes 110,790 high confidence genes, 158,793 low confidence genes and 13,044 long coding RNAs.
    +98,270 high confidence genes from the TGACv1 annotation were aligned to the assembly using Exonerate. For each gene up to 3 alignments are displayed, compromising 196,243 alignments of which 90,686 are protein coding.

    + +

    + + + +

    Variation

    + +

    768664 markers from the 820K Axiom SNP array from CerealsDB were aligned to the assembly.
    +This was done by CerealsDB[1] using Blast with a cutoff of 1e-05. The top three hits were parsed and compared to CerealsDB genetic map data. In cases where two or more of the top three hits had an identical score, the hit agreed with the genetic map was selected. In cases of no genetic map information for a particular SNP then the top hit was selected.

    + +

    + + +

    References

    1. CerealsDB 3.0: expansion of resources and data integration.
      Paul A. Wilkinson, Mark O. Winfield, Gary L. A. Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Caccamo et al. 2016. BMC Bioinformatics. 17:256
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Triticum_urartu.html b/gramene/htdocs/ssi/species/about_Triticum_urartu.html new file mode 100644 index 00000000..58315baf --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Triticum_urartu.html @@ -0,0 +1,73 @@ + +

    Wheat genomics resources are developed as part of our involvement in the consortium Triticeae Genomics For Sustainable Agriculture, funded by the BBSRC, and led by TGAC.

    + +

    BBSRC logo

    +
    + + +

    About Triticum urartu

    + +

    Triticum urartu is the diploid progenitor of the bread wheat A-genome, providing important evolutionary information for bread and durum wheat. It is closely related to einkorn wheat, T. monococcum.

    + + + +

    Assembly

    + +

    The genome of Triticum urartu accession G1812 was sequenced by the BGI using a whole-genome shotgum strategy, and assembled using SOAPdenovo software. The genome assembly reached 3.92 Gbp with a N50 size of 3.42 kbp. After gap closure, the draft assembly was 4.66 Gbp, with a scaffold N50 length of 63.69 kbp.

    + +

    The chloroplast genome component and its gene annotation are also present. This was imported from ENA entry, KC912693.

    + + + +

    Annotation

    + +

    34,879 protein-coding genes were predicted. For more details about genome sequencing and the protein_coding gene prediction protocol, see [1].

    + +

    Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

    + +

    Triticeae Repeats from TREP were aligned to the T. urartu genome using RepeatMasker.

    + + + +

    Regulation and sequence alignment

    + +

    RNA-Seq data, ESTs and UniGene datasets have also been aligned to the Triticum urartu genome:

    + +

    Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. [4]

    + +

    The wheat genome assemblies previously generated by Brenchley et al. (PMID:23192148) have been aligned to the bread wheat survey sequence, Brachypodium, barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii). Homoeologous variants inferred between the three wheat genomes (A, B, and D) are displayed in the context of the gene models of these five genomes.

    + +

    Sequences of diploid progenitor and ancestral species permitted homoeologous variants to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.

    + +

    The wheat gene alignments and the projected wheat SNPs are available on the Location view, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for example.

    + +

    Transcriptome assembly in diploid einkorn wheat Triticum monococcum - Fox et al. [5]

    + +

    Genome-wide transcriptomes of two Triticum monococcum subspecies were constructed, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC projects PRJNA203221 and PRJNA195398.

    + +

    The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. They were mapped to the bread wheat, barley and Triticum urartu genomes using STAR. Click here for a Triticum urartu example.

    + + + +

    Links

    + +

    Links (Triticum urartu)

    + +
    • GigaDB
      • +
    • ENA study: SRP002455: Discovery of SNPs and genome-specific mutations by comparative analysis of transcriptomes of hexaploid wheat and its diploid ancestors
      • +
    • TREP, the Triticeae Repeat Sequence Database
      • +

    Links (Triticum aestivum)

    + + + +

    References

    1. Draft genome of the wheat A-genome progenitor Triticum urartu.
      Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y et al. 2013. Nature. 496:87-90.
      2. +
    2. Image credit: Mark Nesbitt [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons.
      3. +
    3. Homoeolog-specific transcriptional bias in allopolyploid wheat.
      Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Vigna_angularis.html b/gramene/htdocs/ssi/species/about_Vigna_angularis.html new file mode 100644 index 00000000..7d818b21 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Vigna_angularis.html @@ -0,0 +1,18 @@ + +

    About Vigna angularis

    + +

    Vigna angularis (adzuki bean) is an annual legume crop, widely grown throughout East Asia and the Himalayas for food. It is widely used as an ingredient for traditional dessert cuisines due to its sweet taste, as well as its nutritious protein and starch contents. It is a diploid (2n = 2x = 22) with an estimated genome size of 538 Mbp.

    + + + +

    Assembly

    + +

    Paired-end (180 bp) and mate-pair (5 and 10 kbp) libraries were prepared using 100 bp short reads (Illumina HiSeq 2000) and were combined with a single unpaired library of average read length of 458 bp (Roche GS-FLX+) for a total physical coverage of 291x. The assembly produced 3,883 scaffolds with N50 length of 703 kbp, covering 75% of the estimated genome size. Scaffolds were assembled into pseudo-molecules using synteny and genetic mapping of a population of 133 F4 lines (814 SNPs in 11 linkage groups).

    + + + +

    Annotation

    + +

    Gene prediction using the MAKER pipeline revealed 26,857 high confidence protein-coding genes using RNA-Seq of flower, pod, leaf, and root tissues. In total, 86% of the 248 core eukaryotic genes in CEGMA pipeline were matched to the genome assembly.

    + +

    References

    1. Draft genome sequence of adzuki bean, Vigna angularis.
      Kang YJ, Satyawan D, Shim S, Lee T, Lee J, Hwang WJ, Kim SK, Lestari P, Laosatit K, Kim KH et al. 2015. Sci Rep. :8069.

    Picture credit: By Sanjay Acharya [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], from Wikimedia Commons

    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Vitis_vinifera.html b/gramene/htdocs/ssi/species/about_Vitis_vinifera.html new file mode 100644 index 00000000..bda7c0e5 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Vitis_vinifera.html @@ -0,0 +1,40 @@ + +

    About Vitis vinifera

    + +

    Vitis vinifera (grape) is the most widely cultivated and economically important grape species. It has a diploid genome with haploid chromosome number of 19, and an estimated genome size of ~500 Mbp.

    + + + +

    Assembly

    + +

    This release is based on a 12x whole genome shotgun sequence assembly and the V1 annotation of the Vitis vinifera genome [1]. These data were prepared by a French-Italian Public Consortium for Grapevine Genome Characterization under the auspices of the International Grape Genome Program (IGGP). Further details of the sequencing and assembly are available from Genoscope.

    + + + +

    Annotation

    + +

    Protein-coding genes were predicted by combining ab initio models, V. vinifera complementary DNA alignments, and alignments of proteins and genomic DNA from other species. The integration of the data was performed with GAZE [2].

    + + + +

    Regulation

    + +

    Oligo probes from the GeneChip Vitis vinifera Genome Array have been aligned using the standard Ensembl mapping procedure. For example, see the the results for 1609916_s_at (a probe that comes up when browsing the sol1 gene (VIT_18s0157g00050).

    + + + +

    Variation

    + +

    Single nucleotide polymorphisms identified by re-sequencing a collection of grape cultivars and wild Vitis species from the USDA germplasm collection [3].

    + + + +

    Links

    + + + +

    References

    1. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
      Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al. 2007. Nature. 449:463-467.
      2. +
    2. GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
      Howe KL, Chothia T, Durbin R. 2002. Genome Res. 9:1418-27.
      3. +
    3. Rapid genomic characterization of the genus vitis.
      Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D. 2010. PLoS ONE. 5:e8219.
    \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/about_Zea_mays.html b/gramene/htdocs/ssi/species/about_Zea_mays.html new file mode 100644 index 00000000..7094e925 --- /dev/null +++ b/gramene/htdocs/ssi/species/about_Zea_mays.html @@ -0,0 +1,84 @@ + +

    About Zea mays

    + +

    Zea mays (maize) has the highest world-wide production of all grain crops, yielding 875 million tonnes in 2012 (http://faostat.fao.org/). Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. Maize was domesticated from wild teosinte in Central America and its cultivation spread throughout the Americas by Pre-Columbian civilizations. In addition to its economic value, maize is an important model organism for studies in plant genetics, physiology, and development. It has a large genome of of about 2.4 gigabases with a haploid chromosome number of 10 (Schnable et al., 2009; Zhang et al., 2009). Maize is distinguished from other grasses in that its genome arose from an ancient tetraploidy event unique to its lineage.

    + + + +

    Assembly

    + +

    This entirely new assembly of the maize genome (B73 RefGen_v4) is constructed from PacBio Single Molecule Real-Time (SMRT) sequencing at approximately 60-fold coverage and scaffolded with the aid of a high-resolution whole-genome restriction (optical) mapping. The pseudomolecules of maize B73 RefGen_v4 are assembled nearly end-to-end, representing a 52-fold improvement in average contig size relative to the previous reference (B73 RefGen_v3).

    + + + +

    Annotation

    + +

    Nomenclature of Maize RefGen_V4 gene models

    + +

    The gene models of Maize RefGen_V4 were named following the standard of Maize Genetics Nomenclature: www.maizegdb.org/nomenclature#GENEMODEL. Previous identifiers (e.g. GRMZM) are retained as synonyms and can be searched.

    + +

    Method

    + +

    Genes were annotated with Maker pipeline (Campbell et al. 2014) using 111,000 transcripts obtained by single-molecule sequencing. These long read Iso-Seq data (Wang et al. 2016) improved annotation of alternative splicing, more than doubling the number of alternative transcripts from 1.5 to 3.8 per gene, thereby improving our knowledge of gene structure and transcript variation, resulting in substantial improvements including resolved gaps and misassembles, corrections to strand, consolidation of gene models, and anchoring of unanchored genes.

    + +

    Gene annotation was performed in the laboratory of Doreen Ware (CSHL/USDA). Protein-coding genes were identified using MAKER-P software version 3.1 (Campbell et al 2014) with the following transcript evidence: 111,151 PacBio Iso-Seq long-reads from 6 tissues (Wang et al. 2016), 69,163 full-length cDNAs deposited in Genbank (Alexandrov et al. 2008; Soderlund et al. 2009), 1,574,442 Trinity-assembled transcripts from 94 B73 RNA-Seq experiments (Law et al 2015), and 112,963 transcripts assembled from deep sequencing of a B73 seedling (Martin et al 2014). Additional evidence included annotated proteins from Sorghum bicolor, Oryza sativa, Setaria italica, Brachypodium distachyon, and Arabidopsis thaliana downloaded from Ensembl Plants Release 29 (Oct-2015). Gene calling was assisted by Augustus (Keller et al. 2011) and FGENESH (Salamov & Solovyev, 2000) trained on maize and monocots, respectively. Low-confidence gene calls were filtered on the basis of AED score and other criteria and are viewable as a separate track. In the end, the higher confidence set (called filtered gene set) has 39,324 protein coding genes. Gene annotations from B73 RefGen_v3 were mapped to the new assembly and are also available as a separate track. In addition, 2,532 Long non-coding RNA (lncRNA) genes were mapped and annotated from prior studies (Li et al., 2014; Wang et al., 2016), while 2,290 tRNA genes were identified using tRNAscan-SE (Lowe & Eddy 1997), and 154 miRNA genes mapped from miRBase (Kozomara & Griffiths-Jones 2014).

    + +

    Repeats

    + +

    Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 1,335,693 Low complexity (Dust) features, covering 56 Mb (2.6% of the genome); 787,462 RepeatMasker features (with the reDAT library), covering 1,417 Mb (66.3% of the genome); 1,105,314 RepeatMasker features (with the RepBase library), covering 1,646 Mb (77.1% of the genome); 950,012 Tandem repeats (TRF) features, covering 103 Mb (4.8% of the genome).

    + + + +

    Regulation

    + +

    Gene expression probes

    + +

    Oligo probes from the GeneChip Maize Genome Array have been aligned using the standard Ensembl 2-step mapping procedure. For example, see the the results for Zm.155.1.A1_a_at.

    + +

    DNA methylation

    + +

    Genomewide patterns of DNA methylation for two maize inbred lines, B73 and Mo17, are now displayed on the maize genome browser. Cytosine methylation in symmetric (CG and CHG, where H is A, C, or T) context is associated with DNA replication and histone modification. CG (65%) and CHG (50%) methylation is also highest in transposons. Source: Maize methylome publication by Regulski et al. (2013).

    + + + +

    Variation

    + +

    HapMap2 dataset

    + +

    A variation set which comprises the maize HapMap2 data (Chia et al., 2012). This dataset incorporates approximately 55 million SNPs and InDels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass). Each line was sequenced to an average of 4.5-fold coverage using the Illumina GAIIx platform. The reads can be accessed from the SRA, with accession ID: SRA051245. Reads were initially mapped to the B73 RefGen_v3 reference genome using a combination of Bowtie, Novoalign and SOAP, then remapped to the most recent B73 RefGen_v4 reference genome. The variations were scored by taking into account identity-by-descent blocks that are shared among the lines.

    + +

    The Panzea 2.7 genotyped-by-sequencing (GBS) dataset

    + +

    This variation data set consists of 719,472 SNPs (excluding 332 SNPs that were removed for mapping to scaffolds) typed in 16,718 maize and teosinte lines, and grouped in 14 overlapping populations according to the germplasm set in the corresponding metadata table.

    + + + +

    Links

    + + + +

    References

    1. A genome-wide characterization of microRNA genes in maize.
      Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. 2009. PLoS Genet.. 5:e1000716.
      2. +
    2. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
      Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S et al. 2014. Sci Rep. 4:4519.
      3. +
    3. A novel hybrid gene prediction method employing protein multiple sequence alignments.
      Keller O, Kollmar M, Stanke M, Waack S. 2011. Bioinformatics. 27:757-763.
      4. +
    4. Ab initio gene finding in Drosophila genomic DNA.
      Salamov AA, Solovyev VV. 2000. Genome Res.. 10:516-522.
      5. +
    5. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.
      Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM et al. 2015. Plant Physiol.. 167:25-39.
      6. +
    6. Genome-wide discovery and characterization of maize long non-coding RNAs.
      Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE et al. 2014. Genome Biol.. 15:R40.
      7. +
    7. Insights into corn genes derived from large-scale cDNA sequencing.
      Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB et al. 2009. Plant Mol. Biol.. 69:179-194.
      8. +
    8. Maize HapMap2 identifies extant variation from a genome in flux.
      Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC et al. 2012. Nat. Genet.. 44:803-807.
      9. +
    9. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.
      Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ et al. 2014. Plant Physiol.. 164:513-524.
      10. +
    10. miRBase: annotating high confidence microRNAs using deep sequencing data.
      Kozomara A, Griffiths-Jones S. 2014. Nucleic Acids Res.. 42:D68-73.
      11. +
    11. Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
      Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E et al. 2009. PLoS Genet.. 5:e1000740.
      12. +
    12. The B73 maize genome: complexity, diversity, and dynamics.
      Schnable PS, Ware D, et al.. 2009. Science. 326:1112-1115.
      13. +
    13. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
      Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D. 2016. Nat Commun. 7:11708.
      14. +
    14. FAOSTAT.
      15. +
    15. Comparative population genomics of maize domestication and improvement.
      Hufford MB, Xu X, van Heerwaarden J, Pyhjrvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM et al. 2012. Nat. Genet.. 44:808-811.
      16. +
    16. A first-generation haplotype map of maize.
      Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J et al. 2009. Science. 326:1115-1117.
      17. +
    17. Detailed analysis of a contiguous 22-Mb region of the maize genome.
      Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y et al. 2009. PLoS Genet.. 5:e1000728.
      18. +
    18. The physical and genetic framework of the maize B73 genome.
      Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W et al. 2009. PLoS Genet.. 5:e1000715.
      19. +
    19. A single molecule scaffold for the maize genome.
      Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S et al. 2009. PLoS Genet.. 5:e1000711.
      20. +
    20. Evidence-based gene predictions in plant genomes.
      Liang C, Mao L, Ware D, Stein L. 2009. Genome Res.. 19:1912-1923.

    Picture credit: Nicolle Rager Fuller, National Science Foundation.

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    Summary

    Database version: - 93.11 + 87.11 Base Pairs: @@ -17,16 +17,16 @@

    Summary

    Golden Path Length: 119,667,750 - Genebuild by: Araport11 Genebuild method: Imported from Araport Genebuild started: Jun 2016 Genebuild released: Sep 2010 Genebuild last updated/patched: Sep 2010 Genebuild version: 2016-06-Araport11 + Genebuild by: Araport11 Genebuild method: Imported from TAIR Genebuild started: Jun 2016 Genebuild released: Sep 2010 Genebuild last updated/patched: Sep 2010 Genebuild version: 2016-06-Araport11

    Gene counts

    - + - - + +
    Coding genesHASH(0x68bff40):Coding genes

    Genes and/or transcript that contains an open reading frame (ORF).

    :    		 27,655
    Gene transcriptsHASH(0x68ce400):55,442Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:54,013
    @@ -52,7 +52,7 @@

    Coordinate Systems

    Mt366924Pt154478 -
    +
@@ -66,8 +66,4 @@

Other

FGENESH gene predictions: 20,579 - - Short Variants (SNPs, indels, somatic mutations): - 12,883,854 - \ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Arabidopsis_thaliana_IPtop500.html b/gramene/htdocs/ssi/species/stats_Arabidopsis_thaliana_IPtop500.html index ef8b69c6..45817853 100644 --- a/gramene/htdocs/ssi/species/stats_Arabidopsis_thaliana_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Arabidopsis_thaliana_IPtop500.html @@ -17,519 +17,519 @@ 1 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1104 - 3232 + 1113 + 5392 2 IPR011009
Protein kinase-like domain superfamily 1082 - 2384 + 4342 3 - IPR000719
  + IPR000719
Protein kinase domain 1037 - 15213 + 9548 4 IPR008271
Serine/threonine-protein kinase, active site 805 - 1596 + 1317 5 - IPR032675
  - 778 - 5164 + IPR032675
Leucine-rich repeat domain, L domain-like + 793 + 2211 6 - IPR013083
  - 713 - 2916 + IPR013083
Zinc finger, RING/FYVE/PHD-type + 750 + 1219 7 - IPR011990
  - 682 - 13617 + IPR017441
Protein kinase, ATP binding site + 680 + 1057 8 - IPR017441
Protein kinase, ATP binding site - 680 - 1282 + IPR036047
F-box-like domain superfamily + 656 + 904 9 - IPR036047
F-box-like domain superfamily - 656 - 1005 + IPR001810
F-box domain + 627 + 3666 10 - IPR001810
  - 625 - 5667 + IPR011990
Tetratricopeptide-like helical + 592 + 2385 11 - IPR002885
  - 471 - 36978 + IPR013320
Concanavalin A-like lectin/glucanase, subgroup + 517 + 1069 12 - IPR001841
  - 466 - 3714 + IPR001841
Zinc finger, RING-type + 471 + 3460 13 - IPR009057
Homeobox-like domain superfamily - 406 - 809 + IPR002885
Pentatricopeptide repeat + 471 + 27386 14 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 392 - 1141 + IPR009057
Homeobox-like domain superfamily + 435 + 3358 15 - IPR001611
  - 372 - 8985 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 397 + 2280 16 IPR016024
Armadillo-type fold 371 - 1804 + 1814 17 - IPR036291
NAD(P)-binding domain superfamily - 344 - 700 + IPR016040
NAD(P)-binding domain + 371 + 805 18 - IPR029058
  - 338 - 2944 + IPR001611
Leucine-rich repeat + 370 + 2950 19 - IPR003593
AAA+ ATPase domain - 321 - 765 + IPR036291
NAD(P)-binding domain superfamily + 344 + 632 20 - IPR001005
SANT/Myb domain - 290 - 1871 + IPR029058
Alpha/Beta hydrolase fold + 338 + 1398 21 - IPR035979
RNA-binding domain superfamily - 282 - 977 + IPR003593
AAA+ ATPase domain + 320 + 1320 22 - IPR012677
  - 278 - 2064 + IPR001005
SANT/Myb domain + 295 + 6581 23 - IPR017451
F-box associated interaction domain - 269 - 315 + IPR011989
Armadillo-like helical + 286 + 918 24 - IPR015943
  - 261 - 2517 + IPR012677
Nucleotide-binding, alpha-beta plait + 284 + 797 25 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 261 - 632 + IPR015943
WD40/YVTN repeat-like-containing domain + 282 + 800 26 - IPR000504
  - 258 - 8019 + IPR035979
RNA-binding domain superfamily + 282 + 905 27 - IPR036322
WD40-repeat-containing domain superfamily - 255 - 821 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like + 269 + 1108 28 - IPR036396
  - 251 - 2184 + IPR017451
F-box associated interaction domain + 264 + 301 29 - IPR036249
Thioredoxin-like superfamily - 249 - 438 + IPR017930
Myb domain + 258 + 1292 30 - IPR001128
Cytochrome P450 - 249 - 1474 + IPR000504
RNA recognition motif domain + 257 + 4884 31 - IPR011989
  - 247 - 1402 + IPR036322
WD40-repeat-containing domain superfamily + 255 + 544 32 - IPR001680
  - 239 - 14868 + IPR036396
Cytochrome P450 superfamily + 251 + 362 33 - IPR002401
Cytochrome P450, E-class, group I - 229 - 2131 + IPR001128
Cytochrome P450 + 251 + 3644 34 - IPR017930
  - 229 - 1252 + IPR036249
Thioredoxin-like superfamily + 249 + 422 35 - IPR036259
MFS transporter superfamily - 226 - 675 + IPR012336
Thioredoxin-like fold + 241 + 794 36 - IPR017972
Cytochrome P450, conserved site - 225 - 293 + IPR001680
WD40 repeat + 239 + 9094 37 - IPR017986
  - 220 - 1428 + IPR002401
Cytochrome P450, E-class, group I + 229 + 4262 38 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 217 - 323 + IPR036259
MFS transporter superfamily + 226 + 454 39 - IPR017853
Glycoside hydrolase superfamily - 215 - 436 + IPR017972
Cytochrome P450, conserved site + 225 + 275 40 - IPR036390
Winged helix DNA-binding domain superfamily - 199 - 450 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 218 + 652 41 - IPR011992
EF-hand domain pair - 193 - 402 + IPR017853
Glycoside hydrolase superfamily + 215 + 788 42 - IPR006566
FBD domain - 175 - 401 + IPR036390
Winged helix DNA-binding domain superfamily + 199 + 450 43 - IPR020846
  - 171 - 1124 + IPR011992
EF-hand domain pair + 195 + 1586 44 - IPR003591
Leucine-rich repeat, typical subtype - 170 - 1941 + IPR013781
Glycoside hydrolase, catalytic domain + 183 + 316 45 - IPR002182
NB-ARC - 167 - 426 + IPR006566
FBD domain + 175 + 714 46 - IPR002048
  - 165 - 6939 + IPR044974
Disease resistance protein, plants + 172 + 750 47 - IPR011050
Pectin lyase fold/virulence factor - 164 - 220 + IPR003591
Leucine-rich repeat, typical subtype + 170 + 1756 48 - IPR011598
  - 164 - 3747 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 168 + 2396 49 - IPR036638
  - 163 - 2097 + IPR002182
NB-ARC + 166 + 848 50 - IPR012334
  - 160 - 418 + IPR002048
EF-hand domain + 165 + 4174 51 - IPR006527
F-box associated domain, type 1 - 159 - 180 + IPR011050
Pectin lyase fold/virulence factor + 164 + 434 52 - IPR016177
DNA-binding domain superfamily - 158 - 284 + IPR012334
Pectin lyase fold + 164 + 208 53 - IPR036412
HAD-like superfamily - 156 - 469 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 163 + 365 54 - IPR029044
  - 153 - 1108 + IPR006527
F-box associated domain, type 1 + 159 + 360 55 - IPR013087
  - 153 - 3207 + IPR016177
DNA-binding domain superfamily + 158 + 568 56 - IPR014001
  - 152 - 1354 + IPR036412
HAD-like superfamily + 156 + 328 57 - IPR018247
EF-Hand 1, calcium-binding site - 151 - 654 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 153 + 1242 58 IPR004146
DC1 151 - 872 + 1668 59 - IPR019775
WD40 repeat, conserved site - 149 - 473 + IPR007087
Zinc finger, C2H2 + 151 + 901 60 - IPR001650
  - 147 - 2568 + IPR018247
EF-Hand 1, calcium-binding site + 151 + 562 61 - IPR001471
  - 146 - 4146 + IPR019775
WD40 repeat, conserved site + 149 + 404 62 - IPR036955
  - 146 - 783 + IPR015915
Kelch-type beta propeller + 147 + 316 63 - IPR015915
  - 142 - 1350 + IPR001650
Helicase, C-terminal + 147 + 1796 64 - IPR035897
  - 140 - 1354 + IPR001471
AP2/ERF domain + 146 + 3164 65 - IPR023214
  - 139 - 900 + IPR029044
Nucleotide-diphospho-sugar transferases + 144 + 408 66 - IPR012337
Ribonuclease H-like superfamily - 138 - 283 + IPR011991
Winged helix-turn-helix DNA-binding domain + 144 + 239 67 - IPR036388
  - 136 - 554 + IPR012337
Ribonuclease H-like superfamily + 140 + 764 68 - IPR029071
Ubiquitin-like domain superfamily - 135 - 339 + IPR000157
Toll/interleukin-1 receptor homology (TIR) domain + 140 + 2330 69 - IPR000157
  - 135 - 2769 + IPR035897
Toll/interleukin-1 receptor homology (TIR) domain superfamily + 139 + 337 70 IPR001965
Zinc finger, PHD-type 135 - 513 + 456 71 - IPR012340
Nucleic acid-binding, OB-fold - 134 - 317 + IPR029071
Ubiquitin-related domain + 135 + 339 72 - IPR013101
Leucine-rich repeat 2 - 131 - 242 + IPR012340
Nucleic acid-binding, OB-fold + 134 + 588 73 - IPR013026
  - 129 - 888 + IPR013101
Leucine-rich repeat 2 + 131 + 484 74 - IPR036188
  - 128 - 1786 + IPR023214
HAD-like domain + 127 + 375 @@ -541,702 +541,702 @@ 76 - IPR015300
  - 126 - 1588 + IPR036188
FAD/NAD(P)-binding domain superfamily + 127 + 279 77 - IPR005123
  - 125 - 1236 + IPR015300
DNA-binding pseudobarrel domain superfamily + 125 + 1552 78 IPR006501
Pectinesterase inhibitor domain 125 - 395 + 1080 79 - IPR035513
  + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily 124 - 560 + 141 80 IPR005225
Small GTP-binding protein domain 124 - 203 + 159 81 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 122 - 241 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 124 + 1010 82 - IPR038765
Papain-like cysteine peptidase superfamily - 121 - 262 + IPR014729
Rossmann-like alpha/beta/alpha sandwich fold + 123 + 227 83 - IPR003959
ATPase, AAA-type, core - 121 - 221 + IPR023753
FAD/NAD(P)-binding domain + 122 + 961 84 - IPR036770
  - 120 - 1200 + IPR003959
ATPase, AAA-type, core + 122 + 444 85 - IPR019734
  - 118 - 4518 + IPR020683
Ankyrin repeat-containing domain + 121 + 1018 86 - IPR020683
  - 118 - 1630 + IPR038765
Papain-like cysteine peptidase superfamily + 121 + 228 87 - IPR003439
  - 118 - 2115 + IPR019734
Tetratricopeptide repeat + 120 + 2218 88 - IPR036869
  - 118 - 892 + IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain + 119 + 175 89 - IPR003340
  - 117 - 4260 + IPR036770
Ankyrin repeat-containing domain superfamily + 119 + 244 90 - IPR036514
  - 116 - 346 + IPR003439
ABC transporter-like, ATP-binding domain + 118 + 1402 91 - IPR003441
  - 115 - 1110 + IPR003340
B3 DNA binding domain + 117 + 2772 92 - IPR036397
  - 115 - 576 + IPR001623
DnaJ domain + 117 + 2984 93 - IPR036093
  - 115 - 1116 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 116 + 758 94 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 115 - 143 + IPR036869
Chaperone J-domain superfamily + 116 + 223 95 - IPR036236
Zinc finger C2H2 superfamily - 115 - 320 + IPR003441
NAC domain + 115 + 1307 96 - IPR014729
  - 114 - 502 + IPR036236
Zinc finger C2H2 superfamily + 115 + 257 97 - IPR001623
  - 112 - 2736 + IPR001087
GDSL lipase/esterase + 113 + 338 98 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 111 - 218 + IPR013830
SGNH hydrolase-type esterase domain + 112 + 167 99 - IPR036879
  - 110 - 1182 + IPR035892
C2 domain superfamily + 111 + 284 100 - IPR013187
F-box associated domain, type 3 - 109 - 129 + IPR036879
Transcription factor, MADS-box superfamily + 110 + 198 101 - IPR006652
Kelch repeat type 1 - 109 - 475 + IPR000008
C2 domain + 110 + 2134 102 - IPR002100
  + IPR002100
Transcription factor, MADS-box 109 - 3516 + 2266 103 - IPR001087
GDSL lipase/esterase - 108 - 158 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 109 + 418 104 - IPR002110
  - 108 - 4404 + IPR013187
F-box associated domain, type 3 + 109 + 258 105 - IPR027443
  - 107 - 382 + IPR006652
Kelch repeat type 1 + 109 + 852 106 - IPR035892
  - 106 - 574 + IPR002110
Ankyrin repeat + 108 + 2634 107 - IPR011011
Zinc finger, FYVE/PHD-type - 105 - 285 + IPR015916
Galactose oxidase, beta-propeller + 108 + 125 108 - IPR035669
GDSL lipase/esterase-like, plant - 104 - 138 + IPR027443
Isopenicillin N synthase-like + 107 + 178 109 - IPR008502
Prolamin-like domain - 104 - 106 + IPR011011
Zinc finger, FYVE/PHD-type + 105 + 568 110 - IPR020472
G-protein beta WD-40 repeat - 103 - 537 + IPR008502
Prolamin-like domain + 105 + 214 111 - IPR011333
SKP1/BTB/POZ domain superfamily - 101 - 201 + IPR035669
GDSL lipase/esterase-like, plant + 104 + 138 112 - IPR000008
  - 100 - 1636 + IPR020472
G-protein beta WD-40 repeat + 103 + 1074 113 - IPR014710
  - 99 - 450 + IPR014710
RmlC-like jelly roll fold + 102 + 190 114 - IPR026992
Non-haem dioxygenase N-terminal domain - 97 - 150 + IPR011333
SKP1/BTB/POZ domain superfamily + 101 + 390 115 - IPR001356
  - 97 - 1905 + IPR026992
Non-haem dioxygenase N-terminal domain + 97 + 300 116 - IPR008974
  - 97 - 1290 + IPR020846
Major facilitator superfamily domain + 97 + 428 117 - IPR038408
  - 96 - 644 + IPR001356
Homeobox domain + 97 + 1192 118 - IPR002902
  + IPR002902
Gnk2-homologous domain 96 - 1276 + 1272 119 IPR011545
DEAD/DEAH box helicase domain 95 - 193 + 386 120 IPR017907
Zinc finger, RING-type, conserved site 95 - 204 + 152 121 IPR011043
Galactose oxidase/kelch, beta-propeller 95 - 136 + 252 122 IPR000073
Alpha/beta hydrolase fold-1 - 94 - 362 + 95 + 726 123 - IPR015421
  - 93 - 564 + IPR013785
Aldolase-type TIM barrel + 93 + 192 124 - IPR015424
Pyridoxal phosphate-dependent transferase - 92 - 198 + IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1 + 92 + 150 125 - IPR000626
  - 91 - 1944 + IPR015424
Pyridoxal phosphate-dependent transferase + 92 + 376 126 - IPR017871
ABC transporter, conserved site - 91 - 223 + IPR013766
Thioredoxin domain + 92 + 520 127 - IPR013785
  - 90 - 702 + IPR017871
ABC transporter, conserved site + 91 + 191 128 - IPR002347
Short-chain dehydrogenase/reductase SDR - 90 - 1204 + IPR000626
Ubiquitin-like domain + 91 + 1174 129 - IPR008972
  - 90 - 1016 - + IPR002347
Short-chain dehydrogenase/reductase SDR + 90 + 2414 + 130 - IPR032867
DYW domain - 90 - 110 + IPR008972
Cupredoxin + 90 + 974 131 - IPR000270
  - 87 - 1020 + IPR032867
DYW domain + 89 + 109 132 - IPR009072
  + IPR009072
Histone-fold 87 - 837 + 488 133 - IPR013766
  - 86 - 765 + IPR000270
PB1 domain + 87 + 594 134 IPR006447
Myb domain, plants 86 - 167 + 135 135 IPR011713
Leucine-rich repeat 3 - 86 - 289 + 85 + 574 136 - IPR010255
Haem peroxidase + IPR010255
Haem peroxidase superfamily 84 - 120 + 230 137 - IPR001806
Small GTPase superfamily - 83 - 138 + IPR023393
START-like domain + 84 + 133 138 - IPR036457
  - 82 - 872 + IPR001806
Small GTPase + 83 + 490 139 - IPR019786
Zinc finger, PHD-type, conserved site - 82 - 179 + IPR036457
PPM-type phosphatase domain superfamily + 82 + 191 140 - IPR002016
  + IPR002016
Haem peroxidase 82 - 2223 + 1482 141 - IPR001932
  - 82 - 2394 + IPR019786
Zinc finger, PHD-type, conserved site + 82 + 160 142 - IPR015422
  - 81 - 810 + IPR001932
PPM-type phosphatase domain + 82 + 1872 143 - IPR000225
  + IPR000225
Armadillo 81 - 3969 + 2158 144 - IPR023393
  - 80 - 282 + IPR008974
TRAF-like + 81 + 176 145 - IPR002083
  + IPR002083
MATH/TRAF domain 79 - 2151 + 1390 146 - IPR036961
  - 79 - 972 + IPR003676
Small auxin-up RNA + 78 + 172 147 - IPR003676
Small auxin-up RNA - 78 - 86 + IPR015880
Zinc finger, C2H2-like + 77 + 363 148 - IPR035595
UDP-glycosyltransferase family, conserved site - 77 - 90 + IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2 + 76 + 132 149 - IPR023213
  - 76 - 314 + IPR000210
BTB/POZ domain + 75 + 658 150 - IPR021109
  - 75 - 698 + IPR024788
Malectin-like domain + 74 + 264 151 - IPR000210
  - 75 - 1020 + IPR000823
Plant peroxidase + 74 + 1498 152 - IPR015655
Protein phosphatase 2C family - 75 - 180 + IPR004827
Basic-leucine zipper domain + 74 + 1054 153 - IPR024788
Malectin-like carbohydrate-binding domain - 74 - 132 + IPR000571
Zinc finger, CCCH-type + 74 + 1964 154 - IPR004827
  - 74 - 1824 + IPR003657
WRKY domain + 73 + 1726 155 - IPR000571
  - 74 - 2658 + IPR033905
Secretory peroxidase + 73 + 82 156 - IPR000823
Plant peroxidase - 74 - 749 + IPR011051
RmlC-like cupin domain superfamily + 73 + 236 157 - IPR036576
  - 73 - 996 + IPR044810
WRKY transcription factor, plant + 73 + 131 158 - IPR033905
Secretory peroxidase - 73 - 82 + IPR021109
Aspartic peptidase domain superfamily + 72 + 674 159 - IPR003657
  - 73 - 1479 + IPR023213
Chloramphenicol acetyltransferase-like domain + 72 + 145 160 - IPR011051
RmlC-like cupin domain superfamily - 73 - 126 + IPR020568
Ribosomal protein S5 domain 2-type fold + 72 + 314 161 - IPR020568
Ribosomal protein S5 domain 2-type fold - 72 - 176 + IPR011993
Pleckstrin homology-like domain + 71 + 137 162 IPR005828
Major facilitator, sugar transporter-like 71 - 178 + 356 163 - IPR019793
Peroxidases heam-ligand binding site - 71 - 91 + IPR029052
Metallo-dependent phosphatase-like + 70 + 263 164 - IPR033121
  - 70 - 248 + IPR019793
Peroxidases heam-ligand binding site + 70 + 81 165 - IPR001461
Aspartic peptidase A1 family - 70 - 310 + IPR033121
Peptidase family A1 domain + 70 + 124 166 - IPR000048
  + IPR000048
IQ motif, EF-hand binding site 70 - 3414 + 2142 167 IPR003960
ATPase, AAA-type, conserved site 69 - 112 + 100 168 - IPR019787
  - 68 - 550 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 68 + 100 169 - IPR008979
  - 68 - 672 + IPR010987
Glutathione S-transferase, C-terminal-like + 68 + 348 170 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 68 - 101 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 67 + 234 171 - IPR000070
Pectinesterase, catalytic - 68 - 80 + IPR012946
X8 domain + 67 + 386 172 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 67 - 117 + IPR000070
Pectinesterase, catalytic + 67 + 158 173 - IPR012946
X8 domain - 67 - 204 + IPR010264
Plant self-incompatibility S1 + 67 + 282 174 IPR000743
Glycoside hydrolase, family 28 67 - 144 + 288 175 - IPR027640
Kinesin-like protein - 65 - 237 + IPR019787
Zinc finger, PHD-finger + 65 + 542 @@ -1248,16 +1248,16 @@ 177 - IPR036163
Heavy metal-associated domain superfamily - 65 - 141 + IPR003613
U box domain + 65 + 586 178 - IPR003613
  - 65 - 936 + IPR036163
Heavy metal-associated domain superfamily + 65 + 141 @@ -1269,30 +1269,30 @@ 180 - IPR006121
  - 63 - 1011 + IPR004045
Glutathione S-transferase, N-terminal + 63 + 354 181 - IPR004045
  - 63 - 528 + IPR003480
Transferase + 63 + 140 182 - IPR003480
Transferase - 63 - 70 + IPR006626
Parallel beta-helix repeat + 62 + 363 183 - IPR006626
Parallel beta-helix repeat - 62 - 381 + IPR005174
Domain unknown function DUF295 + 62 + 144 @@ -1304,2214 +1304,2214 @@ 185 - IPR010264
Plant self-incompatibility S1 - 62 - 66 + IPR013763
Cyclin-like + 62 + 990 186 - IPR013783
  - 61 - 306 + IPR008979
Galactose-binding-like domain superfamily + 62 + 600 187 - IPR001752
  - 61 - 3435 + IPR006121
Heavy metal-associated domain, HMA + 61 + 660 188 - IPR019794
Peroxidase, active site - 60 - 73 + IPR002156
Ribonuclease H domain + 61 + 188 189 - IPR010987
  - 60 - 178 + IPR001752
Kinesin motor domain + 61 + 2498 190 - IPR018108
  + IPR018108
Mitochondrial substrate/solute carrier 59 - 1154 + 1134 191 - IPR023395
  - 59 - 458 + IPR019794
Peroxidase, active site + 59 + 65 192 - IPR011993
  - 59 - 228 + IPR023395
Mitochondrial carrier domain superfamily + 59 + 380 193 - IPR016135
  - 58 - 532 + IPR044707
Egg cell-secreted protein 1.2/1.3/1.4 + 58 + 60 194 - IPR029052
  - 58 - 212 + IPR005829
Sugar transporter, conserved site + 57 + 157 195 - IPR005829
Sugar transporter, conserved site - 57 - 218 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 57 + 460 196 IPR002528
Multi antimicrobial extrusion protein 57 - 275 + 536 197 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 56 - 87 + IPR036852
Peptidase S8/S53 domain superfamily + 56 + 90 198 - IPR036852
  - 56 - 1179 + IPR023828
Peptidase S8, subtilisin, Ser-active site + 56 + 77 199 - IPR000209
Peptidase S8/S53 domain - 56 - 90 + IPR015500
Peptidase S8, subtilisin-related + 56 + 746 200 - IPR008949
  - 55 - 408 + IPR000209
Peptidase S8/S53 domain + 56 + 536 201 - IPR014014
  - 55 - 196 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 55 + 80 202 - IPR015500
Peptidase S8, subtilisin-related - 55 - 253 + IPR043129
ATPase, nucleotide binding domain + 55 + 238 203 - IPR001563
Peptidase S10, serine carboxypeptidase - 54 - 622 + IPR008949
Isoprenoid synthase domain superfamily + 55 + 330 204 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 54 - 86 + IPR001461
Aspartic peptidase A1 family + 55 + 564 205 - IPR018253
DnaJ domain, conserved site - 54 - 97 + IPR016181
Acyl-CoA N-acyltransferase + 54 + 408 206 - IPR001220
Legume lectin domain - 54 - 149 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 54 + 252 207 - IPR008978
  - 53 - 292 + IPR001878
Zinc finger, CCHC-type + 54 + 1004 208 - IPR000109
Proton-dependent oligopeptide transporter family - 53 - 163 + IPR001563
Peptidase S10, serine carboxypeptidase + 54 + 1240 209 - IPR003663
Sugar/inositol transporter - 53 - 662 + IPR001220
Legume lectin domain + 54 + 298 210 - IPR037045
  - 53 - 166 + IPR044965
Glycoside hydrolase family 17, plant + 53 + 82 211 - IPR016181
Acyl-CoA N-acyltransferase - 52 - 107 + IPR000109
Proton-dependent oligopeptide transporter family + 53 + 324 212 - IPR036318
FAD-binding, type 2-like superfamily - 52 - 77 + IPR018253
DnaJ domain, conserved site + 53 + 80 213 - IPR013763
Cyclin-like - 52 - 315 + IPR003663
Sugar/inositol transporter + 53 + 1278 214 - IPR034197
Cucumisin-like catalytic domain - 52 - 84 + IPR036318
FAD-binding, type PCMH-like superfamily + 52 + 77 215 - IPR004314
Neprosin - 52 - 63 + IPR034197
Cucumisin-like catalytic domain + 52 + 84 216 - IPR001878
  - 52 - 1308 + IPR004314
Neprosin + 52 + 124 217 - IPR019821
Kinesin motor domain, conserved site - 51 - 144 + IPR041569
AAA ATPase, AAA+ lid domain + 52 + 97 218 - IPR009060
UBA-like superfamily - 51 - 106 + IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2 + 52 + 71 219 - IPR000490
Glycoside hydrolase family 17 - 51 - 136 + IPR019821
Kinesin, motor region, conserved site + 51 + 110 220 IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid 51 - 144 + 414 221 - IPR016166
  - 50 - 222 + IPR008978
HSP20-like chaperone + 51 + 258 222 - IPR005174
Domain unknown function DUF295 - 50 - 59 + IPR009060
UBA-like superfamily + 51 + 212 223 - IPR036404
  - 50 - 1032 + IPR014014
RNA helicase, DEAD-box type, Q motif + 51 + 184 224 - IPR012341
  - 50 - 255 + IPR000490
Glycoside hydrolase family 17 + 51 + 260 225 - IPR001229
  - 50 - 1520 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 50 + 77 226 - IPR036426
  - 49 - 568 + IPR001229
Jacalin-like lectin domain + 50 + 1806 227 - IPR001480
  - 49 - 696 + IPR016166
FAD-binding domain, PCMH-type + 50 + 148 228 - IPR030184
WAT1-related protein - 49 - 128 + IPR036404
Jacalin-like lectin domain superfamily + 50 + 256 229 - IPR000608
  - 48 - 650 + IPR036426
Bulb-type lectin domain superfamily + 49 + 126 230 - IPR008250
P-type ATPase, A domain superfamily - 48 - 123 + IPR001480
Bulb-type lectin domain + 49 + 1084 231 - IPR029055
  - 48 - 368 + IPR000608
Ubiquitin-conjugating enzyme E2 + 48 + 654 232 - IPR033131
Pectinesterase, Asp active site - 48 - 55 + IPR008928
Six-hairpin glycosidase superfamily + 48 + 160 233 - IPR008928
Six-hairpin glycosidase superfamily - 48 - 99 + IPR001757
P-type ATPase + 48 + 658 234 - IPR023299
  - 48 - 510 + IPR023298
P-type ATPase, transmembrane domain + 48 + 200 235 - IPR001757
P-type ATPase - 48 - 379 + IPR036855
Zinc finger, CCCH-type superfamily + 48 + 219 236 - IPR002109
  - 48 - 351 + IPR008250
P-type ATPase, A domain superfamily + 48 + 390 237 - IPR023298
P-type ATPase, transmembrane domain superfamily - 48 - 291 + IPR029055
Nucleophile aminohydrolases, N-terminal + 48 + 155 238 - IPR036855
Zinc finger, CCCH-type superfamily - 48 - 219 + IPR033131
Pectinesterase, Asp active site + 48 + 55 239 - IPR001214
  - 48 - 1014 + IPR023299
P-type ATPase, cytoplasmic domain N + 48 + 312 240 - IPR008942
  - 47 - 316 + IPR030184
WAT1-related protein + 48 + 126 241 - IPR033896
MADS MEF2-like - 47 - 113 + IPR001214
SET domain + 48 + 606 242 - IPR001360
Glycoside hydrolase family 1 - 47 - 634 + IPR033896
MADS MEF2-like + 47 + 113 243 - IPR026057
PC-Esterase - 47 - 79 + IPR001360
Glycoside hydrolase family 1 + 47 + 1266 244 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 47 - 55 + IPR026057
PC-Esterase + 47 + 158 245 - IPR025521
Neprosin activation peptide - 47 - 56 + IPR018303
P-type ATPase, phosphorylation site + 47 + 71 246 - IPR018303
P-type ATPase, phosphorylation site - 47 - 98 + IPR033897
MADS SRF-like + 47 + 58 247 - IPR033897
MADS SRF-like - 47 - 58 + IPR014756
Immunoglobulin E-set + 47 + 194 248 - IPR014756
Immunoglobulin E-set - 47 - 110 + IPR000620
EamA domain + 47 + 324 249 - IPR000620
EamA domain - 47 - 162 + IPR033389
AUX/IAA domain + 46 + 99 250 - IPR033389
AUX/IAA domain - 46 - 95 + IPR011032
GroES-like superfamily + 46 + 362 251 - IPR011032
GroES-like superfamily - 46 - 114 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 46 + 184 252 - IPR036640
  - 46 - 1011 + IPR025846
PMR5 N-terminal domain + 46 + 148 253 - IPR013057
Amino acid transporter, transmembrane domain - 46 - 84 + IPR002109
Glutaredoxin + 46 + 116 254 - IPR011527
  - 46 - 1098 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 46 + 106 255 - IPR025846
PMR5 N-terminal domain - 46 - 74 + IPR013057
Amino acid transporter, transmembrane domain + 46 + 168 256 - IPR029962
Trichome birefringence-like family - 45 - 88 + IPR011527
ABC transporter type 1, transmembrane domain + 46 + 732 257 IPR000873
AMP-dependent synthetase/ligase 45 - 81 + 162 258 - IPR033734
Jacalin-like lectin domain, plant - 45 - 235 + IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup + 45 + 75 259 - IPR038770
  - 44 - 140 + IPR017884
SANT domain + 45 + 184 260 - IPR003245
  - 44 - 468 + IPR029962
Trichome birefringence-like family + 45 + 82 261 - IPR038718
  - 44 - 336 + IPR025521
Neprosin activation peptide + 45 + 108 262 IPR006094
FAD linked oxidase, N-terminal 44 - 60 + 120 263 - IPR017877
  - 44 - 174 + IPR033734
Jacalin-like lectin domain, plant + 44 + 234 264 - IPR006016
UspA - 43 - 73 + IPR008942
ENTH/VHS + 44 + 270 265 - IPR009000
Translation protein, beta-barrel domain superfamily - 43 - 96 + IPR003245
Phytocyanin domain + 44 + 312 266 - IPR004883
  - 43 - 232 + IPR010851
Defensin-like protein + 43 + 142 267 - IPR017970
Homeobox, conserved site - 43 - 80 + IPR004883
Lateral organ boundaries, LOB + 43 + 232 268 - IPR014721
  - 43 - 186 + IPR016167
FAD-binding, type 2, subdomain 1 + 43 + 58 269 - IPR001789
  - 43 - 939 + IPR031127
E3 ubiquitin ligase RBR family + 43 + 69 270 - IPR002921
Fungal lipase-like domain - 42 - 80 + IPR001789
Signal transduction response regulator, receiver domain + 43 + 438 271 - IPR010920
LSM domain superfamily - 42 - 85 + IPR009000
Translation protein, beta-barrel domain superfamily + 43 + 186 272 - IPR024171
S-receptor-like serine/threonine-protein kinase - 42 - 116 + IPR017970
Homeobox, conserved site + 43 + 61 273 - IPR010851
S locus-related glycoprotein 1 binding pollen coat protein - 42 - 42 + IPR010920
LSM domain superfamily + 42 + 168 274 - IPR016167
  - 42 - 195 + IPR004263
Exostosin-like + 42 + 325 275 IPR006045
Cupin 1 42 - 134 + 270 276 - IPR002219
  + IPR002219
Protein kinase C-like, phorbol ester/diacylglycerol-binding domain 42 - 603 + 394 277 IPR006671
Cyclin, N-terminal 42 - 147 + 282 278 IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site 42 - 78 + 75 279 IPR015947
PUA-like superfamily 42 - 93 + 192 280 - IPR001117
Multicopper oxidase, type 1 - 41 - 63 + IPR002921
Fungal lipase-like domain + 42 + 160 281 - IPR006153
Cation/H+ exchanger - 41 - 60 + IPR004853
Sugar phosphate transporter domain + 41 + 172 282 - IPR013525
ABC-2 type transporter - 41 - 119 + IPR011701
Major facilitator superfamily + 41 + 210 283 - IPR004853
Sugar phosphate transporter domain - 41 - 86 + IPR000330
SNF2, N-terminal + 41 + 234 284 - IPR011701
Major facilitator superfamily - 41 - 105 + IPR003609
PAN/Apple domain + 41 + 646 285 - IPR000330
SNF2-related, N-terminal domain - 41 - 117 + IPR026961
PGG domain + 41 + 174 286 - IPR003137
PA domain - 41 - 64 + IPR003594
Histidine kinase/HSP90-like ATPase + 41 + 326 287 - IPR003609
  - 41 - 682 + IPR045087
Multicopper oxidase + 41 + 63 288 - IPR036890
  - 41 - 330 + IPR001117
Multicopper oxidase, type 1 + 41 + 126 289 - IPR026961
PGG domain - 41 - 87 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 41 + 140 290 - IPR004839
Aminotransferase, class I/classII - 41 - 84 + IPR006016
UspA + 41 + 142 291 - IPR011006
CheY-like superfamily - 41 - 92 + IPR006153
Cation/H+ exchanger + 41 + 120 292 - IPR019378
GDP-fucose protein O-fucosyltransferase - 41 - 60 + IPR004839
Aminotransferase, class I/classII + 41 + 168 293 - IPR011706
Multicopper oxidase, type 2 - 41 - 63 + IPR011006
CheY-like superfamily + 41 + 180 294 - IPR036465
  - 41 - 232 + IPR011706
Multicopper oxidase, C-terminal + 41 + 126 295 - IPR010402
  - 40 - 432 + IPR011042
Six-bladed beta-propeller, TolB-like + 41 + 71 296 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 40 - 369 + IPR010402
CCT domain + 40 + 288 297 - IPR022742
Serine aminopeptidase, S33 - 40 - 74 + IPR013525
ABC-2 type transporter + 40 + 236 298 - IPR002495
Glycosyl transferase, family 8 - 40 - 64 + IPR013783
Immunoglobulin-like fold + 40 + 83 299 - IPR016159
Cullin repeat-like-containing domain superfamily - 40 - 77 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 40 + 75 300 - IPR031127
E3 ubiquitin ligase RBR family - 40 - 66 + IPR044066
TRIAD supradomain + 40 + 62 301 - IPR002487
  + IPR002487
Transcription factor, K-box 40 - 780 + 520 302 - IPR016040
NAD(P)-binding domain - 39 - 79 + IPR006553
Leucine-rich repeat, cysteine-containing subtype + 40 + 325 303 - IPR002867
IBR domain - 39 - 210 + IPR039391
Phytocyanin + 40 + 52 304 - IPR011016
  - 39 - 723 + IPR022742
Serine aminopeptidase, S33 + 40 + 148 305 - IPR004263
Exostosin-like - 39 - 61 - - + IPR016159
Cullin repeat-like-containing domain superfamily + 40 + 110 + + 306 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 39 - 56 + IPR011707
Multicopper oxidase, N-termianl + 40 + 122 307 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 39 - 75 + IPR019378
GDP-fucose protein O-fucosyltransferase + 39 + 116 308 - IPR020845
AMP-binding, conserved site - 39 - 72 + IPR002495
Glycosyl transferase, family 8 + 39 + 122 309 - IPR002067
Mitochondrial carrier protein - 39 - 312 + IPR036465
von Willebrand factor A-like domain superfamily + 39 + 70 310 - IPR011707
Multicopper oxidase, type 3 - 39 - 60 + IPR002867
IBR domain + 39 + 388 311 - IPR006702
Casparian strip membrane protein domain - 39 - 49 + IPR011016
Zinc finger, RING-CH-type + 39 + 422 312 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 38 - 56 + IPR007125
Histone H2A/H2B/H3 + 39 + 108 313 - IPR023271
  - 38 - 238 + IPR020845
AMP-binding, conserved site + 39 + 61 314 - IPR000222
PPM-type phosphatase, divalent cation binding - 38 - 68 + IPR002067
Mitochondrial carrier protein + 39 + 624 315 - IPR011012
Longin-like domain superfamily - 38 - 66 + IPR006702
Casparian strip membrane protein domain + 39 + 98 316 - IPR007125
Histone H2A/H2B/H3 - 38 - 52 + IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site + 38 + 54 317 - IPR036908
  - 38 - 226 + IPR011012
Longin-like domain superfamily + 38 + 132 318 - IPR036875
Zinc finger, CCHC-type superfamily - 38 - 110 + IPR032710
NTF2-like domain + 38 + 142 319 - IPR000182
  - 37 - 238 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 38 + 220 320 - IPR000858
S-locus glycoprotein domain - 37 - 108 + IPR023271
Aquaporin-like + 38 + 232 321 - IPR013149
Alcohol dehydrogenase, C-terminal - 37 - 70 + IPR036908
RlpA-like domain superfamily + 38 + 56 322 - IPR013216
Methyltransferase type 11 - 37 - 51 + IPR036875
Zinc finger, CCHC-type superfamily + 38 + 110 323 - IPR001969
Aspartic peptidase, active site - 37 - 97 + IPR003614
Knottin, scorpion toxin-like + 38 + 150 324 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 37 - 55 + IPR000182
GNAT domain + 37 + 238 325 - IPR034294
Aquaporin transporter - 37 - 59 + IPR000858
S-locus glycoprotein domain + 37 + 216 326 - IPR007112
  - 37 - 214 + IPR013216
Methyltransferase type 11 + 37 + 102 327 - IPR000425
Major intrinsic protein - 37 - 449 + IPR001969
Peptidase aspartic, active site + 37 + 108 328 - IPR000727
  - 36 - 364 + IPR020904
Short-chain dehydrogenase/reductase, conserved site + 37 + 53 329 - IPR032710
NTF2-like domain superfamily - 36 - 89 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 37 + 946 330 - IPR013128
Peptidase C1A - 36 - 50 + IPR013149
Alcohol dehydrogenase, C-terminal + 37 + 134 331 - IPR002068
  - 36 - 152 + IPR007112
Expansin/pollen allergen, DPBB domain + 37 + 212 332 - IPR036691
  - 36 - 542 + IPR000425
Major intrinsic protein + 37 + 892 333 - IPR036612
  - 36 - 876 + IPR044788
Carbohydrate-binding X8 domain-containing protein, plant + 37 + 55 334 - IPR001509
NAD-dependent epimerase/dehydratase - 36 - 60 + IPR000727
Target SNARE coiled-coil homology domain + 36 + 332 335 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 36 - 475 + IPR036612
K Homology domain, type 1 superfamily + 36 + 172 336 - IPR029045
ClpP/crotonase-like domain superfamily - 36 - 95 + IPR003137
PA domain + 36 + 102 337 - IPR008801
Rapid ALkalinization Factor - 36 - 40 + IPR002913
START domain + 36 + 400 338 - IPR000668
Peptidase C1A, papain C-terminal - 36 - 196 + IPR002068
Alpha crystallin/Hsp20 domain + 36 + 152 339 - IPR003851
  - 36 - 624 + IPR024171
S-receptor-like serine/threonine-protein kinase + 36 + 71 340 - IPR002913
  - 36 - 657 + IPR029045
ClpP/crotonase-like domain + 36 + 129 341 - IPR001251
  - 35 - 736 + IPR008801
Rapid ALkalinization Factor + 36 + 80 342 - IPR007118
Expansin/Lol pI - 35 - 283 + IPR004088
K Homology domain, type 1 + 36 + 570 343 - IPR008991
Translation protein SH3-like domain superfamily - 35 - 47 + IPR000668
Peptidase C1A, papain C-terminal + 36 + 390 344 - IPR000315
  - 35 - 909 + IPR003851
Zinc finger, Dof-type + 36 + 396 345 - IPR016039
  - 35 - 573 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 35 + 52 346 - IPR036865
  - 35 - 368 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 35 + 140 347 - IPR036749
  - 35 - 208 + IPR015797
NUDIX hydrolase-like domain superfamily + 35 + 308 348 - IPR003594
Histidine kinase/HSP90-like ATPase - 35 - 146 + IPR043926
ABC transporter family G domain + 35 + 96 349 - IPR038538
  - 35 - 178 + IPR001251
CRAL-TRIO lipid binding domain + 35 + 814 350 - IPR001849
  - 35 - 324 + IPR007118
Expansin/Lol pI + 35 + 566 351 - IPR007117
  - 35 - 202 + IPR008991
Translation protein SH3-like domain superfamily + 35 + 94 352 - IPR015797
NUDIX hydrolase-like domain superfamily - 35 - 88 + IPR016039
Thiolase-like + 35 + 450 353 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 34 - 130 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 35 + 108 354 - IPR034161
Pepsin-like domain, plant - 34 - 45 + IPR002035
von Willebrand factor, type A + 35 + 230 355 - IPR005630
Terpene synthase, metal-binding domain - 34 - 52 + IPR001849
Pleckstrin homology domain + 35 + 304 356 - IPR005202
  - 34 - 192 + IPR007117
Expansin, cellulose-binding-like domain + 35 + 304 357 - IPR029062
  - 34 - 308 + IPR000315
B-box-type zinc finger + 34 + 408 358 - IPR000644
  - 34 - 584 + IPR005630
Terpene synthase, metal-binding domain + 34 + 104 359 - IPR002912
  - 34 - 456 + IPR034294
Aquaporin transporter + 34 + 54 360 - IPR025110
AMP-binding enzyme, C-terminal domain - 33 - 46 + IPR029062
Class I glutamine amidotransferase-like + 34 + 144 361 - IPR018490
Cyclic nucleotide-binding-like - 33 - 79 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 34 + 256 362 - IPR029000
  - 33 - 274 + IPR001509
NAD-dependent epimerase/dehydratase + 34 + 116 363 - IPR024709
Putative O-fucosyltransferase, plant - 33 - 99 + IPR034161
Pepsin-like domain, plant + 34 + 45 364 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 33 - 42 + IPR005135
Endonuclease/exonuclease/phosphatase + 34 + 416 365 - IPR027356
  - 33 - 320 + IPR005202
Transcription factor GRAS + 34 + 304 366 - IPR003406
Glycosyl transferase, family 14 - 33 - 62 + IPR002912
ACT domain + 34 + 416 367 - IPR017937
Thioredoxin, conserved site - 33 - 59 + IPR012341
Six-hairpin glycosidase + 34 + 51 368 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 33 - 43 + IPR018490
Cyclic nucleotide-binding-like + 33 + 158 369 - IPR011042
  - 33 - 118 + IPR016455
Xyloglucan endotransglucosylase/hydrolase + 33 + 148 370 - IPR000757
  - 33 - 264 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 91 371 - IPR036965
  - 32 - 159 + IPR043454
NPH3/RPT2-like family + 33 + 81 372 - IPR025659
  - 32 - 184 + IPR017937
Thioredoxin, conserved site + 33 + 58 373 - IPR017392
AP2/ERF transcription factor ERF/PTI6 - 32 - 61 + IPR044791
Beta-glucanase/XTH + 33 + 45 374 - IPR023313
Ubiquitin-conjugating enzyme, active site - 32 - 75 + IPR025110
AMP-binding enzyme, C-terminal domain + 33 + 92 375 - IPR022357
Major intrinsic protein, conserved site - 32 - 51 + IPR029000
Cyclophilin-like domain + 33 + 119 376 - IPR001906
Terpene synthase, N-terminal domain - 32 - 50 + IPR024709
Putative O-fucosyltransferase, plant + 33 + 184 377 - IPR028889
  - 32 - 130 + IPR027356
NPH3 domain + 33 + 320 378 - IPR000595
  - 32 - 560 + IPR003406
Glycosyl transferase, family 14 + 33 + 124 379 - IPR008889
VQ - 32 - 45 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 33 + 86 380 - IPR005175
  - 32 - 292 + IPR039361
Cyclin + 33 + 80 381 - IPR015940
  - 31 - 342 + IPR000757
Glycoside hydrolase family 16 + 33 + 176 382 - IPR001929
Germin - 31 - 113 + IPR022357
Major intrinsic protein, conserved site + 32 + 48 383 - IPR002130
  - 31 - 1002 + IPR001906
Terpene synthase, N-terminal domain + 32 + 188 384 - IPR004367
Cyclin, C-terminal domain - 31 - 93 + IPR000595
Cyclic nucleotide-binding domain + 32 + 546 385 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 31 - 80 + IPR044730
Ribonuclease H-like domain, plant type + 32 + 35 386 - IPR005746
Thioredoxin - 31 - 67 + IPR008889
VQ + 32 + 90 387 - IPR006073
GTP binding domain - 31 - 146 + IPR025659
Tubby-like, C-terminal + 32 + 128 388 - IPR017927
  - 30 - 180 + IPR023313
Ubiquitin-conjugating enzyme, active site + 32 + 54 389 - IPR006594
  - 30 - 486 + IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain + 32 + 65 390 - IPR017938
Riboflavin synthase-like beta-barrel - 30 - 57 + IPR005175
PPC domain + 32 + 290 391 - IPR017946
  - 30 - 384 + IPR006073
GTP binding domain + 32 + 298 392 - IPR013088
  - 30 - 126 + IPR015940
Ubiquitin-associated domain + 31 + 334 393 - IPR029021
  - 30 - 272 + IPR012675
Beta-grasp domain + 31 + 44 394 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 30 - 75 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 31 + 60 395 - IPR001296
Glycosyl transferase, family 1 - 30 - 52 + IPR001929
Germin + 31 + 226 396 - IPR008265
Lipase, GDSL, active site - 30 - 40 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 31 + 668 397 - IPR025886
Phloem protein 2-like - 30 - 40 + IPR004367
Cyclin, C-terminal domain + 31 + 184 398 - IPR011013
Galactose mutarotase-like domain superfamily - 30 - 93 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 31 + 78 399 - IPR027923
Hydrophobic seed protein - 30 - 68 + IPR000644
CBS domain + 31 + 468 400 - IPR005821
Ion transport domain - 30 - 73 + IPR006594
LIS1 homology motif + 30 + 288 401 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 30 - 112 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 30 + 360 402 - IPR000086
  - 30 - 432 + IPR017938
Riboflavin synthase-like beta-barrel + 30 + 110 403 - IPR020843
Polyketide synthase, enoylreductase domain - 30 - 42 + IPR013088
Zinc finger, NHR/GATA-type + 30 + 34 404 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 47 + IPR044814
Terpene cyclases, class 1, plant + 30 + 42 405 - IPR000679
  - 30 - 495 + IPR027923
Hydrophobic seed protein + 30 + 68 406 - IPR000717
  - 29 - 206 + IPR005821
Ion transport domain + 30 + 146 407 - IPR000795
  - 29 - 1164 + IPR015655
Protein phosphatase 2C + 30 + 69 408 - IPR008480
Protein of unknown function DUF761, plant - 29 - 30 + IPR000086
NUDIX hydrolase domain + 30 + 288 409 - IPR014722
  - 29 - 96 + IPR000679
Zinc finger, GATA-type + 30 + 382 410 - IPR000916
Bet v I/Major latex protein - 29 - 93 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 30 + 120 411 - IPR036427
  - 29 - 387 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 30 + 244 412 - IPR003311
AUX/IAA protein - 29 - 59 + IPR029021
Protein-tyrosine phosphatase-like + 30 + 130 413 - IPR009091
  - 29 - 478 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 30 + 148 414 - IPR036574
  - 29 - 116 + IPR025886
Phloem protein 2-like + 30 + 80 415 - IPR025322
Protein of unknown function DUF4228, plant - 28 - 32 + IPR011013
Galactose mutarotase-like domain superfamily + 30 + 136 416 - IPR005135
Endonuclease/exonuclease/phosphatase - 28 - 77 + IPR014720
Double-stranded RNA-binding domain + 30 + 201 417 - IPR013154
Alcohol dehydrogenase, N-terminal - 28 - 52 + IPR020843
Polyketide synthase, enoylreductase + 30 + 40 418 - IPR024768
Meiosis regulator and mRNA stability factor 1 - 28 - 70 + IPR018202
Peptidase S10, serine carboxypeptidase, active site + 30 + 45 419 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 28 - 75 + IPR000717
Proteasome component (PCI) domain + 29 + 200 420 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 28 - 59 + IPR039417
Papain-like cysteine endopeptidase + 29 + 37 421 - IPR004087
K Homology domain - 28 - 162 + IPR018957
Zinc finger, C3HC4 RING-type + 29 + 140 422 - IPR000169
Cysteine peptidase, cysteine active site - 28 - 40 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 29 + 50 423 - IPR001487
  - 28 - 993 + IPR000795
Translational (tr)-type GTP-binding domain + 29 + 776 424 - IPR025660
Cysteine peptidase, histidine active site - 28 - 33 + IPR000916
Bet v I/Major latex protein + 29 + 178 425 - IPR036600
Paired amphipathic helix superfamily - 27 - 104 + IPR003311
AUX/IAA protein + 29 + 122 426 - IPR018200
Ubiquitin specific protease, conserved site - 27 - 89 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 29 + 316 427 - IPR012951
Berberine/berberine-like - 27 - 33 + IPR001487
Bromodomain + 29 + 732 428 - IPR023753
FAD/NAD(P)-binding domain - 27 - 51 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 28 + 31 429 - IPR010989
SNARE - 27 - 53 + IPR007592
GLABROUS1 enhancer-binding protein family + 28 + 122 430 - IPR004265
Dirigent protein - 27 - 31 + IPR008480
Protein of unknown function DUF761, plant + 28 + 58 431 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 27 - 58 + IPR004087
K Homology domain + 28 + 126 432 - IPR000960
Flavin monooxygenase FMO - 27 - 192 + IPR000169
Cysteine peptidase, cysteine active site + 28 + 36 433 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 27 - 99 + IPR036427
Bromodomain-like superfamily + 28 + 64 434 - IPR022796
Chlorophyll A-B binding protein - 27 - 40 + IPR025660
Cysteine peptidase, histidine active site + 28 + 32 435 - IPR020946
Flavin monooxygenase-like - 27 - 66 + IPR025322
Protein of unknown function DUF4228, plant + 28 + 64 436 - IPR004088
K Homology domain, type 1 - 27 - 152 + IPR040256
Uncharacterized protein At4g02000-like + 28 + 32 437 - IPR001701
Glycoside hydrolase family 9 - 27 - 40 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 28 + 44 438 - IPR004158
Protein of unknown function DUF247, plant - 27 - 50 + IPR001296
Glycosyl transferase, family 1 + 28 + 100 439 - IPR034741
Terpene cyclase-like 1, C-terminal domain - 27 - 34 + IPR013154
Alcohol dehydrogenase, N-terminal + 28 + 104 440 - IPR004274
  - 27 - 308 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 28 + 210 441 - IPR004041
NAF domain - 26 - 44 + IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site + 28 + 47 442 - IPR018957
Zinc finger, C3HC4 RING-type - 26 - 67 + IPR010682
Plant self-incompatibility response + 28 + 108 443 - IPR018451
  - 26 - 129 + IPR036600
Paired amphipathic helix superfamily + 27 + 104 444 - IPR001163
LSM domain, eukaryotic/archaea-type - 26 - 103 + IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site + 27 + 70 445 - IPR004161
Translation elongation factor EFTu-like, domain 2 - 26 - 53 + IPR012951
Berberine/berberine-like + 27 + 66 446 - IPR003822
  - 26 - 570 + IPR001279
Metallo-beta-lactamase + 27 + 252 447 - IPR002022
Pectate lyase - 26 - 72 + IPR008265
Lipase, GDSL, active site + 27 + 36 448 - IPR012675
  - 26 - 94 + IPR003822
Paired amphipathic helix + 27 + 534 449 - IPR011074
CRAL/TRIO, N-terminal domain - 26 - 113 + IPR004265
Dirigent protein + 27 + 62 450 - IPR005150
Cellulose synthase - 26 - 55 + IPR024768
Meiosis arrest female protein 1 + 27 + 62 451 - IPR031107
Small heat shock protein HSP20 - 26 - 39 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 27 + 170 452 - IPR013780
  - 26 - 106 + IPR033443
Pentacotripeptide-repeat region of PROPR + 27 + 45 453 - IPR029006
  - 26 - 360 + IPR001701
Glycoside hydrolase family 9 + 27 + 80 454 - IPR025661
Cysteine peptidase, asparagine active site - 26 + IPR036574
Knottin, scorpion toxin-like superfamily + 27 29 455 - IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase - 26 - 435 + IPR004274
FCP1 homology domain + 27 + 282 456 - IPR018082
AmbAllergen - 26 - 252 + IPR010989
SNARE + 27 + 100 457 - IPR000528
Plant lipid transfer protein/Par allergen - 25 - 157 + IPR020946
Flavin monooxygenase-like + 27 + 132 458 - IPR000782
  - 25 - 210 + IPR004158
Protein of unknown function DUF247, plant + 27 + 174 459 - IPR019956
Ubiquitin - 25 - 138 + IPR004041
NAF domain + 26 + 88 460 - IPR005299
SAM dependent carboxyl methyltransferase - 25 - 88 + IPR018451
NAF/FISL domain + 26 + 86 461 - IPR029061
Thiamin diphosphate-binding fold - 25 - 71 + IPR045032
Pectin lyase family + 26 + 36 462 - IPR001938
  - 25 - 794 + IPR002022
Pectate lyase + 26 + 140 463 - IPR036866
  - 25 - 326 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 26 + 112 464 - IPR014002
Agenet domain, plant type - 25 - 126 + IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase + 26 + 846 465 - IPR002963
Expansin - 25 - 303 + IPR018082
AmbAllergen + 26 + 504 466 - IPR004046
Glutathione S-transferase, C-terminal - 25 - 38 + IPR001163
LSM domain, eukaryotic/archaea-type + 26 + 174 467 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 25 - 55 + IPR011074
CRAL/TRIO, N-terminal domain + 26 + 180 468 - IPR019780
Germin, manganese binding site - 25 - 30 + IPR005150
Cellulose synthase + 26 + 110 469 - IPR001313
  - 25 - 2499 + IPR029006
ADF-H/Gelsolin-like domain + 26 + 100 470 - IPR034086
Pectinesterase inhibitor, plant - 25 - 26 + IPR043519
Nucleotidyltransferase superfamily + 26 + 89 471 - IPR013809
  - 25 - 184 + IPR025661
Cysteine peptidase, asparagine active site + 26 + 29 472 - IPR029033
  - 25 - 330 + IPR029060
PIN domain-like + 25 + 110 473 - IPR037176
  - 25 - 182 + IPR000782
FAS1 domain + 25 + 278 474 - IPR017884
  - 24 - 92 + IPR019956
Ubiquitin domain + 25 + 276 475 - IPR006689
Small GTPase superfamily, ARF/SAR type - 24 - 210 + IPR005299
SAM dependent carboxyl methyltransferase + 25 + 170 476 - IPR036378
  - 24 - 142 + IPR029061
Thiamin diphosphate-binding fold + 25 + 132 477 - IPR025753
AAA-type ATPase, N-terminal domain - 24 - 30 + IPR001938
Thaumatin family + 25 + 844 478 - IPR003954
RNA recognition motif domain, eukaryote - 24 - 75 + IPR029056
Ribokinase-like + 25 + 86 479 - IPR027725
Heat shock transcription factor family - 24 - 43 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 25 + 63 480 - IPR001594
Palmitoyltransferase, DHHC domain - 24 - 36 + IPR014002
Tudor-like, plant + 25 + 108 481 - IPR005333
Transcription factor, TCP - 24 - 42 + IPR002963
Expansin + 25 + 606 482 - IPR017887
  - 24 - 82 + IPR022796
Chlorophyll A-B binding protein + 25 + 76 483 - IPR001353
Proteasome, subunit alpha/beta - 24 - 45 + IPR014722
Ribosomal protein L2 domain 2 + 25 + 32 484 - IPR012552
DVL - 24 - 25 + IPR034086
Pectinesterase inhibitor, plant + 25 + 26 485 - IPR029056
  - 24 - 174 + IPR013809
ENTH domain + 25 + 170 486 - IPR017926
  - 24 - 148 + IPR029033
Histidine phosphatase superfamily + 25 + 152 487 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 24 - 74 + IPR037176
Osmotin/thaumatin-like superfamily + 25 + 45 488 - IPR000408
  - 24 - 2358 + IPR004161
Translation elongation factor EFTu-like, domain 2 + 25 + 100 489 - IPR006459
Casparian strip membrane protein - 24 - 26 + IPR039774
Transcriptional regulatory protein Sin3-like + 25 + 55 490 - IPR001876
  - 24 - 518 + IPR004046
Glutathione S-transferase, C-terminal + 25 + 76 491 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 24 - 53 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 25 + 110 492 - IPR025486
Domain of unknown function DUF4378 - 24 - 67 + IPR019780
Germin, manganese binding site + 25 + 30 493 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 24 - 170 + IPR025753
AAA-type ATPase, N-terminal domain + 24 + 60 494 - IPR000836
Phosphoribosyltransferase domain - 24 - 76 + IPR044835
Auxin response factor + 24 + 59 495 - IPR033133
  - 23 - 120 + IPR027725
Heat shock transcription factor family + 24 + 35 496 - IPR001179
  - 23 - 186 + IPR001594
Palmitoyltransferase, DHHC domain + 24 + 72 497 - IPR021820
S-locus receptor kinase, C-terminal - 23 - 60 + IPR017887
Transcription factor TCP subgroup + 24 + 82 498 - IPR035940
  - 23 - 94 + IPR001353
Proteasome, subunit alpha/beta + 24 + 90 499 - IPR002423
Chaperonin Cpn60/TCP-1 family - 23 - 48 + IPR039218
REM family + 24 + 153 500 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 23 - 63 + IPR000408
Regulator of chromosome condensation, RCC1 + 24 + 2366 diff --git a/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii.html b/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii.html index 09b415e6..bfa02aea 100644 --- a/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii.html +++ b/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.3 + 87.3 Base Pairs: @@ -21,11 +21,11 @@

Summary

Gene counts

- + - + @@ -62,7 +62,7 @@

Coordinate Systems

16
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 17,743
Gene transcriptsHASH(0x68ce400):Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.: 19,528
7783580
177188315
-
+
@@ -112,7 +112,7 @@

Coordinate Systems

KZ4549796241KZ4549802479 -
+
diff --git a/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii_IPtop500.html b/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii_IPtop500.html index f1ccc046..684b0ec9 100644 --- a/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Chlamydomonas_reinhardtii_IPtop500.html @@ -16,35 +16,35 @@ 1 - IPR011009
Protein kinase-like domain superfamily + IPR011009
  729 - 1546 + 1750 2 - IPR027417
P-loop containing nucleoside triphosphate hydrolase + IPR027417
  696 - 1557 + 2018 3 IPR000719
  - 621 - 9772 + 614 + 3746 4 - IPR008271
Serine/threonine-protein kinase, active site + IPR008271
  437 486 5 - IPR017441
Protein kinase, ATP binding site + IPR017441
  313 351 @@ -53,3309 +53,3309 @@ 6 IPR036770
  245 - 3831 + 1448 7 IPR013083
  232 - 1674 + 279 8 IPR015943
  216 - 3824 + 478 9 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + IPR029063
  211 - 331 + 478 10 - IPR036322
WD40-repeat-containing domain superfamily + IPR036322
  209 - 532 + 530 11 - IPR001680
  - 202 - 13272 + IPR032675
  + 201 + 469 12 - IPR032675
  - 201 - 2814 + IPR016024
  + 198 + 514 13 - IPR016024
Armadillo-type fold - 198 - 604 + IPR001245
  + 192 + 772 14 - IPR003593
AAA+ ATPase domain - 195 - 320 + IPR036291
  + 184 + 450 15 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 195 - 394 + IPR017986
  + 179 + 262 16 - IPR036291
NAD(P)-binding domain superfamily - 184 - 270 + IPR001680
  + 177 + 3896 17 - IPR017986
  - 179 - 2096 + IPR011990
  + 175 + 1046 18 - IPR011990
  - 175 - 3504 + IPR038772
  + 170 + 410 19 - IPR020683
  - 165 - 2844 + IPR029058
  + 165 + 738 20 - IPR029058
  - 165 - 1938 + IPR020683
  + 153 + 838 21 IPR002110
  - 148 - 9828 + 144 + 2894 22 IPR002048
  140 - 5324 + 1932 23 IPR029787
  140 - 2499 + 942 24 IPR009072
  138 - 1676 + 558 25 - IPR011992
EF-hand domain pair + IPR011992
  138 - 236 + 358 26 IPR001054
  127 - 1611 + 1064 27 - IPR019775
WD40 repeat, conserved site + IPR019775
  125 286 28 - IPR018247
EF-Hand 1, calcium-binding site + IPR018247
  122 274 29 - IPR002893
  - 122 - 1053 + IPR036249
  + 121 + 286 30 - IPR036249
Thioredoxin-like superfamily - 121 - 146 + IPR002893
  + 120 + 684 31 IPR036188
  119 - 2253 + 754 32 IPR001841
  116 - 1233 + 604 33 IPR011989
  113 - 1098 + 183 34 - IPR035979
RNA-binding domain superfamily + IPR035979
  111 - 220 + 388 35 IPR012677
  110 - 1344 + 224 36 IPR014001
  - 110 - 1050 + 106 + 460 37 IPR001650
  - 105 - 1695 + 103 + 674 38 IPR000504
  - 105 - 3048 + 103 + 1132 39 IPR000477
  - 105 - 897 + 103 + 592 40 - IPR019734
  - 98 - 4396 + IPR036412
  + 94 + 234 41 - IPR036412
HAD-like superfamily - 94 - 179 + IPR007125
  + 93 + 186 42 - IPR007125
Histone H2A/H2B/H3 - 93 - 93 + IPR001611
  + 92 + 1188 43 - IPR001611
  - 91 - 3096 + IPR036691
  + 89 + 404 44 - IPR036691
  - 89 - 1023 + IPR013783
  + 87 + 176 45 - IPR013783
  - 87 - 1056 + IPR013026
  + 87 + 135 46 - IPR013026
  - 87 - 1080 + IPR038765
  + 85 + 198 47 - IPR038765
Papain-like cysteine peptidase superfamily - 85 - 150 + IPR023214
  + 82 + 169 48 - IPR038772
Sphingomyelin phosphodiesterase 2-like - 84 - 86 + IPR039606
Phytol/farnesol kinase + 80 + 89 49 - IPR023214
  - 82 - 1014 + IPR003439
  + 80 + 782 50 - IPR003439
  - 80 - 1576 + IPR012337
  + 77 + 190 51 - IPR012337
Ribonuclease H-like superfamily - 77 - 131 + IPR003959
  + 73 + 194 52 IPR036869
  73 - 690 + 306 53 - IPR003959
ATPase, AAA-type, core - 72 - 96 + IPR036259
  + 71 + 168 54 - IPR024616
Pherophorin - 71 - 126 + IPR019734
  + 70 + 998 55 - IPR036259
MFS transporter superfamily - 71 - 141 + IPR001623
  + 69 + 950 56 - IPR001623
  - 69 - 1638 + IPR012340
  + 69 + 198 57 - IPR012340
Nucleic acid-binding, OB-fold - 69 - 108 + IPR011333
  + 69 + 150 58 - IPR011333
SKP1/BTB/POZ domain superfamily - 69 - 89 + IPR009057
  + 67 + 164 59 - IPR009057
Homeobox-like domain superfamily - 67 - 82 + IPR029044
  + 66 + 244 60 - IPR029044
  - 66 - 564 + IPR020472
  + 66 + 426 61 - IPR020472
G-protein beta WD-40 repeat - 66 - 213 + IPR016181
  + 63 + 136 62 - IPR016181
Acyl-CoA N-acyltransferase - 63 - 72 + IPR011545
  + 63 + 138 63 - IPR011545
DEAD/DEAH box helicase domain - 63 - 69 + IPR024616
  + 62 + 218 64 - IPR017871
ABC transporter, conserved site + IPR017871
  62 90 65 - IPR029071
Ubiquitin-like domain superfamily + IPR029071
  62 - 77 + 154 66 IPR000210
  - 61 - 928 + 60 + 350 67 IPR013785
  59 - 616 + 77 68 - IPR020846
  - 58 - 441 + IPR001214
  + 58 + 330 69 - IPR001214
  - 58 - 748 + IPR036047
  + 57 + 116 70 - IPR001005
SANT/Myb domain - 58 - 220 + IPR001005
  + 57 + 633 71 - IPR036047
F-box-like domain superfamily - 57 - 58 + IPR013032
  + 54 + 134 72 - IPR013032
EGF-like, conserved site - 54 - 134 + IPR013766
  + 53 + 316 73 IPR014729
  53 - 438 + 73 74 - IPR011011
Zinc finger, FYVE/PHD-type + IPR011011
  53 - 63 + 124 75 - IPR014756
Immunoglobulin E-set + IPR014756
  53 - 83 + 158 76 - IPR017907
Zinc finger, RING-type, conserved site + IPR017907
  52 56 77 - IPR015424
Pyridoxal phosphate-dependent transferase + IPR015424
  52 - 79 + 120 78 IPR036397
  51 - 480 + 60 79 - IPR013766
  - 51 - 628 + IPR017853
  + 51 + 130 80 - IPR017853
Glycoside hydrolase superfamily - 51 - 97 + IPR005225
  + 51 + 57 81 - IPR027090
Enoyl-CoA hydratase 2 - 51 - 151 + IPR043502
DNA/RNA polymerase superfamily + 50 + 57 82 - IPR005225
Small GTP-binding protein domain - 51 - 57 + IPR036388
  + 49 + 61 83 - IPR036388
  - 49 - 366 + IPR014710
  + 49 + 78 84 - IPR014710
  - 49 - 468 + IPR006598
  + 49 + 128 85 - IPR006598
Lipopolysaccharide-modifying protein - 49 - 125 + IPR017930
  + 49 + 264 86 - IPR001965
Zinc finger, PHD-type - 49 - 69 + IPR000182
  + 48 + 286 87 - IPR000182
  - 48 - 429 + IPR015421
  + 48 + 58 88 - IPR015421
  - 48 - 464 + IPR008266
  + 48 + 55 89 - IPR008266
Tyrosine-protein kinase, active site - 48 - 55 + IPR008752
  + 48 + 108 90 - IPR008752
Peptidase M11, gametolysin - 48 - 54 + IPR000626
  + 47 + 316 91 - IPR000742
  - 48 - 552 + IPR010095
  + 47 + 98 92 - IPR005821
Ion transport domain - 48 - 86 + IPR005821
  + 47 + 168 93 - IPR000626
  - 47 - 780 + IPR011047
  + 45 + 120 94 - IPR010095
Transposase IS605, OrfB, C-terminal - 47 - 49 + IPR000742
  + 45 + 240 95 - IPR027640
Kinesin-like protein - 47 - 85 + IPR036390
  + 45 + 108 96 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 45 - 125 + IPR001190
  + 45 + 1242 97 - IPR036390
Winged helix DNA-binding domain superfamily - 45 - 54 + IPR018297
  + 45 + 49 98 - IPR001190
  - 45 - 1869 + IPR002347
  + 44 + 590 99 - IPR018297
Adenylyl cyclase class-4/guanylyl cyclase, conserved site - 45 - 49 + IPR000048
  + 44 + 662 100 - IPR002347
Short-chain dehydrogenase/reductase SDR - 44 - 295 + IPR018490
  + 43 + 138 101 IPR001810
  - 44 - 368 + 43 + 164 102 - IPR000048
  - 44 - 1812 + IPR011050
  + 43 + 164 103 - IPR018490
Cyclic nucleotide-binding-like - 43 - 97 + IPR030616
  + 43 + 110 104 - IPR011050
Pectin lyase fold/virulence factor - 43 - 125 + IPR018108
  + 43 + 812 105 - IPR018108
  - 43 - 1227 + IPR023395
  + 43 + 260 106 - IPR023395
  - 43 - 687 + IPR036772
  + 43 + 662 107 - IPR036772
  - 43 - 1494 + IPR000595
  + 43 + 438 108 - IPR000595
  - 43 - 777 + IPR029052
  + 42 + 164 109 - IPR017930
  - 42 - 378 + IPR036396
  + 41 + 240 110 - IPR036396
  - 41 - 964 + IPR004263
  + 41 + 240 111 IPR019787
  41 - 366 + 244 112 IPR036961
  41 - 520 + 65 113 IPR015422
  41 - 568 + 71 114 - IPR001128
Cytochrome P450 + IPR001128
  41 - 196 + 392 115 - IPR004263
Exostosin-like - 40 - 48 + IPR008979
  + 40 + 188 116 - IPR008979
  - 40 - 414 + IPR020568
  + 40 + 96 117 - IPR020568
Ribosomal protein S5 domain 2-type fold - 40 - 56 + IPR009003
  + 39 + 90 118 - IPR006502
Protein of unknown function PDDEXK-like - 40 - 67 + IPR001752
  + 39 + 584 119 - IPR006626
Parallel beta-helix repeat - 39 - 559 + IPR017972
  + 39 + 42 120 - IPR003591
Leucine-rich repeat, typical subtype - 39 - 357 + IPR035892
  + 38 + 166 121 - IPR009003
Peptidase S1, PA clan - 39 - 65 + IPR005123
  + 38 + 259 122 - IPR001752
  - 39 - 1344 + IPR005135
  + 38 + 86 123 - IPR017972
Cytochrome P450, conserved site - 39 - 42 + IPR011701
  + 37 + 84 124 - IPR011701
Major facilitator superfamily - 38 - 43 + IPR036457
  + 37 + 156 125 - IPR005123
  - 38 - 452 + IPR020846
  + 37 + 156 126 - IPR005135
Endonuclease/exonuclease/phosphatase - 38 - 43 + IPR032710
  + 36 + 80 127 - IPR013584
  - 38 - 336 + IPR003960
  + 36 + 42 128 - IPR036457
  - 37 - 429 + IPR014014
  + 36 + 128 129 - IPR017448
SRCR-like domain - 37 - 147 + IPR001763
  + 36 + 198 130 - IPR032710
NTF2-like domain superfamily - 36 - 40 + IPR019786
  + 36 + 44 131 - IPR003607
  - 36 - 130 + IPR022796
  + 36 + 78 132 - IPR003960
ATPase, AAA-type, conserved site - 36 + IPR018253
  + 36 42 133 - IPR014014
  - 36 - 222 + IPR001932
  + 36 + 304 134 - IPR019786
Zinc finger, PHD-type, conserved site - 36 - 44 + IPR000164
  + 35 + 670 135 - IPR022796
Chlorophyll A-B binding protein - 36 - 40 + IPR016135
  + 35 + 154 136 - IPR018253
DnaJ domain, conserved site - 36 - 42 + IPR043129
ATPase, nucleotide binding domain + 35 + 72 137 - IPR001932
  - 36 - 816 + IPR029000
  + 34 + 176 138 - IPR035892
  - 35 - 252 + IPR009000
  + 34 + 80 139 - IPR000164
Histone H3/CENP-A - 35 - 370 + IPR000073
  + 34 + 138 140 - IPR016135
  - 35 - 348 + IPR023329
  + 34 + 37 141 - IPR029000
  - 34 - 399 + IPR004843
  + 33 + 70 142 - IPR009000
Translation protein, beta-barrel domain superfamily - 34 - 41 + IPR000008
  + 33 + 196 143 - IPR000073
Alpha/beta hydrolase fold-1 - 34 - 69 + IPR006502
  + 33 + 98 144 - IPR023329
  - 34 - 222 + IPR036873
  + 32 + 130 145 - IPR003613
  - 33 - 536 + IPR003607
  + 32 + 78 146 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 32 - 34 + IPR035425
  + 32 + 66 147 - IPR036873
  - 32 - 318 + IPR001951
  + 32 + 462 148 - IPR035425
CENP-T/Histone H4, histone fold - 32 + IPR019809
  + 32 33 149 - IPR001951
Histone H4 - 32 - 264 + IPR013584
  + 32 + 172 150 - IPR001763
  - 32 - 369 + IPR003613
  + 32 + 194 151 - IPR019809
Histone H4, conserved site - 32 - 33 + IPR000571
  + 32 + 348 152 - IPR000571
  - 32 - 996 + IPR015797
  + 32 + 64 153 - IPR015797
NUDIX hydrolase-like domain superfamily - 32 - 34 + IPR002073
  + 31 + 230 154 - IPR000008
  - 31 - 363 + IPR036465
  + 31 + 144 155 - IPR002073
  - 31 - 460 + IPR035965
  + 31 + 98 156 - IPR036465
  - 31 - 342 + IPR043519
Nucleotidyltransferase superfamily + 31 + 41 157 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 31 - 54 + IPR011042
  + 31 + 46 158 - IPR035965
PAS domain superfamily - 31 - 49 + IPR000014
  + 30 + 422 159 - IPR011042
  - 31 - 276 + IPR004853
  + 30 + 62 160 - IPR000225
  - 31 - 944 + IPR000330
  + 30 + 74 161 - IPR000014
  - 30 - 819 + IPR002119
  + 30 + 352 162 - IPR004853
Sugar phosphate transporter domain - 30 - 31 + IPR041569
AAA ATPase, AAA+ lid domain + 30 + 34 163 - IPR000330
SNF2-related, N-terminal domain - 30 - 37 + IPR023088
  + 29 + 288 164 - IPR002119
Histone H2A - 30 - 206 + IPR002130
  + 29 + 460 165 - IPR023088
3'5'-cyclic nucleotide phosphodiesterase - 29 - 144 + IPR019821
  + 29 + 32 166 - IPR002130
  - 29 - 920 + IPR029021
  + 29 + 124 167 - IPR019821
Kinesin motor domain, conserved site - 29 - 32 + IPR032454
  + 29 + 58 168 - IPR029021
  - 29 - 309 + IPR038718
  + 29 + 47 169 - IPR032454
Histone H2A, C-terminal domain - 29 - 29 + IPR015915
  + 29 + 204 170 - IPR038718
  - 29 - 282 + IPR005069
  + 29 + 62 171 - IPR029052
  - 29 - 204 + IPR006073
  + 29 + 174 172 - IPR015915
  - 29 - 716 + IPR016187
  + 29 + 336 173 - IPR005069
Nucleotide-diphospho-sugar transferase - 29 - 31 + IPR000558
  + 28 + 392 174 - IPR006073
GTP binding domain - 29 - 87 + IPR002401
  + 28 + 310 175 - IPR016187
C-type lectin fold - 29 - 177 + IPR029055
  + 28 + 116 176 - IPR000558
Histone H2B - 28 - 224 + IPR036890
  + 28 + 126 177 - IPR002401
Cytochrome P450, E-class, group I - 28 - 155 + IPR027640
  + 28 + 66 178 - IPR029055
  - 28 - 267 + IPR011043
  + 28 + 68 179 - IPR036890
  - 28 - 279 + IPR032458
  + 28 + 28 180 - IPR011043
Galactose oxidase/kelch, beta-propeller - 28 - 40 + IPR000608
  + 27 + 222 181 - IPR032458
Histone H2A conserved site - 28 - 28 + IPR039123
Protein phosphatase 2C + 27 + 52 182 - IPR013525
ABC-2 type transporter - 27 - 43 + IPR006311
  + 27 + 112 183 - IPR000608
  - 27 - 339 + IPR015947
  + 27 + 58 184 - IPR015655
Protein phosphatase 2C family - 27 - 46 + IPR044515
Ankyrin repeat and BTB/POZ domain-containing protein 1-like + 26 + 28 185 - IPR006311
  - 27 - 168 + IPR016177
  + 26 + 74 186 - IPR015947
PUA-like superfamily - 27 - 34 + IPR029045
  + 26 + 66 187 - IPR006620
Prolyl 4-hydroxylase, alpha subunit - 26 - 28 + IPR000086
  + 26 + 148 188 - IPR016177
DNA-binding domain superfamily - 26 - 37 + IPR029033
  + 26 + 112 189 - IPR029045
ClpP/crotonase-like domain superfamily - 26 - 47 + IPR013525
  + 25 + 82 190 - IPR029033
  - 26 - 342 + IPR000387
  + 25 + 104 191 - IPR013216
Methyltransferase type 11 - 25 - 29 + IPR008250
  + 25 + 62 192 - IPR008250
P-type ATPase, A domain superfamily - 25 - 35 + IPR001344
  + 25 + 56 193 - IPR001344
Chlorophyll A-B binding protein, plant - 25 - 28 + IPR000629
  + 25 + 26 194 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 25 - 152 - + IPR018303
  + 25 + 31 + 195 - IPR000511
Cytochrome c/c1 haem-lyase - 25 - 34 + IPR006189
  + 25 + 128 196 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 25 - 26 + IPR001202
  + 25 + 266 197 - IPR018303
P-type ATPase, phosphorylation site - 25 - 31 + IPR036282
  + 25 + 50 198 - IPR006189
  - 25 - 246 + IPR017850
  + 25 + 64 199 - IPR001202
  - 25 - 648 + IPR014721
  + 25 + 32 200 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 25 - 27 + IPR009060
  + 24 + 66 201 - IPR000086
  - 25 - 292 + IPR010920
  + 24 + 48 202 - IPR017850
Alkaline-phosphatase-like, core domain superfamily - 25 - 55 + IPR036893
  + 24 + 112 203 - IPR014721
  - 25 - 192 + IPR000795
  + 24 + 350 204 - IPR000387
  - 24 - 200 + IPR004333
  + 24 + 168 205 - IPR009060
UBA-like superfamily - 24 - 33 + IPR036866
  + 24 + 102 206 - IPR010920
LSM domain superfamily - 24 - 25 + IPR023299
  + 24 + 120 207 - IPR036893
  - 24 - 336 + IPR036514
  + 24 + 31 208 - IPR000795
  - 24 - 700 + IPR023298
  + 24 + 60 209 - IPR003594
Histidine kinase/HSP90-like ATPase - 24 - 71 + IPR036915
  + 24 + 80 210 - IPR004333
  - 24 - 336 + IPR002921
  + 23 + 56 211 - IPR036866
  - 24 - 282 + IPR013216
  + 23 + 54 212 - IPR023299
  - 24 - 408 + IPR036020
  + 23 + 58 213 - IPR036514
  - 24 - 186 + IPR036971
  + 23 + 46 214 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 24 - 39 + IPR001757
  + 23 + 172 215 - IPR023298
P-type ATPase, transmembrane domain superfamily - 24 - 95 + IPR011010
  + 23 + 54 216 - IPR036915
Cyclin-like superfamily - 24 - 43 + IPR009091
  + 23 + 194 217 - IPR002921
Fungal lipase-like domain - 23 - 28 + IPR044817
Squamosa promoter-binding-like protein + 23 + 35 218 - IPR036020
WW domain superfamily - 23 - 29 + IPR001179
  + 22 + 168 219 - IPR036971
  - 23 - 368 + IPR001471
  + 22 + 260 220 - IPR001757
P-type ATPase - 23 - 86 + IPR013762
  + 22 + 30 221 - IPR011010
DNA breaking-rejoining enzyme, catalytic core - 23 - 28 + IPR000408
  + 22 + 758 222 - IPR004827
  - 23 - 304 + IPR036955
  + 22 + 33 223 - IPR009091
  - 23 - 549 + IPR017849
  + 22 + 31 224 - IPR000679
  - 23 - 428 + IPR020103
  + 22 + 50 225 - IPR001179
  - 22 - 255 + IPR011527
  + 22 + 238 226 - IPR001471
  - 22 - 648 + IPR041679
DNA2/NAM7 helicase-like, AAA domain + 22 + 44 227 - IPR013762
  - 22 - 180 + IPR000668
  + 22 + 114 228 - IPR000408
  - 22 - 1128 + IPR008927
  + 22 + 50 229 - IPR036955
  - 22 - 264 + IPR017937
  + 22 + 26 230 - IPR017849
  - 22 - 248 + IPR000679
  + 22 + 192 231 - IPR020103
Pseudouridine synthase, catalytic domain superfamily - 22 - 54 + IPR011993
  + 22 + 27 232 - IPR011527
  - 22 - 476 + IPR011032
  + 21 + 78 233 - IPR000668
Peptidase C1A, papain C-terminal - 22 - 76 + IPR013784
  + 21 + 66 234 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 22 - 28 + IPR036640
  + 21 + 156 235 - IPR017937
Thioredoxin, conserved site - 22 - 26 + IPR013320
  + 21 + 64 236 - IPR011993
  - 22 - 162 + IPR007197
  + 21 + 124 237 - IPR011032
GroES-like superfamily - 21 - 43 + IPR018392
  + 21 + 248 238 - IPR013784
Carbohydrate-binding-like fold - 21 - 33 + IPR011012
  + 21 + 44 239 - IPR036640
  - 21 - 516 + IPR029062
  + 21 + 82 240 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 21 - 39 + IPR036852
  + 21 + 104 241 - IPR007197
Radical SAM - 21 - 42 + IPR036855
  + 21 + 70 242 - IPR018392
  - 21 - 498 + IPR016040
  + 20 + 48 243 - IPR011012
Longin-like domain superfamily - 21 - 22 + IPR000782
  + 20 + 236 244 - IPR029062
  - 21 - 192 + IPR036378
  + 20 + 164 245 - IPR036852
  - 21 - 432 + IPR035952
  + 20 + 74 246 - IPR002889
  - 21 - 315 + IPR023753
  + 20 + 52 247 - IPR036855
Zinc finger, CCCH-type superfamily - 21 - 35 + IPR012675
  + 20 + 26 248 - IPR000209
Peptidase S8/S53 domain - 21 - 24 + IPR013763
  + 20 + 50 249 - IPR000782
  - 20 - 459 + IPR015202
  + 20 + 88 250 - IPR036378
  - 20 - 372 + IPR016186
  + 20 + 135 251 - IPR013128
Peptidase C1A - 20 - 27 + IPR004045
  + 20 + 110 252 - IPR011016
  - 20 - 316 + IPR040521
Kyakuja-Dileera-Zisupton transposase + 20 + 23 253 - IPR023753
FAD/NAD(P)-binding domain - 20 - 26 + IPR036779
  + 20 + 90 254 - IPR012675
  - 20 - 156 + IPR004827
  + 20 + 110 255 - IPR013763
Cyclin-like - 20 - 43 + IPR036034
  + 20 + 46 256 - IPR015202
Galactose oxidase-like, Early set domain - 20 - 44 + IPR045054
Prolyl 4-hydroxylase + 20 + 22 257 - IPR003582
  - 20 - 321 + IPR000209
  + 20 + 46 258 - IPR016186
  - 20 - 810 + IPR037293
  + 19 + 22 259 - IPR004045
  - 20 - 212 + IPR001251
  + 19 + 160 260 - IPR036779
  - 20 - 168 + IPR011016
  + 19 + 114 261 - IPR036034
PDZ superfamily - 20 - 23 + IPR036865
  + 19 + 82 262 - IPR016040
NAD(P)-binding domain - 19 - 23 + IPR036361
  + 19 + 88 263 - IPR037293
  - 19 - 132 + IPR000917
  + 19 + 46 264 - IPR001251
  - 19 - 288 + IPR022742
  + 19 + 44 265 - IPR003347
  - 19 - 165 + IPR038538
  + 19 + 20 266 - IPR036865
  - 19 - 186 + IPR011006
  + 19 + 50 267 - IPR036361
  - 19 - 207 + IPR002044
  + 19 + 178 268 - IPR000917
Sulfatase, N-terminal - 19 - 23 + IPR010987
  + 19 + 74 269 - IPR022742
Serine aminopeptidase, S33 - 19 - 22 + IPR023210
  + 19 + 44 270 - IPR013087
  - 19 - 280 + IPR036812
  + 19 + 88 271 - IPR038538
  - 19 - 120 + IPR001789
  + 19 + 142 272 - IPR011006
CheY-like superfamily - 19 - 26 + IPR033205
  + 18 + 44 273 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 19 - 25 + IPR001304
  + 18 + 560 274 - IPR002044
  - 19 - 472 + IPR036922
  + 18 + 78 275 - IPR002035
  - 19 - 237 + IPR008978
  + 18 + 76 276 - IPR010987
  - 19 - 114 + IPR003034
  + 18 + 144 277 - IPR023210
NADP-dependent oxidoreductase domain - 19 - 43 + IPR013088
  + 18 + 21 278 - IPR036812
  - 19 - 204 + IPR036612
  + 18 + 126 279 - IPR001789
  - 19 - 480 + IPR003609
  + 18 + 242 280 - IPR001304
  - 18 - 1272 + IPR002938
  + 18 + 60 281 - IPR036922
  - 18 - 244 + IPR029016
  + 18 + 23 282 - IPR008978
  - 18 - 180 + IPR013087
  + 18 + 96 283 - IPR003034
  - 18 - 282 + IPR004839
  + 18 + 42 284 - IPR013088
  - 18 - 168 + IPR001394
  + 18 + 48 285 - IPR036612
  - 18 - 380 + IPR002067
  + 18 + 182 286 - IPR003609
  - 18 - 468 + IPR011051
  + 18 + 38 287 - IPR002938
FAD-binding domain - 18 - 29 + IPR004147
  + 18 + 42 288 - IPR029016
  - 18 - 138 + IPR028889
  + 18 + 80 289 - IPR004839
Aminotransferase, class I/classII - 18 - 21 + IPR016130
  + 18 + 20 290 - IPR002067
Mitochondrial carrier protein - 18 - 91 + IPR018957
  + 17 + 42 291 - IPR011051
RmlC-like cupin domain superfamily - 18 - 20 + IPR003347
  + 17 + 78 292 - IPR004147
UbiB domain - 18 - 21 + IPR017941
  + 17 + 108 293 - IPR028889
  - 18 - 120 + IPR008972
  + 17 + 148 294 - IPR016130
Protein-tyrosine phosphatase, active site - 18 - 20 + IPR036420
  + 17 + 98 295 - IPR009880
Glyoxal oxidase, N-terminal - 18 - 21 + IPR000340
  + 17 + 34 296 - IPR015940
  - 17 - 228 + IPR041698
Methyltransferase domain 25 + 17 + 18 297 - IPR017941
  - 17 - 216 + IPR009030
  + 17 + 76 298 - IPR008972
  - 17 - 351 + IPR029056
  + 17 + 72 299 - IPR036420
  - 17 - 234 + IPR035706
  + 17 + 36 300 - IPR000340
Dual specificity phosphatase, catalytic domain - 17 + IPR020904
  + 17 17 301 - IPR009030
Growth factor receptor cysteine-rich domain superfamily - 17 - 54 + IPR013078
  + 17 + 74 302 - IPR029056
  - 17 - 180 + IPR023828
  + 17 + 19 303 - IPR035706
Dynein heavy chain, ATP-binding dynein motor region D5 - 17 - 18 + IPR016035
  + 17 + 40 304 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 17 - 17 + IPR013815
  + 17 + 20 305 - IPR013078
Histidine phosphatase superfamily, clade-1 - 17 - 53 + IPR024743
  + 17 + 34 306 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 17 - 19 + IPR039633
Plastid-lipid-associated protein + 17 + 22 307 - IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase - 17 - 24 + IPR041677
DNA2/NAM7 helicase, AAA domain + 17 + 26 308 - IPR013815
  - 17 - 160 + IPR006671
  + 17 + 42 309 - IPR024743
Dynein heavy chain, coiled coil stalk - 17 - 17 + IPR000644
  + 17 + 158 310 - IPR026983
Dynein heavy chain - 17 - 31 + IPR002889
  + 17 + 162 311 - IPR006671
Cyclin, N-terminal - 17 - 21 + IPR015500
  + 17 + 106 312 - IPR000644
  - 17 - 342 + IPR036875
  + 17 + 48 313 - IPR015500
Peptidase S8, subtilisin-related - 17 - 53 + IPR001806
  + 17 + 66 314 - IPR036875
Zinc finger, CCHC-type superfamily - 17 - 24 + IPR000225
  + 17 + 172 315 - IPR001806
Small GTPase superfamily - 17 - 19 + IPR022764
  + 16 + 34 316 - IPR022764
Peptidase S54, rhomboid domain - 16 - 17 + IPR006689
  + 16 + 160 317 - IPR006689
Small GTPase superfamily, ARF/SAR type - 16 - 80 + IPR043926
ABC transporter family G domain + 16 + 27 318 - IPR021133
  - 16 - 186 + IPR015940
  + 16 + 112 319 - IPR013328
  - 16 - 152 + IPR021133
  + 16 + 124 320 - IPR006195
  - 16 - 96 + IPR013328
  + 16 + 19 321 - IPR000104
Antifreeze protein, type I - 16 - 54 + IPR006195
  + 16 + 64 322 - IPR018200
Ubiquitin specific protease, conserved site - 16 - 31 - + IPR000104
  + 16 + 108 + 323 - IPR008984
SMAD/FHA domain superfamily - 16 - 18 + IPR018200
  + 16 + 31 324 - IPR013602
Dynein heavy chain, domain-2 - 16 - 16 + IPR008984
  + 16 + 34 325 - IPR000717
  - 16 - 189 + IPR013602
  + 16 + 32 326 - IPR001163
LSM domain, eukaryotic/archaea-type - 16 - 31 + IPR000717
  + 16 + 98 327 IPR000253
  16 - 304 + 126 328 IPR027359
  16 - 312 + 52 329 - IPR007657
Glycosyltransferase 61 - 16 - 37 + IPR001353
  + 16 + 36 330 - IPR001353
Proteasome, subunit alpha/beta - 16 - 18 + IPR000511
  + 16 + 50 331 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 16 - 24 + IPR003594
  + 16 + 38 332 - IPR013761
Sterile alpha motif/pointed domain superfamily - 16 - 18 + IPR003582
  + 16 + 128 333 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 16 - 42 + IPR013761
  + 16 + 36 334 - IPR002528
Multi antimicrobial extrusion protein - 16 - 41 + IPR015813
  + 16 + 52 335 - IPR006843
Plastid lipid-associated protein/fibrillin conserved domain - 16 - 24 + IPR041228
Dynein heavy chain, C-terminal domain + 16 + 17 336 - IPR029028
Alpha/beta knot methyltransferases - 16 - 27 + IPR002528
  + 16 + 82 337 - IPR010998
  - 16 - 120 + IPR006843
  + 16 + 48 338 - IPR006059
Bacterial extracellular solute-binding protein - 16 - 16 + IPR029028
  + 16 + 46 339 - IPR035699
Dynein heavy chain, hydrolytic ATP-binding dynein motor region D1 - 16 - 16 + IPR010998
  + 16 + 20 340 - IPR004273
Dynein heavy chain domain - 16 - 20 + IPR019410
  + 16 + 66 341 - IPR002937
Amine oxidase - 16 - 18 + IPR006059
  + 16 + 32 342 - IPR024317
Dynein heavy chain, AAA module D4 - 16 - 16 + IPR035699
  + 16 + 34 343 - IPR017927
  - 15 - 120 + IPR045055
DNA2/NAM7-like helicase + 16 + 29 344 - IPR017938
Riboflavin synthase-like beta-barrel - 15 - 18 + IPR004273
  + 16 + 32 345 - IPR003035
  - 15 - 144 + IPR041658
Dynein heavy chain AAA lid domain + 16 + 17 346 - IPR016123
  - 15 - 132 + IPR002937
  + 16 + 36 347 - IPR001357
  - 15 - 258 + IPR024317
  + 16 + 32 348 - IPR008991
Translation protein SH3-like domain superfamily - 15 - 17 + IPR017927
  + 15 + 60 349 - IPR001296
Glycosyl transferase, family 1 - 15 - 17 + IPR024862
  + 15 + 46 350 - IPR023801
Histone deacetylase domain - 15 - 18 + IPR017938
  + 15 + 32 351 - IPR001478
  - 15 - 228 + IPR003035
  + 15 + 96 352 - IPR002423
Chaperonin Cpn60/TCP-1 family - 15 - 19 + IPR041466
Dynein heavy chain, AAA 5 extension domain + 15 + 15 353 - IPR036010
2Fe-2S ferredoxin-like superfamily - 15 - 17 + IPR016123
  + 15 + 58 354 - IPR032466
Metal-dependent hydrolase - 15 - 24 + IPR001357
  + 15 + 118 355 - IPR022812
Dynamin superfamily - 15 - 74 + IPR008991
  + 15 + 34 356 - IPR011761
  - 15 - 144 + IPR001163
  + 15 + 30 357 - IPR013154
Alcohol dehydrogenase, N-terminal - 15 - 20 + IPR007657
  + 15 + 54 358 - IPR035969
Rab-GTPase-TBC domain superfamily - 15 - 35 + IPR001296
  + 15 + 34 359 - IPR011705
BTB/Kelch-associated - 15 - 21 + IPR023801
  + 15 + 36 360 - IPR023696
Ureohydrolase domain superfamily - 15 - 27 + IPR002423
  + 15 + 36 361 - IPR000286
Histone deacetylase family - 15 - 65 + IPR036010
  + 15 + 34 362 - IPR027409
  - 15 - 138 + IPR032466
  + 15 + 32 363 - IPR024607
Sulfatase, conserved site - 15 - 27 + IPR022812
  + 15 + 170 364 - IPR005746
Thioredoxin - 15 - 21 + IPR011761
  + 15 + 72 365 - IPR019410
Lysine methyltransferase - 15 - 17 + IPR013154
  + 15 + 40 366 - IPR004087
K Homology domain - 15 - 30 + IPR035969
  + 15 + 60 367 - IPR002912
  - 15 - 144 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 15 + 17 368 - IPR001878
  - 15 - 324 + IPR011705
  + 15 + 30 369 - IPR001041
  - 15 - 220 + IPR023696
  + 15 + 40 370 - IPR003029
  - 15 - 320 + IPR033031
  + 15 + 46 371 - IPR024156
  - 15 - 144 + IPR027409
  + 15 + 60 372 - IPR003611
Nuclease associated modular domain 3 - 14 - 69 + IPR015655
  + 15 + 42 373 - IPR008942
  - 14 - 123 + IPR024607
  + 15 + 27 374 - IPR000727
  - 14 - 144 + IPR002035
  + 15 + 114 375 - IPR000467
  - 14 - 212 + IPR041589
Dynein heavy chain 3, AAA+ lid domain + 15 + 15 376 - IPR017946
  - 14 - 236 + IPR002912
  + 15 + 88 377 - IPR000953
  - 14 - 162 + IPR001041
  + 15 + 110 378 - IPR035952
  - 14 - 90 + IPR003029
  + 15 + 160 379 - IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site - 14 - 15 + IPR024156
  + 15 + 18 380 - IPR011629
Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal - 14 - 28 + IPR003611
  + 14 + 58 381 - IPR000873
AMP-dependent synthetase/ligase - 14 - 22 + IPR008942
  + 14 + 52 382 - IPR023393
  - 14 - 96 + IPR000467
  + 14 + 80 383 - IPR029061
Thiamin diphosphate-binding fold - 14 - 28 + IPR017946
  + 14 + 68 384 - IPR001509
NAD-dependent epimerase/dehydratase - 14 - 15 + IPR013149
  + 14 + 52 385 - IPR035940
  - 14 - 153 + IPR001412
  + 14 + 15 386 - IPR002562
3'-5' exonuclease domain - 14 - 23 + IPR011629
  + 14 + 28 387 - IPR001199
  - 14 - 264 + IPR000873
  + 14 + 44 388 - IPR006652
Kelch repeat type 1 - 14 - 55 + IPR023393
  + 14 + 16 389 - IPR020422
  - 14 - 188 + IPR029061
  + 14 + 48 390 - IPR011053
Single hybrid motif - 14 - 17 + IPR001478
  + 14 + 78 391 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 14 - 16 + IPR035940
  + 14 + 68 392 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 14 - 29 + IPR001199
  + 14 + 142 393 - IPR036910
  - 14 - 168 + IPR020422
  + 14 + 52 394 - IPR029057
Phosphoribosyltransferase-like - 14 - 16 + IPR011053
  + 14 + 34 395 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 14 - 64 + IPR036273
  + 14 + 30 396 - IPR004344
  - 14 - 168 + IPR004014
  + 14 + 30 397 - IPR020892
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site - 14 - 16 + IPR036910
  + 14 + 76 398 - IPR014044
CAP domain - 14 - 34 + IPR029057
  + 14 + 30 399 - IPR004088
K Homology domain, type 1 - 14 - 27 + IPR004344
  + 14 + 84 400 - IPR036400
  - 14 - 171 + IPR020892
  + 14 + 16 401 - IPR029026
  - 14 - 114 + IPR014044
  + 14 + 34 402 - IPR037138
  - 14 - 120 + IPR041492
Haloacid dehalogenase-like hydrolase + 14 + 15 403 - IPR029069
HotDog domain superfamily - 14 - 23 + IPR004088
  + 14 + 54 404 - IPR000195
  - 14 - 165 + IPR036400
  + 14 + 76 405 - IPR036427
  - 14 - 196 + IPR029026
  + 14 + 19 406 - IPR003903
  - 14 - 204 + IPR037138
  + 14 + 20 407 - IPR020843
Polyketide synthase, enoylreductase domain - 14 - 24 + IPR029069
  + 14 + 42 408 - IPR003409
MORN motif - 14 - 148 + IPR000195
  + 14 + 84 409 - IPR011709
Domain of unknown function DUF1605 - 14 - 15 + IPR036427
  + 14 + 66 410 - IPR027410
  - 14 - 219 + IPR003903
  + 14 + 106 411 - IPR036236
Zinc finger C2H2 superfamily - 14 - 18 + IPR003409
  + 14 + 152 412 - IPR008974
  - 14 - 160 + IPR011709
  + 14 + 30 413 - IPR013149
Alcohol dehydrogenase, C-terminal - 13 - 25 + IPR027410
  + 14 + 78 414 - IPR018957
Zinc finger, C3HC4 RING-type - 13 - 17 + IPR001878
  + 14 + 120 415 - IPR016039
  - 13 - 472 + IPR036236
  + 14 + 34 416 - IPR000089
  - 13 - 135 + IPR045122
Calcium permeable stress-gated cation channel 1-like + 13 + 15 417 - IPR004161
Translation elongation factor EFTu-like, domain 2 - 13 - 14 + IPR016039
  + 13 + 134 418 - IPR001279
Metallo-beta-lactamase - 13 - 22 + IPR000089
  + 13 + 90 419 - IPR027413
  - 13 - 264 + IPR004161
  + 13 + 28 420 - IPR038770
  - 13 - 102 + IPR001509
  + 13 + 28 421 - IPR007112
  - 13 - 102 + IPR001279
  + 13 + 34 422 - IPR003107
HAT (Half-A-TPR) repeat - 13 - 113 + IPR027413
  + 13 + 90 423 - IPR006076
FAD dependent oxidoreductase - 13 - 13 + IPR002562
  + 13 + 30 424 - IPR003689
Zinc/iron permease - 13 - 15 + IPR038770
  + 13 + 17 425 - IPR014722
  - 13 - 114 + IPR007112
  + 13 + 52 426 - IPR036908
  - 13 - 129 + IPR002372
  + 13 + 64 427 - IPR022398
Peptidase S8, subtilisin, His-active site - 13 - 14 + IPR003690
  + 13 + 38 428 - IPR016161
Aldehyde/histidinol dehydrogenase - 13 - 14 + IPR000286
  + 13 + 88 429 - IPR013780
  - 13 - 90 + IPR006076
  + 13 + 26 430 - IPR003882
Pistil-specific extensin-like protein - 13 - 42 + IPR001283
  + 13 + 126 431 - IPR013126
Heat shock protein 70 family - 13 - 100 + IPR003689
  + 13 + 30 432 - IPR006439
HAD hydrolase, subfamily IA - 13 - 27 + IPR014722
  + 13 + 19 433 - IPR001660
  - 13 - 180 + IPR036908
  + 13 + 56 434 - IPR007248
Mpv17/PMP22 - 13 - 26 + IPR022398
  + 13 + 14 435 - IPR001487
  - 13 - 340 + IPR016161
  + 13 + 26 436 - IPR002683
PsbP family - 13 - 13 + IPR013780
  + 13 + 15 437 - IPR006342
Methyltransferase FkbM - 13 - 29 + IPR003882
  + 13 + 84 438 - IPR006638
Elp3/MiaB/NifB - 12 - 12 + IPR013126
  + 13 + 62 439 - IPR007502
Helicase-associated domain - 12 - 30 + IPR006439
  + 13 + 54 440 - IPR019956
Ubiquitin - 12 - 33 + IPR001660
  + 13 + 76 441 - IPR036525
  - 12 - 114 + IPR001487
  + 13 + 144 442 - IPR009078
Ferritin-like superfamily - 12 - 15 + IPR002683
  + 13 + 26 443 - IPR009071
  - 12 - 168 + IPR006342
  + 13 + 58 444 - IPR005467
  - 12 - 90 + IPR000727
  + 12 + 66 445 - IPR002885
  - 12 - 684 + IPR019956
  + 12 + 66 446 - IPR001594
Palmitoyltransferase, DHHC domain - 12 - 12 + IPR036525
  + 12 + 48 447 - IPR024950
Dual specificity phosphatase - 12 - 16 + IPR009078
  + 12 + 30 448 - IPR003495
CobW/HypB/UreG, nucleotide-binding domain - 12 - 16 + IPR005467
  + 12 + 60 449 - IPR005828
Major facilitator, sugar transporter-like - 12 - 13 + IPR002885
  + 12 + 384 450 - IPR020084
NUDIX hydrolase, conserved site - 12 - 12 + IPR001594
  + 12 + 24 451 - IPR011611
Carbohydrate kinase PfkB - 12 - 19 + IPR003495
  + 12 + 32 452 - IPR011044
Quinoprotein amine dehydrogenase, beta chain-like - 12 - 20 + IPR005828
  + 12 + 28 453 - IPR009050
Globin-like superfamily - 12 - 20 + IPR020084
  + 12 + 12 454 - IPR031112
AP2-like ethylene-responsive transcription factor - 12 - 41 + IPR011611
  + 12 + 32 455 - IPR003323
  - 12 - 105 + IPR011044
  + 12 + 26 456 - IPR016166
  - 12 - 104 + IPR009050
  + 12 + 40 457 - IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme - 12 - 17 + IPR003323
  + 12 + 70 458 - IPR016021
  - 12 - 120 + IPR016166
  + 12 + 52 459 - IPR037252
  - 12 - 90 + IPR036052
  + 12 + 26 460 - IPR001375
Peptidase S9, prolyl oligopeptidase, catalytic domain - 12 - 13 + IPR016021
  + 12 + 20 461 - IPR011060
Ribulose-phosphate binding barrel - 12 - 12 + IPR037252
  + 12 + 44 462 - IPR027443
  - 12 - 78 + IPR001375
  + 12 + 26 463 - IPR002372
Pyrrolo-quinoline quinone repeat - 12 - 30 + IPR011060
  + 12 + 24 464 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 12 - 40 + IPR027443
  + 12 + 13 465 - IPR011704
ATPase, dynein-related, AAA domain - 12 - 26 + IPR001537
  + 12 + 36 466 - IPR001537
tRNA/rRNA methyltransferase, SpoU type - 12 - 18 + IPR023313
  + 12 + 12 467 - IPR006461
PLAC8 motif-containing protein - 12 - 57 + IPR001494
  + 12 + 66 468 - IPR023313
Ubiquitin-conjugating enzyme, active site - 12 - 12 + IPR012292
  + 12 + 19 469 - IPR001494
  - 12 - 176 + IPR009836
  + 12 + 58 470 - IPR011641
Tyrosine-protein kinase ephrin type A/B receptor-like - 12 - 100 + IPR031157
  + 12 + 13 471 - IPR012292
  - 12 - 152 + IPR001926
  + 12 + 26 472 - IPR031157
Tr-type G domain, conserved site - 12 - 13 + IPR016197
  + 12 + 36 473 - IPR001926
Pyridoxal-phosphate dependent enzyme - 12 - 13 + IPR025476
  + 12 + 30 474 - IPR016197
Chromo-like domain superfamily - 12 - 22 + IPR044607
Transcription factor RKD-like + 12 + 37 475 - IPR025476
Helitron helicase-like domain - 12 - 14 + IPR008974
  + 12 + 13 476 - IPR013122
Polycystin cation channel, PKD1/PKD2 + IPR013122
  12 - 17 + 34 477 IPR016163
  12 - 96 + 12 478 - IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site + IPR002464
  12 15 @@ -3364,154 +3364,154 @@ 479 IPR004274
  12 - 153 + 78 480 - IPR001204
Phosphate transporter + IPR001204
  12 - 28 + 72 481 - IPR001940
Peptidase S1C + IPR001940
  11 - 57 + 114 482 IPR006594
  11 - 132 + 56 483 - IPR008254
  - 11 - 144 + IPR007502
  + 11 + 28 484 - IPR006593
  - 11 - 111 + IPR008254
  + 11 + 72 485 - IPR036318
FAD-binding, type 2-like superfamily - 11 - 14 + IPR006593
  + 11 + 54 486 - IPR003018
GAF domain - 11 - 17 + IPR036318
  + 11 + 26 487 - IPR015353
Rubisco LSMT, substrate-binding domain - 11 - 11 + IPR037518
  + 11 + 44 488 - IPR037518
  - 11 - 66 + IPR003864
  + 11 + 24 489 - IPR003864
Calcium-dependent channel, 7TM region, putative phosphate - 11 - 12 + IPR009071
  + 11 + 84 490 - IPR006068
Cation-transporting P-type ATPase, C-terminal + IPR006068
  11 - 13 + 26 491 IPR023198
  11 - 66 + 11 492 - IPR009009
RlpA-like protein, double-psi beta-barrel domain + IPR009009
  11 - 11 + 22 493 - IPR000222
PPM-type phosphatase, divalent cation binding - 11 - 12 + IPR039091
Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor + 11 + 19 494 - IPR037219
Peptidase M41-like - 11 - 13 + IPR000222
  + 11 + 12 495 - IPR002083
  - 11 - 164 + IPR037219
  + 11 + 22 496 - IPR003008
Tubulin/FtsZ, GTPase domain - 11 - 30 + IPR002083
  + 11 + 72 497 - IPR000569
  - 11 - 240 + IPR006652
  + 11 + 42 498 - IPR035983
HECT, E3 ligase catalytic domain - 11 - 19 + IPR000569
  + 11 + 94 499 - IPR017956
AT hook, DNA-binding motif - 11 - 80 + IPR035983
  + 11 + 28 500 - IPR029039
  - 11 - 120 + IPR006461
  + 11 + 92 diff --git a/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster.html b/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster.html new file mode 100644 index 00000000..8c158526 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster.html @@ -0,0 +1,82 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:BDGP6, Jul 2014
Database version:87.6
Base Pairs:142,573,017
Golden Path Length:143,725,995
Genebuild by: FlyBase
Genebuild method: Import
Genebuild started: May 2014
Genebuild released: Sep 2014
Genebuild last updated/patched: Sep 2014
Genebuild version: dmel_r6.02_FB2014_05
+

Gene counts

+ + + + + + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		13,918
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		257
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:34,749
+ + +

Coordinate Systems

+ + + + + + + + + + + + + + + + +
chromosome
+
8 sequences
+
+ +
+ + + +
SequenceLength (bp)
2L23513712
2R25286936
3L28110227
3R32079331
41348131
X23542271
Y3667352
dmel_mitochondrion_genome19517
+
+
scaffold1862 sequences
contig2442 sequences
chunk5137 sequences
+ +

Other

+ + + + + +
Genscan gene predictions:18,548
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster_IPtop500.html b/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster_IPtop500.html new file mode 100644 index 00000000..869c6d92 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Drosophila_melanogaster_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		5133140
2IPR011009
Protein kinase-like domain		294914
3IPR007087
Zinc finger, C2H2		2935905
4IPR015880
Zinc finger, C2H2-like		2713531
5IPR009003
Trypsin-like cysteine/serine peptidase domain		259353
6IPR001254
Peptidase S1		253987
7IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		2332069
8IPR001314
Peptidase S1A, chymotrypsin-type		223846
9IPR000719
Protein kinase domain		2221679
10IPR013083
Zinc finger, RING/FYVE/PHD-type		215555
11IPR015943
WD40/YVTN repeat-like-containing domain		212668
12IPR016024
Armadillo-type fold		1961086
13IPR017986
WD40-repeat-containing domain		194870
14IPR018114
Peptidase S1, trypsin family, active site		183241
15IPR013783
Immunoglobulin-like fold		1805127
16IPR001680
WD40 repeat		1733207
17IPR032675
Leucine-rich repeat domain, L domain-like		1711069
18IPR020846
Major facilitator superfamily domain		171715
19IPR017441
Protein kinase, ATP binding site		164497
20IPR016040
NAD(P)-binding domain		163763
21IPR012677
Nucleotide-binding alpha-beta plait domain		1631569
22IPR029058
Alpha/Beta hydrolase fold		157721
23IPR011993
Pleckstrin homology-like domain		1521216
24IPR009057
Homeodomain-like		150702
25IPR011990
Tetratricopeptide-like helical domain		150767
26IPR008271
Serine/threonine-protein kinase, active site		147442
27IPR033116
Serine proteases, trypsin family, serine active site		146193
28IPR007110
Immunoglobulin-like domain		1356451
29IPR000504
RNA recognition motif domain		1352107
30IPR003593
AAA+ ATPase domain		123385
31IPR001841
Zinc finger, RING-type		122501
32IPR011989
Armadillo-like helical		120558
33IPR011992
EF-hand domain pair		117906
34IPR012336
Thioredoxin-like fold		116577
35IPR011991
Winged helix-turn-helix DNA-binding domain		114435
36IPR001611
Leucine-rich repeat		1142785
37IPR003599
Immunoglobulin subtype		1113223
38IPR003598
Immunoglobulin subtype 2		1092902
39IPR000618
Insect cuticle protein		107512
40IPR002557
Chitin binding domain		1062235
41IPR001356
Homeobox domain		102681
42IPR019775
WD40 repeat, conserved site		99305
43IPR010512
Protein of unknown function DUF1091		99191
44IPR002048
EF-hand domain		951450
45IPR017970
Homeobox, conserved site		92197
46IPR029071
Ubiquitin-related domain		92282
47IPR012934
Zinc finger, AD-type		92267
48IPR001128
Cytochrome P450		88849
49IPR020683
Ankyrin repeat-containing domain		851688
50IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		85276
51IPR011333
BTB/POZ fold		85319
52IPR018247
EF-Hand 1, calcium-binding site		84388
53IPR005225
Small GTP-binding protein domain		84145
54IPR002110
Ankyrin repeat		833508
55IPR011701
Major facilitator superfamily		82162
56IPR031311
Chitin-binding type R&R consensus		82104
57IPR017972
Cytochrome P450, conserved site		80110
58IPR003591
Leucine-rich repeat, typical subtype		781754
59IPR002401
Cytochrome P450, E-class, group I		77617
60IPR013026
Tetratricopeptide repeat-containing domain		77170
61IPR000276
G protein-coupled receptor, rhodopsin-like		761487
62IPR017452
GPCR, rhodopsin-like, 7TM		76173
63IPR001650
Helicase, C-terminal		75401
64IPR019734
Tetratricopeptide repeat		741028
65IPR000210
BTB/POZ-like		74739
66IPR000742
Epidermal growth factor-like domain		749859
67IPR014001
Helicase superfamily 1/2, ATP-binding domain		74270
68IPR001849
Pleckstrin homology domain		71704
69IPR001478
PDZ domain		692323
70IPR011011
Zinc finger, FYVE/PHD-type		68235
71IPR014756
Immunoglobulin E-set		68446
72IPR001452
SH3 domain		681813
73IPR013098
Immunoglobulin I-set		661852
74IPR001806
Small GTPase superfamily		66142
75IPR003961
Fibronectin type III		644776
76IPR013032
EGF-like, conserved site		613516
77IPR013320
Concanavalin A-like lectin/glucanase domain		60766
78IPR004117
Olfactory receptor, Drosophila		60133
79IPR005828
General substrate transporter		59105
80IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		58536
81IPR002347
Glucose/ribitol dehydrogenase		57825
82IPR023753
Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain		57423
83IPR020472
G-protein beta WD-40 repeat		57276
84IPR023214
HAD-like domain		56475
85IPR003439
ABC transporter-like		56345
86IPR012340
Nucleic acid-binding, OB-fold		55123
87IPR017853
Glycoside hydrolase superfamily		54156
88IPR024079
Metallopeptidase, catalytic domain		53134
89IPR013604
7TM chemoreceptor		5267
90IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		52514
91IPR004119
Protein of unknown function DUF227		5166
92IPR000008
C2 domain		511523
93IPR011545
DEAD/DEAH box helicase domain		5192
94IPR015897
CHK kinase-like		5166
95IPR010987
Glutathione S-transferase, C-terminal-like		50226
96IPR017907
Zinc finger, RING-type, conserved site		5085
97IPR029044
Nucleotide-diphospho-sugar transferases		49182
98IPR018108
Mitochondrial substrate/solute carrier		49527
99IPR023395
Mitochondrial carrier domain		49212
100IPR016181
Acyl-CoA N-acyltransferase		48191
101IPR013781
Glycoside hydrolase, catalytic domain		48167
102IPR006578
MADF domain		48294
103IPR017871
ABC transporter, conserved site		47135
104IPR006170
Pheromone/general odorant binding protein		47237
105IPR016187
C-type lectin fold		46102
106IPR002223
Proteinase inhibitor I2, Kunitz metazoa		45521
107IPR013761
Sterile alpha motif/pointed domain		44293
108IPR017850
Alkaline-phosphatase-like, core domain		4473
109IPR017849
Alkaline phosphatase-like, alpha/beta/alpha		4365
110IPR016186
C-type lectin-like		4386
111IPR003959
ATPase, AAA-type, core		43107
112IPR016135
Ubiquitin-conjugating enzyme/RWD-like		42180
113IPR001304
C-type lectin		41189
114IPR029055
Nucleophile aminohydrolases, N-terminal		41143
115IPR001623
DnaJ domain		41579
116IPR014729
Rossmann-like alpha/beta/alpha sandwich fold		4091
117IPR001965
Zinc finger, PHD-type		40173
118IPR004045
Glutathione S-transferase, N-terminal		39122
119IPR011042
Six-bladed beta-propeller, TolB-like		39150
120IPR029021
Protein-tyrosine phosphatase-like		38299
121IPR019786
Zinc finger, PHD-type, conserved site		38106
122IPR020479
Homeodomain, metazoa		38204
123IPR013106
Immunoglobulin V-set domain		37187
124IPR005829
Sugar transporter, conserved site		37102
125IPR002172
Low-density lipoprotein (LDL) receptor class A repeat		373690
126IPR002350
Kazal domain		36196
127IPR001881
EGF-like calcium-binding domain		361820
128IPR008952
Tetraspanin, EC2 domain		3662
129IPR013766
Thioredoxin domain		36153
130IPR019787
Zinc finger, PHD-finger		36217
131IPR004046
Glutathione S-transferase, C-terminal		3654
132IPR029052
Metallo-dependent phosphatase-like		36152
133IPR009072
Histone-fold		36105
134IPR000048
IQ motif, EF-hand binding site		36460
135IPR009060
UBA-like		3586
136IPR018499
Tetraspanin/Peripherin		3563
137IPR008266
Tyrosine-protein kinase, active site		3597
138IPR002018
Carboxylesterase, type B		3569
139IPR012337
Ribonuclease H-like domain		35127
140IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		35128
141IPR001781
Zinc finger, LIM-type		351860
142IPR001251
CRAL-TRIO domain		34349
143IPR009030
Insulin-like growth factor binding protein, N-terminal		34329
144IPR005821
Ion transport domain		34528
145IPR015424
Pyridoxal phosphate-dependent transferase		3473
146IPR013818
Lipase, N-terminal		3353
147IPR004843
Calcineurin-like phosphoesterase domain, apaH type		3368
148IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1		3362
149IPR000734
Triacylglycerol lipase family		33205
150IPR001660
Sterile alpha motif domain		33344
151IPR000980
SH2 domain		33832
152IPR000608
Ubiquitin-conjugating enzyme E2		32141
153IPR009071
High mobility group box domain		32334
154IPR014014
RNA helicase, DEAD-box type, Q motif		3260
155IPR001810
F-box domain		32191
156IPR008979
Galactose-binding domain-like		32156
157IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		3294
158IPR014044
CAP domain		32178
159IPR000626
Ubiquitin-like		31242
160IPR001873
Na+ channel, amiloride-sensitive		31274
161IPR001320
Ionotropic glutamate receptor		3187
162IPR001715
Calponin homology domain		31972
163IPR000571
Zinc finger, CCCH-type		31348
164IPR010562
Haemolymph juvenile hormone binding		3085
165IPR000387
Protein-tyrosine/Dual specificity phosphatase		30106
166IPR005123
Oxoglutarate/iron-dependent dioxygenase		3075
167IPR000215
Serpin family		3061
168IPR000859
CUB domain		30679
169IPR000152
EGF-type aspartate/asparagine hydroxylation site		30597
170IPR004088
K Homology domain, type 1		30950
171IPR018097
EGF-like calcium-binding, conserved site		30537
172IPR023796
Serpin domain		30154
173IPR006631
Protein of unknown function DM4/12		3068
174IPR008936
Rho GTPase activation protein		29104
175IPR016130
Protein-tyrosine phosphatase, active site		2999
176IPR017981
GPCR, family 2-like		2865
177IPR000873
AMP-dependent synthetase/ligase		2859
178IPR003960
ATPase, AAA-type, conserved site		2863
179IPR011074
CRAL/TRIO, N-terminal domain		2886
180IPR000718
Peptidase M13		2863
181IPR002219
Protein kinase C-like, phorbol ester/diacylglycerol-binding domain		28597
182IPR023415
Low-density lipoprotein (LDL) receptor class A, conserved site		28594
183IPR013785
Aldolase-type TIM barrel		2767
184IPR000182
GNAT domain		2780
185IPR014352
FERM/acyl-CoA-binding protein, 3-helical bundle		2780
186IPR008984
SMAD/FHA domain		2762
187IPR000301
Tetraspanin		27220
188IPR014710
RmlC-like jelly roll fold		27118
189IPR004087
K Homology domain		27237
190IPR028082
Periplasmic binding protein-like I		2780
191IPR020635
Tyrosine-protein kinase, catalytic domain		2773
192IPR001752
Kinesin motor domain		27427
193IPR001214
SET domain		27123
194IPR006620
Prolyl 4-hydroxylase, alpha subunit		2634
195IPR008753
Peptidase M13, N-terminal domain		2640
196IPR013088
Zinc finger, NHR/GATA-type		2687
197IPR000961
AGC-kinase, C-terminal		26163
198IPR013547
Prolyl 4-hydroxylase alpha-subunit, N-terminal		2636
199IPR027640
Kinesin-like protein		26171
200IPR029787
Nucleotide cyclase		2695
201IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2		2653
202IPR001828
Extracellular ligand-binding receptor		2665
203IPR001054
Adenylyl cyclase class-3/4/guanylyl cyclase		26353
204IPR004145
Domain of unknown function DUF243		2658
205IPR009000
Translation protein, beta-barrel domain		2547
206IPR001353
Proteasome, subunit alpha/beta		2531
207IPR011705
BTB/Kelch-associated		25104
208IPR020568
Ribosomal protein S5 domain 2-type fold		2549
209IPR015940
Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote		24165
210IPR014782
Peptidase M1, membrane alanine aminopeptidase, N-terminal		24237
211IPR000253
Forkhead-associated (FHA) domain		24161
212IPR011527
ABC transporter type 1, transmembrane domain		24296
213IPR000195
Rab-GTPase-TBC domain		24284
214IPR000219
Dbl homology (DH) domain		24527
215IPR025110
AMP-binding enzyme C-terminal domain		2342
216IPR008978
HSP20-like chaperone		2359
217IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2397
218IPR019749
Band 4.1 domain		23184
219IPR020904
Short-chain dehydrogenase/reductase, conserved site		2337
220IPR000834
Peptidase M14, carboxypeptidase A		23348
221IPR001930
Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase		2358
222IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site		2343
223IPR006201
Neurotransmitter-gated ion-channel		23484
224IPR007588
Zinc finger, FLYWCH-type		2358
225IPR012464
Protein of unknown function DUF1676		2364
226IPR001202
WW domain		23546
227IPR028889
Ubiquitin specific protease domain		2362
228IPR016197
Chromo domain-like		2364
229IPR018497
Peptidase M13, C-terminal domain		23123
230IPR006202
Neurotransmitter-gated ion-channel ligand-binding domain		23244
231IPR004210
BESS motif		2369
232IPR022700
Proteinase, regulatory CLIP domain		2358
233IPR019748
FERM central domain		22141
234IPR000175
Sodium:neurotransmitter symporter		22459
235IPR006029
Neurotransmitter-gated ion-channel transmembrane domain		22193
236IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		2260
237IPR000198
Rho GTPase-activating protein domain		22298
238IPR001628
Zinc finger, nuclear hormone receptor-type		22481
239IPR000595
Cyclic nucleotide-binding domain		22263
240IPR018297
Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site		2259
241IPR000299
FERM domain		2175
242IPR018490
Cyclic nucleotide-binding-like		21106
243IPR002999
Tudor domain		21142
244IPR000483
Cysteine-rich flanking region, C-terminal		2170
245IPR013763
Cyclin-like		21179
246IPR000073
Alpha/beta hydrolase fold-1		2174
247IPR018253
DnaJ domain, conserved site		2144
248IPR029034
Cystine-knot cytokine		2173
249IPR002893
Zinc finger, MYND-type		2184
250IPR024571
ERAP1-like C-terminal domain		2139
251IPR002076
ELO family		2055
252IPR013162
CD80-like, immunoglobulin C2-set		2090
253IPR019821
Kinesin motor domain, conserved site		2044
254IPR000536
Nuclear hormone receptor, ligand-binding, core		20316
255IPR011047
Quinonprotein alcohol dehydrogenase-like superfamily		2077
256IPR032466
Metal-dependent hydrolase		2042
257IPR023313
Ubiquitin-conjugating enzyme, active site		2043
258IPR002067
Mitochondrial carrier protein		20219
259IPR008967
p53-like transcription factor, DNA-binding		2061
260IPR004827
Basic-leucine zipper domain		20220
261IPR018000
Neurotransmitter-gated ion-channel, conserved site		2059
262IPR009020
Proteinase inhibitor, propeptide		2034
263IPR001487
Bromodomain		20555
264IPR003595
Protein-tyrosine phosphatase, catalytic		1983
265IPR020849
Small GTPase superfamily, Ras type		1990
266IPR000953
Chromo/chromo shadow domain		1995
267IPR029000
Cyclophilin-like domain		1946
268IPR018200
Ubiquitin specific protease, conserved site		1999
269IPR001791
Laminin G domain		19766
270IPR010920
Like-Sm (LSM) domain		1935
271IPR020901
Proteinase inhibitor I2, Kunitz, conserved site		1956
272IPR001766
Transcription factor, fork head		19211
273IPR002656
Acyltransferase 3		1925
274IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		19340
275IPR001507
Zona pellucida domain		18109
276IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		18130
277IPR015919
Cadherin-like		18634
278IPR001163
Ribonucleoprotein LSM domain		1849
279IPR000832
GPCR, family 2, secretin-like		18162
280IPR000795
Elongation factor, GTP-binding domain		18171
281IPR020845
AMP-binding, conserved site		1835
282IPR025483
Lipase, eukaryotic		1824
283IPR023795
Serpin, conserved site		1825
284IPR013780
Glycosyl hydrolase, family 13, all-beta		1830
285IPR014720
Double-stranded RNA-binding domain		18336
286IPR011021
Arrestin-like, N-terminal		1828
287IPR006629
LPS-induced tumour necrosis factor alpha factor		1852
288IPR001005
SANT/Myb domain		1893
289IPR001071
Cellular retinaldehyde binding/alpha-tocopherol transport		18130
290IPR019594
Ionotropic glutamate receptor, L-glutamate and glycine-binding domain		1873
291IPR007889
DNA binding HTH domain, Psq-type		17122
292IPR003146
Proteinase inhibitor, carboxypeptidase propeptide		1742
293IPR000330
SNF2-related		1737
294IPR006693
Partial AB-hydrolase lipase domain		1724
295IPR033640
Fatty acyl-CoA reductase, C-terminal		1731
296IPR001199
Cytochrome b5-like heme/steroid binding domain		17144
297IPR011022
Arrestin C-terminal-like domain		1754
298IPR006621
Nose resistant-to-fluoxetine protein, N-terminal		1723
299IPR006020
PTB/PI domain		17115
300IPR000884
Thrombospondin, type 1 repeat		17590
301IPR029045
ClpP/crotonase-like domain		1781
302IPR002035
von Willebrand factor, type A		17117
303IPR017455
Zinc finger, FYVE-related		1742
304IPR013120
Male sterility, NAD-binding		1732
305IPR011583
Chitinase II		1738
306IPR030456
Fork head domain conserved site 2		1733
307IPR001223
Glycoside hydrolase, family 18, catalytic domain		1738
308IPR001173
Glycosyltransferase 2-like		1727
309IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup		1729
310IPR026055
Fatty acyl-CoA reductase		1732
311IPR000727
Target SNARE coiled-coil domain		1665
312IPR000242
Protein-tyrosine phosphatase, receptor/non-receptor type		16529
313IPR006594
LIS1 homology motif		1656
314IPR000467
G-patch domain		1689
315IPR000014
PAS domain		16281
316IPR019819
Carboxylesterase type B, conserved site		1631
317IPR008250
P-type ATPase, A domain		16177
318IPR004245
Protein of unknown function DUF229		1645
319IPR002126
Cadherin		162569
320IPR023346
Lysozyme-like domain		1621
321IPR029070
Chitinase insertion domain		1674
322IPR001723
Steroid hormone receptor		16261
323IPR016021
MIF4-like, type 1/2/3		1655
324IPR013057
Amino acid transporter, transmembrane domain		1639
325IPR011012
Longin-like domain		1626
326IPR001683
Phox homologous domain		16135
327IPR029033
Histidine phosphatase superfamily		16148
328IPR001878
Zinc finger, CCHC-type		16121
329IPR015797
NUDIX hydrolase domain-like		1676
330IPR000225
Armadillo		16255
331IPR006689
Small GTPase superfamily, ARF/SAR type		1590
332IPR004000
Actin family		15175
333IPR013525
ABC-2 type transporter		1532
334IPR001734
Sodium/solute symporter		15132
335IPR001357
BRCT domain		15193
336IPR000772
Ricin B lectin domain		1596
337IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site		1520
338IPR000717
Proteasome component (PCI) domain		1545
339IPR012675
Beta-grasp domain		1521
340IPR000436
Sushi/SCR/CCP domain		15640
341IPR011013
Galactose mutarotase-like domain		1535
342IPR000172
Glucose-methanol-choline oxidoreductase, N-terminal		1552
343IPR007867
Glucose-methanol-choline oxidoreductase, C-terminal		1520
344IPR023561
Carbonic anhydrase, alpha-class		1527
345IPR001494
Importin-beta, N-terminal domain		1582
346IPR019826
Carboxylesterase type B, active site		1530
347IPR006026
Peptidase, metallopeptidase		1529
348IPR015902
Glycoside hydrolase, family 13		1538
349IPR023299
P-type ATPase, cytoplasmic domain N		15154
350IPR017937
Thioredoxin, conserved site		1531
351IPR003604
Zinc finger, U1-type		1564
352IPR006671
Cyclin, N-terminal		1539
353IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase		1528
354IPR007484
Peptidase M28		1525
355IPR000086
NUDIX hydrolase domain		1546
356IPR011330
Glycoside hydrolase/deacetylase, beta/alpha-barrel		1533
357IPR006047
Glycosyl hydrolase, family 13, catalytic domain		1544
358IPR001148
Alpha carbonic anhydrase		15135
359IPR006073
GTP binding domain		1558
360IPR001932
Protein phosphatase 2C (PP2C)-like domain		15167
361IPR008942
ENTH/VHS		1488
362IPR007502
Helicase-associated domain		1446
363IPR000433
Zinc finger, ZZ-type		14167
364IPR002181
Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain		1498
365IPR006195
Aminoacyl-tRNA synthetase, class II		1429
366IPR014716
Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1		1424
367IPR013602
Dynein heavy chain, domain-2		1427
368IPR000340
Dual specificity phosphatase, catalytic domain		1440
369IPR021109
Aspartic peptidase domain		1455
370IPR006652
Kelch repeat type 1		14257
371IPR000569
HECT		14223
372IPR023780
Chromo domain		1440
373IPR007125
Histone core		1417
374IPR018303
P-type ATPase, phosphorylation site		1465
375IPR001876
Zinc finger, RanBP2-type		14304
376IPR017996
Major royal jelly protein/Protein yellow		1463
377IPR009075
Acyl-CoA dehydrogenase/oxidase C-terminal		1447
378IPR001757
P-type ATPase		14154
379IPR026983
Dynein heavy chain		1499
380IPR000306
FYVE zinc finger		1454
381IPR016149
Casein kinase II, regulatory subunit, alpha-helical		1421
382IPR000704
Casein kinase II, regulatory subunit		14226
383IPR023311
Methuselah ectodomain, domain 2		1427
384IPR009100
Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain		1420
385IPR003663
Sugar/inositol transporter		14190
386IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		1465
387IPR002159
CD36 antigen		14232
388IPR015510
Peptidoglycan recognition protein		1434
389IPR024977
Anaphase-promoting complex subunit 4, WD40 domain		1420
390IPR001609
Myosin head, motor domain		14523
391IPR020894
Cadherin conserved site		14314
392IPR006611
Protein of unknown function DUF1431, cysteine-rich, Drosophila		1344
393IPR001952
Alkaline phosphatase		13138
394IPR006091
Acyl-CoA oxidase/dehydrogenase, central domain		1319
395IPR011032
GroES (chaperonin 10)-like		1340
396IPR006619
Peptidoglycan recognition protein family domain, metazoa/bacteria		1330
397IPR001506
Peptidase M12A, astacin		13108
398IPR012132
Glucose-methanol-choline oxidoreductase		1317
399IPR002068
Alpha crystallin/Hsp20 domain		1340
400IPR003347
JmjC domain		1373
401IPR007931
Protein of unknown function DUF725		1319
402IPR016050
Proteasome beta-type subunit, conserved site		1316
403IPR013099
Two pore domain potassium channel domain		1363
404IPR006601
Uncharacterised protein family DM11, Drosophila melanogaster		1313
405IPR000159
Ras-association		13179
406IPR002423
Chaperonin Cpn60/TCP-1 family		1315
407IPR003656
Zinc finger, BED-type		1352
408IPR019799
Glycoside hydrolase, family 22, conserved site		1317
409IPR001508
Ionotropic glutamate receptor, metazoa		1388
410IPR029056
Ribokinase-like		1334
411IPR013816
ATP-grasp fold, subdomain 2		1342
412IPR000408
Regulator of chromosome condensation, RCC1		13268
413IPR003008
Tubulin/FtsZ, GTPase domain		1372
414IPR001916
Glycoside hydrolase, family 22		13142
415IPR027409
GroEL-like apical domain		1330
416IPR001007
von Willebrand factor, type C		13119
417IPR033121
Peptidase family A1 domain		1332
418IPR016150
Casein kinase II, regulatory subunit, beta-sheet		1320
419IPR024743
Dynein heavy chain, coiled coil stalk		1326
420IPR001461
Aspartic peptidase		1384
421IPR016161
Aldehyde/histidinol dehydrogenase		1334
422IPR013126
Heat shock protein 70 family		13197
423IPR029006
ADF-H/Gelsolin-like domain		13108
424IPR002049
EGF-like, laminin		131145
425IPR001604
DNA/RNA non-specific endonuclease		1332
426IPR004273
Dynein heavy chain domain		1326
427IPR023210
NADP-dependent oxidoreductase domain		1381
428IPR011709
Domain of unknown function DUF1605		1322
429IPR003650
Orange		1343
430IPR009080
Aminoacyl-tRNA synthetase, class 1a, anticodon-binding		1341
431IPR002502
N-acetylmuramoyl-L-alanine amidase domain		13106
432IPR014715
Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2		1322
433IPR010596
Methuselah, N-terminal domain		1325
434IPR020821
Extracellular Endonuclease, subunit A		1324
435IPR024317
Dynein heavy chain, P-loop containing D4 domain		1326
436IPR002464
DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site		1321
437IPR024156
Small GTPase superfamily, ARF type		1320
438IPR017892
Protein kinase, C-terminal		1252
439IPR029277
Single domain Von Willebrand factor type C domain		1236
440IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		1271
441IPR016064
NAD kinase/diacylglycerol kinase-like domain		1291
442IPR000217
Tubulin		12161
443IPR023333
Proteasome B-type subunit		1215
444IPR013128
Peptidase C1A		1220
445IPR001753
Crotonase superfamily		1220
446IPR016039
Thiolase-like		1282
447IPR004161
Translation elongation factor EFTu/EF1A, domain 2		1225
448IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		1248
449IPR008280
Tubulin/FtsZ, C-terminal		1216
450IPR005135
Endonuclease/exonuclease/phosphatase		1298
451IPR018181
Heat shock protein 70, conserved site		1249
452IPR027413
GroEL-like equatorial domain		1229
453IPR013786
Acyl-CoA dehydrogenase/oxidase, N-terminal		1223
454IPR000047
Helix-turn-helix motif		1250
455IPR009038
GOLD		1264
456IPR006028
Gamma-aminobutyric acid A receptor/Glycine receptor alpha		12185
457IPR011704
ATPase, dynein-related, AAA domain		1235
458IPR003877
SPRY domain		12112
459IPR028846
Recoverin family		1228
460IPR031107
Small heat shock protein HSP20		1222
461IPR030457
ELO family, conserved site		1212
462IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		1229
463IPR023123
Tubulin, C-terminal		1216
464IPR003378
Fringe-like		1219
465IPR029047
Heat shock protein 70kD, peptide-binding domain		1247
466IPR018979
FERM, N-terminal		1242
467IPR001395
Aldo/keto reductase		1246
468IPR016163
Aldehyde dehydrogenase, C-terminal		1231
469IPR029048
Heat shock protein 70kD, C-terminal domain		1242
470IPR027267
Arfaptin homology (AH) domain/BAR domain		1130
471IPR029060
PIN domain-like		1134
472IPR003131
Potassium channel tetramerisation-type BTB domain		1142
473IPR001107
Band 7 protein		11116
474IPR018359
Bromodomain, conserved site		1149
475IPR017975
Tubulin, conserved site		1115
476IPR008991
Translation protein SH3-like domain		1116
477IPR027359
Voltage-dependent channel, four helix bundle domain		11422
478IPR029061
Thiamin diphosphate-binding fold		1168
479IPR001279
Beta-lactamase-like		1156
480IPR001969
Aspartic peptidase, active site		1121
481IPR031732
Protein of unknown function DUF4729		1113
482IPR007614
Retinin-like protein		1114
483IPR003280
Two pore domain potassium channel		1140
484IPR006553
Leucine-rich repeat, cysteine-containing subtype		11197
485IPR018980
FERM, C-terminal PH-like domain		1166
486IPR002123
Phospholipid/glycerol acyltransferase		1153
487IPR020422
Dual specificity phosphatase, subgroup, catalytic domain		1155
488IPR001496
SOCS protein, C-terminal		1190
489IPR003475
Insect protein of unknown function		1113
490IPR004344
Tubulin-tyrosine ligase/Tubulin polyglutamylase		1134
491IPR000157
Toll/interleukin-1 receptor homology (TIR) domain		11122
492IPR001870
B30.2/SPRY domain		1154
493IPR011038
Calycin-like		1121
494IPR000426
Proteasome alpha-subunit, N-terminal domain		1142
495IPR012674
Calycin		1120
496IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		1180
497IPR004011
GYR motif		1191
498IPR018122
Fork head domain conserved site1		1124
499IPR026906
Leucine rich repeat 5		1122
500IPR023332
Proteasome A-type subunit		1114
+
diff --git a/gramene/htdocs/ssi/species/stats_Leersia_perrieri.html b/gramene/htdocs/ssi/species/stats_Leersia_perrieri.html index 23cf9793..059c1ab8 100644 --- a/gramene/htdocs/ssi/species/stats_Leersia_perrieri.html +++ b/gramene/htdocs/ssi/species/stats_Leersia_perrieri.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.14 + 87.14 Base Pairs: @@ -21,12 +21,12 @@

Summary

Gene counts

- + - - + +
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 29,078
Gene transcriptsHASH(0x68ce400):41,422Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:40,939
@@ -57,7 +57,7 @@

Coordinate Systems

11210469601217761961 -
+
diff --git a/gramene/htdocs/ssi/species/stats_Leersia_perrieri_IPtop500.html b/gramene/htdocs/ssi/species/stats_Leersia_perrieri_IPtop500.html index 0d0d131c..7c87ab6f 100644 --- a/gramene/htdocs/ssi/species/stats_Leersia_perrieri_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Leersia_perrieri_IPtop500.html @@ -18,3500 +18,3500 @@ 1 IPR011009
Protein kinase-like domain superfamily 1381 - 2395 + 2236 2 - IPR000719
  - 1312 - 15630 + IPR000719
Protein kinase domain + 1311 + 3527 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase 1269 - 2741 + 2371 4 - IPR008271
Serine/threonine-protein kinase, active site - 1038 - 1625 + IPR036047
F-box-like domain superfamily + 528 + 795 5 - IPR032675
  - 1013 - 5762 + IPR002885
Pentatricopeptide repeat + 453 + 7697 6 - IPR017441
Protein kinase, ATP binding site - 879 - 1344 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 448 + 1053 7 - IPR011990
  - 681 - 11238 + IPR044974
Disease resistance protein, plants + 417 + 908 8 - IPR013083
  - 647 - 1920 + IPR001841
Zinc finger, RING-type + 399 + 854 9 - IPR036047
F-box-like domain superfamily - 528 - 810 + IPR001611
Leucine-rich repeat + 388 + 1374 10 - IPR002885
  - 454 - 29388 + IPR001810
F-box domain + 372 + 818 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 446 - 1031 + IPR002182
NB-ARC + 369 + 610 12 - IPR001841
  - 398 - 2642 + IPR029058
Alpha/Beta hydrolase fold + 357 + 633 13 - IPR001611
  - 391 - 8373 + IPR036291
NAD(P)-binding domain superfamily + 352 + 548 14 - IPR002182
NB-ARC - 385 - 633 + IPR009057
Homeobox-like domain superfamily + 346 + 470 15 - IPR001810
  - 384 - 3699 + IPR016024
Armadillo-type fold + 344 + 643 16 - IPR029058
  - 357 - 2710 + IPR011990
Tetratricopeptide-like helical domain superfamily + 324 + 571 17 - IPR036291
NAD(P)-binding domain superfamily - 352 - 610 + IPR036396
Cytochrome P450 superfamily + 303 + 419 18 - IPR009057
Homeobox-like domain superfamily - 346 - 474 + IPR001128
Cytochrome P450 + 297 + 1474 19 - IPR016024
Armadillo-type fold - 344 - 1284 + IPR041118
Rx, N-terminal + 287 + 418 20 - IPR036396
  - 305 - 2622 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 276 + 396 21 - IPR001128
Cytochrome P450 - 297 - 1476 + IPR035979
RNA-binding domain superfamily + 267 + 575 22 - IPR003593
AAA+ ATPase domain - 288 - 572 + IPR002401
Cytochrome P450, E-class, group I + 246 + 1765 23 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 276 - 395 + IPR000504
RNA recognition motif domain + 246 + 1123 24 - IPR035979
RNA-binding domain superfamily - 267 - 616 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 237 + 429 25 - IPR012677
  - 261 - 1322 + IPR036322
WD40-repeat-containing domain superfamily + 235 + 387 26 - IPR003591
Leucine-rich repeat, typical subtype - 247 - 2347 + IPR036259
MFS transporter superfamily + 231 + 420 27 - IPR002401
Cytochrome P450, E-class, group I - 246 - 1765 + IPR017853
Glycoside hydrolase superfamily + 228 + 377 28 - IPR000504
  - 246 - 5097 + IPR036249
Thioredoxin-like superfamily + 215 + 325 29 - IPR015943
  - 245 - 1764 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 211 + 294 30 - IPR017972
Cytochrome P450, conserved site - 245 - 329 + IPR001680
WD40 repeat + 210 + 1729 31 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 237 - 514 + IPR017930
Myb domain + 203 + 614 32 IPR001005
SANT/Myb domain - 236 - 983 + 196 + 630 33 - IPR001680
  - 235 - 10716 + IPR011992
EF-hand domain pair + 176 + 254 34 - IPR036322
WD40-repeat-containing domain superfamily - 235 - 587 + IPR002048
EF-hand domain + 167 + 962 35 - IPR036259
MFS transporter superfamily - 231 - 607 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 167 + 209 36 - IPR017853
Glycoside hydrolase superfamily - 228 - 424 + IPR016177
DNA-binding domain superfamily + 167 + 222 37 - IPR011989
  - 225 - 1056 + IPR036093
NAC domain superfamily + 166 + 193 38 - IPR036249
Thioredoxin-like superfamily - 215 - 329 + IPR003441
NAC domain + 163 + 376 39 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 211 - 294 + IPR036412
HAD-like superfamily + 162 + 258 40 - IPR017986
  - 203 - 1095 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 158 + 367 41 - IPR011992
EF-hand domain pair - 176 - 270 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 156 + 453 42 - IPR017930
  - 170 - 588 + IPR038765
Papain-like cysteine peptidase superfamily + 155 + 229 43 - IPR002048
  - 167 - 4716 + IPR001471
AP2/ERF domain + 154 + 813 44 - IPR036638
  - 167 - 1191 + IPR011333
SKP1/BTB/POZ domain superfamily + 145 + 220 45 - IPR016177
DNA-binding domain superfamily - 167 - 222 + IPR036770
Ankyrin repeat-containing domain superfamily + 143 + 244 46 - IPR036093
  - 166 - 1158 + IPR036390
Winged helix DNA-binding domain superfamily + 142 + 207 47 - IPR020846
  - 166 - 890 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 139 + 173 48 - IPR003441
  - 163 - 1125 + IPR029044
Nucleotide-diphospho-sugar transferases + 137 + 185 49 - IPR013087
  - 162 - 2253 + IPR036236
Zinc finger C2H2 superfamily + 136 + 191 50 - IPR036412
HAD-like superfamily - 162 - 381 + IPR001650
Helicase, C-terminal + 134 + 425 51 - IPR011598
  - 160 - 2103 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 133 + 229 52 - IPR001471
  - 155 - 3015 + IPR013087
Zinc finger C2H2-type + 132 + 245 53 - IPR036955
  - 155 - 582 + IPR002110
Ankyrin repeat + 129 + 670 54 - IPR038765
Papain-like cysteine peptidase superfamily - 155 - 280 + IPR003480
Transferase + 124 + 143 55 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 152 - 222 + IPR003439
ABC transporter-like, ATP-binding domain + 123 + 601 56 - IPR036388
  - 151 - 474 + IPR003959
ATPase, AAA-type, core + 120 + 201 57 - IPR018247
EF-Hand 1, calcium-binding site - 150 - 449 + IPR036188
FAD/NAD(P)-binding domain superfamily + 119 + 210 58 - IPR029044
  - 149 - 936 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 118 + 129 59 - IPR023214
  - 146 - 696 + IPR012340
Nucleic acid-binding, OB-fold + 112 + 233 60 - IPR011333
SKP1/BTB/POZ domain superfamily - 145 - 233 + IPR011011
Zinc finger, FYVE/PHD-type + 111 + 202 61 - IPR020683
  - 143 - 1646 + IPR000210
BTB/POZ domain + 109 + 322 62 - IPR023213
  - 143 - 540 + IPR036869
Chaperone J-domain superfamily + 109 + 157 63 - IPR036770
  - 143 - 1244 + IPR020683
Ankyrin repeat-containing domain + 106 + 245 64 - IPR036390
Winged helix DNA-binding domain superfamily - 142 - 209 + IPR036426
Bulb-type lectin domain superfamily + 103 + 133 65 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 139 - 209 + IPR001623
DnaJ domain + 102 + 765 66 - IPR014001
  - 138 - 908 + IPR012337
Ribonuclease H-like superfamily + 102 + 168 67 - IPR036236
Zinc finger C2H2 superfamily - 136 - 232 + IPR005174
Domain unknown function DUF295 + 102 + 135 68 - IPR001650
  - 134 - 1746 + IPR035892
C2 domain superfamily + 101 + 218 69 - IPR002110
  - 134 - 5118 + IPR036576
WRKY domain superfamily + 100 + 136 70 - IPR019775
WD40 repeat, conserved site - 127 - 302 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 100 + 195 71 - IPR013026
  - 125 - 744 + IPR001087
GDSL lipase/esterase + 99 + 147 72 - IPR003480
Transferase - 124 - 143 + IPR003657
WRKY domain + 99 + 268 73 - IPR014729
  - 123 - 394 + IPR001480
Bulb-type lectin domain + 99 + 346 74 - IPR003439
  - 123 - 1803 + IPR008972
Cupredoxin + 98 + 211 75 - IPR036188
  - 122 - 1322 + IPR019734
Tetratricopeptide repeat + 97 + 367 76 - IPR019734
  - 121 - 4194 + IPR011050
Pectin lyase fold/virulence factor + 97 + 109 77 - IPR003959
ATPase, AAA-type, core - 121 - 203 + IPR001356
Homeobox domain + 96 + 309 78 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 118 - 131 + IPR029071
Ubiquitin-like domain superfamily + 94 + 143 79 - IPR035595
UDP-glycosyltransferase family, conserved site - 113 - 141 + IPR020846
Major facilitator superfamily domain + 94 + 149 80 - IPR000210
  - 113 - 1395 + IPR044810
WRKY transcription factor, plant + 94 + 114 81 - IPR012340
Nucleic acid-binding, OB-fold - 112 - 247 + IPR021109
Aspartic peptidase domain superfamily + 93 + 134 82 - IPR011011
Zinc finger, FYVE/PHD-type - 111 - 202 + IPR036457
PPM-type phosphatase domain superfamily + 92 + 153 83 - IPR036869
  - 111 - 620 + IPR015424
Pyridoxal phosphate-dependent transferase + 92 + 151 84 - IPR008974
  - 111 - 1053 + IPR001932
PPM-type phosphatase domain + 91 + 444 85 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 110 - 182 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 90 + 180 86 - IPR036514
  - 106 - 316 + IPR000008
C2 domain + 89 + 434 87 - IPR036426
  - 103 - 622 + IPR035669
GDSL lipase/esterase-like, plant + 88 + 132 88 - IPR001623
  - 102 - 1800 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 88 + 95 89 - IPR012337
Ribonuclease H-like superfamily - 102 - 185 + IPR003609
PAN/Apple domain + 87 + 206 90 - IPR001480
  - 101 - 736 + IPR011545
DEAD/DEAH box helicase domain + 87 + 133 91 - IPR036576
  - 100 - 813 + IPR002347
Short-chain dehydrogenase/reductase SDR + 85 + 793 92 - IPR003657
  - 100 - 1209 + IPR007658
Protein of unknown function DUF594 + 85 + 103 93 - IPR005225
Small GTP-binding protein domain - 99 - 149 + IPR025315
Domain of unknown function DUF4220 + 85 + 116 94 - IPR008972
  - 98 - 890 + IPR015300
DNA-binding pseudobarrel domain superfamily + 85 + 189 95 - IPR014710
  - 98 - 370 + IPR033121
Peptidase family A1 domain + 84 + 131 96 - IPR013785
  - 97 - 567 + IPR009072
Histone-fold + 84 + 94 97 - IPR011050
Pectin lyase fold/virulence factor - 97 - 110 + IPR002083
MATH/TRAF domain + 83 + 362 98 - IPR001356
  - 96 - 1272 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 83 + 160 99 - IPR012334
  - 96 - 226 + IPR013766
Thioredoxin domain + 82 + 179 100 - IPR021109
  - 95 - 810 + IPR005828
Major facilitator, sugar transporter-like + 81 + 145 101 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 94 - 190 + IPR032799
Xylanase inhibitor, C-terminal + 80 + 108 102 - IPR005123
  - 94 - 1086 + IPR003340
B3 DNA binding domain + 79 + 527 103 - IPR006447
Myb domain, plants - 94 - 115 + IPR000858
S-locus glycoprotein domain + 79 + 106 104 - IPR029071
Ubiquitin-like domain superfamily - 94 - 143 + IPR000073
Alpha/beta hydrolase fold-1 + 79 + 280 105 - IPR035892
  - 93 - 420 + IPR020472
G-protein beta WD-40 repeat + 78 + 333 106 - IPR001087
GDSL lipase/esterase - 92 - 131 + IPR032861
Xylanase inhibitor, N-terminal + 78 + 98 107 - IPR036457
  - 92 - 696 + IPR004827
Basic-leucine zipper domain + 78 + 209 108 - IPR036397
  - 92 - 510 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 77 + 170 109 - IPR015424
Pyridoxal phosphate-dependent transferase - 92 - 156 + IPR011676
Domain of unknown function DUF1618 + 76 + 97 110 - IPR015421
  - 91 - 453 + IPR011051
RmlC-like cupin domain superfamily + 76 + 109 111 - IPR001932
  - 91 - 1866 + IPR036163
Heavy metal-associated domain superfamily + 75 + 100 112 - IPR001461
Aspartic peptidase A1 family - 89 - 323 + IPR032867
DYW domain + 75 + 96 113 - IPR035669
GDSL lipase/esterase-like, plant - 88 - 132 + IPR001461
Aspartic peptidase A1 family + 74 + 280 114 - IPR003609
  - 88 - 590 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 73 + 80 115 - IPR000008
  - 87 - 1182 + IPR043129
ATPase, nucleotide binding domain + 73 + 193 116 - IPR011545
DEAD/DEAH box helicase domain - 87 - 133 + IPR003613
U box domain + 73 + 184 117 - IPR009072
  - 87 - 576 + IPR006121
Heavy metal-associated domain, HMA + 72 + 241 118 - IPR015300
  - 87 - 756 + IPR026992
Non-haem dioxygenase N-terminal domain + 72 + 154 119 - IPR017871
ABC transporter, conserved site - 86 - 168 + IPR000109
Proton-dependent oligopeptide transporter family + 70 + 239 120 - IPR002347
Short-chain dehydrogenase/reductase SDR - 85 - 794 + IPR001220
Legume lectin domain + 69 + 147 121 - IPR007658
Protein of unknown function DUF594 - 85 - 103 + IPR036879
Transcription factor, MADS-box superfamily + 69 + 96 122 - IPR025315
Domain of unknown function DUF4220 - 85 - 116 + IPR002100
Transcription factor, MADS-box + 68 + 436 123 - IPR002083
  - 84 - 1326 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 68 + 104 124 - IPR027443
  - 84 - 400 + IPR036915
Cyclin-like superfamily + 67 + 186 125 - IPR033121
  - 84 - 260 + IPR000270
PB1 domain + 67 + 124 126 - IPR005174
Domain unknown function DUF295 - 82 - 105 + IPR019787
Zinc finger, PHD-finger + 66 + 186 127 - IPR001965
Zinc finger, PHD-type - 82 - 189 + IPR002902
Gnk2-homologous domain + 66 + 378 128 - IPR024171
S-receptor-like serine/threonine-protein kinase - 81 - 141 + IPR006501
Pectinesterase inhibitor domain + 65 + 70 129 - IPR005828
Major facilitator, sugar transporter-like - 81 - 145 + IPR029052
Metallo-dependent phosphatase-like + 63 + 91 130 - IPR032799
Xylanase inhibitor, C-terminal - 81 - 109 + IPR016039
Thiolase-like + 62 + 134 131 - IPR000858
S-locus glycoprotein domain - 80 - 107 + IPR036908
RlpA-like domain superfamily + 62 + 77 132 - IPR032867
DYW domain - 80 - 102 + IPR000571
Zinc finger, CCCH-type + 62 + 307 133 - IPR015422
  - 80 - 618 + IPR026961
PGG domain + 61 + 155 134 - IPR017907
Zinc finger, RING-type, conserved site - 80 - 124 + IPR000626
Ubiquitin-like domain + 60 + 149 135 - IPR004827
  - 80 - 1194 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 60 + 89 136 - IPR003340
  - 79 - 2100 + IPR001806
Small GTPase + 60 + 182 137 - IPR032861
Xylanase inhibitor, N-terminal - 79 - 100 + IPR013057
Amino acid transporter, transmembrane domain + 59 + 73 138 - IPR015655
Protein phosphatase 2C family - 79 - 158 + IPR004045
Glutathione S-transferase, N-terminal + 59 + 202 139 - IPR020472
G-protein beta WD-40 repeat - 78 - 333 + IPR000048
IQ motif, EF-hand binding site + 58 + 353 140 - IPR013766
  - 77 - 522 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 57 + 84 141 - IPR000073
Alpha/beta hydrolase fold-1 - 77 - 276 + IPR045051
Subtilisin-like protease + 57 + 109 142 - IPR011676
Domain of unknown function DUF1618 - 76 - 98 + IPR003245
Phytocyanin domain + 57 + 133 143 - IPR011051
RmlC-like cupin domain superfamily - 76 - 135 + IPR023395
Mitochondrial carrier domain superfamily + 57 + 79 144 - IPR003960
ATPase, AAA-type, conserved site - 75 - 120 + IPR036852
Peptidase S8/S53 domain superfamily + 57 + 83 145 - IPR036163
Heavy metal-associated domain superfamily - 75 - 100 + IPR010987
Glutathione S-transferase, C-terminal-like + 57 + 87 146 - IPR006121
  - 74 - 729 + IPR017884
SANT domain + 56 + 79 147 - IPR035513
  - 73 - 302 + IPR013763
Cyclin-like + 56 + 150 148 - IPR026992
Non-haem dioxygenase N-terminal domain - 73 - 155 + IPR039391
Phytocyanin + 56 + 66 149 - IPR003613
  - 73 - 828 + IPR018108
Mitochondrial substrate/solute carrier + 56 + 436 150 - IPR000109
Proton-dependent oligopeptide transporter family - 70 - 245 + IPR016159
Cullin repeat-like-containing domain superfamily + 56 + 72 151 - IPR001220
Legume lectin domain - 69 - 147 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 55 + 61 152 - IPR036879
  - 69 - 573 + IPR020568
Ribosomal protein S5 domain 2-type fold + 55 + 88 153 - IPR000225
  - 69 - 2316 + IPR044965
Glycoside hydrolase family 17, plant + 55 + 89 154 - IPR002100
  - 68 - 1752 + IPR000209
Peptidase S8/S53 domain + 55 + 82 155 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 68 - 106 + IPR000225
Armadillo + 55 + 256 156 - IPR036915
Cyclin-like superfamily - 67 - 190 + IPR013525
ABC-2 type transporter + 54 + 129 157 - IPR000270
  - 67 - 501 + IPR007112
Expansin/pollen allergen, DPBB domain + 54 + 63 158 - IPR019787
  - 66 - 372 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 54 + 78 159 - IPR002902
  - 66 - 758 + IPR005202
Transcription factor GRAS + 54 + 188 160 - IPR036961
  - 66 - 636 + IPR006566
FBD domain + 54 + 59 161 - IPR038408
  - 65 - 386 + IPR013094
Alpha/beta hydrolase fold-3 + 54 + 63 162 - IPR006501
Pectinesterase inhibitor domain - 65 - 178 + IPR001752
Kinesin motor domain + 54 + 574 163 - IPR013783
  - 64 - 226 + IPR000490
Glycoside hydrolase family 17 + 53 + 76 164 - IPR006566
FBD domain - 63 - 75 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 52 + 74 165 - IPR016039
  - 62 - 786 + IPR015500
Peptidase S8, subtilisin-related + 52 + 194 166 - IPR000742
  - 62 - 514 + IPR016181
Acyl-CoA N-acyltransferase + 51 + 86 167 - IPR036908
  - 62 - 310 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 51 + 75 168 - IPR000571
  - 62 - 1539 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 51 + 60 169 - IPR026961
PGG domain - 61 - 155 + IPR022059
Protein of unknown function DUF3615 + 51 + 76 170 - IPR004045
  - 61 - 609 + IPR007117
Expansin, cellulose-binding-like domain + 51 + 120 171 - IPR000626
  - 60 - 609 + IPR041569
AAA ATPase, AAA+ lid domain + 51 + 93 172 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 60 - 89 + IPR003676
Small auxin-up RNA + 51 + 63 173 - IPR019786
Zinc finger, PHD-type, conserved site - 60 - 101 + IPR008949
Isoprenoid synthase domain superfamily + 50 + 73 174 - IPR011993
  - 60 - 184 + IPR026057
PC-Esterase + 50 + 83 175 - IPR001806
Small GTPase superfamily - 60 - 104 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 50 + 60 176 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 59 - 87 + IPR036465
von Willebrand factor A-like domain superfamily + 50 + 71 177 - IPR013057
Amino acid transporter, transmembrane domain - 59 - 73 + IPR007118
Expansin/Lol pI + 49 + 280 178 - IPR036852
  - 59 - 1020 + IPR003663
Sugar/inositol transporter + 49 + 326 179 - IPR010987
  - 58 - 178 + IPR002921
Fungal lipase-like domain + 48 + 68 180 - IPR000048
  - 58 - 1716 + IPR011032
GroES-like superfamily + 48 + 98 181 - IPR003245
  - 57 - 588 + IPR001563
Peptidase S10, serine carboxypeptidase + 48 + 608 182 - IPR023395
  - 57 - 366 + IPR029962
Trichome birefringence-like family + 48 + 85 183 - IPR015915
  - 57 - 555 + IPR001509
NAD-dependent epimerase/dehydratase + 48 + 77 184 - IPR013763
Cyclin-like - 56 - 276 + IPR012946
X8 domain + 48 + 60 185 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 56 - 62 + IPR008979
Galactose-binding-like domain superfamily + 48 + 127 186 - IPR016135
  - 56 - 336 + IPR002528
Multi antimicrobial extrusion protein + 48 + 159 187 - IPR018108
  - 56 - 892 + IPR015915
Kelch-type beta propeller + 48 + 75 188 - IPR008979
  - 56 - 512 - + IPR024788
Malectin-like domain + 48 + 116 + 189 - IPR016159
Cullin repeat-like-containing domain superfamily - 56 - 95 + IPR036855
Zinc finger, CCCH-type superfamily + 48 + 137 190 - IPR013525
ABC-2 type transporter - 55 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 47 131 191 - IPR027640
Kinesin-like protein - 55 - 169 + IPR000873
AMP-dependent synthetase/ligase + 47 + 71 192 - IPR020568
Ribosomal protein S5 domain 2-type fold - 55 - 102 + IPR011527
ABC transporter type 1, transmembrane domain + 47 + 271 193 - IPR029052
  - 55 - 166 + IPR025846
PMR5 N-terminal domain + 47 + 74 194 - IPR034090
BPM, C-terminal - 55 - 94 + IPR030184
WAT1-related protein + 46 + 77 195 - IPR000209
Peptidase S8/S53 domain - 55 - 83 + IPR000620
EamA domain + 46 + 104 196 - IPR007112
  - 54 - 238 + IPR043926
ABC transporter family G domain + 45 + 91 197 - IPR005202
  - 54 - 250 + IPR000608
Ubiquitin-conjugating enzyme E2 + 45 + 184 198 - IPR013094
Alpha/beta hydrolase fold-3 - 54 - 63 + IPR029055
Nucleophile aminohydrolases, N-terminal + 45 + 53 199 - IPR001752
  - 54 - 2025 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 45 + 77 200 - IPR000490
Glycoside hydrolase family 17 - 53 - 114 + IPR034197
Cucumisin-like catalytic domain + 45 + 64 201 - IPR018097
EGF-like calcium-binding, conserved site - 53 - 99 + IPR008928
Six-hairpin glycosidase superfamily + 45 + 68 202 - IPR013128
Peptidase C1A - 52 - 67 + IPR009003
Peptidase S1, PA clan + 45 + 78 203 - IPR001881
EGF-like calcium-binding domain - 52 - 158 + IPR023298
P-type ATPase, transmembrane domain superfamily + 45 + 86 204 - IPR005829
Sugar transporter, conserved site - 52 - 131 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 45 + 97 205 - IPR015500
Peptidase S8, subtilisin-related - 52 - 194 + IPR008250
P-type ATPase, A domain superfamily + 44 + 79 206 - IPR016181
Acyl-CoA N-acyltransferase - 51 - 88 + IPR006671
Cyclin, N-terminal + 44 + 76 207 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 51 - 78 + IPR004158
Protein of unknown function DUF247, plant + 44 + 111 208 - IPR001509
NAD-dependent epimerase/dehydratase - 51 - 78 + IPR044808
Ethylene-responsive transcription factor + 44 + 51 209 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 51 - 61 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 115 210 - IPR036749
  - 51 - 238 + IPR014014
RNA helicase, DEAD-box type, Q motif + 43 + 58 211 - IPR022059
Protein of unknown function DUF3615 - 51 - 75 + IPR011006
CheY-like superfamily + 43 + 61 212 - IPR036465
  - 51 - 258 + IPR007125
Histone H2A/H2B/H3 + 43 + 48 213 - IPR007117
  - 51 - 240 + IPR000668
Peptidase C1A, papain C-terminal + 43 + 164 214 - IPR003676
Small auxin-up RNA - 51 - 63 + IPR000070
Pectinesterase, catalytic + 43 + 47 215 - IPR008949
  - 50 - 352 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 42 + 46 216 - IPR026057
PC-Esterase - 50 - 83 + IPR006045
Cupin 1 + 42 + 75 217 - IPR007118
Expansin/Lol pI - 49 - 280 + IPR014756
Immunoglobulin E-set + 42 + 77 218 - IPR000222
PPM-type phosphatase, divalent cation binding - 49 - 77 + IPR006016
UspA + 41 + 45 219 - IPR003663
Sugar/inositol transporter - 49 - 381 + IPR036318
FAD-binding, type PCMH-like superfamily + 41 + 56 220 - IPR002921
Fungal lipase-like domain - 48 - 68 + IPR008978
HSP20-like chaperone + 41 + 50 221 - IPR011032
GroES-like superfamily - 48 - 100 + IPR034161
Pepsin-like domain, plant + 41 + 49 222 - IPR001563
Peptidase S10, serine carboxypeptidase - 48 - 626 + IPR000742
EGF-like domain + 41 + 68 223 - IPR029962
Trichome birefringence-like family - 48 - 90 + IPR010255
Haem peroxidase superfamily + 41 + 60 224 - IPR012946
X8 domain - 48 - 120 + IPR001214
SET domain + 41 + 107 225 - IPR002528
Multi antimicrobial extrusion protein - 48 - 223 + IPR000743
Glycoside hydrolase, family 28 + 41 + 50 226 - IPR030184
WAT1-related protein - 48 - 84 + IPR033389
AUX/IAA domain + 40 + 58 227 - IPR024788
Malectin-like carbohydrate-binding domain - 48 - 112 + IPR007493
Protein of unknown function DUF538 + 40 + 89 228 - IPR036855
Zinc finger, CCCH-type superfamily - 48 - 137 + IPR000330
SNF2, N-terminal + 40 + 68 229 - IPR036640
  - 47 - 810 + IPR004140
Exocyst complex component Exo70 + 40 + 92 230 - IPR000873
AMP-dependent synthetase/ligase - 47 - 71 + IPR016166
FAD-binding domain, PCMH-type + 40 + 53 231 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 47 - 563 + IPR036758
At5g01610-like superfamily + 40 + 46 232 - IPR011527
  - 47 - 813 + IPR011706
Multicopper oxidase, C-terminal + 40 + 49 233 - IPR025846
PMR5 N-terminal domain - 47 - 74 + IPR045087
Multicopper oxidase + 40 + 53 234 - IPR037045
  - 47 - 140 + IPR002016
Haem peroxidase + 40 + 267 235 - IPR017451
F-box associated interaction domain - 46 - 60 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 40 + 52 236 - IPR014014
  - 46 - 134 + IPR001117
Multicopper oxidase, type 1 + 39 + 47 237 - IPR017970
Homeobox, conserved site - 46 - 49 + IPR008942
ENTH/VHS + 39 + 62 238 - IPR023299
  - 46 - 405 + IPR010402
CCT domain + 39 + 112 239 - IPR001757
P-type ATPase - 46 - 326 + IPR033896
MADS MEF2-like + 39 + 62 240 - IPR000620
EamA domain - 46 - 105 + IPR025659
Tubby-like, C-terminal + 39 + 55 241 - IPR000608
  - 45 - 368 + IPR011701
Major facilitator superfamily + 39 + 95 242 - IPR023393
  - 45 - 142 + IPR009000
Translation protein, beta-barrel domain superfamily + 39 + 66 243 - IPR029055
  - 45 - 214 + IPR002912
ACT domain + 39 + 119 244 - IPR036890
  - 45 - 332 + IPR000182
GNAT domain + 38 + 101 245 - IPR034197
Cucumisin-like catalytic domain - 45 - 64 + IPR003137
PA domain + 38 + 52 246 - IPR008928
Six-hairpin glycosidase superfamily - 45 - 80 + IPR001296
Glycosyl transferase, family 1 + 38 + 62 247 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 45 - 67 + IPR039417
Papain-like cysteine endopeptidase + 38 + 43 248 - IPR009003
Peptidase S1, PA clan - 45 - 83 + IPR004314
Neprosin + 38 + 43 249 - IPR023298
P-type ATPase, transmembrane domain superfamily - 45 - 244 + IPR011043
Galactose oxidase/kelch, beta-propeller + 38 + 44 250 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 45 - 109 + IPR008889
VQ + 38 + 39 251 - IPR008250
P-type ATPase, A domain superfamily - 44 - 98 + IPR004853
Sugar phosphate transporter domain + 37 + 61 252 - IPR018253
DnaJ domain, conserved site - 44 - 59 + IPR009060
UBA-like superfamily + 37 + 53 253 - IPR006671
Cyclin, N-terminal - 44 - 108 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 37 + 38 254 - IPR004158
Protein of unknown function DUF247, plant - 44 - 56 + IPR004263
Exostosin-like + 37 + 57 255 - IPR001789
  - 44 - 663 + IPR011012
Longin-like domain superfamily + 37 + 55 256 - IPR008942
  - 43 - 260 + IPR004883
Lateral organ boundaries, LOB + 37 + 74 257 - IPR008978
  - 43 - 204 + IPR013126
Heat shock protein 70 family + 37 + 100 258 - IPR011006
CheY-like superfamily - 43 - 62 + IPR011707
Multicopper oxidase, N-termianl + 37 + 45 259 - IPR020845
AMP-binding, conserved site - 43 - 60 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 36 + 51 260 - IPR018303
P-type ATPase, phosphorylation site - 43 - 76 + IPR023271
Aquaporin-like + 36 + 44 261 - IPR000668
Peptidase C1A, papain C-terminal - 43 - 209 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 36 + 68 262 - IPR000070
Pectinesterase, catalytic - 43 - 47 + IPR015655
Protein phosphatase 2C family + 36 + 89 263 - IPR011042
  - 43 - 142 + IPR000425
Major intrinsic protein + 36 + 321 264 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 42 - 92 + IPR002487
Transcription factor, K-box + 36 + 111 265 - IPR006045
Cupin 1 - 42 - 145 + IPR036612
K Homology domain, type 1 superfamily + 35 + 139 266 - IPR013780
  - 42 - 144 + IPR004265
Dirigent protein + 35 + 45 267 - IPR014756
Immunoglobulin E-set - 42 - 78 + IPR004046
Glutathione S-transferase, C-terminal + 35 + 57 268 - IPR012341
  - 42 - 237 + IPR028889
Ubiquitin specific protease domain + 35 + 58 269 - IPR006016
UspA - 41 - 45 + IPR039361
Cyclin + 35 + 68 270 - IPR036318
FAD-binding, type 2-like superfamily - 41 - 56 + IPR015947
PUA-like superfamily + 35 + 44 271 - IPR034161
Pepsin-like domain, plant - 41 - 49 + IPR025322
Protein of unknown function DUF4228, plant + 34 + 35 272 - IPR010255
Haem peroxidase - 41 - 61 + IPR002156
Ribonuclease H domain + 34 + 49 273 - IPR001214
  - 41 - 474 + IPR029021
Protein-tyrosine phosphatase-like + 34 + 55 274 - IPR000743
Glycoside hydrolase, family 28 - 41 - 74 + IPR034294
Aquaporin transporter + 34 + 47 275 - IPR007493
Protein of unknown function DUF538 - 40 - 89 + IPR002495
Glycosyl transferase, family 8 + 34 + 46 276 - IPR011701
Major facilitator superfamily - 40 - 96 + IPR000644
CBS domain + 34 + 168 277 - IPR000330
SNF2-related, N-terminal domain - 40 - 68 + IPR001878
Zinc finger, CCHC-type + 34 + 129 278 - IPR003137
PA domain - 40 - 54 + IPR004041
NAF domain + 33 + 37 279 - IPR001938
  - 40 - 714 + IPR027214
Cystatin + 33 + 40 280 - IPR004140
Exocyst complex component Exo70 - 40 - 97 + IPR013149
Alcohol dehydrogenase, C-terminal + 33 + 53 281 - IPR016166
  - 40 - 159 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 145 - 282 - IPR036758
  - 40 - 184 + 282 + IPR018451
NAF/FISL domain + 33 + 37 283 - IPR011706
Multicopper oxidase, type 2 - 40 - 49 + IPR035940
CAP superfamily + 33 + 42 284 - IPR002016
  - 40 - 801 + IPR001938
Thaumatin family + 33 + 262 285 - IPR001117
Multicopper oxidase, type 1 - 39 - 47 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 49 286 - IPR010402
  - 39 - 336 + IPR029045
ClpP/crotonase-like domain superfamily + 33 + 52 287 - IPR033896
MADS MEF2-like - 39 - 62 + IPR019378
GDP-fucose protein O-fucosyltransferase + 33 + 54 288 - IPR025659
  - 39 - 176 + IPR006094
FAD linked oxidase, N-terminal + 33 + 39 289 - IPR036691
  - 39 - 304 + IPR002067
Mitochondrial carrier protein + 33 + 223 290 - IPR009000
Translation protein, beta-barrel domain superfamily - 39 - 67 + IPR040911
Exostosin, GT47 domain + 33 + 50 291 - IPR003594
Histidine kinase/HSP90-like ATPase - 39 - 130 + IPR043519
Nucleotidyltransferase superfamily + 33 + 47 292 - IPR007125
Histone H2A/H2B/H3 - 39 - 43 + IPR037176
Osmotin/thaumatin-like superfamily + 33 + 44 293 - IPR002912
  - 39 - 268 + IPR016040
NAD(P)-binding domain + 32 + 44 294 - IPR033389
AUX/IAA domain - 38 - 55 + IPR032710
NTF2-like domain superfamily + 32 + 39 295 - IPR000182
  - 38 - 202 + IPR006153
Cation/H+ exchanger + 32 + 52 296 - IPR006626
Parallel beta-helix repeat - 38 - 216 + IPR002659
Glycosyl transferase, family 31 + 32 + 93 297 - IPR011016
  - 38 - 330 + IPR005135
Endonuclease/exonuclease/phosphatase + 32 + 42 298 - IPR001969
Aspartic peptidase, active site - 38 - 74 + IPR004367
Cyclin, C-terminal domain + 32 + 47 299 - IPR000644
  - 38 - 630 + IPR022742
Serine aminopeptidase, S33 + 32 + 55 300 - IPR004314
Neprosin - 38 - 43 + IPR003406
Glycosyl transferase, family 14 + 32 + 38 301 - IPR011043
Galactose oxidase/kelch, beta-propeller - 38 - 49 + IPR004839
Aminotransferase, class I/classII + 32 + 63 302 - IPR008889
VQ - 38 - 39 + IPR006458
Ovate protein family, C-terminal + 32 + 62 303 - IPR004853
Sugar phosphate transporter domain - 37 - 61 + IPR002109
Glutaredoxin + 32 + 35 304 - IPR009060
UBA-like superfamily - 37 - 53 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 32 + 34 305 - IPR001296
Glycosyl transferase, family 1 - 37 - 61 + IPR006702
Casparian strip membrane protein domain + 32 + 41 306 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 37 - 67 + IPR036378
FAS1 domain superfamily + 31 + 42 307 - IPR011012
Longin-like domain superfamily - 37 - 55 + IPR005630
Terpene synthase, metal-binding domain + 31 + 34 308 - IPR004883
  - 37 - 148 + IPR013154
Alcohol dehydrogenase, N-terminal + 31 + 46 309 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 37 - 70 + IPR000010
Cystatin domain + 31 + 54 310 - IPR038718
  - 37 - 146 + IPR018490
Cyclic nucleotide-binding-like + 30 + 56 311 - IPR013126
Heat shock protein 70 family - 37 - 347 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 30 + 41 312 - IPR025661
Cysteine peptidase, asparagine active site - 37 - 40 + IPR002068
Alpha crystallin/Hsp20 domain + 30 + 67 313 - IPR011707
Multicopper oxidase, type 3 - 37 - 45 + IPR038933
Ovate protein family + 30 + 32 314 - IPR017877
  - 37 - 114 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 30 + 122 315 - IPR027214
Cystatin - 36 - 43 + IPR014044
CAP domain + 30 + 39 316 - IPR029021
  - 36 - 236 + IPR036875
Zinc finger, CCHC-type superfamily + 30 + 54 317 - IPR036612
  - 36 - 714 + IPR000823
Plant peroxidase + 30 + 219 318 - IPR023271
  - 36 - 182 + IPR006073
GTP binding domain + 30 + 98 319 - IPR036865
  - 36 - 204 + IPR025110
AMP-binding enzyme, C-terminal domain + 29 + 42 320 - IPR034294
Aquaporin transporter - 36 - 51 + IPR008991
Translation protein SH3-like domain superfamily + 29 + 34 321 - IPR000425
Major intrinsic protein - 36 - 345 + IPR036420
BRCT domain superfamily + 29 + 76 322 - IPR002487
  - 36 - 345 + IPR001283
Cysteine-rich secretory protein-related + 29 + 140 323 - IPR004265
Dirigent protein - 35 - 45 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 324 - IPR028889
  - 35 - 116 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 29 + 60 325 - IPR002109
  - 35 - 216 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 29 + 51 326 - IPR001878
  - 35 - 600 + IPR002423
Chaperonin Cpn60/TCP-1 family + 28 + 41 327 - IPR015947
PUA-like superfamily - 35 - 52 + IPR027356
NPH3 domain + 28 + 80 328 - IPR025322
Protein of unknown function DUF4228, plant - 34 - 35 + IPR006652
Kelch repeat type 1 + 28 + 73 329 - IPR019378
GDP-fucose protein O-fucosyltransferase - 34 - 55 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 28 + 43 330 - IPR002495
Glycosyl transferase, family 8 - 34 - 46 + IPR043454
NPH3/RPT2-like family + 28 + 49 331 - IPR000169
Cysteine peptidase, cysteine active site - 34 - 35 + IPR027409
GroEL-like apical domain superfamily + 28 + 36 332 - IPR025660
Cysteine peptidase, histidine active site - 34 - 38 + IPR005821
Ion transport domain + 28 + 47 333 - IPR004041
NAF domain - 33 - 37 + IPR004088
K Homology domain, type 1 + 28 + 120 334 - IPR013149
Alcohol dehydrogenase, C-terminal - 33 - 53 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 28 + 50 335 - IPR001251
  - 33 - 386 + IPR003851
Zinc finger, Dof-type + 28 + 60 336 - IPR018451
  - 33 - 111 + IPR003311
AUX/IAA protein + 28 + 44 337 - IPR035940
  - 33 - 166 + IPR000595
Cyclic nucleotide-binding domain + 28 + 139 338 - IPR004263
Exostosin-like - 33 - 50 + IPR000727
Target SNARE coiled-coil homology domain + 27 + 48 339 - IPR004367
Cyclin, C-terminal domain - 33 - 90 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 27 + 124 340 - IPR022742
Serine aminopeptidase, S33 - 33 - 57 + IPR017938
Riboflavin synthase-like beta-barrel + 27 + 37 341 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 33 - 53 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 27 + 84 342 - IPR029045
ClpP/crotonase-like domain superfamily - 33 - 61 + IPR001357
BRCT domain + 27 + 126 343 - IPR002035
  - 33 - 208 + IPR024709
Putative O-fucosyltransferase, plant + 27 + 53 344 - IPR022357
Major intrinsic protein, conserved site - 33 - 39 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 27 + 34 345 - IPR004046
Glutathione S-transferase, C-terminal - 33 - 52 + IPR000717
Proteasome component (PCI) domain + 27 + 58 346 - IPR006094
FAD linked oxidase, N-terminal - 33 - 39 + IPR013216
Methyltransferase type 11 + 27 + 43 - - 347 - IPR002067
Mitochondrial carrier protein - 33 - 223 + + 347 + IPR000795
Translational (tr)-type GTP-binding domain + 27 + 246 348 - IPR029047
  - 33 - 144 + IPR007650
Zf-FLZ domain + 27 + 59 349 - IPR037176
  - 33 - 190 + IPR005150
Cellulose synthase + 27 + 58 350 - IPR032710
NTF2-like domain superfamily - 32 - 41 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 27 + 35 351 - IPR006153
Cation/H+ exchanger - 32 - 52 + IPR002963
Expansin + 27 + 217 352 - IPR019821
Kinesin motor domain, conserved site - 32 - 51 + IPR033443
Pentacotripeptide-repeat region of PRORP + 27 + 56 353 - IPR002659
Glycosyl transferase, family 31 - 32 - 98 + IPR001906
Terpene synthase, N-terminal domain + 27 + 29 354 - IPR005630
Terpene synthase, metal-binding domain - 32 - 37 + IPR044791
Beta-glucanase/XTH + 27 + 35 355 - IPR005135
Endonuclease/exonuclease/phosphatase - 32 - 42 + IPR000757
Glycoside hydrolase family 16 + 27 + 68 356 - IPR003406
Glycosyl transferase, family 14 - 32 - 38 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 26 + 35 357 - IPR004839
Aminotransferase, class I/classII - 32 - 63 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 26 + 29 358 - IPR006458
  - 32 - 184 + IPR016461
O-methyltransferase COMT-type + 26 + 73 359 - IPR014721
  - 32 - 116 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 26 + 30 360 - IPR006702
Casparian strip membrane protein domain - 32 - 41 + IPR008422
Homeobox KN domain + 26 + 29 361 - IPR016040
NAD(P)-binding domain - 31 - 42 + IPR029061
Thiamin diphosphate-binding fold + 26 + 69 362 - IPR036378
  - 31 - 146 + IPR044848
PHR1-like + 26 + 42 363 - IPR013154
Alcohol dehydrogenase, N-terminal - 31 - 46 + IPR001594
Palmitoyltransferase, DHHC domain + 26 + 41 364 - IPR038770
  - 31 - 92 + IPR001763
Rhodanese-like domain + 26 + 65 365 - IPR006652
Kelch repeat type 1 - 31 - 178 + IPR003594
Histidine kinase/HSP90-like ATPase + 26 + 36 366 - IPR008480
Protein of unknown function DUF761, plant - 31 - 31 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 26 + 35 367 - IPR020843
Polyketide synthase, enoylreductase domain - 31 - 37 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 26 + 48 368 - IPR000010
Cystatin domain - 31 - 66 + IPR000863
Sulfotransferase domain + 26 + 39 369 - IPR018490
Cyclic nucleotide-binding-like - 30 - 57 + IPR001077
O-methyltransferase domain + 26 + 36 370 - IPR018200
Ubiquitin specific protease, conserved site - 30 - 82 + IPR002035
von Willebrand factor, type A + 26 + 62 371 - IPR002068
  - 30 - 134 + IPR001757
P-type ATPase + 26 + 186 372 - IPR038933
Ovate protein family - 30 - 35 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 26 + 32 373 - IPR018181
Heat shock protein 70, conserved site - 30 - 75 + IPR003855
Potassium transporter + 26 + 89 374 - IPR033131
Pectinesterase, Asp active site - 30 - 30 + IPR005175
PPC domain + 26 + 76 375 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 30 - 283 + IPR036085
PAZ domain superfamily + 25 + 58 376 - IPR038538
  - 30 - 118 + IPR015940
Ubiquitin-associated domain + 25 + 76 377 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 30 - 144 + IPR000782
FAS1 domain + 25 + 63 378 - IPR014044
CAP domain - 30 - 77 + IPR013601
FAE1/Type III polyketide synthase-like protein + 25 + 27 379 - IPR004088
K Homology domain, type 1 - 30 - 125 + IPR010920
LSM domain superfamily + 25 + 44 380 - IPR004087
K Homology domain - 30 - 128 + IPR044835
Auxin response factor + 25 + 60 381 - IPR036875
Zinc finger, CCHC-type superfamily - 30 - 54 + IPR007657
Glycosyltransferase 61 + 25 + 80 382 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 53 + IPR027725
Heat shock transcription factor family + 25 + 30 383 - IPR000823
Plant peroxidase - 30 - 219 + IPR001353
Proteasome, subunit alpha/beta + 25 + 30 384 - IPR006073
GTP binding domain - 30 - 98 + IPR000408
Regulator of chromosome condensation, RCC1 + 25 + 611 385 - IPR025110
AMP-binding enzyme, C-terminal domain - 29 - 42 + IPR002123
Phospholipid/glycerol acyltransferase + 25 + 27 386 - IPR008991
Translation protein SH3-like domain superfamily - 29 - 34 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 25 + 26 387 - IPR036420
  - 29 - 314 + IPR011013
Galactose mutarotase-like domain superfamily + 25 + 43 388 - IPR031112
AP2-like ethylene-responsive transcription factor - 29 - 45 + IPR044839
Protein NDR1-like + 25 + 30 389 - IPR002123
Phospholipid/glycerol acyltransferase - 29 - 56 + IPR004813
Oligopeptide transporter, OPT superfamily + 25 + 62 390 - IPR009091
  - 29 - 268 + IPR023299
P-type ATPase, cytoplasmic domain N + 25 + 39 391 - IPR036965
  - 28 - 114 + IPR025486
Domain of unknown function DUF4378 + 25 + 40 392 - IPR000315
  - 28 - 492 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 111 393 - IPR013216
Methyltransferase type 11 - 28 - 44 + IPR036034
PDZ superfamily + 25 + 37 394 - IPR002423
Chaperonin Cpn60/TCP-1 family - 28 - 41 + IPR002913
START domain + 25 + 79 395 - IPR027356
  - 28 - 160 + IPR003100
PAZ domain + 24 + 109 396 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 28 - 47 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 24 + 42 397 - IPR019793
Peroxidases heam-ligand binding site - 28 - 40 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 24 + 240 398 - IPR019794
Peroxidase, active site - 28 - 38 + IPR007612
LURP-one-related + 24 + 60 399 - IPR027409
  - 28 - 144 + IPR029000
Cyclophilin-like domain superfamily + 24 + 42 400 - IPR005821
Ion transport domain - 28 - 47 + IPR025753
AAA-type ATPase, N-terminal domain + 24 + 28 401 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 28 - 50 + IPR000315
B-box-type zinc finger + 24 + 69 402 - IPR017937
Thioredoxin, conserved site - 28 - 40 + IPR011016
Zinc finger, RING-CH-type + 24 + 62 403 - IPR003851
  - 28 - 357 + IPR023753
FAD/NAD(P)-binding domain + 24 + 31 404 - IPR003311
AUX/IAA protein - 28 - 45 + IPR002293
Amino acid/polyamine transporter I + 24 + 39 405 - IPR000595
  - 28 - 358 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 24 + 52 406 - IPR017884
  - 27 - 84 + IPR027923
Hydrophobic seed protein domain + 24 + 54 407 - IPR000727
  - 27 - 142 + IPR001701
Glycoside hydrolase family 9 + 24 + 30 408 - IPR017938
Riboflavin synthase-like beta-barrel - 27 - 43 + IPR000679
Zinc finger, GATA-type + 24 + 100 409 - IPR004141
Strictosidine synthase - 27 - 33 + IPR015797
NUDIX hydrolase-like domain superfamily + 24 + 35 410 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 27 - 81 + IPR010525
Auxin response factor domain + 24 + 41 411 - IPR001357
  - 27 - 500 + IPR001929
Germin + 23 + 80 412 - IPR000717
  - 27 - 156 + IPR001360
Glycoside hydrolase family 1 + 23 + 395 413 - IPR000795
  - 27 - 738 + IPR013581
Plant PDR ABC transporter associated + 23 + 42 414 - IPR007650
  - 27 - 118 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 23 + 30 415 - IPR033124
Serine carboxypeptidases, histidine active site - 27 - 49 + IPR003337
Trehalose-phosphatase + 23 + 31 416 - IPR005150
Cellulose synthase - 27 - 58 + IPR020946
Flavin monooxygenase-like + 23 + 38 417 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 48 + IPR029062
Class I glutamine amidotransferase-like + 23 + 41 418 - IPR002963
Expansin - 27 - 217 + IPR017923
Transcription factor IIS, N-terminal + 23 + 73 419 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 27 - 41 + IPR006594
LIS1 homology motif + 22 + 66 420 - IPR014722
  - 27 - 84 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 64 421 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 27 - 51 + IPR006195
Aminoacyl-tRNA synthetase, class II + 22 + 29 422 - IPR001906
Terpene synthase, N-terminal domain - 27 - 29 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 22 + 79 423 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 27 - 29 + IPR001440
Tetratricopeptide repeat 1 + 22 + 36 424 - IPR000757
  - 27 - 204 + IPR003347
JmjC domain + 22 + 69 425 - IPR017927
  - 26 - 105 + IPR025422
Transcription factor TGA like domain + 22 + 82 426 - IPR000528
Plant lipid transfer protein/Par allergen - 26 - 119 + IPR008963
Purple acid phosphatase-like, N-terminal + 22 + 30 427 - IPR000782
  - 26 - 182 + IPR002939
Chaperone DnaJ, C-terminal + 22 + 32 428 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 26 - 52 + IPR036404
Jacalin-like lectin domain superfamily + 22 + 31 429 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 26 - 30 + IPR035441
TFIIS/LEDGF domain superfamily + 22 + 37 430 - IPR024709
Putative O-fucosyltransferase, plant - 26 - 78 + IPR029033
Histidine phosphatase superfamily + 22 + 35 431 - IPR013088
  - 26 - 114 + IPR001099
Chalcone/stilbene synthase, N-terminal + 22 + 23 432 - IPR008422
Homeobox KN domain - 26 - 29 + IPR004274
FCP1 homology domain + 22 + 75 433 - IPR029061
Thiamin diphosphate-binding fold - 26 - 71 + IPR006689
Small GTPase superfamily, ARF/SAR type + 21 + 130 434 - IPR001594
Palmitoyltransferase, DHHC domain - 26 - 41 + IPR003106
Leucine zipper, homeobox-associated + 21 + 21 435 - IPR002355
Multicopper oxidase, copper-binding site - 26 - 36 + IPR006593
Cytochrome b561/ferric reductase transmembrane + 21 + 44 436 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 26 - 89 + IPR035952
Rhomboid-like superfamily + 21 + 26 437 - IPR000863
Sulfotransferase domain - 26 - 39 + IPR036873
Rhodanese-like domain superfamily + 21 + 29 438 - IPR023313
Ubiquitin-conjugating enzyme, active site - 26 - 32 + IPR044815
Serine/threonine-protein kinase-like protein CCR3/CCR4 + 21 + 41 439 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 26 - 27 + IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain + 21 + 29 440 - IPR001077
O-methyltransferase, family 2 - 26 - 37 + IPR044778
Sugar transport protein STP/MST-like, plant + 21 + 32 441 - IPR005746
Thioredoxin - 26 - 40 + IPR036186
Serpin superfamily + 21 + 38 442 - IPR001849
  - 26 - 194 + IPR018392
LysM domain + 21 + 67 443 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 26 - 32 + IPR005333
Transcription factor, TCP + 21 + 27 444 - IPR003855
Potassium transporter - 26 - 118 + IPR005516
Remorin, C-terminal + 21 + 31 445 - IPR005175
  - 26 - 152 + IPR001881
EGF-like calcium-binding domain + 21 + 53 446 - IPR036085
PAZ domain superfamily - 25 - 85 + IPR017887
Transcription factor TCP subgroup + 21 + 47 447 - IPR015940
  - 25 - 218 + IPR004320
Protein of unknown function DUF241, plant + 21 + 46 448 - IPR013601
FAE1/Type III polyketide synthase-like protein - 25 + IPR036010
2Fe-2S ferredoxin-like superfamily + 21 27 449 - IPR016461
  - 25 - 177 + IPR006694
Fatty acid hydroxylase + 21 + 37 450 - IPR010920
LSM domain superfamily - 25 - 44 + IPR033905
Secretory peroxidase + 21 + 33 451 - IPR007657
Glycosyltransferase 61 - 25 - 79 + IPR016897
S-phase kinase-associated protein 1 + 21 + 31 452 - IPR027725
Heat shock transcription factor family - 25 - 31 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 21 + 33 453 - IPR001353
Proteasome, subunit alpha/beta - 25 - 28 + IPR001849
Pleckstrin homology domain + 21 + 59 454 - IPR011074
CRAL/TRIO, N-terminal domain - 25 - 67 + IPR039421
Type 1 protein exporter + 21 + 54 455 - IPR000408
  - 25 - 1328 + IPR016161
Aldehyde/histidinol dehydrogenase + 21 + 37 456 - IPR008266
Tyrosine-protein kinase, active site - 25 - 39 + IPR036427
Bromodomain-like superfamily + 21 + 31 457 - IPR011013
Galactose mutarotase-like domain superfamily - 25 - 48 + IPR000086
NUDIX hydrolase domain + 21 + 59 458 - IPR036866
  - 25 - 278 + IPR041792
Purple acid phosphatase, metallophosphatase domain + 21 + 28 459 - IPR036537
  - 25 - 96 + IPR010399
Tify domain + 21 + 69 460 - IPR004813
Oligopeptide transporter, OPT superfamily - 25 - 117 + IPR044730
Ribonuclease H-like domain, plant type + 21 + 23 461 - IPR025486
Domain of unknown function DUF4378 - 25 - 43 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 21 + 41 462 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 25 - 166 + IPR011141
Polyketide synthase, type III + 21 + 24 463 - IPR036034
PDZ superfamily - 25 - 37 + IPR023210
NADP-dependent oxidoreductase domain + 21 + 48 464 - IPR002913
  - 25 - 327 + IPR012967
Plant methyltransferase dimerisation + 21 + 28 465 - IPR003100
  - 24 - 444 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 21 + 26 466 - IPR017946
  - 24 - 273 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 21 + 44 467 - IPR002130
  - 24 - 720 + IPR023796
Serpin domain + 21 + 43 468 - IPR007612
LURP-one-related - 24 - 61 + IPR018119
Strictosidine synthase, conserved region + 21 + 24 469 - IPR029000
  - 24 - 176 + IPR006867
Domain of unknown function DUF632 + 21 + 32 470 - IPR025753
AAA-type ATPase, N-terminal domain - 24 - 28 + IPR002403
Cytochrome P450, E-class, group IV + 20 + 134 471 - IPR023753
FAD/NAD(P)-binding domain - 24 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 20 31 472 - IPR001763
  - 24 - 180 + IPR036893
SBP domain superfamily + 20 + 26 473 - IPR038595
  - 24 - 60 + IPR001163
LSM domain, eukaryotic/archaea-type + 20 + 27 474 - IPR002293
Amino acid/polyamine transporter I - 24 - 73 + IPR027413
GroEL-like equatorial domain superfamily + 20 + 23 475 - IPR000960
Flavin monooxygenase FMO - 24 - 85 + IPR011257
DNA glycosylase + 20 + 32 476 - IPR027923
Hydrophobic seed protein - 24 - 54 + IPR010989
SNARE + 20 + 25 477 - IPR031107
Small heat shock protein HSP20 - 24 - 26 + IPR045048
F-box only protein 31/39 + 20 + 72 478 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 24 - 58 + IPR000215
Serpin family + 20 + 41 479 - IPR001701
Glycoside hydrolase family 9 - 24 - 30 + IPR004333
SBP domain + 20 + 52 480 - IPR029006
  - 24 - 218 + IPR006015
Universal stress protein A family + 20 + 61 481 - IPR000679
  - 24 - 399 + IPR005018
DOMON domain + 20 + 39 482 - IPR015797
NUDIX hydrolase-like domain superfamily - 24 - 35 + IPR020103
Pseudouridine synthase, catalytic domain superfamily + 20 + 40 483 - IPR010525
Auxin response factor - 24 - 41 + IPR003165
Piwi domain + 20 + 105 484 - IPR003106
Leucine zipper, homeobox-associated - 23 - 34 + IPR011004
Trimeric LpxA-like superfamily + 20 + 30 485 - IPR001929
Germin - 23 - 80 + IPR029069
HotDog domain superfamily + 20 + 46 486 - IPR001360
Glycoside hydrolase family 1 - 23 - 398 + IPR015914
Purple acid phosphatase, N-terminal + 20 + 27 487 - IPR036873
  - 23 - 132 + IPR006868
Domain of unknown function DUF630 + 20 + 30 488 - IPR003954
RNA recognition motif domain, eukaryote - 23 - 52 + IPR002641
Patatin-like phospholipase domain + 20 + 60 489 - IPR013581
Plant PDR ABC transporter associated - 23 - 42 + IPR000836
Phosphoribosyltransferase domain + 20 + 50 490 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 23 - 28 + IPR044066
TRIAD supradomain + 20 + 37 491 - IPR012675
  - 23 - 56 + IPR001487
Bromodomain + 20 + 161 492 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 23 - 61 + IPR013809
ENTH domain + 20 + 32 493 - IPR003337
Trehalose-phosphatase - 23 - 54 + IPR002937
Amine oxidase + 20 + 35 494 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 23 - 40 + IPR044817
Squamosa promoter-binding-like protein + 20 + 28 495 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 23 - 28 + IPR015590
Aldehyde dehydrogenase domain + 20 + 39 496 - IPR016167
  - 23 - 129 + IPR001229
Jacalin-like lectin domain + 20 + 58 497 - IPR020946
Flavin monooxygenase-like - 23 - 38 + IPR004000
Actin family + 19 + 171 498 - IPR033443
Pentacotripeptide-repeat region of PRORP - 23 - 50 + IPR002867
IBR domain + 19 + 57 499 - IPR029062
  - 23 - 174 + IPR016064
NAD kinase/diacylglycerol kinase-like domain superfamily + 19 + 34 500 - IPR017923
  - 23 - 219 + IPR004316
SWEET sugar transporter + 19 + 44 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_aus.html b/gramene/htdocs/ssi/species/stats_Oryza_aus.html new file mode 100644 index 00000000..5bbea977 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_aus.html @@ -0,0 +1,181 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OsN22RS2, Jan 2020
Database version:87.2
Base Pairs:388,175,468
Golden Path Length:388,175,468
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,319
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,131
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
142787722
237316900
338991741
434943064
530810063
631706320
729491485
829456214
924344104
1024739695
1131893087
1226473654
+
+
scaffold
+
93 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg56222058
UN-Ctg57211407
UN-Ctg58173819
UN-Ctg59159409
UN-Ctg60136213
UN-Ctg61132210
UN-Ctg62120029
UN-Ctg63119394
UN-Ctg64114669
UN-Ctg65107302
UN-Ctg6699253
UN-Ctg6792754
UN-Ctg6891482
UN-Ctg6983988
UN-Ctg7081969
UN-Ctg7181735
UN-Ctg7279778
UN-Ctg7378090
UN-Ctg7477423
UN-Ctg7575500
UN-Ctg7670438
UN-Ctg7769082
UN-Ctg7866630
UN-Ctg7963950
UN-Ctg8062766
UN-Ctg8162189
UN-Ctg8261860
UN-Ctg8356127
UN-Ctg8455280
UN-Ctg8554708
UN-Ctg8653762
UN-Ctg8752425
UN-Ctg8852256
UN-Ctg8951852
UN-Ctg9050953
UN-Ctg9150914
UN-Ctg9250128
UN-Ctg9349923
UN-Ctg9449570
UN-Ctg9549149
UN-Ctg9648796
UN-Ctg9748535
UN-Ctg9848298
UN-Ctg9948168
UN-Ctg10047015
UN-Ctg10145630
UN-Ctg10245551
UN-Ctg10345436
UN-Ctg10445280
UN-Ctg10544973
UN-Ctg10644691
UN-Ctg10742339
UN-Ctg10841301
UN-Ctg10940412
UN-Ctg11040102
UN-Ctg11139394
UN-Ctg11238344
UN-Ctg11338333
UN-Ctg11436491
UN-Ctg11535576
UN-Ctg11635228
UN-Ctg11735416
UN-Ctg11834985
UN-Ctg11934961
UN-Ctg12034727
UN-Ctg12133956
UN-Ctg12233760
UN-Ctg12332963
UN-Ctg12432813
UN-Ctg12532416
UN-Ctg12631496
UN-Ctg12730931
UN-Ctg12831086
UN-Ctg12930710
UN-Ctg13028954
UN-Ctg13128356
UN-Ctg13226436
UN-Ctg13326276
UN-Ctg13425736
UN-Ctg13525372
UN-Ctg13625048
UN-Ctg13724790
UN-Ctg13823895
UN-Ctg13923385
UN-Ctg14023270
UN-Ctg14122831
UN-Ctg14222479
UN-Ctg14320132
UN-Ctg14419580
UN-Ctg14519199
UN-Ctg14613765
UN-Ctg14710026
UN-Ctg1489332
+
+
chunk3940 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):19,343,353
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		15012058
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14172132
3IPR000719
Protein kinase domain		13993194
4IPR036047
F-box-like domain superfamily		667831
5IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		527880
6IPR044974
Disease resistance protein, plants		511880
7IPR002885
Pentatricopeptide repeat		4996350
8IPR001611
Leucine-rich repeat		4821562
9IPR001810
F-box domain		480875
10IPR002182
NB-ARC		474563
11IPR001841
Zinc finger, RING-type		428895
12IPR016024
Armadillo-type fold		388647
13IPR009057
Homeobox-like domain superfamily		386506
14IPR036291
NAD(P)-binding domain superfamily		372561
15IPR029058
Alpha/Beta hydrolase fold		372513
16IPR041118
Rx, N-terminal		369416
17IPR011990
Tetratricopeptide-like helical domain superfamily		347526
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		328417
19IPR036396
Cytochrome P450 superfamily		323424
20IPR001128
Cytochrome P450		3161488
21IPR035979
RNA-binding domain superfamily		303610
22IPR000504
RNA recognition motif domain		2681145
23IPR002401
Cytochrome P450, E-class, group I		2671813
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		263410
25IPR017853
Glycoside hydrolase superfamily		258387
26IPR036259
MFS transporter superfamily		255403
27IPR038005
Virus X resistance protein-like, coiled-coil domain		251280
28IPR038765
Papain-like cysteine peptidase superfamily		239288
29IPR017930
Myb domain		239736
30IPR036322
WD40-repeat-containing domain superfamily		237365
31IPR001005
SANT/Myb domain		237724
32IPR036249
Thioredoxin-like superfamily		232341
33IPR001680
WD40 repeat		2131739
34IPR011992
EF-hand domain pair		189254
35IPR036770
Ankyrin repeat-containing domain superfamily		185260
36IPR002048
EF-hand domain		177963
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		176403
38IPR016177
DNA-binding domain superfamily		171235
39IPR002110
Ankyrin repeat		170693
40IPR036412
HAD-like superfamily		169225
41IPR036638
Helix-loop-helix DNA-binding domain superfamily		167203
42IPR012337
Ribonuclease H-like superfamily		160202
43IPR011333
SKP1/BTB/POZ domain superfamily		158239
44IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		157348
45IPR036390
Winged helix DNA-binding domain superfamily		156207
46IPR001471
AP2/ERF domain		155815
47IPR036093
NAC domain superfamily		151175
48IPR003441
NAC domain		147336
49IPR020683
Ankyrin repeat-containing domain		142289
50IPR029044
Nucleotide-diphospho-sugar transferases		141181
51IPR012340
Nucleic acid-binding, OB-fold		140264
52IPR010255
Haem peroxidase superfamily		140182
53IPR001650
Helicase, C-terminal		139394
54IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		139163
55IPR036236
Zinc finger C2H2 superfamily		138198
56IPR014001
Helicase superfamily 1/2, ATP-binding domain		137205
57IPR002016
Haem peroxidase		136630
58IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		135179
59IPR013087
Zinc finger C2H2-type		133247
60IPR036188
FAD/NAD(P)-binding domain superfamily		131239
61IPR005174
Domain unknown function DUF295		129151
62IPR003439
ABC transporter-like, ATP-binding domain		128504
63IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		125185
64IPR000210
BTB/POZ domain		122376
65IPR003480
Transferase		118141
66IPR036426
Bulb-type lectin domain superfamily		117156
67IPR021109
Aspartic peptidase domain superfamily		114148
68IPR001480
Bulb-type lectin domain		114397
69IPR020846
Major facilitator superfamily domain		114154
70IPR003959
ATPase, AAA-type, core		113167
71IPR001087
GDSL lipase/esterase		111136
72IPR007658
Protein of unknown function DUF594		111118
73IPR036869
Chaperone J-domain superfamily		111148
74IPR025315
Domain of unknown function DUF4220		110119
75IPR019734
Tetratricopeptide repeat		109324
76IPR008972
Cupredoxin		108222
77IPR011011
Zinc finger, FYVE/PHD-type		107156
78IPR001623
DnaJ domain		106737
79IPR033121
Peptidase family A1 domain		103147
80IPR003657
WRKY domain		103272
81IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		103118
82IPR036576
WRKY domain superfamily		102137
83IPR015424
Pyridoxal phosphate-dependent transferase		102139
84IPR029071
Ubiquitin-like domain superfamily		101160
85IPR035892
C2 domain superfamily		100187
86IPR032799
Xylanase inhibitor, C-terminal		97121
87IPR044810
WRKY transcription factor, plant		96126
88IPR005123
Oxoglutarate/iron-dependent dioxygenase		95136
89IPR045005
BTB/POZ and MATH domain-containing protein 1-6		95165
90IPR011050
Pectin lyase fold/virulence factor		94107
91IPR032861
Xylanase inhibitor, N-terminal		94118
92IPR011051
RmlC-like cupin domain superfamily		94118
93IPR036457
PPM-type phosphatase domain superfamily		93132
94IPR003609
PAN/Apple domain		93225
95IPR011676
Domain of unknown function DUF1618		93120
96IPR015300
DNA-binding pseudobarrel domain superfamily		92154
97IPR005828
Major facilitator, sugar transporter-like		91144
98IPR001932
PPM-type phosphatase domain		91379
99IPR000858
S-locus glycoprotein domain		90117
100IPR001356
Homeobox domain		90284
101IPR000823
Plant peroxidase		90377
102IPR000008
C2 domain		89396
103IPR026961
PGG domain		89177
104IPR011545
DEAD/DEAH box helicase domain		89134
105IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		88127
106IPR009072
Histone-fold		8898
107IPR035669
GDSL lipase/esterase-like, plant		86101
108IPR002083
MATH/TRAF domain		86290
109IPR000073
Alpha/beta hydrolase fold-1		86243
110IPR036875
Zinc finger, CCHC-type superfamily		86104
111IPR002347
Short-chain dehydrogenase/reductase SDR		85761
112IPR020472
G-protein beta WD-40 repeat		82384
113IPR026992
Non-haem dioxygenase N-terminal domain		82118
114IPR003340
B3 DNA binding domain		81380
115IPR013766
Thioredoxin domain		81183
116IPR004827
Basic-leucine zipper domain		81206
117IPR001461
Aspartic peptidase A1 family		80272
118IPR001878
Zinc finger, CCHC-type		80168
119IPR000109
Proton-dependent oligopeptide transporter family		79303
120IPR012871
Protein of unknown function DUF1677, Oryza sativa		7896
121IPR031052
FHY3/FAR1 family		78150
122IPR003653
Ulp1 protease family, C-terminal catalytic domain		78146
123IPR004158
Protein of unknown function DUF247, plant		78206
124IPR043129
ATPase, nucleotide binding domain		77194
125IPR036282
Glutathione S-transferase, C-terminal domain superfamily		74107
126IPR008949
Isoprenoid synthase domain superfamily		7390
127IPR003613
U box domain		73158
128IPR016039
Thiolase-like		71158
129IPR002100
Transcription factor, MADS-box		71405
130IPR036163
Heavy metal-associated domain superfamily		71100
131IPR036879
Transcription factor, MADS-box superfamily		7188
132IPR004330
FAR1 DNA binding domain		7179
133IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		71120
134IPR006121
Heavy metal-associated domain, HMA		70236
135IPR000270
PB1 domain		69118
136IPR024788
Malectin-like domain		6989
137IPR016159
Cullin repeat-like-containing domain superfamily		6883
138IPR007527
Zinc finger, SWIM-type		67114
139IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6670
140IPR002902
Gnk2-homologous domain		66327
141IPR004045
Glutathione S-transferase, N-terminal		66200
142IPR001220
Legume lectin domain		66162
143IPR036908
RlpA-like domain superfamily		6481
144IPR044965
Glycoside hydrolase family 17, plant		6492
145IPR029052
Metallo-dependent phosphatase-like		6489
146IPR000626
Ubiquitin-like domain		63161
147IPR019787
Zinc finger, PHD-finger		63143
148IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6369
149IPR013057
Amino acid transporter, transmembrane domain		6388
150IPR036915
Cyclin-like superfamily		63146
151IPR000571
Zinc finger, CCCH-type		63283
152IPR000048
IQ motif, EF-hand binding site		63348
153IPR036749
Expansin, cellulose-binding-like domain superfamily		6277
154IPR018108
Mitochondrial substrate/solute carrier		62471
155IPR023395
Mitochondrial carrier domain superfamily		6284
156IPR010987
Glutathione S-transferase, C-terminal-like		6292
157IPR009003
Peptidase S1, PA clan		62101
158IPR001806
Small GTPase		62140
159IPR020568
Ribosomal protein S5 domain 2-type fold		61103
160IPR003663
Sugar/inositol transporter		61358
161IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6085
162IPR005202
Transcription factor GRAS		60224
163IPR007117
Expansin, cellulose-binding-like domain		60148
164IPR026057
PC-Esterase		5987
165IPR003245
Phytocyanin domain		59123
166IPR036852
Peptidase S8/S53 domain superfamily		5989
167IPR006501
Pectinesterase inhibitor domain		5962
168IPR000490
Glycoside hydrolase family 17		5979
169IPR015915
Kelch-type beta propeller		5985
170IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5878
171IPR002156
Ribonuclease H domain		5877
172IPR039391
Phytocyanin		5867
173IPR029962
Trichome birefringence-like family		5789
174IPR045051
Subtilisin-like protease		56109
175IPR022059
Protein of unknown function DUF3615		5672
176IPR006045
Cupin 1		5689
177IPR000209
Peptidase S8/S53 domain		5686
178IPR025846
PMR5 N-terminal domain		5575
179IPR041469
Subtilisin-like protease, fibronectin type-III domain		5482
180IPR013525
ABC-2 type transporter		54111
181IPR007112
Expansin/pollen allergen, DPBB domain		5468
182IPR002921
Fungal lipase-like domain		5362
183IPR002528
Multi antimicrobial extrusion protein		53127
184IPR036465
von Willebrand factor A-like domain superfamily		5375
185IPR013094
Alpha/beta hydrolase fold-3		5371
186IPR001752
Kinesin motor domain		53455
187IPR000225
Armadillo		53226
188IPR001563
Peptidase S10, serine carboxypeptidase		52434
189IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5268
190IPR005630
Terpene synthase, metal-binding domain		5264
191IPR013763
Cyclin-like		52113
192IPR011032
GroES-like superfamily		5178
193IPR016181
Acyl-CoA N-acyltransferase		5160
194IPR009009
RlpA-like protein, double-psi beta-barrel domain		5164
195IPR023298
P-type ATPase, transmembrane domain superfamily		5175
196IPR003676
Small auxin-up RNA		5154
197IPR000608
Ubiquitin-conjugating enzyme E2		50201
198IPR008250
P-type ATPase, A domain superfamily		5066
199IPR013201
Cathepsin propeptide inhibitor domain (I29)		5054
200IPR006566
FBD domain		5060
201IPR030184
WAT1-related protein		5084
202IPR008978
HSP20-like chaperone		4963
203IPR004140
Exocyst complex component Exo70		49139
204IPR008979
Galactose-binding-like domain superfamily		4987
205IPR015500
Peptidase S8, subtilisin-related		49162
206IPR044808
Ethylene-responsive transcription factor		4956
207IPR045087
Multicopper oxidase		4867
208IPR001906
Terpene synthase, N-terminal domain		4862
209IPR000620
EamA domain		48111
210IPR017884
SANT domain		4765
211IPR036640
ABC transporter type 1, transmembrane domain superfamily		47105
212IPR007118
Expansin/Lol pI		47297
213IPR034161
Pepsin-like domain, plant		4759
214IPR011527
ABC transporter type 1, transmembrane domain		47209
215IPR041569
AAA ATPase, AAA+ lid domain		4770
216IPR009060
UBA-like superfamily		4671
217IPR011701
Major facilitator superfamily		4669
218IPR000873
AMP-dependent synthetase/ligase		4671
219IPR029055
Nucleophile aminohydrolases, N-terminal		4663
220IPR033905
Secretory peroxidase		4652
221IPR008928
Six-hairpin glycosidase superfamily		4661
222IPR036855
Zinc finger, CCCH-type superfamily		46111
223IPR001117
Multicopper oxidase, type 1		4552
224IPR036318
FAD-binding, type PCMH-like superfamily		4553
225IPR004853
Sugar phosphate transporter domain		4578
226IPR009000
Translation protein, beta-barrel domain superfamily		4565
227IPR034197
Cucumisin-like catalytic domain		4566
228IPR011706
Multicopper oxidase, C-terminal		4552
229IPR006671
Cyclin, N-terminal		4566
230IPR032867
DYW domain		4547
231IPR033896
MADS MEF2-like		4461
232IPR014014
RNA helicase, DEAD-box type, Q motif		4463
233IPR012946
X8 domain		4458
234IPR011006
CheY-like superfamily		4458
235IPR007125
Histone H2A/H2B/H3		4446
236IPR000742
EGF-like domain		4448
237IPR014756
Immunoglobulin E-set		4471
238IPR044730
Ribonuclease H-like domain, plant type		4445
239IPR008889
VQ		4445
240IPR011707
Multicopper oxidase, N-termianl		4449
241IPR000182
GNAT domain		4385
242IPR001509
NAD-dependent epimerase/dehydratase		4364
243IPR004263
Exostosin-like		4353
244IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4361
245IPR001214
SET domain		43103
246IPR001789
Signal transduction response regulator, receiver domain		4392
247IPR006016
UspA		4254
248IPR016461
O-methyltransferase COMT-type		4291
249IPR004265
Dirigent protein		4251
250IPR029045
ClpP/crotonase-like domain superfamily		4262
251IPR000070
Pectinesterase, catalytic		4252
252IPR024752
Myb/SANT-like domain		4244
253IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4250
254IPR033389
AUX/IAA domain		4156
255IPR010402
CCT domain		41102
256IPR043926
ABC transporter family G domain		4170
257IPR000330
SNF2, N-terminal		4167
258IPR036612
K Homology domain, type 1 superfamily		41111
259IPR000668
Peptidase C1A, papain C-terminal		41160
260IPR000743
Glycoside hydrolase, family 28		4150
261IPR016040
NAD(P)-binding domain		4063
262IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4061
263IPR011012
Longin-like domain superfamily		4071
264IPR011043
Galactose oxidase/kelch, beta-propeller		4047
265IPR015947
PUA-like superfamily		4053
266IPR006702
Casparian strip membrane protein domain		4042
267IPR025322
Protein of unknown function DUF4228, plant		3941
268IPR004046
Glutathione S-transferase, C-terminal		3953
269IPR002495
Glycosyl transferase, family 8		3950
270IPR039361
Cyclin		3959
271IPR037176
Osmotin/thaumatin-like superfamily		3944
272IPR002068
Alpha crystallin/Hsp20 domain		3893
273IPR029021
Protein-tyrosine phosphatase-like		3861
274IPR003137
PA domain		3847
275IPR016166
FAD-binding domain, PCMH-type		3846
276IPR015655
Protein phosphatase 2C family		3866
277IPR039417
Papain-like cysteine endopeptidase		3844
278IPR040911
Exostosin, GT47 domain		3844
279IPR002109
Glutaredoxin		3846
280IPR008942
ENTH/VHS		3752
281IPR025659
Tubby-like, C-terminal		3747
282IPR001938
Thaumatin family		37251
283IPR004839
Aminotransferase, class I/classII		3752
284IPR004883
Lateral organ boundaries, LOB		3779
285IPR001077
O-methyltransferase domain		3744
286IPR000644
CBS domain		37163
287IPR013126
Heat shock protein 70 family		37104
288IPR002912
ACT domain		3797
289IPR004041
NAF domain		3645
290IPR007493
Protein of unknown function DUF538		3678
291IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3640
292IPR013154
Alcohol dehydrogenase, N-terminal		3645
293IPR043454
NPH3/RPT2-like family		3660
294IPR036758
At5g01610-like superfamily		3640
295IPR019378
GDP-fucose protein O-fucosyltransferase		3651
296IPR002067
Mitochondrial carrier protein		36228
297IPR018451
NAF/FISL domain		3544
298IPR023271
Aquaporin-like		3547
299IPR022742
Serine aminopeptidase, S33		3543
300IPR000425
Major intrinsic protein		35305
301IPR002487
Transcription factor, K-box		35105
302IPR001360
Glycoside hydrolase family 1		34371
303IPR004367
Cyclin, C-terminal domain		3441
304IPR006652
Kelch repeat type 1		3479
305IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3449
306IPR004088
K Homology domain, type 1		3497
307IPR006094
FAD linked oxidase, N-terminal		3442
308IPR028889
Ubiquitin specific protease domain		3446
309IPR043519
Nucleotidyltransferase superfamily		3460
310IPR001251
CRAL-TRIO lipid binding domain		33133
311IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3349
312IPR005135
Endonuclease/exonuclease/phosphatase		3346
313IPR000795
Translational (tr)-type GTP-binding domain		33268
314IPR036865
CRAL-TRIO lipid binding domain superfamily		3345
315IPR004314
Neprosin		3338
316IPR012967
Plant methyltransferase dimerisation		3334
317IPR006311
Twin-arginine translocation pathway, signal sequence		3335
318IPR013149
Alcohol dehydrogenase, C-terminal		3241
319IPR038933
Ovate protein family		3233
320IPR034294
Aquaporin transporter		3251
321IPR000863
Sulfotransferase domain		3242
322IPR006458
Ovate protein family, C-terminal		3262
323IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3261
324IPR018490
Cyclic nucleotide-binding-like		3140
325IPR032710
NTF2-like domain superfamily		3136
326IPR000315
B-box-type zinc finger		3184
327IPR001296
Glycosyl transferase, family 1		3158
328IPR027356
NPH3 domain		3187
329IPR003690
Transcription termination factor, mitochondrial/chloroplastic		31106
330IPR027923
Hydrophobic seed protein domain		3171
331IPR033443
Pentacotripeptide-repeat region of PRORP		3138
332IPR036041
Ribosome-inactivating protein superfamily		3135
333IPR011141
Polyketide synthase, type III		3138
334IPR006073
GTP binding domain		31112
335IPR001099
Chalcone/stilbene synthase, N-terminal		3137
336IPR015940
Ubiquitin-associated domain		3090
337IPR001929
Germin		3099
338IPR005299
SAM dependent carboxyl methyltransferase		3096
339IPR008991
Translation protein SH3-like domain superfamily		3045
340IPR044835
Auxin response factor		3058
341IPR044822
Myb/SANT-like DNA-binding domain 4		3041
342IPR000717
Proteasome component (PCI) domain		3074
343IPR029061
Thiamin diphosphate-binding fold		3082
344IPR035940
CAP superfamily		3041
345IPR002423
Chaperonin Cpn60/TCP-1 family		3044
346IPR045048
F-box only protein 31/39		3054
347IPR003406
Glycosyl transferase, family 14		3036
348IPR003851
Zinc finger, Dof-type		3068
349IPR003855
Potassium transporter		30125
350IPR001574
Ribosome-inactivating protein		3065
351IPR006153
Cation/H+ exchanger		2938
352IPR029000
Cyclophilin-like domain superfamily		2942
353IPR001594
Palmitoyltransferase, DHHC domain		2947
354IPR011013
Galactose mutarotase-like domain superfamily		2941
355IPR005150
Cellulose synthase		2957
356IPR001283
Cysteine-rich secretory protein-related		29113
357IPR027409
GroEL-like apical domain superfamily		2939
358IPR023299
P-type ATPase, cytoplasmic domain N		2940
359IPR012328
Chalcone/stilbene synthase, C-terminal		2930
360IPR000595
Cyclic nucleotide-binding domain		2995
361IPR001223
Glycoside hydrolase family 18, catalytic domain		2968
362IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28237
363IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		2898
364IPR024709
Putative O-fucosyltransferase, plant		2843
365IPR010920
LSM domain superfamily		2837
366IPR044848
PHR1-like		2843
367IPR005333
Transcription factor, TCP		2831
368IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2838
369IPR002963
Expansin		28240
370IPR008480
Protein of unknown function DUF761, plant		2828
371IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2842
372IPR003311
AUX/IAA protein		2842
373IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2836
374IPR000727
Target SNARE coiled-coil homology domain		2750
375IPR013601
FAE1/Type III polyketide synthase-like protein		2736
376IPR036378
FAS1 domain superfamily		2740
377IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2738
378IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2796
379IPR002659
Glycosyl transferase, family 31		2795
380IPR007650
Zf-FLZ domain		2774
381IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2736
382IPR003337
Trehalose-phosphatase		2735
383IPR002123
Phospholipid/glycerol acyltransferase		2729
384IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2737
385IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2742
386IPR005821
Ion transport domain		2736
387IPR014044
CAP domain		2734
388IPR001701
Glycoside hydrolase family 9		2736
389IPR044791
Beta-glucanase/XTH		2742
390IPR000757
Glycoside hydrolase family 16		2774
391IPR005175
PPC domain		2789
392IPR002913
START domain		2790
393IPR025110
AMP-binding enzyme, C-terminal domain		2634
394IPR017938
Riboflavin synthase-like beta-barrel		2637
395IPR029466
No apical meristem-associated, C-terminal domain		2628
396IPR044778
Sugar transport protein STP/MST-like, plant		2630
397IPR036420
BRCT domain superfamily		2643
398IPR001881
EGF-like calcium-binding domain		2636
399IPR004320
Protein of unknown function DUF241, plant		2632
400IPR001763
Rhodanese-like domain		2665
401IPR000408
Regulator of chromosome condensation, RCC1		26661
402IPR036273
CRAL/TRIO, N-terminal domain superfamily		2634
403IPR004014
Cation-transporting P-type ATPase, N-terminal		2638
404IPR004813
Oligopeptide transporter, OPT superfamily		2656
405IPR029062
Class I glutamine amidotransferase-like		2649
406IPR036812
NADP-dependent oxidoreductase domain superfamily		2644
407IPR000679
Zinc finger, GATA-type		26105
408IPR015797
NUDIX hydrolase-like domain superfamily		2635
409IPR000528
Plant non-specific lipid-transfer protein/Par allergen		25148
410IPR036085
PAZ domain superfamily		2542
411IPR004316
SWEET sugar transporter		2544
412IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2532
413IPR001357
BRCT domain		2572
414IPR036186
Serpin superfamily		2535
415IPR040417
Glycine-rich cell wall structural protein 1/2		2535
416IPR007657
Glycosyltransferase 61		2571
417IPR027725
Heat shock transcription factor family		2532
418IPR044839
Protein NDR1-like		2526
419IPR002035
von Willebrand factor, type A		2564
420IPR001757
P-type ATPase		25123
421IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2534
422IPR036034
PDZ superfamily		2533
423IPR002937
Amine oxidase		2537
424IPR023796
Serpin domain		2543
425IPR010525
Auxin response factor domain		2538
426IPR017927
FAD-binding domain, ferredoxin reductase-type		2436
427IPR000782
FAS1 domain		2464
428IPR008971
HSP40/DnaJ peptide-binding		2461
429IPR013187
F-box associated domain, type 3		2430
430IPR008422
Homeobox KN domain		2429
431IPR023753
FAD/NAD(P)-binding domain		2437
432IPR026960
Reverse transcriptase zinc-binding domain		2424
433IPR009030
Growth factor receptor cysteine-rich domain superfamily		2432
434IPR016897
S-phase kinase-associated protein 1		2433
435IPR034285
Laccase, second cupredoxin domain		2427
436IPR001849
Pleckstrin homology domain		2458
437IPR002939
Chaperone DnaJ, C-terminal		2434
438IPR036296
SKP1-like, dimerisation domain superfamily		2432
439IPR036427
Bromodomain-like superfamily		2435
440IPR025486
Domain of unknown function DUF4378		2442
441IPR000086
NUDIX hydrolase domain		2464
442IPR000232
Heat shock factor (HSF)-type, DNA-binding		24105
443IPR023210
NADP-dependent oxidoreductase domain		2448
444IPR029033
Histidine phosphatase superfamily		2429
445IPR003100
PAZ domain		2379
446IPR003106
Leucine zipper, homeobox-associated		2323
447IPR002867
IBR domain		2344
448IPR000387
Tyrosine specific protein phosphatases domain		2340
449IPR001440
Tetratricopeptide repeat 1		2334
450IPR021790
PTBP1, RNA recognition motif 2-like		2331
451IPR013581
Plant PDR ABC transporter associated		2332
452IPR011016
Zinc finger, RING-CH-type		2382
453IPR001163
LSM domain, eukaryotic/archaea-type		2330
454IPR013216
Methyltransferase type 11		2332
455IPR018392
LysM domain		2381
456IPR001353
Proteasome, subunit alpha/beta		2331
457IPR003594
Histidine kinase/HSP90-like ATPase		2334
458IPR020103
Pseudouridine synthase, catalytic domain superfamily		2333
459IPR016072
SKP1 component, dimerisation		2330
460IPR007592
GLABROUS1 enhancer-binding protein family		2350
461IPR039421
Type 1 protein exporter		2341
462IPR029069
HotDog domain superfamily		2353
463IPR036404
Jacalin-like lectin domain superfamily		2335
464IPR036392
PLAT/LH2 domain superfamily		2325
465IPR001487
Bromodomain		23172
466IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2332
467IPR006689
Small GTPase superfamily, ARF/SAR type		22143
468IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2233
469IPR002403
Cytochrome P450, E-class, group IV		22123
470IPR025753
AAA-type ATPase, N-terminal domain		2225
471IPR019557
Aminotransferase-like, plant mobile domain		2225
472IPR017887
Transcription factor TCP subgroup		2246
473IPR036010
2Fe-2S ferredoxin-like superfamily		2226
474IPR044675
E3 ubiquitin-protein ligase RING1-like		2226
475IPR000215
Serpin family		2239
476IPR021720
Malectin domain		2241
477IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2232
478IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2224
479IPR020946
Flavin monooxygenase-like		2242
480IPR041679
DNA2/NAM7 helicase-like, C-terminal		2258
481IPR041677
DNA2/NAM7 helicase, helicase domain		2240
482IPR016161
Aldehyde/histidinol dehydrogenase		2237
483IPR031127
E3 ubiquitin ligase RBR family		2245
484IPR006868
Domain of unknown function DUF630		2225
485IPR044066
TRIAD supradomain		2228
486IPR035952
Rhomboid-like superfamily		2128
487IPR007612
LURP-one-related		2152
488IPR036873
Rhodanese-like domain superfamily		2131
489IPR003347
JmjC domain		2144
490IPR012416
CALMODULIN-BINDING PROTEIN60		2165
491IPR000340
Dual specificity phosphatase, catalytic domain		2138
492IPR005516
Remorin, C-terminal		2126
493IPR027413
GroEL-like equatorial domain superfamily		2129
494IPR025422
Transcription factor TGA like domain		2148
495IPR010989
SNARE		2123
496IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2133
497IPR002293
Amino acid/polyamine transporter I		2137
498IPR004252
Probable transposase, Ptta/En/Spm, plant		2127
499IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2133
500IPR020422
Dual specificity protein phosphatase domain		2134
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_barthii.html b/gramene/htdocs/ssi/species/stats_Oryza_barthii.html index 21b2c425..be87e7ab 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_barthii.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_barthii.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:O.barthii_v1, Apr 2014AGI_PacBIO, Jul 2018
Database version:93.387.4
Base Pairs:308,272,304347,715,970
Golden Path Length:308,272,304347,715,970
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: May 2014
Genebuild version: 2014-05-OGE
+ Genebuild by: CSHL Genebuild method: Imported from OGE MAKER annotation Genebuild started: Jul 2018 Genebuild version: 2018-07-CSHL

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):34,575Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		40,481
Gene transcriptsHASH(0x68ce400):44,891Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:50,335
@@ -37,38 +37,69 @@

Coordinate Systems

chromosome
-
12 sequences
+
51 sequences
+1
SequenceLength (bp)
136915442
231686972
333311619
427574323
524206129
625711811
724128185
822678724
919219615
1019274048
1123014695
1220550741
40334623
235048755
335242676
431651462
526101924
628978289
727336505
825358699
921309684
1021777534
1127108482
1224666841
UN-Ctg46257872
UN-Ctg47147837
UN-Ctg48136788
UN-Ctg49116299
UN-Ctg50112779
UN-Ctg51111671
UN-Ctg52100749
UN-Ctg5398486
UN-Ctg5496606
UN-Ctg5594846
UN-Ctg5680252
UN-Ctg5778563
UN-Ctg5876998
UN-Ctg5975269
UN-Ctg6073233
UN-Ctg6173074
UN-Ctg6271326
UN-Ctg6367265
UN-Ctg6465897
UN-Ctg6563534
UN-Ctg6662300
UN-Ctg6761378
UN-Ctg6851349
UN-Ctg6949076
UN-Ctg7048752
UN-Ctg7148404
UN-Ctg7244069
UN-Ctg7343843
UN-Ctg7443713
UN-Ctg7542423
UN-Ctg7642351
UN-Ctg7740592
UN-Ctg7838136
UN-Ctg7935934
UN-Ctg8035589
UN-Ctg8133221
UN-Ctg8230242
UN-Ctg8325193
UN-Ctg8424587
-
+
chunk - 3090 sequences + 3503 sequences - -

Other

- - - - - -
FGENESH gene predictions:43,127
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop500.html index b8f75f21..077a886c 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_barthii_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1393 - 2237 + 1498 + 2190 2 - IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1349 - 2514 + IPR000719
Protein kinase domain + 1423 + 3459 3 - IPR000719
  - 1319 - 14592 + IPR027417
P-loop containing nucleoside triphosphate hydrolase + 1409 + 2329 4 - IPR032675
  - 1211 - 6476 + IPR036047
F-box-like domain superfamily + 714 + 928 5 - IPR008271
Serine/threonine-protein kinase, active site - 1041 - 1554 + IPR001810
F-box domain + 511 + 990 6 - IPR017441
Protein kinase, ATP binding site - 883 - 1283 + IPR044974
Disease resistance protein, plants + 509 + 949 7 - IPR011990
  - 709 - 10404 + IPR002885
Pentatricopeptide repeat + 497 + 7308 8 - IPR013083
  - 608 - 1720 + IPR001611
Leucine-rich repeat + 496 + 1774 9 - IPR036047
F-box-like domain superfamily - 570 - 847 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 479 + 974 10 - IPR002885
  - 484 - 27624 + IPR002182
NB-ARC + 462 + 611 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 461 - 953 + IPR001841
Zinc finger, RING-type + 447 + 886 12 - IPR002182
NB-ARC - 457 - 626 + IPR009057
Homeobox-like domain superfamily + 397 + 513 13 - IPR001611
  - 453 - 11637 + IPR036291
NAD(P)-binding domain superfamily + 396 + 601 14 - IPR001810
  - 427 - 4050 + IPR029058
Alpha/Beta hydrolase fold + 391 + 570 15 - IPR036291
NAD(P)-binding domain superfamily - 376 - 613 + IPR016024
Armadillo-type fold + 386 + 645 16 - IPR001841
  - 366 - 2312 + IPR041118
Rx, N-terminal + 371 + 480 17 - IPR016024
Armadillo-type fold - 360 - 1303 + IPR011990
Tetratricopeptide-like helical domain superfamily + 353 + 602 18 - IPR029058
  - 357 - 2232 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 344 + 466 19 - IPR003591
Leucine-rich repeat, typical subtype - 330 - 3028 + IPR036396
Cytochrome P450 superfamily + 335 + 451 20 - IPR009057
Homeobox-like domain superfamily - 322 - 420 + IPR001128
Cytochrome P450 + 328 + 1596 21 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 302 - 432 + IPR035979
RNA-binding domain superfamily + 314 + 612 22 - IPR036396
  - 299 - 2772 + IPR002401
Cytochrome P450, E-class, group I + 280 + 2109 23 - IPR035979
RNA-binding domain superfamily - 289 - 548 + IPR017853
Glycoside hydrolase superfamily + 278 + 375 24 - IPR001128
Cytochrome P450 - 288 - 1470 + IPR000504
RNA recognition motif domain + 277 + 1176 25 - IPR012677
  - 279 - 1150 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 270 + 418 26 - IPR003593
AAA+ ATPase domain - 261 - 512 + IPR036259
MFS transporter superfamily + 264 + 391 27 - IPR017853
Glycoside hydrolase superfamily - 261 - 427 + IPR012337
Ribonuclease H-like superfamily + 259 + 339 28 - IPR000504
  - 257 - 4500 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 254 + 317 29 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 250 - 456 + IPR001005
SANT/Myb domain + 250 + 809 30 - IPR036259
MFS transporter superfamily - 240 - 653 + IPR017930
Myb domain + 247 + 781 31 - IPR011989
  - 239 - 942 + IPR036249
Thioredoxin-like superfamily + 236 + 375 32 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 239 - 300 + IPR036322
WD40-repeat-containing domain superfamily + 233 + 360 33 - IPR002401
Cytochrome P450, E-class, group I - 237 - 1701 + IPR038765
Papain-like cysteine peptidase superfamily + 232 + 327 34 - IPR015943
  - 235 - 1590 + IPR001680
WD40 repeat + 213 + 1655 35 - IPR017972
Cytochrome P450, conserved site - 235 - 327 + IPR011992
EF-hand domain pair + 192 + 253 36 - IPR036249
Thioredoxin-like superfamily - 231 - 341 + IPR016177
DNA-binding domain superfamily + 191 + 266 37 - IPR036322
WD40-repeat-containing domain superfamily - 231 - 551 + IPR002048
EF-hand domain + 182 + 993 38 - IPR001680
  - 220 - 9768 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 182 + 410 39 - IPR001005
SANT/Myb domain - 215 - 839 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 177 + 219 40 - IPR017986
  - 201 - 1020 + IPR036770
Ankyrin repeat-containing domain superfamily + 176 + 254 41 - IPR011992
EF-hand domain pair - 193 - 261 + IPR001471
AP2/ERF domain + 173 + 953 42 - IPR038765
Papain-like cysteine peptidase superfamily - 192 - 329 + IPR011333
SKP1/BTB/POZ domain superfamily + 169 + 241 43 - IPR002048
  - 176 - 4311 + IPR036412
HAD-like superfamily + 169 + 245 44 - IPR036388
  - 172 - 442 + IPR043502
DNA/RNA polymerase superfamily + 166 + 191 45 - IPR020846
  - 171 - 904 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 166 + 358 46 - IPR036412
HAD-like superfamily - 164 - 316 + IPR002110
Ankyrin repeat + 163 + 649 47 - IPR018247
EF-Hand 1, calcium-binding site - 163 - 429 + IPR036390
Winged helix DNA-binding domain superfamily + 160 + 203 48 - IPR017930
  - 163 - 530 + IPR036236
Zinc finger C2H2 superfamily + 159 + 215 49 - IPR036638
  - 158 - 1089 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 152 + 185 50 - IPR011333
SKP1/BTB/POZ domain superfamily - 158 - 257 + IPR021109
Aspartic peptidase domain superfamily + 152 + 176 51 - IPR023214
  - 155 - 670 + IPR036093
NAC domain superfamily + 152 + 167 52 - IPR036390
Winged helix DNA-binding domain superfamily - 155 - 191 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 148 + 171 53 - IPR020683
  - 150 - 1670 + IPR005174
Domain unknown function DUF295 + 148 + 169 54 - IPR036770
  - 150 - 1188 + IPR003441
NAC domain + 147 + 317 55 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 148 - 198 + IPR010255
Haem peroxidase superfamily + 145 + 182 56 - IPR011598
  - 148 - 1848 + IPR029044
Nucleotide-diphospho-sugar transferases + 143 + 197 57 - IPR014001
  - 145 - 846 + IPR013087
Zinc finger C2H2-type + 143 + 257 58 - IPR001650
  - 144 - 1658 + IPR002016
Haem peroxidase + 143 + 1024 59 - IPR013087
  - 144 - 2361 + IPR001650
Helicase, C-terminal + 141 + 425 60 - IPR029044
  - 142 - 932 + IPR012340
Nucleic acid-binding, OB-fold + 140 + 292 61 - IPR036093
  - 140 - 885 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 139 + 218 62 - IPR002110
  - 140 - 4896 + IPR020683
Ankyrin repeat-containing domain + 132 + 277 63 - IPR016177
DNA-binding domain superfamily - 138 - 189 + IPR003439
ABC transporter-like, ATP-binding domain + 132 + 569 64 - IPR003441
  - 137 - 864 + IPR036188
FAD/NAD(P)-binding domain superfamily + 130 + 235 65 - IPR036188
  - 137 - 1408 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 129 + 223 66 - IPR019775
WD40 repeat, conserved site - 134 - 335 + IPR000210
BTB/POZ domain + 128 + 362 67 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 132 - 162 + IPR000823
Plant peroxidase + 126 + 1106 68 - IPR013026
  - 129 - 690 + IPR036875
Zinc finger, CCHC-type superfamily + 123 + 176 69 - IPR019734
  - 128 - 3813 + IPR036426
Bulb-type lectin domain superfamily + 121 + 200 70 - IPR000210
  - 123 - 1548 + IPR003480
Transferase + 121 + 152 71 - IPR023213
  - 123 - 490 + IPR001878
Zinc finger, CCHC-type + 120 + 364 72 - IPR036236
Zinc finger C2H2 superfamily - 122 - 230 + IPR036869
Chaperone J-domain superfamily + 116 + 151 73 - IPR014729
  - 121 - 424 + IPR033905
Secretory peroxidase + 115 + 137 74 - IPR003439
  - 121 - 1773 + IPR001480
Bulb-type lectin domain + 115 + 527 75 - IPR001471
  - 120 - 2358 + IPR020846
Major facilitator superfamily domain + 115 + 152 76 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 119 - 135 + IPR003959
ATPase, AAA-type, core + 115 + 178 77 - IPR036955
  - 118 - 447 + IPR011676
Domain of unknown function DUF1618 + 114 + 146 78 - IPR012340
Nucleic acid-binding, OB-fold - 118 - 235 + IPR029071
Ubiquitin-like domain superfamily + 114 + 178 79 - IPR036514
  - 113 - 322 + IPR019734
Tetratricopeptide repeat + 112 + 370 80 - IPR003959
ATPase, AAA-type, core - 113 - 165 + IPR001623
DnaJ domain + 112 + 746 81 - IPR036869
  - 113 - 560 + IPR001087
GDSL lipase/esterase + 110 + 144 82 - IPR014710
  - 112 - 368 + IPR033121
Peptidase family A1 domain + 109 + 131 83 - IPR008974
  - 111 - 1026 + IPR011011
Zinc finger, FYVE/PHD-type + 108 + 187 84 - IPR021109
  - 109 - 838 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 107 + 134 85 - IPR036426
  - 108 - 892 + IPR025315
Domain of unknown function DUF4220 + 107 + 117 86 - IPR011011
Zinc finger, FYVE/PHD-type - 107 - 164 + IPR036576
WRKY domain superfamily + 105 + 137 87 - IPR015424
Pyridoxal phosphate-dependent transferase - 107 - 147 + IPR008972
Cupredoxin + 105 + 218 88 - IPR001623
  - 106 - 1644 + IPR003657
WRKY domain + 105 + 274 89 - IPR013785
  - 105 - 543 + IPR011050
Pectin lyase fold/virulence factor + 104 + 113 90 - IPR005174
Domain unknown function DUF295 - 105 - 123 + IPR015424
Pyridoxal phosphate-dependent transferase + 103 + 136 91 - IPR001461
Aspartic peptidase A1 family - 105 - 321 + IPR007658
Protein of unknown function DUF594 + 102 + 107 92 - IPR005123
  - 103 - 756 + IPR032799
Xylanase inhibitor, C-terminal + 102 + 119 93 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 103 - 176 + IPR032861
Xylanase inhibitor, N-terminal + 102 + 123 94 - IPR015421
  - 102 - 417 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 102 + 178 95 - IPR001480
  - 102 - 1030 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 101 + 125 96 - IPR003480
Transferase - 102 - 144 + IPR035892
C2 domain superfamily + 100 + 199 97 - IPR008972
  - 101 - 846 + IPR044810
WRKY transcription factor, plant + 98 + 114 98 - IPR005225
Small GTP-binding protein domain - 101 - 127 + IPR015300
DNA-binding pseudobarrel domain superfamily + 98 + 179 99 - IPR025315
Domain of unknown function DUF4220 - 101 - 110 + IPR036457
PPM-type phosphatase domain superfamily + 97 + 166 100 - IPR011050
Pectin lyase fold/virulence factor - 100 - 114 + IPR002083
MATH/TRAF domain + 96 + 338 101 - IPR029071
Ubiquitin-like domain superfamily - 100 - 142 + IPR001356
Homeobox domain + 96 + 306 102 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 99 - 183 + IPR009072
Histone-fold + 95 + 106 103 - IPR012334
  - 99 - 230 + IPR003609
PAN/Apple domain + 94 + 298 104 - IPR027443
  - 98 - 274 + IPR001932
PPM-type phosphatase domain + 94 + 466 105 - IPR036576
  - 97 - 750 + IPR035669
GDSL lipase/esterase-like, plant + 93 + 112 106 - IPR011676
Domain of unknown function DUF1618 - 97 - 131 + IPR002347
Short-chain dehydrogenase/reductase SDR + 93 + 887 107 - IPR003657
  - 97 - 1122 + IPR000477
Reverse transcriptase domain + 92 + 159 108 - IPR033121
  - 95 - 252 + IPR000109
Proton-dependent oligopeptide transporter family + 91 + 279 109 - IPR035595
UDP-glycosyltransferase family, conserved site - 94 - 111 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 91 + 113 110 - IPR036457
  - 94 - 670 + IPR011545
DEAD/DEAH box helicase domain + 90 + 138 111 - IPR009072
  - 94 - 597 + IPR000073
Alpha/beta hydrolase fold-1 + 89 + 258 112 - IPR007658
Protein of unknown function DUF594 - 93 - 96 + IPR011051
RmlC-like cupin domain superfamily + 89 + 117 113 - IPR002083
  - 93 - 1209 + IPR005828
Major facilitator, sugar transporter-like + 88 + 130 114 - IPR015300
  - 93 - 692 + IPR003340
B3 DNA binding domain + 87 + 471 115 - IPR012337
Ribonuclease H-like superfamily - 92 - 165 + IPR000858
S-locus glycoprotein domain + 87 + 150 116 - IPR001087
GDSL lipase/esterase - 91 - 114 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 87 + 104 117 - IPR011051
RmlC-like cupin domain superfamily - 91 - 144 + IPR000008
C2 domain + 86 + 412 118 - IPR001932
  - 91 - 1695 + IPR032867
DYW domain + 85 + 91 119 - IPR032867
DYW domain - 90 - 102 + IPR007527
Zinc finger, SWIM-type + 85 + 152 120 - IPR015422
  - 89 - 519 + IPR004827
Basic-leucine zipper domain + 85 + 229 121 - IPR035892
  - 88 - 346 + IPR020472
G-protein beta WD-40 repeat + 84 + 375 122 - IPR003609
  - 88 - 806 + IPR026992
Non-haem dioxygenase N-terminal domain + 83 + 99 123 - IPR015655
Protein phosphatase 2C family - 88 - 151 + IPR001461
Aspartic peptidase A1 family + 82 + 260 124 - IPR001356
  - 88 - 1137 + IPR000270
PB1 domain + 82 + 129 125 - IPR011545
DEAD/DEAH box helicase domain - 87 - 124 + IPR013766
Thioredoxin domain + 81 + 225 126 - IPR004827
  - 87 - 1236 + IPR003613
U box domain + 80 + 191 127 - IPR000109
Proton-dependent oligopeptide transporter family - 86 - 345 + IPR000626
Ubiquitin-like domain + 78 + 199 128 - IPR002347
Short-chain dehydrogenase/reductase SDR - 86 - 756 + IPR002100
Transcription factor, MADS-box + 78 + 466 129 - IPR035669
GDSL lipase/esterase-like, plant - 85 - 116 + IPR036879
Transcription factor, MADS-box superfamily + 78 + 104 130 - IPR000858
S-locus glycoprotein domain - 85 - 145 + IPR026961
PGG domain + 77 + 170 131 - IPR032799
Xylanase inhibitor, C-terminal - 85 - 113 + IPR036163
Heavy metal-associated domain superfamily + 77 + 106 132 - IPR017871
ABC transporter, conserved site - 85 - 162 + IPR004158
Protein of unknown function DUF247, plant + 77 + 175 133 - IPR000008
  - 84 - 912 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 77 + 106 134 - IPR005828
Major facilitator, sugar transporter-like - 84 - 152 + IPR043129
ATPase, nucleotide binding domain + 76 + 196 135 - IPR006447
Myb domain, plants - 83 - 97 + IPR001220
Legume lectin domain + 76 + 166 136 - IPR032861
Xylanase inhibitor, N-terminal - 83 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 75 106 137 - IPR003340
  - 82 - 1863 + IPR006121
Heavy metal-associated domain, HMA + 74 + 254 138 - IPR024171
S-receptor-like serine/threonine-protein kinase - 82 - 124 + IPR002156
Ribonuclease H domain + 74 + 106 139 - IPR020472
G-protein beta WD-40 repeat - 80 - 372 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 74 + 76 140 - IPR000073
Alpha/beta hydrolase fold-1 - 80 - 198 + IPR018289
MULE transposase domain + 74 + 78 141 - IPR001965
Zinc finger, PHD-type - 80 - 166 + IPR008949
Isoprenoid synthase domain superfamily + 73 + 105 142 - IPR000742
  - 79 - 606 + IPR000571
Zinc finger, CCCH-type + 72 + 285 143 - IPR000270
  - 77 - 489 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 72 + 138 144 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 76 - 98 + IPR002902
Gnk2-homologous domain + 71 + 374 145 - IPR036397
  - 76 - 399 + IPR016039
Thiolase-like + 69 + 134 146 - IPR013766
  - 76 - 531 + IPR004045
Glutathione S-transferase, N-terminal + 69 + 202 147 - IPR017907
Zinc finger, RING-type, conserved site - 76 - 109 + IPR019787
Zinc finger, PHD-finger + 67 + 185 148 - IPR002100
  - 75 - 1803 + IPR005202
Transcription factor GRAS + 67 + 213 149 - IPR036879
  - 74 - 591 + IPR036908
RlpA-like domain superfamily + 67 + 85 150 - IPR008949
  - 73 - 524 + IPR010987
Glutathione S-transferase, C-terminal-like + 67 + 94 151 - IPR026961
PGG domain - 72 - 163 + IPR044965
Glycoside hydrolase family 17, plant + 67 + 93 152 - IPR036163
Heavy metal-associated domain superfamily - 72 - 94 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 66 + 75 153 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 72 - 108 + IPR016159
Cullin repeat-like-containing domain superfamily + 66 + 87 154 - IPR006121
  - 70 - 690 + IPR007117
Expansin, cellulose-binding-like domain + 66 + 147 155 - IPR016039
  - 70 - 795 + IPR001806
Small GTPase + 65 + 150 156 - IPR013783
  - 70 - 206 + IPR018108
Mitochondrial substrate/solute carrier + 64 + 467 157 - IPR001220
Legume lectin domain - 70 - 147 + IPR022059
Protein of unknown function DUF3615 + 64 + 82 158 - IPR034090
BPM, C-terminal - 69 - 125 + IPR013057
Amino acid transporter, transmembrane domain + 64 + 90 159 - IPR026992
Non-haem dioxygenase N-terminal domain - 68 - 86 + IPR020568
Ribosomal protein S5 domain 2-type fold + 64 + 90 160 - IPR036961
  - 68 - 450 + IPR023395
Mitochondrial carrier domain superfamily + 64 + 86 161 - IPR004045
  - 68 - 594 + IPR006501
Pectinesterase inhibitor domain + 64 + 66 162 - IPR000571
  - 68 - 1299 + IPR029052
Metallo-dependent phosphatase-like + 64 + 84 163 - IPR013057
Amino acid transporter, transmembrane domain - 67 - 103 + IPR000490
Glycoside hydrolase family 17 + 64 + 78 164 - IPR036908
  - 67 - 306 + IPR024788
Malectin-like domain + 64 + 90 165 - IPR000225
  - 66 - 1710 + IPR026960
Reverse transcriptase zinc-binding domain + 63 + 66 166 - IPR003960
ATPase, AAA-type, conserved site - 65 - 81 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 63 + 70 167 - IPR004158
Protein of unknown function DUF247, plant - 65 - 76 + IPR000048
IQ motif, EF-hand binding site + 63 + 375 168 - IPR003613
  - 65 - 681 + IPR036852
Peptidase S8/S53 domain superfamily + 62 + 86 169 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 65 - 173 + IPR013094
Alpha/beta hydrolase fold-3 + 62 + 71 170 - IPR006566
FBD domain - 64 - 114 + IPR000209
Peptidase S8/S53 domain + 62 + 83 171 - IPR010255
Haem peroxidase - 64 - 95 + IPR031052
FHY3/FAR1 family + 61 + 111 172 - IPR000626
  - 63 - 618 + IPR036915
Cyclin-like superfamily + 61 + 140 173 - IPR020568
Ribosomal protein S5 domain 2-type fold - 63 - 97 + IPR001584
Integrase, catalytic core + 60 + 98 174 - IPR010987
  - 63 - 192 + IPR045051
Subtilisin-like protease + 60 + 93 175 - IPR000490
Glycoside hydrolase family 17 - 63 - 116 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 60 + 100 176 - IPR018097
EGF-like calcium-binding, conserved site - 62 - 101 + IPR002528
Multi antimicrobial extrusion protein + 60 + 153 177 - IPR001881
EGF-like calcium-binding domain - 61 - 142 + IPR011032
GroES-like superfamily + 59 + 94 178 - IPR018108
  - 61 - 820 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 59 + 78 179 - IPR023395
  - 61 - 348 + IPR001563
Peptidase S10, serine carboxypeptidase + 59 + 506 180 - IPR002016
  - 61 - 1107 + IPR003663
Sugar/inositol transporter + 59 + 348 181 - IPR016159
Cullin repeat-like-containing domain superfamily - 61 - 96 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 58 + 70 182 - IPR000048
  - 61 - 1179 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 57 + 70 183 - IPR001806
Small GTPase superfamily - 61 - 77 + IPR007112
Expansin/pollen allergen, DPBB domain + 57 + 66 184 - IPR013128
Peptidase C1A - 60 - 97 + IPR006566
FBD domain + 57 + 74 185 - IPR019787
  - 60 - 300 + IPR003245
Phytocyanin domain + 56 + 132 186 - IPR038408
  - 60 - 324 + IPR030184
WAT1-related protein + 56 + 87 187 - IPR002902
  - 60 - 646 + IPR009003
Peptidase S1, PA clan + 56 + 98 188 - IPR035513
  - 59 - 226 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 55 + 70 189 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 59 - 68 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 55 + 65 190 - IPR016135
  - 59 - 428 + IPR039391
Phytocyanin + 55 + 66 191 - IPR005829
Sugar transporter, conserved site - 59 - 132 + IPR001752
Kinesin motor domain + 55 + 471 192 - IPR008979
  - 59 - 380 + IPR000620
EamA domain + 55 + 125 193 - IPR011993
  - 59 - 160 + IPR015500
Peptidase S8, subtilisin-related + 55 + 197 194 - IPR017451
F-box associated interaction domain - 58 - 79 + IPR000225
Armadillo + 55 + 225 195 - IPR036749
  - 58 - 288 + IPR026057
PC-Esterase + 54 + 73 196 - IPR022059
Protein of unknown function DUF3615 - 58 - 85 + IPR034161
Pepsin-like domain, plant + 54 + 56 197 - IPR030184
WAT1-related protein - 58 - 98 + IPR006045
Cupin 1 + 54 + 92 198 - IPR007117
  - 58 - 284 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 54 + 57 199 - IPR026057
PC-Esterase - 57 - 76 + IPR008978
HSP20-like chaperone + 53 + 61 200 - IPR024788
Malectin-like carbohydrate-binding domain - 57 - 95 + IPR029962
Trichome birefringence-like family + 53 + 76 201 - IPR011032
GroES-like superfamily - 56 - 93 + IPR001509
NAD-dependent epimerase/dehydratase + 53 + 80 202 - IPR029962
Trichome birefringence-like family - 56 - 83 + IPR008979
Galactose-binding-like domain superfamily + 53 + 95 203 - IPR027640
Kinesin-like protein - 56 - 125 + IPR025846
PMR5 N-terminal domain + 53 + 70 204 - IPR001563
Peptidase S10, serine carboxypeptidase - 55 - 528 + IPR001906
Terpene synthase, N-terminal domain + 53 + 68 205 - IPR023393
  - 55 - 146 + IPR003676
Small auxin-up RNA + 53 + 61 206 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 55 - 514 + IPR016181
Acyl-CoA N-acyltransferase + 52 + 70 207 - IPR019786
Zinc finger, PHD-type, conserved site - 55 - 77 + IPR013525
ABC-2 type transporter + 52 + 120 208 - IPR003245
  - 55 - 567 + IPR007118
Expansin/Lol pI + 52 + 317 209 - IPR002528
Multi antimicrobial extrusion protein - 55 - 235 + IPR034197
Cucumisin-like catalytic domain + 52 + 64 210 - IPR006045
Cupin 1 - 55 - 166 + IPR015915
Kelch-type beta propeller + 52 + 65 211 - IPR015915
  - 55 - 405 + IPR004330
FAR1 DNA binding domain + 52 + 64 212 - IPR001752
  - 55 - 1545 + IPR005630
Terpene synthase, metal-binding domain + 51 + 64 213 - IPR007112
  - 54 - 236 + IPR013763
Cyclin-like + 51 + 106 214 - IPR036915
Cyclin-like superfamily - 54 - 128 + IPR002921
Fungal lipase-like domain + 50 + 66 215 - IPR036852
  - 53 - 1023 + IPR017884
SANT domain + 50 + 67 216 - IPR000620
EamA domain - 53 - 123 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 50 + 120 217 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 52 - 79 + IPR000608
Ubiquitin-conjugating enzyme E2 + 50 + 196 218 - IPR018253
DnaJ domain, conserved site - 52 - 65 + IPR011701
Major facilitator superfamily + 50 + 77 219 - IPR005202
  - 52 - 226 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 50 + 99 220 - IPR029052
  - 52 - 182 + IPR011527
ABC transporter type 1, transmembrane domain + 50 + 240 221 - IPR000209
Peptidase S8/S53 domain - 52 - 82 + IPR036465
von Willebrand factor A-like domain superfamily + 50 + 77 222 - IPR008978
  - 51 - 220 + IPR023298
P-type ATPase, transmembrane domain superfamily + 50 + 86 223 - IPR001509
NAD-dependent epimerase/dehydratase - 51 - 84 + IPR044808
Ethylene-responsive transcription factor + 50 + 53 224 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 51 - 59 + IPR008906
HAT, C-terminal dimerisation domain + 49 + 52 225 - IPR005630
Terpene synthase, metal-binding domain - 51 - 87 + IPR004140
Exocyst complex component Exo70 + 49 + 123 226 - IPR014014
  - 51 - 136 + IPR004265
Dirigent protein + 49 + 54 227 - IPR025846
PMR5 N-terminal domain - 51 - 58 + IPR008928
Six-hairpin glycosidase superfamily + 49 + 63 228 - IPR006501
Pectinesterase inhibitor domain - 51 - 133 + IPR000668
Peptidase C1A, papain C-terminal + 49 + 194 229 - IPR003663
Sugar/inositol transporter - 51 - 371 + IPR008250
P-type ATPase, A domain superfamily + 48 + 78 230 - IPR016181
Acyl-CoA N-acyltransferase - 50 - 61 + IPR006016
UspA + 47 + 55 231 - IPR036640
  - 50 - 705 + IPR005162
Retrotransposon gag domain + 47 + 49 232 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 50 - 107 + IPR007125
Histone H2A/H2B/H3 + 47 + 49 233 - IPR036465
  - 50 - 232 + IPR045087
Multicopper oxidase + 47 + 56 234 - IPR009003
Peptidase S1, PA clan - 50 - 90 + IPR041569
AAA ATPase, AAA+ lid domain + 47 + 74 235 - IPR023298
P-type ATPase, transmembrane domain superfamily - 50 - 189 + IPR036855
Zinc finger, CCCH-type superfamily + 47 + 111 236 - IPR036965
  - 49 - 303 + IPR001214
SET domain + 47 + 143 237 - IPR013525
ABC-2 type transporter - 49 - 125 + IPR033389
AUX/IAA domain + 46 + 63 238 - IPR007118
Expansin/Lol pI - 49 - 280 + IPR043926
ABC transporter family G domain + 46 + 80 239 - IPR036855
Zinc finger, CCCH-type superfamily - 49 - 110 + IPR029055
Nucleophile aminohydrolases, N-terminal + 46 + 63 240 - IPR000608
  - 48 - 352 + IPR009000
Translation protein, beta-barrel domain superfamily + 46 + 73 241 - IPR008928
Six-hairpin glycosidase superfamily - 48 - 66 + IPR014014
RNA helicase, DEAD-box type, Q motif + 46 + 59 242 - IPR011527
  - 48 - 717 + IPR012946
X8 domain + 46 + 59 243 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 47 - 66 + IPR011006
CheY-like superfamily + 46 + 68 244 - IPR000873
AMP-dependent synthetase/ligase - 47 - 75 + IPR000070
Pectinesterase, catalytic + 46 + 52 245 - IPR008250
P-type ATPase, A domain superfamily - 47 - 76 + IPR036318
FAD-binding, type PCMH-like superfamily + 45 + 56 246 - IPR013763
Cyclin-like - 47 - 176 + IPR000873
AMP-dependent synthetase/ligase + 45 + 79 247 - IPR023299
  - 47 - 363 + IPR004263
Exostosin-like + 45 + 58 248 - IPR001906
Terpene synthase, N-terminal domain - 47 - 81 + IPR014756
Immunoglobulin E-set + 45 + 71 249 - IPR013094
Alpha/beta hydrolase fold-3 - 47 - 61 + IPR000743
Glycoside hydrolase, family 28 + 45 + 50 250 - IPR037045
  - 47 - 130 + IPR009060
UBA-like superfamily + 44 + 58 251 - IPR019794
Peroxidase, active site - 46 - 65 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 44 + 72 252 - IPR033389
AUX/IAA domain - 45 - 66 + IPR004046
Glutathione S-transferase, C-terminal + 44 + 56 253 - IPR000222
PPM-type phosphatase, divalent cation binding - 45 - 71 + IPR011706
Multicopper oxidase, C-terminal + 44 + 50 254 - IPR004265
Dirigent protein - 45 - 50 + IPR006671
Cyclin, N-terminal + 44 + 61 255 - IPR018303
P-type ATPase, phosphorylation site - 45 - 59 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 127 256 - IPR014756
Immunoglobulin E-set - 45 - 72 + IPR016461
O-methyltransferase COMT-type + 43 + 89 257 - IPR015500
Peptidase S8, subtilisin-related - 45 - 168 + IPR011012
Longin-like domain superfamily + 43 + 59 258 - IPR001214
  - 45 - 531 + IPR011043
Galactose oxidase/kelch, beta-propeller + 43 + 47 259 - IPR001878
  - 45 - 831 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 43 + 55 260 - IPR000823
Plant peroxidase - 45 - 311 + IPR008889
VQ + 43 + 44 261 - IPR012341
  - 45 - 168 + IPR011707
Multicopper oxidase, N-termianl + 43 + 48 262 - IPR000743
Glycoside hydrolase, family 28 - 45 - 73 + IPR001117
Multicopper oxidase, type 1 + 42 + 48 263 - IPR002921
Fungal lipase-like domain - 44 - 54 + IPR000182
GNAT domain + 42 + 92 264 - IPR029055
  - 44 - 184 + IPR002068
Alpha crystallin/Hsp20 domain + 42 + 89 265 - IPR011006
CheY-like superfamily - 44 - 63 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 42 + 143 266 - IPR029021
  - 43 - 252 + IPR000742
EGF-like domain + 42 + 60 267 - IPR012946
X8 domain - 43 - 117 + IPR044730
Ribonuclease H-like domain, plant type + 42 + 46 268 - IPR004140
Exocyst complex component Exo70 - 43 - 117 + IPR015947
PUA-like superfamily + 42 + 53 269 - IPR003676
Small auxin-up RNA - 43 - 63 + IPR010402
CCT domain + 41 + 108 270 - IPR001789
  - 43 - 684 + IPR004853
Sugar phosphate transporter domain + 41 + 53 271 - IPR033896
MADS MEF2-like - 42 - 65 + IPR013149
Alcohol dehydrogenase, C-terminal + 41 + 55 272 - IPR004853
Sugar phosphate transporter domain - 42 - 46 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 41 + 49 273 - IPR036890
  - 42 - 252 + IPR004883
Lateral organ boundaries, LOB + 41 + 91 274 - IPR004046
Glutathione S-transferase, C-terminal - 42 - 55 + IPR001077
O-methyltransferase domain + 41 + 44 275 - IPR001757
P-type ATPase - 42 - 215 + IPR029045
ClpP/crotonase-like domain superfamily + 41 + 62 276 - IPR000070
Pectinesterase, catalytic - 42 - 52 + IPR039417
Papain-like cysteine endopeptidase + 41 + 55 277 - IPR014721
  - 42 - 116 + IPR024752
Myb/SANT-like domain + 41 + 43 278 - IPR009060
UBA-like superfamily - 41 + IPR016040
NAD(P)-binding domain + 40 57 279 - IPR000330
SNF2-related, N-terminal domain - 41 - 74 + IPR033896
MADS MEF2-like + 40 + 63 280 - IPR036612
  - 41 - 678 + IPR025659
Tubby-like, C-terminal + 40 + 53 281 - IPR001117
Multicopper oxidase, type 1 - 40 - 44 + IPR000330
SNF2, N-terminal + 40 + 71 282 - IPR006016
UspA - 40 - 44 + IPR036612
K Homology domain, type 1 superfamily + 40 + 129 283 - IPR025659
  - 40 - 192 + IPR016166
FAD-binding domain, PCMH-type + 40 + 51 284 - IPR001938
  - 40 - 544 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 40 + 58 285 - IPR011012
Longin-like domain superfamily - 40 - 67 + IPR028889
Ubiquitin specific protease domain + 40 + 58 286 - IPR007125
Histone H2A/H2B/H3 - 40 - 42 + IPR037176
Osmotin/thaumatin-like superfamily + 40 + 43 287 - IPR017970
Homeobox, conserved site - 40 - 45 + IPR025322
Protein of unknown function DUF4228, plant + 39 + 42 288 - IPR011706
Multicopper oxidase, type 2 - 40 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 39 45 289 - IPR000668
Peptidase C1A, papain C-terminal - 40 - 191 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 39 + 52 290 - IPR038718
  - 40 - 174 + IPR036041
Ribosome-inactivating protein superfamily + 39 + 40 291 - IPR000644
  - 40 - 550 + IPR002487
Transcription factor, K-box + 39 + 114 292 - IPR002109
  - 40 - 255 + IPR008942
ENTH/VHS + 38 + 47 293 - IPR002912
  - 40 - 242 + IPR001360
Glycoside hydrolase family 1 + 38 + 403 294 - IPR011042
  - 40 - 128 + IPR029021
Protein-tyrosine phosphatase-like + 38 + 65 295 - IPR000182
  - 39 - 142 + IPR001938
Thaumatin family + 38 + 259 296 - IPR016461
  - 39 - 246 + IPR004839
Aminotransferase, class I/classII + 38 + 53 297 - IPR006626
Parallel beta-helix repeat - 39 - 213 + IPR015655
Protein phosphatase 2C family + 38 + 89 298 - IPR002068
  - 39 - 158 + IPR000644
CBS domain + 38 + 188 299 - IPR004839
Aminotransferase, class I/classII - 39 - 53 + IPR039361
Cyclin + 38 + 58 300 - IPR001077
O-methyltransferase, family 2 - 39 - 44 + IPR002912
ACT domain + 38 + 114 301 - IPR029045
ClpP/crotonase-like domain superfamily - 39 - 80 + IPR001574
Ribosome-inactivating protein + 38 + 70 302 - IPR006671
Cyclin, N-terminal - 39 - 74 + IPR006702
Casparian strip membrane protein domain + 38 + 42 303 - IPR011707
Multicopper oxidase, type 3 - 39 + IPR004041
NAF domain + 37 43 304 - IPR008942
  - 38 - 196 + IPR007493
Protein of unknown function DUF538 + 37 + 84 305 - IPR036318
FAD-binding, type 2-like superfamily - 38 - 41 + IPR003137
PA domain + 37 + 51 306 - IPR011701
Major facilitator superfamily - 38 - 99 + IPR023271
Aquaporin-like + 37 + 44 307 - IPR009000
Translation protein, beta-barrel domain superfamily - 38 - 62 + IPR013154
Alcohol dehydrogenase, N-terminal + 37 + 44 308 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 38 - 65 + IPR043454
NPH3/RPT2-like family + 37 + 42 309 - IPR019378
GDP-fucose protein O-fucosyltransferase - 38 - 64 + IPR036758
At5g01610-like superfamily + 37 + 42 310 - IPR013780
  - 38 - 112 + IPR000425
Major intrinsic protein + 37 + 291 311 - IPR017877
  - 38 - 104 + IPR002495
Glycosyl transferase, family 8 + 37 + 48 312 - IPR004041
NAF domain - 37 - 41 + IPR040911
Exostosin, GT47 domain + 37 + 47 313 - IPR013149
Alcohol dehydrogenase, C-terminal - 37 - 46 + IPR002109
Glutaredoxin + 37 + 42 314 - IPR007493
Protein of unknown function DUF538 - 37 - 90 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 37 + 75 315 - IPR018451
  - 37 - 123 + IPR012967
Plant methyltransferase dimerisation + 37 + 37 316 - IPR034161
Pepsin-like domain, plant - 37 - 45 + IPR025525
hAT-like transposase, RNase-H fold + 36 + 41 317 - IPR028889
  - 37 - 110 + IPR018451
NAF/FISL domain + 36 + 42 318 - IPR002487
  - 37 - 354 + IPR003656
Zinc finger, BED-type + 36 + 70 319 - IPR010402
  - 36 - 243 + IPR019378
GDP-fucose protein O-fucosyltransferase + 36 + 63 320 - IPR036691
  - 36 - 316 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 35 + 56 321 - IPR003137
PA domain - 36 - 49 + IPR004332
Transposase, MuDR, plant + 35 + 35 322 - IPR036865
  - 36 - 182 + IPR019557
Aminotransferase-like, plant mobile domain + 35 + 46 323 - IPR034197
Cucumisin-like catalytic domain - 36 - 54 + IPR022742
Serine aminopeptidase, S33 + 35 + 42 324 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 36 - 55 + IPR006094
FAD linked oxidase, N-terminal + 35 + 40 325 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 36 - 55 + IPR002067
Mitochondrial carrier protein + 35 + 220 326 - IPR036758
  - 36 - 170 + IPR006458
Ovate protein family, C-terminal + 35 + 68 327 - IPR011043
Galactose oxidase/kelch, beta-propeller - 36 - 44 + IPR036404
Jacalin-like lectin domain superfamily + 35 + 63 328 - IPR015947
PUA-like superfamily - 36 - 48 + IPR043519
Nucleotidyltransferase superfamily + 35 + 54 329 - IPR006702
Casparian strip membrane protein domain - 36 - 38 + IPR001229
Jacalin-like lectin domain + 35 + 124 330 - IPR001251
  - 35 - 350 + IPR038933
Ovate protein family + 34 + 35 331 - IPR013154
Alcohol dehydrogenase, N-terminal - 35 - 49 + IPR027356
NPH3 domain + 34 + 72 332 - IPR036875
Zinc finger, CCHC-type superfamily - 35 - 63 + IPR025452
Domain of unknown function DUF4218 + 34 + 35 333 - IPR012967
Plant methyltransferase dimerisation - 35 - 36 + IPR034294
Aquaporin transporter + 34 + 44 334 - IPR001296
Glycosyl transferase, family 1 - 34 - 51 + IPR000863
Sulfotransferase domain + 34 + 48 335 - IPR004263
Exostosin-like - 34 - 47 + IPR013126
Heat shock protein 70 family + 34 + 87 336 - IPR023271
  - 34 - 194 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 117 337 - IPR027356
  - 34 - 132 + IPR001296
Glycosyl transferase, family 1 + 33 + 49 338 - IPR034294
Aquaporin transporter - 34 + IPR005135
Endonuclease/exonuclease/phosphatase + 33 54 339 - IPR003594
Histidine kinase/HSP90-like ATPase - 34 - 106 + IPR035940
CAP superfamily + 33 + 45 340 - IPR008266
Tyrosine-protein kinase, active site - 34 - 44 + IPR044814
Terpene cyclases, class 1, plant + 33 + 40 341 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 34 - 46 + IPR003311
AUX/IAA protein + 33 + 50 342 - IPR019793
Peroxidases heam-ligand binding site - 34 - 53 + IPR006073
GTP binding domain + 33 + 117 343 - IPR004883
  - 34 - 140 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 32 + 177 344 - IPR000425
Major intrinsic protein - 34 - 310 + IPR029466
No apical meristem-associated, C-terminal domain + 32 + 32 345 - IPR004088
K Homology domain, type 1 - 34 - 120 + IPR005299
SAM dependent carboxyl methyltransferase + 32 + 90 346 - IPR016040
NAD(P)-binding domain - 33 - 45 + IPR008991
Translation protein SH3-like domain superfamily + 32 + 41 347 - IPR031112
AP2-like ethylene-responsive transcription factor - 33 - 44 + IPR000795
Translational (tr)-type GTP-binding domain + 32 + 327 348 - IPR016166
  - 33 - 102 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 32 + 43 349 - IPR003653
  - 33 - 249 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 32 + 41 350 - IPR013126
Heat shock protein 70 family - 33 - 319 + IPR004367
Cyclin, C-terminal domain + 32 + 42 351 - IPR001360
Glycoside hydrolase family 1 - 32 - 476 + IPR006652
Kelch repeat type 1 + 32 + 62 352 - IPR019821
Kinesin motor domain, conserved site - 32 - 40 + IPR014044
CAP domain + 32 + 44 353 - IPR018200
Ubiquitin specific protease, conserved site - 32 - 70 + IPR004314
Neprosin + 32 + 53 354 - IPR038770
  - 32 - 84 + IPR000595
Cyclic nucleotide-binding domain + 32 + 115 355 - IPR020845
AMP-binding, conserved site - 32 - 50 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 32 + 48 356 - IPR031107
Small heat shock protein HSP20 - 32 - 37 + IPR013601
FAE1/Type III polyketide synthase-like protein + 31 + 34 357 - IPR022357
Major intrinsic protein, conserved site - 32 - 39 + IPR018490
Cyclic nucleotide-binding-like + 31 + 46 358 - IPR002495
Glycosyl transferase, family 8 - 32 - 44 + IPR032710
NTF2-like domain superfamily + 31 + 41 359 - IPR003311
AUX/IAA protein - 32 - 54 + IPR000717
Proteasome component (PCI) domain + 31 + 64 360 - IPR004314
Neprosin - 32 - 51 + IPR013216
Methyltransferase type 11 + 31 + 40 361 - IPR000595
  - 32 - 282 + IPR029061
Thiamin diphosphate-binding fold + 31 + 68 362 - IPR020843
Polyketide synthase, enoylreductase domain - 32 - 39 + IPR029480
Transposase-associated domain + 31 + 33 363 - IPR036041
Ribosome-inactivating protein superfamily - 32 - 38 + IPR003406
Glycosyl transferase, family 14 + 31 + 39 364 - IPR036812
  - 32 - 220 + IPR001283
Cysteine-rich secretory protein-related + 31 + 161 365 - IPR006073
GTP binding domain - 32 - 118 + IPR004088
K Homology domain, type 1 + 31 + 114 366 - IPR037176
  - 32 - 146 + IPR025724
GAG-pre-integrase domain + 31 + 31 367 - IPR015940
  - 31 - 222 + IPR002913
START domain + 31 + 88 368 - IPR018490
Cyclic nucleotide-binding-like - 31 - 42 + IPR015940
Ubiquitin-associated domain + 30 + 74 369 - IPR011016
  - 31 - 318 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 30 + 31 370 - IPR001969
Aspartic peptidase, active site - 31 - 54 + IPR001929
Germin + 30 + 95 371 - IPR033131
Pectinesterase, Asp active site - 31 - 34 + IPR029000
Cyclophilin-like domain superfamily + 30 + 38 372 - IPR000863
Sulfotransferase domain - 31 - 41 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 30 + 126 373 - IPR027409
  - 31 - 154 + IPR010920
LSM domain superfamily + 30 + 39 374 - IPR004087
K Homology domain - 31 - 119 + IPR000315
B-box-type zinc finger + 30 + 75 375 - IPR025661
Cysteine peptidase, asparagine active site - 31 - 36 + IPR001594
Palmitoyltransferase, DHHC domain + 30 + 44 376 - IPR003855
Potassium transporter - 31 - 121 + IPR002963
Expansin + 30 + 267 377 - IPR011141
Polyketide synthase, type III - 31 - 61 + IPR027409
GroEL-like apical domain superfamily + 30 + 39 378 - IPR023210
NADP-dependent oxidoreductase domain - 31 - 103 + IPR033443
Pentacotripeptide-repeat region of PRORP + 30 + 53 379 - IPR000717
  - 30 - 154 + IPR003851
Zinc finger, Dof-type + 30 + 60 380 - IPR029061
Thiamin diphosphate-binding fold - 30 - 61 + IPR004242
Transposon, En/Spm-like + 30 + 33 381 - IPR002423
Chaperonin Cpn60/TCP-1 family - 30 - 41 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 30 + 50 382 - IPR006652
Kelch repeat type 1 - 30 - 125 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 29 + 210 383 - IPR038538
  - 30 - 168 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 29 + 76 384 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 30 - 44 + IPR024709
Putative O-fucosyltransferase, plant + 29 + 59 385 - IPR002067
Mitochondrial carrier protein - 30 - 158 + IPR044835
Auxin response factor + 29 + 45 386 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 30 + IPR005333
Transcription factor, TCP + 29 32 387 - IPR000757
  - 30 - 204 + IPR002423
Chaperonin Cpn60/TCP-1 family + 29 + 39 388 - IPR001929
Germin - 29 - 94 + IPR007650
Zf-FLZ domain + 29 + 64 389 - IPR024709
Putative O-fucosyltransferase, plant - 29 - 102 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 390 - IPR027725
Heat shock transcription factor family - 29 - 43 + IPR027923
Hydrophobic seed protein domain + 29 + 67 391 - IPR004367
Cyclin, C-terminal domain - 29 - 69 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 29 + 47 392 - IPR022742
Serine aminopeptidase, S33 - 29 - 36 + IPR000679
Zinc finger, GATA-type + 29 + 95 393 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 29 - 408 + IPR000757
Glycoside hydrolase family 16 + 29 + 72 394 - IPR002035
  - 29 - 162 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 28 + 39 395 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 29 - 48 + IPR017938
Riboflavin synthase-like beta-barrel + 28 + 40 396 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 29 - 70 + IPR025312
Domain of unknown function DUF4216 + 28 + 28 397 - IPR036404
  - 29 - 198 + IPR002659
Glycosyl transferase, family 31 + 28 + 109 398 - IPR009091
  - 29 - 284 + IPR044848
PHR1-like + 28 + 43 399 - IPR008889
VQ - 29 - 31 + IPR005150
Cellulose synthase + 28 + 64 400 - IPR001099
Chalcone/stilbene synthase, N-terminal - 29 - 36 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 28 + 33 401 - IPR032710
NTF2-like domain superfamily - 28 - 41 + IPR005821
Ion transport domain + 28 + 37 402 - IPR002130
  - 28 - 558 + IPR001701
Glycoside hydrolase family 9 + 28 + 29 403 - IPR029000
  - 28 - 162 + IPR003855
Potassium transporter + 28 + 85 404 - IPR001179
  - 28 - 226 + IPR011141
Polyketide synthase, type III + 28 + 33 405 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 28 - 84 + IPR023210
NADP-dependent oxidoreductase domain + 28 + 58 406 - IPR008991
Translation protein SH3-like domain superfamily - 28 - 33 + IPR006311
Twin-arginine translocation pathway, signal sequence + 28 + 35 407 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 28 - 35 + IPR033734
Jacalin-like lectin domain, plant + 28 + 55 408 - IPR002659
Glycosyl transferase, family 31 - 28 - 83 + IPR000727
Target SNARE coiled-coil homology domain + 27 + 58 409 - IPR001594
Palmitoyltransferase, DHHC domain - 28 - 37 + IPR036378
FAS1 domain superfamily + 27 + 38 410 - IPR005135
Endonuclease/exonuclease/phosphatase - 28 + IPR006153
Cation/H+ exchanger + 27 39 411 - IPR035940
  - 28 - 154 + IPR027725
Heat shock transcription factor family + 27 + 33 412 - IPR000795
  - 28 - 840 + IPR001763
Rhodanese-like domain + 27 + 60 413 - IPR000408
  - 28 - 1388 + IPR000408
Regulator of chromosome condensation, RCC1 + 27 + 554 414 - IPR003406
Glycosyl transferase, family 14 - 28 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 27 30 415 - IPR033905
Secretory peroxidase - 28 - 50 + IPR011013
Galactose mutarotase-like domain superfamily + 27 + 43 416 - IPR008480
Protein of unknown function DUF761, plant - 28 - 28 + IPR004264
Transposase, Tnp1/En/Spm-like + 27 + 30 417 - IPR000169
Cysteine peptidase, cysteine active site - 28 - 35 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 27 + 33 418 - IPR036034
PDZ superfamily - 28 - 44 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 37 419 - IPR018202
Serine carboxypeptidase, serine active site - 28 - 38 + IPR039421
Type 1 protein exporter + 27 + 42 420 - IPR025322
Protein of unknown function DUF4228, plant - 27 - 33 + IPR023299
P-type ATPase, cytoplasmic domain N + 27 + 53 421 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 27 - 57 + IPR044791
Beta-glucanase/XTH + 27 + 36 422 - IPR038933
Ovate protein family - 27 - 36 + IPR036034
PDZ superfamily + 27 + 43 423 - IPR007650
  - 27 - 124 + IPR001099
Chalcone/stilbene synthase, N-terminal + 27 + 32 424 - IPR005150
Cellulose synthase - 27 - 61 + IPR025110
AMP-binding enzyme, C-terminal domain + 26 + 41 425 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 27 - 33 + IPR002867
IBR domain + 26 + 65 426 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 51 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 26 + 26 427 - IPR002963
Expansin - 27 - 227 + IPR027806
Harbinger transposase-derived nuclease domain + 26 + 26 428 - IPR005821
Ion transport domain - 27 - 36 + IPR011016
Zinc finger, RING-CH-type + 26 + 75 429 - IPR014722
  - 27 - 82 + IPR023753
FAD/NAD(P)-binding domain + 26 + 36 430 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 27 - 64 + IPR001881
EGF-like calcium-binding domain + 26 + 41 431 - IPR006458
  - 27 - 148 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 26 + 40 432 - IPR025660
Cysteine peptidase, histidine active site - 27 - 34 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 26 + 29 433 - IPR001229
  - 27 - 266 + IPR004320
Protein of unknown function DUF241, plant + 26 + 41 434 - IPR017938
Riboflavin synthase-like beta-barrel - 26 - 42 + IPR002123
Phospholipid/glycerol acyltransferase + 26 + 35 435 - IPR036378
  - 26 - 110 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 26 + 54 436 - IPR006153
Cation/H+ exchanger - 26 - 40 + IPR044839
Protein NDR1-like + 26 + 27 437 - IPR011013
Galactose mutarotase-like domain superfamily - 26 - 40 + IPR001849
Pleckstrin homology domain + 26 + 72 438 - IPR036866
  - 26 - 236 + IPR029069
HotDog domain superfamily + 26 + 46 439 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 26 - 136 + IPR012328
Chalcone/stilbene synthase, C-terminal + 26 + 29 440 - IPR014044
CAP domain - 26 - 73 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 26 + 33 441 - IPR006094
FAD linked oxidase, N-terminal - 26 - 27 + IPR036296
SKP1-like, dimerisation domain superfamily + 26 + 36 442 - IPR001701
Glycoside hydrolase family 9 - 26 - 28 + IPR031127
E3 ubiquitin ligase RBR family + 26 + 59 443 - IPR029047
  + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily 26 - 130 + 31 444 - IPR001574
Ribosome-inactivating protein - 26 - 28 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 26 + 35 445 - IPR010525
Auxin response factor - 26 - 35 + IPR005175
PPC domain + 26 + 80 446 - IPR017884
  - 25 - 76 + IPR015797
NUDIX hydrolase-like domain superfamily + 26 + 35 447 - IPR000727
  - 25 - 182 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 27 448 - IPR025110
AMP-binding enzyme, C-terminal domain - 25 - 34 + IPR036420
BRCT domain superfamily + 25 + 52 449 - IPR002403
Cytochrome P450, E-class, group IV - 25 - 121 + IPR007657
Glycosyltransferase 61 + 25 + 60 450 - IPR004316
SWEET sugar transporter - 25 - 54 + IPR017887
Transcription factor TCP subgroup + 25 + 49 451 - IPR005299
SAM dependent carboxyl methyltransferase - 25 - 88 + IPR016072
SKP1 component, dimerisation + 25 + 33 452 - IPR036420
  - 25 - 200 + IPR016897
S-phase kinase-associated protein 1 + 25 + 36 453 - IPR023753
FAD/NAD(P)-binding domain - 25 - 30 + IPR002035
von Willebrand factor, type A + 25 + 66 454 - IPR007657
Glycosyltransferase 61 - 25 - 80 + IPR004813
Oligopeptide transporter, OPT superfamily + 25 + 50 455 - IPR018181
Heat shock protein 70, conserved site - 25 - 71 + IPR029062
Class I glutamine amidotransferase-like + 25 + 42 456 - IPR003337
Trehalose-phosphatase - 25 - 56 + IPR001757
P-type ATPase + 25 + 117 457 - IPR002355
Multicopper oxidase, copper-binding site - 25 - 28 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 113 458 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 25 - 29 + IPR044066
TRIAD supradomain + 25 + 43 459 - IPR025875
Leucine rich repeat 4 - 25 - 30 + IPR036443
Zinc finger, RanBP2-type superfamily + 25 + 72 460 - IPR005746
Thioredoxin - 25 - 42 + IPR000782
FAS1 domain + 24 + 60 461 - IPR029069
HotDog domain superfamily - 25 - 41 + IPR003106
Leucine zipper, homeobox-associated + 24 + 26 462 - IPR019780
Germin, manganese binding site - 25 - 30 + IPR022149
Protein of unknown function DUF3681 + 24 + 51 463 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 25 - 29 + IPR004316
SWEET sugar transporter + 24 + 59 464 - IPR016138
  - 25 - 60 + IPR021790
PTBP1, RNA recognition motif 2-like + 24 + 31 465 - IPR006439
HAD hydrolase, subfamily IA - 25 - 82 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 24 + 32 466 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 25 - 145 + IPR025422
Transcription factor TGA like domain + 24 + 86 467 - IPR027410
  - 25 - 194 + IPR003337
Trehalose-phosphatase + 24 + 29 468 - IPR015797
NUDIX hydrolase-like domain superfamily - 25 - 28 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 24 + 34 469 - IPR017927
  - 24 - 99 + IPR034285
Laccase, second cupredoxin domain + 24 + 27 470 - IPR013601
FAE1/Type III polyketide synthase-like protein - 24 - 28 + IPR025486
Domain of unknown function DUF4378 + 24 + 31 471 - IPR017946
  - 24 - 261 + IPR016197
Chromo-like domain superfamily + 24 + 46 472 - IPR010920
LSM domain superfamily - 24 - 31 + IPR002937
Amine oxidase + 24 + 39 473 - IPR013216
Methyltransferase type 11 - 24 - 26 + IPR010525
Auxin response factor domain + 24 + 30 474 - IPR033124
Serine carboxypeptidases, histidine active site - 24 - 33 + IPR036085
PAZ domain superfamily + 23 + 46 475 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 24 - 32 + IPR019956
Ubiquitin domain + 23 + 77 476 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 24 - 59 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 23 + 43 477 - IPR016072
SKP1 component, dimerisation - 24 - 31 + IPR000864
Proteinase inhibitor I13, potato inhibitor I + 23 + 94 478 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 24 - 27 + IPR002403
Cytochrome P450, E-class, group IV + 23 + 126 479 - IPR004776
Membrane transport protein - 24 - 50 + IPR007612
LURP-one-related + 23 + 56 480 - IPR001876
  - 24 - 296 + IPR001357
BRCT domain + 23 + 85 481 - IPR004813
Oligopeptide transporter, OPT superfamily - 24 - 104 + IPR018957
Zinc finger, C3HC4 RING-type + 23 + 26 482 - IPR029062
  - 24 - 178 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 30 483 - IPR017937
Thioredoxin, conserved site - 24 - 39 + IPR008422
Homeobox KN domain + 23 + 30 484 - IPR016161
Aldehyde/histidinol dehydrogenase - 24 - 29 + IPR001353
Proteasome, subunit alpha/beta + 23 + 27 485 - IPR036296
SKP1-like, dimerisation domain superfamily - 24 - 33 + IPR002293
Amino acid/polyamine transporter I + 23 + 32 486 - IPR025486
Domain of unknown function DUF4378 - 24 - 31 + IPR003594
Histidine kinase/HSP90-like ATPase + 23 + 34 487 - IPR031127
E3 ubiquitin ligase RBR family - 24 - 74 + IPR011332
Zinc-binding ribosomal protein + 23 + 32 488 - IPR034741
Terpene cyclase-like 1, C-terminal domain - 24 - 28 + IPR034288
Laccase, first cupredoxin domain + 23 + 26 489 - IPR002913
  - 24 - 300 + IPR004776
Membrane transport protein + 23 + 41 490 - IPR008971
HSP40/DnaJ peptide-binding - 23 - 67 + IPR016161
Aldehyde/histidinol dehydrogenase + 23 + 31 491 - IPR007612
LURP-one-related - 23 - 75 + IPR036427
Bromodomain-like superfamily + 23 + 34 492 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 23 + IPR036354
Proteinase inhibitor I13, potato inhibitor I superfamily + 23 23 493 - IPR001357
  - 23 - 306 + IPR000086
NUDIX hydrolase domain + 23 + 56 494 - IPR008422
Homeobox KN domain - 23 - 33 + IPR036392
PLAT/LH2 domain superfamily + 23 + 25 495 - IPR012675
  - 23 - 54 + IPR029033
Histidine phosphatase superfamily + 23 + 35 496 - IPR025422
  - 23 - 234 + IPR003100
PAZ domain + 22 + 87 497 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 23 - 40 + IPR006689
Small GTPase superfamily, ARF/SAR type + 22 + 146 498 - IPR027923
Hydrophobic seed protein - 23 - 53 + IPR004000
Actin family + 22 + 156 499 - IPR001849
  - 23 - 166 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 52 500 - IPR033443
Pentacotripeptide-repeat region of PRORP - 23 - 30 + IPR025753
AAA-type ATPase, N-terminal domain + 22 + 27 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_brachyantha.html b/gramene/htdocs/ssi/species/stats_Oryza_brachyantha.html index 984edd09..b55f07be 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_brachyantha.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_brachyantha.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:Oryza_brachyantha.v1.4b, May 2011AGI_PacBIO,
Database version:93.1487.4
Base Pairs:260,838,168263,195,077
Golden Path Length:260,838,168263,195,077
Genebuild by: OGE
Genebuild method: Imported from OGE
Genebuild started: May 2011
Genebuild version: OGEv1.4
+

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):32,038Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		29,820
Gene transcriptsHASH(0x68ce400):34,598Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:41,684
@@ -37,42 +37,77 @@

Coordinate Systems

chromosome
-
12 sequences
+
59 sequences
+1
SequenceLength (bp)
133916305
227085147
329620734
421479432
520131956
621794218
718603524
818224760
914107269
1014643570
1116001410
1215318893
33554891
227476678
329856040
421827379
520245399
621974636
719450094
818299912
915506556
1016246320
1117534090
1216931956
UN-Ctg4456751
UN-Ctg45120491
UN-Ctg46705295
UN-Ctg47278345
UN-Ctg48232093
UN-Ctg49207166
UN-Ctg50201584
UN-Ctg51164390
UN-Ctg52155163
UN-Ctg53145019
UN-Ctg54106328
UN-Ctg5599473
UN-Ctg5692129
UN-Ctg5790675
UN-Ctg5887736
UN-Ctg5982649
UN-Ctg6082116
UN-Ctg6177768
UN-Ctg6277474
UN-Ctg6373099
UN-Ctg6464398
UN-Ctg6563165
UN-Ctg6659948
UN-Ctg6758844
UN-Ctg6857773
UN-Ctg6956880
UN-Ctg7052260
UN-Ctg7151046
UN-Ctg7249779
UN-Ctg7346557
UN-Ctg7446712
UN-Ctg7543054
UN-Ctg7641780
UN-Ctg7741140
UN-Ctg7840355
UN-Ctg7939538
UN-Ctg8037402
UN-Ctg8136362
UN-Ctg8236421
UN-Ctg8336016
UN-Ctg8435832
UN-Ctg8534500
UN-Ctg8630170
UN-Ctg8726420
UN-Ctg8823840
UN-Ctg8923378
UN-Ctg9021812
-
+
- superscaffold - 7473 sequences - - chunk - 10000 sequences + 2662 sequences - -

Other

- - - - - -
FGENESH gene predictions:26,828
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_brachyantha_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_brachyantha_IPtop500.html index 39cde67a..a4a18279 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_brachyantha_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_brachyantha_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1298 - 1415 + 1250 + 2002 2 - IPR000719
  - 1223 - 9153 + IPR000719
Protein kinase domain + 1186 + 3141 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1148 - 1532 + 1129 + 2070 4 - IPR008271
Serine/threonine-protein kinase, active site - 958 - 964 + IPR002885
Pentatricopeptide repeat + 466 + 6968 5 - IPR017441
Protein kinase, ATP binding site - 808 - 814 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 415 + 909 6 - IPR032675
  - 786 - 3074 + IPR001841
Zinc finger, RING-type + 406 + 882 7 - IPR011990
  - 662 - 7566 + IPR009057
Homeobox-like domain superfamily + 378 + 539 8 - IPR013083
  - 561 - 1222 + IPR029058
Alpha/Beta hydrolase fold + 347 + 572 9 - IPR002885
  - 460 - 20580 + IPR036291
NAD(P)-binding domain superfamily + 344 + 559 10 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 413 - 627 + IPR001611
Leucine-rich repeat + 344 + 1134 11 - IPR036291
NAD(P)-binding domain superfamily - 353 - 401 + IPR036047
F-box-like domain superfamily + 340 + 406 12 - IPR001611
  - 351 - 5316 + IPR016024
Armadillo-type fold + 330 + 641 13 - IPR009057
Homeobox-like domain superfamily - 350 - 375 + IPR011990
Tetratricopeptide-like helical domain superfamily + 304 + 521 14 - IPR029058
  - 348 - 1482 + IPR036396
Cytochrome P450 superfamily + 276 + 354 15 - IPR016024
Armadillo-type fold - 337 - 758 + IPR044974
Disease resistance protein, plants + 263 + 483 16 - IPR001841
  - 335 - 1538 + IPR001128
Cytochrome P450 + 263 + 1302 17 - IPR036396
  - 296 - 1932 + IPR035979
RNA-binding domain superfamily + 261 + 622 18 - IPR001128
Cytochrome P450 - 283 - 1095 + IPR002182
NB-ARC + 250 + 322 19 - IPR002182
NB-ARC - 279 - 294 + IPR017930
Myb domain + 246 + 835 20 - IPR003593
AAA+ ATPase domain - 267 - 358 + IPR001810
F-box domain + 245 + 417 21 - IPR001005
SANT/Myb domain - 251 - 945 + IPR017853
Glycoside hydrolase superfamily + 245 + 446 22 - IPR035979
RNA-binding domain superfamily - 248 - 364 + IPR000504
RNA recognition motif domain + 241 + 1232 23 - IPR017853
Glycoside hydrolase superfamily - 246 - 274 + IPR001005
SANT/Myb domain + 240 + 820 24 IPR036259
MFS transporter superfamily - 245 - 387 + 239 + 411 25 - IPR036047
F-box-like domain superfamily - 244 - 253 + IPR036322
WD40-repeat-containing domain superfamily + 231 + 439 26 - IPR012677
  - 238 - 758 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 225 + 414 27 - IPR015943
  - 237 - 1050 + IPR002401
Cytochrome P450, E-class, group I + 224 + 1694 28 - IPR002401
Cytochrome P450, E-class, group I - 232 - 1377 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 222 + 280 29 - IPR036322
WD40-repeat-containing domain superfamily - 228 - 364 + IPR036249
Thioredoxin-like superfamily + 217 + 346 30 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 228 - 298 + IPR012337
Ribonuclease H-like superfamily + 211 + 254 31 - IPR000504
  - 225 - 3063 + IPR001680
WD40 repeat + 204 + 2025 32 - IPR001680
  - 221 - 6810 + IPR041118
Rx, N-terminal + 197 + 240 33 - IPR003591
Leucine-rich repeat, typical subtype - 214 - 1443 + IPR011992
EF-hand domain pair + 186 + 274 34 - IPR011989
  - 213 - 594 + IPR016177
DNA-binding domain superfamily + 179 + 245 35 - IPR017972
Cytochrome P450, conserved site - 208 - 208 + IPR002048
EF-hand domain + 171 + 995 36 - IPR036249
Thioredoxin-like superfamily - 203 - 240 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 168 + 233 37 - IPR017986
  - 199 - 666 + IPR001471
AP2/ERF domain + 165 + 946 38 - IPR017930
  - 195 - 612 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 160 + 398 39 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 187 - 190 + IPR036412
HAD-like superfamily + 157 + 256 40 - IPR011992
EF-hand domain pair - 178 - 195 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 144 + 338 41 - IPR020846
  - 174 - 568 + IPR010255
Haem peroxidase superfamily + 142 + 181 42 - IPR001810
  - 168 - 981 + IPR038765
Papain-like cysteine peptidase superfamily + 140 + 238 43 - IPR002048
  - 161 - 3612 + IPR002016
Haem peroxidase + 137 + 981 44 - IPR012337
Ribonuclease H-like superfamily - 158 - 177 + IPR036236
Zinc finger C2H2 superfamily + 137 + 216 45 - IPR038765
Papain-like cysteine peptidase superfamily - 155 - 191 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 136 + 161 46 - IPR036412
HAD-like superfamily - 155 - 219 + IPR001650
Helicase, C-terminal + 134 + 442 47 - IPR036638
  - 154 - 858 + IPR029044
Nucleotide-diphospho-sugar transferases + 133 + 201 48 - IPR018247
EF-Hand 1, calcium-binding site - 153 - 360 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 132 + 230 49 - IPR010255
Haem peroxidase - 152 - 166 + IPR003441
NAC domain + 128 + 282 50 - IPR002016
  - 150 - 2703 + IPR036093
NAC domain superfamily + 128 + 144 51 - IPR011598
  - 146 - 1431 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 127 + 152 52 - IPR014001
  - 140 - 550 + IPR013087
Zinc finger C2H2-type + 127 + 274 53 - IPR029044
  - 139 - 620 + IPR036390
Winged helix DNA-binding domain superfamily + 127 + 193 54 - IPR001650
  - 138 - 1100 + IPR003439
ABC transporter-like, ATP-binding domain + 127 + 604 55 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 138 - 139 + IPR036188
FAD/NAD(P)-binding domain superfamily + 121 + 245 56 - IPR023214
  - 136 - 428 + IPR036770
Ankyrin repeat-containing domain superfamily + 120 + 192 57 - IPR013087
  - 135 - 1596 + IPR000823
Plant peroxidase + 120 + 1040 58 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 132 - 155 + IPR012340
Nucleic acid-binding, OB-fold + 118 + 311 59 - IPR000823
Plant peroxidase - 131 - 976 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 115 + 135 60 - IPR019775
WD40 repeat, conserved site - 130 - 215 + IPR011333
SKP1/BTB/POZ domain superfamily + 114 + 147 61 - IPR003439
  - 128 - 1116 + IPR043502
DNA/RNA polymerase superfamily + 113 + 128 62 - IPR036188
  - 127 - 912 + IPR001087
GDSL lipase/esterase + 111 + 152 63 - IPR036388
  - 125 - 276 + IPR020846
Major facilitator superfamily domain + 108 + 157 64 - IPR036093
  - 124 - 738 + IPR002110
Ankyrin repeat + 108 + 507 65 - IPR003441
  - 123 - 723 + IPR036869
Chaperone J-domain superfamily + 106 + 155 66 - IPR036390
Winged helix DNA-binding domain superfamily - 121 - 127 + IPR003480
Transferase + 106 + 125 67 - IPR036770
  - 120 - 652 + IPR033905
Secretory peroxidase + 104 + 125 68 - IPR016177
DNA-binding domain superfamily - 119 - 144 + IPR003959
ATPase, AAA-type, core + 103 + 178 69 - IPR020683
  - 119 - 880 + IPR029071
Ubiquitin-like domain superfamily + 102 + 158 70 - IPR036514
  - 118 - 252 + IPR008972
Cupredoxin + 100 + 210 71 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 118 - 119 + IPR001623
DnaJ domain + 100 + 786 72 - IPR023213
  - 115 - 356 + IPR011011
Zinc finger, FYVE/PHD-type + 100 + 180 73 - IPR036236
Zinc finger C2H2 superfamily - 115 - 179 + IPR035892
C2 domain superfamily + 99 + 203 74 - IPR036397
  - 112 - 354 + IPR015424
Pyridoxal phosphate-dependent transferase + 97 + 155 75 - IPR014729
  - 112 - 262 + IPR036576
WRKY domain superfamily + 96 + 114 76 - IPR019793
Peroxidases heam-ligand binding site - 112 - 112 + IPR011050
Pectin lyase fold/virulence factor + 95 + 138 77 - IPR013026
  - 111 - 435 + IPR003657
WRKY domain + 95 + 222 78 - IPR008972
  - 110 - 742 + IPR044810
WRKY transcription factor, plant + 94 + 105 79 - IPR021109
  - 110 - 582 + IPR035669
GDSL lipase/esterase-like, plant + 93 + 120 80 - IPR002110
  - 110 - 2535 + IPR036457
PPM-type phosphatase domain superfamily + 93 + 146 81 - IPR036955
  - 109 - 384 + IPR019734
Tetratricopeptide repeat + 91 + 387 82 - IPR001471
  - 108 - 1872 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 91 + 112 83 - IPR014710
  - 108 - 262 + IPR036426
Bulb-type lectin domain superfamily + 91 + 110 84 - IPR011333
SKP1/BTB/POZ domain superfamily - 108 - 119 + IPR032867
DYW domain + 91 + 107 85 - IPR019734
  - 107 - 2487 + IPR001356
Homeobox domain + 91 + 327 86 - IPR033905
Secretory peroxidase - 105 - 105 + IPR001932
PPM-type phosphatase domain + 91 + 423 87 - IPR029071
Ubiquitin-like domain superfamily - 104 - 130 + IPR021109
Aspartic peptidase domain superfamily + 90 + 116 88 - IPR011011
Zinc finger, FYVE/PHD-type - 104 - 123 + IPR020683
Ankyrin repeat-containing domain + 90 + 202 89 - IPR003959
ATPase, AAA-type, core - 103 - 126 + IPR001480
Bulb-type lectin domain + 88 + 292 90 - IPR003480
Transferase - 103 - 119 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 87 + 94 91 - IPR013785
  - 101 - 348 + IPR000008
C2 domain + 86 + 419 92 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 99 - 104 + IPR020472
G-protein beta WD-40 repeat + 86 + 432 93 - IPR019794
Peroxidase, active site - 99 - 99 + IPR011545
DEAD/DEAH box helicase domain + 85 + 141 94 - IPR012340
Nucleic acid-binding, OB-fold - 99 - 142 + IPR004827
Basic-leucine zipper domain + 84 + 248 95 - IPR015424
Pyridoxal phosphate-dependent transferase - 99 - 111 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 83 + 98 96 - IPR011050
Pectin lyase fold/virulence factor - 97 - 100 + IPR036875
Zinc finger, CCHC-type superfamily + 83 + 114 97 - IPR036869
  - 96 - 374 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 82 + 109 98 - IPR012334
  - 96 - 202 + IPR011051
RmlC-like cupin domain superfamily + 82 + 103 99 - IPR001087
GDSL lipase/esterase - 95 - 95 + IPR001584
Integrase, catalytic core + 81 + 137 100 - IPR015421
  - 95 - 294 + IPR013766
Thioredoxin domain + 79 + 226 101 - IPR005225
Small GTP-binding protein domain - 93 - 94 + IPR002347
Short-chain dehydrogenase/reductase SDR + 78 + 729 102 - IPR032867
DYW domain - 93 - 93 + IPR005828
Major facilitator, sugar transporter-like + 78 + 125 103 - IPR005123
  - 92 - 507 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 78 + 92 104 - IPR001461
Aspartic peptidase A1 family - 92 - 208 + IPR033121
Peptidase family A1 domain + 78 + 114 105 - IPR000109
Proton-dependent oligopeptide transporter family - 90 - 208 + IPR000270
PB1 domain + 78 + 143 106 - IPR036576
  - 89 - 600 + IPR015300
DNA-binding pseudobarrel domain superfamily + 78 + 173 107 - IPR001623
  - 89 - 1138 + IPR009072
Histone-fold + 77 + 83 108 - IPR003657
  - 89 - 876 + IPR000109
Proton-dependent oligopeptide transporter family + 75 + 267 109 - IPR036457
  - 88 - 418 + IPR032799
Xylanase inhibitor, C-terminal + 75 + 89 110 - IPR035669
GDSL lipase/esterase-like, plant - 87 - 87 + IPR000073
Alpha/beta hydrolase fold-1 + 75 + 239 111 - IPR036426
  - 87 - 434 + IPR032861
Xylanase inhibitor, N-terminal + 74 + 91 112 - IPR001356
  - 87 - 912 + IPR036163
Heavy metal-associated domain superfamily + 74 + 100 113 - IPR001932
  - 87 - 1128 + IPR001878
Zinc finger, CCHC-type + 74 + 215 114 - IPR027443
  - 86 - 182 + IPR000210
BTB/POZ domain + 73 + 197 115 - IPR011545
DEAD/DEAH box helicase domain - 86 - 89 + IPR025315
Domain of unknown function DUF4220 + 73 + 86 116 - IPR017871
ABC transporter, conserved site - 85 - 111 + IPR026992
Non-haem dioxygenase N-terminal domain + 72 + 87 117 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 85 - 131 + IPR003613
U box domain + 72 + 197 118 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 84 - 91 + IPR000858
S-locus glycoprotein domain + 71 + 84 119 - IPR001480
  - 84 - 500 + IPR006121
Heavy metal-associated domain, HMA + 71 + 230 120 - IPR006447
Myb domain, plants - 83 - 83 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 71 + 74 121 - IPR011051
RmlC-like cupin domain superfamily - 83 - 110 + IPR000626
Ubiquitin-like domain + 70 + 201 122 - IPR035892
  - 82 - 262 + IPR003340
B3 DNA binding domain + 70 + 445 123 - IPR002347
Short-chain dehydrogenase/reductase SDR - 82 - 490 + IPR003609
PAN/Apple domain + 70 + 161 124 - IPR032799
Xylanase inhibitor, C-terminal - 82 - 83 + IPR043129
ATPase, nucleotide binding domain + 69 + 194 125 - IPR015655
Protein phosphatase 2C family - 81 - 96 + IPR005174
Domain unknown function DUF295 + 68 + 77 126 - IPR015422
  - 81 - 387 + IPR001461
Aspartic peptidase A1 family + 67 + 263 127 - IPR004827
  - 81 - 852 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 67 + 83 128 - IPR025315
Domain of unknown function DUF4220 - 81 - 84 + IPR007658
Protein of unknown function DUF594 + 66 + 70 129 - IPR035595
UDP-glycosyltransferase family, conserved site - 80 - 80 + IPR018108
Mitochondrial substrate/solute carrier + 64 + 521 130 - IPR000008
  - 80 - 754 + IPR023395
Mitochondrial carrier domain superfamily + 64 + 94 131 - IPR005828
Major facilitator, sugar transporter-like - 79 - 93 + IPR036879
Transcription factor, MADS-box superfamily + 64 + 91 132 - IPR020472
G-protein beta WD-40 repeat - 79 - 237 + IPR000571
Zinc finger, CCCH-type + 64 + 365 133 - IPR033121
  - 79 - 168 + IPR002100
Transcription factor, MADS-box + 63 + 432 134 - IPR017907
Zinc finger, RING-type, conserved site - 79 - 81 + IPR029052
Metallo-dependent phosphatase-like + 63 + 96 135 - IPR001965
Zinc finger, PHD-type - 79 - 121 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 62 + 70 136 - IPR009072
  - 78 - 474 + IPR000048
IQ motif, EF-hand binding site + 62 + 421 137 - IPR015300
  - 78 - 384 + IPR036908
RlpA-like domain superfamily + 61 + 71 138 - IPR000626
  - 75 - 738 + IPR013057
Amino acid transporter, transmembrane domain + 60 + 88 139 - IPR000270
  - 74 - 351 + IPR036852
Peptidase S8/S53 domain superfamily + 60 + 69 140 - IPR024171
S-receptor-like serine/threonine-protein kinase - 73 - 88 + IPR044965
Glycoside hydrolase family 17, plant + 60 + 91 141 - IPR000210
  - 73 - 588 + IPR036915
Cyclin-like superfamily + 60 + 156 142 - IPR007658
Protein of unknown function DUF594 - 73 - 73 + IPR000209
Peptidase S8/S53 domain + 60 + 68 143 - IPR000073
Alpha/beta hydrolase fold-1 - 73 - 138 + IPR004045
Glutathione S-transferase, N-terminal + 59 + 134 144 - IPR000858
S-locus glycoprotein domain - 72 - 72 + IPR006501
Pectinesterase inhibitor domain + 59 + 62 145 - IPR003609
  - 71 - 358 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 58 + 87 146 - IPR003340
  - 70 - 1014 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 58 + 97 147 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 70 - 75 + IPR003245
Phytocyanin domain + 58 + 128 148 - IPR008974
  - 70 - 408 + IPR020568
Ribosomal protein S5 domain 2-type fold + 58 + 113 149 - IPR013766
  - 69 - 384 + IPR010987
Glutathione S-transferase, C-terminal-like + 58 + 68 150 - IPR036163
Heavy metal-associated domain superfamily - 69 - 83 + IPR000490
Glycoside hydrolase family 17 + 58 + 81 151 - IPR032861
Xylanase inhibitor, N-terminal - 68 - 68 + IPR004158
Protein of unknown function DUF247, plant + 58 + 147 152 - IPR006121
  - 67 - 588 + IPR001806
Small GTPase + 58 + 159 153 - IPR013057
Amino acid transporter, transmembrane domain - 66 - 71 + IPR016039
Thiolase-like + 57 + 133 154 - IPR003960
ATPase, AAA-type, conserved site - 65 - 69 + IPR045051
Subtilisin-like protease + 57 + 79 155 - IPR004045
  - 65 - 378 + IPR039391
Phytocyanin + 57 + 64 156 - IPR013783
  - 64 - 138 + IPR013094
Alpha/beta hydrolase fold-3 + 57 + 67 157 - IPR000742
  - 64 - 304 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 56 + 66 158 - IPR036852
  - 64 - 744 + IPR019787
Zinc finger, PHD-finger + 56 + 161 159 - IPR018108
  - 63 - 676 + IPR007117
Expansin, cellulose-binding-like domain + 56 + 132 160 - IPR023395
  - 63 - 288 + IPR003676
Small auxin-up RNA + 56 + 62 161 - IPR003613
  - 63 - 558 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 55 + 62 162 - IPR026057
PC-Esterase - 62 - 64 + IPR005202
Transcription factor GRAS + 55 + 192 163 - IPR003245
  - 62 - 546 + IPR003663
Sugar/inositol transporter + 55 + 357 164 - IPR036961
  - 62 - 258 + IPR026961
PGG domain + 54 + 120 165 - IPR004158
Protein of unknown function DUF247, plant - 62 - 67 + IPR002902
Gnk2-homologous domain + 54 + 347 166 - IPR000209
Peptidase S8/S53 domain - 62 - 65 + IPR001220
Legume lectin domain + 54 + 115 167 - IPR019787
  - 61 - 224 + IPR015500
Peptidase S8, subtilisin-related + 54 + 169 168 - IPR010987
  - 61 - 126 + IPR013525
ABC-2 type transporter + 53 + 123 169 - IPR036879
  - 61 - 360 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 52 + 58 170 - IPR036875
Zinc finger, CCHC-type superfamily - 61 - 73 + IPR024788
Malectin-like domain + 52 + 76 171 - IPR001878
  - 61 - 726 + IPR026057
PC-Esterase + 51 + 82 172 - IPR001881
EGF-like calcium-binding domain - 60 - 88 + IPR029962
Trichome birefringence-like family + 51 + 84 173 - IPR020568
Ribosomal protein S5 domain 2-type fold - 60 - 72 + IPR007112
Expansin/pollen allergen, DPBB domain + 51 + 61 174 - IPR001220
Legume lectin domain - 60 - 117 + IPR002528
Multi antimicrobial extrusion protein + 51 + 149 175 - IPR018097
EGF-like calcium-binding, conserved site - 59 - 59 + IPR006045
Cupin 1 + 51 + 83 176 - IPR002100
  - 58 - 1083 + IPR001752
Kinesin motor domain + 51 + 568 177 - IPR036908
  - 58 - 230 + IPR001563
Peptidase S10, serine carboxypeptidase + 50 + 453 178 - IPR000571
  - 58 - 1044 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 50 + 153 179 - IPR011993
  - 58 - 122 + IPR007118
Expansin/Lol pI + 50 + 334 180 - IPR016039
  - 57 - 591 + IPR034197
Cucumisin-like catalytic domain + 50 + 55 181 - IPR029962
Trichome birefringence-like family - 57 - 64 + IPR025846
PMR5 N-terminal domain + 50 + 76 182 - IPR016135
  - 57 - 226 + IPR015915
Kelch-type beta propeller + 50 + 78 183 - IPR036915
Cyclin-like superfamily - 57 - 96 + IPR025724
GAG-pre-integrase domain + 50 + 50 184 - IPR005829
Sugar transporter, conserved site - 56 - 90 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 49 + 57 185 - IPR008979
  - 56 - 256 + IPR013763
Cyclin-like + 49 + 114 186 - IPR000048
  - 56 - 936 + IPR023298
P-type ATPase, transmembrane domain superfamily + 49 + 88 187 - IPR001806
Small GTPase superfamily - 56 - 57 + IPR001214
SET domain + 49 + 179 188 - IPR000225
  - 56 - 1299 + IPR000225
Armadillo + 49 + 263 189 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 55 - 55 + IPR017884
SANT domain + 48 + 68 190 - IPR013525
ABC-2 type transporter - 55 - 78 + IPR008978
HSP20-like chaperone + 48 + 50 191 - IPR036691
  - 55 - 282 + IPR008250
P-type ATPase, A domain superfamily + 48 + 84 192 - IPR038408
  - 55 - 192 + IPR012946
X8 domain + 48 + 63 193 - IPR002902
  - 55 - 382 + IPR018289
MULE transposase domain + 48 + 52 194 - IPR026992
Non-haem dioxygenase N-terminal domain - 55 - 56 + IPR016181
Acyl-CoA N-acyltransferase + 47 + 81 195 - IPR005174
Domain unknown function DUF295 - 55 - 55 + IPR000608
Ubiquitin-conjugating enzyme E2 + 47 + 214 196 - IPR019786
Zinc finger, PHD-type, conserved site - 54 - 59 + IPR029055
Nucleophile aminohydrolases, N-terminal + 47 + 70 197 - IPR005202
  - 54 - 228 + IPR011527
ABC transporter type 1, transmembrane domain + 47 + 293 198 - IPR000490
Glycoside hydrolase family 17 - 54 - 85 + IPR036855
Zinc finger, CCCH-type superfamily + 47 + 155 199 - IPR003663
Sugar/inositol transporter - 54 - 274 + IPR002921
Fungal lipase-like domain + 46 + 66 200 - IPR001563
Peptidase S10, serine carboxypeptidase - 53 - 295 + IPR008949
Isoprenoid synthase domain superfamily + 46 + 71 201 - IPR036640
  - 53 - 525 + IPR008979
Galactose-binding-like domain superfamily + 46 + 119 202 - IPR006045
Cupin 1 - 53 - 134 + IPR008928
Six-hairpin glycosidase superfamily + 46 + 63 203 - IPR029052
  - 53 - 108 + IPR033389
AUX/IAA domain + 45 + 82 204 - IPR024788
Malectin-like carbohydrate-binding domain - 53 - 55 + IPR011032
GroES-like superfamily + 45 + 91 205 - IPR036749
  - 52 - 204 + IPR010811
Domain of unknown function DUF1409 + 45 + 47 206 - IPR007117
  - 52 - 206 + IPR002083
MATH/TRAF domain + 45 + 136 207 - IPR003676
Small auxin-up RNA - 52 - 53 + IPR036465
von Willebrand factor A-like domain superfamily + 45 + 65 208 - IPR026961
PGG domain - 51 - 104 + IPR007527
Zinc finger, SWIM-type + 45 + 85 209 - IPR027640
Kinesin-like protein - 51 - 66 + IPR044808
Ethylene-responsive transcription factor + 45 + 50 210 - IPR002528
Multi antimicrobial extrusion protein - 51 - 128 + IPR000873
AMP-dependent synthetase/ligase + 44 + 77 211 - IPR011527
  - 51 - 537 + IPR041569
AAA ATPase, AAA+ lid domain + 44 + 71 212 - IPR001752
  - 51 - 1020 + IPR000070
Pectinesterase, catalytic + 43 + 63 213 - IPR016181
Acyl-CoA N-acyltransferase - 50 - 57 + IPR043926
ABC transporter family G domain + 42 + 73 214 - IPR018289
MULE transposase domain - 50 - 50 + IPR011701
Major facilitator superfamily + 42 + 73 215 - IPR030184
WAT1-related protein - 50 - 58 + IPR014014
RNA helicase, DEAD-box type, Q motif + 42 + 66 216 - IPR007118
Expansin/Lol pI - 49 - 250 + IPR030184
WAT1-related protein + 42 + 93 217 - IPR000873
AMP-dependent synthetase/ligase - 49 - 51 + IPR008889
VQ + 42 + 43 218 - IPR013763
Cyclin-like - 49 - 143 + IPR000743
Glycoside hydrolase, family 28 + 42 + 66 219 - IPR023298
P-type ATPase, transmembrane domain superfamily - 49 - 135 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 42 + 84 220 - IPR037045
  - 49 - 98 + IPR033896
MADS MEF2-like + 41 + 67 221 - IPR033389
AUX/IAA domain - 48 - 50 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 41 + 85 222 - IPR011032
GroES-like superfamily - 48 - 63 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 41 + 48 223 - IPR008949
  - 48 - 208 + IPR004263
Exostosin-like + 41 + 61 224 - IPR035513
  - 48 - 174 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 41 + 75 225 - IPR002083
  - 48 - 429 + IPR006671
Cyclin, N-terminal + 41 + 61 226 - IPR007112
  - 48 - 176 + IPR016159
Cullin repeat-like-containing domain superfamily + 41 + 54 227 - IPR015915
  - 48 - 339 + IPR014756
Immunoglobulin E-set + 41 + 65 228 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 47 - 47 + IPR000620
EamA domain + 41 + 109 229 - IPR013128
Peptidase C1A - 47 - 62 + IPR001117
Multicopper oxidase, type 1 + 40 + 47 230 - IPR008250
P-type ATPase, A domain superfamily - 47 - 58 + IPR006016
UspA + 40 + 57 231 - IPR029055
  - 47 - 196 + IPR004853
Sugar phosphate transporter domain + 40 + 75 232 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 47 - 47 + IPR003137
PA domain + 40 + 54 233 - IPR018303
P-type ATPase, phosphorylation site - 47 - 47 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 40 + 58 234 - IPR023299
  - 47 - 228 + IPR000668
Peptidase C1A, papain C-terminal + 40 + 171 235 - IPR008978
  - 46 - 180 + IPR045087
Multicopper oxidase + 40 + 51 236 - IPR000608
  - 46 - 262 + IPR011707
Multicopper oxidase, N-termianl + 40 + 49 237 - IPR000222
PPM-type phosphatase, divalent cation binding - 46 - 46 + IPR036318
FAD-binding, type PCMH-like superfamily + 39 + 50 238 - IPR018253
DnaJ domain, conserved site - 46 - 46 + IPR009060
UBA-like superfamily + 39 + 65 239 - IPR025846
PMR5 N-terminal domain - 46 - 46 + IPR001509
NAD-dependent epimerase/dehydratase + 39 + 70 240 - IPR000620
EamA domain - 46 - 81 + IPR023271
Aquaporin-like + 39 + 46 241 - IPR011701
Major facilitator superfamily - 45 - 45 + IPR000742
EGF-like domain + 39 + 51 242 - IPR001509
NAD-dependent epimerase/dehydratase - 45 - 49 + IPR000425
Major intrinsic protein + 39 + 322 243 - IPR014014
  - 45 - 90 + IPR011706
Multicopper oxidase, C-terminal + 39 + 47 244 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 45 - 328 + IPR033443
Pentacotripeptide-repeat region of PRORP + 39 + 61 245 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 45 - 47 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 39 + 56 246 - IPR001757
P-type ATPase - 45 - 164 + IPR006702
Casparian strip membrane protein domain + 39 + 44 247 - IPR007527
  - 45 - 243 + IPR016040
NAD(P)-binding domain + 38 + 54 248 - IPR015500
Peptidase S8, subtilisin-related - 45 - 127 + IPR016166
FAD-binding domain, PCMH-type + 38 + 49 249 - IPR001214
  - 45 - 357 + IPR011006
CheY-like superfamily + 38 + 62 250 - IPR000743
Glycoside hydrolase, family 28 - 45 - 67 + IPR015655
Protein phosphatase 2C family + 38 + 71 251 - IPR036890
  - 44 - 188 + IPR002109
Glutaredoxin + 38 + 41 252 - IPR008928
Six-hairpin glycosidase superfamily - 44 - 56 + IPR008942
ENTH/VHS + 37 + 50 253 - IPR000668
Peptidase C1A, papain C-terminal - 44 - 181 + IPR010402
CCT domain + 37 + 96 254 - IPR036465
  - 44 - 164 + IPR025659
Tubby-like, C-terminal + 37 + 45 255 - IPR036855
Zinc finger, CCCH-type superfamily - 44 - 89 + IPR002068
Alpha crystallin/Hsp20 domain + 37 + 73 256 - IPR012341
  - 44 - 159 + IPR000330
SNF2, N-terminal + 37 + 77 257 - IPR023393
  - 43 - 94 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 37 + 38 258 - IPR012946
X8 domain - 43 - 94 + IPR009000
Translation protein, beta-barrel domain superfamily + 37 + 53 259 - IPR016159
Cullin repeat-like-containing domain superfamily - 43 - 57 + IPR039417
Papain-like cysteine endopeptidase + 37 + 45 260 - IPR031052
FHY3/FAR1 family - 42 + IPR040911
Exostosin, GT47 domain + 37 54 261 - IPR013094
Alpha/beta hydrolase fold-3 - 42 - 42 + IPR000644
CBS domain + 37 + 188 262 - IPR000070
Pectinesterase, catalytic - 42 - 43 + IPR025322
Protein of unknown function DUF4228, plant + 36 + 37 263 - IPR004853
Sugar phosphate transporter domain - 41 - 41 + IPR029021
Protein-tyrosine phosphatase-like + 36 + 60 264 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 41 - 41 + IPR034294
Aquaporin transporter + 36 + 46 265 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 41 - 61 + IPR031052
FHY3/FAR1 family + 36 + 62 266 - IPR023271
  - 40 - 168 + IPR007125
Histone H2A/H2B/H3 + 36 + 39 267 - IPR034294
Aquaporin transporter - 40 - 45 + IPR019378
GDP-fucose protein O-fucosyltransferase + 36 + 59 268 - IPR004265
Dirigent protein - 40 - 40 + IPR043519
Nucleotidyltransferase superfamily + 36 + 62 269 - IPR000425
Major intrinsic protein - 40 - 272 + IPR011043
Galactose oxidase/kelch, beta-propeller + 36 + 42 270 - IPR014756
Immunoglobulin E-set - 40 - 42 + IPR015947
PUA-like superfamily + 36 + 51 271 - IPR002921
Fungal lipase-like domain - 39 - 39 + IPR001789
Signal transduction response regulator, receiver domain + 36 + 109 272 - IPR001117
Multicopper oxidase, type 1 - 39 - 39 + IPR036612
K Homology domain, type 1 superfamily + 35 + 128 273 - IPR000330
SNF2-related, N-terminal domain - 39 - 39 + IPR034161
Pepsin-like domain, plant + 35 + 42 274 - IPR034197
Cucumisin-like catalytic domain - 39 - 39 + IPR001938
Thaumatin family + 35 + 252 275 - IPR020845
AMP-binding, conserved site - 39 - 39 + IPR004839
Aminotransferase, class I/classII + 35 + 62 276 - IPR011706
Multicopper oxidase, type 2 - 39 - 39 + IPR011012
Longin-like domain superfamily + 35 + 50 277 - IPR013780
  - 39 - 86 + IPR029045
ClpP/crotonase-like domain superfamily + 35 + 66 278 - IPR033896
MADS MEF2-like - 38 - 38 + IPR002067
Mitochondrial carrier protein + 35 + 239 279 - IPR007493
Protein of unknown function DUF538 - 38 - 76 + IPR028889
Ubiquitin specific protease domain + 35 + 56 280 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 38 - 76 + IPR039361
Cyclin + 35 + 65 281 - IPR009000
Translation protein, beta-barrel domain superfamily - 38 - 41 + IPR002912
ACT domain + 35 + 129 282 - IPR036758
  - 38 - 152 + IPR037176
Osmotin/thaumatin-like superfamily + 35 + 40 283 - IPR038718
  - 38 - 96 + IPR000182
GNAT domain + 34 + 89 284 - IPR006671
Cyclin, N-terminal - 38 - 63 + IPR004265
Dirigent protein + 34 + 46 285 - IPR000644
  - 38 - 444 + IPR006652
Kelch repeat type 1 + 34 + 69 286 - IPR034090
BPM, C-terminal - 38 - 38 + IPR002495
Glycosyl transferase, family 8 + 34 + 45 287 - IPR002487
  - 38 - 219 + IPR002487
Transcription factor, K-box + 34 + 117 288 - IPR011707
Multicopper oxidase, type 3 - 38 - 38 + IPR013149
Alcohol dehydrogenase, C-terminal + 33 + 51 289 - IPR017877
  - 38 - 90 + IPR007493
Protein of unknown function DUF538 + 33 + 77 290 - IPR010402
  - 37 - 219 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 166 291 - IPR000182
  - 37 - 136 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 57 292 - IPR029021
  - 37 - 162 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 33 + 56 293 - IPR006564
Zinc finger, PMZ-type - 37 - 37 + IPR036758
At5g01610-like superfamily + 33 + 38 294 - IPR004839
Aminotransferase, class I/classII - 37 - 37 + IPR006458
Ovate protein family, C-terminal + 33 + 64 295 - IPR011006
CheY-like superfamily - 37 - 41 + IPR013126
Heat shock protein 70 family + 33 + 80 296 - IPR017970
Homeobox, conserved site - 37 - 37 + IPR006073
GTP binding domain + 33 + 142 297 - IPR019378
GDP-fucose protein O-fucosyltransferase - 37 - 37 + IPR004041
NAF domain + 32 + 45 298 - IPR013126
Heat shock protein 70 family - 37 - 298 + IPR032710
NTF2-like domain superfamily + 32 + 48 299 - IPR000477
  - 37 - 110 + IPR006153
Cation/H+ exchanger + 32 + 46 300 - IPR014721
  - 37 - 90 + IPR001360
Glycoside hydrolase family 1 + 32 + 582 301 - IPR025659
  - 36 - 116 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 32 + 34 302 - IPR013149
Alcohol dehydrogenase, C-terminal - 36 - 36 + IPR008991
Translation protein SH3-like domain superfamily + 32 + 49 303 - IPR003137
PA domain - 36 - 36 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 32 + 42 304 - IPR026960
Reverse transcriptase zinc-binding domain - 36 - 36 + IPR013154
Alcohol dehydrogenase, N-terminal + 32 + 47 305 - IPR022742
Serine aminopeptidase, S33 - 36 - 36 + IPR004367
Cyclin, C-terminal domain + 32 + 48 306 - IPR029045
ClpP/crotonase-like domain superfamily - 36 - 50 + IPR022742
Serine aminopeptidase, S33 + 32 + 44 307 - IPR006501
Pectinesterase inhibitor domain - 36 - 94 + IPR006094
FAD linked oxidase, N-terminal + 32 + 41 308 - IPR028889
  - 36 - 76 + IPR029466
No apical meristem-associated, C-terminal domain + 31 + 32 309 - IPR025661
Cysteine peptidase, asparagine active site - 36 - 36 + IPR018451
NAF/FISL domain + 31 + 44 310 - IPR002912
  - 36 - 144 + IPR038933
Ovate protein family + 31 + 34 311 - IPR008942
  - 35 - 130 + IPR002659
Glycosyl transferase, family 31 + 31 + 103 312 - IPR036612
  - 35 - 345 + IPR005135
Endonuclease/exonuclease/phosphatase + 31 + 51 313 - IPR003594
Histidine kinase/HSP90-like ATPase - 35 - 80 + IPR011676
Domain of unknown function DUF1618 + 31 + 34 314 - IPR004330
FAR1 DNA binding domain - 35 - 41 + IPR004883
Lateral organ boundaries, LOB + 31 + 65 315 - IPR001789
  - 35 - 417 + IPR044839
Protein NDR1-like + 31 + 32 316 - IPR006016
UspA - 34 - 34 + IPR008480
Protein of unknown function DUF761, plant + 31 + 31 317 - IPR001360
Glycoside hydrolase family 1 - 34 - 224 + IPR004046
Glutathione S-transferase, C-terminal + 31 + 36 318 - IPR006626
Parallel beta-helix repeat - 34 - 169 + IPR003311
AUX/IAA protein + 31 + 55 319 - IPR002659
Glycosyl transferase, family 31 - 34 - 67 + IPR003855
Potassium transporter + 31 + 125 320 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 34 - 36 + IPR000315
B-box-type zinc finger + 30 + 76 321 - IPR015947
PUA-like superfamily - 34 - 38 + IPR001296
Glycosyl transferase, family 1 + 30 + 57 322 - IPR006702
Casparian strip membrane protein domain - 34 - 34 + IPR003406
Glycosyl transferase, family 14 + 30 + 58 323 - IPR001251
  - 33 - 254 + IPR003851
Zinc finger, Dof-type + 30 + 62 324 - IPR034161
Pepsin-like domain, plant - 33 - 33 + IPR044791
Beta-glucanase/XTH + 30 + 35 325 - IPR005135
Endonuclease/exonuclease/phosphatase - 33 - 33 + IPR009003
Peptidase S1, PA clan + 30 + 65 326 - IPR004263
Exostosin-like - 33 - 38 + IPR023210
NADP-dependent oxidoreductase domain + 30 + 60 327 - IPR036865
  - 33 - 130 + IPR004330
FAR1 DNA binding domain + 30 + 41 328 - IPR013154
Alcohol dehydrogenase, N-terminal - 33 - 33 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 30 + 56 329 - IPR011012
Longin-like domain superfamily - 33 - 34 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 29 + 140 330 - IPR007125
Histone H2A/H2B/H3 - 33 - 34 + IPR044835
Auxin response factor + 29 + 58 331 - IPR022357
Major intrinsic protein, conserved site - 33 - 33 + IPR026960
Reverse transcriptase zinc-binding domain + 29 + 31 332 - IPR036318
FAD-binding, type 2-like superfamily - 32 - 32 + IPR005630
Terpene synthase, metal-binding domain + 29 + 43 333 - IPR009060
UBA-like superfamily - 32 - 37 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 29 + 50 334 - IPR029466
No apical meristem-associated, C-terminal domain - 32 - 33 + IPR043454
NPH3/RPT2-like family + 29 + 34 335 - IPR011016
  - 32 - 210 + IPR002963
Expansin + 29 + 266 336 - IPR038933
Ovate protein family - 32 - 43 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 29 + 62 337 - IPR001938
  - 32 - 444 + IPR000757
Glycoside hydrolase family 16 + 29 + 64 338 - IPR038770
  - 32 - 68 + IPR000727
Target SNARE coiled-coil homology domain + 28 + 47 339 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 32 - 32 + IPR025110
AMP-binding enzyme, C-terminal domain + 28 + 43 340 - IPR033443
Pentacotripeptide-repeat region of PRORP - 32 - 34 + IPR018490
Cyclic nucleotide-binding-like + 28 + 60 341 - IPR004041
NAF domain - 31 - 31 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 28 + 273 342 - IPR036965
  - 31 - 108 + IPR029000
Cyclophilin-like domain superfamily + 28 + 47 343 - IPR001929
Germin - 31 - 90 + IPR044848
PHR1-like + 28 + 60 344 - IPR006153
Cation/H+ exchanger - 31 - 33 + IPR001594
Palmitoyltransferase, DHHC domain + 28 + 45 345 - IPR019821
Kinesin motor domain, conserved site - 31 + IPR035940
CAP superfamily + 28 31 346 - IPR018200
Ubiquitin specific protease, conserved site - 31 - 54 + IPR027356
NPH3 domain + 28 + 62 347 - IPR018451
  - 31 - 93 + IPR011013
Galactose mutarotase-like domain superfamily + 28 + 52 348 - IPR002068
  - 31 - 118 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 28 + 106 349 - IPR004813
Oligopeptide transporter, OPT superfamily - 31 - 60 + IPR004088
K Homology domain, type 1 + 28 + 113 350 - IPR002495
Glycosyl transferase, family 8 - 31 - 32 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 28 + 30 351 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 31 - 42 + IPR036378
FAS1 domain superfamily + 27 + 41 352 - IPR006458
  - 31 - 168 + IPR024709
Putative O-fucosyltransferase, plant + 27 + 50 353 - IPR003311
AUX/IAA protein - 31 - 34 + IPR010920
LSM domain superfamily + 27 + 38 354 - IPR000595
  - 31 - 218 + IPR002423
Chaperonin Cpn60/TCP-1 family + 27 + 43 355 - IPR003855
Potassium transporter - 31 - 91 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 27 + 40 356 - IPR011042
  - 31 - 76 + IPR027409
GroEL-like apical domain superfamily + 27 + 41 357 - IPR036812
  - 31 - 124 + IPR001757
P-type ATPase + 27 + 144 358 - IPR006073
GTP binding domain - 31 - 87 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 27 + 32 359 - IPR000727
  - 30 - 142 + IPR024752
Myb/SANT-like domain + 27 + 32 360 - IPR001969
Aspartic peptidase, active site - 30 - 39 + IPR000679
Zinc finger, GATA-type + 27 + 85 361 - IPR035940
  - 30 - 124 + IPR005175
PPC domain + 27 + 96 362 - IPR004367
Cyclin, C-terminal domain - 30 - 55 + IPR001929
Germin + 26 + 92 363 - IPR005150
Cellulose synthase - 30 - 45 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 26 + 99 364 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 30 - 180 + IPR000717
Proteasome component (PCI) domain + 26 + 62 365 - IPR038538
  - 30 - 80 + IPR008422
Homeobox KN domain + 26 + 38 366 - IPR004046
Glutathione S-transferase, C-terminal - 30 - 31 + IPR007650
Zf-FLZ domain + 26 + 56 367 - IPR004087
K Homology domain - 30 - 63 + IPR004140
Exocyst complex component Exo70 + 26 + 69 368 - IPR020843
Polyketide synthase, enoylreductase domain - 30 - 30 + IPR002123
Phospholipid/glycerol acyltransferase + 26 + 32 369 - IPR029047
  - 30 - 124 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 26 + 45 370 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 30 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 26 + 33 371 - IPR000757
  - 30 - 177 + IPR005821
Ion transport domain + 26 + 46 372 - IPR037176
  - 30 - 144 + IPR004813
Oligopeptide transporter, OPT superfamily + 26 + 87 373 - IPR018490
Cyclic nucleotide-binding-like - 29 - 30 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 26 + 45 374 - IPR032710
NTF2-like domain superfamily - 29 - 30 + IPR000595
Cyclic nucleotide-binding domain + 26 + 160 375 - IPR001179
  - 29 - 174 + IPR015940
Ubiquitin-associated domain + 25 + 79 376 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 29 - 60 + IPR000782
FAS1 domain + 25 + 69 377 - IPR010920
LSM domain superfamily - 29 - 29 + IPR013216
Methyltransferase type 11 + 25 + 34 378 - IPR001296
Glycosyl transferase, family 1 - 29 - 29 + IPR023753
FAD/NAD(P)-binding domain + 25 + 44 379 - IPR005630
Terpene synthase, metal-binding domain - 29 - 30 + IPR007657
Glycosyltransferase 61 + 25 + 76 380 - IPR004320
Protein of unknown function DUF241, plant - 29 - 29 + IPR027725
Heat shock transcription factor family + 25 + 37 381 - IPR006652
Kelch repeat type 1 - 29 - 111 + IPR000795
Translational (tr)-type GTP-binding domain + 25 + 212 382 - IPR005162
Retrotransposon gag domain - 29 - 29 + IPR001763
Rhodanese-like domain + 25 + 80 383 - IPR003406
Glycosyl transferase, family 14 - 29 - 30 + IPR000408
Regulator of chromosome condensation, RCC1 + 25 + 700 384 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 29 - 39 + IPR005150
Cellulose synthase + 25 + 62 385 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 29 - 101 + IPR001849
Pleckstrin homology domain + 25 + 64 386 - IPR004088
K Homology domain, type 1 - 29 - 62 + IPR023299
P-type ATPase, cytoplasmic domain N + 25 + 50 387 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 29 - 33 + IPR029062
Class I glutamine amidotransferase-like + 25 + 52 388 - IPR002067
Mitochondrial carrier protein - 29 - 144 + IPR001906
Terpene synthase, N-terminal domain + 25 + 31 389 - IPR004314
Neprosin - 29 - 33 + IPR036296
SKP1-like, dimerisation domain superfamily + 25 + 27 390 - IPR009003
Peptidase S1, PA clan - 29 - 36 + IPR001701
Glycoside hydrolase family 9 + 25 + 29 391 - IPR023210
NADP-dependent oxidoreductase domain - 29 - 57 + IPR036427
Bromodomain-like superfamily + 25 + 40 392 - IPR025660
Cysteine peptidase, histidine active site - 29 - 29 + IPR025486
Domain of unknown function DUF4378 + 25 + 32 393 - IPR002130
  - 28 - 510 + IPR004314
Neprosin + 25 + 35 394 - IPR029000
  - 28 - 118 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 132 395 - IPR001594
Palmitoyltransferase, DHHC domain - 28 - 28 + IPR000477
Reverse transcriptase domain + 25 + 40 396 - IPR002423
Chaperonin Cpn60/TCP-1 family - 28 - 28 + IPR002913
START domain + 25 + 78 397 - IPR004140
Exocyst complex component Exo70 - 28 - 60 + IPR010525
Auxin response factor domain + 25 + 44 398 - IPR033131
Pectinesterase, Asp active site - 28 - 28 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 24 + 154 399 - IPR031112
AP2-like ethylene-responsive transcription factor - 28 - 33 + IPR017938
Riboflavin synthase-like beta-barrel + 24 + 38 400 - IPR011676
Domain of unknown function DUF1618 - 28 - 28 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 24 + 25 401 - IPR008480
Protein of unknown function DUF761, plant - 28 - 28 + IPR003106
Leucine zipper, homeobox-associated + 24 + 25 402 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 28 - 28 + IPR013581
Plant PDR ABC transporter associated + 24 + 42 403 - IPR000169
Cysteine peptidase, cysteine active site - 28 - 28 + IPR044778
Sugar transport protein STP/MST-like, plant + 24 + 26 404 - IPR001906
Terpene synthase, N-terminal domain - 28 - 28 + IPR029061
Thiamin diphosphate-binding fold + 24 + 65 405 - IPR002109
  - 28 - 177 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 24 + 27 406 - IPR016040
NAD(P)-binding domain - 27 - 32 + IPR007592
GLABROUS1 enhancer-binding protein family + 24 + 49 407 - IPR025110
AMP-binding enzyme, C-terminal domain - 27 - 27 + IPR000863
Sulfotransferase domain + 24 + 31 408 - IPR017451
F-box associated interaction domain - 27 - 27 + IPR001283
Cysteine-rich secretory protein-related + 24 + 103 409 - IPR007650
  - 27 - 108 + IPR014044
CAP domain + 24 + 26 410 - IPR027356
  - 27 - 110 + IPR039421
Type 1 protein exporter + 24 + 50 411 - IPR031107
Small heat shock protein HSP20 - 27 - 28 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 24 + 52 412 - IPR019780
Germin, manganese binding site - 27 - 27 + IPR015797
NUDIX hydrolase-like domain superfamily + 24 + 32 413 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 27 - 42 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 23 + 34 414 - IPR011043
Galactose oxidase/kelch, beta-propeller - 27 - 28 + IPR013601
FAE1/Type III polyketide synthase-like protein + 23 + 23 415 - IPR009091
  - 27 - 172 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 23 + 24 416 - IPR002913
  - 27 - 210 + IPR036420
BRCT domain superfamily + 23 + 72 417 - IPR027806
Harbinger transposase-derived nuclease domain - 26 - 26 + IPR011016
Zinc finger, RING-CH-type + 23 + 70 418 - IPR008991
Translation protein SH3-like domain superfamily - 26 - 26 + IPR001353
Proteasome, subunit alpha/beta + 23 + 36 419 - IPR000717
  - 26 - 126 + IPR010989
SNARE + 23 + 30 420 - IPR000795
  - 26 - 468 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 23 + 34 421 - IPR033124
Serine carboxypeptidases, histidine active site - 26 - 26 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 23 + 51 422 - IPR000408
  - 26 - 870 + IPR016897
S-phase kinase-associated protein 1 + 23 + 25 423 - IPR004883
  - 26 - 104 + IPR044817
Squamosa promoter-binding-like protein + 23 + 35 424 - IPR027409
  - 26 - 104 + IPR003100
PAZ domain + 22 + 90 425 - IPR005821
Ion transport domain - 26 - 27 + IPR006594
LIS1 homology motif + 22 + 63 426 - IPR014044
CAP domain - 26 + IPR036085
PAZ domain superfamily + 22 50 427 - IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase - 26 - 27 + IPR016461
O-methyltransferase COMT-type + 22 + 57 428 - IPR017938
Riboflavin synthase-like beta-barrel - 25 - 29 + IPR002156
Ribonuclease H domain + 22 + 33 429 - IPR019956
Ubiquitin - 25 - 69 + IPR000387
Tyrosine specific protein phosphatases domain + 22 + 33 430 - IPR036378
  - 25 - 112 + IPR001357
BRCT domain + 22 + 125 431 - IPR024709
Putative O-fucosyltransferase, plant - 25 - 49 + IPR036893
SBP domain superfamily + 22 + 26 432 - IPR008422
Homeobox KN domain - 25 - 25 + IPR003347
JmjC domain + 22 + 63 433 - IPR013216
Methyltransferase type 11 - 25 - 25 + IPR025422
Transcription factor TGA like domain + 22 + 85 434 - IPR007657
Glycosyltransferase 61 - 25 - 58 + IPR003337
Trehalose-phosphatase + 22 + 37 435 - IPR027725
Heat shock transcription factor family - 25 - 31 + IPR003594
Histidine kinase/HSP90-like ATPase + 22 + 42 436 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 25 - 48 + IPR004333
SBP domain + 22 + 52 437 - IPR018181
Heat shock protein 70, conserved site - 25 - 59 + IPR016072
SKP1 component, dimerisation + 22 + 22 438 - IPR002355
Multicopper oxidase, copper-binding site - 25 - 25 + IPR000086
NUDIX hydrolase domain + 22 + 57 439 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 25 - 25 + IPR001487
Bromodomain + 22 + 190 440 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 25 - 28 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 22 + 35 441 - IPR027923
Hydrophobic seed protein - 25 - 49 + IPR029033
Histidine phosphatase superfamily + 22 + 40 442 - IPR002035
  - 25 - 120 + IPR006689
Small GTPase superfamily, ARF/SAR type + 21 + 119 443 - IPR017937
Thioredoxin, conserved site - 25 - 30 + IPR019956
Ubiquitin domain + 21 + 73 444 - IPR006566
FBD domain - 25 - 25 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 21 + 48 445 - IPR006439
HAD hydrolase, subfamily IA - 25 - 62 + IPR006593
Cytochrome b561/ferric reductase transmembrane + 21 + 56 446 - IPR015797
NUDIX hydrolase-like domain superfamily - 25 - 26 + IPR002403
Cytochrome P450, E-class, group IV + 21 + 124 447 - IPR010525
Auxin response factor - 25 - 25 + IPR035952
Rhomboid-like superfamily + 21 + 34 448 - IPR025322
Protein of unknown function DUF4228, plant - 24 - 24 + IPR007612
LURP-one-related + 21 + 44 449 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 24 - 40 + IPR036873
Rhodanese-like domain superfamily + 21 + 41 450 - IPR036420
  - 24 - 156 + IPR008984
SMAD/FHA domain superfamily + 21 + 29 451 - IPR023753
FAD/NAD(P)-binding domain - 24 - 25 + IPR005333
Transcription factor, TCP + 21 + 23 452 - IPR029061
Thiamin diphosphate-binding fold - 24 - 41 + IPR005516
Remorin, C-terminal + 21 + 26 453 - IPR008906
HAT, C-terminal dimerisation domain - 24 - 24 + IPR017887
Transcription factor TCP subgroup + 21 + 42 454 - IPR001353
Proteasome, subunit alpha/beta - 24 - 24 + IPR036010
2Fe-2S ferredoxin-like superfamily + 21 + 27 455 - IPR011074
CRAL/TRIO, N-terminal domain - 24 - 44 + IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain + 21 + 41 456 - IPR016166
  - 24 - 72 + IPR011332
Zinc-binding ribosomal protein + 21 + 24 457 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 24 - 47 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 21 + 25 458 - IPR036866
  - 24 - 126 + IPR036610
PEBP-like superfamily + 21 + 26 459 - IPR000863
Sulfotransferase domain - 24 - 24 + IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily + 21 + 31 460 - IPR023313
Ubiquitin-conjugating enzyme, active site - 24 - 24 + IPR034285
Laccase, second cupredoxin domain + 21 + 23 461 - IPR002963
Expansin - 24 - 196 + IPR002035
von Willebrand factor, type A + 21 + 48 462 - IPR014722
  - 24 - 58 + IPR029069
HotDog domain superfamily + 21 + 47 463 - IPR029062
  - 24 - 118 + IPR016161
Aldehyde/histidinol dehydrogenase + 21 + 43 464 - IPR001701
Glycoside hydrolase family 9 - 24 - 28 + IPR017923
Transcription factor IIS, N-terminal + 21 + 47 465 - IPR036427
  - 24 - 144 + IPR010399
Tify domain + 21 + 45 466 - IPR001487
  - 24 - 408 + IPR036034
PDZ superfamily + 21 + 40 467 - IPR027410
  - 24 - 144 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 21 + 35 468 - IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site - 24 - 24 + IPR044800
B3 domain-containing transcription factor LEC2-like + 21 + 25 469 - IPR017927
  - 23 - 69 + IPR035441
TFIIS/LEDGF domain superfamily + 21 + 23 470 - IPR006689
Small GTPase superfamily, ARF/SAR type - 23 - 96 + IPR006195
Aminoacyl-tRNA synthetase, class II + 20 + 38 471 - IPR015940
  - 23 - 130 + IPR025753
AAA-type ATPase, N-terminal domain + 20 + 21 472 - IPR001357
  - 23 - 260 + IPR001163
LSM domain, eukaryotic/archaea-type + 20 + 26 473 - IPR013581
Plant PDR ABC transporter associated - 23 - 23 + IPR018499
Tetraspanin/Peripherin + 20 + 25 474 - IPR002293
Amino acid/polyamine transporter I - 23 - 45 + IPR000340
Dual specificity phosphatase, catalytic domain + 20 + 32 475 - IPR011332
Zinc-binding ribosomal protein - 23 - 23 + IPR008914
Phosphatidylethanolamine-binding protein + 20 + 25 476 - IPR011013
Galactose mutarotase-like domain superfamily - 23 - 26 + IPR018392
LysM domain + 20 + 79 477 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 23 - 23 + IPR004320
Protein of unknown function DUF241, plant + 20 + 30 478 - IPR020946
Flavin monooxygenase-like - 23 - 33 + IPR027413
GroEL-like equatorial domain superfamily + 20 + 30 479 - IPR005746
Thioredoxin - 23 - 39 + IPR011257
DNA glycosylase + 20 + 37 480 - IPR001849
  - 23 - 124 + IPR002293
Amino acid/polyamine transporter I + 20 + 55 481 - IPR029069
HotDog domain superfamily - 23 - 33 + IPR006694
Fatty acid hydroxylase + 20 + 32 482 - IPR025486
Domain of unknown function DUF4378 - 23 - 23 + IPR020103
Pseudouridine synthase, catalytic domain superfamily + 20 + 61 483 - IPR000086
  - 23 - 135 + IPR034288
Laccase, first cupredoxin domain + 20 + 22 484 - IPR029006
  - 23 - 94 + IPR027923
Hydrophobic seed protein domain + 20 + 47 485 - IPR029033
  - 23 - 106 + IPR020946
Flavin monooxygenase-like + 20 + 34 486 - IPR000679
  - 23 - 234 + IPR001876
Zinc finger, RanBP2-type + 20 + 106 487 - IPR000782
  - 22 - 136 + IPR035810
Phosphatidylethanolamine-binding protein, eukaryotic + 20 + 48 488 - IPR013601
FAE1/Type III polyketide synthase-like protein - 22 - 22 + IPR003388
Reticulon + 20 + 51 489 - IPR036873
  - 22 - 100 + IPR000836
Phosphoribosyltransferase domain + 20 + 49 490 - IPR013088
  - 22 - 66 + IPR002937
Amine oxidase + 20 + 43 491 - IPR003347
  - 22 - 114 + IPR006311
Twin-arginine translocation pathway, signal sequence + 20 + 25 492 - IPR012675
  - 22 - 50 + IPR036443
Zinc finger, RanBP2-type superfamily + 20 + 59 493 - IPR001763
  - 22 - 124 + IPR015590
Aldehyde dehydrogenase domain + 20 + 43 494 - IPR016021
  - 22 - 76 + IPR001574
Ribosome-inactivating protein + 20 + 35 495 - IPR015679
Phospholipase D family - 22 - 23 + IPR016073
SKP1 component, POZ domain + 19 + 20 496 - IPR001876
  - 22 - 240 + IPR008971
HSP40/DnaJ peptide-binding + 19 + 48 497 - IPR016161
Aldehyde/histidinol dehydrogenase - 22 - 22 + IPR016064
NAD kinase/diacylglycerol kinase-like domain superfamily + 19 + 34 498 - IPR036296
SKP1-like, dimerisation domain superfamily - 22 - 24 + IPR004316
SWEET sugar transporter + 19 + 57 499 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 22 - 22 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 19 + 24 500 - IPR031127
E3 ubiquitin ligase RBR family - 22 - 32 + IPR027806
Harbinger transposase-derived nuclease domain + 19 + 20 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_carolina.html b/gramene/htdocs/ssi/species/stats_Oryza_carolina.html new file mode 100644 index 00000000..be5273f5 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_carolina.html @@ -0,0 +1,263 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:CGRFv1,
Database version:87.1
Base Pairs:386,338,064
Golden Path Length:386,338,064
Genebuild by: Maker
Genebuild method: Warelab Maker-P annotation
Genebuild started: Jul 2018
Genebuild version: 2018-07-Maker
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,885
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:54,344
+ + +

Coordinate Systems

+ + + + + + + + +
contig
+
209 sequences
+
+ +
+ + + +
SequenceLength (bp)
tig00000002160227
tig0000000477407
tig0000000895889
tig0000001360103
tig00000014129457
tig00000016129375
tig0000001859560
tig0000001980998
tig0000002166449
tig0000002351030
tig0000002791183
tig0000003580216
tig00000038124001
tig0000003961408
tig00000049105692
tig00000074a8614523
tig00000074b9386108
tig000000782032043
tig000000857664127
tig000001033958330
tig0000015637043
tig00000176118536
tig0000021952186
tig0000025620220626
tig0000026025653
tig00000338990607
tig0000036266705
tig00000364545125
tig000004366619025
tig00000460555095
tig0000063581473
tig0000104439992
tig000010624439422
tig0000109652312
tig000012741762723
tig0000129048696
tig0000132611032741
tig000014859685813
tig0000150242553
tig0000152841571
tig0000162742479
tig00001716583222
tig0000178059238
tig000019853096471
tig0000218170085
tig0000225039330
tig0000225557758
tig0000252552182
tig000026111384223
tig0000271196339
tig0000278349553
tig0000281430305
tig00002831107271
tig00002838135671
tig0000284049261
tig0000285075194
tig0000287249272
tig0000288142016
tig00002888124878
tig0000291360471
tig00002922138091
tig0000296339610
tig00002969159510
tig0000297271339
tig0000299498894
tig0000301247742
tig00003033108768
tig0000309957824
tig0000310248934
tig00003141156148
tig0000318729262
tig0000319144748
tig00003200109170
tig00003201120889
tig00003202108079
tig0000321032922
tig00003241106751
tig00003243109049
tig0000325355148
tig0000332127869
tig0000335976960
tig0000336274092
tig0000340256343
tig0000340468614
tig0000341062368
tig0000341370157
tig0000343953383
tig0000345264794
tig0000346873959
tig0000350142264
tig0000350731909
tig0000353766623
tig0000355149086
tig0000361138512
tig0000362436072
tig0000364741240
tig0000369439939
tig0000369924055
tig0000370552001
tig0000373814779
tig0000376975738
tig0000383648272
tig0000384251348
tig0000384732086
tig0000386055533
tig0000391237510
tig000039895974
tig000041254136
tig000041517477
tig000041823972
tig0000422219603
tig00027329164847
tig0002733022269229
tig0002733121064
tig000273322338332
tig000273343029434
tig0002733723390289
tig0002733843617
tig00027339992608
tig0002734120461179
tig0002734256961
tig000273431830093
tig0002734414135645
tig0002734543822
tig0002734656356
tig000273482935044
tig0002734950773
tig00027350688067
tig000273522174261
tig000273548654799
tig0002735552001
tig00027356384091
tig0002735748150
tig0002735998992
tig0002736551546
tig0002737063554
tig0002737260324
tig00027374154539
tig0002737733742
tig000273834564581
tig0002738519062658
tig00027386594076
tig0002738745621
tig0002738883762
tig0002738913413199
tig0002739057047
tig000273916545815
tig000273928241
tig000273931591272
tig0002739544568
tig000273961019373
tig0002739739539
tig0002739810193138
tig000274009682158
tig00027402799915
tig000274032286359
tig0002740465140
tig0002740514711342
tig0002741253718
tig0002741415929712
tig00027415188104
tig00027416136877
tig0002741786576
tig0002741871976
tig0002741999582
tig000274206289440
tig000274216025335
tig00027423648608
tig0002742442781
tig0002742512880937
tig00027426206798
tig000274276237148
tig0002742844062
tig00027429148793
tig00027430193460
tig00027431113746
tig0002743211627331
tig000274339727910
tig0002743564817
tig000274369217371
tig0002743835458
tig000274393896075
tig0002744023938
tig000274412737666
tig0002744258680
tig000274433081249
tig0002744429242
tig00027447112778
tig000274485642938
tig0002744963498
tig0002745163035
tig00027452133069
tig000274531476636
tig00027456132092
tig00027458106940
tig00027459126490
tig0002746082787
tig0002746136414
tig0002746275827
tig0002746497443
tig00027467125767
tig0002746859829
tig0002747028935
tig0002747134870
tig0002747234457
tig0002747664338
tig0002747852443
tig0002748748136
tig0002748910001
+
+
chunk3967 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_carolina_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_carolina_IPtop500.html new file mode 100644 index 00000000..7108981f --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_carolina_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain		14492361
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		13862574
3IPR000719
Protein kinase domain		13793745
4IPR036047
F-box-like domain superfamily		705926
5IPR001810
F-box domain		509993
6IPR044974
Disease resistance protein, plants		503907
7IPR002885
Pentatricopeptide repeat		4668138
8IPR001245
Serine-threonine/tyrosine-protein kinase catalytic domain		4571039
9IPR001841
Zinc finger, RING-type		4561020
10IPR002182
NB-ARC		445623
11IPR001611
Leucine-rich repeat		4341558
12IPR036291
NAD(P)-binding domain superfamily		390666
13IPR029058
Alpha/Beta hydrolase fold		373613
14IPR016024
Armadillo-type fold		372722
15IPR009057
Homeodomain-like		360569
16IPR041118
Rx, N-terminal		350465
17IPR036396
Cytochrome P450 superfamily		324392
18IPR001128
Cytochrome P450		3171497
19IPR011990
Tetratricopeptide-like helical domain		316625
20IPR035979
RNA-binding domain superfamily		297763
21IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		286401
22IPR002401
Cytochrome P450, E-class, group I		2731995
23IPR038765
Papain-like cysteine peptidase superfamily		272397
24IPR036259
MFS transporter superfamily		271459
25IPR012337
Ribonuclease H-like domain		265361
26IPR001005
SANT/Myb domain		2652107
27IPR017853
Glycoside hydrolase superfamily		264458
28IPR000504
RNA recognition motif domain		2631509
29IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		258485
30IPR038005
Virus X resistance protein-like, coiled-coil domain		237319
31IPR036249
Thioredoxin-like superfamily		234405
32IPR017930
Myb domain		221425
33IPR036322
WD40-repeat-containing domain superfamily		209419
34IPR001680
WD40 repeat		1911994
35IPR011333
SKP1/BTB/POZ domain		188241
36IPR011992
EF-hand domain pair		188264
37IPR016177
DNA-binding domain		178264
38IPR002048
EF-hand domain		1741013
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		174359
40IPR036412
HAD-like superfamily		164298
41IPR036770
Ankyrin repeat-containing domain superfamily		162266
42IPR001471
AP2/ERF domain		160942
43IPR013320
Concanavalin A-like lectin/glucanase domain		159208
44IPR036638
Helix-loop-helix DNA-binding domain superfamily		158244
45IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		157168
46IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		154437
47IPR036390
Winged helix DNA-binding domain superfamily		153230
48IPR021109
Aspartic peptidase domain		149187
49IPR002110
Ankyrin repeat		146739
50IPR003441
NAC domain		143698
51IPR000210
BTB/POZ domain		143359
52IPR036236
Zinc finger C2H2 superfamily		142227
53IPR012340
Nucleic acid-binding, OB-fold		141325
54IPR010255
Haem peroxidase		141160
55IPR005174
Domain unknown function DUF295		139160
56IPR002016
Haem peroxidase, plant/fungal/bacterial		137931
57IPR036875
Zinc finger, CCHC-type superfamily		135233
58IPR029044
Nucleotide-diphospho-sugar transferases		132203
59IPR001878
Zinc finger, CCHC-type		132444
60IPR036188
FAD/NAD(P)-binding domain superfamily		131271
61IPR001650
Helicase, C-terminal		129511
62IPR007087
Zinc finger, C2H2		129514
63IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain		12935
64IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		128185
65IPR045005
BTB/POZ and MATH domain-containing protein 1-6		128163
66IPR014001
Helicase superfamily 1/2, ATP-binding domain		128250
67IPR020683
Ankyrin repeat-containing domain		125307
68IPR003480
Transferase		124132
69IPR043502
DNA/RNA polymerase superfamily		123149
70IPR033121
Peptidase family A1 domain		122141
71IPR000823
Plant peroxidase		1191013
72IPR036426
Bulb-type lectin domain superfamily		117180
73IPR020846
Major facilitator superfamily domain		115188
74IPR003439
ABC transporter-like		115522
75IPR002083
MATH/TRAF domain		114306
76IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		114123
77IPR032799
Xylanase inhibitor, C-terminal		113125
78IPR032861
Xylanase inhibitor, N-terminal		113134
79IPR001480
Bulb-type lectin domain		113464
80IPR007527
Zinc finger, SWIM-type		112223
81IPR018289
MULE transposase domain		109128
82IPR033905
Secretory peroxidase		109119
83IPR036869
Chaperone J-domain superfamily		109181
84IPR008972
Cupredoxin		107203
85IPR031052
FHY3/FAR1 family		105192
86IPR019734
Tetratricopeptide repeat		104441
87IPR003653
Ulp1 protease family, C-terminal catalytic domain		103232
88IPR011676
Domain of unknown function DUF1618		103138
89IPR003959
ATPase, AAA-type, core		103198
90IPR025315
Domain of unknown function DUF4220		103112
91IPR001623
DnaJ domain		102837
92IPR011011
Zinc finger, FYVE/PHD-type		101202
93IPR029071
Ubiquitin-related domain		100178
94IPR005123
Oxoglutarate/iron-dependent dioxygenase		98372
95IPR003609
PAN/Apple domain		97289
96IPR003657
WRKY domain		97664
97IPR000109
Proton-dependent oligopeptide transporter family		96304
98IPR007658
Protein of unknown function DUF594		96101
99IPR002347
Glucose/ribitol dehydrogenase		95609
100IPR015424
Pyridoxal phosphate-dependent transferase		95149
101IPR000858
S-locus glycoprotein domain		94146
102IPR035892
C2 domain superfamily		93200
103IPR001087
GDSL lipase/esterase		93120
104IPR005828
Major facilitator, sugar transporter-like		93153
105IPR001461
Aspartic peptidase		93351
106IPR011051
RmlC-like cupin domain		93131
107IPR036282
Glutathione S-transferase, C-terminal domain superfamily		90117
108IPR044810
WRKY transcription factor, plant		90129
109IPR036457
PPM-type phosphatase domain superfamily		89163
110IPR011050
Pectin lyase fold/virulence factor		88114
111IPR001220
Legume lectin domain		88179
112IPR002198
Short-chain dehydrogenase/reductase SDR		87694
113IPR001356
Homeobox domain		87342
114IPR001932
PPM-type phosphatase domain		86443
115IPR015300
DNA-binding pseudobarrel domain		85207
116IPR004330
FAR1 DNA binding domain		84113
117IPR002902
Gnk2-homologous domain		83409
118IPR004045
Glutathione S-transferase, N-terminal		82232
119IPR009072
Histone-fold		82103
120IPR004158
Protein of unknown function DUF247, plant		81179
121IPR035669
GDSL lipase/esterase-like, plant		8089
122IPR002156
Ribonuclease H domain		79107
123IPR000008
C2 domain		79394
124IPR000073
Alpha/beta hydrolase fold-1		79248
125IPR003340
B3 DNA binding domain		78530
126IPR012871
Protein of unknown function DUF1677, Oryza sativa		7897
127IPR026961
PGG domain		78168
128IPR020472
G-protein beta WD-40 repeat		78420
129IPR010987
Glutathione S-transferase, C-terminal-like		78101
130IPR011545
DEAD/DEAH box helicase domain		78159
131IPR032867
DYW domain		7898
132IPR004827
Basic-leucine zipper domain		78253
133IPR043129
ATPase, nucleotide binding domain		76220
134IPR013766
Thioredoxin domain		75103
135IPR026992
Non-haem dioxygenase N-terminal domain		7593
136IPR003613
U box domain		74213
137IPR000477
Reverse transcriptase domain		71129
138IPR002100
Transcription factor, MADS-box		70480
139IPR044965
Glycoside hydrolase family 17, plant		70119
140IPR036879
Transcription factor, MADS-box superfamily		70105
141IPR016039
Thiolase-like		69166
142IPR012336
Thioredoxin-like fold		68271
143IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6868
144IPR036915
Cyclin-like superfamily		68187
145IPR000270
PB1 domain		68163
146IPR006121
Heavy metal-associated domain, HMA		67239
147IPR036908
RlpA-like domain superfamily		6774
148IPR036691
Endonuclease/exonuclease/phosphatase superfamily		66116
149IPR036163
Heavy metal-associated domain superfamily		6695
150IPR026960
Reverse transcriptase zinc-binding domain		6568
151IPR000490
Glycoside hydrolase family 17		6596
152IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		64175
153IPR000626
Ubiquitin domain		63181
154IPR036749
Expansin, cellulose-binding-like domain superfamily		6369
155IPR013094
Alpha/beta hydrolase fold-3		6372
156IPR019787
Zinc finger, PHD-finger		62185
157IPR003676
Small auxin-up RNA		6264
158IPR008949
Isoprenoid synthase domain		61102
159IPR016159
Cullin repeat-like-containing domain		6192
160IPR007117
Expansin, cellulose-binding-like domain		61134
161IPR013057
Amino acid transporter, transmembrane domain		6091
162IPR006501
Pectinesterase inhibitor domain		6060
163IPR029052
Metallo-dependent phosphatase-like		6097
164IPR009003
Peptidase S1, PA clan		60179
165IPR024788
Malectin-like carbohydrate-binding domain		6088
166IPR000048
IQ motif, EF-hand binding site		60513
167IPR026057
PC-Esterase		5977
168IPR022059
Protein of unknown function DUF3615		5984
169IPR020568
Ribosomal protein S5 domain 2-type fold		59136
170IPR005202
Transcription factor GRAS		59227
171IPR004864
Late embryogenesis abundant protein, LEA-14		5864
172IPR006045
Cupin 1		5883
173IPR003663
Sugar/inositol transporter		58362
174IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		5759
175IPR029962
Trichome birefringence-like family		5771
176IPR001509
NAD-dependent epimerase/dehydratase, N-terminal domain		57101
177IPR003245
Phytocyanin domain		57118
178IPR015500
Peptidase S8, subtilisin-related		57309
179IPR044730
Ribonuclease H-like domain, plant type		5759
180IPR001806
Small GTPase superfamily		57157
181IPR004843
Calcineurin-like phosphoesterase domain, apaH type		5690
182IPR034161
Pepsin-like domain, plant		5660
183IPR013763
Cyclin-like		56147
184IPR029045
ClpP/crotonase-like domain		5678
185IPR036852
Peptidase S8/S53 domain superfamily		5670
186IPR001563
Peptidase S10, serine carboxypeptidase		55562
187IPR019557
Aminotransferase-like, plant mobile domain		5574
188IPR039391
Phytocyanin		5558
189IPR025846
PMR5 N-terminal domain		5569
190IPR006566
FBD domain		5575
191IPR000571
Zinc finger, CCCH-type		55393
192IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5490
193IPR018108
Mitochondrial substrate/solute carrier		54506
194IPR023395
Mitochondrial carrier domain		5496
195IPR000209
Peptidase S8/S53 domain		5469
196IPR004265
Plant disease resistance response protein		5355
197IPR002528
Multi antimicrobial extrusion protein		53180
198IPR007112
Expansin/pollen allergen, DPBB domain		5259
199IPR041469
Subtilisin-like protease, fibronectin type-III domain		5160
200IPR001584
Integrase, catalytic core		5173
201IPR016181
Acyl-CoA N-acyltransferase		5181
202IPR009009
RlpA-like double-psi beta-barrel domain		5158
203IPR015915
Kelch-type beta propeller		51104
204IPR000225
Armadillo		51265
205IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5058
206IPR011701
Major facilitator superfamily		50108
207IPR004332
Transposase, MuDR, plant		5050
208IPR013201
Cathepsin propeptide inhibitor domain (I29)		5059
209IPR036465
von Willebrand factor A-like domain superfamily		5089
210IPR002921
Fungal lipase-like domain		4985
211IPR006671
Cyclin, N-terminal		4991
212IPR001752
Kinesin motor domain		49559
213IPR013525
ABC-2 type transporter		48119
214IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		4860
215IPR004140
Exocyst complex protein Exo70		48155
216IPR000668
Peptidase C1A, papain C-terminal		48200
217IPR000620
EamA domain		48145
218IPR044808
Ethylene-responsive transcription factor		4853
219IPR011032
GroES-like		4775
220IPR008250
P-type ATPase, A domain		4782
221IPR000742
EGF-like domain		4760
222IPR023298
P-type ATPase, transmembrane domain		4783
223IPR007118
Expansin/Lol pI		46287
224IPR012946
X8 domain		4671
225IPR030184
WAT1-related protein		46103
226IPR000608
Ubiquitin-conjugating enzyme E2		45186
227IPR034197
Cucumisin-like catalytic domain		4554
228IPR008979
Galactose-binding domain-like		45110
229IPR045087
Multicopper oxidase		4554
230IPR001906
Terpene synthase, N-terminal domain		4561
231IPR005630
Terpene synthase, metal-binding domain		4464
232IPR017884
SANT domain		4370
233IPR008978
HSP20-like chaperone		4361
234IPR004100
ATPase, F1 complex alpha/beta subunit, N-terminal domain		4345
235IPR000330
SNF2-related, N-terminal domain		4390
236IPR001214
SET domain		43129
237IPR011707
Multicopper oxidase, type 3		4347
238IPR001117
Multicopper oxidase, type 1		4245
239IPR000182
GNAT domain		42114
240IPR029055
Nucleophile aminohydrolases, N-terminal		4274
241IPR008928
Six-hairpin glycosidase-like		4265
242IPR011706
Multicopper oxidase, type 2		4245
243IPR014756
Immunoglobulin E-set		4290
244IPR024752
Myb/SANT-like domain		4247
245IPR015947
PUA-like domain		4271
246IPR043926
ABC transporter family G domain		4182
247IPR036318
FAD-binding, type PCMH-like superfamily		4150
248IPR000873
AMP-dependent synthetase/ligase		4175
249IPR036121
ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily		4142
250IPR004046
Glutathione S-transferase, C-terminal		4154
251IPR041569
AAA ATPase, AAA+ lid domain		4174
252IPR008889
VQ		4141
253IPR001929
Germin		40122
254IPR006016
UspA		4071
255IPR033896
MADS MEF2-like		4068
256IPR036001
Photosystem antenna protein-like superfamily		4041
257IPR044822
Myb/SANT-like DNA-binding domain 4		4058
258IPR009000
Translation protein, beta-barrel domain		4069
259IPR004263
Exostosin-like		40154
260IPR014014
RNA helicase, DEAD-box type, Q motif		4070
261IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4077
262IPR011006
CheY-like superfamily		4054
263IPR007125
Histone H2A/H2B/H3		4048
264IPR000932
Photosystem antenna protein-like		40122
265IPR039417
Papain-like cysteine endopeptidase		4048
266IPR011043
Galactose oxidase/kelch, beta-propeller		4050
267IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4068
268IPR000743
Glycoside hydrolase, family 28		4060
269IPR001789
Signal transduction response regulator, receiver domain		40101
270IPR004853
Sugar phosphate transporter domain		3989
271IPR029466
No apical meristem-associated, C-terminal domain		3941
272IPR037176
Osmotin/thaumatin-like superfamily		3943
273IPR010402
CCT domain		38130
274IPR025659
Tubby C-terminal-like domain		3859
275IPR036640
ABC transporter type 1, transmembrane domain superfamily		38108
276IPR009060
UBA-like		3872
277IPR011012
Longin-like domain		3875
278IPR015655
Protein phosphatase 2C family		3872
279IPR002495
Glycosyl transferase, family 8		3856
280IPR000644
CBS domain		38207
281IPR002109
Glutaredoxin		3846
282IPR039361
Cyclin		3866
283IPR001223
Glycoside hydrolase family 18, catalytic domain		3880
284IPR036855
Zinc finger, CCCH-type superfamily		38149
285IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3741
286IPR008906
HAT, C-terminal dimerisation domain		3745
287IPR004320
Protein of unknown function DUF241, plant		3739
288IPR001938
Thaumatin		37262
289IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3760
290IPR011527
ABC transporter type 1, transmembrane domain		37214
291IPR028889
Ubiquitin specific protease domain		3758
292IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase		3742
293IPR006702
Domain of unknown function DUF588		3748
294IPR016461
O-methyltransferase COMT-type		3686
295IPR007493
Protein of unknown function DUF538		36155
296IPR005299
SAM dependent carboxyl methyltransferase		36110
297IPR029021
Protein-tyrosine phosphatase-like		3679
298IPR003137
PA domain		3657
299IPR016166
FAD-binding, type 2		3645
300IPR003690
Mitochodrial transcription termination factor		36116
301IPR027923
Hydrophobic seed protein		3671
302IPR013126
Heat shock protein 70 family		3683
303IPR003311
AUX/IAA protein		36185
304IPR000070
Pectinesterase, catalytic		3642
305IPR004041
NAF domain		3555
306IPR018451
NAF/FISL domain		3555
307IPR043454
NPH3/RPT2-like family		3547
308IPR004314
Domain of unknown function DUF239		3551
309IPR002912
ACT domain		35120
310IPR036041
Ribosome-inactivating protein superfamily		3538
311IPR001574
Ribosome-inactivating protein		3568
312IPR008942
ENTH/VHS		3458
313IPR000528
Plant lipid transfer protein/Par allergen		34169
314IPR025322
Protein of unknown function DUF4228, plant		3434
315IPR035940
CAP superfamily		3439
316IPR019378
GDP-fucose protein O-fucosyltransferase		3480
317IPR002487
Transcription factor, K-box		34123
318IPR036612
K Homology domain, type 1 superfamily		33116
319IPR002659
Glycosyl transferase, family 31		33115
320IPR027356
NPH3 domain		3382
321IPR004367
Cyclin, C-terminal domain		3347
322IPR000863
Sulfotransferase domain		3337
323IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related		33153
324IPR001077
O-methyltransferase, family 2		3339
325IPR014044
CAP domain		3338
326IPR001099
Chalcone/stilbene synthase, N-terminal		3337
327IPR016040
NAD(P)-binding domain		3256
328IPR001360
Glycoside hydrolase, family 1		32467
329IPR002068
Alpha crystallin/Hsp20 domain		3277
330IPR038933
Ovate protein family		3233
331IPR044824
Protein MAINTENANCE OF MERISTEMS-like		3260
332IPR005135
Endonuclease/exonuclease/phosphatase		3260
333IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3243
334IPR013154
Alcohol dehydrogenase, N-terminal		3245
335IPR000484
Photosynthetic reaction centre, L/M		32136
336IPR044675
E3 ubiquitin-protein ligase RING1-like		3232
337IPR005150
Cellulose synthase		3273
338IPR004883
Lateral organ boundaries, LOB		3277
339IPR006458
Ovate protein family, C-terminal		3262
340IPR043519
Nucleotidyltransferase superfamily		3269
341IPR011141
Polyketide synthase, type III		3240
342IPR012967
Plant methyltransferase dimerisation		3235
343IPR036854
Photosystem II protein D1/D2 superfamily		3232
344IPR013149
Alcohol dehydrogenase, C-terminal		3140
345IPR001251
CRAL-TRIO lipid binding domain		31149
346IPR003656
Zinc finger, BED-type		3152
347IPR036865
CRAL-TRIO lipid binding domain superfamily		3152
348IPR006652
Kelch repeat type 1		31101
349IPR006311
Twin-arginine translocation pathway, signal sequence		3136
350IPR006073
GTP binding domain		31123
351IPR000315
B-box-type zinc finger		30105
352IPR044848
PHR1-like		3069
353IPR001296
Glycosyl transferase, family 1		3059
354IPR001907
ATP-dependent Clp protease proteolytic subunit		30134
355IPR000795
Transcription factor, GTP-binding domain		30296
356IPR022742
Serine aminopeptidase, S33		3056
357IPR004839
Aminotransferase, class I/classII		3051
358IPR033443
Pentacotripeptide-repeat region of PRORP		3053
359IPR006094
FAD linked oxidase, N-terminal		3034
360IPR002067
Mitochondrial carrier protein		30246
361IPR036296
SKP1-like, dimerisation domain superfamily		3031
362IPR023562
Clp protease proteolytic subunit /Translocation-enhancing protein TepA		3062
363IPR036812
NADP-dependent oxidoreductase domain superfamily		3054
364IPR040417
Glycine-rich cell wall structural protein 1/2		2938
365IPR029061
Thiamin diphosphate-binding fold		2968
366IPR023271
Aquaporin-like		2935
367IPR007650
Zf-FLZ domain		2970
368IPR045048
F-box only protein 31/39		2951
369IPR016897
S-phase kinase-associated protein 1		2931
370IPR000425
Major intrinsic protein		29256
371IPR023299
P-type ATPase, cytoplasmic domain N		2958
372IPR000793
ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal		2958
373IPR008927
6-phosphogluconate dehydrogenase C-terminal domain-like		2965
374IPR044791
Beta-glucanase/XTH		2938
375IPR004242
Transposon, En/Spm-like		2936
376IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		2976
377IPR002867
IBR domain		2863
378IPR024709
O-fucosyltransferase, plant		2872
379IPR007641
RNA polymerase Rpb2, domain 7		2831
380IPR001881
EGF-like calcium-binding domain		2835
381IPR034294
Aquaporin transporter		2840
382IPR003337
Trehalose-phosphatase		2849
383IPR005162
Retrotransposon gag domain		2828
384IPR008480
Protein of unknown function DUF761, plant		2828
385IPR034285
Laccase, second cupredoxin domain		2829
386IPR012328
Chalcone/stilbene synthase, C-terminal		2830
387IPR023210
NADP-dependent oxidoreductase domain		2853
388IPR000757
Glycoside hydrolase, family 16		2872
389IPR025110
AMP-binding enzyme C-terminal domain		2739
390IPR015940
Ubiquitin-associated domain		2791
391IPR032710
NTF2-like domain		2743
392IPR025753
AAA-type ATPase, N-terminal domain		2728
393IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2790
394IPR036376
Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily		2727
395IPR027806
Harbinger transposase-derived nuclease domain		2727
396IPR036186
Serpin superfamily		2729
397IPR000717
Proteasome component (PCI) domain		2764
398IPR013216
Methyltransferase type 11		2745
399IPR009068
S15/NS1, RNA-binding		2732
400IPR036422
RuBisCO large subunit, N-terminal domain superfamily		2727
401IPR000215
Serpin family		2731
402IPR017443
Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal		2729
403IPR015712
DNA-directed RNA polymerase, subunit 2		27102
404IPR016072
SKP1 component, dimerisation		2728
405IPR034288
Laccase, first cupredoxin domain		2729
406IPR044839
Protein NDR1-like		2727
407IPR004813
Oligopeptide transporter, OPT superfamily		2750
408IPR004088
K Homology domain, type 1		27100
409IPR001849
Pleckstrin homology domain		2787
410IPR025724
GAG-pre-integrase domain		2727
411IPR031127
E3 ubiquitin ligase RBR family		2761
412IPR003855
Potassium transporter		27105
413IPR029047
Heat shock protein 70kD, peptide-binding domain		2731
414IPR036603
RNA polymerase, RBP11-like subunit		2730
415IPR044066
TRIAD supradomain		2737
416IPR023796
Serpin domain		2731
417IPR000589
Ribosomal protein S15		2660
418IPR018490
Cyclic nucleotide-binding-like		2645
419IPR006153
Cation/H+ exchanger		2643
420IPR025525
hAT-like transposase, RNase-H fold		2632
421IPR013187
F-box associated domain, type 3		2630
422IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		26150
423IPR010920
LSM domain		2634
424IPR000685
Ribulose bisphosphate carboxylase, large subunit, C-terminal		2637
425IPR044835
Auxin response factor		2663
426IPR036420
BRCT domain superfamily		2672
427IPR001594
Zinc finger, DHHC-type, palmitoyltransferase		2650
428IPR005333
Transcription factor, TCP		2676
429IPR002423
Chaperonin Cpn60/TCP-1 family		2648
430IPR007120
DNA-directed RNA polymerase, subunit 2, domain 6		2629
431IPR003406
Glycosyl transferase, family 14		2642
432IPR033966
RuBisCO		2639
433IPR001971
Ribosomal protein S11		2643
434IPR002963
Expansin		26225
435IPR001469
ATPase, F1 complex, delta/epsilon subunit		2629
436IPR002035
von Willebrand factor, type A		2664
437IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2631
438IPR036404
Jacalin-like lectin domain superfamily		2645
439IPR000595
Cyclic nucleotide-binding domain		26108
440IPR000722
RNA polymerase, alpha subunit		2640
441IPR005175
PPC domain		2699
442IPR002913
START domain		26106
443IPR000727
Target SNARE coiled-coil homology domain		2555
444IPR016073
SKP1 component, POZ domain		2525
445IPR036378
FAS1 domain superfamily		2547
446IPR009025
DNA-directed RNA polymerase, RBP11-like dimerisation domain		2552
447IPR029000
Cyclophilin-like domain		2544
448IPR008991
Translation protein SH3-like domain		2541
449IPR007657
Glycosyltransferase AER61, uncharacterised		2582
450IPR009030
Growth factor receptor cysteine-rich domain		2530
451IPR002123
Phospholipid/glycerol acyltransferase		2534
452IPR011013
Galactose mutarotase-like domain		2548
453IPR044814
Terpene cyclases, class 1, plant		2534
454IPR004014
Cation-transporting P-type ATPase, N-terminal		2535
455IPR027409
GroEL-like apical domain		2543
456IPR020546
ATPase, F1 complex, delta/epsilon subunit, N-terminal		2525
457IPR036771
F0F1 ATP synthase delta/epsilon subunit, N-terminal		2525
458IPR000679
Zinc finger, GATA-type		25134
459IPR001229
Jacalin-like lectin domain		2588
460IPR036643
DNA-directed RNA polymerase, insert domain superfamily		2527
461IPR036085
PAZ domain superfamily		2444
462IPR013601
FAE1/Type III polyketide synthase-like protein		2429
463IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2429
464IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		24247
465IPR004316
SWEET sugar transporter		2445
466IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C-terminal		2430
467IPR001357
BRCT domain		24121
468IPR044778
Sugar transport protein STP/MST-like, plant		2427
469IPR027725
Heat shock transcription factor family		2433
470IPR029480
Transposase-associated domain		2424
471IPR004252
Probable transposase, Ptta/En/Spm, plant		2433
472IPR005821
Ion transport domain		2441
473IPR007642
RNA polymerase Rpb2, domain 2		2427
474IPR007645
RNA polymerase Rpb2, domain 3		2426
475IPR034289
Laccase, third cupredoxin domain		2425
476IPR041677
DNA2/NAM7 helicase, helicase domain		2462
477IPR015797
NUDIX hydrolase domain-like		2430
478IPR011262
DNA-directed RNA polymerase, insert domain		2426
479IPR017938
Riboflavin synthase-like beta-barrel		2347
480IPR003106
Leucine zipper, homeobox-associated		2327
481IPR007612
LURP1-related protein domain		2360
482IPR017887
Transcription factor TCP subgroup		2323
483IPR001763
Rhodanese-like domain		2366
484IPR000408
Regulator of chromosome condensation, RCC1		23872
485IPR036273
CRAL/TRIO, N-terminal domain superfamily		2335
486IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2343
487IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2351
488IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain		2334
489IPR041679
DNA2/NAM7 helicase-like, C-terminal		2389
490IPR004146
DC1		2338
491IPR029069
HotDog domain		2350
492IPR003851
Zinc finger, Dof-type		2356
493IPR001701
Glycoside hydrolase, family 9		2330
494IPR000232
Heat shock factor (HSF)-type, DNA-binding		23118
495IPR002937
Amine oxidase		2349
496IPR010525
Auxin response factor		2345
497IPR017927
Ferredoxin reductase-type FAD-binding domain		2240
498IPR009606
Protein of unknown function DUF1218		2230
499IPR000782
FAS1 domain		2274
500IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain		2241
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_glaberrima.html b/gramene/htdocs/ssi/species/stats_Oryza_glaberrima.html index e2cd2ac9..a7c6592e 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_glaberrima.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_glaberrima.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:AGI1.1, May 2011AGI_PacBIO,
Database version:93.287.4
Base Pairs:316,419,574347,321,046
Golden Path Length:316,419,574347,321,046
Genebuild by: AGI
Genebuild method: Imported from MIPS
Genebuild started: May 2011
Genebuild version: 2011-05-AGI
+ Genebuild by: CSHL Genebuild started: Jul 2018 Genebuild version: 2018-07-CSHL

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):33,164Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		37,833
Gene transcriptsHASH(0x68ce400):74,579Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:51,231
@@ -37,46 +37,77 @@

Coordinate Systems

chromosome
-
12 sequences
+
59 sequences
+1
SequenceLength (bp)
132613412
229142869
333053699
426299011
523192814
624174485
721799424
820292731
917607432
1016910673
1120796451
1219154523
39656875
234451706
335526804
431572834
526274045
629275208
726599614
825472747
921796211
1022418184
1126393634
1225020143
UN-Ctg37241712
UN-Ctg38285771
UN-Ctg39220846
UN-Ctg40136550
UN-Ctg41104094
UN-Ctg4299044
UN-Ctg4392801
UN-Ctg4490830
UN-Ctg4589626
UN-Ctg4682446
UN-Ctg4774458
UN-Ctg4873113
UN-Ctg4970610
UN-Ctg5067074
UN-Ctg5162711
UN-Ctg5262187
UN-Ctg5360608
UN-Ctg5457716
UN-Ctg5554206
UN-Ctg5648475
UN-Ctg5747599
UN-Ctg5843218
UN-Ctg5942752
UN-Ctg6040563
UN-Ctg6137872
UN-Ctg6236687
UN-Ctg6335359
UN-Ctg6434083
UN-Ctg6533756
UN-Ctg6633214
UN-Ctg6732611
UN-Ctg6832466
UN-Ctg6932005
UN-Ctg7030676
UN-Ctg7129811
UN-Ctg7228023
UN-Ctg7327666
UN-Ctg7427637
UN-Ctg7523984
UN-Ctg7623015
UN-Ctg7721693
UN-Ctg7821053
UN-Ctg7919363
UN-Ctg8015054
UN-Ctg8113998
UN-Ctg8213471
UN-Ctg8310534
-
+
- scaffold - 1939 sequences - - chunk - 4890 sequences + 3504 sequences - -

Other

- - - - - - - - - -
FGENESH gene predictions:27,943
Short Variants (SNPs, indels, somatic mutations):7,704,409
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_glaberrima_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_glaberrima_IPtop500.html index 58a8c8be..12fb5b13 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_glaberrima_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_glaberrima_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1327 - 1436 + 1489 + 2188 2 - IPR000719
  - 1264 - 9498 + IPR000719
Protein kinase domain + 1417 + 3463 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1193 - 1575 + 1411 + 2293 4 - IPR008271
Serine/threonine-protein kinase, active site - 1009 - 1011 + IPR036047
F-box-like domain superfamily + 717 + 975 5 - IPR032675
  - 945 - 3570 + IPR044974
Disease resistance protein, plants + 520 + 896 6 - IPR017441
Protein kinase, ATP binding site - 872 - 874 + IPR001810
F-box domain + 516 + 1041 7 - IPR013083
  - 647 - 1404 + IPR001611
Leucine-rich repeat + 505 + 1872 8 - IPR011990
  - 640 - 7245 + IPR002885
Pentatricopeptide repeat + 491 + 7255 9 - IPR036047
F-box-like domain superfamily - 558 - 572 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 476 + 940 10 - IPR002885
  - 422 - 19238 + IPR002182
NB-ARC + 468 + 605 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 419 - 615 + IPR001841
Zinc finger, RING-type + 447 + 884 12 - IPR001810
  - 414 - 2370 + IPR009057
Homeobox-like domain superfamily + 396 + 534 13 - IPR001841
  - 409 - 1994 + IPR036291
NAD(P)-binding domain superfamily + 389 + 615 14 - IPR001611
  - 389 - 6036 + IPR016024
Armadillo-type fold + 385 + 638 15 - IPR036291
NAD(P)-binding domain superfamily - 376 - 413 + IPR029058
Alpha/Beta hydrolase fold + 385 + 569 16 - IPR029058
  - 353 - 1438 + IPR041118
Rx, N-terminal + 380 + 473 17 - IPR009057
Homeobox-like domain superfamily - 352 - 387 + IPR011990
Tetratricopeptide-like helical domain superfamily + 355 + 589 18 - IPR016024
Armadillo-type fold - 348 - 790 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 346 + 467 19 - IPR002182
NB-ARC - 306 - 322 + IPR036396
Cytochrome P450 superfamily + 338 + 480 20 - IPR036396
  - 300 - 1854 + IPR001128
Cytochrome P450 + 330 + 1651 21 - IPR001128
Cytochrome P450 - 296 - 1231 + IPR035979
RNA-binding domain superfamily + 313 + 644 22 - IPR035979
RNA-binding domain superfamily - 288 - 425 + IPR002401
Cytochrome P450, E-class, group I + 287 + 2159 23 - IPR012677
  - 287 - 894 + IPR012337
Ribonuclease H-like superfamily + 286 + 371 24 IPR017853
Glycoside hydrolase superfamily - 268 - 305 + 275 + 398 25 - IPR000504
  - 261 - 3459 + IPR000504
RNA recognition motif domain + 275 + 1222 26 - IPR036259
MFS transporter superfamily - 259 - 427 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 273 + 440 27 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 258 - 324 + IPR036259
MFS transporter superfamily + 262 + 395 28 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 256 - 260 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 252 + 313 29 - IPR002401
Cytochrome P450, E-class, group I - 252 - 1651 + IPR001005
SANT/Myb domain + 247 + 827 30 - IPR001005
SANT/Myb domain - 249 - 935 + IPR017930
Myb domain + 242 + 801 31 - IPR003593
AAA+ ATPase domain - 245 - 319 + IPR038765
Papain-like cysteine peptidase superfamily + 236 + 330 32 - IPR017972
Cytochrome P450, conserved site - 243 - 243 + IPR036249
Thioredoxin-like superfamily + 231 + 376 33 - IPR003591
Leucine-rich repeat, typical subtype - 238 - 1591 + IPR036322
WD40-repeat-containing domain superfamily + 226 + 376 34 - IPR011989
  - 233 - 654 + IPR001680
WD40 repeat + 209 + 1748 35 - IPR015943
  - 231 - 1056 + IPR011992
EF-hand domain pair + 190 + 250 36 - IPR038765
Papain-like cysteine peptidase superfamily - 219 - 246 + IPR016177
DNA-binding domain superfamily + 185 + 261 37 - IPR036249
Thioredoxin-like superfamily - 212 - 242 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 184 + 407 38 - IPR001680
  - 209 - 6681 + IPR036770
Ankyrin repeat-containing domain superfamily + 181 + 254 39 - IPR036322
WD40-repeat-containing domain superfamily - 205 - 314 + IPR002048
EF-hand domain + 178 + 1013 40 - IPR017930
  - 202 - 612 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 177 + 220 41 - IPR017986
  - 194 - 663 + IPR011333
SKP1/BTB/POZ domain superfamily + 172 + 268 42 - IPR012337
Ribonuclease H-like superfamily - 190 - 228 + IPR001471
AP2/ERF domain + 171 + 985 43 - IPR020846
  - 186 - 608 + IPR036412
HAD-like superfamily + 169 + 260 44 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 172 - 172 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 168 + 365 45 - IPR011992
EF-hand domain pair - 168 - 188 + IPR043502
DNA/RNA polymerase superfamily + 167 + 183 46 - IPR036638
  - 166 - 924 + IPR002110
Ankyrin repeat + 164 + 659 47 - IPR011333
SKP1/BTB/POZ domain superfamily - 164 - 177 + IPR036390
Winged helix DNA-binding domain superfamily + 155 + 194 48 - IPR036388
  - 161 - 348 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 154 + 169 49 - IPR011598
  - 161 - 1602 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 152 + 193 50 - IPR020683
  - 160 - 1146 + IPR036093
NAC domain superfamily + 151 + 169 51 - IPR036770
  - 160 - 806 + IPR021109
Aspartic peptidase domain superfamily + 150 + 178 52 - IPR002048
  - 159 - 3495 + IPR036236
Zinc finger C2H2 superfamily + 150 + 223 53 - IPR002110
  - 154 - 3129 + IPR003441
NAC domain + 146 + 320 54 - IPR036412
HAD-like superfamily - 152 - 216 + IPR010255
Haem peroxidase superfamily + 146 + 182 55 - IPR016177
DNA-binding domain superfamily - 150 - 178 + IPR002016
Haem peroxidase + 144 + 1011 56 - IPR036390
Winged helix DNA-binding domain superfamily - 147 - 154 + IPR029044
Nucleotide-diphospho-sugar transferases + 143 + 208 57 - IPR013087
  - 146 - 1941 + IPR005174
Domain unknown function DUF295 + 142 + 179 58 - IPR018247
EF-Hand 1, calcium-binding site - 145 - 346 + IPR001650
Helicase, C-terminal + 139 + 415 59 - IPR029044
  - 142 - 662 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 139 + 209 60 - IPR002016
  - 142 - 2769 + IPR013087
Zinc finger C2H2-type + 137 + 264 61 - IPR010255
Haem peroxidase - 142 - 144 + IPR020683
Ankyrin repeat-containing domain + 135 + 285 62 - IPR023214
  - 141 - 470 + IPR036188
FAD/NAD(P)-binding domain superfamily + 133 + 255 63 - IPR036955
  - 139 - 480 + IPR000210
BTB/POZ domain + 131 + 409 64 - IPR014001
  - 139 - 538 + IPR012340
Nucleic acid-binding, OB-fold + 131 + 269 65 - IPR001471
  - 138 - 2619 + IPR003439
ABC transporter-like, ATP-binding domain + 131 + 575 66 - IPR036397
  - 136 - 441 + IPR000823
Plant peroxidase + 126 + 1099 67 - IPR036236
Zinc finger C2H2 superfamily - 136 - 214 + IPR036875
Zinc finger, CCHC-type superfamily + 124 + 180 68 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 133 - 135 + IPR003480
Transferase + 124 + 151 69 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 133 - 133 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 123 + 207 70 - IPR035595
UDP-glycosyltransferase family, conserved site - 132 - 132 + IPR001878
Zinc finger, CCHC-type + 123 + 367 71 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 132 - 158 + IPR029071
Ubiquitin-like domain superfamily + 118 + 193 72 - IPR001650
  - 131 - 1036 + IPR036426
Bulb-type lectin domain superfamily + 118 + 215 73 - IPR012340
Nucleic acid-binding, OB-fold - 130 - 197 + IPR020846
Major facilitator superfamily domain + 118 + 153 74 - IPR000823
Plant peroxidase - 129 - 1059 + IPR036869
Chaperone J-domain superfamily + 116 + 151 75 - IPR000210
  - 128 - 1035 + IPR033905
Secretory peroxidase + 115 + 135 76 - IPR023213
  - 126 - 444 + IPR001087
GDSL lipase/esterase + 114 + 146 77 - IPR008974
  - 124 - 690 + IPR003959
ATPase, AAA-type, core + 114 + 184 78 - IPR036188
  - 123 - 940 + IPR001623
DnaJ domain + 112 + 765 79 - IPR021109
  - 122 - 704 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 112 + 140 80 - IPR013026
  - 122 - 456 + IPR001480
Bulb-type lectin domain + 112 + 563 81 - IPR019775
WD40 repeat, conserved site - 121 - 209 + IPR019734
Tetratricopeptide repeat + 110 + 350 82 - IPR019793
Peroxidases heam-ligand binding site - 121 - 121 + IPR011011
Zinc finger, FYVE/PHD-type + 110 + 204 83 - IPR036093
  - 121 - 729 + IPR011676
Domain of unknown function DUF1618 + 109 + 146 84 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 121 - 178 + IPR033121
Peptidase family A1 domain + 107 + 134 85 - IPR014729
  - 119 - 284 + IPR003657
WRKY domain + 106 + 290 86 - IPR036514
  - 119 - 240 + IPR036576
WRKY domain superfamily + 105 + 145 87 - IPR003441
  - 118 - 708 + IPR011050
Pectin lyase fold/virulence factor + 105 + 116 88 - IPR033905
Secretory peroxidase - 117 - 117 + IPR025315
Domain of unknown function DUF4220 + 105 + 118 89 - IPR019734
  - 116 - 2493 + IPR015424
Pyridoxal phosphate-dependent transferase + 103 + 133 90 - IPR036869
  - 113 - 442 + IPR008972
Cupredoxin + 102 + 210 91 - IPR036426
  - 111 - 534 + IPR032799
Xylanase inhibitor, C-terminal + 102 + 122 92 - IPR001461
Aspartic peptidase A1 family - 111 - 269 + IPR032861
Xylanase inhibitor, N-terminal + 102 + 126 93 - IPR014710
  - 109 - 292 + IPR035892
C2 domain superfamily + 101 + 223 94 - IPR029071
Ubiquitin-like domain superfamily - 107 - 131 + IPR015300
DNA-binding pseudobarrel domain superfamily + 101 + 184 95 - IPR003439
  - 107 - 945 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 100 + 193 96 - IPR003480
Transferase - 107 - 118 + IPR002083
MATH/TRAF domain + 99 + 374 97 - IPR013785
  - 106 - 345 + IPR044810
WRKY transcription factor, plant + 99 + 114 98 - IPR001480
  - 106 - 614 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 98 + 135 99 - IPR011011
Zinc finger, FYVE/PHD-type - 105 - 117 + IPR001356
Homeobox domain + 98 + 313 100 - IPR019794
Peroxidase, active site - 104 - 104 + IPR036457
PPM-type phosphatase domain superfamily + 97 + 149 101 - IPR003959
ATPase, AAA-type, core - 104 - 125 + IPR003609
PAN/Apple domain + 94 + 331 102 - IPR005123
  - 102 - 579 + IPR009072
Histone-fold + 94 + 105 103 - IPR001623
  - 102 - 1248 + IPR001932
PPM-type phosphatase domain + 94 + 421 104 - IPR033121
  - 102 - 216 + IPR007658
Protein of unknown function DUF594 + 93 + 100 105 - IPR002347
Short-chain dehydrogenase/reductase SDR - 101 - 759 + IPR035669
GDSL lipase/esterase-like, plant + 92 + 109 106 - IPR032861
Xylanase inhibitor, N-terminal - 101 - 102 + IPR011051
RmlC-like cupin domain superfamily + 91 + 129 107 - IPR001087
GDSL lipase/esterase - 100 - 100 + IPR005828
Major facilitator, sugar transporter-like + 90 + 133 108 - IPR008972
  - 99 - 728 + IPR002347
Short-chain dehydrogenase/reductase SDR + 89 + 918 109 - IPR002083
  - 99 - 747 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 89 + 127 110 - IPR005225
Small GTP-binding protein domain - 98 - 101 + IPR000073
Alpha/beta hydrolase fold-1 + 88 + 236 111 - IPR032799
Xylanase inhibitor, C-terminal - 97 - 97 + IPR011545
DEAD/DEAH box helicase domain + 88 + 138 112 - IPR027443
  - 96 - 200 + IPR000858
S-locus glycoprotein domain + 87 + 170 113 - IPR015424
Pyridoxal phosphate-dependent transferase - 96 - 106 + IPR000008
C2 domain + 87 + 440 114 - IPR015421
  - 95 - 294 + IPR003340
B3 DNA binding domain + 86 + 472 115 - IPR003609
  - 94 - 452 + IPR000477
Reverse transcriptase domain + 86 + 146 116 - IPR035669
GDSL lipase/esterase-like, plant - 92 - 92 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 85 + 101 117 - IPR005828
Major facilitator, sugar transporter-like - 92 - 103 + IPR032867
DYW domain + 85 + 93 118 - IPR011051
RmlC-like cupin domain superfamily - 91 - 118 + IPR007527
Zinc finger, SWIM-type + 85 + 158 119 - IPR005174
Domain unknown function DUF295 - 90 - 90 + IPR020472
G-protein beta WD-40 repeat + 84 + 384 120 - IPR024171
S-receptor-like serine/threonine-protein kinase - 89 - 103 + IPR004827
Basic-leucine zipper domain + 84 + 228 121 - IPR003657
  - 89 - 897 + IPR002156
Ribonuclease H domain + 82 + 125 122 - IPR036576
  - 88 - 600 + IPR000270
PB1 domain + 82 + 141 123 - IPR000858
S-locus glycoprotein domain - 88 - 88 + IPR000109
Proton-dependent oligopeptide transporter family + 81 + 291 124 - IPR011545
DEAD/DEAH box helicase domain - 86 - 88 + IPR013766
Thioredoxin domain + 81 + 214 125 - IPR009072
  - 86 - 501 + IPR026992
Non-haem dioxygenase N-terminal domain + 81 + 116 126 - IPR011050
Pectin lyase fold/virulence factor - 85 - 87 + IPR026961
PGG domain + 80 + 187 127 - IPR032867
DYW domain - 85 - 85 + IPR018289
MULE transposase domain + 80 + 82 128 - IPR000109
Proton-dependent oligopeptide transporter family - 84 - 170 + IPR000626
Ubiquitin-like domain + 79 + 204 129 - IPR015300
  - 84 - 448 + IPR001461
Aspartic peptidase A1 family + 79 + 274 130 - IPR012334
  - 83 - 174 + IPR001584
Integrase, catalytic core + 78 + 129 131 - IPR017907
Zinc finger, RING-type, conserved site - 82 - 83 + IPR043129
ATPase, nucleotide binding domain + 78 + 209 132 - IPR001356
  - 82 - 882 + IPR002100
Transcription factor, MADS-box + 76 + 479 133 - IPR006447
Myb domain, plants - 81 - 81 + IPR003613
U box domain + 76 + 170 134 - IPR011676
Domain of unknown function DUF1618 - 81 - 82 + IPR036879
Transcription factor, MADS-box superfamily + 76 + 107 135 - IPR000073
Alpha/beta hydrolase fold-1 - 80 - 169 + IPR001220
Legume lectin domain + 75 + 178 136 - IPR017871
ABC transporter, conserved site - 80 - 102 + IPR006121
Heavy metal-associated domain, HMA + 74 + 260 137 - IPR035892
  - 79 - 230 + IPR016039
Thiolase-like + 74 + 142 138 - IPR000270
  - 79 - 387 + IPR036163
Heavy metal-associated domain superfamily + 74 + 105 139 - IPR036457
  - 78 - 366 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 74 + 104 140 - IPR015422
  - 78 - 390 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 72 + 149 141 - IPR001965
Zinc finger, PHD-type - 78 - 112 + IPR008949
Isoprenoid synthase domain superfamily + 71 + 104 142 - IPR001932
  - 77 - 1017 + IPR004158
Protein of unknown function DUF247, plant + 71 + 170 143 - IPR003340
  - 76 - 1203 + IPR000571
Zinc finger, CCCH-type + 71 + 309 144 - IPR003613
  - 76 - 675 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 68 + 71 145 - IPR020472
G-protein beta WD-40 repeat - 75 - 225 + IPR004045
Glutathione S-transferase, N-terminal + 68 + 201 146 - IPR034090
BPM, C-terminal - 75 - 76 + IPR002902
Gnk2-homologous domain + 67 + 365 147 - IPR004827
  - 75 - 816 + IPR036908
RlpA-like domain superfamily + 67 + 79 148 - IPR000008
  - 74 - 642 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 66 + 93 149 - IPR026992
Non-haem dioxygenase N-terminal domain - 74 - 74 + IPR019787
Zinc finger, PHD-finger + 66 + 205 150 - IPR026961
PGG domain - 73 - 160 + IPR044965
Glycoside hydrolase family 17, plant + 66 + 100 151 - IPR000626
  - 72 - 639 + IPR029052
Metallo-dependent phosphatase-like + 66 + 89 152 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 72 - 75 + IPR000048
IQ motif, EF-hand binding site + 66 + 355 153 - IPR013783
  - 72 + IPR001806
Small GTPase + 66 154 154 - IPR015655
Protein phosphatase 2C family - 72 - 79 + IPR020568
Ribosomal protein S5 domain 2-type fold + 65 + 106 155 - IPR000571
  - 72 - 1164 + IPR036852
Peptidase S8/S53 domain superfamily + 65 + 79 156 - IPR006121
  - 70 - 630 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 64 + 73 157 - IPR013766
  - 69 - 393 + IPR013057
Amino acid transporter, transmembrane domain + 64 + 94 158 - IPR036163
Heavy metal-associated domain superfamily - 67 - 83 + IPR005202
Transcription factor GRAS + 64 + 232 159 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 66 - 71 + IPR010987
Glutathione S-transferase, C-terminal-like + 64 + 91 160 - IPR036908
  - 66 - 266 - + IPR016159
Cullin repeat-like-containing domain superfamily + 64 + 85 + 161 - IPR001220
Legume lectin domain - 66 - 126 + IPR000209
Peptidase S8/S53 domain + 64 + 77 162 - IPR005829
Sugar transporter, conserved site - 64 - 105 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 63 + 68 163 - IPR002100
  - 64 - 1158 + IPR007117
Expansin, cellulose-binding-like domain + 63 + 141 164 - IPR003663
Sugar/inositol transporter - 64 - 340 + IPR036915
Cyclin-like superfamily + 63 + 126 165 - IPR001806
Small GTPase superfamily - 64 - 65 + IPR024788
Malectin-like domain + 63 + 90 166 - IPR000225
  - 64 - 1494 + IPR003676
Small auxin-up RNA + 63 + 64 167 - IPR019787
  - 63 - 230 + IPR045051
Subtilisin-like protease + 62 + 83 168 - IPR015915
  - 63 - 423 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 468 169 - IPR036879
  - 63 - 369 + IPR023395
Mitochondrial carrier domain superfamily + 62 + 85 170 - IPR025315
Domain of unknown function DUF4220 - 63 - 69 + IPR000490
Glycoside hydrolase family 17 + 62 + 84 171 - IPR001878
  - 63 - 795 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 61 + 82 172 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 62 - 62 + IPR022059
Protein of unknown function DUF3615 + 61 + 95 173 - IPR026057
PC-Esterase - 62 - 63 + IPR003663
Sugar/inositol transporter + 61 + 342 174 - IPR016039
  - 62 - 654 + IPR006501
Pectinesterase inhibitor domain + 60 + 63 175 - IPR029962
Trichome birefringence-like family - 62 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 59 66 176 - IPR013057
Amino acid transporter, transmembrane domain - 61 - 61 + IPR026960
Reverse transcriptase zinc-binding domain + 59 + 63 177 - IPR000490
Glycoside hydrolase family 17 - 61 - 98 + IPR031052
FHY3/FAR1 family + 59 + 109 178 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 61 - 63 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 59 + 92 179 - IPR035513
  - 60 - 230 + IPR002528
Multi antimicrobial extrusion protein + 59 + 161 180 - IPR002902
  - 60 - 438 + IPR013094
Alpha/beta hydrolase fold-3 + 59 + 70 181 - IPR036961
  - 60 - 243 + IPR001563
Peptidase S10, serine carboxypeptidase + 58 + 495 182 - IPR008949
  - 59 - 264 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 58 + 65 183 - IPR003960
ATPase, AAA-type, conserved site - 59 - 64 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 58 + 123 184 - IPR007658
Protein of unknown function DUF594 - 59 - 60 + IPR005162
Retrotransposon gag domain + 58 + 62 185 - IPR038408
  - 59 - 220 + IPR000225
Armadillo + 58 + 229 186 - IPR018108
  - 59 - 674 + IPR026057
PC-Esterase + 57 + 74 187 - IPR020568
Ribosomal protein S5 domain 2-type fold - 59 - 73 + IPR015500
Peptidase S8, subtilisin-related + 57 + 191 188 - IPR006045
Cupin 1 - 59 - 153 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 57 + 61 189 - IPR023395
  - 59 - 276 + IPR011032
GroES-like superfamily + 56 + 88 190 - IPR036852
  - 59 - 720 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 56 + 71 191 - IPR007527
  - 59 - 315 + IPR029962
Trichome birefringence-like family + 55 + 74 192 - IPR001509
NAD-dependent epimerase/dehydratase - 58 - 59 + IPR030184
WAT1-related protein + 55 + 92 193 - IPR036749
  - 58 - 240 + IPR015915
Kelch-type beta propeller + 55 + 73 194 - IPR000742
  - 58 - 256 + IPR009003
Peptidase S1, PA clan + 55 + 107 195 - IPR007117
  - 58 - 240 + IPR034161
Pepsin-like domain, plant + 54 + 55 196 - IPR031052
FHY3/FAR1 family - 57 - 74 + IPR007112
Expansin/pollen allergen, DPBB domain + 54 + 63 197 - IPR007112
  - 57 - 228 + IPR034197
Cucumisin-like catalytic domain + 54 + 61 198 - IPR003245
  - 57 - 501 + IPR003245
Phytocyanin domain + 54 + 122 199 - IPR008979
  - 57 - 278 + IPR006045
Cupin 1 + 54 + 94 200 - IPR005202
  - 57 - 242 + IPR025846
PMR5 N-terminal domain + 54 + 70 201 - IPR004045
  - 57 - 345 + IPR001752
Kinesin motor domain + 54 + 476 202 - IPR029052
  - 57 + IPR000620
EamA domain + 54 120 203 - IPR000209
Peptidase S8/S53 domain - 57 - 57 + IPR013525
ABC-2 type transporter + 53 + 122 204 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 56 - 57 + IPR013763
Cyclin-like + 53 + 96 205 - IPR019786
Zinc finger, PHD-type, conserved site - 56 + IPR039391
Phytocyanin + 53 60 206 - IPR025846
PMR5 N-terminal domain - 56 - 56 + IPR006566
FBD domain + 53 + 73 207 - IPR036875
Zinc finger, CCHC-type superfamily - 56 - 73 + IPR001906
Terpene synthase, N-terminal domain + 53 + 68 208 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 56 - 78 + IPR001509
NAD-dependent epimerase/dehydratase + 52 + 85 209 - IPR010987
  - 55 - 110 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 52 + 62 210 - IPR006501
Pectinesterase inhibitor domain - 55 - 145 + IPR008979
Galactose-binding-like domain superfamily + 52 + 90 211 - IPR006566
FBD domain - 55 + IPR008978
HSP20-like chaperone + 51 59 212 - IPR016159
Cullin repeat-like-containing domain superfamily - 55 - 74 + IPR023298
P-type ATPase, transmembrane domain superfamily + 51 + 83 213 - IPR036915
Cyclin-like superfamily - 55 - 89 + IPR017884
SANT domain + 50 + 79 214 - IPR003676
Small auxin-up RNA - 55 - 55 + IPR016181
Acyl-CoA N-acyltransferase + 50 + 72 215 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 54 - 54 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 50 + 125 216 - IPR023393
  - 54 - 110 + IPR007118
Expansin/Lol pI + 50 + 297 217 - IPR015500
Peptidase S8, subtilisin-related - 54 - 160 + IPR011701
Major facilitator superfamily + 50 + 71 218 - IPR011993
  - 54 - 112 + IPR005630
Terpene synthase, metal-binding domain + 50 + 65 219 - IPR037045
  - 54 - 108 + IPR004140
Exocyst complex component Exo70 + 50 + 134 220 - IPR013128
Peptidase C1A - 53 - 62 + IPR011527
ABC transporter type 1, transmembrane domain + 50 + 250 221 - IPR018289
MULE transposase domain - 53 - 53 + IPR000668
Peptidase C1A, papain C-terminal + 50 + 192 222 - IPR016135
  - 53 - 208 + IPR044808
Ethylene-responsive transcription factor + 50 + 57 223 - IPR024788
Malectin-like carbohydrate-binding domain - 53 - 55 + IPR002921
Fungal lipase-like domain + 49 + 62 224 - IPR027640
Kinesin-like protein - 52 - 71 + IPR000608
Ubiquitin-conjugating enzyme E2 + 49 + 185 225 - IPR013094
Alpha/beta hydrolase fold-3 - 52 - 53 + IPR008250
P-type ATPase, A domain superfamily + 49 + 77 226 - IPR000048
  - 52 - 843 + IPR036465
von Willebrand factor A-like domain superfamily + 49 + 75 227 - IPR007118
Expansin/Lol pI - 51 - 290 + IPR004330
FAR1 DNA binding domain + 49 + 63 228 - IPR017451
F-box associated interaction domain - 51 - 52 + IPR008906
HAT, C-terminal dimerisation domain + 48 + 57 229 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 51 - 53 + IPR007125
Histone H2A/H2B/H3 + 48 + 52 230 - IPR034197
Cucumisin-like catalytic domain - 50 - 50 + IPR033389
AUX/IAA domain + 47 + 66 231 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 50 - 50 + IPR043926
ABC transporter family G domain + 47 + 80 232 - IPR018253
DnaJ domain, conserved site - 50 + IPR006016
UspA + 47 50 233 - IPR001752
  - 50 - 945 + IPR012946
X8 domain + 47 + 62 234 - IPR014014
  - 49 - 98 + IPR041569
AAA ATPase, AAA+ lid domain + 47 + 75 235 - IPR001938
  - 49 - 626 + IPR001214
SET domain + 47 + 133 236 - IPR002528
Multi antimicrobial extrusion protein - 49 - 131 + IPR036318
FAD-binding, type PCMH-like superfamily + 46 + 57 237 - IPR030184
WAT1-related protein - 49 - 55 + IPR029055
Nucleophile aminohydrolases, N-terminal + 46 + 66 238 - IPR018097
EGF-like calcium-binding, conserved site - 49 - 49 + IPR009000
Translation protein, beta-barrel domain superfamily + 46 + 69 239 - IPR011032
GroES-like superfamily - 48 - 60 + IPR014014
RNA helicase, DEAD-box type, Q motif + 46 + 63 240 - IPR001563
Peptidase S10, serine carboxypeptidase - 48 - 269 + IPR004265
Dirigent protein + 46 + 52 241 - IPR036318
FAD-binding, type 2-like superfamily - 48 - 48 + IPR011006
CheY-like superfamily + 46 + 63 242 - IPR006564
Zinc finger, PMZ-type - 48 - 48 + IPR045087
Multicopper oxidase + 46 + 53 243 - IPR036465
  - 48 - 174 + IPR036855
Zinc finger, CCCH-type superfamily + 46 + 119 244 - IPR000620
EamA domain - 48 - 86 + IPR000743
Glycoside hydrolase, family 28 + 46 + 52 245 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 47 - 92 + IPR001789
Signal transduction response regulator, receiver domain + 46 + 115 246 - IPR001881
EGF-like calcium-binding domain - 47 - 65 + IPR009060
UBA-like superfamily + 45 + 60 247 - IPR009003
Peptidase S1, PA clan - 47 - 63 + IPR000873
AMP-dependent synthetase/ligase + 45 + 60 248 - IPR036640
  - 46 - 459 + IPR004263
Exostosin-like + 45 + 67 249 - IPR034161
Pepsin-like domain, plant - 46 - 46 + IPR008928
Six-hairpin glycosidase superfamily + 45 + 57 250 - IPR000222
PPM-type phosphatase, divalent cation binding - 46 - 46 + IPR000742
EGF-like domain + 45 + 61 251 - IPR004158
Protein of unknown function DUF247, plant - 46 - 51 + IPR014756
Immunoglobulin E-set + 45 + 69 252 - IPR036855
Zinc finger, CCCH-type superfamily - 46 - 94 + IPR008889
VQ + 45 + 45 253 - IPR016181
Acyl-CoA N-acyltransferase - 45 - 50 + IPR016461
O-methyltransferase COMT-type + 44 + 91 254 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 45 - 323 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 44 + 75 255 - IPR016166
  - 45 - 135 + IPR011706
Multicopper oxidase, C-terminal + 44 + 50 256 - IPR011527
  - 45 - 459 + IPR006671
Cyclin, N-terminal + 44 + 54 257 - IPR002109
  - 45 - 255 + IPR000070
Pectinesterase, catalytic + 44 + 52 258 - IPR000873
AMP-dependent synthetase/ligase - 44 - 44 + IPR033896
MADS MEF2-like + 43 + 69 259 - IPR004265
Dirigent protein - 44 - 44 + IPR004853
Sugar phosphate transporter domain + 43 + 66 260 - IPR023299
  - 44 - 237 + IPR044730
Ribonuclease H-like domain, plant type + 43 + 49 261 - IPR023298
P-type ATPase, transmembrane domain superfamily - 44 - 127 + IPR001117
Multicopper oxidase, type 1 + 42 + 48 262 - IPR002921
Fungal lipase-like domain - 43 - 43 + IPR011012
Longin-like domain superfamily + 42 + 61 263 - IPR008250
P-type ATPase, A domain superfamily - 43 - 53 + IPR001077
O-methyltransferase domain + 42 + 46 264 - IPR013763
Cyclin-like - 43 - 129 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 42 + 54 265 - IPR022059
Protein of unknown function DUF3615 - 43 - 44 + IPR015947
PUA-like superfamily + 42 + 53 266 - IPR017970
Homeobox, conserved site - 43 - 43 + IPR010402
CCT domain + 41 + 107 267 - IPR014756
Immunoglobulin E-set - 43 - 48 + IPR000182
GNAT domain + 41 + 96 268 - IPR033389
AUX/IAA domain - 42 - 44 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 41 + 49 269 - IPR000608
  - 42 - 240 + IPR004332
Transposase, MuDR, plant + 41 + 41 270 - IPR009000
Translation protein, beta-barrel domain superfamily - 42 - 45 + IPR004883
Lateral organ boundaries, LOB + 41 + 87 271 - IPR008928
Six-hairpin glycosidase superfamily - 42 - 52 + IPR004046
Glutathione S-transferase, C-terminal + 41 + 50 272 - IPR012341
  - 42 - 126 + IPR039417
Papain-like cysteine endopeptidase + 41 + 55 273 - IPR001360
Glycoside hydrolase family 1 - 41 - 259 + IPR011043
Galactose oxidase/kelch, beta-propeller + 41 + 46 274 - IPR000330
SNF2-related, N-terminal domain - 41 - 42 + IPR011707
Multicopper oxidase, N-termianl + 41 + 46 275 - IPR012946
X8 domain - 41 - 92 + IPR006702
Casparian strip membrane protein domain + 41 + 43 276 - IPR020845
AMP-binding, conserved site - 41 - 41 + IPR025322
Protein of unknown function DUF4228, plant + 40 + 44 277 - IPR000668
Peptidase C1A, papain C-terminal - 41 - 186 + IPR025659
Tubby-like, C-terminal + 40 + 54 278 - IPR017877
  - 41 - 100 + IPR002068
Alpha crystallin/Hsp20 domain + 40 + 86 279 - IPR008942
  - 40 - 154 + IPR000330
SNF2, N-terminal + 40 + 61 280 - IPR000182
  - 40 - 138 + IPR036612
K Homology domain, type 1 superfamily + 40 + 124 281 - IPR033896
MADS MEF2-like - 40 - 40 + IPR003656
Zinc finger, BED-type + 40 + 79 282 - IPR004853
Sugar phosphate transporter domain - 40 - 40 + IPR016166
FAD-binding domain, PCMH-type + 40 + 50 283 - IPR011006
CheY-like superfamily - 40 - 43 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 40 + 138 284 - IPR011012
Longin-like domain superfamily - 40 + IPR024752
Myb/SANT-like domain + 40 40 285 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 40 - 42 + IPR013149
Alcohol dehydrogenase, C-terminal + 39 + 53 286 - IPR001757
P-type ATPase - 40 - 151 + IPR029021
Protein-tyrosine phosphatase-like + 39 + 67 287 - IPR028889
  - 40 - 80 + IPR008942
ENTH/VHS + 38 + 42 288 - IPR001214
  - 40 - 321 + IPR004041
NAF domain + 38 + 44 289 - IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase - 40 - 40 + IPR001360
Glycoside hydrolase family 1 + 38 + 475 290 - IPR001117
Multicopper oxidase, type 1 - 39 - 39 + IPR007493
Protein of unknown function DUF538 + 38 + 90 291 - IPR010402
  - 39 - 234 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 38 + 43 292 - IPR036965
  - 39 - 144 + IPR019557
Aminotransferase-like, plant mobile domain + 38 + 51 293 - IPR013525
ABC-2 type transporter - 39 - 52 + IPR023271
Aquaporin-like + 38 + 51 294 - IPR009060
UBA-like superfamily - 39 - 46 + IPR004839
Aminotransferase, class I/classII + 38 + 57 295 - IPR003137
PA domain - 39 - 39 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 38 + 59 296 - IPR029055
  - 39 - 164 + IPR036758
At5g01610-like superfamily + 38 + 47 297 - IPR001969
Aspartic peptidase, active site - 39 - 49 + IPR029045
ClpP/crotonase-like domain superfamily + 38 + 62 298 - IPR005630
Terpene synthase, metal-binding domain - 39 - 43 + IPR015655
Protein phosphatase 2C family + 38 + 71 299 - IPR036890
  - 39 - 166 + IPR000425
Major intrinsic protein + 38 + 316 300 - IPR029045
ClpP/crotonase-like domain superfamily - 39 - 50 + IPR000644
CBS domain + 38 + 184 301 - IPR018303
P-type ATPase, phosphorylation site - 39 - 39 + IPR028889
Ubiquitin specific protease domain + 38 + 58 302 - IPR038718
  - 39 - 102 + IPR013126
Heat shock protein 70 family + 38 + 91 303 - IPR000644
  - 39 - 494 + IPR039361
Cyclin + 38 + 54 304 - IPR000743
Glycoside hydrolase, family 28 - 39 - 58 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 38 + 76 305 - IPR001789
  - 39 - 468 + IPR002912
ACT domain + 38 + 106 306 - IPR008978
  - 38 - 148 + IPR036041
Ribosome-inactivating protein superfamily + 38 + 46 307 - IPR005299
SAM dependent carboxyl methyltransferase - 38 - 81 + IPR012967
Plant methyltransferase dimerisation + 38 + 38 308 - IPR004140
Exocyst complex component Exo70 - 38 - 81 + IPR002487
Transcription factor, K-box + 38 + 116 309 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 38 - 38 + IPR018451
NAF/FISL domain + 37 + 43 310 - IPR019378
GDP-fucose protein O-fucosyltransferase - 38 - 39 + IPR003137
PA domain + 37 + 55 311 - IPR011706
Multicopper oxidase, type 2 - 38 - 38 + IPR001938
Thaumatin family + 37 + 252 312 - IPR006094
FAD linked oxidase, N-terminal - 38 - 38 + IPR002495
Glycosyl transferase, family 8 + 37 + 55 313 - IPR001929
Germin - 37 - 110 + IPR002109
Glutaredoxin + 37 + 44 314 - IPR006016
UspA - 37 - 37 + IPR037176
Osmotin/thaumatin-like superfamily + 37 + 42 315 - IPR008906
HAT, C-terminal dimerisation domain - 37 - 37 + IPR001574
Ribosome-inactivating protein + 37 + 74 316 - IPR006652
Kelch repeat type 1 - 37 - 130 + IPR016040
NAD(P)-binding domain + 36 + 52 317 - IPR007125
Histone H2A/H2B/H3 - 37 + IPR038933
Ovate protein family + 36 37 318 - IPR011043
Galactose oxidase/kelch, beta-propeller - 37 - 46 + IPR013154
Alcohol dehydrogenase, N-terminal + 36 + 43 319 - IPR014721
  - 37 - 96 + IPR000863
Sulfotransferase domain + 36 + 48 320 - IPR011707
Multicopper oxidase, type 3 - 37 - 37 + IPR019378
GDP-fucose protein O-fucosyltransferase + 36 + 69 321 - IPR025322
Protein of unknown function DUF4228, plant - 36 - 36 + IPR040911
Exostosin, GT47 domain + 36 + 50 322 - IPR004252
Probable transposase, Ptta/En/Spm, plant - 36 - 36 + IPR036404
Jacalin-like lectin domain superfamily + 36 + 72 323 - IPR004839
Aminotransferase, class I/classII - 36 - 37 + IPR034294
Aquaporin transporter + 35 + 51 324 - IPR027923
Hydrophobic seed protein - 36 - 68 + IPR043454
NPH3/RPT2-like family + 35 + 40 325 - IPR001077
O-methyltransferase, family 2 - 36 - 36 + IPR006094
FAD linked oxidase, N-terminal + 35 + 42 326 - IPR006671
Cyclin, N-terminal - 36 - 55 + IPR002067
Mitochondrial carrier protein + 35 + 212 327 - IPR013780
  - 36 - 80 + IPR006458
Ovate protein family, C-terminal + 35 + 68 328 - IPR001906
Terpene synthase, N-terminal domain - 36 - 36 + IPR001229
Jacalin-like lectin domain + 35 + 139 329 - IPR000070
Pectinesterase, catalytic - 36 - 38 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 34 + 168 330 - IPR008889
VQ - 36 - 36 + IPR035940
CAP superfamily + 34 + 42 331 - IPR004041
NAF domain - 35 - 35 + IPR027356
NPH3 domain + 34 + 74 332 - IPR025659
  - 35 - 120 + IPR022742
Serine aminopeptidase, S33 + 34 + 42 333 - IPR016461
  - 35 - 201 + IPR043519
Nucleotidyltransferase superfamily + 34 + 56 334 - IPR006626
Parallel beta-helix repeat - 35 - 185 + IPR032710
NTF2-like domain superfamily + 33 + 45 335 - IPR018451
  - 35 - 105 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 119 336 - IPR011701
Major facilitator superfamily - 35 - 36 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 33 + 57 337 - IPR029021
  - 35 - 150 + IPR029466
No apical meristem-associated, C-terminal domain + 33 + 33 338 - IPR002912
  - 35 - 166 + IPR001296
Glycosyl transferase, family 1 + 33 + 52 339 - IPR037176
  - 35 - 146 + IPR005135
Endonuclease/exonuclease/phosphatase + 33 + 48 340 - IPR001251
  - 34 - 254 + IPR025452
Domain of unknown function DUF4218 + 33 + 33 341 - IPR036612
  - 34 - 333 + IPR006652
Kelch repeat type 1 + 33 + 64 342 - IPR004263
Exostosin-like - 34 - 34 + IPR003311
AUX/IAA protein + 33 + 50 343 - IPR036865
  - 34 - 134 + IPR004314
Neprosin + 33 + 48 344 - IPR003594
Histidine kinase/HSP90-like ATPase - 34 - 77 + IPR004242
Transposon, En/Spm-like + 33 + 35 345 - IPR004883
  - 34 - 140 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 33 + 62 346 - IPR004046
Glutathione S-transferase, C-terminal - 34 - 34 + IPR006073
GTP binding domain + 33 + 121 347 - IPR002495
Glycosyl transferase, family 8 - 34 - 35 + IPR008991
Translation protein SH3-like domain superfamily + 32 + 44 348 - IPR013126
Heat shock protein 70 family - 34 - 315 + IPR000315
B-box-type zinc finger + 32 + 83 349 - IPR025661
Cysteine peptidase, asparagine active site - 34 - 34 + IPR002659
Glycosyl transferase, family 31 + 32 + 100 350 - IPR004330
FAR1 DNA binding domain - 34 - 38 + IPR000795
Translational (tr)-type GTP-binding domain + 32 + 309 351 - IPR011042
  - 34 - 84 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 32 + 41 352 - IPR015947
PUA-like superfamily - 34 - 40 + IPR004367
Cyclin, C-terminal domain + 32 + 38 353 - IPR007493
Protein of unknown function DUF538 - 33 - 66 + IPR014044
CAP domain + 32 + 40 354 - IPR018200
Ubiquitin specific protease, conserved site - 33 - 48 + IPR011141
Polyketide synthase, type III + 32 + 37 355 - IPR023271
  - 33 - 134 + IPR015940
Ubiquitin-associated domain + 31 + 83 356 - IPR034294
Aquaporin transporter - 33 - 36 + IPR025525
hAT-like transposase, RNase-H fold + 31 + 43 357 - IPR022742
Serine aminopeptidase, S33 - 33 - 33 + IPR005299
SAM dependent carboxyl methyltransferase + 31 + 78 358 - IPR036758
  - 33 - 132 + IPR000717
Proteasome component (PCI) domain + 31 + 62 359 - IPR000425
Major intrinsic protein - 33 - 254 + IPR005333
Transcription factor, TCP + 31 + 33 360 - IPR019780
Germin, manganese binding site - 33 - 33 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 31 + 42 361 - IPR012967
Plant methyltransferase dimerisation - 33 - 33 + IPR044814
Terpene cyclases, class 1, plant + 31 + 34 362 - IPR010666
Zinc finger, GRF-type - 32 - 33 + IPR003406
Glycosyl transferase, family 14 + 31 + 42 363 - IPR038933
Ovate protein family - 32 - 39 + IPR001283
Cysteine-rich secretory protein-related + 31 + 152 364 - IPR004320
Protein of unknown function DUF241, plant - 32 - 35 + IPR004088
K Homology domain, type 1 + 31 + 110 365 - IPR027356
  - 32 - 126 + IPR000595
Cyclic nucleotide-binding domain + 31 + 100 366 - IPR002487
  - 32 - 192 + IPR025724
GAG-pre-integrase domain + 31 + 31 367 - IPR006073
GTP binding domain - 32 - 87 + IPR006311
Twin-arginine translocation pathway, signal sequence + 31 + 36 368 - IPR036378
  - 31 - 142 + IPR001099
Chalcone/stilbene synthase, N-terminal + 31 + 35 369 - IPR013149
Alcohol dehydrogenase, C-terminal - 31 - 31 + IPR033734
Jacalin-like lectin domain, plant + 31 + 61 370 - IPR008991
Translation protein SH3-like domain superfamily - 31 + IPR013601
FAE1/Type III polyketide synthase-like protein + 30 32 371 - IPR036691
  - 31 - 182 + IPR018490
Cyclic nucleotide-binding-like + 30 + 40 372 - IPR001296
Glycosyl transferase, family 1 - 31 - 31 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 30 + 32 373 - IPR000795
  - 31 - 564 + IPR001929
Germin + 30 + 97 374 - IPR003653
  - 31 - 159 + IPR029000
Cyclophilin-like domain superfamily + 30 + 41 375 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 31 - 201 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 30 + 121 376 - IPR038538
  - 31 - 82 + IPR010920
LSM domain superfamily + 30 + 40 377 - IPR002963
Expansin - 31 - 254 + IPR029061
Thiamin diphosphate-binding fold + 30 + 65 378 - IPR002035
  - 31 - 148 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 30 + 50 379 - IPR000169
Cysteine peptidase, cysteine active site - 31 - 31 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 30 + 40 380 - IPR002067
Mitochondrial carrier protein - 31 - 166 + IPR027409
GroEL-like apical domain superfamily + 30 + 37 381 - IPR006458
  - 31 - 176 + IPR027923
Hydrophobic seed protein domain + 30 + 68 382 - IPR020843
Polyketide synthase, enoylreductase domain - 31 - 31 + IPR003851
Zinc finger, Dof-type + 30 + 64 383 - IPR006702
Casparian strip membrane protein domain - 31 - 31 + IPR003855
Potassium transporter + 30 + 116 384 - IPR016040
NAD(P)-binding domain - 30 - 33 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 30 + 48 385 - IPR032710
NTF2-like domain superfamily - 30 - 30 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 29 + 229 386 - IPR013154
Alcohol dehydrogenase, N-terminal - 30 - 30 + IPR024709
Putative O-fucosyltransferase, plant + 29 + 63 387 - IPR031112
AP2-like ethylene-responsive transcription factor - 30 - 36 + IPR013216
Methyltransferase type 11 + 29 + 37 388 - IPR008480
Protein of unknown function DUF761, plant - 30 - 30 + IPR044848
PHR1-like + 29 + 45 389 - IPR022357
Major intrinsic protein, conserved site - 30 - 30 + IPR001594
Palmitoyltransferase, DHHC domain + 29 + 49 390 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 30 - 30 + IPR007650
Zf-FLZ domain + 29 + 66 391 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 30 + IPR021720
Malectin domain + 29 + 65 392 - IPR013216
Methyltransferase type 11 - 29 - 29 + IPR005150
Cellulose synthase + 29 + 73 393 - IPR002659
Glycosyl transferase, family 31 - 29 - 60 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 394 - IPR002423
Chaperonin Cpn60/TCP-1 family - 29 - 29 + IPR033443
Pentacotripeptide-repeat region of PRORP + 29 + 47 395 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 29 - 59 + IPR044791
Beta-glucanase/XTH + 29 + 39 396 - IPR038770
  - 29 - 58 + IPR016197
Chromo-like domain superfamily + 29 + 46 397 - IPR008266
Tyrosine-protein kinase, active site - 29 - 29 + IPR000679
Zinc finger, GATA-type + 29 + 96 398 - IPR003406
Glycosyl transferase, family 14 - 29 - 29 + IPR000757
Glycoside hydrolase family 16 + 29 + 72 399 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 29 + IPR002913
START domain + 29 + 77 400 - IPR031127
E3 ubiquitin ligase RBR family - 29 - 34 + IPR000727
Target SNARE coiled-coil homology domain + 28 + 56 401 - IPR003855
Potassium transporter - 29 - 86 + IPR036378
FAS1 domain superfamily + 28 + 40 402 - IPR011141
Polyketide synthase, type III - 29 - 58 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 28 + 90 403 - IPR024752
Myb/SANT-like domain - 29 - 29 + IPR027725
Heat shock transcription factor family + 28 + 33 404 - IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site - 29 - 29 + IPR002423
Chaperonin Cpn60/TCP-1 family + 28 + 39 405 - IPR001099
Chalcone/stilbene synthase, N-terminal - 29 - 31 + IPR004320
Protein of unknown function DUF241, plant + 28 + 35 406 - IPR000727
  - 28 - 146 + IPR000408
Regulator of chromosome condensation, RCC1 + 28 + 686 407 - IPR025110
AMP-binding enzyme, C-terminal domain - 28 - 28 + IPR029480
Transposase-associated domain + 28 + 29 408 - IPR000315
  - 28 - 381 + IPR002123
Phospholipid/glycerol acyltransferase + 28 + 38 409 - IPR007657
Glycosyltransferase 61 - 28 - 57 + IPR011013
Galactose mutarotase-like domain superfamily + 28 + 47 410 - IPR001594
Palmitoyltransferase, DHHC domain - 28 - 29 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 28 + 36 411 - IPR005135
Endonuclease/exonuclease/phosphatase - 28 - 28 + IPR002963
Expansin + 28 + 252 412 - IPR011013
Galactose mutarotase-like domain superfamily - 28 - 33 + IPR005821
Ion transport domain + 28 + 39 413 - IPR027409
  - 28 - 110 + IPR001849
Pleckstrin homology domain + 28 + 69 414 - IPR014722
  - 28 - 62 + IPR023299
P-type ATPase, cytoplasmic domain N + 28 + 53 415 - IPR004088
K Homology domain, type 1 - 28 - 57 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 28 + 39 416 IPR012328
Chalcone/stilbene synthase, C-terminal 28 - 28 + 30 417 - IPR003311
AUX/IAA protein - 28 - 28 + IPR036034
PDZ superfamily + 28 + 43 418 - IPR009091
  - 28 - 178 + IPR023210
NADP-dependent oxidoreductase domain + 28 + 56 419 - IPR006311
  - 28 - 56 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 27 + 35 420 - IPR000757
  - 28 - 168 + IPR017938
Riboflavin synthase-like beta-barrel + 27 + 37 421 - IPR000782
  - 27 - 180 + IPR006153
Cation/H+ exchanger + 27 + 34 422 - IPR001179
  - 27 - 146 + IPR044835
Auxin response factor + 27 + 39 423 - IPR010920
LSM domain superfamily - 27 - 29 + IPR023753
FAD/NAD(P)-binding domain + 27 + 36 424 - IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain - 27 - 27 + IPR007657
Glycosyltransferase 61 + 27 + 65 425 - IPR011016
  - 27 - 192 + IPR001881
EGF-like calcium-binding domain + 27 + 38 426 - IPR019557
Aminotransferase-like, plant mobile domain - 27 - 27 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 27 + 29 427 - IPR018181
Heat shock protein 70, conserved site - 27 - 66 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 27 + 34 428 - IPR003656
  - 27 - 183 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 35 429 - IPR002355
Multicopper oxidase, copper-binding site - 27 - 27 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 27 + 34 430 - IPR002123
Phospholipid/glycerol acyltransferase - 27 - 52 + IPR001701
Glycoside hydrolase family 9 + 27 + 30 431 - IPR036866
  - 27 - 142 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 27 + 30 432 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 27 - 28 + IPR015797
NUDIX hydrolase-like domain superfamily + 27 + 33 433 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 38 + IPR003106
Leucine zipper, homeobox-associated + 26 + 29 434 - IPR004087
K Homology domain - 27 - 57 + IPR002867
IBR domain + 26 + 60 435 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 27 - 33 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 26 + 26 436 - IPR025486
Domain of unknown function DUF4378 - 27 - 27 + IPR044778
Sugar transport protein STP/MST-like, plant + 26 + 29 437 - IPR029047
  - 27 - 110 + IPR011016
Zinc finger, RING-CH-type + 26 + 72 438 - IPR025660
Cysteine peptidase, histidine active site - 27 - 27 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 26 + 35 439 - IPR002913
  - 27 - 207 + IPR001763
Rhodanese-like domain + 26 + 56 440 - IPR015797
NUDIX hydrolase-like domain superfamily - 27 - 27 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 26 + 38 441 - IPR015940
  - 26 - 156 + IPR044839
Protein NDR1-like + 26 + 27 442 - IPR002867
IBR domain - 26 - 89 + IPR029069
HotDog domain superfamily + 26 + 48 443 - IPR019821
Kinesin motor domain, conserved site - 26 - 26 + IPR001757
P-type ATPase + 26 + 123 444 - IPR001440
Tetratricopeptide repeat 1 - 26 - 31 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 26 + 110 445 - IPR024709
Putative O-fucosyltransferase, plant - 26 - 48 + IPR005175
PPC domain + 26 + 83 446 - IPR002068
  - 26 - 102 + IPR000782
FAS1 domain + 25 + 63 447 - IPR000717
  - 26 - 128 + IPR004316
SWEET sugar transporter + 25 + 53 448 - IPR029061
Thiamin diphosphate-binding fold - 26 - 41 + IPR021790
PTBP1, RNA recognition motif 2-like + 25 + 31 449 - IPR035940
  - 26 - 108 + IPR017887
Transcription factor TCP subgroup + 25 + 49 450 - IPR033131
Pectinesterase, Asp active site - 26 - 26 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 25 + 30 451 - IPR004367
Cyclin, C-terminal domain - 26 - 46 + IPR002035
von Willebrand factor, type A + 25 + 64 452 - IPR000863
Sulfotransferase domain - 26 - 27 + IPR004813
Oligopeptide transporter, OPT superfamily + 25 + 44 453 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 26 - 31 + IPR039421
Type 1 protein exporter + 25 + 45 454 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 26 - 39 + IPR029062
Class I glutamine amidotransferase-like + 25 + 36 455 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 26 - 26 + IPR036296
SKP1-like, dimerisation domain superfamily + 25 + 35 456 - IPR002130
  - 25 - 459 + IPR031127
E3 ubiquitin ligase RBR family + 25 + 53 457 - IPR029000
  - 25 - 110 + IPR044066
TRIAD supradomain + 25 + 39 458 - IPR013088
  - 25 - 84 + IPR002937
Amine oxidase + 25 + 39 459 - IPR036420
  - 25 - 156 + IPR025110
AMP-binding enzyme, C-terminal domain + 24 + 33 460 - IPR008422
Homeobox KN domain - 25 - 25 + IPR025312
Domain of unknown function DUF4216 + 24 + 24 461 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 25 - 29 + IPR036420
BRCT domain superfamily + 24 + 57 462 - IPR011332
Zinc-binding ribosomal protein - 25 - 25 + IPR008422
Homeobox KN domain + 24 + 36 463 - IPR005150
Cellulose synthase - 25 - 36 + IPR025422
Transcription factor TGA like domain + 24 + 79 464 - IPR016167
  - 25 - 102 + IPR003337
Trehalose-phosphatase + 24 + 32 465 - IPR008963
  - 25 - 111 + IPR016072
SKP1 component, dimerisation + 24 + 32 466 - IPR014044
CAP domain - 25 - 52 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 24 + 56 467 - IPR005746
Thioredoxin - 25 - 36 + IPR016897
S-phase kinase-associated protein 1 + 24 + 35 468 - IPR029069
HotDog domain superfamily - 25 - 36 + IPR034285
Laccase, second cupredoxin domain + 24 + 27 469 - IPR003851
  - 25 - 291 + IPR025486
Domain of unknown function DUF4378 + 24 + 30 470 - IPR036404
  - 25 - 128 + IPR000086
NUDIX hydrolase domain + 24 + 56 471 - IPR015914
Purple acid phosphatase, N-terminal - 25 - 25 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 24 + 32 472 - IPR036812
  - 25 - 102 + IPR010525
Auxin response factor domain + 24 + 29 473 - IPR000679
  - 25 - 315 + IPR006689
Small GTPase superfamily, ARF/SAR type + 23 + 147 474 - IPR008552
Domain of unknown function DUF834 - 25 - 28 + IPR036085
PAZ domain superfamily + 23 + 47 475 - IPR001229
  - 25 - 186 + IPR019956
Ubiquitin domain + 23 + 77 476 - IPR017884
  - 24 - 54 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 23 + 44 477 - IPR000528
Plant lipid transfer protein/Par allergen - 24 - 108 + IPR022149
Protein of unknown function DUF3681 + 23 + 51 478 - IPR013601
FAE1/Type III polyketide synthase-like protein - 24 - 24 + IPR002403
Cytochrome P450, E-class, group IV + 23 + 126 479 - IPR018490
Cyclic nucleotide-binding-like - 24 - 25 + IPR007612
LURP-one-related + 23 + 58 480 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 24 - 44 + IPR027806
Harbinger transposase-derived nuclease domain + 23 + 23 481 - IPR006153
Cation/H+ exchanger - 24 - 26 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 29 482 - IPR001357
  - 24 - 266 + IPR036010
2Fe-2S ferredoxin-like superfamily + 23 + 29 483 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 24 - 26 + IPR001353
Proteasome, subunit alpha/beta + 23 + 32 484 - IPR033124
Serine carboxypeptidases, histidine active site - 24 - 24 + IPR011257
DNA glycosylase + 23 + 35 485 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 24 - 24 + IPR003594
Histidine kinase/HSP90-like ATPase + 23 + 30 486 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 24 - 24 + IPR016161
Aldehyde/histidinol dehydrogenase + 23 + 32 487 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 24 - 110 + IPR036392
PLAT/LH2 domain superfamily + 23 + 25 488 - IPR001876
  - 24 - 278 + IPR035441
TFIIS/LEDGF domain superfamily + 23 + 27 489 - IPR029062
  - 24 - 122 + IPR029033
Histidine phosphatase superfamily + 23 + 35 490 - IPR016161
Aldehyde/histidinol dehydrogenase - 24 - 25 + IPR036443
Zinc finger, RanBP2-type superfamily + 23 + 65 491 - IPR001701
Glycoside hydrolase family 9 - 24 - 24 + IPR003100
PAZ domain + 22 + 90 492 - IPR036427
  - 24 - 138 + IPR006594
LIS1 homology motif + 22 + 51 493 - IPR004314
Neprosin - 24 - 25 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 48 494 - IPR000595
  - 24 - 176 + IPR025753
AAA-type ATPase, N-terminal domain + 22 + 28 495 - IPR023210
NADP-dependent oxidoreductase domain - 24 - 45 + IPR001357
BRCT domain + 22 + 95 496 - IPR005175
  - 24 - 144 + IPR013581
Plant PDR ABC transporter associated + 22 + 39 497 - IPR017896
  - 24 - 112 + IPR018392
LysM domain + 22 + 76 498 - IPR017938
Riboflavin synthase-like beta-barrel - 23 - 26 + IPR014977
WRC domain + 22 + 51 499 - IPR004316
SWEET sugar transporter - 23 - 46 + IPR041577
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain + 22 + 22 500 - IPR004161
Translation elongation factor EFTu-like, domain 2 - 23 - 23 + IPR027413
GroEL-like equatorial domain superfamily + 22 + 27 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula.html b/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula.html index 0a5045cf..5c0b4222 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:ALNU02000000, Aug 2013AGI_PacBIO,
Database version:93.1587.4
Base Pairs:372,860,283388,593,428
Golden Path Length:372,860,283388,593,428
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09
+ Genebuild by: CSHL Genebuild started: Jul 2018 Genebuild version: 2018-07-CSHL

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):35,735Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		41,158
Gene transcriptsHASH(0x68ce400):50,860Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:52,718
@@ -37,42 +37,65 @@

Coordinate Systems

chromosome
-
12 sequences
+
47 sequences
+1
SequenceLength (bp)
146529941
238039368
337594838
432884216
530429317
631548187
728350858
827185770
923490084
1022967634
1127098305
1226741765
45664349
236906571
339367850
434316930
530257704
633537877
729772470
828865088
923906556
1024753583
1131489372
1227342405
UN-Ctg53205312
UN-Ctg54160854
UN-Ctg55119319
UN-Ctg56107666
UN-Ctg57103248
UN-Ctg5888329
UN-Ctg5984894
UN-Ctg6078225
UN-Ctg6177729
UN-Ctg6275317
UN-Ctg6373669
UN-Ctg6470339
UN-Ctg6569311
UN-Ctg6662568
UN-Ctg6761938
UN-Ctg6861225
UN-Ctg6960586
UN-Ctg7060091
UN-Ctg7158435
UN-Ctg7258369
UN-Ctg7354937
UN-Ctg7453901
UN-Ctg7553452
UN-Ctg7652680
UN-Ctg7751047
UN-Ctg7849442
UN-Ctg7948922
UN-Ctg8048264
UN-Ctg8146330
UN-Ctg8246690
UN-Ctg8344485
UN-Ctg8440041
UN-Ctg8538075
UN-Ctg8628892
UN-Ctg8718091
-
+
chunk - 3733 sequences + 3909 sequences - -

Other

- - - - - - - - - -
FGENESH gene predictions:44,113
Short Variants (SNPs, indels, somatic mutations):4,901,344
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula_IPtop500.html index 75a591f2..461757b2 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_glumaepatula_IPtop500.html @@ -17,3500 +17,3500 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1415 - 2363 + 1447 + 2085 2 - IPR000719
  - 1360 - 15699 + IPR000719
Protein kinase domain + 1379 + 3330 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1335 - 2919 + 1377 + 2328 4 - IPR032675
  - 1190 - 6790 + IPR036047
F-box-like domain superfamily + 701 + 955 5 - IPR008271
Serine/threonine-protein kinase, active site - 1083 - 1667 + IPR036875
Zinc finger, CCHC-type superfamily + 608 + 920 6 - IPR017441
Protein kinase, ATP binding site - 951 - 1431 + IPR001878
Zinc finger, CCHC-type + 594 + 1505 7 - IPR011990
  - 706 - 12036 + IPR001810
F-box domain + 510 + 1059 8 - IPR013083
  - 675 - 2132 + IPR002885
Pentatricopeptide repeat + 490 + 7515 9 - IPR036047
F-box-like domain superfamily - 664 - 1079 + IPR001611
Leucine-rich repeat + 487 + 1588 10 - IPR001810
  - 491 - 5322 + IPR044974
Disease resistance protein, plants + 480 + 940 11 - IPR002885
  - 480 - 32346 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 456 + 883 12 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 463 - 987 + IPR001841
Zinc finger, RING-type + 452 + 897 13 - IPR001611
  - 458 - 10977 + IPR002182
NB-ARC + 436 + 607 14 - IPR002182
NB-ARC - 426 - 716 + IPR009057
Homeobox-like domain superfamily + 383 + 525 15 - IPR001841
  - 423 - 2874 + IPR036291
NAD(P)-binding domain superfamily + 382 + 570 16 - IPR029058
  - 385 - 2250 + IPR029058
Alpha/Beta hydrolase fold + 380 + 571 17 - IPR036291
NAD(P)-binding domain superfamily - 369 - 671 + IPR012337
Ribonuclease H-like superfamily + 376 + 458 18 IPR016024
Armadillo-type fold - 364 - 1290 + 367 + 601 19 - IPR036396
  - 342 - 2922 + IPR041118
Rx, N-terminal + 357 + 494 20 - IPR009057
Homeobox-like domain superfamily - 341 - 469 + IPR011990
Tetratricopeptide-like helical domain superfamily + 340 + 578 21 - IPR001128
Cytochrome P450 - 328 - 1609 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 331 + 397 22 - IPR003591
Leucine-rich repeat, typical subtype - 321 - 2922 + IPR036396
Cytochrome P450 superfamily + 328 + 449 23 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 320 - 436 + IPR001128
Cytochrome P450 + 322 + 1607 24 IPR035979
RNA-binding domain superfamily - 302 - 637 + 309 + 603 25 - IPR012677
  - 291 - 1314 + IPR002401
Cytochrome P450, E-class, group I + 272 + 2075 26 - IPR000504
  - 271 - 5277 + IPR017853
Glycoside hydrolase superfamily + 270 + 399 27 - IPR002401
Cytochrome P450, E-class, group I - 270 - 2045 + IPR000504
RNA recognition motif domain + 270 + 1133 28 - IPR003593
AAA+ ATPase domain - 266 - 569 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 270 + 448 29 - IPR017853
Glycoside hydrolase superfamily - 260 - 509 + IPR005162
Retrotransposon gag domain + 266 + 267 30 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 260 - 490 + IPR043502
DNA/RNA polymerase superfamily + 256 + 277 31 - IPR017972
Cytochrome P450, conserved site - 254 - 343 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 247 + 329 32 IPR036259
MFS transporter superfamily - 252 - 734 + 245 + 398 33 - IPR015943
  - 242 - 1803 + IPR017930
Myb domain + 240 + 818 34 - IPR011989
  - 235 - 988 + IPR036249
Thioredoxin-like superfamily + 239 + 367 35 - IPR036249
Thioredoxin-like superfamily - 232 - 371 + IPR038765
Papain-like cysteine peptidase superfamily + 233 + 349 36 - IPR036322
WD40-repeat-containing domain superfamily - 229 - 625 + IPR001005
SANT/Myb domain + 233 + 835 37 - IPR001680
  - 227 - 10605 + IPR021109
Aspartic peptidase domain superfamily + 232 + 261 38 - IPR001005
SANT/Myb domain - 226 - 999 + IPR036322
WD40-repeat-containing domain superfamily + 225 + 386 39 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 224 - 334 + IPR001680
WD40 repeat + 203 + 1708 40 - IPR017986
  - 201 - 1116 + IPR011992
EF-hand domain pair + 188 + 252 41 - IPR038765
Papain-like cysteine peptidase superfamily - 190 - 350 + IPR016177
DNA-binding domain superfamily + 187 + 264 42 - IPR011992
EF-hand domain pair - 186 - 289 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 180 + 409 43 - IPR020846
  - 179 - 984 + IPR002048
EF-hand domain + 175 + 996 44 - IPR002048
  - 176 - 5097 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 174 + 214 45 - IPR016177
DNA-binding domain superfamily - 173 - 246 + IPR000477
Reverse transcriptase domain + 173 + 330 46 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 172 - 195 + IPR001471
AP2/ERF domain + 171 + 966 47 - IPR036638
  - 171 - 1257 + IPR036412
HAD-like superfamily + 170 + 250 48 - IPR017930
  - 171 - 604 + IPR001584
Integrase, catalytic core + 166 + 220 49 - IPR036388
  - 167 - 448 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 165 + 362 50 - IPR013087
  - 164 - 2649 + IPR036770
Ankyrin repeat-containing domain superfamily + 164 + 234 51 - IPR018247
EF-Hand 1, calcium-binding site - 163 - 498 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 163 + 211 52 - IPR011598
  - 162 - 2160 + IPR011333
SKP1/BTB/POZ domain superfamily + 161 + 243 53 - IPR011333
SKP1/BTB/POZ domain superfamily - 161 - 252 + IPR036093
NAC domain superfamily + 155 + 170 54 - IPR036412
HAD-like superfamily - 161 - 358 + IPR036390
Winged helix DNA-binding domain superfamily + 154 + 187 55 - IPR036770
  - 157 - 1206 + IPR002110
Ankyrin repeat + 151 + 608 56 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 156 - 209 + IPR003441
NAC domain + 150 + 318 57 - IPR020683
  - 156 - 1668 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 150 + 184 58 - IPR001471
  - 153 - 3111 + IPR036236
Zinc finger C2H2 superfamily + 149 + 212 59 - IPR036955
  - 153 - 579 + IPR010255
Haem peroxidase superfamily + 141 + 173 60 - IPR029044
  - 151 - 1074 + IPR002016
Haem peroxidase + 140 + 1020 61 - IPR036390
Winged helix DNA-binding domain superfamily - 150 - 197 + IPR013087
Zinc finger C2H2-type + 139 + 257 62 - IPR023214
  - 148 - 696 + IPR036188
FAD/NAD(P)-binding domain superfamily + 137 + 251 63 - IPR036188
  - 148 - 1500 + IPR029044
Nucleotide-diphospho-sugar transferases + 135 + 189 64 - IPR036093
  - 147 - 1005 + IPR001650
Helicase, C-terminal + 133 + 400 65 - IPR002110
  - 146 - 4794 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 133 + 205 66 - IPR003441
  - 144 - 960 + IPR005174
Domain unknown function DUF295 + 128 + 160 67 - IPR014001
  - 143 - 872 + IPR000823
Plant peroxidase + 127 + 1147 68 - IPR001650
  - 141 - 1730 + IPR020683
Ankyrin repeat-containing domain + 125 + 251 69 - IPR036236
Zinc finger C2H2 superfamily - 138 - 255 + IPR012340
Nucleic acid-binding, OB-fold + 125 + 286 70 - IPR023213
  - 137 - 520 + IPR036426
Bulb-type lectin domain superfamily + 125 + 179 71 - IPR019775
WD40 repeat, conserved site - 134 - 352 + IPR003439
ABC transporter-like, ATP-binding domain + 122 + 534 72 - IPR035595
UDP-glycosyltransferase family, conserved site - 130 - 144 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 121 + 207 73 - IPR013026
  - 130 - 744 + IPR001480
Bulb-type lectin domain + 121 + 466 74 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 126 - 142 + IPR001087
GDSL lipase/esterase + 118 + 149 75 - IPR014729
  - 125 - 520 + IPR000210
BTB/POZ domain + 118 + 371 76 - IPR003439
  - 125 - 1869 + IPR003480
Transferase + 117 + 135 77 - IPR019734
  - 124 - 4053 + IPR033905
Secretory peroxidase + 114 + 137 78 - IPR000210
  - 123 - 1560 + IPR003959
ATPase, AAA-type, core + 114 + 190 79 - IPR012340
Nucleic acid-binding, OB-fold - 118 - 233 + IPR041588
Integrase zinc-binding domain + 114 + 114 80 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 116 - 228 + IPR029071
Ubiquitin-like domain superfamily + 113 + 169 81 - IPR036869
  - 116 - 630 + IPR019734
Tetratricopeptide repeat + 112 + 378 82 - IPR003480
Transferase - 116 + IPR033121
Peptidase family A1 domain + 111 145 83 - IPR021109
  - 115 - 804 + IPR036869
Chaperone J-domain superfamily + 111 + 147 84 - IPR036514
  - 115 - 368 + IPR008972
Cupredoxin + 109 + 214 85 - IPR003959
ATPase, AAA-type, core - 115 - 191 + IPR011011
Zinc finger, FYVE/PHD-type + 107 + 182 86 - IPR001461
Aspartic peptidase A1 family - 111 - 323 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 107 + 133 87 - IPR014710
  - 110 - 412 + IPR032799
Xylanase inhibitor, C-terminal + 105 + 120 88 - IPR036426
  - 110 - 838 + IPR020846
Major facilitator superfamily domain + 105 + 146 89 - IPR008974
  - 110 - 1047 + IPR016197
Chromo-like domain superfamily + 105 + 122 90 - IPR001623
  - 108 - 1784 + IPR001623
DnaJ domain + 104 + 729 91 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 108 - 180 + IPR003657
WRKY domain + 102 + 245 92 - IPR011011
Zinc finger, FYVE/PHD-type - 107 - 204 + IPR015424
Pyridoxal phosphate-dependent transferase + 102 + 138 93 - IPR001480
  - 107 - 948 + IPR011050
Pectin lyase fold/virulence factor + 101 + 109 94 - IPR008972
  - 106 - 902 + IPR036576
WRKY domain superfamily + 100 + 122 95 - IPR005123
  - 106 - 861 + IPR003609
PAN/Apple domain + 100 + 264 96 - IPR005174
Domain unknown function DUF295 - 104 - 141 + IPR007658
Protein of unknown function DUF594 + 100 + 106 97 - IPR029071
Ubiquitin-like domain superfamily - 103 - 145 + IPR032861
Xylanase inhibitor, N-terminal + 100 + 118 98 - IPR013785
  - 101 - 594 + IPR025315
Domain of unknown function DUF4220 + 100 + 108 99 - IPR015421
  - 101 - 447 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 99 + 134 100 - IPR015424
Pyridoxal phosphate-dependent transferase - 101 - 150 + IPR035892
C2 domain superfamily + 98 + 209 101 - IPR011050
Pectin lyase fold/virulence factor - 99 - 123 + IPR011676
Domain of unknown function DUF1618 + 98 + 131 102 - IPR005225
Small GTP-binding protein domain - 99 - 136 + IPR041373
Reverse transcriptase, RNase H-like domain + 98 + 98 103 - IPR033121
  - 98 - 264 + IPR044810
WRKY transcription factor, plant + 97 + 105 104 - IPR003657
  - 98 - 1191 + IPR001356
Homeobox domain + 95 + 319 105 - IPR036576
  - 97 - 807 + IPR000858
S-locus glycoprotein domain + 94 + 138 106 - IPR032799
Xylanase inhibitor, C-terminal - 96 + IPR035669
GDSL lipase/esterase-like, plant + 92 110 107 - IPR032861
Xylanase inhibitor, N-terminal - 96 - 113 + IPR036457
PPM-type phosphatase domain superfamily + 92 + 135 108 - IPR012337
Ribonuclease H-like superfamily - 95 - 175 + IPR011051
RmlC-like cupin domain superfamily + 92 + 117 109 - IPR011676
Domain of unknown function DUF1618 - 95 - 129 + IPR015300
DNA-binding pseudobarrel domain superfamily + 92 + 174 110 - IPR012334
  - 95 - 232 + IPR001932
PPM-type phosphatase domain + 91 + 398 111 - IPR027443
  - 94 - 304 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 90 + 162 112 - IPR025315
Domain of unknown function DUF4220 - 94 - 106 + IPR002347
Short-chain dehydrogenase/reductase SDR + 88 + 821 113 - IPR001087
GDSL lipase/esterase - 93 - 129 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 88 + 127 114 - IPR001356
  - 93 - 1212 + IPR001220
Legume lectin domain + 88 + 212 115 - IPR015300
  - 93 - 722 + IPR001461
Aspartic peptidase A1 family + 87 + 269 116 - IPR032867
DYW domain - 91 - 115 + IPR009072
Histone-fold + 87 + 93 117 - IPR035892
  - 90 - 418 + IPR000008
C2 domain + 86 + 425 118 - IPR035669
GDSL lipase/esterase-like, plant - 89 - 129 + IPR005828
Major facilitator, sugar transporter-like + 86 + 130 119 - IPR009072
  - 89 - 591 + IPR002083
MATH/TRAF domain + 86 + 319 120 - IPR000109
Proton-dependent oligopeptide transporter family - 88 - 374 + IPR032867
DYW domain + 86 + 98 121 - IPR036457
  - 88 - 558 + IPR000073
Alpha/beta hydrolase fold-1 + 85 + 272 122 - IPR007658
Protein of unknown function DUF594 - 88 - 97 + IPR003340
B3 DNA binding domain + 84 + 438 123 - IPR011051
RmlC-like cupin domain superfamily - 88 - 150 + IPR011545
DEAD/DEAH box helicase domain + 84 + 131 124 - IPR002347
Short-chain dehydrogenase/reductase SDR - 87 - 866 + IPR000109
Proton-dependent oligopeptide transporter family + 83 + 287 125 - IPR003609
  - 87 - 786 + IPR026992
Non-haem dioxygenase N-terminal domain + 83 + 119 126 - IPR000008
  - 86 - 1144 + IPR007527
Zinc finger, SWIM-type + 83 + 150 127 - IPR005828
Major facilitator, sugar transporter-like - 86 - 151 + IPR013766
Thioredoxin domain + 82 + 208 128 - IPR015422
  - 86 - 591 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 82 + 110 129 - IPR001932
  - 86 - 1458 + IPR004827
Basic-leucine zipper domain + 82 + 208 130 - IPR000858
S-locus glycoprotein domain - 85 - 137 + IPR002156
Ribonuclease H domain + 80 + 115 131 - IPR006447
Myb domain, plants - 85 - 106 + IPR020472
G-protein beta WD-40 repeat + 80 + 351 132 - IPR011545
DEAD/DEAH box helicase domain - 84 - 142 + IPR043129
ATPase, nucleotide binding domain + 79 + 209 133 - IPR004827
  - 84 - 1227 + IPR002100
Transcription factor, MADS-box + 79 + 449 134 - IPR003340
  - 83 - 1863 + IPR036879
Transcription factor, MADS-box superfamily + 79 + 98 135 - IPR015655
Protein phosphatase 2C family - 83 - 132 + IPR000270
PB1 domain + 78 + 135 136 - IPR001965
Zinc finger, PHD-type - 83 - 212 + IPR000953
Chromo/chromo shadow domain + 77 + 89 137 - IPR017907
Zinc finger, RING-type, conserved site - 82 - 129 + IPR026961
PGG domain + 77 + 157 138 - IPR024171
S-receptor-like serine/threonine-protein kinase - 81 - 129 + IPR018289
MULE transposase domain + 77 + 84 139 - IPR002083
  - 81 - 1254 + IPR000626
Ubiquitin-like domain + 75 + 195 140 - IPR026992
Non-haem dioxygenase N-terminal domain - 81 - 124 + IPR006121
Heavy metal-associated domain, HMA + 75 + 235 141 - IPR017871
ABC transporter, conserved site - 81 - 174 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 75 + 98 142 - IPR020472
G-protein beta WD-40 repeat - 80 - 390 + IPR002902
Gnk2-homologous domain + 75 + 365 143 - IPR001220
Legume lectin domain - 80 - 166 + IPR004045
Glutathione S-transferase, N-terminal + 75 + 213 144 - IPR000073
Alpha/beta hydrolase fold-1 - 79 - 238 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 73 + 75 145 - IPR000270
  - 78 - 555 + IPR036163
Heavy metal-associated domain superfamily + 73 + 92 146 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 77 - 109 + IPR016039
Thiolase-like + 72 + 136 147 - IPR006121
  - 76 - 756 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 72 + 85 148 - IPR036397
  - 76 - 423 + IPR003613
U box domain + 72 + 175 149 - IPR013766
  - 76 - 564 + IPR010987
Glutathione S-transferase, C-terminal-like + 71 + 96 150 - IPR000742
  - 75 - 548 + IPR004158
Protein of unknown function DUF247, plant + 71 + 156 151 - IPR026961
PGG domain - 74 - 170 + IPR008949
Isoprenoid synthase domain superfamily + 70 + 101 152 - IPR038408
  - 74 - 394 + IPR000571
Zinc finger, CCCH-type + 70 + 347 153 - IPR002902
  - 74 - 762 + IPR036908
RlpA-like domain superfamily + 69 + 80 154 - IPR002100
  - 74 - 1782 + IPR036852
Peptidase S8/S53 domain superfamily + 68 + 77 155 - IPR016039
  - 73 - 852 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 66 + 163 156 - IPR006566
FBD domain - 73 - 122 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 65 + 74 157 - IPR003613
  - 73 - 948 + IPR031052
FHY3/FAR1 family + 65 + 114 158 - IPR036879
  - 73 - 570 + IPR001806
Small GTPase + 65 + 149 159 - IPR036163
Heavy metal-associated domain superfamily - 72 - 98 + IPR019787
Zinc finger, PHD-finger + 64 + 173 160 - IPR000626
  - 70 - 642 + IPR013057
Amino acid transporter, transmembrane domain + 64 + 85 161 - IPR004045
  - 70 - 600 + IPR044965
Glycoside hydrolase family 17, plant + 64 + 86 162 - IPR000225
  - 70 - 2160 + IPR029052
Metallo-dependent phosphatase-like + 64 + 80 163 - IPR017451
F-box associated interaction domain - 69 - 105 + IPR007117
Expansin, cellulose-binding-like domain + 64 + 143 164 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 69 - 85 + IPR045051
Subtilisin-like protease + 63 + 82 165 - IPR035513
  - 69 - 272 + IPR006501
Pectinesterase inhibitor domain + 63 + 65 166 - IPR036961
  - 69 - 546 + IPR000209
Peptidase S8/S53 domain + 63 + 72 167 - IPR013783
  - 68 - 226 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 62 + 163 168 - IPR036908
  - 68 - 336 + IPR005202
Transcription factor GRAS + 62 + 226 169 - IPR000571
  - 68 - 1752 + IPR000048
IQ motif, EF-hand binding site + 62 + 363 170 - IPR003960
ATPase, AAA-type, conserved site - 67 - 103 + IPR020568
Ribosomal protein S5 domain 2-type fold + 61 + 106 171 - IPR010987
  - 67 - 190 + IPR023395
Mitochondrial carrier domain superfamily + 61 + 84 172 - IPR004158
Protein of unknown function DUF247, plant - 66 - 78 + IPR036915
Cyclin-like superfamily + 61 + 131 173 - IPR013057
Amino acid transporter, transmembrane domain - 65 - 97 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 61 + 68 174 - IPR036852
  - 65 - 1131 + IPR026960
Reverse transcriptase zinc-binding domain + 60 + 61 175 - IPR011993
  - 65 - 252 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 60 + 68 176 - IPR008949
  - 64 - 518 + IPR018108
Mitochondrial substrate/solute carrier + 60 + 464 177 - IPR001881
EGF-like calcium-binding domain - 63 - 158 + IPR003245
Phytocyanin domain + 60 + 128 178 - IPR020568
Ribosomal protein S5 domain 2-type fold - 63 - 125 + IPR002528
Multi antimicrobial extrusion protein + 60 + 159 179 - IPR015915
  - 63 - 552 + IPR013094
Alpha/beta hydrolase fold-3 + 60 + 67 180 - IPR016159
Cullin repeat-like-containing domain superfamily - 62 - 118 + IPR003663
Sugar/inositol transporter + 60 + 348 181 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 62 - 172 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 59 + 75 182 - IPR000209
Peptidase S8/S53 domain - 62 - 91 + IPR016159
Cullin repeat-like-containing domain superfamily + 59 + 77 183 - IPR001563
Peptidase S10, serine carboxypeptidase - 61 - 458 + IPR000490
Glycoside hydrolase family 17 + 59 + 72 184 - IPR036749
  - 61 - 304 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 58 + 64 185 - IPR005829
Sugar transporter, conserved site - 61 - 150 + IPR001563
Peptidase S10, serine carboxypeptidase + 58 + 517 186 - IPR006501
Pectinesterase inhibitor domain - 61 - 165 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 58 + 63 187 - IPR000048
  - 61 - 1680 + IPR026057
PC-Esterase + 58 + 71 188 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 60 - 88 + IPR039391
Phytocyanin + 58 + 63 189 - IPR016135
  - 60 - 400 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 58 + 88 190 - IPR000490
Glycoside hydrolase family 17 - 60 - 119 + IPR006566
FBD domain + 58 + 81 191 - IPR007117
  - 60 - 298 + IPR007112
Expansin/pollen allergen, DPBB domain + 57 + 66 192 - IPR036915
Cyclin-like superfamily - 60 - 131 + IPR022059
Protein of unknown function DUF3615 + 56 + 80 193 - IPR001806
Small GTPase superfamily - 60 - 87 + IPR006045
Cupin 1 + 56 + 95 194 - IPR026057
PC-Esterase - 59 - 81 + IPR015500
Peptidase S8, subtilisin-related + 56 + 177 195 - IPR008979
  - 59 - 410 + IPR011032
GroES-like superfamily + 55 + 102 196 - IPR005202
  - 59 - 272 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 55 + 64 197 - IPR030184
WAT1-related protein - 59 - 121 + IPR025846
PMR5 N-terminal domain + 55 + 67 198 - IPR034090
BPM, C-terminal - 59 - 101 + IPR024788
Malectin-like domain + 55 + 80 199 - IPR018097
EGF-like calcium-binding, conserved site - 59 - 102 + IPR029962
Trichome birefringence-like family + 54 + 68 200 - IPR019787
  - 58 - 332 + IPR015915
Kelch-type beta propeller + 54 + 73 201 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 57 - 81 + IPR001752
Kinesin motor domain + 54 + 486 202 - IPR018108
  - 57 - 1082 + IPR000620
EamA domain + 54 + 120 203 - IPR022059
Protein of unknown function DUF3615 - 57 - 98 + IPR000225
Armadillo + 54 + 237 204 - IPR023395
  - 57 - 472 + IPR008979
Galactose-binding-like domain superfamily + 53 + 85 205 - IPR016181
Acyl-CoA N-acyltransferase - 56 - 91 + IPR030184
WAT1-related protein + 53 + 89 206 - IPR013128
Peptidase C1A - 56 - 96 + IPR001509
NAD-dependent epimerase/dehydratase + 52 + 76 207 - IPR027640
Kinesin-like protein - 56 - 170 + IPR016181
Acyl-CoA N-acyltransferase + 51 + 75 208 - IPR003245
  - 56 - 537 + IPR007118
Expansin/Lol pI + 51 + 316 209 - IPR013094
Alpha/beta hydrolase fold-3 - 56 - 62 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 51 + 60 210 - IPR001752
  - 56 - 2019 + IPR013525
ABC-2 type transporter + 50 + 111 211 - IPR003663
Sugar/inositol transporter - 56 - 430 + IPR013763
Cyclin-like + 50 + 96 212 - IPR015500
Peptidase S8, subtilisin-related - 56 - 200 + IPR034197
Cucumisin-like catalytic domain + 50 + 56 213 - IPR007112
  - 55 - 260 + IPR036465
von Willebrand factor A-like domain superfamily + 50 + 65 214 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 55 - 58 + IPR023298
P-type ATPase, transmembrane domain superfamily + 50 + 78 215 - IPR011032
GroES-like superfamily - 54 - 104 + IPR044730
Ribonuclease H-like domain, plant type + 50 + 53 216 - IPR029962
Trichome birefringence-like family - 54 - 82 + IPR003676
Small auxin-up RNA + 50 + 78 217 - IPR019786
Zinc finger, PHD-type, conserved site - 54 - 95 + IPR008978
HSP20-like chaperone + 49 + 53 218 - IPR002528
Multi antimicrobial extrusion protein - 54 - 259 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 49 + 126 219 - IPR024788
Malectin-like carbohydrate-binding domain - 54 - 88 + IPR008250
P-type ATPase, A domain superfamily + 49 + 74 220 - IPR037045
  - 54 - 154 + IPR034161
Pepsin-like domain, plant + 49 + 52 221 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 53 - 120 + IPR000668
Peptidase C1A, papain C-terminal + 49 + 174 222 - IPR023393
  - 53 - 196 + IPR002921
Fungal lipase-like domain + 48 + 56 223 - IPR001509
NAD-dependent epimerase/dehydratase - 53 - 101 + IPR000608
Ubiquitin-conjugating enzyme E2 + 48 + 181 224 - IPR006045
Cupin 1 - 53 - 182 + IPR005630
Terpene synthase, metal-binding domain + 48 + 75 225 - IPR025846
PMR5 N-terminal domain - 53 - 74 + IPR004265
Dirigent protein + 48 + 54 226 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 52 - 63 + IPR011527
ABC transporter type 1, transmembrane domain + 48 + 247 227 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 52 - 568 + IPR045087
Multicopper oxidase + 48 + 58 228 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 52 - 79 + IPR036855
Zinc finger, CCCH-type superfamily + 48 + 143 229 - IPR029052
  - 52 - 166 + IPR004330
FAR1 DNA binding domain + 48 + 64 230 - IPR000620
EamA domain - 52 - 131 + IPR012946
X8 domain + 47 + 59 231 - IPR008978
  - 51 - 260 + IPR000742
EGF-like domain + 47 + 52 232 - IPR013763
Cyclin-like - 51 - 185 + IPR044808
Ethylene-responsive transcription factor + 47 + 55 233 - IPR023298
P-type ATPase, transmembrane domain superfamily - 51 - 214 + IPR008928
Six-hairpin glycosidase superfamily + 46 + 63 234 - IPR036640
  - 50 - 858 + IPR001906
Terpene synthase, N-terminal domain + 46 + 64 235 - IPR000608
  - 50 - 334 + IPR041569
AAA ATPase, AAA+ lid domain + 46 + 67 236 - IPR014014
  - 50 - 160 + IPR000743
Glycoside hydrolase, family 28 + 46 + 50 237 - IPR034197
Cucumisin-like catalytic domain - 50 - 71 + IPR033389
AUX/IAA domain + 45 + 64 238 - IPR018253
DnaJ domain, conserved site - 50 - 68 + IPR043926
ABC transporter family G domain + 45 + 79 239 - IPR010255
Haem peroxidase - 50 - 71 + IPR036318
FAD-binding, type PCMH-like superfamily + 45 + 61 240 - IPR011043
Galactose oxidase/kelch, beta-propeller - 50 - 65 + IPR016461
O-methyltransferase COMT-type + 45 + 96 241 - IPR003676
Small auxin-up RNA - 50 - 67 + IPR009060
UBA-like superfamily + 45 + 60 242 - IPR002921
Fungal lipase-like domain - 49 - 61 + IPR029055
Nucleophile aminohydrolases, N-terminal + 45 + 63 243 - IPR008250
P-type ATPase, A domain superfamily - 49 - 95 + IPR009000
Translation protein, beta-barrel domain superfamily + 45 + 69 244 - IPR004265
Dirigent protein - 49 - 52 + IPR011043
Galactose oxidase/kelch, beta-propeller + 45 + 51 245 - IPR008928
Six-hairpin glycosidase superfamily - 49 - 76 + IPR025724
GAG-pre-integrase domain + 45 + 45 246 - IPR011527
  - 49 - 852 + IPR001214
SET domain + 45 + 121 247 - IPR002016
  - 49 - 852 + IPR011707
Multicopper oxidase, N-termianl + 45 + 49 248 - IPR036465
  - 49 - 254 + IPR017884
SANT domain + 44 + 68 249 - IPR001878
  - 49 - 813 + IPR011012
Longin-like domain superfamily + 44 + 68 250 - IPR013525
ABC-2 type transporter - 48 - 132 + IPR011706
Multicopper oxidase, C-terminal + 44 + 48 251 - IPR007118
Expansin/Lol pI - 48 - 307 + IPR014756
Immunoglobulin E-set + 44 + 67 252 - IPR034161
Pepsin-like domain, plant - 48 - 52 + IPR015947
PUA-like superfamily + 44 + 57 253 - IPR004140
Exocyst complex component Exo70 - 48 - 143 + IPR001117
Multicopper oxidase, type 1 + 43 + 47 254 - IPR023299
  - 47 - 405 + IPR010402
CCT domain + 43 + 148 255 - IPR036855
Zinc finger, CCCH-type superfamily - 47 - 139 + IPR004041
NAF domain + 43 + 54 256 - IPR000873
AMP-dependent synthetase/ligase - 46 - 89 + IPR006016
UspA + 43 + 49 257 - IPR012946
X8 domain - 46 - 114 + IPR033896
MADS MEF2-like + 43 + 59 258 - IPR014756
Immunoglobulin E-set - 46 - 89 + IPR018451
NAF/FISL domain + 43 + 54 259 - IPR012341
  - 46 - 192 + IPR014014
RNA helicase, DEAD-box type, Q motif + 43 + 56 260 - IPR017877
  - 46 - 150 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 43 + 74 261 - IPR033389
AUX/IAA domain - 45 - 62 + IPR011006
CheY-like superfamily + 43 + 67 262 - IPR000182
  - 45 - 178 + IPR007125
Histone H2A/H2B/H3 + 43 + 46 263 - IPR036318
FAD-binding, type 2-like superfamily - 45 - 57 + IPR001077
O-methyltransferase domain + 43 + 44 264 - IPR016461
  - 45 - 282 + IPR009003
Peptidase S1, PA clan + 43 + 105 265 - IPR001938
  - 45 - 636 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 43 + 55 266 - IPR000222
PPM-type phosphatase, divalent cation binding - 45 - 58 + IPR004853
Sugar phosphate transporter domain + 42 + 60 267 - IPR000668
Peptidase C1A, papain C-terminal - 45 - 247 + IPR011701
Major facilitator superfamily + 42 + 68 268 - IPR001757
P-type ATPase - 45 - 261 + IPR004140
Exocyst complex component Exo70 + 42 + 103 269 - IPR009003
Peptidase S1, PA clan - 45 - 98 + IPR004046
Glutathione S-transferase, C-terminal + 42 + 55 270 - IPR036875
Zinc finger, CCHC-type superfamily - 45 - 75 + IPR000070
Pectinesterase, catalytic + 42 + 47 271 - IPR033896
MADS MEF2-like - 44 - 69 + IPR008889
VQ + 42 + 43 272 - IPR009060
UBA-like superfamily - 44 - 69 + IPR001789
Signal transduction response regulator, receiver domain + 42 + 122 273 - IPR011701
Major facilitator superfamily - 44 - 95 + IPR000182
GNAT domain + 41 + 99 274 - IPR029055
  - 44 - 208 + IPR004332
Transposase, MuDR, plant + 41 + 41 275 - IPR017970
Homeobox, conserved site - 44 - 52 + IPR000873
AMP-dependent synthetase/ligase + 41 + 68 276 - IPR002109
  - 44 - 348 + IPR006671
Cyclin, N-terminal + 41 + 53 277 - IPR000070
Pectinesterase, catalytic - 44 - 55 + IPR000330
SNF2, N-terminal + 40 + 60 278 - IPR001214
  - 44 - 594 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 40 + 46 279 - IPR036965
  - 43 - 267 + IPR004263
Exostosin-like + 40 + 58 280 - IPR036890
  - 43 - 346 + IPR029045
ClpP/crotonase-like domain superfamily + 40 + 64 281 - IPR018303
P-type ATPase, phosphorylation site - 43 - 66 + IPR039417
Papain-like cysteine endopeptidase + 40 + 45 282 - IPR011706
Multicopper oxidase, type 2 - 43 - 52 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 40 + 81 283 - IPR006016
UspA - 42 - 56 + IPR006702
Casparian strip membrane protein domain + 40 + 45 284 - IPR009000
Translation protein, beta-barrel domain superfamily - 42 - 62 + IPR025322
Protein of unknown function DUF4228, plant + 39 + 40 285 - IPR005630
Terpene synthase, metal-binding domain - 42 - 83 + IPR025659
Tubby-like, C-terminal + 39 + 49 286 - IPR011006
CheY-like superfamily - 42 - 70 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 39 + 52 287 - IPR001077
O-methyltransferase, family 2 - 42 - 51 + IPR029021
Protein-tyrosine phosphatase-like + 39 + 72 288 - IPR006671
Cyclin, N-terminal - 42 - 78 + IPR036612
K Homology domain, type 1 superfamily + 39 + 110 289 - IPR001906
Terpene synthase, N-terminal domain - 42 - 73 + IPR016166
FAD-binding domain, PCMH-type + 39 + 53 290 - IPR011707
Multicopper oxidase, type 3 - 42 - 48 + IPR002487
Transcription factor, K-box + 39 + 98 291 - IPR000743
Glycoside hydrolase, family 28 - 42 - 75 + IPR008942
ENTH/VHS + 38 + 49 292 - IPR001789
  - 42 - 702 + IPR016040
NAD(P)-binding domain + 38 + 54 293 - IPR001117
Multicopper oxidase, type 1 - 41 - 50 + IPR003137
PA domain + 38 + 53 294 - IPR008942
  - 41 - 216 + IPR023271
Aquaporin-like + 38 + 45 295 - IPR020845
AMP-binding, conserved site - 41 - 69 + IPR000425
Major intrinsic protein + 38 + 297 296 - IPR025322
Protein of unknown function DUF4228, plant - 40 - 42 + IPR000644
CBS domain + 38 + 206 297 - IPR004853
Sugar phosphate transporter domain - 40 - 57 + IPR002109
Glutaredoxin + 38 + 40 298 - IPR000330
SNF2-related, N-terminal domain - 40 - 64 + IPR013126
Heat shock protein 70 family + 38 + 79 299 - IPR001969
Aspartic peptidase, active site - 40 - 66 + IPR037176
Osmotin/thaumatin-like superfamily + 38 + 41 300 - IPR016166
  - 40 - 138 + IPR013149
Alcohol dehydrogenase, C-terminal + 37 + 51 301 - IPR011012
Longin-like domain superfamily - 40 - 60 + IPR001938
Thaumatin family + 37 + 247 302 - IPR038718
  - 40 - 150 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 37 + 149 303 - IPR008889
VQ - 40 - 40 + IPR001360
Glycoside hydrolase family 1 + 36 + 512 304 - IPR025659
  - 39 - 174 + IPR002068
Alpha crystallin/Hsp20 domain + 36 + 80 305 - IPR003653
  - 39 - 255 + IPR022742
Serine aminopeptidase, S33 + 36 + 51 306 - IPR029045
ClpP/crotonase-like domain superfamily - 39 - 76 + IPR004839
Aminotransferase, class I/classII + 36 + 53 307 - IPR028889
  - 39 - 128 + IPR015655
Protein phosphatase 2C family + 36 + 73 308 - IPR011042
  - 39 - 148 + IPR033443
Pentacotripeptide-repeat region of PRORP + 36 + 54 309 - IPR014721
  - 39 - 150 + IPR002067
Mitochondrial carrier protein + 36 + 208 310 - IPR015947
PUA-like superfamily - 39 - 64 + IPR028889
Ubiquitin specific protease domain + 36 + 57 311 - IPR036691
  - 38 - 424 + IPR004314
Neprosin + 36 + 51 312 - IPR036612
  - 38 - 633 + IPR012967
Plant methyltransferase dimerisation + 36 + 37 313 - IPR004839
Aminotransferase, class I/classII - 38 - 55 + IPR038933
Ovate protein family + 35 + 36 314 - IPR007125
Histone H2A/H2B/H3 - 38 - 41 + IPR019557
Aminotransferase-like, plant mobile domain + 35 + 47 315 - IPR004046
Glutathione S-transferase, C-terminal - 38 - 50 + IPR005135
Endonuclease/exonuclease/phosphatase + 35 + 48 316 - IPR013780
  - 38 - 174 + IPR013154
Alcohol dehydrogenase, N-terminal + 35 + 52 317 - IPR000644
  - 38 - 666 + IPR034294
Aquaporin transporter + 35 + 46 318 - IPR002912
  - 38 - 276 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 35 + 55 319 - IPR010402
  - 37 - 258 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 35 + 57 320 - IPR002068
  - 37 - 168 + IPR002495
Glycosyl transferase, family 8 + 35 + 44 321 - IPR029021
  - 37 - 306 + IPR040911
Exostosin, GT47 domain + 35 + 47 322 - IPR003137
PA domain - 37 - 45 + IPR043519
Nucleotidyltransferase superfamily + 35 + 53 323 - IPR022742
Serine aminopeptidase, S33 - 37 - 46 + IPR039361
Cyclin + 35 + 53 324 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 37 - 42 + IPR001296
Glycosyl transferase, family 1 + 34 + 55 325 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 37 - 67 + IPR006094
FAD linked oxidase, N-terminal + 34 + 43 326 - IPR002495
Glycosyl transferase, family 8 - 37 - 51 + IPR006458
Ovate protein family, C-terminal + 34 + 66 327 - IPR002487
  - 37 - 342 + IPR002912
ACT domain + 34 + 93 328 - IPR037176
  - 37 - 160 + IPR005299
SAM dependent carboxyl methyltransferase + 33 + 121 329 - IPR006626
Parallel beta-helix repeat - 36 - 208 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 33 + 48 330 - IPR003594
Histidine kinase/HSP90-like ATPase - 36 - 142 + IPR000795
Translational (tr)-type GTP-binding domain + 33 + 318 331 - IPR004883
  - 36 - 164 + IPR043454
NPH3/RPT2-like family + 33 + 43 332 - IPR019378
GDP-fucose protein O-fucosyltransferase - 36 - 65 + IPR004883
Lateral organ boundaries, LOB + 33 + 74 333 - IPR006702
Casparian strip membrane protein domain - 36 - 42 + IPR027923
Hydrophobic seed protein domain + 33 + 82 334 - IPR004041
NAF domain - 35 - 43 + IPR007493
Protein of unknown function DUF538 + 32 + 76 335 - IPR013149
Alcohol dehydrogenase, C-terminal - 35 - 47 + IPR001251
CRAL-TRIO lipid binding domain + 32 + 112 336 - IPR018451
  - 35 - 129 + IPR008991
Translation protein SH3-like domain superfamily + 32 + 41 337 - IPR011016
  - 35 - 378 + IPR035940
CAP superfamily + 32 + 40 338 - IPR004263
Exostosin-like - 35 - 52 + IPR006652
Kelch repeat type 1 + 32 + 66 339 - IPR027356
  - 35 - 148 + IPR036758
At5g01610-like superfamily + 32 + 38 340 - IPR027923
Hydrophobic seed protein - 35 - 73 + IPR011141
Polyketide synthase, type III + 32 + 39 341 - IPR006094
FAD linked oxidase, N-terminal - 35 - 40 + IPR006073
GTP binding domain + 32 + 113 342 - IPR004314
Neprosin - 35 - 55 + IPR001929
Germin + 31 + 106 343 - IPR012967
Plant methyltransferase dimerisation - 35 - 38 + IPR032710
NTF2-like domain superfamily + 31 + 41 344 - IPR001296
Glycosyl transferase, family 1 - 34 - 57 + IPR013216
Methyltransferase type 11 + 31 + 43 345 - IPR023271
  - 34 - 182 + IPR008906
HAT, C-terminal dimerisation domain + 31 + 39 346 - IPR013154
Alcohol dehydrogenase, N-terminal - 34 - 55 + IPR007650
Zf-FLZ domain + 31 + 70 347 - IPR006652
Kelch repeat type 1 - 34 - 186 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 31 + 45 348 - IPR000425
Major intrinsic protein - 34 - 336 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 31 + 38 349 - IPR013126
Heat shock protein 70 family - 34 - 315 + IPR027356
NPH3 domain + 31 + 72 350 - IPR025661
Cysteine peptidase, asparagine active site - 34 - 42 + IPR004367
Cyclin, C-terminal domain + 31 + 41 351 - IPR019821
Kinesin motor domain, conserved site - 33 - 55 + IPR003406
Glycosyl transferase, family 14 + 31 + 42 352 - IPR007493
Protein of unknown function DUF538 - 33 - 86 + IPR000863
Sulfotransferase domain + 31 + 47 353 - IPR001251
  - 33 - 362 + IPR001283
Cysteine-rich secretory protein-related + 31 + 158 354 - IPR018200
Ubiquitin specific protease, conserved site - 33 - 90 + IPR014044
CAP domain + 31 + 39 355 - IPR005299
SAM dependent carboxyl methyltransferase - 33 - 125 + IPR019378
GDP-fucose protein O-fucosyltransferase + 31 + 55 356 - IPR038933
Ovate protein family - 33 - 39 + IPR004088
K Homology domain, type 1 + 31 + 93 357 - IPR036865
  - 33 - 186 + IPR003311
AUX/IAA protein + 31 + 49 358 - IPR034294
Aquaporin transporter - 33 - 45 + IPR023210
NADP-dependent oxidoreductase domain + 31 + 48 359 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 33 - 331 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 31 + 44 360 - IPR038538
  - 33 - 120 + IPR006311
Twin-arginine translocation pathway, signal sequence + 31 + 40 361 - IPR019794
Peroxidase, active site - 33 - 43 + IPR001099
Chalcone/stilbene synthase, N-terminal + 31 + 36 362 - IPR002067
Mitochondrial carrier protein - 33 - 227 + IPR015940
Ubiquitin-associated domain + 30 + 68 363 - IPR006458
  - 33 - 188 + IPR018490
Cyclic nucleotide-binding-like + 30 + 47 364 - IPR016040
NAD(P)-binding domain - 32 - 48 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 30 + 32 365 - IPR001360
Glycoside hydrolase family 1 - 32 - 467 + IPR010920
LSM domain superfamily + 30 + 39 366 - IPR033131
Pectinesterase, Asp active site - 32 - 33 + IPR000315
B-box-type zinc finger + 30 + 73 367 - IPR008266
Tyrosine-protein kinase, active site - 32 - 43 + IPR002659
Glycosyl transferase, family 31 + 30 + 104 368 - IPR000863
Sulfotransferase domain - 32 - 45 + IPR001594
Palmitoyltransferase, DHHC domain + 30 + 48 369 - IPR036758
  - 32 - 196 + IPR002423
Chaperonin Cpn60/TCP-1 family + 30 + 45 370 - IPR027409
  - 32 - 214 + IPR029480
Transposase-associated domain + 30 + 30 371 - IPR002035
  - 32 - 178 + IPR027409
GroEL-like apical domain superfamily + 30 + 40 372 - IPR022357
Major intrinsic protein, conserved site - 32 - 43 + IPR003851
Zinc finger, Dof-type + 30 + 64 373 - IPR001099
Chalcone/stilbene synthase, N-terminal - 32 - 35 + IPR004242
Transposon, En/Spm-like + 30 + 30 374 - IPR015940
  - 31 - 246 + IPR002913
START domain + 30 + 99 375 - IPR018490
Cyclic nucleotide-binding-like - 31 - 51 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 29 + 173 376 - IPR001929
Germin - 31 - 110 + IPR013601
FAE1/Type III polyketide synthase-like protein + 29 + 31 377 - IPR000315
  - 31 - 507 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 29 + 245 378 - IPR002659
Glycosyl transferase, family 31 - 31 - 97 + IPR029000
Cyclophilin-like domain superfamily + 29 + 43 379 - IPR002423
Chaperonin Cpn60/TCP-1 family - 31 - 56 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 29 + 37 380 - IPR000795
  - 31 - 765 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 29 + 45 381 - IPR004088
K Homology domain, type 1 - 31 - 103 + IPR045048
F-box only protein 31/39 + 29 + 63 382 - IPR003311
AUX/IAA protein - 31 - 48 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 53 383 - IPR000595
  - 31 - 362 + IPR002963
Expansin + 29 + 268 384 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 31 - 36 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 385 - IPR009091
  - 31 - 356 + IPR016897
S-phase kinase-associated protein 1 + 29 + 36 386 - IPR011141
Polyketide synthase, type III - 31 - 70 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 29 + 45 387 - IPR000823
Plant peroxidase - 31 - 211 + IPR036296
SKP1-like, dimerisation domain superfamily + 29 + 34 388 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 30 - 53 + IPR036404
Jacalin-like lectin domain superfamily + 29 + 49 389 - IPR032710
NTF2-like domain superfamily - 30 - 40 + IPR000595
Cyclic nucleotide-binding domain + 29 + 116 390 - IPR013187
F-box associated domain, type 3 - 30 - 51 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 29 + 49 391 - IPR000717
  - 30 - 178 + IPR000679
Zinc finger, GATA-type + 29 + 99 392 - IPR005135
Endonuclease/exonuclease/phosphatase - 30 - 51 + IPR001229
Jacalin-like lectin domain + 29 + 98 393 - IPR038770
  - 30 - 86 + IPR017938
Riboflavin synthase-like beta-barrel + 28 + 42 394 - IPR003406
Glycosyl transferase, family 14 - 30 - 41 + IPR006153
Cation/H+ exchanger + 28 + 43 395 - IPR008480
Protein of unknown function DUF761, plant - 30 - 30 + IPR002403
Cytochrome P450, E-class, group IV + 28 + 163 396 - IPR004087
K Homology domain - 30 - 100 + IPR013187
F-box associated domain, type 3 + 28 + 43 397 - IPR000169
Cysteine peptidase, cysteine active site - 30 - 37 + IPR044835
Auxin response factor + 28 + 46 398 - IPR036404
  - 30 - 186 + IPR000717
Proteasome component (PCI) domain + 28 + 60 399 - IPR020843
Polyketide synthase, enoylreductase domain - 30 - 46 + IPR029061
Thiamin diphosphate-binding fold + 28 + 68 400 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 37 + IPR027725
Heat shock transcription factor family + 28 + 31 401 - IPR000757
  - 30 - 219 + IPR025452
Domain of unknown function DUF4218 + 28 + 28 402 - IPR006073
GTP binding domain - 30 - 113 + IPR002123
Phospholipid/glycerol acyltransferase + 28 + 38 403 - IPR001229
  - 30 - 266 + IPR012328
Chalcone/stilbene synthase, C-terminal + 28 + 29 404 - IPR035940
  - 29 - 144 + IPR036041
Ribosome-inactivating protein superfamily + 28 + 30 405 - IPR007650
  - 29 - 130 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 27 + 39 406 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 29 - 89 + IPR036378
FAS1 domain superfamily + 27 + 40 407 - IPR004367
Cyclin, C-terminal domain - 29 - 65 + IPR001440
Tetratricopeptide repeat 1 + 27 + 44 408 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 29 - 136 + IPR044848
PHR1-like + 27 + 40 409 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 52 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 27 + 27 410 - IPR005821
Ion transport domain - 29 - 44 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 40 411 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 29 - 43 + IPR016072
SKP1 component, dimerisation + 27 + 32 412 - IPR012328
Chalcone/stilbene synthase, C-terminal - 29 - 30 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 27 + 33 413 - IPR003851
  - 29 - 366 + IPR004813
Oligopeptide transporter, OPT superfamily + 27 + 53 414 - IPR003855
Potassium transporter - 29 - 138 + IPR044791
Beta-glucanase/XTH + 27 + 39 415 - IPR036041
Ribosome-inactivating protein superfamily - 29 - 37 + IPR003855
Potassium transporter + 27 + 85 416 - IPR025660
Cysteine peptidase, histidine active site - 29 - 43 + IPR000757
Glycoside hydrolase family 16 + 27 + 74 417 - IPR013601
FAE1/Type III polyketide synthase-like protein - 28 - 29 + IPR001574
Ribosome-inactivating protein + 27 + 54 418 - IPR029061
Thiamin diphosphate-binding fold - 28 - 62 + IPR000727
Target SNARE coiled-coil homology domain + 26 + 44 419 - IPR009030
Growth factor receptor cysteine-rich domain superfamily - 28 - 44 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 26 + 26 420 - IPR004320
Protein of unknown function DUF241, plant - 28 - 37 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 26 + 88 421 - IPR002355
Multicopper oxidase, copper-binding site - 28 - 30 + IPR024709
Putative O-fucosyltransferase, plant + 26 + 42 422 - IPR002123
Phospholipid/glycerol acyltransferase - 28 - 82 + IPR044778
Sugar transport protein STP/MST-like, plant + 26 + 28 423 - IPR011013
Galactose mutarotase-like domain superfamily - 28 - 46 + IPR005333
Transcription factor, TCP + 26 + 32 424 - IPR005150
Cellulose synthase - 28 - 64 + IPR041577
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain + 26 + 26 425 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 28 - 41 + IPR005150
Cellulose synthase + 26 + 63 426 - IPR002963
Expansin - 28 - 268 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 26 + 31 427 - IPR020946
Flavin monooxygenase-like - 28 - 45 + IPR005821
Ion transport domain + 26 + 39 428 - IPR031107
Small heat shock protein HSP20 - 28 - 32 + IPR002035
von Willebrand factor, type A + 26 + 60 429 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 28 - 55 + IPR023299
P-type ATPase, cytoplasmic domain N + 26 + 48 430 - IPR036296
SKP1-like, dimerisation domain superfamily - 28 - 31 + IPR029069
HotDog domain superfamily + 26 + 41 431 - IPR025110
AMP-binding enzyme, C-terminal domain - 27 - 49 + IPR029062
Class I glutamine amidotransferase-like + 26 + 48 432 - IPR036378
  - 27 - 140 + IPR001701
Glycoside hydrolase family 9 + 26 + 33 433 - IPR001179
  - 27 - 208 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 26 + 27 434 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 27 - 85 + IPR005175
PPC domain + 26 + 83 435 - IPR024709
Putative O-fucosyltransferase, plant - 27 - 89 + IPR015797
NUDIX hydrolase-like domain superfamily + 26 + 32 436 - IPR013088
  - 27 - 105 + IPR036085
PAZ domain superfamily + 25 + 57 437 - IPR010920
LSM domain superfamily - 27 + IPR025110
AMP-binding enzyme, C-terminal domain + 25 36 438 - IPR023753
FAD/NAD(P)-binding domain - 27 - 35 + IPR019956
Ubiquitin domain + 25 + 78 439 - IPR005333
Transcription factor, TCP - 27 - 29 + IPR025753
AAA-type ATPase, N-terminal domain + 25 + 31 440 - IPR031112
AP2-like ethylene-responsive transcription factor - 27 - 45 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 25 + 77 441 - IPR000408
  - 27 - 1618 + IPR027806
Harbinger transposase-derived nuclease domain + 25 + 25 442 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 42 + IPR029466
No apical meristem-associated, C-terminal domain + 25 + 27 443 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 27 - 28 + IPR007657
Glycosyltransferase 61 + 25 + 65 444 - IPR014044
CAP domain - 27 - 68 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 25 + 33 445 - IPR004813
Oligopeptide transporter, OPT superfamily - 27 - 100 + IPR003656
Zinc finger, BED-type + 25 + 56 446 - IPR001849
  - 27 - 262 + IPR001763
Rhodanese-like domain + 25 + 78 447 - IPR019780
Germin, manganese binding site - 27 - 37 + IPR000408
Regulator of chromosome condensation, RCC1 + 25 + 479 448 - IPR001701
Glycoside hydrolase family 9 - 27 - 28 + IPR044814
Terpene cyclases, class 1, plant + 25 + 34 449 - IPR029047
  - 27 - 118 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 25 + 34 450 - IPR023210
NADP-dependent oxidoreductase domain - 27 - 103 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 25 + 54 451 - IPR027410
  - 27 - 230 + IPR044839
Protein NDR1-like + 25 + 26 452 - IPR036812
  - 27 - 210 + IPR020946
Flavin monooxygenase-like + 25 + 42 453 - IPR006311
  - 27 - 64 + IPR034285
Laccase, second cupredoxin domain + 25 + 28 454 - IPR000679
  - 27 - 402 + IPR001757
P-type ATPase + 25 + 125 455 - IPR001574
Ribosome-inactivating protein - 27 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 25 35 456 - IPR017938
Riboflavin synthase-like beta-barrel - 26 - 50 + IPR024752
Myb/SANT-like domain + 25 + 26 457 - IPR002130
  - 26 - 762 + IPR010525
Auxin response factor domain + 25 + 33 458 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 26 - 26 + IPR033734
Jacalin-like lectin domain, plant + 25 + 45 459 - IPR029000
  - 26 - 194 + IPR003100
PAZ domain + 24 + 108 460 - IPR025753
AAA-type ATPase, N-terminal domain - 26 - 30 + IPR000782
FAS1 domain + 24 + 64 461 - IPR008991
Translation protein SH3-like domain superfamily - 26 - 31 + IPR002867
IBR domain + 24 + 50 462 - IPR036420
  - 26 - 384 + IPR004316
SWEET sugar transporter + 24 + 51 463 - IPR013216
Methyltransferase type 11 - 26 - 31 + IPR007612
LURP-one-related + 24 + 56 464 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 26 - 36 + IPR011016
Zinc finger, RING-CH-type + 24 + 71 465 - IPR007657
Glycosyltransferase 61 - 26 - 90 + IPR023753
FAD/NAD(P)-binding domain + 24 + 34 466 - IPR027725
Heat shock transcription factor family - 26 - 38 + IPR002293
Amino acid/polyamine transporter I + 24 + 33 467 - IPR017887
  - 26 - 56 + IPR003594
Histidine kinase/HSP90-like ATPase + 24 + 33 468 - IPR000960
Flavin monooxygenase FMO - 26 - 69 + IPR013010
Zinc finger, SIAH-type + 24 + 31 469 - IPR016072
SKP1 component, dimerisation - 26 - 29 + IPR034288
Laccase, first cupredoxin domain + 24 + 27 470 - IPR016167
  - 26 - 117 + IPR001849
Pleckstrin homology domain + 24 + 80 471 - IPR033443
Pentacotripeptide-repeat region of PRORP - 26 - 38 + IPR017923
Transcription factor IIS, N-terminal + 24 + 74 472 - IPR029062
  - 26 - 188 + IPR000086
NUDIX hydrolase domain + 24 + 58 473 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 26 - 74 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 24 + 101 474 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 26 - 32 + IPR031127
E3 ubiquitin ligase RBR family + 24 + 48 475 IPR036034
PDZ superfamily - 26 - 38 + 24 + 47 476 - IPR005175
  - 26 - 160 + IPR044066
TRIAD supradomain + 24 + 32 477 - IPR002913
  - 26 - 393 + IPR035441
TFIIS/LEDGF domain superfamily + 24 + 40 478 - IPR010525
Auxin response factor - 26 - 36 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 23 + 48 479 - IPR017927
  - 25 - 120 + IPR016073
SKP1 component, POZ domain + 23 + 28 480 - IPR000727
  - 25 - 192 + IPR003106
Leucine zipper, homeobox-associated + 23 + 26 481 - IPR006153
Cation/H+ exchanger - 25 - 36 + IPR021790
PTBP1, RNA recognition motif 2-like + 23 + 26 482 - IPR007612
LURP-one-related - 25 - 58 + IPR036420
BRCT domain superfamily + 23 + 51 483 - IPR012675
  - 25 - 62 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 31 484 - IPR018181
Heat shock protein 70, conserved site - 25 - 68 + IPR008422
Homeobox KN domain + 23 + 33 485 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 25 - 47 + IPR025422
Transcription factor TGA like domain + 23 + 70 486 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 25 - 66 + IPR003337
Trehalose-phosphatase + 23 + 29 487 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 25 - 33 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 23 + 25 488 - IPR019793
Peroxidases heam-ligand binding site - 25 - 35 + IPR021720
Malectin domain + 23 + 85 489 - IPR001876
  - 25 - 414 + IPR001876
Zinc finger, RanBP2-type + 23 + 115 490 - IPR001232
S-phase kinase-associated protein 1-like - 25 - 27 + IPR039421
Type 1 protein exporter + 23 + 39 491 - IPR017937
Thioredoxin, conserved site - 25 - 42 + IPR016161
Aldehyde/histidinol dehydrogenase + 23 + 29 492 - IPR029993
Plant galacturonosyltransferase GAUT - 25 - 47 + IPR025486
Domain of unknown function DUF4378 + 23 + 33 493 - IPR025486
Domain of unknown function DUF4378 - 25 - 35 + IPR002937
Amine oxidase + 23 + 39 494 - IPR036085
PAZ domain superfamily - 24 - 65 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 23 + 33 495 - IPR000782
  - 24 - 184 + IPR029033
Histidine phosphatase superfamily + 23 + 33 496 - IPR003954
RNA recognition motif domain, eukaryote - 24 - 61 + IPR036443
Zinc finger, RanBP2-type superfamily + 23 + 70 497 - IPR001357
  - 24 - 598 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 47 498 - IPR018957
Zinc finger, C3HC4 RING-type - 24 - 28 + IPR025312
Domain of unknown function DUF4216 + 22 + 22 499 - IPR008422
Homeobox KN domain - 24 - 29 + IPR004161
Translation elongation factor EFTu-like, domain 2 + 22 + 32 500 - IPR001594
Palmitoyltransferase, DHHC domain - 24 + IPR017887
Transcription factor TCP subgroup + 22 46 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_indica.html b/gramene/htdocs/ssi/species/stats_Oryza_indica.html index a76ac818..e3a05950 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_indica.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_indica.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:ASM465v1, Jan 2005ASM386521v1, Dec 2018
Database version:93.287.3
Base Pairs:411,710,190395,354,355
Golden Path Length:427,004,890395,354,355
Genebuild by: BGI
Genebuild method: Imported from BGI
Genebuild started: Jul 2010
Genebuild released: Jan 2005
Genebuild last updated/patched: Jul 2010
Genebuild version: 2010-07-BGI
+ Genebuild by: Ensembl Genebuild started: Apr 2021

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):40,745Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		35,897
Gene transcriptsHASH(0x68ce400):89,723Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:50,457
@@ -35,48 +35,143 @@

Gene counts

Coordinate Systems

- + - - - - - - - -
chromosomeprimary_assembly
-
12 sequences
+
127 sequences
-
- +
+
- +
SequenceLength (bp)
147283185
238103930
341884883
434718618
531240961
632913967
727957088
830396518
921757032
1022204031
1123035369
1223049917
PKRX01000013.145777
PKRX01000014.137687
PKRX01000015.153894
PKRX01000016.135475
PKRX01000017.1272205
PKRX01000018.1116040
PKRX01000019.172221
PKRX01000020.164048
PKRX01000021.178537
PKRX01000022.1132305
PKRX01000023.145053
PKRX01000024.1142770
PKRX01000025.161090
PKRX01000026.165606
PKRX01000027.143480
PKRX01000028.164505
PKRX01000029.167075
PKRX01000030.141410
PKRX01000031.138016
PKRX01000032.149130
PKRX01000033.1145827
PKRX01000034.165977
PKRX01000035.158209
PKRX01000036.151299
PKRX01000037.190627
PKRX01000038.154858
PKRX01000039.174771
PKRX01000040.137474
PKRX01000041.145109
PKRX01000042.174721
PKRX01000043.170721
PKRX01000044.182198
PKRX01000045.131900
PKRX01000046.174047
PKRX01000047.147781
PKRX01000048.147258
PKRX01000049.161371
PKRX01000050.127145
PKRX01000051.172101
PKRX01000052.134640
PKRX01000053.168546
PKRX01000054.127535
PKRX01000055.133091
PKRX01000056.146364
PKRX01000057.157981
PKRX01000058.149010
PKRX01000059.133551
PKRX01000060.124549
PKRX01000061.124513
PKRX01000062.148824
PKRX01000063.142652
PKRX01000064.124365
PKRX01000065.136056
PKRX01000066.132288
PKRX01000067.143666
PKRX01000068.150813
PKRX01000069.147889
PKRX01000070.127281
PKRX01000071.137817
PKRX01000072.136651
PKRX01000073.121652
PKRX01000074.128914
PKRX01000075.184871
PKRX01000076.144418
PKRX01000077.1142251
PKRX01000078.134004
PKRX01000079.1119167
PKRX01000080.143798
PKRX01000081.194756
PKRX01000082.127412
PKRX01000083.175765
PKRX01000084.152405
PKRX01000085.1134384
PKRX01000086.175184
PKRX01000087.1206605
PKRX01000088.195239
PKRX01000089.1274625
PKRX01000090.166989
PKRX01000091.126316
PKRX01000092.147553
PKRX01000093.145970
PKRX01000094.151582
PKRX01000095.144376
PKRX01000096.156326
PKRX01000097.181970
PKRX01000098.138198
PKRX01000099.149549
PKRX01000100.128968
PKRX01000101.1172473
PKRX01000102.173198
PKRX01000103.132351
PKRX01000104.138091
PKRX01000105.1130731
PKRX01000106.144505
PKRX01000107.1444941
PKRX01000108.1112857
PKRX01000109.160190
PKRX01000110.183352
PKRX01000111.173933
PKRX01000112.143234
PKRX01000113.177365
PKRX01000114.142936
PKRX01000115.1102993
PKRX01000116.144541
PKRX01000117.122166
PKRX01000118.1110388
PKRX01000119.181351
PKRX01000120.137048
PKRX01000121.120025
PKRX01000122.185706
PKRX01000123.141478
PKRX01000124.135657
PKRX01000125.135087
PKRX01000126.129552
PKRX01000127.143444
144347626
248423113
339024662
435928712
530593392
632158464
720293094
829283865
924258770
1025547656
1131741312
1225973049
-
+
supscaffold10627 sequences
scaffold39922 sequences
- -

Other

- - - - - - - - - -
FGENESH gene predictions:59,695
Short Variants (SNPs, indels, somatic mutations):4,747,883
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_indica_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_indica_IPtop500.html index 24775071..18162eb9 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_indica_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_indica_IPtop500.html @@ -16,3502 +16,3502 @@ 1 - IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1711 - 2218 + IPR011009
Protein kinase-like domain superfamily + 1463 + 2408 2 - IPR011009
Protein kinase-like domain superfamily - 1552 - 1729 + IPR027417
P-loop containing nucleoside triphosphate hydrolase + 1357 + 2501 3 - IPR032675
  - 1468 - 5522 + IPR000719
Protein kinase domain + 1356 + 3710 4 - IPR000719
  - 1449 - 11013 + IPR036047
F-box-like domain superfamily + 658 + 931 5 - IPR008271
Serine/threonine-protein kinase, active site - 1119 - 1134 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 492 + 1066 6 - IPR017441
Protein kinase, ATP binding site - 945 - 959 + IPR002885
Pentatricopeptide repeat + 486 + 8197 7 - IPR036047
F-box-like domain superfamily - 772 - 806 + IPR044974
Disease resistance protein, plants + 475 + 947 8 - IPR011990
  - 766 - 8007 + IPR001611
Leucine-rich repeat + 475 + 1652 9 - IPR013083
  - 702 - 1500 + IPR001810
F-box domain + 459 + 1001 10 - IPR036291
NAD(P)-binding domain superfamily - 566 - 624 + IPR002182
NB-ARC + 446 + 639 11 - IPR001810
  - 560 - 3357 + IPR001841
Zinc finger, RING-type + 423 + 970 12 - IPR001611
  - 554 - 8772 + IPR016024
Armadillo-type fold + 381 + 686 13 - IPR002182
NB-ARC - 539 - 579 + IPR009057
Homeobox-like domain superfamily + 373 + 544 14 - IPR002885
  - 509 - 20700 + IPR029058
Alpha/Beta hydrolase fold + 359 + 608 15 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 496 - 704 + IPR036291
NAD(P)-binding domain superfamily + 358 + 620 16 - IPR029058
  - 458 - 1898 + IPR041118
Rx, N-terminal + 342 + 478 17 - IPR001841
  - 440 - 2196 + IPR011990
Tetratricopeptide-like helical domain superfamily + 330 + 637 18 - IPR009057
Homeobox-like domain superfamily - 438 - 471 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 319 + 433 19 - IPR036396
  - 422 - 2637 + IPR036396
Cytochrome P450 superfamily + 310 + 433 20 - IPR001128
Cytochrome P450 - 402 - 1517 + IPR035979
RNA-binding domain superfamily + 302 + 732 21 - IPR016024
Armadillo-type fold - 399 - 875 + IPR001128
Cytochrome P450 + 301 + 1566 22 - IPR003593
AAA+ ATPase domain - 384 - 499 + IPR000504
RNA recognition motif domain + 271 + 1368 23 - IPR036259
MFS transporter superfamily - 365 - 556 + IPR002401
Cytochrome P450, E-class, group I + 261 + 1924 24 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 357 - 365 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 253 + 469 25 - IPR003591
Leucine-rich repeat, typical subtype - 343 - 2331 + IPR036259
MFS transporter superfamily + 252 + 477 26 - IPR012337
Ribonuclease H-like superfamily - 342 - 389 + IPR017853
Glycoside hydrolase superfamily + 248 + 409 27 - IPR017853
Glycoside hydrolase superfamily - 339 - 386 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 240 + 324 28 - IPR035979
RNA-binding domain superfamily - 322 - 452 + IPR017930
Myb domain + 235 + 794 29 - IPR012677
  - 314 - 946 + IPR038765
Papain-like cysteine peptidase superfamily + 234 + 320 30 - IPR002401
Cytochrome P450, E-class, group I - 314 - 1954 + IPR036249
Thioredoxin-like superfamily + 232 + 392 31 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 306 - 391 + IPR001005
SANT/Myb domain + 232 + 782 32 - IPR036249
Thioredoxin-like superfamily - 301 - 342 + IPR036322
WD40-repeat-containing domain superfamily + 231 + 418 33 - IPR001005
SANT/Myb domain - 292 - 1075 + IPR001680
WD40 repeat + 209 + 1987 34 - IPR036388
  - 287 - 602 + IPR011992
EF-hand domain pair + 187 + 274 35 - IPR000504
  - 283 - 3624 + IPR002048
EF-hand domain + 174 + 1045 36 - IPR017972
Cytochrome P450, conserved site - 283 - 283 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 172 + 396 37 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 281 - 283 + IPR036412
HAD-like superfamily + 166 + 309 38 - IPR011989
  - 269 - 756 + IPR036770
Ankyrin repeat-containing domain superfamily + 166 + 270 39 - IPR020846
  - 269 - 894 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 158 + 239 40 - IPR015943
  - 268 - 1218 + IPR016177
DNA-binding domain superfamily + 157 + 244 41 - IPR036397
  - 252 - 825 + IPR002110
Ankyrin repeat + 153 + 745 42 - IPR003439
  - 249 - 1935 + IPR036390
Winged helix DNA-binding domain superfamily + 151 + 226 43 - IPR036322
WD40-repeat-containing domain superfamily - 248 - 391 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 149 + 413 44 - IPR001680
  - 247 - 7545 + IPR011333
SKP1/BTB/POZ domain superfamily + 148 + 242 45 - IPR036390
Winged helix DNA-binding domain superfamily - 235 - 243 + IPR001471
AP2/ERF domain + 144 + 888 46 - IPR011333
SKP1/BTB/POZ domain superfamily - 230 - 252 + IPR036093
NAC domain superfamily + 144 + 191 47 - IPR038765
Papain-like cysteine peptidase superfamily - 229 - 271 + IPR029044
Nucleotide-diphospho-sugar transferases + 142 + 199 48 - IPR017930
  - 227 - 688 + IPR003441
NAC domain + 141 + 359 49 - IPR017986
  - 220 - 750 + IPR001650
Helicase, C-terminal + 140 + 485 50 - IPR020683
  - 208 - 1502 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 139 + 241 51 - IPR036770
  - 208 - 1088 + IPR012340
Nucleic acid-binding, OB-fold + 138 + 318 52 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 200 - 201 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 137 + 192 53 - IPR036188
  - 197 - 1480 + IPR012337
Ribonuclease H-like superfamily + 136 + 213 54 - IPR021109
  - 194 - 1004 + IPR010255
Haem peroxidase superfamily + 135 + 173 55 - IPR011992
EF-hand domain pair - 194 - 215 + IPR036236
Zinc finger C2H2 superfamily + 135 + 222 56 - IPR016177
DNA-binding domain superfamily - 193 - 227 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 130 + 153 57 - IPR036412
HAD-like superfamily - 192 - 264 + IPR013087
Zinc finger C2H2-type + 130 + 278 58 - IPR036638
  - 191 - 1077 + IPR005174
Domain unknown function DUF295 + 130 + 160 59 - IPR002110
  - 190 - 4158 + IPR036188
FAD/NAD(P)-binding domain superfamily + 129 + 250 60 - IPR010255
Haem peroxidase - 189 - 197 + IPR002016
Haem peroxidase + 128 + 605 61 - IPR008974
  - 185 - 1074 + IPR003439
ABC transporter-like, ATP-binding domain + 127 + 626 62 - IPR002016
  - 183 - 3372 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 122 + 204 63 - IPR000210
  - 182 - 1530 + IPR025315
Domain of unknown function DUF4220 + 121 + 132 64 - IPR011598
  - 180 - 1824 + IPR003480
Transferase + 121 + 149 65 - IPR015424
Pyridoxal phosphate-dependent transferase - 180 - 195 + IPR020683
Ankyrin repeat-containing domain + 119 + 300 66 - IPR002048
  - 179 - 3876 + IPR036426
Bulb-type lectin domain superfamily + 119 + 188 67 - IPR017871
ABC transporter, conserved site - 179 - 212 + IPR001480
Bulb-type lectin domain + 116 + 459 68 - IPR036955
  - 178 - 615 + IPR007658
Protein of unknown function DUF594 + 115 + 123 69 - IPR001471
  - 176 - 3174 + IPR003959
ATPase, AAA-type, core + 113 + 207 70 - IPR001878
  - 176 - 1776 + IPR036869
Chaperone J-domain superfamily + 113 + 184 71 - IPR013087
  - 175 - 2244 + IPR020846
Major facilitator superfamily domain + 112 + 181 72 - IPR015421
  - 174 - 546 + IPR021109
Aspartic peptidase domain superfamily + 109 + 145 73 - IPR023214
  - 170 - 544 + IPR000210
BTB/POZ domain + 109 + 377 74 - IPR029044
  - 169 - 764 + IPR008972
Cupredoxin + 106 + 210 75 - IPR036875
Zinc finger, CCHC-type superfamily - 168 - 189 + IPR001623
DnaJ domain + 106 + 874 76 - IPR036236
Zinc finger C2H2 superfamily - 166 - 255 + IPR011011
Zinc finger, FYVE/PHD-type + 105 + 195 77 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 164 - 181 + IPR019734
Tetratricopeptide repeat + 104 + 388 78 - IPR013785
  - 163 - 573 + IPR001087
GDSL lipase/esterase + 103 + 141 79 - IPR000823
Plant peroxidase - 163 - 1257 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 102 + 116 80 - IPR018247
EF-Hand 1, calcium-binding site - 163 - 378 + IPR015424
Pyridoxal phosphate-dependent transferase + 102 + 153 81 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 162 - 189 + IPR029071
Ubiquitin-like domain superfamily + 101 + 165 82 - IPR023213
  - 162 - 568 + IPR011676
Domain of unknown function DUF1618 + 100 + 143 83 - IPR014001
  - 162 - 622 + IPR035892
C2 domain superfamily + 98 + 229 84 - IPR036093
  - 161 - 966 + IPR033121
Peptidase family A1 domain + 98 + 145 85 - IPR003441
  - 159 - 939 + IPR003657
WRKY domain + 98 + 302 86 - IPR035595
UDP-glycosyltransferase family, conserved site - 155 - 155 + IPR036576
WRKY domain superfamily + 97 + 151 87 - IPR001650
  - 154 - 1206 + IPR000858
S-locus glycoprotein domain + 94 + 152 88 - IPR012340
Nucleic acid-binding, OB-fold - 154 - 223 + IPR011050
Pectin lyase fold/virulence factor + 94 + 119 89 - IPR002083
  - 152 - 1209 + IPR011051
RmlC-like cupin domain superfamily + 94 + 139 90 - IPR015422
  - 152 - 684 + IPR003609
PAN/Apple domain + 93 + 274 91 - IPR002347
Short-chain dehydrogenase/reductase SDR - 152 - 1077 + IPR032861
Xylanase inhibitor, N-terminal + 93 + 116 92 - IPR014729
  - 150 - 366 + IPR032799
Xylanase inhibitor, C-terminal + 92 + 115 93 - IPR014710
  - 145 - 376 + IPR044810
WRKY transcription factor, plant + 92 + 132 94 - IPR036514
  - 145 - 298 + IPR036457
PPM-type phosphatase domain superfamily + 90 + 188 95 - IPR036426
  - 144 - 740 + IPR011545
DEAD/DEAH box helicase domain + 89 + 159 96 - IPR019793
Peroxidases heam-ligand binding site - 144 - 144 + IPR001356
Homeobox domain + 89 + 346 97 - IPR019775
WD40 repeat, conserved site - 143 - 231 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 88 + 129 98 - IPR001480
  - 143 - 848 + IPR001932
PPM-type phosphatase domain + 88 + 508 99 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 141 - 144 + IPR009072
Histone-fold + 87 + 103 100 - IPR033905
Secretory peroxidase - 140 - 140 + IPR015300
DNA-binding pseudobarrel domain superfamily + 87 + 169 101 - IPR003480
Transferase - 139 - 150 + IPR000008
C2 domain + 85 + 475 102 - IPR013026
  - 138 - 528 + IPR000109
Proton-dependent oligopeptide transporter family + 85 + 357 103 - IPR001461
Aspartic peptidase A1 family - 137 - 312 + IPR005828
Major facilitator, sugar transporter-like + 85 + 144 104 - IPR029071
Ubiquitin-like domain superfamily - 135 - 179 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 84 + 121 105 - IPR005162
Retrotransposon gag domain - 133 - 133 + IPR020472
G-protein beta WD-40 repeat + 84 + 447 106 - IPR019734
  - 132 - 2871 + IPR036875
Zinc finger, CCHC-type superfamily + 84 + 131 107 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 130 - 204 + IPR000823
Plant peroxidase + 84 + 378 108 - IPR005123
  - 128 - 732 + IPR002347
Short-chain dehydrogenase/reductase SDR + 83 + 801 109 - IPR033121
  - 128 - 274 + IPR035669
GDSL lipase/esterase-like, plant + 81 + 102 110 - IPR025315
Domain of unknown function DUF4220 - 128 - 139 + IPR000073
Alpha/beta hydrolase fold-1 + 80 + 254 111 - IPR019794
Peroxidase, active site - 127 - 127 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 80 + 158 112 - IPR005174
Domain unknown function DUF295 - 126 - 129 + IPR004158
Protein of unknown function DUF247, plant + 80 + 195 113 - IPR036869
  - 126 - 500 + IPR031052
FHY3/FAR1 family + 79 + 160 114 - IPR003959
ATPase, AAA-type, core - 122 - 149 + IPR003340
B3 DNA binding domain + 78 + 451 115 - IPR027443
  - 121 - 260 + IPR013766
Thioredoxin domain + 78 + 205 116 - IPR007658
Protein of unknown function DUF594 - 121 - 121 + IPR043129
ATPase, nucleotide binding domain + 78 + 221 117 - IPR011051
RmlC-like cupin domain superfamily - 119 - 152 + IPR001878
Zinc finger, CCHC-type + 78 + 236 118 - IPR034090
BPM, C-terminal - 118 - 121 + IPR002083
MATH/TRAF domain + 77 + 289 119 - IPR003609
  - 117 - 606 + IPR001461
Aspartic peptidase A1 family + 77 + 267 120 - IPR011676
Domain of unknown function DUF1618 - 117 - 119 + IPR026992
Non-haem dioxygenase N-terminal domain + 76 + 108 121 - IPR032861
Xylanase inhibitor, N-terminal - 117 - 117 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 75 + 111 122 - IPR032799
Xylanase inhibitor, C-terminal - 116 - 120 + IPR004827
Basic-leucine zipper domain + 75 + 232 123 - IPR008972
  - 115 - 762 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 74 + 97 124 - IPR011050
Pectin lyase fold/virulence factor - 115 - 118 + IPR003613
U box domain + 74 + 212 125 - IPR001623
  - 114 - 1434 + IPR004330
FAR1 DNA binding domain + 74 + 92 126 - IPR000477
  - 113 - 384 + IPR026961
PGG domain + 73 + 182 127 - IPR005225
Small GTP-binding protein domain - 112 - 113 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 71 + 150 128 - IPR012334
  - 112 - 234 + IPR000270
PB1 domain + 71 + 162 129 - IPR001087
GDSL lipase/esterase - 111 - 111 + IPR036879
Transcription factor, MADS-box superfamily + 71 + 109 130 - IPR003657
  - 111 - 1110 + IPR016039
Thiolase-like + 70 + 161 131 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 111 - 115 + IPR002902
Gnk2-homologous domain + 70 + 386 132 - IPR000109
Proton-dependent oligopeptide transporter family - 111 - 239 + IPR002100
Transcription factor, MADS-box + 70 + 494 133 - IPR036576
  - 109 - 738 + IPR004045
Glutathione S-transferase, N-terminal + 70 + 219 134 - IPR000858
S-locus glycoprotein domain - 108 - 112 + IPR001220
Legume lectin domain + 70 + 171 135 - IPR004045
  - 108 - 645 + IPR007527
Zinc finger, SWIM-type + 70 + 127 136 - IPR005828
Major facilitator, sugar transporter-like - 106 - 122 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 67 + 73 137 - IPR035669
GDSL lipase/esterase-like, plant - 104 - 104 + IPR008949
Isoprenoid synthase domain superfamily + 66 + 94 138 - IPR031052
FHY3/FAR1 family - 104 - 178 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 65 + 81 139 - IPR010987
  - 103 - 206 + IPR016159
Cullin repeat-like-containing domain superfamily + 65 + 101 140 - IPR036457
  - 102 - 482 + IPR036908
RlpA-like domain superfamily + 64 + 85 141 - IPR011011
Zinc finger, FYVE/PHD-type - 102 - 118 + IPR007117
Expansin, cellulose-binding-like domain + 64 + 159 142 - IPR011545
DEAD/DEAH box helicase domain - 100 - 103 + IPR013057
Amino acid transporter, transmembrane domain + 63 + 94 143 - IPR000073
Alpha/beta hydrolase fold-1 - 100 - 213 + IPR020568
Ribosomal protein S5 domain 2-type fold + 63 + 125 144 - IPR004158
Protein of unknown function DUF247, plant - 100 - 111 + IPR036163
Heavy metal-associated domain superfamily + 63 + 96 145 - IPR007527
  - 100 - 534 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 63 + 140 146 - IPR016039
  - 99 - 1053 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 62 + 67 147 - IPR001356
  - 98 - 1035 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 610 148 - IPR009072
  - 98 - 573 + IPR023395
Mitochondrial carrier domain superfamily + 62 + 111 149 - IPR011701
Major facilitator superfamily - 96 - 97 + IPR029052
Metallo-dependent phosphatase-like + 62 + 111 150 - IPR018289
MULE transposase domain - 96 - 98 + IPR001806
Small GTPase + 62 + 155 151 - IPR001932
  - 96 - 1209 + IPR006121
Heavy metal-associated domain, HMA + 61 + 231 152 - IPR032867
DYW domain - 95 - 96 + IPR019787
Zinc finger, PHD-finger + 61 + 173 153 - IPR015300
  - 95 - 532 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 61 + 93 154 - IPR015655
Protein phosphatase 2C family - 94 - 114 + IPR036852
Peptidase S8/S53 domain superfamily + 61 + 80 155 - IPR006447
Myb domain, plants - 94 - 95 + IPR044965
Glycoside hydrolase family 17, plant + 61 + 106 156 - IPR035892
  - 93 - 280 + IPR000048
IQ motif, EF-hand binding site + 61 + 457 157 - IPR038408
  - 93 - 350 + IPR000209
Peptidase S8/S53 domain + 61 + 78 158 - IPR000626
  - 92 - 984 + IPR000626
Ubiquitin-like domain + 60 + 168 159 - IPR002902
  - 92 - 682 + IPR005202
Transcription factor GRAS + 60 + 250 160 - IPR004827
  - 92 - 1005 + IPR010987
Glutathione S-transferase, C-terminal-like + 60 + 94 161 - IPR020472
G-protein beta WD-40 repeat - 90 - 270 + IPR036915
Cyclin-like superfamily + 60 + 171 162 - IPR026992
Non-haem dioxygenase N-terminal domain - 90 - 92 + IPR000571
Zinc finger, CCCH-type + 60 + 387 163 - IPR024171
S-receptor-like serine/threonine-protein kinase - 89 - 126 - + IPR006501
Pectinesterase inhibitor domain + 59 + 64 + 164 - IPR013766
  - 87 - 492 + IPR009003
Peptidase S1, PA clan + 59 + 111 165 - IPR000270
  - 87 - 414 + IPR003663
Sugar/inositol transporter + 59 + 346 166 - IPR036890
  - 86 - 354 + IPR024788
Malectin-like domain + 58 + 85 167 - IPR026961
PGG domain - 86 - 154 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 57 + 103 168 - IPR017907
Zinc finger, RING-type, conserved site - 86 - 86 + IPR039391
Phytocyanin + 57 + 71 169 - IPR000008
  - 86 - 756 + IPR003245
Phytocyanin domain + 57 + 123 170 - IPR003340
  - 85 - 1449 + IPR006045
Cupin 1 + 57 + 100 171 - IPR005829
Sugar transporter, conserved site - 85 - 140 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 56 + 68 172 - IPR036163
Heavy metal-associated domain superfamily - 85 - 101 + IPR045051
Subtilisin-like protease + 56 + 83 173 - IPR006121
  - 84 - 735 + IPR000490
Glycoside hydrolase family 17 + 56 + 86 174 - IPR036908
  - 83 - 334 + IPR015915
Kelch-type beta propeller + 56 + 108 175 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 82 - 90 + IPR011032
GroES-like superfamily + 54 + 92 176 - IPR006564
Zinc finger, PMZ-type - 82 - 82 + IPR007112
Expansin/pollen allergen, DPBB domain + 54 + 69 177 - IPR011006
CheY-like superfamily - 82 - 90 + IPR022059
Protein of unknown function DUF3615 + 54 + 84 178 - IPR001220
Legume lectin domain - 82 - 151 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 53 + 62 179 - IPR001789
  - 81 - 963 + IPR000225
Armadillo + 53 + 272 180 - IPR013783
  - 80 - 176 + IPR002921
Fungal lipase-like domain + 52 + 79 181 - IPR000742
  - 80 - 310 + IPR013525
ABC-2 type transporter + 52 + 137 182 - IPR003594
Histidine kinase/HSP90-like ATPase - 79 - 203 + IPR001563
Peptidase S10, serine carboxypeptidase + 51 + 428 183 - IPR020568
Ribosomal protein S5 domain 2-type fold - 79 - 97 + IPR016181
Acyl-CoA N-acyltransferase + 51 + 78 184 - IPR001965
Zinc finger, PHD-type - 78 - 116 + IPR000608
Ubiquitin-conjugating enzyme E2 + 51 + 199 185 - IPR008949
  - 77 - 354 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 51 + 65 186 - IPR036691
  - 77 - 380 + IPR036465
von Willebrand factor A-like domain superfamily + 51 + 77 187 - IPR000490
Glycoside hydrolase family 17 - 77 - 119 + IPR001752
Kinesin motor domain + 51 + 514 188 - IPR017451
F-box associated interaction domain - 75 - 76 + IPR015500
Peptidase S8, subtilisin-related + 51 + 174 189 - IPR016159
Cullin repeat-like-containing domain superfamily - 75 - 100 + IPR013763
Cyclin-like + 50 + 130 190 - IPR013094
Alpha/beta hydrolase fold-3 - 74 - 81 + IPR026057
PC-Esterase + 49 + 77 191 - IPR001584
  - 73 - 396 + IPR002528
Multi antimicrobial extrusion protein + 49 + 171 192 - IPR001509
NAD-dependent epimerase/dehydratase - 73 - 74 + IPR023298
P-type ATPase, transmembrane domain superfamily + 49 + 91 193 - IPR013057
Amino acid transporter, transmembrane domain - 73 - 77 + IPR017884
SANT domain + 48 + 66 194 - IPR000571
  - 73 - 1128 + IPR011701
Major facilitator superfamily + 48 + 111 195 - IPR011032
GroES-like superfamily - 72 - 91 + IPR004140
Exocyst complex component Exo70 + 48 + 167 196 - IPR016181
Acyl-CoA N-acyltransferase - 72 - 76 + IPR003676
Small auxin-up RNA + 48 + 62 197 - IPR036852
  - 72 - 786 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 47 + 138 198 - IPR003613
  - 72 - 648 + IPR007118
Expansin/Lol pI + 47 + 317 199 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 72 - 110 + IPR029962
Trichome birefringence-like family + 47 + 75 200 - IPR000225
  - 72 - 1530 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 47 + 54 201 - IPR026960
Reverse transcriptase zinc-binding domain - 72 - 72 + IPR005630
Terpene synthase, metal-binding domain + 47 + 62 202 - IPR001806
Small GTPase superfamily - 71 - 73 + IPR008979
Galactose-binding-like domain superfamily + 47 + 89 203 - IPR036961
  - 71 - 312 + IPR011527
ABC transporter type 1, transmembrane domain + 47 + 277 204 - IPR006045
Cupin 1 - 70 - 183 + IPR008978
HSP20-like chaperone + 46 + 67 205 - IPR024788
Malectin-like carbohydrate-binding domain - 70 - 74 + IPR004853
Sugar phosphate transporter domain + 46 + 110 206 - IPR001881
EGF-like calcium-binding domain - 70 - 96 + IPR008250
P-type ATPase, A domain superfamily + 46 + 86 207 - IPR000873
AMP-dependent synthetase/ligase - 69 - 81 + IPR009000
Translation protein, beta-barrel domain superfamily + 46 + 70 208 - IPR035513
  - 69 - 258 + IPR034197
Cucumisin-like catalytic domain + 46 + 57 209 - IPR002100
  - 69 - 1233 + IPR045087
Multicopper oxidase + 46 + 67 210 - IPR036879
  - 69 - 405 + IPR014756
Immunoglobulin E-set + 46 + 75 211 - IPR003663
Sugar/inositol transporter - 69 - 357 + IPR001214
SET domain + 46 + 128 212 - IPR036640
  - 68 - 627 + IPR009060
UBA-like superfamily + 45 + 73 213 - IPR026057
PC-Esterase - 68 - 70 + IPR001509
NAD-dependent epimerase/dehydratase + 45 + 80 214 - IPR008979
  - 68 - 302 + IPR029055
Nucleophile aminohydrolases, N-terminal + 45 + 66 215 - IPR000620
EamA domain - 68 - 118 + IPR008928
Six-hairpin glycosidase superfamily + 45 + 60 216 - IPR001969
Aspartic peptidase, active site - 67 - 78 + IPR007125
Histone H2A/H2B/H3 + 45 + 48 217 - IPR006566
FBD domain - 67 - 72 + IPR000742
EGF-like domain + 45 + 55 218 - IPR004330
FAR1 DNA binding domain - 67 - 73 + IPR025846
PMR5 N-terminal domain + 45 + 64 219 - IPR023395
  - 67 - 320 + IPR006566
FBD domain + 45 + 64 220 - IPR030184
WAT1-related protein - 67 - 82 + IPR013094
Alpha/beta hydrolase fold-3 + 45 + 70 221 - IPR018108
  - 66 - 720 + IPR000873
AMP-dependent synthetase/ligase + 44 + 69 222 - IPR036465
  - 66 - 246 + IPR034161
Pepsin-like domain, plant + 44 + 55 223 - IPR029962
Trichome birefringence-like family - 66 - 75 + IPR032867
DYW domain + 44 + 56 224 - IPR011527
  - 66 - 657 + IPR030184
WAT1-related protein + 44 + 94 225 - IPR000048
  - 66 - 975 + IPR041569
AAA ATPase, AAA+ lid domain + 44 + 68 226 - IPR000209
Peptidase S8/S53 domain - 66 - 69 + IPR007811
DNA-directed RNA polymerase III subunit RPC4 + 44 + 95 227 - IPR013128
Peptidase C1A - 65 - 72 + IPR033389
AUX/IAA domain + 43 + 68 228 - IPR003960
ATPase, AAA-type, conserved site - 65 - 68 + IPR000182
GNAT domain + 43 + 114 229 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 65 - 65 + IPR014014
RNA helicase, DEAD-box type, Q motif + 43 + 72 230 - IPR029055
  - 65 - 238 + IPR012946
X8 domain + 43 + 69 231 - IPR002528
Multi antimicrobial extrusion protein - 65 - 165 + IPR011706
Multicopper oxidase, C-terminal + 43 + 48 232 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 64 - 64 + IPR001906
Terpene synthase, N-terminal domain + 43 + 58 233 - IPR022059
Protein of unknown function DUF3615 - 64 - 66 + IPR000620
EamA domain + 43 + 105 234 - IPR029045
ClpP/crotonase-like domain superfamily - 64 - 83 + IPR015947
PUA-like superfamily + 43 + 63 235 - IPR004332
Transposase, MuDR, plant - 63 - 65 + IPR001117
Multicopper oxidase, type 1 + 42 + 47 236 - IPR025846
PMR5 N-terminal domain - 63 - 63 + IPR002156
Ribonuclease H domain + 42 + 66 237 - IPR001563
Peptidase S10, serine carboxypeptidase - 63 - 332 + IPR000330
SNF2, N-terminal + 42 + 77 238 - IPR005202
  - 63 - 254 + IPR004265
Dirigent protein + 42 + 49 239 - IPR006501
Pectinesterase inhibitor domain - 63 - 154 + IPR033905
Secretory peroxidase + 42 + 50 240 - IPR018097
EGF-like calcium-binding, conserved site - 63 - 63 + IPR011006
CheY-like superfamily + 42 + 57 241 - IPR000182
  - 62 - 218 + IPR006671
Cyclin, N-terminal + 42 + 82 242 - IPR036749
  - 62 - 250 + IPR036855
Zinc finger, CCCH-type superfamily + 42 + 144 243 - IPR023298
P-type ATPase, transmembrane domain superfamily - 62 - 168 + IPR044808
Ethylene-responsive transcription factor + 42 + 50 244 - IPR011993
  - 62 - 130 + IPR043926
ABC transporter family G domain + 41 + 92 245 - IPR027640
Kinesin-like protein - 62 - 93 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 41 + 70 246 - IPR007112
  - 62 - 236 + IPR011012
Longin-like domain superfamily + 41 + 73 247 - IPR036318
FAD-binding, type 2-like superfamily - 61 - 61 + IPR011043
Galactose oxidase/kelch, beta-propeller + 41 + 51 248 - IPR004265
Dirigent protein - 61 - 61 + IPR000070
Pectinesterase, catalytic + 41 + 53 249 - IPR008928
Six-hairpin glycosidase superfamily - 61 - 76 + IPR011707
Multicopper oxidase, N-termianl + 41 + 46 250 - IPR036915
Cyclin-like superfamily - 61 - 102 + IPR000743
Glycoside hydrolase, family 28 + 41 + 57 251 - IPR007117
  - 61 - 248 + IPR037176
Osmotin/thaumatin-like superfamily + 41 + 45 252 - IPR003676
Small auxin-up RNA - 61 - 61 + IPR010402
CCT domain + 40 + 123 253 - IPR004140
Exocyst complex component Exo70 - 60 - 136 + IPR033896
MADS MEF2-like + 40 + 76 254 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 60 - 62 + IPR004263
Exostosin-like + 40 + 54 255 - IPR016135
  - 60 - 244 + IPR000668
Peptidase C1A, papain C-terminal + 40 + 165 256 - IPR004839
Aminotransferase, class I/classII - 60 - 61 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 40 + 69 257 - IPR003245
  - 60 - 528 + IPR006702
Casparian strip membrane protein domain + 40 + 44 258 - IPR009003
Peptidase S1, PA clan - 60 - 74 + IPR001789
Signal transduction response regulator, receiver domain + 40 + 95 259 - IPR019787
  - 59 - 214 + IPR006016
UspA + 39 + 64 260 - IPR015915
  - 59 - 402 + IPR029021
Protein-tyrosine phosphatase-like + 39 + 74 261 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 59 - 59 + IPR029045
ClpP/crotonase-like domain superfamily + 39 + 64 262 - IPR023299
  - 59 - 294 + IPR000644
CBS domain + 39 + 201 263 - IPR013525
ABC-2 type transporter - 58 - 78 + IPR013126
Heat shock protein 70 family + 39 + 109 264 - IPR007118
Expansin/Lol pI - 58 - 318 + IPR025322
Protein of unknown function DUF4228, plant + 38 + 40 265 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 58 - 111 + IPR025659
Tubby-like, C-terminal + 38 + 61 266 - IPR025312
Domain of unknown function DUF4216 - 57 - 57 + IPR036318
FAD-binding, type PCMH-like superfamily + 38 + 54 267 - IPR005119
LysR, substrate-binding - 57 - 57 + IPR016461
O-methyltransferase COMT-type + 38 + 83 268 - IPR029052
  - 57 - 122 + IPR036612
K Homology domain, type 1 superfamily + 38 + 137 269 - IPR008978
  - 57 - 226 + IPR015655
Protein phosphatase 2C family + 38 + 99 270 - IPR001752
  - 57 - 1125 + IPR002495
Glycosyl transferase, family 8 + 38 + 53 271 - IPR017877
  - 57 - 126 + IPR008889
VQ + 38 + 38 272 - IPR034161
Pepsin-like domain, plant - 56 + IPR008942
ENTH/VHS + 37 56 273 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 56 - 365 + IPR016040
NAD(P)-binding domain + 37 + 67 274 - IPR018253
DnaJ domain, conserved site - 56 + IPR003137
PA domain + 37 56 275 - IPR001757
P-type ATPase - 55 - 197 + IPR001938
Thaumatin family + 37 + 256 276 - IPR002921
Fungal lipase-like domain - 55 - 55 + IPR002109
Glutaredoxin + 37 + 45 277 - IPR023393
  - 55 - 116 + IPR002912
ACT domain + 37 + 168 278 - IPR014014
  - 55 - 110 + IPR024752
Myb/SANT-like domain + 37 + 38 279 - IPR019786
Zinc finger, PHD-type, conserved site - 55 - 57 + IPR004041
NAF domain + 36 + 53 280 - IPR020845
AMP-binding, conserved site - 55 - 57 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 36 + 55 281 - IPR012341
  - 55 - 183 + IPR018451
NAF/FISL domain + 36 + 52 282 - IPR001938
  - 54 - 788 + IPR002068
Alpha crystallin/Hsp20 domain + 36 + 91 283 - IPR013149
Alcohol dehydrogenase, C-terminal - 54 - 54 + IPR008991
Translation protein SH3-like domain superfamily + 36 + 49 284 - IPR008250
P-type ATPase, A domain superfamily - 54 - 63 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 36 + 72 285 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 54 - 56 + IPR004839
Aminotransferase, class I/classII + 36 + 54 286 - IPR029061
Thiamin diphosphate-binding fold - 53 - 86 + IPR001077
O-methyltransferase domain + 36 + 47 287 - IPR005467
  - 53 - 106 + IPR039417
Papain-like cysteine endopeptidase + 36 + 43 288 - IPR008906
HAT, C-terminal dimerisation domain - 53 - 54 + IPR002067
Mitochondrial carrier protein + 36 + 286 289 - IPR013763
Cyclin-like - 53 - 156 + IPR002487
Transcription factor, K-box + 36 + 140 290 - IPR013154
Alcohol dehydrogenase, N-terminal - 53 - 54 + IPR013149
Alcohol dehydrogenase, C-terminal + 35 + 49 291 - IPR005630
Terpene synthase, metal-binding domain - 52 - 54 + IPR007493
Protein of unknown function DUF538 + 35 + 84 292 - IPR000222
PPM-type phosphatase, divalent cation binding - 52 - 53 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 35 + 39 293 - IPR000668
Peptidase C1A, papain C-terminal - 52 - 218 + IPR023271
Aquaporin-like + 35 + 46 294 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 51 - 52 + IPR004883
Lateral organ boundaries, LOB + 35 + 82 295 - IPR001906
Terpene synthase, N-terminal domain - 51 - 52 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 35 + 57 296 - IPR001360
Glycoside hydrolase family 1 - 51 - 327 + IPR036758
At5g01610-like superfamily + 35 + 42 297 - IPR012946
X8 domain - 51 - 110 + IPR019378
GDP-fucose protein O-fucosyltransferase + 35 + 78 298 - IPR013780
  - 51 - 116 + IPR000425
Major intrinsic protein + 35 + 281 299 - IPR033389
AUX/IAA domain - 50 - 54 + IPR004046
Glutathione S-transferase, C-terminal + 35 + 48 300 - IPR000847
  - 50 - 326 + IPR028889
Ubiquitin specific protease domain + 35 + 51 301 - IPR002109
  - 50 - 285 + IPR001929
Germin + 34 + 119 302 - IPR036855
Zinc finger, CCCH-type superfamily - 50 - 92 + IPR001360
Glycoside hydrolase family 1 + 34 + 438 303 - IPR018303
P-type ATPase, phosphorylation site - 50 - 50 + IPR013154
Alcohol dehydrogenase, N-terminal + 34 + 46 304 - IPR004046
Glutathione S-transferase, C-terminal - 50 - 50 + IPR016166
FAD-binding domain, PCMH-type + 34 + 49 305 - IPR011042
  - 50 - 130 + IPR040911
Exostosin, GT47 domain + 34 + 43 306 - IPR036965
  - 49 - 174 + IPR043519
Nucleotidyltransferase superfamily + 34 + 63 307 - IPR029062
  - 49 - 222 + IPR039361
Cyclin + 34 + 58 308 - IPR000644
  - 49 - 562 + IPR044730
Ribonuclease H-like domain, plant type + 34 + 37 309 - IPR009000
Translation protein, beta-barrel domain superfamily - 48 - 51 + IPR038933
Ovate protein family + 33 + 34 310 - IPR006702
Casparian strip membrane protein domain - 48 - 49 + IPR000795
Translational (tr)-type GTP-binding domain + 33 + 314 311 - IPR014721
  - 47 - 114 + IPR006652
Kelch repeat type 1 + 33 + 122 312 - IPR015947
PUA-like superfamily - 47 - 53 + IPR043454
NPH3/RPT2-like family + 33 + 61 313 - IPR016166
  - 47 - 141 + IPR006458
Ovate protein family, C-terminal + 33 + 64 314 - IPR016161
Aldehyde/histidinol dehydrogenase - 47 - 49 + IPR001296
Glycosyl transferase, family 1 + 32 + 64 315 - IPR023210
NADP-dependent oxidoreductase domain - 47 - 95 + IPR034294
Aquaporin transporter + 32 + 48 316 - IPR036812
  - 47 - 202 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 31 + 152 317 - IPR016461
  - 46 - 228 + IPR018490
Cyclic nucleotide-binding-like + 31 + 51 318 - IPR000608
  - 46 - 260 + IPR027356
NPH3 domain + 31 + 87 319 - IPR037176
  - 46 - 194 + IPR022742
Serine aminopeptidase, S33 + 31 + 55 320 - IPR006016
UspA - 46 - 47 + IPR004088
K Homology domain, type 1 + 31 + 120 321 - IPR029466
No apical meristem-associated, C-terminal domain - 46 - 47 + IPR033443
Pentacotripeptide-repeat region of PRORP + 31 + 49 322 - IPR014756
Immunoglobulin E-set - 46 - 51 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 31 + 83 323 - IPR013126
Heat shock protein 70 family - 46 - 309 + IPR011141
Polyketide synthase, type III + 31 + 38 324 - IPR015500
Peptidase S8, subtilisin-related - 46 - 132 + IPR012967
Plant methyltransferase dimerisation + 31 + 32 325 - IPR000070
Pectinesterase, catalytic - 46 - 49 + IPR006311
Twin-arginine translocation pathway, signal sequence + 31 + 40 326 - IPR024752
Myb/SANT-like domain - 46 - 46 + IPR006073
GTP binding domain + 31 + 112 327 - IPR001214
  - 46 - 375 + IPR032710
NTF2-like domain superfamily + 30 + 42 328 - IPR011043
Galactose oxidase/kelch, beta-propeller - 45 + IPR029000
Cyclophilin-like domain superfamily + 30 54 329 - IPR002068
  - 45 - 176 + IPR001251
CRAL-TRIO lipid binding domain + 30 + 160 330 - IPR000743
Glycoside hydrolase, family 28 - 45 - 65 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 30 + 43 331 - IPR004853
Sugar phosphate transporter domain - 44 - 44 + IPR000315
B-box-type zinc finger + 30 + 91 332 - IPR036612
  - 44 - 408 + IPR000717
Proteasome component (PCI) domain + 30 + 73 333 - IPR012675
  - 44 - 92 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 30 + 56 334 - IPR001077
O-methyltransferase, family 2 - 44 - 46 + IPR004367
Cyclin, C-terminal domain + 30 + 42 335 - IPR006671
Cyclin, N-terminal - 44 - 66 + IPR005150
Cellulose synthase + 30 + 56 336 - IPR016162
  - 44 - 246 + IPR023299
P-type ATPase, cytoplasmic domain N + 30 + 61 337 - IPR025110
AMP-binding enzyme, C-terminal domain - 44 - 47 + IPR004314
Neprosin + 30 + 46 338 - IPR023271
  - 44 - 184 + IPR000595
Cyclic nucleotide-binding domain + 30 + 117 339 - IPR007125
Histone H2A/H2B/H3 - 44 - 44 + IPR001099
Chalcone/stilbene synthase, N-terminal + 30 + 35 340 - IPR017970
Homeobox, conserved site - 44 - 44 + IPR025110
AMP-binding enzyme, C-terminal domain + 29 + 38 341 - IPR000425
Major intrinsic protein - 44 - 330 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 29 + 284 342 - IPR020843
Polyketide synthase, enoylreductase domain - 44 - 44 + IPR029061
Thiamin diphosphate-binding fold + 29 + 79 343 - IPR002912
  - 44 - 194 + IPR001594
Palmitoyltransferase, DHHC domain + 29 + 65 344 - IPR011707
Multicopper oxidase, type 3 - 44 - 45 + IPR003406
Glycosyl transferase, family 14 + 29 + 47 345 - IPR037045
  - 44 - 90 + IPR002963
Expansin + 29 + 276 346 - IPR033896
MADS MEF2-like - 43 - 43 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 29 + 54 347 - IPR034294
Aquaporin transporter - 43 - 48 + IPR006094
FAD linked oxidase, N-terminal + 29 + 42 348 - IPR004883
  - 43 - 172 + IPR003311
AUX/IAA protein + 29 + 54 349 - IPR008889
VQ - 43 - 43 + IPR003855
Potassium transporter + 29 + 120 350 - IPR025322
Protein of unknown function DUF4228, plant - 43 - 43 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 29 + 38 351 - IPR009060
UBA-like superfamily - 43 - 50 + IPR015940
Ubiquitin-associated domain + 28 + 87 352 - IPR036758
  - 43 - 170 + IPR013601
FAE1/Type III polyketide synthase-like protein + 28 + 36 353 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 43 - 52 + IPR010920
LSM domain superfamily + 28 + 37 354 - IPR015590
Aldehyde dehydrogenase domain - 43 - 45 + IPR002659
Glycosyl transferase, family 31 + 28 + 99 355 - IPR007493
Protein of unknown function DUF538 - 42 - 84 + IPR005333
Transcription factor, TCP + 28 + 31 356 - IPR000330
SNF2-related, N-terminal domain - 42 - 45 + IPR005135
Endonuclease/exonuclease/phosphatase + 28 + 55 357 - IPR038718
  - 42 - 108 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 28 + 37 358 - IPR008942
  - 42 - 156 + IPR002423
Chaperonin Cpn60/TCP-1 family + 28 + 49 359 - IPR003653
  - 42 - 225 + IPR011013
Galactose mutarotase-like domain superfamily + 28 + 44 360 - IPR028889
  - 42 - 84 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 28 + 110 361 - IPR010402
  - 41 - 243 + IPR000863
Sulfotransferase domain + 28 + 38 362 - IPR004041
NAF domain - 41 - 41 + IPR027409
GroEL-like apical domain superfamily + 28 + 43 363 - IPR018451
  - 41 - 123 + IPR012328
Chalcone/stilbene synthase, C-terminal + 28 + 29 364 - IPR004263
Exostosin-like - 41 - 42 + IPR003851
Zinc finger, Dof-type + 28 + 62 365 - IPR004252
Probable transposase, Ptta/En/Spm, plant - 41 - 42 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 28 + 71 366 - IPR034197
Cucumisin-like catalytic domain - 41 - 42 + IPR002913
START domain + 28 + 136 367 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 41 - 43 + IPR036378
FAS1 domain superfamily + 27 + 46 368 - IPR036537
  - 41 - 123 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 27 + 36 369 - IPR025659
  - 41 - 132 + IPR006153
Cation/H+ exchanger + 27 + 46 370 - IPR003661
Signal transduction histidine kinase, dimerisation/phosphoacceptor domain - 41 - 117 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 27 + 126 371 - IPR036097
Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily - 41 - 41 + IPR025753
AAA-type ATPase, N-terminal domain + 27 + 32 372 - IPR002035
  - 41 - 208 + IPR024709
Putative O-fucosyltransferase, plant + 27 + 60 373 - IPR016163
  - 41 - 132 + IPR029466
No apical meristem-associated, C-terminal domain + 27 + 27 374 - IPR006626
Parallel beta-helix repeat - 40 - 203 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 27 + 37 375 - IPR011012
Longin-like domain superfamily - 40 - 40 + IPR044848
PHR1-like + 27 + 52 376 - IPR004358
Signal transduction histidine kinase-related protein, C-terminal - 40 - 130 + IPR007650
Zf-FLZ domain + 27 + 65 377 - IPR006094
FAD linked oxidase, N-terminal - 40 - 40 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 27 + 42 378 - IPR006311
  - 40 - 80 + IPR008480
Protein of unknown function DUF761, plant + 27 + 27 379 - IPR001117
Multicopper oxidase, type 1 - 40 - 40 + IPR001849
Pleckstrin homology domain + 27 + 65 380 - IPR001929
Germin - 40 - 120 + IPR044791
Beta-glucanase/XTH + 27 + 42 381 - IPR023753
FAD/NAD(P)-binding domain - 40 - 44 + IPR000757
Glycoside hydrolase family 16 + 27 + 73 382 - IPR002495
Glycosyl transferase, family 8 - 39 - 39 + IPR005175
PPC domain + 27 + 103 383 - IPR036041
Ribosome-inactivating protein superfamily - 39 - 41 + IPR000727
Target SNARE coiled-coil homology domain + 26 + 51 384 - IPR002487
  - 39 - 234 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 26 + 105 385 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 39 - 51 + IPR044835
Auxin response factor + 26 + 62 386 - IPR011706
Multicopper oxidase, type 2 - 39 - 39 + IPR036420
BRCT domain superfamily + 26 + 71 387 - IPR025661
Cysteine peptidase, asparagine active site - 39 - 40 + IPR035940
CAP superfamily + 26 + 32 388 - IPR003137
PA domain - 38 - 38 + IPR004320
Protein of unknown function DUF241, plant + 26 + 40 389 - IPR035940
  - 38 - 156 + IPR003337
Trehalose-phosphatase + 26 + 47 390 - IPR036010
2Fe-2S ferredoxin-like superfamily - 38 - 38 + IPR002123
Phospholipid/glycerol acyltransferase + 26 + 33 391 - IPR003656
  - 38 - 306 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 26 + 41 392 - IPR038770
  - 38 - 80 + IPR005821
Ion transport domain + 26 + 42 393 - IPR019378
GDP-fucose protein O-fucosyltransferase - 38 - 39 + IPR004813
Oligopeptide transporter, OPT superfamily + 26 + 66 394 - IPR022357
Major intrinsic protein, conserved site - 38 - 38 + IPR001701
Glycoside hydrolase family 9 + 26 + 29 395 - IPR000169
Cysteine peptidase, cysteine active site - 38 - 38 + IPR036041
Ribosome-inactivating protein superfamily + 26 + 33 396 - IPR028082
Periplasmic binding protein-like I - 38 - 51 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 26 + 49 397 - IPR029021
  - 38 - 160 + IPR015797
NUDIX hydrolase-like domain superfamily + 26 + 38 398 - IPR008991
Translation protein SH3-like domain superfamily - 38 - 39 + IPR001574
Ribosome-inactivating protein + 26 + 58 399 - IPR004320
Protein of unknown function DUF241, plant - 38 - 39 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 25 + 31 400 - IPR004088
K Homology domain, type 1 - 38 - 70 + IPR001357
BRCT domain + 25 + 119 401 - IPR025558
Domain of unknown function DUF4283 - 38 - 38 + IPR005299
SAM dependent carboxyl methyltransferase + 25 + 77 402 - IPR002659
Glycosyl transferase, family 31 - 37 - 76 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 28 403 - IPR036865
  - 37 - 152 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 25 + 36 404 - IPR016138
  - 37 - 76 + IPR000408
Regulator of chromosome condensation, RCC1 + 25 + 967 405 - IPR001574
Ribosome-inactivating protein - 37 - 39 + IPR045048
F-box only protein 31/39 + 25 + 69 406 - IPR014044
CAP domain - 37 - 74 + IPR016072
SKP1 component, dimerisation + 25 + 26 407 - IPR036404
  - 37 - 192 + IPR016897
S-phase kinase-associated protein 1 + 25 + 27 408 - IPR003855
Potassium transporter - 37 - 108 + IPR027923
Hydrophobic seed protein domain + 25 + 65 409 - IPR011141
Polyketide synthase, type III - 37 - 68 + IPR029062
Class I glutamine amidotransferase-like + 25 + 48 410 - IPR012967
Plant methyltransferase dimerisation - 37 - 37 + IPR036296
SKP1-like, dimerisation domain superfamily + 25 + 26 411 - IPR013601
FAE1/Type III polyketide synthase-like protein - 36 - 37 + IPR000679
Zinc finger, GATA-type + 25 + 119 412 - IPR018200
Ubiquitin specific protease, conserved site - 36 - 58 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 24 + 40 413 - IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme - 36 - 39 + IPR017938
Riboflavin synthase-like beta-barrel + 24 + 42 414 - IPR038538
  - 36 - 82 + IPR000782
FAS1 domain + 24 + 73 415 - IPR036866
  - 36 - 178 + IPR002867
IBR domain + 24 + 50 416 - IPR004314
Neprosin - 36 - 38 + IPR011016
Zinc finger, RING-CH-type + 24 + 105 417 - IPR001099
Chalcone/stilbene synthase, N-terminal - 36 - 39 + IPR023753
FAD/NAD(P)-binding domain + 24 + 36 418 - IPR001296
Glycosyl transferase, family 1 - 36 - 36 + IPR007657
Glycosyltransferase 61 + 24 + 71 419 - IPR027356
  - 36 - 140 + IPR027725
Heat shock transcription factor family + 24 + 33 420 - IPR031112
AP2-like ethylene-responsive transcription factor - 36 - 40 + IPR001763
Rhodanese-like domain + 24 + 58 421 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 36 - 148 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 24 + 40 422 - IPR019780
Germin, manganese binding site - 36 - 36 + IPR001283
Cysteine-rich secretory protein-related + 24 + 79 423 - IPR003311
AUX/IAA protein - 36 - 39 + IPR044839
Protein NDR1-like + 24 + 25 424 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 36 - 36 + IPR002035
von Willebrand factor, type A + 24 + 58 425 - IPR017938
Riboflavin synthase-like beta-barrel - 35 - 42 + IPR001757
P-type ATPase + 24 + 142 426 - IPR014722
  - 35 - 82 + IPR036427
Bromodomain-like superfamily + 24 + 46 427 - IPR029069
HotDog domain superfamily - 35 + IPR025486
Domain of unknown function DUF4378 + 24 48 428 - IPR000595
  - 35 - 254 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 24 + 121 429 - IPR001229
  - 35 - 268 + IPR031127
E3 ubiquitin ligase RBR family + 24 + 45 430 - IPR016040
NAD(P)-binding domain - 35 - 39 + IPR023210
NADP-dependent oxidoreductase domain + 24 + 54 431 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 35 - 68 + IPR029033
Histidine phosphatase superfamily + 24 + 43 432 - IPR001251
  - 35 - 256 + IPR010525
Auxin response factor domain + 24 + 47 433 - IPR011016
  - 35 - 234 + IPR036085
PAZ domain superfamily + 23 + 43 434 - IPR038933
Ovate protein family - 35 - 43 + IPR003106
Leucine zipper, homeobox-associated + 23 + 25 435 - IPR022742
Serine aminopeptidase, S33 - 35 - 35 + IPR000387
Tyrosine specific protein phosphatases domain + 23 + 44 436 - IPR006652
Kelch repeat type 1 - 35 - 129 + IPR013187
F-box associated domain, type 3 + 23 + 30 437 - IPR005150
Cellulose synthase - 35 - 49 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 28 438 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 35 - 35 + IPR013216
Methyltransferase type 11 + 23 + 40 439 - IPR006458
  - 35 - 196 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 23 + 45 440 - IPR036034
PDZ superfamily - 35 - 41 + IPR014044
CAP domain + 23 + 28 441 - IPR006073
GTP binding domain - 35 - 90 + IPR034285
Laccase, second cupredoxin domain + 23 + 25 442 - IPR018490
Cyclic nucleotide-binding-like - 34 - 35 + IPR004776
Membrane transport protein + 23 + 52 443 - IPR025525
hAT-like transposase, RNase-H fold - 34 - 34 + IPR029069
HotDog domain superfamily + 23 + 64 444 - IPR019821
Kinesin motor domain, conserved site - 34 - 34 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 23 + 32 445 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 34 - 209 + IPR000086
NUDIX hydrolase domain + 23 + 65 446 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 34 - 35 + IPR044066
TRIAD supradomain + 23 + 32 447 - IPR000863
Sulfotransferase domain - 34 - 40 + IPR001487
Bromodomain + 23 + 226 448 - IPR002963
Expansin - 34 - 274 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 23 + 36 449 - IPR027923
Hydrophobic seed protein - 34 - 66 + IPR003100
PAZ domain + 22 + 82 450 - IPR031107
Small heat shock protein HSP20 - 34 - 36 + IPR006689
Small GTPase superfamily, ARF/SAR type + 22 + 145 451 - IPR004087
K Homology domain - 34 - 68 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 22 + 37 452 - IPR001701
Glycoside hydrolase family 9 - 34 - 35 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 71 453 - IPR001926
Pyridoxal-phosphate dependent enzyme - 34 - 35 + IPR008999
Actin-crosslinking + 22 + 30 454 - IPR000795
  - 34 - 600 + IPR021790
PTBP1, RNA recognition motif 2-like + 22 + 35 455 - IPR033131
Pectinesterase, Asp active site - 34 - 34 + IPR008422
Homeobox KN domain + 22 + 30 456 - IPR002067
Mitochondrial carrier protein - 34 - 166 + IPR012416
CALMODULIN-BINDING PROTEIN60 + 22 + 102 457 - IPR029047
  - 34 - 128 + IPR018392
LysM domain + 22 + 85 458 - IPR019956
Ubiquitin - 33 - 94 + IPR019557
Aminotransferase-like, plant mobile domain + 22 + 25 459 - IPR013088
  - 33 - 105 + IPR017887
Transcription factor TCP subgroup + 22 + 46 460 - IPR019557
Aminotransferase-like, plant mobile domain - 33 - 34 + IPR001353
Proteasome, subunit alpha/beta + 22 + 30 461 - IPR007650
  - 33 - 130 + IPR025422
Transcription factor TGA like domain + 22 + 83 462 - IPR004813
Oligopeptide transporter, OPT superfamily - 33 - 66 + IPR003594
Histidine kinase/HSP90-like ATPase + 22 + 31 463 - IPR017937
Thioredoxin, conserved site - 33 - 40 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 22 + 26 464 - IPR031127
E3 ubiquitin ligase RBR family - 33 - 47 + IPR020103
Pseudouridine synthase, catalytic domain superfamily + 22 + 52 465 - IPR000679
  - 33 - 390 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 22 + 30 466 - IPR001041
  - 33 - 255 + IPR039421
Type 1 protein exporter + 22 + 44 467 - IPR015797
NUDIX hydrolase-like domain superfamily - 33 - 33 + IPR002939
Chaperone DnaJ, C-terminal + 22 + 39 468 - IPR001179
  - 33 - 194 + IPR036034
PDZ superfamily + 22 + 29 469 - IPR008266
Tyrosine-protein kinase, active site - 33 - 33 + IPR036443
Zinc finger, RanBP2-type superfamily + 22 + 96 470 - IPR011013
Galactose mutarotase-like domain superfamily - 33 - 38 + IPR004000
Actin family + 21 + 175 471 - IPR003406
Glycosyl transferase, family 14 - 33 - 33 + IPR035952
Rhomboid-like superfamily + 21 + 31 472 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 33 - 45 + IPR004316
SWEET sugar transporter + 21 + 41 473 - IPR018202
Serine carboxypeptidase, serine active site - 33 - 33 + IPR007612
LURP-one-related + 21 + 71 474 - IPR000757
  - 33 - 207 + IPR003347
JmjC domain + 21 + 59 475 - IPR000528
Plant lipid transfer protein/Par allergen - 32 - 147 + IPR000340
Dual specificity phosphatase, catalytic domain + 21 + 38 476 - IPR010920
LSM domain superfamily - 32 - 33 + IPR005516
Remorin, C-terminal + 21 + 39 477 - IPR005299
SAM dependent carboxyl methyltransferase - 32 - 72 + IPR036010
2Fe-2S ferredoxin-like superfamily + 21 + 26 478 - IPR029056
  - 32 - 130 + IPR011257
DNA glycosylase + 21 + 39 479 - IPR008480
Protein of unknown function DUF761, plant - 32 - 32 + IPR020422
Dual specificity protein phosphatase domain + 21 + 34 480 - IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase - 32 - 38 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 21 + 35 481 - IPR027409
  - 32 - 126 + IPR022796
Chlorophyll A-B binding protein + 21 + 30 482 - IPR006439
HAD hydrolase, subfamily IA - 32 - 76 + IPR036928
Amidase signature (AS) superfamily + 21 + 38 483 - IPR017927
  - 32 - 96 + IPR003616
Post-SET domain + 21 + 32 484 - IPR032710
NTF2-like domain superfamily - 32 - 32 + IPR017923
Transcription factor IIS, N-terminal + 21 + 51 485 - IPR006153
Cation/H+ exchanger - 32 - 34 + IPR021864
Domain of unknown function DUF3475 + 21 + 28 486 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 32 - 36 + IPR007679
Domain of unknown function DUF569 + 21 + 23 487 - IPR002423
Chaperonin Cpn60/TCP-1 family - 32 - 36 + IPR013809
ENTH domain + 21 + 37 488 - IPR004367
Cyclin, C-terminal domain - 32 - 57 + IPR035441
TFIIS/LEDGF domain superfamily + 21 + 26 489 - IPR006195
  - 31 - 62 + IPR006867
Domain of unknown function DUF632 + 21 + 30 490 - IPR013216
Methyltransferase type 11 - 31 - 31 + IPR004274
FCP1 homology domain + 21 + 104 491 - IPR001594
Palmitoyltransferase, DHHC domain - 31 - 31 + IPR016073
SKP1 component, POZ domain + 20 + 21 492 - IPR025660
Cysteine peptidase, histidine active site - 31 - 31 + IPR006593
Cytochrome b561/ferric reductase transmembrane + 20 + 49 493 - IPR029000
  - 31 - 136 + IPR006195
Aminoacyl-tRNA synthetase, class II + 20 + 29 494 - IPR005135
Endonuclease/exonuclease/phosphatase - 31 - 31 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 20 + 30 495 - IPR036296
SKP1-like, dimerisation domain superfamily - 31 - 31 + IPR001440
Tetratricopeptide repeat 1 + 20 + 37 496 - IPR009091
  - 31 - 198 + IPR013581
Plant PDR ABC transporter associated + 20 + 40 497 - IPR000727
  - 30 - 150 + IPR036186
Serpin superfamily + 20 + 31 498 - IPR036873
  - 30 - 144 + IPR004161
Translation elongation factor EFTu-like, domain 2 + 20 + 28 499 - IPR000315
  - 30 - 423 + IPR001881
EGF-like calcium-binding domain + 20 + 30 500 - IPR000717
  - 30 - 140 + IPR014977
WRC domain + 20 + 56 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_indicair8.html b/gramene/htdocs/ssi/species/stats_Oryza_indicair8.html new file mode 100644 index 00000000..1890a7db --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_indicair8.html @@ -0,0 +1,159 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Rice_IR8_v1.7, Dec 2016
Database version:87.1
Base Pairs:389,082,167
Golden Path Length:389,088,367
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		35,508
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:56,823
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144746683
237475564
339065119
435713470
531269760
632072649
730380234
830236384
924243884
1025246678
1132337678
1225963606
+
+
supercontig
+
3 sequences
+
+ +
+ + + +
SequenceLength (bp)
IR8_Chr00_Ctg130_0006588843
IR8_Chr00_Ctg291_0006798459
IR8_Chr00_Ctg1520_00066149356
+
+
contig
+
66 sequences
+
+ +
+ + + +
SequenceLength (bp)
MPPV01000001.113957568
MPPV01000002.1772818
MPPV01000003.12829530
MPPV01000004.1599510
MPPV01000005.1493967
MPPV01000006.126092790
MPPV01000007.114714266
MPPV01000008.1850289
MPPV01000009.13255014
MPPV01000010.118655595
MPPV01000011.13811878
MPPV01000012.116902864
MPPV01000013.11058269
MPPV01000014.117121279
MPPV01000015.1170329
MPPV01000016.12251857
MPPV01000017.16057010
MPPV01000018.1831905
MPPV01000019.183630
MPPV01000020.1566450
MPPV01000021.1377629
MPPV01000022.118891260
MPPV01000023.16653029
MPPV01000024.11348859
MPPV01000025.17352252
MPPV01000026.16974593
MPPV01000027.115493534
MPPV01000028.1100022
MPPV01000029.16320144
MPPV01000030.13931259
MPPV01000031.11171307
MPPV01000032.15379507
MPPV01000033.1705275
MPPV01000034.114564657
MPPV01000035.116690981
MPPV01000036.113689053
MPPV01000037.16240730
MPPV01000038.11305531
MPPV01000039.1963550
MPPV01000040.14540254
MPPV01000041.14076855
MPPV01000042.11073145
MPPV01000043.11305338
MPPV01000044.1897330
MPPV01000045.14679785
MPPV01000046.15152866
MPPV01000047.13031427
MPPV01000048.12190648
MPPV01000049.11234270
MPPV01000050.18012759
MPPV01000051.15527597
MPPV01000052.1988256
MPPV01000053.13258227
MPPV01000054.13173925
MPPV01000055.1667642
MPPV01000056.1595836
MPPV01000057.120808775
MPPV01000058.14918926
MPPV01000059.19001889
MPPV01000060.13726225
MPPV01000061.113380425
MPPV01000062.11309713
MPPV01000063.125963406
MPPV01000064.188843
MPPV01000065.1149356
MPPV01000066.198459
+
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_indicair8_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_indicair8_IPtop500.html new file mode 100644 index 00000000..c89d6eaa --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_indicair8_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		13662777
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		13013312
3IPR000719
Protein kinase domain		12924311
4IPR036047
F-box-like domain superfamily		5991102
5IPR044974
Disease resistance protein, plants		4611240
6IPR002885
Pentatricopeptide repeat		4559799
7IPR001611
Leucine-rich repeat		4431895
8IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		4411136
9IPR001810
F-box domain		4331197
10IPR002182
NB-ARC		411801
11IPR009057
Homeobox-like domain superfamily		374600
12IPR001841
Zinc finger, RING-type		370898
13IPR036291
NAD(P)-binding domain superfamily		369771
14IPR016024
Armadillo-type fold		3601006
15IPR029058
Alpha/Beta hydrolase fold		353685
16IPR041118
Rx, N-terminal		347658
17IPR011990
Tetratricopeptide-like helical domain superfamily		317821
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		300523
19IPR036396
Cytochrome P450 superfamily		296502
20IPR035979
RNA-binding domain superfamily		291751
21IPR001128
Cytochrome P450		2871705
22IPR000504
RNA recognition motif domain		2651434
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		255580
24IPR017853
Glycoside hydrolase superfamily		250518
25IPR002401
Cytochrome P450, E-class, group I		2402176
26IPR036259
MFS transporter superfamily		240505
27IPR017930
Myb domain		235865
28IPR038005
Virus X resistance protein-like, coiled-coil domain		233438
29IPR036322
WD40-repeat-containing domain superfamily		231580
30IPR001005
SANT/Myb domain		227867
31IPR038765
Papain-like cysteine peptidase superfamily		213488
32IPR036249
Thioredoxin-like superfamily		210415
33IPR001680
WD40 repeat		2052504
34IPR036638
Helix-loop-helix DNA-binding domain superfamily		171264
35IPR011992
EF-hand domain pair		171293
36IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		164443
37IPR036412
HAD-like superfamily		162324
38IPR016177
DNA-binding domain superfamily		161283
39IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		161438
40IPR036770
Ankyrin repeat-containing domain superfamily		160329
41IPR002048
EF-hand domain		1561057
42IPR002110
Ankyrin repeat		149948
43IPR036390
Winged helix DNA-binding domain superfamily		148230
44IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		146235
45IPR001471
AP2/ERF domain		144884
46IPR011333
SKP1/BTB/POZ domain superfamily		140246
47IPR036093
NAC domain superfamily		138192
48IPR003441
NAC domain		136364
49IPR029044
Nucleotide-diphospho-sugar transferases		136247
50IPR001650
Helicase, C-terminal		135646
51IPR014001
Helicase superfamily 1/2, ATP-binding domain		134328
52IPR012340
Nucleic acid-binding, OB-fold		133423
53IPR036188
FAD/NAD(P)-binding domain superfamily		132334
54IPR010255
Haem peroxidase superfamily		132180
55IPR002016
Haem peroxidase		1301010
56IPR020683
Ankyrin repeat-containing domain		127400
57IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		125154
58IPR003439
ABC transporter-like, ATP-binding domain		119893
59IPR000823
Plant peroxidase		1191106
60IPR013087
Zinc finger C2H2-type		118362
61IPR005174
Domain unknown function DUF295		115190
62IPR036236
Zinc finger C2H2 superfamily		115245
63IPR029071
Ubiquitin-like domain superfamily		114236
64IPR036426
Bulb-type lectin domain superfamily		112218
65IPR001480
Bulb-type lectin domain		111567
66IPR003959
ATPase, AAA-type, core		110237
67IPR036869
Chaperone J-domain superfamily		110201
68IPR021109
Aspartic peptidase domain superfamily		109197
69IPR011011
Zinc finger, FYVE/PHD-type		106259
70IPR003480
Transferase		106148
71IPR019734
Tetratricopeptide repeat		105592
72IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		105256
73IPR001623
DnaJ domain		105948
74IPR033905
Secretory peroxidase		104138
75IPR001087
GDSL lipase/esterase		102154
76IPR008972
Cupredoxin		102237
77IPR000210
BTB/POZ domain		101386
78IPR015424
Pyridoxal phosphate-dependent transferase		99184
79IPR036576
WRKY domain superfamily		98144
80IPR003657
WRKY domain		98285
81IPR011050
Pectin lyase fold/virulence factor		97140
82IPR033121
Peptidase family A1 domain		95180
83IPR020846
Major facilitator superfamily domain		95168
84IPR001356
Homeobox domain		95406
85IPR032861
Xylanase inhibitor, N-terminal		94169
86IPR007658
Protein of unknown function DUF594		93110
87IPR044810
WRKY transcription factor, plant		93125
88IPR036457
PPM-type phosphatase domain superfamily		92209
89IPR011676
Domain of unknown function DUF1618		92165
90IPR035892
C2 domain superfamily		91243
91IPR032799
Xylanase inhibitor, C-terminal		91139
92IPR015300
DNA-binding pseudobarrel domain superfamily		91217
93IPR005123
Oxoglutarate/iron-dependent dioxygenase		90169
94IPR003609
PAN/Apple domain		90325
95IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		90108
96IPR025315
Domain of unknown function DUF4220		90123
97IPR001932
PPM-type phosphatase domain		88587
98IPR002347
Short-chain dehydrogenase/reductase SDR		86936
99IPR011051
RmlC-like cupin domain superfamily		86161
100IPR035669
GDSL lipase/esterase-like, plant		85131
101IPR011545
DEAD/DEAH box helicase domain		84192
102IPR000858
S-locus glycoprotein domain		83162
103IPR005828
Major facilitator, sugar transporter-like		83170
104IPR000109
Proton-dependent oligopeptide transporter family		82349
105IPR000008
C2 domain		81529
106IPR003340
B3 DNA binding domain		80565
107IPR026961
PGG domain		80224
108IPR020472
G-protein beta WD-40 repeat		79483
109IPR012337
Ribonuclease H-like superfamily		79178
110IPR032867
DYW domain		79138
111IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		78146
112IPR013766
Thioredoxin domain		78228
113IPR004827
Basic-leucine zipper domain		78252
114IPR000626
Ubiquitin-like domain		77275
115IPR004158
Protein of unknown function DUF247, plant		76198
116IPR000270
PB1 domain		76157
117IPR009072
Histone-fold		7699
118IPR002083
MATH/TRAF domain		75430
119IPR000073
Alpha/beta hydrolase fold-1		75304
120IPR001220
Legume lectin domain		75191
121IPR001461
Aspartic peptidase A1 family		74339
122IPR045005
BTB/POZ and MATH domain-containing protein 1-6		73169
123IPR000571
Zinc finger, CCCH-type		73491
124IPR026992
Non-haem dioxygenase N-terminal domain		72125
125IPR043129
ATPase, nucleotide binding domain		71218
126IPR016039
Thiolase-like		69150
127IPR003613
U box domain		68193
128IPR006121
Heavy metal-associated domain, HMA		67280
129IPR036163
Heavy metal-associated domain superfamily		67118
130IPR008949
Isoprenoid synthase domain superfamily		66131
131IPR012871
Protein of unknown function DUF1677, Oryza sativa		6595
132IPR013057
Amino acid transporter, transmembrane domain		65124
133IPR036908
RlpA-like domain superfamily		6587
134IPR016159
Cullin repeat-like-containing domain superfamily		65107
135IPR036282
Glutathione S-transferase, C-terminal domain superfamily		65124
136IPR029052
Metallo-dependent phosphatase-like		64110
137IPR001806
Small GTPase		64182
138IPR002100
Transcription factor, MADS-box		63483
139IPR036879
Transcription factor, MADS-box superfamily		63108
140IPR026057
PC-Esterase		62111
141IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6268
142IPR019787
Zinc finger, PHD-finger		62232
143IPR002902
Gnk2-homologous domain		62639
144IPR044965
Glycoside hydrolase family 17, plant		62120
145IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		61216
146IPR020568
Ribosomal protein S5 domain 2-type fold		60126
147IPR023395
Mitochondrial carrier domain superfamily		60134
148IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		59104
149IPR018108
Mitochondrial substrate/solute carrier		59671
150IPR045051
Subtilisin-like protease		58107
151IPR029962
Trichome birefringence-like family		58105
152IPR036749
Expansin, cellulose-binding-like domain superfamily		5873
153IPR004045
Glutathione S-transferase, N-terminal		57228
154IPR036852
Peptidase S8/S53 domain superfamily		5791
155IPR000490
Glycoside hydrolase family 17		57114
156IPR007117
Expansin, cellulose-binding-like domain		57144
157IPR000048
IQ motif, EF-hand binding site		57657
158IPR000209
Peptidase S8/S53 domain		5790
159IPR016135
Ubiquitin-conjugating enzyme/RWD-like		56102
160IPR025846
PMR5 N-terminal domain		5694
161IPR005202
Transcription factor GRAS		56230
162IPR036915
Cyclin-like superfamily		56192
163IPR001752
Kinesin motor domain		56742
164IPR001563
Peptidase S10, serine carboxypeptidase		55580
165IPR006501
Pectinesterase inhibitor domain		5559
166IPR003663
Sugar/inositol transporter		55411
167IPR007112
Expansin/pollen allergen, DPBB domain		5469
168IPR003245
Phytocyanin domain		54122
169IPR036465
von Willebrand factor A-like domain superfamily		5494
170IPR009003
Peptidase S1, PA clan		54188
171IPR011032
GroES-like superfamily		53128
172IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5376
173IPR010987
Glutathione S-transferase, C-terminal-like		53109
174IPR013094
Alpha/beta hydrolase fold-3		5363
175IPR041469
Subtilisin-like protease, fibronectin type-III domain		5277
176IPR039391
Phytocyanin		5258
177IPR015915
Kelch-type beta propeller		5284
178IPR003653
Ulp1 protease family, C-terminal catalytic domain		51196
179IPR002528
Multi antimicrobial extrusion protein		51179
180IPR013525
ABC-2 type transporter		50179
181IPR006045
Cupin 1		50112
182IPR024788
Malectin-like domain		50129
183IPR015500
Peptidase S8, subtilisin-related		50205
184IPR007118
Expansin/Lol pI		49318
185IPR013201
Cathepsin propeptide inhibitor domain (I29)		4964
186IPR009009
RlpA-like protein, double-psi beta-barrel domain		4963
187IPR008979
Galactose-binding-like domain superfamily		49132
188IPR000620
EamA domain		49172
189IPR016181
Acyl-CoA N-acyltransferase		4875
190IPR008978
HSP20-like chaperone		4866
191IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		4861
192IPR045087
Multicopper oxidase		4868
193IPR030184
WAT1-related protein		48118
194IPR023298
P-type ATPase, transmembrane domain superfamily		48105
195IPR036855
Zinc finger, CCCH-type superfamily		48207
196IPR036318
FAD-binding, type PCMH-like superfamily		4774
197IPR000608
Ubiquitin-conjugating enzyme E2		47217
198IPR012946
X8 domain		4776
199IPR034197
Cucumisin-like catalytic domain		4772
200IPR041569
AAA ATPase, AAA+ lid domain		4796
201IPR000225
Armadillo		47196
202IPR033389
AUX/IAA domain		4677
203IPR036640
ABC transporter type 1, transmembrane domain superfamily		46217
204IPR008250
P-type ATPase, A domain superfamily		4697
205IPR001509
NAD-dependent epimerase/dehydratase		46126
206IPR013763
Cyclin-like		46152
207IPR022059
Protein of unknown function DUF3615		4689
208IPR008928
Six-hairpin glycosidase superfamily		4679
209IPR011527
ABC transporter type 1, transmembrane domain		46450
210IPR014756
Immunoglobulin E-set		46101
211IPR002921
Fungal lipase-like domain		4576
212IPR017884
SANT domain		4571
213IPR005630
Terpene synthase, metal-binding domain		4592
214IPR004140
Exocyst complex component Exo70		45150
215IPR011707
Multicopper oxidase, N-termianl		4558
216IPR043926
ABC transporter family G domain		44137
217IPR034161
Pepsin-like domain, plant		4459
218IPR004265
Dirigent protein		4458
219IPR001117
Multicopper oxidase, type 1		4357
220IPR029055
Nucleophile aminohydrolases, N-terminal		4381
221IPR001938
Thaumatin family		43333
222IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4389
223IPR011006
CheY-like superfamily		4375
224IPR011706
Multicopper oxidase, C-terminal		4356
225IPR000668
Peptidase C1A, papain C-terminal		43189
226IPR006566
FBD domain		4373
227IPR037176
Osmotin/thaumatin-like superfamily		4357
228IPR006702
Casparian strip membrane protein domain		4347
229IPR004853
Sugar phosphate transporter domain		4283
230IPR000873
AMP-dependent synthetase/ligase		4288
231IPR001906
Terpene synthase, N-terminal domain		4285
232IPR015947
PUA-like superfamily		4273
233IPR044808
Ethylene-responsive transcription factor		4248
234IPR001789
Signal transduction response regulator, receiver domain		42140
235IPR000330
SNF2, N-terminal		41117
236IPR009000
Translation protein, beta-barrel domain superfamily		4189
237IPR004263
Exostosin-like		4169
238IPR016166
FAD-binding domain, PCMH-type		4166
239IPR000070
Pectinesterase, catalytic		4159
240IPR000182
GNAT domain		40110
241IPR033896
MADS MEF2-like		4077
242IPR009060
UBA-like superfamily		4075
243IPR014014
RNA helicase, DEAD-box type, Q motif		4073
244IPR001214
SET domain		40157
245IPR001878
Zinc finger, CCHC-type		40206
246IPR010402
CCT domain		39147
247IPR006016
UspA		3957
248IPR036612
K Homology domain, type 1 superfamily		39165
249IPR011012
Longin-like domain superfamily		3970
250IPR000742
EGF-like domain		3958
251IPR011043
Galactose oxidase/kelch, beta-propeller		3946
252IPR002912
ACT domain		39128
253IPR003676
Small auxin-up RNA		3946
254IPR000743
Glycoside hydrolase, family 28		3971
255IPR016461
O-methyltransferase COMT-type		38102
256IPR001077
O-methyltransferase domain		3853
257IPR006671
Cyclin, N-terminal		3884
258IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		3870
259IPR008942
ENTH/VHS		3777
260IPR013149
Alcohol dehydrogenase, C-terminal		3764
261IPR002068
Alpha crystallin/Hsp20 domain		37102
262IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3742
263IPR015655
Protein phosphatase 2C family		37103
264IPR011701
Major facilitator superfamily		3699
265IPR013154
Alcohol dehydrogenase, N-terminal		3667
266IPR004883
Lateral organ boundaries, LOB		3677
267IPR007125
Histone H2A/H2B/H3		3639
268IPR029045
ClpP/crotonase-like domain superfamily		36100
269IPR039417
Papain-like cysteine endopeptidase		3650
270IPR000644
CBS domain		36191
271IPR028889
Ubiquitin specific protease domain		36102
272IPR002487
Transcription factor, K-box		36128
273IPR008889
VQ		3636
274IPR025659
Tubby-like, C-terminal		3565
275IPR029021
Protein-tyrosine phosphatase-like		3584
276IPR036691
Endonuclease/exonuclease/phosphatase superfamily		35101
277IPR003137
PA domain		3568
278IPR043454
NPH3/RPT2-like family		3550
279IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		35101
280IPR002495
Glycosyl transferase, family 8		3561
281IPR043519
Nucleotidyltransferase superfamily		3579
282IPR023271
Aquaporin-like		3444
283IPR036865
CRAL-TRIO lipid binding domain superfamily		3468
284IPR004839
Aminotransferase, class I/classII		3465
285IPR000425
Major intrinsic protein		34292
286IPR006094
FAD linked oxidase, N-terminal		3452
287IPR016040
NAD(P)-binding domain		3365
288IPR004041
NAF domain		3352
289IPR001251
CRAL-TRIO lipid binding domain		33183
290IPR001296
Glycosyl transferase, family 1		3369
291IPR013126
Heat shock protein 70 family		3387
292IPR039361
Cyclin		3378
293IPR036041
Ribosome-inactivating protein superfamily		3354
294IPR036875
Zinc finger, CCHC-type superfamily		3380
295IPR001574
Ribosome-inactivating protein		3381
296IPR032710
NTF2-like domain superfamily		3257
297IPR018451
NAF/FISL domain		3251
298IPR022742
Serine aminopeptidase, S33		3249
299IPR019378
GDP-fucose protein O-fucosyltransferase		3282
300IPR004046
Glutathione S-transferase, C-terminal		3261
301IPR002067
Mitochondrial carrier protein		32245
302IPR040911
Exostosin, GT47 domain		3248
303IPR003311
AUX/IAA protein		3248
304IPR018490
Cyclic nucleotide-binding-like		3167
305IPR007493
Protein of unknown function DUF538		3179
306IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3158
307IPR027356
NPH3 domain		3179
308IPR003690
Transcription termination factor, mitochondrial/chloroplastic		31119
309IPR036758
At5g01610-like superfamily		3141
310IPR004088
K Homology domain, type 1		31136
311IPR006458
Ovate protein family, C-terminal		3161
312IPR004314
Neprosin		3164
313IPR012967
Plant methyltransferase dimerisation		3136
314IPR006073
GTP binding domain		31120
315IPR008991
Translation protein SH3-like domain superfamily		3053
316IPR038933
Ovate protein family		3032
317IPR002659
Glycosyl transferase, family 31		30142
318IPR005333
Transcription factor, TCP		3039
319IPR002423
Chaperonin Cpn60/TCP-1 family		3052
320IPR004367
Cyclin, C-terminal domain		3058
321IPR003406
Glycosyl transferase, family 14		3044
322IPR002109
Glutaredoxin		3041
323IPR036404
Jacalin-like lectin domain superfamily		3083
324IPR000595
Cyclic nucleotide-binding domain		30166
325IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3064
326IPR001229
Jacalin-like lectin domain		30161
327IPR000528
Plant non-specific lipid-transfer protein/Par allergen		29162
328IPR010920
LSM domain superfamily		2943
329IPR000717
Proteasome component (PCI) domain		2983
330IPR035940
CAP superfamily		2944
331IPR000795
Translational (tr)-type GTP-binding domain		29342
332IPR034294
Aquaporin transporter		2940
333IPR011013
Galactose mutarotase-like domain superfamily		2975
334IPR005150
Cellulose synthase		2994
335IPR002035
von Willebrand factor, type A		2974
336IPR036296
SKP1-like, dimerisation domain superfamily		2937
337IPR001223
Glycoside hydrolase family 18, catalytic domain		2962
338IPR003855
Potassium transporter		29175
339IPR011141
Polyketide synthase, type III		2935
340IPR000679
Zinc finger, GATA-type		29126
341IPR002913
START domain		29124
342IPR001099
Chalcone/stilbene synthase, N-terminal		2935
343IPR017927
FAD-binding domain, ferredoxin reductase-type		2848
344IPR017938
Riboflavin synthase-like beta-barrel		2847
345IPR015940
Ubiquitin-associated domain		28104
346IPR001929
Germin		28106
347IPR001360
Glycoside hydrolase family 1		28616
348IPR005299
SAM dependent carboxyl methyltransferase		28129
349IPR044835
Auxin response factor		2862
350IPR044848
PHR1-like		2851
351IPR005135
Endonuclease/exonuclease/phosphatase		2872
352IPR006652
Kelch repeat type 1		2891
353IPR000863
Sulfotransferase domain		2839
354IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2843
355IPR002963
Expansin		28252
356IPR027409
GroEL-like apical domain superfamily		2844
357IPR023299
P-type ATPase, cytoplasmic domain N		2860
358IPR000757
Glycoside hydrolase family 16		2885
359IPR033734
Jacalin-like lectin domain, plant		2876
360IPR000727
Target SNARE coiled-coil homology domain		2759
361IPR025322
Protein of unknown function DUF4228, plant		2730
362IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2733
363IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		27241
364IPR006153
Cation/H+ exchanger		2762
365IPR029000
Cyclophilin-like domain superfamily		2746
366IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		27158
367IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		27112
368IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		2754
369IPR013216
Methyltransferase type 11		2739
370IPR023753
FAD/NAD(P)-binding domain		2759
371IPR029061
Thiamin diphosphate-binding fold		2773
372IPR001594
Palmitoyltransferase, DHHC domain		2751
373IPR009030
Growth factor receptor cysteine-rich domain superfamily		2741
374IPR036273
CRAL/TRIO, N-terminal domain superfamily		2756
375IPR016072
SKP1 component, dimerisation		2734
376IPR001283
Cysteine-rich secretory protein-related		27139
377IPR014044
CAP domain		2742
378IPR001757
P-type ATPase		27188
379IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2731
380IPR036812
NADP-dependent oxidoreductase domain superfamily		2767
381IPR005175
PPC domain		27113
382IPR024709
Putative O-fucosyltransferase, plant		2668
383IPR007657
Glycosyltransferase 61		2669
384IPR000408
Regulator of chromosome condensation, RCC1		26807
385IPR005821
Ion transport domain		2654
386IPR033443
Pentacotripeptide-repeat region of PRORP		2657
387IPR012328
Chalcone/stilbene synthase, C-terminal		2629
388IPR003851
Zinc finger, Dof-type		2662
389IPR044791
Beta-glucanase/XTH		2638
390IPR015797
NUDIX hydrolase-like domain superfamily		2654
391IPR013601
FAE1/Type III polyketide synthase-like protein		2526
392IPR013187
F-box associated domain, type 3		2537
393IPR000315
B-box-type zinc finger		2570
394IPR044778
Sugar transport protein STP/MST-like, plant		2531
395IPR008422
Homeobox KN domain		2550
396IPR027725
Heat shock transcription factor family		2536
397IPR003337
Trehalose-phosphatase		2541
398IPR002123
Phospholipid/glycerol acyltransferase		2545
399IPR044814
Terpene cyclases, class 1, plant		2546
400IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2543
401IPR016897
S-phase kinase-associated protein 1		2529
402IPR034285
Laccase, second cupredoxin domain		2527
403IPR004813
Oligopeptide transporter, OPT superfamily		2555
404IPR001849
Pleckstrin homology domain		2580
405IPR029069
HotDog domain superfamily		2575
406IPR029062
Class I glutamine amidotransferase-like		2571
407IPR036034
PDZ superfamily		2566
408IPR023210
NADP-dependent oxidoreductase domain		2571
409IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2537
410IPR006311
Twin-arginine translocation pathway, signal sequence		2533
411IPR036378
FAS1 domain superfamily		2444
412IPR003106
Leucine zipper, homeobox-associated		2432
413IPR002403
Cytochrome P450, E-class, group IV		24137
414IPR004316
SWEET sugar transporter		2466
415IPR008999
Actin-crosslinking		2439
416IPR044822
Myb/SANT-like DNA-binding domain 4		2437
417IPR036420
BRCT domain superfamily		2486
418IPR011016
Zinc finger, RING-CH-type		24100
419IPR007650
Zf-FLZ domain		2470
420IPR001763
Rhodanese-like domain		2483
421IPR004014
Cation-transporting P-type ATPase, N-terminal		2447
422IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2469
423IPR034288
Laccase, first cupredoxin domain		2426
424IPR027923
Hydrophobic seed protein domain		2458
425IPR039421
Type 1 protein exporter		2480
426IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2459
427IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2435
428IPR001701
Glycoside hydrolase family 9		2433
429IPR025486
Domain of unknown function DUF4378		2443
430IPR006868
Domain of unknown function DUF630		2431
431IPR010525
Auxin response factor domain		2441
432IPR036085
PAZ domain superfamily		2382
433IPR025110
AMP-binding enzyme, C-terminal domain		2339
434IPR001163
LSM domain, eukaryotic/archaea-type		2335
435IPR025422
Transcription factor TGA like domain		2386
436IPR003594
Histidine kinase/HSP90-like ATPase		2342
437IPR004776
Membrane transport protein		2349
438IPR016161
Aldehyde/histidinol dehydrogenase		2345
439IPR036427
Bromodomain-like superfamily		2348
440IPR000086
NUDIX hydrolase domain		2395
441IPR003100
PAZ domain		22141
442IPR000782
FAS1 domain		2270
443IPR019956
Ubiquitin domain		2287
444IPR008971
HSP40/DnaJ peptide-binding		2269
445IPR001357
BRCT domain		22144
446IPR004320
Protein of unknown function DUF241, plant		2242
447IPR001353
Proteasome, subunit alpha/beta		2234
448IPR010989
SNARE		2238
449IPR006694
Fatty acid hydroxylase		2230
450IPR002939
Chaperone DnaJ, C-terminal		2235
451IPR000232
Heat shock factor (HSF)-type, DNA-binding		2297
452IPR031127
E3 ubiquitin ligase RBR family		2273
453IPR015590
Aldehyde dehydrogenase domain		2245
454IPR006867
Domain of unknown function DUF632		2232
455IPR004000
Actin family		21190
456IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2155
457IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2122
458IPR036873
Rhodanese-like domain superfamily		2142
459IPR005516
Remorin, C-terminal		2134
460IPR027413
GroEL-like equatorial domain superfamily		2131
461IPR011257
DNA glycosylase		2133
462IPR011332
Zinc-binding ribosomal protein		2135
463IPR025521
Neprosin activation peptide		2140
464IPR022796
Chlorophyll A-B binding protein		2129
465IPR001876
Zinc finger, RanBP2-type		21126
466IPR034289
Laccase, third cupredoxin domain		2123
467IPR029993
Plant galacturonosyltransferase GAUT		2150
468IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2		2168
469IPR036392
PLAT/LH2 domain superfamily		2126
470IPR001487
Bromodomain		21203
471IPR002937
Amine oxidase		2141
472IPR036443
Zinc finger, RanBP2-type superfamily		2176
473IPR033133
Pumilio homology domain		2038
474IPR006594
LIS1 homology motif		2060
475IPR006689
Small GTPase superfamily, ARF/SAR type		20146
476IPR016073
SKP1 component, POZ domain		2022
477IPR006593
Cytochrome b561/ferric reductase transmembrane		2049
478IPR002867
IBR domain		2075
479IPR006195
Aminoacyl-tRNA synthetase, class II		2040
480IPR035952
Rhomboid-like superfamily		2035
481IPR001024
PLAT/LH2 domain		2043
482IPR036525
Tubulin/FtsZ, GTPase domain superfamily		2029
483IPR025753
AAA-type ATPase, N-terminal domain		2033
484IPR003347
JmjC domain		2068
485IPR013581
Plant PDR ABC transporter associated		2063
486IPR040417
Glycine-rich cell wall structural protein 1/2		2025
487IPR018392
LysM domain		20122
488IPR001881
EGF-like calcium-binding domain		2035
489IPR017887
Transcription factor TCP subgroup		2042
490IPR036010
2Fe-2S ferredoxin-like superfamily		2028
491IPR002293
Amino acid/polyamine transporter I		2041
492IPR011060
Ribulose-phosphate binding barrel		2036
493IPR020103
Pseudouridine synthase, catalytic domain superfamily		2052
494IPR029057
Phosphoribosyltransferase-like		2045
495IPR044839
Protein NDR1-like		2024
496IPR020946
Flavin monooxygenase-like		2055
497IPR041677
DNA2/NAM7 helicase, helicase domain		2061
498IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain		20108
499IPR003388
Reticulon		2067
500IPR001313
Pumilio RNA-binding repeat		20455
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_meridionalis.html b/gramene/htdocs/ssi/species/stats_Oryza_meridionalis.html index ca759754..c5f6e0cc 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_meridionalis.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_meridionalis.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:Oryza_meridionalis_v1.3, Oct 2014AGI_PacBIO,
Database version:93.1387.4
Base Pairs:335,668,232393,639,427
Golden Path Length:335,668,232393,639,427
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Oct 2014
Genebuild version: 2014-10-MAKER
+

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):29,308Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		41,976
Gene transcriptsHASH(0x68ce400):46,697Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:54,942
@@ -37,30 +37,198 @@

Coordinate Systems

chromosome
-
12 sequences
+
180 sequences
- +
SequenceLength (bp)
141795227
237273066
338314702
430391017
526596109
631808207
726849004
821838022
918641908
1017741381
1124454635
1219964954
142804815
237283348
340595595
434272791
530045131
631576741
730507914
829018812
923643651
1024084775
1129168041
1226254206
UN-Ctg401015623
UN-Ctg41473970
UN-Ctg42356539
UN-Ctg43272270
UN-Ctg44262298
UN-Ctg45260731
UN-Ctg46249267
UN-Ctg47246957
UN-Ctg48230131
UN-Ctg49214515
UN-Ctg50207031
UN-Ctg51187982
UN-Ctg52187415
UN-Ctg53162407
UN-Ctg54160638
UN-Ctg55159482
UN-Ctg56154193
UN-Ctg57150414
UN-Ctg58150036
UN-Ctg59149144
UN-Ctg60148803
UN-Ctg61142810
UN-Ctg62137183
UN-Ctg63135027
UN-Ctg64129649
UN-Ctg65128120
UN-Ctg66126628
UN-Ctg67117047
UN-Ctg68116209
UN-Ctg69115750
UN-Ctg70111134
UN-Ctg71107842
UN-Ctg72106144
UN-Ctg73103230
UN-Ctg74103100
UN-Ctg75100659
UN-Ctg7698428
UN-Ctg7797694
UN-Ctg7897224
UN-Ctg7997709
UN-Ctg8096024
UN-Ctg8191564
UN-Ctg8290991
UN-Ctg8390743
UN-Ctg8490673
UN-Ctg8589767
UN-Ctg8686802
UN-Ctg8787523
UN-Ctg8886199
UN-Ctg8984231
UN-Ctg9084032
UN-Ctg9183027
UN-Ctg9282708
UN-Ctg9381639
UN-Ctg9477053
UN-Ctg9575834
UN-Ctg9674801
UN-Ctg9774776
UN-Ctg9874692
UN-Ctg9973066
UN-Ctg10072663
UN-Ctg10172607
UN-Ctg10271982
UN-Ctg10371954
UN-Ctg10471036
UN-Ctg10570743
UN-Ctg10669934
UN-Ctg10769160
UN-Ctg10869035
UN-Ctg10969000
UN-Ctg11068128
UN-Ctg11167174
UN-Ctg11266478
UN-Ctg11365084
UN-Ctg11465038
UN-Ctg11564737
UN-Ctg11664519
UN-Ctg11763981
UN-Ctg11863261
UN-Ctg11961477
UN-Ctg12061945
UN-Ctg12161854
UN-Ctg12261411
UN-Ctg12361236
UN-Ctg12460607
UN-Ctg12560339
UN-Ctg12659739
UN-Ctg12759102
UN-Ctg12858785
UN-Ctg12958583
UN-Ctg13058153
UN-Ctg13158042
UN-Ctg13255327
UN-Ctg13355483
UN-Ctg13454709
UN-Ctg13554736
UN-Ctg13653689
UN-Ctg13753708
UN-Ctg13853262
UN-Ctg13952817
UN-Ctg14052680
UN-Ctg14150575
UN-Ctg14250569
UN-Ctg14349784
UN-Ctg14449573
UN-Ctg14549474
UN-Ctg14649473
UN-Ctg14748862
UN-Ctg14848114
UN-Ctg14948045
UN-Ctg15047776
UN-Ctg15147762
UN-Ctg15247602
UN-Ctg15347163
UN-Ctg15446957
UN-Ctg15546352
UN-Ctg15645596
UN-Ctg15745002
UN-Ctg15844872
UN-Ctg15944934
UN-Ctg16044443
UN-Ctg16144480
UN-Ctg16244203
UN-Ctg16343468
UN-Ctg16443064
UN-Ctg16543073
UN-Ctg16642861
UN-Ctg16742836
UN-Ctg16842630
UN-Ctg16942624
UN-Ctg17042479
UN-Ctg17142071
UN-Ctg17242103
UN-Ctg17341418
UN-Ctg17440817
UN-Ctg17539781
UN-Ctg17639777
UN-Ctg17737862
UN-Ctg17837838
UN-Ctg17937221
UN-Ctg18036830
UN-Ctg18136581
UN-Ctg18235654
UN-Ctg18335521
UN-Ctg18435432
UN-Ctg18534755
UN-Ctg18635009
UN-Ctg18733403
UN-Ctg18832470
UN-Ctg18932118
UN-Ctg19031626
UN-Ctg19131663
UN-Ctg19230519
UN-Ctg19330426
UN-Ctg19430113
UN-Ctg19529925
UN-Ctg19629586
UN-Ctg19728842
UN-Ctg19828516
UN-Ctg19928256
UN-Ctg20028259
UN-Ctg20126161
UN-Ctg20225339
UN-Ctg20325280
UN-Ctg20421804
UN-Ctg20518699
UN-Ctg20618362
UN-Ctg20717148
-
+
chunk - 3362 sequences + 4024 sequences diff --git a/gramene/htdocs/ssi/species/stats_Oryza_meridionalis_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_meridionalis_IPtop500.html index 936ed5e2..456c192a 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_meridionalis_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_meridionalis_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1230 - 2320 + 1510 + 2174 2 - IPR000719
  - 1171 - 15003 + IPR000719
Protein kinase domain + 1431 + 3434 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 990 - 2520 + 1418 + 2425 4 - IPR008271
Serine/threonine-protein kinase, active site - 926 - 1593 + IPR036047
F-box-like domain superfamily + 675 + 932 5 - IPR032675
  - 843 - 5604 + IPR002885
Pentatricopeptide repeat + 509 + 7675 6 - IPR017441
Protein kinase, ATP binding site - 808 - 1332 + IPR044974
Disease resistance protein, plants + 508 + 947 7 - IPR013083
  - 590 - 1952 + IPR001611
Leucine-rich repeat + 487 + 1659 8 - IPR036047
F-box-like domain superfamily - 478 - 733 + IPR001810
F-box domain + 476 + 1007 9 - IPR011990
  - 466 - 7971 + IPR001841
Zinc finger, RING-type + 468 + 942 10 - IPR001611
  - 390 - 10299 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 467 + 933 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 387 - 1040 + IPR002182
NB-ARC + 435 + 581 12 - IPR001841
  - 367 - 2738 + IPR036291
NAD(P)-binding domain superfamily + 392 + 605 13 - IPR001810
  - 343 - 3252 + IPR009057
Homeobox-like domain superfamily + 392 + 538 14 - IPR016024
Armadillo-type fold - 326 - 1499 + IPR029058
Alpha/Beta hydrolase fold + 391 + 612 15 - IPR029058
  - 318 - 2406 + IPR016024
Armadillo-type fold + 387 + 662 16 - IPR036291
NAD(P)-binding domain superfamily - 297 - 652 + IPR012337
Ribonuclease H-like superfamily + 371 + 475 17 - IPR009057
Homeobox-like domain superfamily - 292 - 457 + IPR041118
Rx, N-terminal + 369 + 463 18 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 285 - 403 + IPR036396
Cytochrome P450 superfamily + 358 + 480 19 - IPR003591
Leucine-rich repeat, typical subtype - 276 - 2754 + IPR011990
Tetratricopeptide-like helical domain superfamily + 356 + 637 20 - IPR035979
RNA-binding domain superfamily - 273 - 695 + IPR001128
Cytochrome P450 + 339 + 1690 21 - IPR002885
  - 271 - 17120 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 325 + 420 22 - IPR012677
  - 266 - 1464 + IPR035979
RNA-binding domain superfamily + 318 + 648 23 - IPR036396
  - 265 - 2661 + IPR043502
DNA/RNA polymerase superfamily + 297 + 324 24 - IPR001128
Cytochrome P450 - 251 - 1406 + IPR017853
Glycoside hydrolase superfamily + 292 + 448 25 - IPR000504
  - 240 - 5805 + IPR038765
Papain-like cysteine peptidase superfamily + 292 + 411 26 - IPR003593
AAA+ ATPase domain - 228 - 556 + IPR002401
Cytochrome P450, E-class, group I + 285 + 2190 27 - IPR011989
  - 226 - 1142 + IPR000504
RNA recognition motif domain + 280 + 1240 28 - IPR017853
Glycoside hydrolase superfamily - 225 - 480 + IPR036259
MFS transporter superfamily + 272 + 435 29 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 221 - 537 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 265 + 316 30 - IPR036259
MFS transporter superfamily - 216 - 591 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 261 + 475 31 - IPR002401
Cytochrome P450, E-class, group I - 215 - 1836 + IPR001878
Zinc finger, CCHC-type + 243 + 690 32 - IPR036249
Thioredoxin-like superfamily - 203 - 384 + IPR001005
SANT/Myb domain + 243 + 815 33 - IPR002182
NB-ARC - 201 - 345 + IPR036875
Zinc finger, CCHC-type superfamily + 240 + 353 34 - IPR015943
  - 201 - 1812 + IPR017930
Myb domain + 240 + 783 35 - IPR001005
SANT/Myb domain - 200 - 932 + IPR036322
WD40-repeat-containing domain superfamily + 238 + 417 36 - IPR036322
WD40-repeat-containing domain superfamily - 189 - 647 + IPR036249
Thioredoxin-like superfamily + 234 + 377 37 - IPR017972
Cytochrome P450, conserved site - 185 - 292 + IPR021109
Aspartic peptidase domain superfamily + 217 + 239 38 - IPR001680
  - 183 - 10110 + IPR001680
WD40 repeat + 214 + 1838 39 IPR016177
DNA-binding domain superfamily - 163 - 257 + 197 + 282 40 - IPR017986
  - 162 - 1071 + IPR011992
EF-hand domain pair + 197 + 266 41 - IPR011992
EF-hand domain pair - 162 - 295 + IPR002048
EF-hand domain + 182 + 1013 42 - IPR038765
Papain-like cysteine peptidase superfamily - 160 - 403 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 181 + 390 43 - IPR002048
  - 152 - 5163 + IPR000477
Reverse transcriptase domain + 181 + 299 44 - IPR020846
  - 152 - 812 + IPR001471
AP2/ERF domain + 178 + 1039 45 - IPR001471
  - 150 - 3261 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 173 + 211 46 - IPR036955
  - 148 - 624 + IPR011333
SKP1/BTB/POZ domain superfamily + 171 + 261 47 - IPR013087
  - 145 - 2772 + IPR036412
HAD-like superfamily + 170 + 257 48 - IPR036638
  - 143 - 1074 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 163 + 370 49 - IPR017930
  - 143 - 536 + IPR036770
Ankyrin repeat-containing domain superfamily + 163 + 241 50 - IPR036412
HAD-like superfamily - 140 - 362 + IPR001584
Integrase, catalytic core + 161 + 237 51 - IPR018247
EF-Hand 1, calcium-binding site - 139 - 495 + IPR036093
NAC domain superfamily + 155 + 171 52 - IPR036388
  - 138 - 468 + IPR003441
NAC domain + 153 + 331 53 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 137 - 166 + IPR036390
Winged helix DNA-binding domain superfamily + 153 + 205 54 - IPR011598
  - 135 - 1854 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 150 + 163 55 - IPR029044
  - 133 - 1076 + IPR002110
Ankyrin repeat + 147 + 663 56 - IPR036390
Winged helix DNA-binding domain superfamily - 132 - 201 + IPR036188
FAD/NAD(P)-binding domain superfamily + 146 + 256 57 - IPR036093
  - 129 - 903 + IPR005162
Retrotransposon gag domain + 144 + 145 58 - IPR003441
  - 128 - 870 + IPR036236
Zinc finger C2H2 superfamily + 144 + 216 59 - IPR023214
  - 126 - 670 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 142 + 185 60 - IPR014001
  - 126 - 866 + IPR001650
Helicase, C-terminal + 141 + 458 61 - IPR036188
  - 124 - 1606 + IPR012340
Nucleic acid-binding, OB-fold + 139 + 307 62 - IPR001650
  - 122 - 1670 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 139 + 236 63 - IPR011333
SKP1/BTB/POZ domain superfamily - 121 - 206 + IPR029044
Nucleotide-diphospho-sugar transferases + 138 + 194 64 - IPR020683
  - 119 - 1350 + IPR002016
Haem peroxidase + 138 + 1026 65 - IPR036770
  - 119 - 992 + IPR010255
Haem peroxidase superfamily + 138 + 182 66 - IPR014729
  - 115 - 512 + IPR013087
Zinc finger C2H2-type + 137 + 278 67 - IPR036236
Zinc finger C2H2 superfamily - 115 - 235 + IPR003439
ABC transporter-like, ATP-binding domain + 134 + 617 68 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 112 - 180 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 128 + 186 69 - IPR002110
  - 112 - 3819 + IPR005174
Domain unknown function DUF295 + 125 + 149 70 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 110 - 133 + IPR000823
Plant peroxidase + 125 + 1090 71 - IPR013026
  - 109 - 789 + IPR036869
Chaperone J-domain superfamily + 125 + 172 72 - IPR021109
  - 106 - 730 + IPR003480
Transferase + 125 + 143 73 - IPR019775
WD40 repeat, conserved site - 105 - 315 + IPR000210
BTB/POZ domain + 122 + 384 74 - IPR036514
  - 105 - 372 + IPR036426
Bulb-type lectin domain superfamily + 120 + 164 75 - IPR036426
  - 105 - 628 + IPR001623
DnaJ domain + 119 + 842 76 - IPR003439
  - 105 - 1737 + IPR033121
Peptidase family A1 domain + 119 + 142 77 - IPR023213
  - 104 - 460 + IPR020683
Ankyrin repeat-containing domain + 116 + 277 78 - IPR036869
  - 104 - 608 + IPR001087
GDSL lipase/esterase + 115 + 149 79 - IPR019734
  - 101 - 4197 + IPR032861
Xylanase inhibitor, N-terminal + 114 + 132 80 - IPR005123
  - 101 - 864 + IPR029071
Ubiquitin-like domain superfamily + 114 + 182 81 - IPR001480
  - 101 - 718 + IPR003959
ATPase, AAA-type, core + 114 + 182 82 - IPR003959
ATPase, AAA-type, core - 101 - 225 + IPR001480
Bulb-type lectin domain + 113 + 418 83 - IPR035595
UDP-glycosyltransferase family, conserved site - 100 - 116 + IPR032799
Xylanase inhibitor, C-terminal + 112 + 124 84 - IPR014710
  - 100 - 424 + IPR011011
Zinc finger, FYVE/PHD-type + 111 + 201 85 - IPR029071
Ubiquitin-like domain superfamily - 98 - 142 + IPR033905
Secretory peroxidase + 110 + 140 86 - IPR012340
Nucleic acid-binding, OB-fold - 97 - 239 + IPR020846
Major facilitator superfamily domain + 110 + 168 87 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 97 - 171 + IPR003657
WRKY domain + 109 + 291 88 - IPR001623
  - 96 - 1692 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 109 + 141 89 - IPR001461
Aspartic peptidase A1 family - 96 - 261 + IPR036576
WRKY domain superfamily + 108 + 148 90 - IPR008972
  - 95 - 944 + IPR025315
Domain of unknown function DUF4220 + 108 + 120 91 - IPR011011
Zinc finger, FYVE/PHD-type - 95 - 190 + IPR019734
Tetratricopeptide repeat + 107 + 368 92 - IPR027443
  - 94 - 296 + IPR008972
Cupredoxin + 107 + 249 93 - IPR013785
  - 93 - 600 + IPR002156
Ribonuclease H domain + 105 + 145 94 - IPR033121
  - 93 - 242 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 104 + 155 95 - IPR036576
  - 92 - 720 + IPR007658
Protein of unknown function DUF594 + 104 + 108 96 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 92 - 190 + IPR015424
Pyridoxal phosphate-dependent transferase + 104 + 151 97 - IPR003657
  - 92 - 1074 + IPR015300
DNA-binding pseudobarrel domain superfamily + 103 + 192 98 - IPR003480
Transferase - 90 - 109 + IPR036457
PPM-type phosphatase domain superfamily + 101 + 146 99 - IPR000210
  - 89 - 1209 + IPR011051
RmlC-like cupin domain superfamily + 101 + 134 100 - IPR032799
Xylanase inhibitor, C-terminal - 89 - 103 + IPR044810
WRKY transcription factor, plant + 101 + 122 101 - IPR012337
Ribonuclease H-like superfamily - 89 - 159 + IPR035892
C2 domain superfamily + 100 + 202 102 - IPR015424
Pyridoxal phosphate-dependent transferase - 89 - 152 + IPR001932
PPM-type phosphatase domain + 99 + 414 103 - IPR005174
Domain unknown function DUF295 - 88 - 116 + IPR035669
GDSL lipase/esterase-like, plant + 98 + 120 104 - IPR005225
Small GTP-binding protein domain - 88 - 155 + IPR000109
Proton-dependent oligopeptide transporter family + 96 + 311 105 - IPR008974
  - 88 - 885 + IPR002347
Short-chain dehydrogenase/reductase SDR + 96 + 920 106 - IPR032861
Xylanase inhibitor, N-terminal - 87 - 105 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 95 + 172 107 - IPR001087
GDSL lipase/esterase - 86 - 141 + IPR011676
Domain of unknown function DUF1618 + 95 + 150 108 - IPR011050
Pectin lyase fold/virulence factor - 85 - 112 + IPR001461
Aspartic peptidase A1 family + 95 + 262 109 - IPR015421
  - 84 - 363 + IPR001356
Homeobox domain + 95 + 310 110 - IPR011676
Domain of unknown function DUF1618 - 84 - 151 + IPR005828
Major facilitator, sugar transporter-like + 94 + 148 111 - IPR015300
  - 84 - 784 + IPR011050
Pectin lyase fold/virulence factor + 94 + 122 112 - IPR012334
  - 84 - 226 + IPR003340
B3 DNA binding domain + 91 + 492 113 - IPR035669
GDSL lipase/esterase-like, plant - 81 - 128 + IPR000858
S-locus glycoprotein domain + 91 + 114 114 - IPR000858
S-locus glycoprotein domain - 81 - 108 + IPR000008
C2 domain + 91 + 405 115 - IPR024171
S-receptor-like serine/threonine-protein kinase - 81 - 120 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 91 + 105 116 - IPR036457
  - 81 - 920 + IPR002083
MATH/TRAF domain + 91 + 357 117 - IPR011051
RmlC-like cupin domain superfamily - 81 - 168 + IPR003609
PAN/Apple domain + 90 + 214 118 - IPR009072
  - 80 - 609 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 90 + 134 119 - IPR003609
  - 79 - 550 + IPR011545
DEAD/DEAH box helicase domain + 90 + 146 120 - IPR004827
  - 78 - 1245 + IPR009072
Histone-fold + 90 + 98 121 - IPR005828
Major facilitator, sugar transporter-like - 77 - 149 + IPR000073
Alpha/beta hydrolase fold-1 + 89 + 255 122 - IPR015422
  - 77 - 510 + IPR032867
DYW domain + 89 + 106 123 - IPR001932
  - 77 - 2184 + IPR007527
Zinc finger, SWIM-type + 88 + 160 124 - IPR036397
  - 76 - 396 + IPR004827
Basic-leucine zipper domain + 88 + 224 125 - IPR001356
  - 76 - 1224 + IPR026960
Reverse transcriptase zinc-binding domain + 85 + 88 126 - IPR003340
  - 75 - 2130 + IPR013766
Thioredoxin domain + 83 + 218 127 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 75 - 114 + IPR020472
G-protein beta WD-40 repeat + 81 + 399 128 - IPR025315
Domain of unknown function DUF4220 - 75 - 84 + IPR018289
MULE transposase domain + 81 + 86 129 - IPR007658
Protein of unknown function DUF594 - 74 - 80 + IPR026992
Non-haem dioxygenase N-terminal domain + 81 + 121 130 - IPR026992
Non-haem dioxygenase N-terminal domain - 74 - 114 + IPR043129
ATPase, nucleotide binding domain + 81 + 217 131 - IPR017871
ABC transporter, conserved site - 74 - 177 + IPR004158
Protein of unknown function DUF247, plant + 80 + 194 132 - IPR011545
DEAD/DEAH box helicase domain - 74 - 133 + IPR000626
Ubiquitin-like domain + 78 + 207 133 - IPR001965
Zinc finger, PHD-type - 74 - 193 + IPR000270
PB1 domain + 78 + 131 134 - IPR000109
Proton-dependent oligopeptide transporter family - 73 - 234 + IPR004242
Transposon, En/Spm-like + 78 + 84 135 - IPR015655
Protein phosphatase 2C family - 73 - 185 + IPR002100
Transcription factor, MADS-box + 77 + 474 136 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 73 - 118 + IPR036879
Transcription factor, MADS-box superfamily + 77 + 107 137 - IPR006447
Myb domain, plants - 72 - 104 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 76 + 81 138 - IPR017907
Zinc finger, RING-type, conserved site - 71 - 121 + IPR026961
PGG domain + 76 + 155 139 - IPR000742
  - 70 - 572 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 76 + 122 140 - IPR032867
DYW domain - 70 - 94 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 76 + 78 141 - IPR000073
Alpha/beta hydrolase fold-1 - 69 - 205 + IPR041588
Integrase zinc-binding domain + 76 + 76 142 - IPR035892
  - 68 - 306 + IPR041373
Reverse transcriptase, RNase H-like domain + 76 + 76 143 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 68 - 81 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 74 + 94 144 - IPR020472
G-protein beta WD-40 repeat - 68 - 347 + IPR002902
Gnk2-homologous domain + 74 + 399 145 - IPR000225
  - 67 - 1818 + IPR036908
RlpA-like domain superfamily + 73 + 83 146 - IPR002347
Short-chain dehydrogenase/reductase SDR - 66 - 849 + IPR024788
Malectin-like domain + 73 + 101 147 - IPR026961
PGG domain - 66 - 139 + IPR006121
Heavy metal-associated domain, HMA + 72 + 239 148 - IPR000270
  - 66 - 678 + IPR044965
Glycoside hydrolase family 17, plant + 72 + 99 149 - IPR010987
  - 65 - 198 + IPR003613
U box domain + 71 + 169 150 - IPR003613
  - 64 - 771 + IPR000571
Zinc finger, CCCH-type + 71 + 320 151 - IPR000626
  - 63 - 588 + IPR004045
Glutathione S-transferase, N-terminal + 70 + 226 152 - IPR006121
  - 63 - 690 + IPR019787
Zinc finger, PHD-finger + 69 + 185 153 - IPR004045
  - 63 - 633 + IPR025452
Domain of unknown function DUF4218 + 69 + 69 154 - IPR000008
  - 62 - 848 + IPR036163
Heavy metal-associated domain superfamily + 69 + 96 155 - IPR002083
  - 62 - 1050 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 69 + 126 156 - IPR000571
  - 62 - 1872 + IPR001220
Legume lectin domain + 68 + 165 157 - IPR003960
ATPase, AAA-type, conserved site - 61 - 127 + IPR006501
Pectinesterase inhibitor domain + 68 + 72 158 - IPR013766
  - 61 - 636 + IPR000490
Glycoside hydrolase family 17 + 68 + 77 159 - IPR013094
Alpha/beta hydrolase fold-3 - 61 - 72 + IPR008949
Isoprenoid synthase domain superfamily + 67 + 95 160 - IPR013783
  - 60 - 218 + IPR026057
PC-Esterase + 67 + 81 161 - IPR002100
  - 60 - 2010 + IPR018108
Mitochondrial substrate/solute carrier + 67 + 539 162 - IPR001881
EGF-like calcium-binding domain - 59 - 142 + IPR013057
Amino acid transporter, transmembrane domain + 67 + 105 163 - IPR036908
  - 59 - 280 + IPR023395
Mitochondrial carrier domain superfamily + 67 + 99 164 - IPR036879
  - 59 - 651 + IPR029962
Trichome birefringence-like family + 66 + 83 165 - IPR026057
PC-Esterase - 58 - 83 + IPR013094
Alpha/beta hydrolase fold-3 + 66 + 77 166 - IPR029962
Trichome birefringence-like family - 58 - 88 + IPR001806
Small GTPase + 66 + 158 167 - IPR035513
  - 58 - 226 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 65 + 73 168 - IPR036163
Heavy metal-associated domain superfamily - 58 - 86 + IPR010987
Glutathione S-transferase, C-terminal-like + 65 + 106 169 - IPR004158
Protein of unknown function DUF247, plant - 58 - 92 + IPR007117
Expansin, cellulose-binding-like domain + 65 + 142 170 - IPR018097
EGF-like calcium-binding, conserved site - 58 - 85 + IPR016039
Thiolase-like + 64 + 142 171 - IPR000490
Glycoside hydrolase family 17 - 57 - 114 + IPR025846
PMR5 N-terminal domain + 64 + 76 172 - IPR016039
  - 56 - 657 + IPR016159
Cullin repeat-like-containing domain superfamily + 64 + 86 173 - IPR038408
  - 56 - 422 + IPR016197
Chromo-like domain superfamily + 63 + 87 174 - IPR002902
  - 56 - 842 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 62 + 74 175 - IPR013057
Amino acid transporter, transmembrane domain - 56 - 90 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 62 + 70 176 - IPR003245
  - 56 - 540 + IPR020568
Ribosomal protein S5 domain 2-type fold + 62 + 117 177 - IPR036961
  - 56 - 585 + IPR029052
Metallo-dependent phosphatase-like + 62 + 97 178 - IPR008949
  - 55 - 522 + IPR007112
Expansin/pollen allergen, DPBB domain + 61 + 69 179 - IPR019787
  - 55 - 314 + IPR000668
Peptidase C1A, papain C-terminal + 61 + 231 180 - IPR001806
Small GTPase superfamily - 55 - 111 + IPR036852
Peptidase S8/S53 domain superfamily + 61 + 86 181 - IPR016135
  - 54 - 348 + IPR036915
Cyclin-like superfamily + 61 + 147 182 - IPR025846
PMR5 N-terminal domain - 54 - 73 + IPR000048
IQ motif, EF-hand binding site + 61 + 382 183 - IPR015915
  - 54 - 669 + IPR003245
Phytocyanin domain + 60 + 131 184 - IPR000048
  - 54 - 1647 + IPR002528
Multi antimicrobial extrusion protein + 60 + 165 185 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 53 - 109 + IPR006045
Cupin 1 + 60 + 92 186 - IPR008979
  - 53 - 468 + IPR000209
Peptidase S8/S53 domain + 60 + 82 187 - IPR020568
Ribosomal protein S5 domain 2-type fold - 53 - 127 + IPR011032
GroES-like superfamily + 59 + 112 188 - IPR036749
  - 52 - 244 + IPR045051
Subtilisin-like protease + 59 + 95 189 - IPR019786
Zinc finger, PHD-type, conserved site - 52 - 93 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 59 + 66 190 - IPR007117
  - 52 - 236 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 59 + 75 191 - IPR006501
Pectinesterase inhibitor domain - 51 - 136 + IPR008979
Galactose-binding-like domain superfamily + 59 + 119 192 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 51 - 140 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 58 + 76 193 - IPR007112
  - 50 - 218 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 58 + 72 194 - IPR036852
  - 50 - 933 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 58 + 126 195 - IPR029052
  - 50 - 224 + IPR005202
Transcription factor GRAS + 58 + 227 196 - IPR011993
  - 50 - 236 + IPR030184
WAT1-related protein + 58 + 101 197 - IPR002921
Fungal lipase-like domain - 49 - 68 + IPR003663
Sugar/inositol transporter + 58 + 362 198 - IPR008978
  - 49 - 200 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 57 + 92 199 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 49 - 55 + IPR007118
Expansin/Lol pI + 57 + 337 200 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 49 - 55 + IPR039391
Phytocyanin + 57 + 63 201 - IPR005829
Sugar transporter, conserved site - 49 - 121 + IPR031052
FHY3/FAR1 family + 57 + 114 202 - IPR016159
Cullin repeat-like-containing domain superfamily - 49 - 91 + IPR001752
Kinesin motor domain + 56 + 509 203 - IPR001878
  - 49 - 1218 + IPR000225
Armadillo + 56 + 251 204 - IPR000209
Peptidase S8/S53 domain - 49 - 75 + IPR025312
Domain of unknown function DUF4216 + 55 + 55 205 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 48 - 61 + IPR029480
Transposase-associated domain + 55 + 55 206 - IPR018108
  - 48 - 774 + IPR022059
Protein of unknown function DUF3615 + 55 + 94 207 - IPR018253
DnaJ domain, conserved site - 48 - 67 + IPR015915
Kelch-type beta propeller + 55 + 85 208 - IPR006045
Cupin 1 - 48 - 168 + IPR025724
GAG-pre-integrase domain + 55 + 57 209 - IPR023395
  - 48 - 346 + IPR015500
Peptidase S8, subtilisin-related + 55 + 189 210 - IPR034090
BPM, C-terminal - 48 - 82 + IPR003676
Small auxin-up RNA + 55 + 87 211 - IPR024788
Malectin-like carbohydrate-binding domain - 48 - 97 + IPR004330
FAR1 DNA binding domain + 55 + 73 212 - IPR011032
GroES-like superfamily - 47 - 107 + IPR016181
Acyl-CoA N-acyltransferase + 54 + 76 213 - IPR016181
Acyl-CoA N-acyltransferase - 47 - 86 + IPR013525
ABC-2 type transporter + 54 + 133 214 - IPR007118
Expansin/Lol pI - 47 - 285 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 54 + 147 215 - IPR017451
F-box associated interaction domain - 47 - 61 + IPR011527
ABC transporter type 1, transmembrane domain + 54 + 291 216 - IPR012946
X8 domain - 47 - 145 + IPR002921
Fungal lipase-like domain + 53 + 71 217 - IPR027640
Kinesin-like protein - 47 - 176 + IPR034161
Pepsin-like domain, plant + 53 + 54 218 - IPR002528
Multi antimicrobial extrusion protein - 47 - 244 + IPR023298
P-type ATPase, transmembrane domain superfamily + 53 + 82 219 - IPR037045
  - 47 - 120 + IPR000620
EamA domain + 53 + 128 220 - IPR000608
  - 46 - 338 + IPR044808
Ethylene-responsive transcription factor + 53 + 61 221 - IPR014014
  - 46 - 154 + IPR036465
von Willebrand factor A-like domain superfamily + 52 + 78 222 - IPR004265
Dirigent protein - 46 - 50 + IPR009003
Peptidase S1, PA clan + 52 + 112 223 - IPR036915
Cyclin-like superfamily - 46 - 140 + IPR008978
HSP20-like chaperone + 51 + 55 224 - IPR001752
  - 46 - 2280 + IPR017884
SANT domain + 50 + 79 225 - IPR003663
Sugar/inositol transporter - 46 - 366 + IPR008250
P-type ATPase, A domain superfamily + 50 + 78 226 - IPR013128
Peptidase C1A - 45 - 76 + IPR000742
EGF-like domain + 50 + 58 227 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 45 - 561 + IPR006566
FBD domain + 50 + 68 228 - IPR022059
Protein of unknown function DUF3615 - 45 - 84 + IPR001509
NAD-dependent epimerase/dehydratase + 49 + 80 229 - IPR015500
Peptidase S8, subtilisin-related - 45 - 186 + IPR005630
Terpene synthase, metal-binding domain + 49 + 59 230 - IPR008250
P-type ATPase, A domain superfamily - 44 - 114 + IPR013763
Cyclin-like + 49 + 102 231 - IPR001220
Legume lectin domain - 44 - 95 + IPR034197
Cucumisin-like catalytic domain + 49 + 64 232 - IPR006566
FBD domain - 44 - 89 + IPR004853
Sugar phosphate transporter domain + 48 + 72 233 - IPR003676
Small auxin-up RNA - 44 - 79 + IPR004332
Transposase, MuDR, plant + 48 + 48 234 - IPR023393
  - 43 - 184 + IPR012946
X8 domain + 48 + 65 235 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 43 - 66 + IPR006016
UspA + 47 + 59 236 - IPR023299
  - 43 - 537 + IPR025659
Tubby-like, C-terminal + 47 + 63 237 - IPR036875
Zinc finger, CCHC-type superfamily - 43 - 95 + IPR009060
UBA-like superfamily + 47 + 71 238 - IPR036640
  - 42 - 882 + IPR000608
Ubiquitin-conjugating enzyme E2 + 47 + 164 239 - IPR036691
  - 42 - 378 + IPR011701
Major facilitator superfamily + 47 + 87 240 - IPR000873
AMP-dependent synthetase/ligase - 42 - 83 + IPR004265
Dirigent protein + 47 + 57 241 - IPR034161
Pepsin-like domain, plant - 42 - 44 + IPR008928
Six-hairpin glycosidase superfamily + 47 + 68 242 - IPR011527
  - 42 - 912 + IPR039417
Papain-like cysteine endopeptidase + 47 + 56 243 - IPR000668
Peptidase C1A, papain C-terminal - 42 - 203 + IPR045087
Multicopper oxidase + 47 + 69 244 - IPR023298
P-type ATPase, transmembrane domain superfamily - 42 - 254 + IPR033389
AUX/IAA domain + 46 + 68 245 IPR001563
Peptidase S10, serine carboxypeptidase - 41 - 515 + 46 + 434 246 - IPR006016
UspA - 41 - 56 + IPR004263
Exostosin-like + 46 + 69 247 - IPR013525
ABC-2 type transporter - 41 - 107 + IPR004140
Exocyst complex component Exo70 + 46 + 124 248 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 41 - 103 + IPR011012
Longin-like domain superfamily + 46 + 75 249 - IPR011006
CheY-like superfamily - 41 - 69 + IPR007125
Histone H2A/H2B/H3 + 46 + 47 250 - IPR005202
  - 41 - 216 + IPR001906
Terpene synthase, N-terminal domain + 46 + 58 251 - IPR036855
Zinc finger, CCCH-type superfamily - 41 - 151 + IPR041569
AAA ATPase, AAA+ lid domain + 46 + 65 252 - IPR000182
  - 40 - 198 + IPR044730
Ribonuclease H-like domain, plant type + 46 + 46 253 - IPR029055
  - 40 - 252 + IPR001214
SET domain + 46 + 148 254 - IPR000222
PPM-type phosphatase, divalent cation binding - 40 - 84 + IPR000182
GNAT domain + 45 + 107 255 - IPR034197
Cucumisin-like catalytic domain - 40 - 55 + IPR000873
AMP-dependent synthetase/ligase + 45 + 65 256 - IPR008928
Six-hairpin glycosidase superfamily - 40 - 71 + IPR029055
Nucleophile aminohydrolases, N-terminal + 45 + 69 257 - IPR018303
P-type ATPase, phosphorylation site - 40 - 83 + IPR014014
RNA helicase, DEAD-box type, Q motif + 45 + 60 258 - IPR001757
P-type ATPase - 40 - 286 + IPR011006
CheY-like superfamily + 45 + 64 259 - IPR030184
WAT1-related protein - 40 - 85 + IPR001789
Signal transduction response regulator, receiver domain + 45 + 122 260 - IPR002109
  - 40 - 252 + IPR043926
ABC transporter family G domain + 44 + 86 261 - IPR001789
  - 40 - 744 + IPR036318
FAD-binding, type PCMH-like superfamily + 44 + 59 262 - IPR033896
MADS MEF2-like - 39 - 80 + IPR019557
Aminotransferase-like, plant mobile domain + 44 + 56 263 - IPR036318
FAD-binding, type 2-like superfamily - 39 - 56 + IPR009000
Translation protein, beta-barrel domain superfamily + 44 + 66 264 - IPR001509
NAD-dependent epimerase/dehydratase - 39 - 80 + IPR036855
Zinc finger, CCCH-type superfamily + 44 + 121 265 - IPR036890
  - 39 - 314 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 44 + 58 266 - IPR004046
Glutathione S-transferase, C-terminal - 39 - 54 + IPR008942
ENTH/VHS + 43 + 58 267 - IPR036465
  - 39 - 246 + IPR033896
MADS MEF2-like + 43 + 69 268 - IPR000644
  - 39 - 742 + IPR007493
Protein of unknown function DUF538 + 43 + 101 269 - IPR001214
  - 39 - 555 + IPR041577
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain + 43 + 43 270 - IPR012341
  - 39 - 204 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 43 + 158 271 - IPR001938
  - 38 - 608 + IPR036758
At5g01610-like superfamily + 43 + 50 272 - IPR013763
Cyclin-like - 38 - 195 + IPR014756
Immunoglobulin E-set + 43 + 65 273 - IPR011012
Longin-like domain superfamily - 38 - 80 + IPR011707
Multicopper oxidase, N-termianl + 43 + 59 274 - IPR020845
AMP-binding, conserved site - 38 - 68 + IPR001117
Multicopper oxidase, type 1 + 42 + 57 275 - IPR014756
Immunoglobulin E-set - 38 - 61 + IPR000330
SNF2, N-terminal + 42 + 72 276 - IPR000620
EamA domain - 38 - 111 + IPR011706
Multicopper oxidase, C-terminal + 42 + 59 277 - IPR017877
  - 38 - 136 + IPR000070
Pectinesterase, catalytic + 42 + 50 278 - IPR025322
Protein of unknown function DUF4228, plant - 37 - 38 + IPR008889
VQ + 42 + 43 279 - IPR002068
  - 37 - 148 + IPR037176
Osmotin/thaumatin-like superfamily + 42 + 45 280 - IPR001969
Aspartic peptidase, active site - 37 - 63 + IPR006702
Casparian strip membrane protein domain + 42 + 48 281 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 37 - 51 + IPR002068
Alpha crystallin/Hsp20 domain + 41 + 89 282 - IPR017970
Homeobox, conserved site - 37 - 48 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 41 + 68 283 - IPR000070
Pectinesterase, catalytic - 37 - 43 + IPR029045
ClpP/crotonase-like domain superfamily + 41 + 66 284 - IPR011707
Multicopper oxidase, type 3 - 37 - 51 + IPR006671
Cyclin, N-terminal + 41 + 63 285 - IPR000743
Glycoside hydrolase, family 28 - 37 - 77 + IPR004314
Neprosin + 41 + 50 286 - IPR033389
AUX/IAA domain - 36 - 85 + IPR015947
PUA-like superfamily + 41 + 63 287 - IPR025659
  - 36 - 176 + IPR013149
Alcohol dehydrogenase, C-terminal + 40 + 60 288 - IPR004853
Sugar phosphate transporter domain - 36 - 56 + IPR029021
Protein-tyrosine phosphatase-like + 40 + 76 289 - IPR009000
Translation protein, beta-barrel domain superfamily - 36 - 68 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 40 + 40 290 - IPR005630
Terpene synthase, metal-binding domain - 36 - 69 + IPR036612
K Homology domain, type 1 superfamily + 40 + 124 291 - IPR016166
  - 36 - 153 + IPR003137
PA domain + 40 + 60 292 - IPR002016
  - 36 - 786 + IPR023271
Aquaporin-like + 40 + 46 293 - IPR010255
Haem peroxidase - 36 - 50 + IPR001938
Thaumatin family + 40 + 268 294 - IPR011042
  - 36 - 146 + IPR004839
Aminotransferase, class I/classII + 40 + 57 295 - IPR001117
Multicopper oxidase, type 1 - 35 - 49 + IPR015655
Protein phosphatase 2C family + 40 + 59 296 - IPR008942
  - 35 - 230 + IPR000425
Major intrinsic protein + 40 + 307 297 - IPR006626
Parallel beta-helix repeat - 35 - 256 + IPR000644
CBS domain + 40 + 194 298 - IPR029021
  - 35 - 312 + IPR002109
Glutaredoxin + 40 + 43 299 - IPR000330
SNF2-related, N-terminal domain - 35 - 67 + IPR036041
Ribosome-inactivating protein superfamily + 40 + 40 300 - IPR003137
PA domain - 35 - 53 + IPR002487
Transcription factor, K-box + 40 + 121 301 - IPR036965
  - 34 - 210 + IPR000743
Glycoside hydrolase, family 28 + 40 + 59 302 - IPR011706
Multicopper oxidase, type 2 - 34 - 54 + IPR010402
CCT domain + 39 + 104 303 - IPR038718
  - 34 - 156 + IPR016166
FAD-binding domain, PCMH-type + 39 + 52 304 - IPR001906
Terpene synthase, N-terminal domain - 34 - 64 + IPR016040
NAD(P)-binding domain + 38 + 51 305 - IPR014721
  - 34 - 172 + IPR016461
O-methyltransferase COMT-type + 38 + 84 306 - IPR007493
Protein of unknown function DUF538 - 33 - 92 + IPR001360
Glycoside hydrolase family 1 + 38 + 565 307 - IPR009060
UBA-like superfamily - 33 - 62 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 38 + 64 308 - IPR003594
Histidine kinase/HSP90-like ATPase - 33 - 148 + IPR013154
Alcohol dehydrogenase, N-terminal + 38 + 57 309 - IPR000863
Sulfotransferase domain - 33 - 46 + IPR025322
Protein of unknown function DUF4228, plant + 37 + 40 310 - IPR004839
Aminotransferase, class I/classII - 33 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 37 52 311 - IPR036758
  - 33 - 188 + IPR034294
Aquaporin transporter + 37 + 45 312 - IPR009003
Peptidase S1, PA clan - 33 - 106 + IPR004883
Lateral organ boundaries, LOB + 37 + 79 313 - IPR002487
  - 33 - 411 + IPR002067
Mitochondrial carrier protein + 37 + 229 314 - IPR036612
  - 32 - 678 + IPR011043
Galactose oxidase/kelch, beta-propeller + 37 + 45 315 - IPR004140
Exocyst complex component Exo70 - 32 - 88 + IPR008991
Translation protein SH3-like domain superfamily + 36 + 47 316 - IPR013154
Alcohol dehydrogenase, N-terminal - 32 - 57 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 36 + 51 317 - IPR007125
Histone H2A/H2B/H3 - 32 - 34 + IPR001077
O-methyltransferase domain + 36 + 40 318 - IPR006671
Cyclin, N-terminal - 32 - 72 + IPR004046
Glutathione S-transferase, C-terminal + 36 + 51 319 - IPR028889
  - 32 - 160 + IPR033443
Pentacotripeptide-repeat region of PRORP + 36 + 52 320 - IPR002912
  - 32 - 380 + IPR040911
Exostosin, GT47 domain + 36 + 56 321 - IPR002423
Chaperonin Cpn60/TCP-1 family - 31 - 62 + IPR028889
Ubiquitin specific protease domain + 36 + 55 322 - IPR002963
Expansin - 31 - 259 + IPR013126
Heat shock protein 70 family + 36 + 84 323 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 31 - 91 + IPR039361
Cyclin + 36 + 59 324 - IPR019378
GDP-fucose protein O-fucosyltransferase - 31 - 55 + IPR001251
CRAL-TRIO lipid binding domain + 35 + 138 325 - IPR002495
Glycosyl transferase, family 8 - 31 - 56 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 35 + 48 326 - IPR006094
FAD linked oxidase, N-terminal - 31 - 41 + IPR035940
CAP superfamily + 35 + 37 327 - IPR011043
Galactose oxidase/kelch, beta-propeller - 31 - 51 + IPR043454
NPH3/RPT2-like family + 35 + 44 328 - IPR015947
PUA-like superfamily - 31 - 58 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 35 + 56 329 - IPR037176
  - 31 - 142 + IPR002495
Glycosyl transferase, family 8 + 35 + 50 330 - IPR006702
Casparian strip membrane protein domain - 31 - 35 + IPR006094
FAD linked oxidase, N-terminal + 35 + 42 331 - IPR010402
  - 30 - 210 + IPR004041
NAF domain + 34 + 40 332 - IPR004263
Exostosin-like - 30 - 52 + IPR001929
Germin + 34 + 119 333 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 30 - 308 + IPR032710
NTF2-like domain superfamily + 34 + 46 334 - IPR027409
  - 30 - 178 + IPR018451
NAF/FISL domain + 34 + 40 335 - IPR029045
ClpP/crotonase-like domain superfamily - 30 - 79 + IPR038933
Ovate protein family + 34 + 36 336 - IPR031107
Small heat shock protein HSP20 - 30 - 39 + IPR002659
Glycosyl transferase, family 31 + 34 + 125 337 - IPR013780
  - 30 - 152 + IPR022742
Serine aminopeptidase, S33 + 34 + 46 338 - IPR006458
  - 30 - 166 + IPR000863
Sulfotransferase domain + 34 + 42 339 - IPR008889
VQ - 30 - 32 + IPR001283
Cysteine-rich secretory protein-related + 34 + 154 340 - IPR011701
Major facilitator superfamily - 29 - 87 + IPR014044
CAP domain + 34 + 36 341 - IPR000315
  - 29 - 534 + IPR019378
GDP-fucose protein O-fucosyltransferase + 34 + 57 342 - IPR000717
  - 29 - 224 + IPR006458
Ovate protein family, C-terminal + 34 + 66 343 - IPR038933
Ovate protein family - 29 - 33 + IPR006073
GTP binding domain + 34 + 141 344 - IPR005135
Endonuclease/exonuclease/phosphatase - 29 - 45 + IPR001574
Ribosome-inactivating protein + 34 + 62 345 - IPR023271
  - 29 - 176 + IPR005135
Endonuclease/exonuclease/phosphatase + 33 + 50 346 - IPR031112
AP2-like ethylene-responsive transcription factor - 29 - 60 + IPR043519
Nucleotidyltransferase superfamily + 33 + 54 347 - IPR038538
  - 29 - 118 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 33 + 70 348 - IPR019793
Peroxidases heam-ligand binding site - 29 - 40 + IPR002912
ACT domain + 33 + 109 349 - IPR000425
Major intrinsic protein - 29 - 291 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 32 + 133 350 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 29 - 63 + IPR015940
Ubiquitin-associated domain + 32 + 90 351 - IPR036041
Ribosome-inactivating protein superfamily - 29 - 34 + IPR018490
Cyclic nucleotide-binding-like + 32 + 43 352 - IPR036812
  - 29 - 196 + IPR001296
Glycosyl transferase, family 1 + 32 + 51 353 - IPR016040
NAD(P)-binding domain - 28 - 59 + IPR002423
Chaperonin Cpn60/TCP-1 family + 32 + 51 354 - IPR001929
Germin - 28 - 109 + IPR027356
NPH3 domain + 32 + 71 355 - IPR013149
Alcohol dehydrogenase, C-terminal - 28 - 48 + IPR004088
K Homology domain, type 1 + 32 + 107 356 - IPR018200
Ubiquitin specific protease, conserved site - 28 - 111 + IPR003311
AUX/IAA protein + 32 + 47 357 - IPR010920
LSM domain superfamily - 28 - 41 + IPR000595
Cyclic nucleotide-binding domain + 32 + 115 358 - IPR005299
SAM dependent carboxyl methyltransferase - 28 - 97 + IPR006153
Cation/H+ exchanger + 31 + 46 359 - IPR011016
  - 28 - 306 + IPR029061
Thiamin diphosphate-binding fold + 31 + 81 360 - IPR002659
Glycosyl transferase, family 31 - 28 - 145 + IPR000795
Translational (tr)-type GTP-binding domain + 31 + 280 361 - IPR001296
Glycosyl transferase, family 1 - 28 - 51 + IPR004367
Cyclin, C-terminal domain + 31 + 42 362 - IPR034294
Aquaporin transporter - 28 - 39 + IPR006652
Kelch repeat type 1 + 31 + 84 363 - IPR002123
Phospholipid/glycerol acyltransferase - 28 - 89 + IPR003406
Glycosyl transferase, family 14 + 31 + 34 364 - IPR006652
Kelch repeat type 1 - 28 - 243 + IPR002963
Expansin + 31 + 256 365 - IPR004314
Neprosin - 28 - 40 + IPR027409
GroEL-like apical domain superfamily + 31 + 49 366 - IPR025661
Cysteine peptidase, asparagine active site - 28 - 34 + IPR027923
Hydrophobic seed protein domain + 31 + 69 367 - IPR023210
NADP-dependent oxidoreductase domain - 28 - 93 + IPR023299
P-type ATPase, cytoplasmic domain N + 31 + 55 368 - IPR004041
NAF domain - 27 - 41 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 31 + 52 369 - IPR001179
  - 27 - 218 + IPR024752
Myb/SANT-like domain + 31 + 32 370 - IPR018451
  - 27 - 123 + IPR007612
LURP-one-related + 30 + 79 371 - IPR008991
Translation protein SH3-like domain superfamily - 27 - 40 + IPR029000
Cyclophilin-like domain superfamily + 30 + 44 372 - IPR036865
  - 27 - 176 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 30 + 147 373 - IPR038770
  - 27 - 82 + IPR005299
SAM dependent carboxyl methyltransferase + 30 + 106 374 - IPR003653
  - 27 - 321 + IPR000315
B-box-type zinc finger + 30 + 77 375 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 27 - 38 + IPR000717
Proteasome component (PCI) domain + 30 + 63 376 - IPR019794
Peroxidase, active site - 27 - 34 + IPR001594
Palmitoyltransferase, DHHC domain + 30 + 56 377 - IPR004088
K Homology domain, type 1 - 27 - 108 + IPR002123
Phospholipid/glycerol acyltransferase + 30 + 34 378 - IPR004087
K Homology domain - 27 - 115 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 30 + 34 379 - IPR002067
Mitochondrial carrier protein - 27 - 170 + IPR003851
Zinc finger, Dof-type + 30 + 60 380 - IPR003851
  - 27 - 378 + IPR003855
Potassium transporter + 30 + 94 381 - IPR020843
Polyketide synthase, enoylreductase domain - 27 - 34 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 30 + 51 382 - IPR018490
Cyclic nucleotide-binding-like - 26 - 49 + IPR002913
START domain + 30 + 78 383 - IPR032710
NTF2-like domain superfamily - 26 - 36 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 29 + 250 384 - IPR016461
  - 26 - 147 + IPR024709
Putative O-fucosyltransferase, plant + 29 + 51 385 - IPR001360
Glycoside hydrolase family 1 - 26 - 495 + IPR010920
LSM domain superfamily + 29 + 45 386 - IPR029000
  - 26 - 184 + IPR013216
Methyltransferase type 11 + 29 + 45 387 - IPR019821
Kinesin motor domain, conserved site - 26 - 65 + IPR005333
Transcription factor, TCP + 29 + 35 388 - IPR001251
  - 26 - 288 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 29 + 34 389 - IPR029061
Thiamin diphosphate-binding fold - 26 - 64 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 43 390 - IPR027725
Heat shock transcription factor family - 26 - 39 + IPR044814
Terpene cyclases, class 1, plant + 29 + 32 391 - IPR035940
  - 26 - 112 + IPR005150
Cellulose synthase + 29 + 59 392 - IPR000795
  - 26 - 744 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 29 + 40 393 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 26 - 90 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 394 - IPR004883
  - 26 - 126 + IPR002035
von Willebrand factor, type A + 29 + 70 395 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 26 - 129 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 29 + 33 396 - IPR008480
Protein of unknown function DUF761, plant - 26 - 26 + IPR011141
Polyketide synthase, type III + 29 + 35 397 - IPR027923
Hydrophobic seed protein - 26 - 55 + IPR012967
Plant methyltransferase dimerisation + 29 + 30 398 - IPR014044
CAP domain - 26 - 56 + IPR000757
Glycoside hydrolase family 16 + 29 + 68 399 - IPR014722
  - 26 - 102 + IPR001099
Chalcone/stilbene synthase, N-terminal + 29 + 35 400 - IPR022357
Major intrinsic protein, conserved site - 26 - 36 + IPR025110
AMP-binding enzyme, C-terminal domain + 28 + 39 401 - IPR013126
Heat shock protein 70 family - 26 - 276 + IPR017938
Riboflavin synthase-like beta-barrel + 28 + 38 402 - IPR000595
  - 26 - 348 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 28 + 111 403 - IPR025660
Cysteine peptidase, histidine active site - 26 - 35 + IPR027806
Harbinger transposase-derived nuclease domain + 28 + 29 404 - IPR001574
Ribosome-inactivating protein - 26 - 29 + IPR021790
PTBP1, RNA recognition motif 2-like + 28 + 37 405 - IPR010525
Auxin response factor - 26 - 57 + IPR044835
Auxin response factor + 28 + 48 406 - IPR013601
FAE1/Type III polyketide synthase-like protein - 25 - 25 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 28 + 35 407 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 25 - 50 + IPR007657
Glycosyltransferase 61 + 28 + 94 408 - IPR002130
  - 25 - 606 + IPR044848
PHR1-like + 28 + 41 409 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 25 - 89 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 28 + 41 410 - IPR023753
FAD/NAD(P)-binding domain - 25 - 43 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 28 + 37 411 - IPR007657
Glycosyltransferase 61 - 25 - 75 + IPR005821
Ion transport domain + 28 + 41 412 - IPR004320
Protein of unknown function DUF241, plant - 25 - 49 + IPR001757
P-type ATPase + 28 + 121 413 - IPR011013
Galactose mutarotase-like domain superfamily - 25 - 42 + IPR012328
Chalcone/stilbene synthase, C-terminal + 28 + 31 414 - IPR005150
Cellulose synthase - 25 - 81 + IPR044791
Beta-glucanase/XTH + 28 + 34 415 - IPR020946
Flavin monooxygenase-like - 25 - 51 + IPR036034
PDZ superfamily + 28 + 50 416 - IPR000169
Cysteine peptidase, cysteine active site - 25 - 29 + IPR023210
NADP-dependent oxidoreductase domain + 28 + 53 417 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 25 - 54 + IPR000679
Zinc finger, GATA-type + 28 + 96 418 - IPR001701
Glycoside hydrolase family 9 - 25 - 30 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 27 + 36 419 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 25 - 178 + IPR013601
FAE1/Type III polyketide synthase-like protein + 27 + 28 420 - IPR003855
Potassium transporter - 25 - 136 + IPR036378
FAS1 domain superfamily + 27 + 44 421 - IPR027410
  - 25 - 224 + IPR023753
FAD/NAD(P)-binding domain + 27 + 38 422 - IPR000727
  - 24 - 182 + IPR027725
Heat shock transcription factor family + 27 + 38 423 - IPR017938
Riboflavin synthase-like beta-barrel - 24 - 45 + IPR004320
Protein of unknown function DUF241, plant + 27 + 39 424 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 24 - 25 + IPR001763
Rhodanese-like domain + 27 + 69 425 - IPR003954
RNA recognition motif domain, eukaryote - 24 - 77 + IPR000408
Regulator of chromosome condensation, RCC1 + 27 + 604 426 - IPR007650
  - 24 - 140 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 37 427 - IPR027356
  - 24 - 122 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 27 + 52 428 - IPR033131
Pectinesterase, Asp active site - 24 - 27 + IPR001701
Glycoside hydrolase family 9 + 27 + 39 429 - IPR004367
Cyclin, C-terminal domain - 24 - 74 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 27 + 29 430 - IPR002355
Multicopper oxidase, copper-binding site - 24 - 34 + IPR015797
NUDIX hydrolase-like domain superfamily + 27 + 38 431 - IPR008266
Tyrosine-protein kinase, active site - 24 - 46 + IPR000727
Target SNARE coiled-coil homology domain + 26 + 62 432 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 24 - 71 + IPR008971
HSP40/DnaJ peptide-binding + 26 + 58 433 - IPR016167
  - 24 - 126 + IPR025525
hAT-like transposase, RNase-H fold + 26 + 31 434 - IPR001077
O-methyltransferase, family 2 - 24 - 30 + IPR004316
SWEET sugar transporter + 26 + 65 435 - IPR019780
Germin, manganese binding site - 24 - 40 + IPR011016
Zinc finger, RING-CH-type + 26 + 106 436 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 24 - 25 + IPR008906
HAT, C-terminal dimerisation domain + 26 + 30 437 - IPR025486
Domain of unknown function DUF4378 - 24 - 43 + IPR027413
GroEL-like equatorial domain superfamily + 26 + 38 438 - IPR009091
  - 24 - 330 + IPR016897
S-phase kinase-associated protein 1 + 26 + 32 439 - IPR018202
Serine carboxypeptidase, serine active site - 24 - 39 + IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily + 26 + 32 440 - IPR000757
  - 24 - 159 + IPR004813
Oligopeptide transporter, OPT superfamily + 26 + 48 441 - IPR002913
  - 24 - 381 + IPR001849
Pleckstrin homology domain + 26 + 74 442 - IPR017884
  - 23 - 86 + IPR039421
Type 1 protein exporter + 26 + 51 443 - IPR025110
AMP-binding enzyme, C-terminal domain - 23 - 39 + IPR029069
HotDog domain superfamily + 26 + 41 444 - IPR015940
  - 23 - 182 + IPR029062
Class I glutamine amidotransferase-like + 26 + 59 445 - IPR018244
Allergen V5/Tpx-1-related, conserved site - 23 - 39 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 26 + 43 446 - IPR006153
Cation/H+ exchanger - 23 - 32 + IPR002939
Chaperone DnaJ, C-terminal + 26 + 31 447 - IPR004162
E3 ubiquitin-protein ligase SIN-like - 23 - 30 + IPR036296
SKP1-like, dimerisation domain superfamily + 26 + 31 448 - IPR008422
Homeobox KN domain - 23 - 36 + IPR036404
Jacalin-like lectin domain superfamily + 26 + 47 449 - IPR027413
  - 23 - 270 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 26 + 124 450 - IPR000960
Flavin monooxygenase FMO - 23 - 61 + IPR006311
Twin-arginine translocation pathway, signal sequence + 26 + 30 451 - IPR003406
Glycosyl transferase, family 14 - 23 - 30 + IPR005175
PPC domain + 26 + 83 452 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 23 - 51 + IPR001229
Jacalin-like lectin domain + 26 + 92 453 - IPR017937
Thioredoxin, conserved site - 23 - 55 + IPR036085
PAZ domain superfamily + 25 + 59 454 - IPR036404
  - 23 - 144 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 31 455 - IPR016138
  - 23 - 52 + IPR036420
BRCT domain superfamily + 25 + 68 456 - IPR036034
PDZ superfamily - 23 + IPR017887
Transcription factor TCP subgroup + 25 54 457 - IPR000823
Plant peroxidase - 23 - 199 + IPR007650
Zf-FLZ domain + 25 + 68 458 - IPR000679
  - 23 - 309 + IPR045048
F-box only protein 31/39 + 25 + 58 459 - IPR005175
  - 23 - 168 + IPR003100
PAZ domain + 24 + 114 460 - IPR017927
  - 22 - 114 + IPR009606
Modifying wall lignin-1/2 + 24 + 29 461 - IPR036085
PAZ domain superfamily - 22 - 56 + IPR000782
FAS1 domain + 24 + 72 462 - IPR008971
HSP40/DnaJ peptide-binding - 22 - 76 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 24 + 26 463 - IPR002867
IBR domain - 22 - 151 + IPR003106
Leucine zipper, homeobox-associated + 24 + 25 464 - IPR007612
LURP-one-related - 22 - 54 + IPR002867
IBR domain + 24 + 63 465 - IPR024709
Putative O-fucosyltransferase, plant - 22 - 69 + IPR025753
AAA-type ATPase, N-terminal domain + 24 + 28 466 - IPR013088
  - 22 - 78 + IPR008422
Homeobox KN domain + 24 + 40 467 - IPR001163
LSM domain, eukaryotic/archaea-type - 22 - 60 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 24 + 29 468 - IPR013216
Methyltransferase type 11 - 22 - 28 + IPR003656
Zinc finger, BED-type + 24 + 49 469 - IPR034111
Pathogenesis-related protein 1-like, SCP domain - 22 - 22 + IPR025422
Transcription factor TGA like domain + 24 + 78 470 - IPR001594
Palmitoyltransferase, DHHC domain - 22 - 46 + IPR011332
Zinc-binding ribosomal protein + 24 + 29 471 - IPR005333
Transcription factor, TCP - 22 - 24 + IPR016072
SKP1 component, dimerisation + 24 + 29 472 - IPR017887
  - 22 - 48 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 24 + 31 473 - IPR014977
  - 22 - 104 + IPR020946
Flavin monooxygenase-like + 24 + 44 474 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 22 - 31 + IPR025486
Domain of unknown function DUF4378 + 24 + 40 475 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 22 - 33 + IPR000086
NUDIX hydrolase domain + 24 + 67 476 - IPR005821
Ion transport domain - 22 - 34 + IPR031127
E3 ubiquitin ligase RBR family + 24 + 48 477 - IPR005746
Thioredoxin - 22 - 50 + IPR013809
ENTH domain + 24 + 39 478 - IPR002035
  - 22 - 160 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 24 + 36 479 - IPR001849
  - 22 - 272 + IPR010525
Auxin response factor domain + 24 + 34 480 - IPR029062
  - 22 - 184 + IPR006594
LIS1 homology motif + 23 + 59 481 - IPR002939
Chaperone DnaJ, C-terminal - 22 - 33 + IPR013187
F-box associated domain, type 3 + 23 + 26 482 - IPR029006
  - 22 - 296 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 23 + 24 483 - IPR012967
Plant methyltransferase dimerisation - 22 - 26 + IPR001440
Tetratricopeptide repeat 1 + 23 + 36 484 - IPR001229
  - 22 - 192 + IPR001357
BRCT domain + 23 + 116 485 - IPR000528
Plant lipid transfer protein/Par allergen - 21 - 108 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 35 486 - IPR006689
Small GTPase superfamily, ARF/SAR type - 21 - 174 + IPR001881
EGF-like calcium-binding domain + 23 + 31 487 - IPR009606
Protein of unknown function DUF1218 - 21 + IPR003337
Trehalose-phosphatase + 23 28 488 - IPR036378
  - 21 - 108 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 23 + 30 489 - IPR004316
SWEET sugar transporter - 21 - 60 + IPR044839
Protein NDR1-like + 23 + 26 490 - IPR036873
  - 21 - 142 + IPR034285
Laccase, second cupredoxin domain + 23 + 30 491 - IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site - 21 - 28 + IPR004776
Membrane transport protein + 23 + 48 492 - IPR036420
  - 21 - 188 + IPR006868
Domain of unknown function DUF630 + 23 + 28 493 - IPR018181
Heat shock protein 70, conserved site - 21 - 53 + IPR002641
Patatin-like phospholipase domain + 23 + 54 494 - IPR033124
Serine carboxypeptidases, histidine active site - 21 - 46 + IPR029033
Histidine phosphatase superfamily + 23 + 34 495 - IPR025422
  - 21 - 213 + IPR006867
Domain of unknown function DUF632 + 23 + 29 496 - IPR001763
  - 21 - 190 + IPR033734
Jacalin-like lectin domain, plant + 23 + 41 497 - IPR038595
  - 21 - 50 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 22 + 34 498 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 21 - 44 + IPR016073
SKP1 component, POZ domain + 22 + 26 499 - IPR000408
  - 21 - 1486 + IPR000953
Chromo/chromo shadow domain + 22 + 34 500 - IPR022742
Serine aminopeptidase, S33 - 21 - 35 + IPR002403
Cytochrome P450, E-class, group IV + 22 + 137 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_nivara.html b/gramene/htdocs/ssi/species/stats_Oryza_nivara.html index effd0c2f..c2bc0455 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_nivara.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_nivara.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:AWHD00000000, Aug 2013AGI_PacBIO,
Database version:93.1087.4
Base Pairs:337,950,324395,534,265
Golden Path Length:337,950,324395,534,265
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09
+ Genebuild by: CSHL Genebuild started: Jul 2018 Genebuild version: 2018-07-CSHL

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):36,313Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		42,429
Gene transcriptsHASH(0x68ce400):50,788Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:53,535
@@ -37,38 +37,44 @@

Coordinate Systems

chromosome
-
12 sequences
+
26 sequences
+1
SequenceLength (bp)
142845077
235065507
336134596
428646061
528014461
629411429
724717764
826703665
920407407
1021549876
1124378308
1220076173
44777331
237617280
339444530
434895103
531081614
631959707
731328962
829944492
923930135
1029664397
1132449966
1226869529
UN-Ctg34304382
UN-Ctg35251620
UN-Ctg36186140
UN-Ctg37178580
UN-Ctg38103931
UN-Ctg3987798
UN-Ctg4075341
UN-Ctg4173934
UN-Ctg4262263
UN-Ctg4360882
UN-Ctg4456571
UN-Ctg4549831
UN-Ctg4639864
UN-Ctg4740082
-
+
chunk - 3387 sequences + 3967 sequences - -

Other

- - - - - -
FGENESH gene predictions:45,102
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_nivara_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_nivara_IPtop500.html index a3168956..cf9745e2 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_nivara_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_nivara_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1477 - 2650 + 1575 + 2291 2 - IPR000719
  - 1401 - 17469 + IPR000719
Protein kinase domain + 1494 + 3668 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1359 - 3049 + 1416 + 2417 4 - IPR032675
  - 1207 - 7648 + IPR036047
F-box-like domain superfamily + 717 + 948 5 - IPR008271
Serine/threonine-protein kinase, active site - 1134 - 1884 + IPR001810
F-box domain + 517 + 1015 6 - IPR017441
Protein kinase, ATP binding site - 983 - 1624 + IPR002885
Pentatricopeptide repeat + 503 + 8740 7 - IPR011990
  - 720 - 12084 + IPR001611
Leucine-rich repeat + 503 + 1755 8 - IPR013083
  - 681 - 2122 + IPR044974
Disease resistance protein, plants + 483 + 986 9 - IPR036047
F-box-like domain superfamily - 655 - 1034 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 478 + 935 10 - IPR001810
  - 486 - 4974 + IPR001841
Zinc finger, RING-type + 443 + 855 11 - IPR002885
  - 481 - 32116 + IPR002182
NB-ARC + 439 + 647 12 - IPR001611
  - 464 - 12453 + IPR009057
Homeobox-like domain superfamily + 400 + 521 13 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 461 - 1045 + IPR029058
Alpha/Beta hydrolase fold + 398 + 623 14 - IPR002182
NB-ARC - 438 - 793 + IPR036291
NAD(P)-binding domain superfamily + 393 + 598 15 - IPR001841
  - 420 - 2978 + IPR016024
Armadillo-type fold + 383 + 608 16 - IPR029058
  - 381 - 2574 + IPR012337
Ribonuclease H-like superfamily + 378 + 474 17 - IPR016024
Armadillo-type fold - 376 - 1479 + IPR011990
Tetratricopeptide-like helical domain superfamily + 365 + 635 18 - IPR036291
NAD(P)-binding domain superfamily - 373 - 646 + IPR041118
Rx, N-terminal + 356 + 531 19 - IPR009057
Homeobox-like domain superfamily - 346 - 484 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 351 + 473 20 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 328 - 517 + IPR036396
Cytochrome P450 superfamily + 343 + 458 21 - IPR036396
  - 324 - 2883 + IPR001128
Cytochrome P450 + 337 + 1683 22 - IPR003591
Leucine-rich repeat, typical subtype - 323 - 3497 + IPR035979
RNA-binding domain superfamily + 310 + 648 23 - IPR001128
Cytochrome P450 - 313 - 1616 + IPR002401
Cytochrome P450, E-class, group I + 293 + 2257 24 - IPR035979
RNA-binding domain superfamily - 298 - 637 + IPR017853
Glycoside hydrolase superfamily + 279 + 403 25 - IPR012677
  - 289 - 1336 + IPR038765
Papain-like cysteine peptidase superfamily + 279 + 358 26 - IPR003593
AAA+ ATPase domain - 277 - 580 + IPR043502
DNA/RNA polymerase superfamily + 275 + 302 27 - IPR017853
Glycoside hydrolase superfamily - 263 - 460 + IPR000504
RNA recognition motif domain + 273 + 1233 28 - IPR000504
  - 263 - 5223 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 272 + 420 29 - IPR002401
Cytochrome P450, E-class, group I - 262 - 1992 + IPR036249
Thioredoxin-like superfamily + 270 + 393 30 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 259 - 494 + IPR001878
Zinc finger, CCHC-type + 266 + 710 31 - IPR011989
  - 258 - 1158 + IPR036259
MFS transporter superfamily + 265 + 427 32 - IPR017972
Cytochrome P450, conserved site - 254 - 353 + IPR036875
Zinc finger, CCHC-type superfamily + 258 + 361 33 - IPR036259
MFS transporter superfamily - 246 - 710 + IPR017930
Myb domain + 250 + 799 34 - IPR015943
  - 241 - 1854 + IPR001005
SANT/Myb domain + 247 + 819 35 IPR038005
Virus X resistance protein-like, coiled-coil domain - 234 - 387 + 243 + 349 36 - IPR001005
SANT/Myb domain - 234 - 972 + IPR036322
WD40-repeat-containing domain superfamily + 237 + 373 37 - IPR036249
Thioredoxin-like superfamily - 231 - 389 + IPR001680
WD40 repeat + 214 + 1694 38 - IPR036322
WD40-repeat-containing domain superfamily - 228 - 656 + IPR021109
Aspartic peptidase domain superfamily + 200 + 245 39 - IPR001680
  - 224 - 11280 + IPR011992
EF-hand domain pair + 195 + 256 40 - IPR038765
Papain-like cysteine peptidase superfamily - 214 - 354 + IPR016177
DNA-binding domain superfamily + 186 + 256 41 - IPR017986
  - 200 - 1143 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 183 + 396 42 - IPR011992
EF-hand domain pair - 193 - 274 + IPR002048
EF-hand domain + 182 + 1011 43 - IPR016177
DNA-binding domain superfamily - 183 - 260 + IPR036770
Ankyrin repeat-containing domain superfamily + 180 + 245 44 - IPR002048
  - 177 - 4932 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 176 + 211 45 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 175 - 217 + IPR036236
Zinc finger C2H2 superfamily + 174 + 244 46 IPR036412
HAD-like superfamily 173 - 394 + 257 47 - IPR036638
  - 172 - 1254 + IPR001471
AP2/ERF domain + 172 + 951 48 - IPR020846
  - 172 - 910 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 169 + 355 49 - IPR017930
  - 172 - 596 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 165 + 183 50 - IPR036955
  - 169 - 657 + IPR002110
Ankyrin repeat + 165 + 643 51 - IPR001471
  - 168 - 3498 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 162 + 202 52 - IPR013087
  - 168 - 2706 + IPR011333
SKP1/BTB/POZ domain superfamily + 162 + 239 53 - IPR036388
  - 167 - 480 + IPR036390
Winged helix DNA-binding domain superfamily + 159 + 193 54 - IPR011598
  - 166 - 2151 + IPR001584
Integrase, catalytic core + 157 + 246 55 - IPR036770
  - 160 - 1256 + IPR000477
Reverse transcriptase domain + 157 + 260 56 - IPR018247
EF-Hand 1, calcium-binding site - 159 - 467 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 156 + 232 57 - IPR020683
  - 158 - 1800 + IPR036093
NAC domain superfamily + 153 + 182 58 - IPR011333
SKP1/BTB/POZ domain superfamily - 156 - 260 + IPR003441
NAC domain + 150 + 345 59 - IPR036093
  - 156 - 1071 + IPR013087
Zinc finger C2H2-type + 148 + 253 60 - IPR023214
  - 155 - 760 + IPR012340
Nucleic acid-binding, OB-fold + 147 + 286 61 - IPR029044
  - 150 - 1112 + IPR010255
Haem peroxidase superfamily + 145 + 171 62 - IPR003441
  - 149 - 1026 + IPR005162
Retrotransposon gag domain + 144 + 145 63 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 148 - 222 + IPR029044
Nucleotide-diphospho-sugar transferases + 143 + 196 64 - IPR036390
Winged helix DNA-binding domain superfamily - 147 - 195 + IPR036188
FAD/NAD(P)-binding domain superfamily + 142 + 276 65 - IPR014001
  - 147 - 1040 + IPR001650
Helicase, C-terminal + 141 + 441 66 - IPR002110
  - 145 - 5220 + IPR002016
Haem peroxidase + 141 + 1008 67 - IPR001650
  - 143 - 2074 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 141 + 240 68 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 141 - 157 + IPR005174
Domain unknown function DUF295 + 137 + 159 69 - IPR035595
UDP-glycosyltransferase family, conserved site - 138 - 162 + IPR029071
Ubiquitin-like domain superfamily + 134 + 201 70 - IPR036188
  - 138 - 1762 + IPR003439
ABC transporter-like, ATP-binding domain + 133 + 565 71 - IPR036236
Zinc finger C2H2 superfamily - 138 - 277 + IPR020683
Ankyrin repeat-containing domain + 132 + 255 72 - IPR023213
  - 133 - 554 + IPR036426
Bulb-type lectin domain superfamily + 128 + 175 73 - IPR019775
WD40 repeat, conserved site - 132 - 358 + IPR000823
Plant peroxidase + 125 + 1109 74 - IPR013026
  - 130 - 738 + IPR001480
Bulb-type lectin domain + 124 + 464 75 - IPR014729
  - 128 - 460 + IPR003480
Transferase + 124 + 141 76 - IPR019734
  - 127 - 4176 + IPR025315
Domain of unknown function DUF4220 + 122 + 134 77 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 127 - 213 + IPR033121
Peptidase family A1 domain + 120 + 159 78 - IPR003439
  - 127 - 1836 + IPR000210
BTB/POZ domain + 119 + 359 79 - IPR012340
Nucleic acid-binding, OB-fold - 122 - 254 + IPR033905
Secretory peroxidase + 118 + 140 80 - IPR036514
  - 122 - 328 + IPR003959
ATPase, AAA-type, core + 118 + 183 81 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 120 - 222 + IPR007658
Protein of unknown function DUF594 + 116 + 121 82 - IPR000210
  - 120 - 1593 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 116 + 156 83 - IPR021109
  - 118 - 986 + IPR036869
Chaperone J-domain superfamily + 115 + 150 84 - IPR003959
ATPase, AAA-type, core - 118 - 204 + IPR001087
GDSL lipase/esterase + 114 + 143 85 - IPR036869
  - 117 - 686 + IPR019734
Tetratricopeptide repeat + 113 + 389 86 - IPR036426
  - 115 - 898 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 113 + 133 87 - IPR003480
Transferase - 115 - 149 + IPR007527
Zinc finger, SWIM-type + 113 + 204 88 - IPR005174
Domain unknown function DUF295 - 112 - 137 + IPR032799
Xylanase inhibitor, C-terminal + 112 + 146 89 - IPR025315
Domain of unknown function DUF4220 - 112 - 127 + IPR020846
Major facilitator superfamily domain + 112 + 168 90 - IPR014710
  - 111 - 442 + IPR015424
Pyridoxal phosphate-dependent transferase + 112 + 143 91 - IPR001461
Aspartic peptidase A1 family - 111 - 366 + IPR001623
DnaJ domain + 111 + 755 92 - IPR001480
  - 111 - 1050 + IPR018289
MULE transposase domain + 111 + 116 93 - IPR001623
  - 110 - 1932 + IPR008972
Cupredoxin + 110 + 229 94 - IPR008974
  - 109 - 969 + IPR032861
Xylanase inhibitor, N-terminal + 110 + 146 95 - IPR011011
Zinc finger, FYVE/PHD-type - 108 - 183 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 108 + 205 96 - IPR005123
  - 105 - 921 + IPR011011
Zinc finger, FYVE/PHD-type + 107 + 189 97 - IPR033121
  - 105 - 324 + IPR004045
Glutathione S-transferase, N-terminal + 105 + 285 98 - IPR015421
  - 104 - 504 + IPR003609
PAN/Apple domain + 104 + 277 99 - IPR001087
GDSL lipase/esterase - 103 - 131 + IPR002156
Ribonuclease H domain + 103 + 153 100 - IPR012337
Ribonuclease H-like superfamily - 103 - 197 + IPR035892
C2 domain superfamily + 102 + 186 101 - IPR029071
Ubiquitin-like domain superfamily - 103 - 158 + IPR036576
WRKY domain superfamily + 102 + 128 102 - IPR013785
  - 102 - 546 + IPR011676
Domain of unknown function DUF1618 + 102 + 131 103 - IPR008972
  - 102 - 944 + IPR003657
WRKY domain + 102 + 254 104 - IPR015424
Pyridoxal phosphate-dependent transferase - 102 - 175 + IPR011050
Pectin lyase fold/virulence factor + 101 + 113 105 - IPR007658
Protein of unknown function DUF594 - 101 - 111 + IPR010987
Glutathione S-transferase, C-terminal-like + 101 + 140 106 - IPR011050
Pectin lyase fold/virulence factor - 100 - 130 + IPR015300
DNA-binding pseudobarrel domain superfamily + 98 + 189 107 - IPR009072
  - 100 - 696 + IPR001356
Homeobox domain + 97 + 312 108 - IPR003657
  - 99 - 1254 + IPR035669
GDSL lipase/esterase-like, plant + 96 + 119 109 - IPR036576
  - 98 - 831 + IPR000858
S-locus glycoprotein domain + 96 + 128 110 - IPR032861
Xylanase inhibitor, N-terminal - 98 - 135 + IPR044810
WRKY transcription factor, plant + 96 + 106 111 - IPR032799
Xylanase inhibitor, C-terminal - 97 - 134 + IPR036457
PPM-type phosphatase domain superfamily + 95 + 137 112 - IPR005225
Small GTP-binding protein domain - 97 - 146 + IPR009072
Histone-fold + 95 + 109 113 - IPR015300
  - 96 - 744 + IPR011051
RmlC-like cupin domain superfamily + 94 + 130 114 - IPR012334
  - 96 - 244 + IPR001932
PPM-type phosphatase domain + 94 + 395 115 - IPR035669
GDSL lipase/esterase-like, plant - 95 - 131 + IPR002347
Short-chain dehydrogenase/reductase SDR + 93 + 883 116 - IPR003609
  - 94 - 830 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 93 + 179 117 - IPR027443
  - 94 - 308 + IPR000073
Alpha/beta hydrolase fold-1 + 93 + 275 118 - IPR036457
  - 93 - 782 + IPR005828
Major facilitator, sugar transporter-like + 92 + 150 119 - IPR032867
DYW domain - 93 - 129 + IPR002083
MATH/TRAF domain + 92 + 329 120 - IPR002347
Short-chain dehydrogenase/reductase SDR - 92 - 888 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 92 + 178 121 - IPR024171
S-receptor-like serine/threonine-protein kinase - 92 - 149 + IPR000626
Ubiquitin-like domain + 91 + 246 122 - IPR000742
  - 92 - 642 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 90 + 195 123 - IPR004827
  - 91 - 1392 + IPR011545
DEAD/DEAH box helicase domain + 90 + 167 124 - IPR001932
  - 91 - 2007 + IPR000008
C2 domain + 89 + 360 125 - IPR035892
  - 90 - 394 + IPR020472
G-protein beta WD-40 repeat + 89 + 375 126 - IPR011676
Domain of unknown function DUF1618 - 90 - 144 + IPR000109
Proton-dependent oligopeptide transporter family + 88 + 322 127 - IPR001356
  - 90 - 1239 + IPR001220
Legume lectin domain + 88 + 188 128 - IPR000109
Proton-dependent oligopeptide transporter family - 89 - 327 + IPR032867
DYW domain + 88 + 98 129 - IPR011051
RmlC-like cupin domain superfamily - 89 + IPR026992
Non-haem dioxygenase N-terminal domain + 87 170 130 - IPR000858
S-locus glycoprotein domain - 88 - 131 + IPR004827
Basic-leucine zipper domain + 85 + 235 131 - IPR017871
ABC transporter, conserved site - 88 - 174 + IPR003340
B3 DNA binding domain + 84 + 462 132 - IPR001965
Zinc finger, PHD-type - 88 - 192 + IPR000270
PB1 domain + 83 + 131 133 - IPR006447
Myb domain, plants - 87 - 108 + IPR013766
Thioredoxin domain + 81 + 186 134 - IPR000073
Alpha/beta hydrolase fold-1 - 87 - 263 + IPR002100
Transcription factor, MADS-box + 81 + 526 135 - IPR036397
  - 86 - 444 + IPR036879
Transcription factor, MADS-box superfamily + 81 + 113 136 - IPR011545
DEAD/DEAH box helicase domain - 86 - 162 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 80 + 102 137 - IPR000008
  - 85 - 1098 + IPR026961
PGG domain + 79 + 163 138 - IPR015422
  - 85 - 600 + IPR041588
Integrase zinc-binding domain + 79 + 79 139 - IPR005828
Major facilitator, sugar transporter-like - 84 - 143 + IPR036908
RlpA-like domain superfamily + 78 + 95 140 - IPR015655
Protein phosphatase 2C family - 84 - 172 + IPR001461
Aspartic peptidase A1 family + 78 + 259 141 - IPR002083
  - 83 - 1116 + IPR002902
Gnk2-homologous domain + 77 + 424 142 - IPR003340
  - 82 - 1884 + IPR043129
ATPase, nucleotide binding domain + 77 + 194 143 - IPR026992
Non-haem dioxygenase N-terminal domain - 80 - 116 + IPR004158
Protein of unknown function DUF247, plant + 77 + 191 144 - IPR017907
Zinc finger, RING-type, conserved site - 80 - 132 + IPR003613
U box domain + 76 + 175 145 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 80 - 123 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 76 + 83 146 - IPR020472
G-protein beta WD-40 repeat - 78 - 387 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 75 + 107 147 - IPR003613
  - 78 - 864 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 75 + 81 148 - IPR000270
  - 77 - 687 + IPR031052
FHY3/FAR1 family + 75 + 119 149 - IPR013766
  - 75 - 630 + IPR008949
Isoprenoid synthase domain superfamily + 74 + 101 150 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 74 - 98 + IPR006121
Heavy metal-associated domain, HMA + 74 + 257 151 - IPR038408
  - 74 - 536 + IPR016039
Thiolase-like + 74 + 135 152 - IPR002902
  - 74 - 1056 + IPR007117
Expansin, cellulose-binding-like domain + 74 + 158 153 - IPR001220
Legume lectin domain - 74 - 186 + IPR000571
Zinc finger, CCCH-type + 74 + 313 154 - IPR002100
  - 73 - 1902 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 73 + 98 155 - IPR004045
  - 73 - 681 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 73 + 76 156 - IPR016039
  - 72 - 810 + IPR036163
Heavy metal-associated domain superfamily + 73 + 102 157 - IPR013783
  - 72 - 232 + IPR041373
Reverse transcriptase, RNase H-like domain + 72 + 72 158 - IPR003960
ATPase, AAA-type, conserved site - 72 - 111 + IPR044965
Glycoside hydrolase family 17, plant + 71 + 99 159 - IPR036163
Heavy metal-associated domain superfamily - 72 - 101 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 71 + 170 160 - IPR018097
EGF-like calcium-binding, conserved site - 72 - 109 + IPR022059
Protein of unknown function DUF3615 + 69 + 105 161 - IPR036879
  - 72 - 618 + IPR016159
Cullin repeat-like-containing domain superfamily + 69 + 83 162 - IPR006121
  - 71 - 714 + IPR036915
Cyclin-like superfamily + 67 + 149 163 - IPR001881
EGF-like calcium-binding domain - 71 - 171 + IPR001806
Small GTPase + 66 + 149 164 - IPR026961
PGG domain - 71 - 202 + IPR045051
Subtilisin-like protease + 65 + 104 165 - IPR010987
  - 69 - 206 + IPR034161
Pepsin-like domain, plant + 65 + 73 166 - IPR000225
  - 69 - 2373 + IPR006501
Pectinesterase inhibitor domain + 65 + 67 167 - IPR016159
Cullin repeat-like-containing domain superfamily - 68 - 115 + IPR029052
Metallo-dependent phosphatase-like + 65 + 87 168 - IPR000571
  - 68 - 1491 + IPR004332
Transposase, MuDR, plant + 64 + 64 169 - IPR035513
  - 67 - 266 + IPR026960
Reverse transcriptase zinc-binding domain + 64 + 64 170 - IPR004158
Protein of unknown function DUF247, plant - 67 - 88 + IPR007112
Expansin/pollen allergen, DPBB domain + 64 + 73 171 - IPR017451
F-box associated interaction domain - 66 - 95 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 64 + 69 172 - IPR036961
  - 66 - 630 + IPR009003
Peptidase S1, PA clan + 64 + 102 173 - IPR036908
  - 65 - 324 + IPR003663
Sugar/inositol transporter + 64 + 375 174 - IPR015915
  - 65 - 660 + IPR000048
IQ motif, EF-hand binding site + 64 + 404 175 - IPR011993
  - 65 - 230 + IPR013057
Amino acid transporter, transmembrane domain + 63 + 84 176 - IPR000626
  - 64 - 654 + IPR000490
Glycoside hydrolase family 17 + 63 + 76 177 - IPR008949
  - 64 - 642 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 62 + 84 178 - IPR019787
  - 64 - 328 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 62 + 69 179 - IPR013057
Amino acid transporter, transmembrane domain - 64 - 91 + IPR019787
Zinc finger, PHD-finger + 62 + 169 180 - IPR000490
Glycoside hydrolase family 17 - 64 - 127 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 62 + 89 181 - IPR000048
  - 64 - 1797 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 518 182 - IPR034090
BPM, C-terminal - 63 - 103 + IPR023395
Mitochondrial carrier domain superfamily + 62 + 90 183 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 63 - 189 + IPR003676
Small auxin-up RNA + 62 + 67 184 - IPR036852
  - 62 - 972 + IPR004330
FAR1 DNA binding domain + 62 + 73 185 - IPR018108
  - 61 - 926 + IPR020568
Ribosomal protein S5 domain 2-type fold + 61 + 102 186 - IPR008979
  - 61 - 432 + IPR001563
Peptidase S10, serine carboxypeptidase + 60 + 543 187 - IPR020568
Ribosomal protein S5 domain 2-type fold - 61 - 104 + IPR036852
Peptidase S8/S53 domain superfamily + 60 + 88 188 - IPR023395
  - 61 - 378 + IPR007118
Expansin/Lol pI + 59 + 353 189 - IPR006501
Pectinesterase inhibitor domain - 61 - 165 + IPR003245
Phytocyanin domain + 59 + 123 190 - IPR009003
Peptidase S1, PA clan - 61 - 139 + IPR000209
Peptidase S8/S53 domain + 59 + 84 191 - IPR001806
Small GTPase superfamily - 61 - 89 + IPR016181
Acyl-CoA N-acyltransferase + 58 + 78 192 - IPR019786
Zinc finger, PHD-type, conserved site - 60 - 95 + IPR026057
PC-Esterase + 58 + 77 193 - IPR016135
  - 60 - 386 + IPR016197
Chromo-like domain superfamily + 58 + 79 194 - IPR026057
PC-Esterase - 59 - 77 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 57 + 78 195 - IPR005202
  - 59 - 286 + IPR039391
Phytocyanin + 57 + 62 196 - IPR013094
Alpha/beta hydrolase fold-3 - 59 - 72 + IPR002528
Multi antimicrobial extrusion protein + 57 + 160 197 - IPR006566
FBD domain - 58 - 109 + IPR005202
Transcription factor GRAS + 57 + 209 198 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 57 - 97 + IPR015915
Kelch-type beta propeller + 57 + 70 199 - IPR029962
Trichome birefringence-like family - 57 - 77 + IPR013094
Alpha/beta hydrolase fold-3 + 57 + 68 200 - IPR005829
Sugar transporter, conserved site - 57 - 141 + IPR024788
Malectin-like domain + 57 + 93 201 - IPR036915
Cyclin-like superfamily - 57 - 153 + IPR029962
Trichome birefringence-like family + 56 + 76 202 - IPR000209
Peptidase S8/S53 domain - 57 - 76 + IPR008906
HAT, C-terminal dimerisation domain + 56 + 60 203 - IPR036749
  - 56 - 272 + IPR013763
Cyclin-like + 56 + 119 204 - IPR022059
Protein of unknown function DUF3615 - 56 - 97 + IPR006045
Cupin 1 + 56 + 96 205 - IPR002528
Multi antimicrobial extrusion protein - 56 - 232 + IPR025846
PMR5 N-terminal domain + 56 + 71 206 - IPR025846
PMR5 N-terminal domain - 56 - 69 + IPR004046
Glutathione S-transferase, C-terminal + 56 + 73 207 - IPR003663
Sugar/inositol transporter - 56 - 420 + IPR025724
GAG-pre-integrase domain + 56 + 57 208 - IPR024788
Malectin-like carbohydrate-binding domain - 56 - 106 + IPR000620
EamA domain + 56 + 127 209 - IPR007112
  - 55 - 248 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 55 + 72 210 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 55 - 59 + IPR030184
WAT1-related protein + 55 + 103 211 - IPR003245
  - 55 - 543 + IPR000225
Armadillo + 55 + 205 212 - IPR007117
  - 55 - 268 + IPR011032
GroES-like superfamily + 54 + 90 213 - IPR011032
GroES-like superfamily - 54 - 98 + IPR019557
Aminotransferase-like, plant mobile domain + 54 + 63 214 - IPR001563
Peptidase S10, serine carboxypeptidase - 54 - 509 + IPR008979
Galactose-binding-like domain superfamily + 54 + 97 215 - IPR036640
  - 54 - 924 + IPR006566
FBD domain + 54 + 65 216 - IPR034161
Pepsin-like domain, plant - 54 - 69 + IPR004140
Exocyst complex component Exo70 + 53 + 139 217 - IPR004140
Exocyst complex component Exo70 - 54 - 153 + IPR001752
Kinesin motor domain + 53 + 445 218 - IPR027640
Kinesin-like protein - 54 - 175 + IPR015500
Peptidase S8, subtilisin-related + 53 + 190 219 - IPR036465
  - 54 - 330 + IPR044730
Ribonuclease H-like domain, plant type + 53 + 56 220 - IPR010255
Haem peroxidase - 54 - 78 + IPR017884
SANT domain + 52 + 72 221 - IPR002921
Fungal lipase-like domain - 53 - 75 + IPR013525
ABC-2 type transporter + 52 + 121 222 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 53 - 66 + IPR008978
HSP20-like chaperone + 52 + 59 223 - IPR013128
Peptidase C1A - 53 - 80 + IPR000608
Ubiquitin-conjugating enzyme E2 + 52 + 187 224 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 53 - 112 + IPR005630
Terpene synthase, metal-binding domain + 52 + 67 225 - IPR023393
  - 53 - 182 + IPR034197
Cucumisin-like catalytic domain + 52 + 70 226 - IPR023298
P-type ATPase, transmembrane domain superfamily - 53 - 217 + IPR036465
von Willebrand factor A-like domain superfamily + 52 + 80 227 - IPR001752
  - 53 - 2100 + IPR002921
Fungal lipase-like domain + 51 + 70 228 - IPR001878
  - 53 - 996 + IPR001509
NAD-dependent epimerase/dehydratase + 51 + 94 229 - IPR037045
  - 53 - 130 + IPR001906
Terpene synthase, N-terminal domain + 51 + 68 230 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 52 - 61 + IPR023298
P-type ATPase, transmembrane domain superfamily + 51 + 87 231 - IPR029052
  - 52 - 188 + IPR044808
Ethylene-responsive transcription factor + 51 + 54 232 - IPR015500
Peptidase S8, subtilisin-related - 52 - 181 + IPR011701
Major facilitator superfamily + 50 + 92 233 - IPR016181
Acyl-CoA N-acyltransferase - 51 - 78 + IPR004265
Dirigent protein + 50 + 57 234 - IPR034197
Cucumisin-like catalytic domain - 51 - 65 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 49 + 123 235 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 51 - 68 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 49 + 53 236 - IPR018253
DnaJ domain, conserved site - 51 - 78 + IPR012946
X8 domain + 49 + 65 237 - IPR002016
  - 51 - 948 + IPR007125
Histone H2A/H2B/H3 + 49 + 53 238 - IPR030184
WAT1-related protein - 51 - 108 + IPR011527
ABC transporter type 1, transmembrane domain + 49 + 243 239 - IPR014014
  - 50 - 162 + IPR045087
Multicopper oxidase + 49 + 63 240 - IPR000222
PPM-type phosphatase, divalent cation binding - 50 - 98 + IPR033389
AUX/IAA domain + 48 + 67 241 - IPR011527
  - 50 - 879 + IPR008250
P-type ATPase, A domain superfamily + 48 + 78 242 - IPR006045
Cupin 1 - 50 - 192 + IPR000742
EGF-like domain + 48 + 57 243 - IPR023299
  - 50 - 423 + IPR001214
SET domain + 48 + 138 244 - IPR013525
ABC-2 type transporter - 49 - 123 + IPR033896
MADS MEF2-like + 47 + 73 245 - IPR000608
  - 49 - 378 + IPR036318
FAD-binding, type PCMH-like superfamily + 47 + 61 246 - IPR007118
Expansin/Lol pI - 49 - 301 + IPR008928
Six-hairpin glycosidase superfamily + 47 + 53 247 - IPR008250
P-type ATPase, A domain superfamily - 49 - 93 + IPR011706
Multicopper oxidase, C-terminal + 47 + 54 248 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 49 - 534 + IPR036855
Zinc finger, CCCH-type superfamily + 47 + 114 249 - IPR013763
Cyclin-like - 49 - 233 + IPR011707
Multicopper oxidase, N-termianl + 47 + 53 250 - IPR000620
EamA domain - 49 - 129 + IPR001117
Multicopper oxidase, type 1 + 46 + 52 251 - IPR008978
  - 48 - 212 + IPR043926
ABC transporter family G domain + 46 + 88 252 - IPR001938
  - 48 - 752 + IPR006016
UspA + 46 + 55 253 - IPR036855
Zinc finger, CCCH-type superfamily - 48 - 131 + IPR009060
UBA-like superfamily + 46 + 65 254 - IPR017877
  - 48 - 160 + IPR036612
K Homology domain, type 1 superfamily + 46 + 161 255 - IPR005630
Terpene synthase, metal-binding domain - 47 - 107 + IPR000873
AMP-dependent synthetase/ligase + 46 + 57 256 - IPR008928
Six-hairpin glycosidase superfamily - 47 + IPR006671
Cyclin, N-terminal + 46 74 257 - IPR012341
  - 47 - 210 + IPR041569
AAA ATPase, AAA+ lid domain + 46 + 68 258 - IPR001509
NAD-dependent epimerase/dehydratase - 46 - 91 + IPR000182
GNAT domain + 45 + 106 259 - IPR012946
X8 domain - 46 - 134 + IPR029055
Nucleophile aminohydrolases, N-terminal + 45 + 62 260 - IPR001757
P-type ATPase - 46 - 267 + IPR011006
CheY-like superfamily + 45 + 63 261 - IPR000070
Pectinesterase, catalytic - 46 - 58 + IPR014756
Immunoglobulin E-set + 45 + 67 262 - IPR003676
Small auxin-up RNA - 46 - 79 + IPR008889
VQ + 45 + 46 263 - IPR033389
AUX/IAA domain - 45 - 72 + IPR009000
Translation protein, beta-barrel domain superfamily + 44 + 63 264 - IPR008942
  - 45 - 226 + IPR004263
Exostosin-like + 44 + 72 265 - IPR036318
FAD-binding, type 2-like superfamily - 45 - 53 + IPR000668
Peptidase C1A, papain C-terminal + 44 + 165 266 - IPR000873
AMP-dependent synthetase/ligase - 45 - 68 + IPR000070
Pectinesterase, catalytic + 44 + 49 267 - IPR004265
Dirigent protein - 45 - 54 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 111 268 - IPR018303
P-type ATPase, phosphorylation site - 45 - 68 + IPR016461
O-methyltransferase COMT-type + 43 + 92 269 - IPR036875
Zinc finger, CCHC-type superfamily - 45 - 86 + IPR004853
Sugar phosphate transporter domain + 43 + 65 270 - IPR036965
  - 44 - 360 + IPR000330
SNF2, N-terminal + 43 + 77 271 - IPR006016
UspA - 44 - 55 + IPR014014
RNA helicase, DEAD-box type, Q motif + 43 + 70 272 - IPR009060
UBA-like superfamily - 44 - 69 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 43 + 66 273 - IPR011701
Major facilitator superfamily - 44 - 102 + IPR027923
Hydrophobic seed protein domain + 43 + 93 274 - IPR029055
  - 44 - 254 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 43 + 57 275 - IPR036890
  - 44 - 332 + IPR025525
hAT-like transposase, RNase-H fold + 42 + 46 276 - IPR000182
  - 43 - 186 + IPR003656
Zinc finger, BED-type + 42 + 76 277 - IPR033896
MADS MEF2-like - 43 - 76 + IPR029045
ClpP/crotonase-like domain superfamily + 42 + 53 278 - IPR000668
Peptidase C1A, papain C-terminal - 43 - 220 + IPR024752
Myb/SANT-like domain + 42 + 42 279 - IPR001906
Terpene synthase, N-terminal domain - 43 - 101 + IPR000743
Glycoside hydrolase, family 28 + 42 + 53 280 - IPR002109
  - 43 - 276 + IPR006702
Casparian strip membrane protein domain + 42 + 45 281 - IPR014756
Immunoglobulin E-set - 43 - 77 + IPR016166
FAD-binding domain, PCMH-type + 41 + 54 282 - IPR011707
Multicopper oxidase, type 3 - 43 - 54 + IPR015947
PUA-like superfamily + 41 + 52 283 - IPR006702
Casparian strip membrane protein domain - 43 - 43 + IPR037176
Osmotin/thaumatin-like superfamily + 41 + 44 284 - IPR001969
Aspartic peptidase, active site - 42 - 71 + IPR010402
CCT domain + 40 + 119 285 - IPR003653
  - 42 - 279 + IPR004041
NAF domain + 40 + 46 286 - IPR011006
CheY-like superfamily - 42 - 80 + IPR018451
NAF/FISL domain + 40 + 46 287 - IPR011706
Multicopper oxidase, type 2 - 42 - 54 + IPR002068
Alpha crystallin/Hsp20 domain + 40 + 81 288 - IPR001214
  - 42 - 510 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 40 + 45 289 - IPR001789
  - 42 - 795 + IPR035940
CAP superfamily + 40 + 51 290 - IPR001117
Multicopper oxidase, type 1 - 41 - 52 + IPR001938
Thaumatin family + 40 + 262 291 - IPR004853
Sugar phosphate transporter domain - 41 - 51 + IPR004839
Aminotransferase, class I/classII + 40 + 61 292 - IPR000330
SNF2-related, N-terminal domain - 41 - 86 + IPR011012
Longin-like domain superfamily + 40 + 63 293 - IPR009000
Translation protein, beta-barrel domain superfamily - 41 - 67 + IPR002109
Glutaredoxin + 40 + 45 294 - IPR016166
  - 41 - 141 + IPR004242
Transposon, En/Spm-like + 40 + 42 295 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 41 - 61 + IPR008942
ENTH/VHS + 39 + 52 296 - IPR020845
AMP-binding, conserved site - 41 - 55 + IPR025659
Tubby-like, C-terminal + 39 + 50 297 - IPR000644
  - 41 - 714 + IPR029021
Protein-tyrosine phosphatase-like + 39 + 66 298 - IPR028889
  - 41 - 110 + IPR003137
PA domain + 39 + 50 299 - IPR037176
  - 41 - 194 + IPR041577
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain + 39 + 40 300 - IPR029021
  - 40 - 304 + IPR023271
Aquaporin-like + 39 + 42 301 - IPR036612
  - 40 - 636 + IPR013154
Alcohol dehydrogenase, N-terminal + 39 + 51 302 - IPR011012
Longin-like domain superfamily - 40 - 62 + IPR029480
Transposase-associated domain + 39 + 39 303 - IPR017970
Homeobox, conserved site - 40 - 43 + IPR001077
O-methyltransferase domain + 39 + 42 304 - IPR019794
Peroxidase, active site - 40 - 51 + IPR014044
CAP domain + 39 + 50 305 - IPR029045
ClpP/crotonase-like domain superfamily - 40 - 84 + IPR015655
Protein phosphatase 2C family + 39 + 70 306 - IPR038718
  - 40 - 204 + IPR000425
Major intrinsic protein + 39 + 283 307 - IPR011043
Galactose oxidase/kelch, beta-propeller - 40 - 63 + IPR000644
CBS domain + 39 + 159 308 - IPR011042
  - 40 - 154 + IPR002487
Transcription factor, K-box + 39 + 110 309 - IPR000743
Glycoside hydrolase, family 28 - 40 - 76 + IPR025322
Protein of unknown function DUF4228, plant + 38 + 41 310 - IPR010402
  - 39 - 324 + IPR001360
Glycoside hydrolase family 1 + 38 + 444 311 - IPR025322
Protein of unknown function DUF4228, plant - 39 - 42 + IPR007493
Protein of unknown function DUF538 + 38 + 88 312 - IPR025659
  - 39 - 190 + IPR029466
No apical meristem-associated, C-terminal domain + 38 + 38 313 - IPR008889
VQ - 39 - 40 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 38 + 112 314 - IPR000823
Plant peroxidase - 39 - 263 + IPR001283
Cysteine-rich secretory protein-related + 38 + 184 315 - IPR004041
NAF domain - 38 - 45 + IPR036758
At5g01610-like superfamily + 38 + 47 316 - IPR016461
  - 38 - 234 + IPR004088
K Homology domain, type 1 + 37 + 144 317 - IPR018451
  - 38 - 135 + IPR039417
Papain-like cysteine endopeptidase + 37 + 41 318 - IPR003137
PA domain - 38 - 55 + IPR002495
Glycosyl transferase, family 8 + 37 + 50 319 - IPR004263
Exostosin-like - 38 - 49 + IPR006094
FAD linked oxidase, N-terminal + 37 + 44 320 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 38 - 51 + IPR028889
Ubiquitin specific protease domain + 37 + 46 321 - IPR004839
Aminotransferase, class I/classII - 38 - 70 + IPR039361
Cyclin + 37 + 59 322 - IPR007125
Histone H2A/H2B/H3 - 38 - 46 + IPR002912
ACT domain + 37 + 107 323 - IPR001077
O-methyltransferase, family 2 - 38 - 43 + IPR012967
Plant methyltransferase dimerisation + 37 + 38 324 - IPR006671
Cyclin, N-terminal - 38 - 90 + IPR016040
NAD(P)-binding domain + 36 + 51 325 - IPR013780
  - 38 - 144 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 36 + 44 326 - IPR002912
  - 38 - 268 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 36 + 48 327 - IPR014721
  - 38 - 134 + IPR034294
Aquaporin transporter + 36 + 39 328 - IPR015947
PUA-like superfamily - 38 - 52 + IPR004883
Lateral organ boundaries, LOB + 36 + 79 329 - IPR006626
Parallel beta-helix repeat - 37 - 240 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 36 + 47 330 - IPR007493
Protein of unknown function DUF538 - 37 - 92 + IPR019378
GDP-fucose protein O-fucosyltransferase + 36 + 75 331 - IPR002068
  - 37 - 148 + IPR040911
Exostosin, GT47 domain + 36 + 52 332 - IPR023271
  - 37 - 204 + IPR013126
Heat shock protein 70 family + 36 + 82 333 - IPR013154
Alcohol dehydrogenase, N-terminal - 37 - 52 + IPR011043
Galactose oxidase/kelch, beta-propeller + 36 + 42 334 - IPR003594
Histidine kinase/HSP90-like ATPase - 37 - 150 + IPR006311
Twin-arginine translocation pathway, signal sequence + 36 + 40 335 - IPR006652
Kelch repeat type 1 - 37 - 215 + IPR013149
Alcohol dehydrogenase, C-terminal + 35 + 51 336 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 37 - 49 + IPR025452
Domain of unknown function DUF4218 + 35 + 35 337 - IPR036758
  - 37 - 182 + IPR043454
NPH3/RPT2-like family + 35 + 43 338 - IPR019378
GDP-fucose protein O-fucosyltransferase - 37 - 64 + IPR002067
Mitochondrial carrier protein + 35 + 235 339 - IPR000425
Major intrinsic protein - 37 - 360 + IPR006458
Ovate protein family, C-terminal + 35 + 68 340 - IPR013149
Alcohol dehydrogenase, C-terminal - 36 - 56 + IPR004314
Neprosin + 35 + 50 341 - IPR000315
  - 36 - 621 + IPR043519
Nucleotidyltransferase superfamily + 35 + 49 342 - IPR011016
  - 36 - 402 + IPR036041
Ribosome-inactivating protein superfamily + 35 + 46 343 - IPR036691
  - 36 - 422 + IPR007811
DNA-directed RNA polymerase III subunit RPC4 + 35 + 89 344 - IPR036865
  - 36 - 178 + IPR001574
Ribosome-inactivating protein + 35 + 71 345 - IPR034294
Aquaporin transporter - 36 - 45 + IPR008991
Translation protein SH3-like domain superfamily + 34 + 43 346 - IPR022742
Serine aminopeptidase, S33 - 36 - 48 + IPR038933
Ovate protein family + 34 + 36 347 - IPR004883
  - 36 - 162 + IPR027356
NPH3 domain + 34 + 76 348 - IPR004046
Glutathione S-transferase, C-terminal - 36 - 54 + IPR006652
Kelch repeat type 1 + 34 + 64 349 - IPR002495
Glycosyl transferase, family 8 - 36 - 50 + IPR003311
AUX/IAA protein + 34 + 46 350 - IPR006094
FAD linked oxidase, N-terminal - 36 - 41 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 34 + 53 351 - IPR002067
Mitochondrial carrier protein - 36 - 231 + IPR001929
Germin + 33 + 111 352 - IPR019793
Peroxidases heam-ligand binding site - 35 - 47 + IPR025312
Domain of unknown function DUF4216 + 33 + 33 353 - IPR018200
Ubiquitin specific protease, conserved site - 34 - 73 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 127 354 - IPR001296
Glycosyl transferase, family 1 - 34 - 55 + IPR027806
Harbinger transposase-derived nuclease domain + 33 + 33 355 - IPR027356
  - 34 - 164 + IPR002423
Chaperonin Cpn60/TCP-1 family + 33 + 47 356 - IPR033131
Pectinesterase, Asp active site - 34 - 36 + IPR000795
Translational (tr)-type GTP-binding domain + 33 + 294 357 - IPR038770
  - 34 - 90 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 47 358 - IPR000863
Sulfotransferase domain - 34 + IPR004367
Cyclin, C-terminal domain + 33 44 359 - IPR022357
Major intrinsic protein, conserved site - 34 - 44 + IPR000863
Sulfotransferase domain + 33 + 42 360 - IPR006458
  - 34 - 194 + IPR027409
GroEL-like apical domain superfamily + 33 + 45 361 - IPR013126
Heat shock protein 70 family - 34 - 303 + IPR011141
Polyketide synthase, type III + 33 + 38 362 - IPR025661
Cysteine peptidase, asparagine active site - 34 - 37 + IPR000315
B-box-type zinc finger + 32 + 84 363 - IPR002487
  - 34 - 372 + IPR001296
Glycosyl transferase, family 1 + 32 + 49 364 - IPR006311
  - 34 - 78 - + IPR001881
EGF-like calcium-binding domain + 32 + 41 + 365 - IPR001251
  - 33 - 312 + IPR005135
Endonuclease/exonuclease/phosphatase + 32 + 50 366 - IPR038933
Ovate protein family - 33 - 38 + IPR022742
Serine aminopeptidase, S33 + 32 + 46 367 - IPR008266
Tyrosine-protein kinase, active site - 33 - 50 + IPR002963
Expansin + 32 + 275 368 - IPR038538
  - 33 - 98 + IPR006073
GTP binding domain + 32 + 105 369 - IPR027923
Hydrophobic seed protein - 33 - 62 + IPR001099
Chalcone/stilbene synthase, N-terminal + 32 + 36 370 - IPR002035
  - 33 - 226 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 31 + 169 371 - IPR004088
K Homology domain, type 1 - 33 - 103 + IPR019956
Ubiquitin domain + 31 + 95 372 - IPR004314
Neprosin - 33 - 55 + IPR018490
Cyclic nucleotide-binding-like + 31 + 49 373 - IPR009091
  - 33 - 320 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 31 + 90 374 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 32 - 261 + IPR029061
Thiamin diphosphate-binding fold + 31 + 64 375 - IPR004087
K Homology domain - 32 - 103 + IPR044848
PHR1-like + 31 + 46 376 - IPR003311
AUX/IAA protein - 32 - 55 + IPR003851
Zinc finger, Dof-type + 31 + 70 377 - IPR020843
Polyketide synthase, enoylreductase domain - 32 - 46 + IPR000595
Cyclic nucleotide-binding domain + 31 + 122 378 IPR001223
Glycoside hydrolase family 18, catalytic domain - 32 - 37 + 31 + 67 379 - IPR012967
Plant methyltransferase dimerisation - 32 - 32 + IPR023210
NADP-dependent oxidoreductase domain + 31 + 52 380 - IPR013601
FAE1/Type III polyketide synthase-like protein - 31 - 33 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 31 + 48 381 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 31 - 58 + IPR000757
Glycoside hydrolase family 16 + 31 + 82 382 - IPR032710
NTF2-like domain superfamily - 31 - 46 + IPR015940
Ubiquitin-associated domain + 30 + 82 383 - IPR001360
Glycoside hydrolase family 1 - 31 - 431 + IPR010920
LSM domain superfamily + 30 + 34 384 - IPR005135
Endonuclease/exonuclease/phosphatase - 31 - 57 + IPR005299
SAM dependent carboxyl methyltransferase + 30 + 89 385 - IPR000795
  - 31 - 828 + IPR000717
Proteasome component (PCI) domain + 30 + 76 386 - IPR003406
Glycosyl transferase, family 14 - 31 - 42 + IPR007657
Glycosyltransferase 61 + 30 + 65 387 - IPR036041
Ribosome-inactivating protein superfamily - 31 - 36 + IPR007650
Zf-FLZ domain + 30 + 75 388 - IPR000757
  - 31 - 213 + IPR005150
Cellulose synthase + 30 + 74 389 - IPR006073
GTP binding domain - 31 - 112 + IPR003406
Glycosyl transferase, family 14 + 30 + 41 390 - IPR016040
NAD(P)-binding domain - 30 - 48 + IPR008480
Protein of unknown function DUF761, plant + 30 + 30 391 - IPR015940
  - 30 - 242 + IPR033443
Pentacotripeptide-repeat region of PRORP + 30 + 42 392 - IPR018490
Cyclic nucleotide-binding-like - 30 - 53 + IPR044791
Beta-glucanase/XTH + 30 + 43 393 - IPR019821
Kinesin motor domain, conserved site - 30 - 56 + IPR000727
Target SNARE coiled-coil homology domain + 29 + 53 394 - IPR025753
AAA-type ATPase, N-terminal domain - 30 - 32 + IPR025110
AMP-binding enzyme, C-terminal domain + 29 + 34 395 - IPR005299
SAM dependent carboxyl methyltransferase - 30 - 103 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 29 + 29 396 - IPR002423
Chaperonin Cpn60/TCP-1 family - 30 - 54 + IPR006153
Cation/H+ exchanger + 29 + 43 397 - IPR031112
AP2-like ethylene-responsive transcription factor - 30 - 54 + IPR013187
F-box associated domain, type 3 + 29 + 30 398 - IPR011013
Galactose mutarotase-like domain superfamily - 30 - 48 + IPR029000
Cyclophilin-like domain superfamily + 29 + 42 399 - IPR008480
Protein of unknown function DUF761, plant - 30 + IPR025753
AAA-type ATPase, N-terminal domain + 29 30 400 - IPR027409
  - 30 - 204 + IPR002659
Glycosyl transferase, family 31 + 29 + 104 401 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 30 + IPR001594
Palmitoyltransferase, DHHC domain + 29 44 402 - IPR000169
Cysteine peptidase, cysteine active site - 30 - 33 + IPR005333
Transcription factor, TCP + 29 + 32 403 - IPR003851
  - 30 - 384 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 29 + 39 404 - IPR013187
F-box associated domain, type 3 - 29 - 33 + IPR003337
Trehalose-phosphatase + 29 + 34 405 - IPR008991
Translation protein SH3-like domain superfamily - 29 - 38 + IPR000408
Regulator of chromosome condensation, RCC1 + 29 + 577 406 - IPR000717
  - 29 - 164 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 43 407 - IPR002659
Glycosyl transferase, family 31 - 29 - 84 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 29 + 33 408 - IPR009030
Growth factor receptor cysteine-rich domain superfamily - 29 - 42 + IPR016897
S-phase kinase-associated protein 1 + 29 + 35 409 - IPR007650
  - 29 - 136 + IPR005821
Ion transport domain + 29 + 41 410 - IPR000408
  - 29 - 1368 + IPR036404
Jacalin-like lectin domain superfamily + 29 + 52 411 - IPR002355
Multicopper oxidase, copper-binding site - 29 - 35 + IPR003855
Potassium transporter + 29 + 93 412 - IPR005150
Cellulose synthase - 29 - 81 + IPR000679
Zinc finger, GATA-type + 29 + 98 413 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 58 + IPR001229
Jacalin-like lectin domain + 29 + 98 414 - IPR000595
  - 29 - 354 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 28 + 36 415 - IPR003855
Potassium transporter - 29 - 128 + IPR017938
Riboflavin synthase-like beta-barrel + 28 + 36 416 - IPR011141
Polyketide synthase, type III - 29 - 55 + IPR036378
FAS1 domain superfamily + 28 + 40 417 - IPR023210
NADP-dependent oxidoreductase domain - 29 - 88 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 28 + 233 418 - IPR036812
  - 29 - 174 + IPR024709
Putative O-fucosyltransferase, plant + 28 + 64 419 - IPR001099
Chalcone/stilbene synthase, N-terminal - 29 - 35 + IPR044835
Auxin response factor + 28 + 50 420 - IPR036378
  - 28 - 144 + IPR013216
Methyltransferase type 11 + 28 + 40 421 - IPR006153
Cation/H+ exchanger - 28 - 51 + IPR001763
Rhodanese-like domain + 28 + 57 422 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 28 - 39 + IPR002123
Phospholipid/glycerol acyltransferase + 28 + 43 423 - IPR027725
Heat shock transcription factor family - 28 - 36 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 28 + 37 424 - IPR001594
Palmitoyltransferase, DHHC domain - 28 - 53 + IPR036296
SKP1-like, dimerisation domain superfamily + 28 + 33 425 - IPR035940
  - 28 - 172 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 28 + 31 426 - IPR004367
Cyclin, C-terminal domain - 28 - 76 + IPR002913
START domain + 28 + 87 427 - IPR002123
Phospholipid/glycerol acyltransferase - 28 - 69 + IPR013601
FAE1/Type III polyketide synthase-like protein + 27 + 27 428 - IPR002963
Expansin - 28 - 243 + IPR032710
NTF2-like domain superfamily + 27 + 36 429 - IPR005821
Ion transport domain - 28 - 45 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 27 + 88 430 - IPR031107
Small heat shock protein HSP20 - 28 - 31 + IPR036420
BRCT domain superfamily + 27 + 64 431 - IPR014722
  - 28 - 96 + IPR011016
Zinc finger, RING-CH-type + 27 + 70 432 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 28 - 32 + IPR008422
Homeobox KN domain + 27 + 37 433 - IPR036404
  - 28 - 192 + IPR027725
Heat shock transcription factor family + 27 + 32 434 - IPR029047
  - 28 - 128 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 27 + 31 435 - IPR018202
Serine carboxypeptidase, serine active site - 28 - 43 + IPR044814
Terpene cyclases, class 1, plant + 27 + 35 436 - IPR001229
  - 28 - 274 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 27 + 34 437 - IPR000727
  - 27 - 190 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 34 438 - IPR001929
Germin - 27 - 111 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 27 + 40 439 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 27 - 90 + IPR039421
Type 1 protein exporter + 27 + 41 440 - IPR024709
Putative O-fucosyltransferase, plant - 27 - 82 + IPR023299
P-type ATPase, cytoplasmic domain N + 27 + 49 441 - IPR010920
LSM domain superfamily - 27 - 34 + IPR001757
P-type ATPase + 27 + 121 442 - IPR023753
FAD/NAD(P)-binding domain - 27 - 40 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 27 + 42 443 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 27 - 33 + IPR005175
PPC domain + 27 + 83 444 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 27 - 72 + IPR033734
Jacalin-like lectin domain, plant + 27 + 45 445 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 27 - 40 + IPR001357
BRCT domain + 26 + 109 446 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 53 + IPR044778
Sugar transport protein STP/MST-like, plant + 26 + 33 447 - IPR016167
  - 27 - 123 + IPR023753
FAD/NAD(P)-binding domain + 26 + 38 448 - IPR014044
CAP domain - 27 - 82 + IPR016072
SKP1 component, dimerisation + 26 + 31 449 - IPR029062
  - 27 - 202 + IPR034288
Laccase, first cupredoxin domain + 26 + 29 450 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 27 - 58 + IPR034285
Laccase, second cupredoxin domain + 26 + 29 451 - IPR000679
  - 27 - 405 + IPR002035
von Willebrand factor, type A + 26 + 63 452 - IPR005175
  - 27 - 184 + IPR001849
Pleckstrin homology domain + 26 + 60 453 - IPR001574
Ribosome-inactivating protein - 27 - 31 + IPR029062
Class I glutamine amidotransferase-like + 26 + 47 454 - IPR033734
Jacalin-like lectin domain, plant - 27 - 44 + IPR012328
Chalcone/stilbene synthase, C-terminal + 26 + 26 455 - IPR017927
  - 26 - 105 + IPR001701
Glycoside hydrolase family 9 + 26 + 28 456 - IPR025110
AMP-binding enzyme, C-terminal domain - 26 - 37 + IPR015797
NUDIX hydrolase-like domain superfamily + 26 + 31 457 - IPR017938
Riboflavin synthase-like beta-barrel - 26 - 41 + IPR000782
FAS1 domain + 25 + 63 458 - IPR002130
  - 26 - 606 + IPR002867
IBR domain + 25 + 63 459 - IPR029000
  - 26 - 146 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 25 + 25 460 - IPR013088
  - 26 - 105 + IPR017887
Transcription factor TCP subgroup + 25 + 50 461 - IPR029061
Thiamin diphosphate-binding fold - 26 - 69 + IPR020946
Flavin monooxygenase-like + 25 + 46 462 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 26 - 33 + IPR004813
Oligopeptide transporter, OPT superfamily + 25 + 52 463 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 26 - 141 + IPR029069
HotDog domain superfamily + 25 + 56 464 - IPR001849
  - 26 - 242 + IPR025486
Domain of unknown function DUF4378 + 25 + 36 465 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 26 - 57 + IPR036085
PAZ domain superfamily + 24 + 44 466 - IPR036296
SKP1-like, dimerisation domain superfamily - 26 - 40 + IPR003106
Leucine zipper, homeobox-associated + 24 + 27 467 - IPR001701
Glycoside hydrolase family 9 - 26 - 34 + IPR006912
Harbinger transposase-derived protein + 24 + 25 468 - IPR025486
Domain of unknown function DUF4378 - 26 - 38 + IPR008999
Actin-crosslinking + 24 + 28 469 - IPR016138
  - 26 - 60 + IPR025422
Transcription factor TGA like domain + 24 + 104 470 - IPR036034
PDZ superfamily - 26 - 44 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 24 + 34 471 - IPR025660
Cysteine peptidase, histidine active site - 26 - 34 + IPR003594
Histidine kinase/HSP90-like ATPase + 24 + 31 472 - IPR002913
  - 26 - 390 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 24 + 24 473 - IPR000528
Plant lipid transfer protein/Par allergen - 25 - 140 + IPR045048
F-box only protein 31/39 + 24 + 57 474 - IPR000782
  - 25 - 186 + IPR006461
PLAC8 motif-containing protein + 24 + 48 475 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 25 - 25 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 24 + 49 476 - IPR001179
  - 25 - 208 + IPR041679
DNA2/NAM7 helicase-like, C-terminal + 24 + 101 477 - IPR036420
  - 25 - 360 + IPR041677
DNA2/NAM7 helicase, helicase domain + 24 + 70 478 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 25 - 27 + IPR045055
DNA2/NAM7-like helicase + 24 + 76 479 - IPR003337
Trehalose-phosphatase - 25 - 72 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 24 + 101 480 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 25 - 33 + IPR031127
E3 ubiquitin ligase RBR family + 24 + 60 481 - IPR033905
Secretory peroxidase - 25 - 41 + IPR036034
PDZ superfamily + 24 + 31 482 - IPR005746
Thioredoxin - 25 - 46 + IPR002937
Amine oxidase + 24 + 42 483 - IPR012328
Chalcone/stilbene synthase, C-terminal - 25 - 26 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 24 + 35 484 - IPR002937
Amine oxidase - 25 - 48 + IPR029033
Histidine phosphatase superfamily + 24 + 37 485 - IPR015797
NUDIX hydrolase-like domain superfamily - 25 - 28 + IPR010525
Auxin response factor domain + 24 + 32 486 - IPR010525
Auxin response factor - 25 - 39 + IPR016073
SKP1 component, POZ domain + 23 + 25 487 - IPR036085
PAZ domain superfamily - 24 - 79 + IPR008971
HSP40/DnaJ peptide-binding + 23 + 55 488 - IPR033138
Multicopper oxidases, conserved site - 24 - 28 + IPR004316
SWEET sugar transporter + 23 + 42 489 - IPR001357
  - 24 - 604 + IPR013581
Plant PDR ABC transporter associated + 23 + 42 490 - IPR013216
Methyltransferase type 11 - 24 - 32 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 + 26 491 - IPR007657
Glycosyltransferase 61 - 24 - 70 + IPR018392
LysM domain + 23 + 91 492 - IPR005333
Transcription factor, TCP - 24 - 24 + IPR036010
2Fe-2S ferredoxin-like superfamily + 23 + 33 493 - IPR017887
  - 24 - 48 + IPR001353
Proteasome, subunit alpha/beta + 23 + 29 494 - IPR018181
Heat shock protein 70, conserved site - 24 - 69 + IPR027413
GroEL-like equatorial domain superfamily + 23 + 32 495 - IPR033124
Serine carboxypeptidases, histidine active site - 24 - 36 + IPR006694
Fatty acid hydroxylase + 23 + 26 496 - IPR025422
  - 24 - 321 + IPR001199
Cytochrome b5-like heme/steroid binding domain + 23 + 97 497 - IPR001763
  - 24 - 180 + IPR000215
Serpin family + 23 + 31 498 - IPR000960
Flavin monooxygenase FMO - 24 - 69 + IPR022796
Chlorophyll A-B binding protein + 23 + 23 499 - IPR016072
SKP1 component, dimerisation - 24 - 38 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 23 + 30 500 - IPR025875
Leucine rich repeat 4 - 24 - 32 + IPR034289
Laccase, third cupredoxin domain + 23 + 24 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_punctata.html b/gramene/htdocs/ssi/species/stats_Oryza_punctata.html index 8294fc97..57e64b30 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_punctata.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_punctata.html @@ -4,29 +4,29 @@

Summary

- + - + - + - + -
Assembly:AVCL00000000, Aug 2013AGI_PacBIO,
Database version:93.1287.4
Base Pairs:393,816,603422,391,326
Golden Path Length:393,816,603422,391,326
Genebuild by: OGE
Genebuild method: Imported from OGE MAKER annotation
Genebuild started: Sep 2013
Genebuild version: 2013-09
+

Gene counts

- - + + - - + +
Coding genesHASH(0x68bff40):31,762Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		35,091
Gene transcriptsHASH(0x68ce400):47,089Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,443
@@ -37,38 +37,79 @@

Coordinate Systems

chromosome
-
12 sequences
+
61 sequences
+1
SequenceLength (bp)
146096743
239559433
338925377
433711903
531082981
634615992
731244610
829853973
926294017
1025992119
1128494620
1227944835
48196116
242391796
340826366
434321815
532501981
637950339
733104438
831250912
928723895
1027915717
1131610942
1230283698
UN-Ctg36365518
UN-Ctg37155778
UN-Ctg38151772
UN-Ctg39131053
UN-Ctg40119123
UN-Ctg4198710
UN-Ctg4296464
UN-Ctg4395309
UN-Ctg4493966
UN-Ctg4585563
UN-Ctg4679482
UN-Ctg4774524
UN-Ctg4873832
UN-Ctg4972033
UN-Ctg5070534
UN-Ctg5166963
UN-Ctg5260476
UN-Ctg5359204
UN-Ctg5457313
UN-Ctg5557041
UN-Ctg5656574
UN-Ctg5755668
UN-Ctg5854526
UN-Ctg5953794
UN-Ctg6053363
UN-Ctg6151294
UN-Ctg6246932
UN-Ctg6348742
UN-Ctg6448628
UN-Ctg6548523
UN-Ctg6648313
UN-Ctg6748276
UN-Ctg6846791
UN-Ctg6943546
UN-Ctg7043808
UN-Ctg7142550
UN-Ctg7242019
UN-Ctg7341150
UN-Ctg7440285
UN-Ctg7539977
UN-Ctg7639429
UN-Ctg7738880
UN-Ctg7838117
UN-Ctg7938232
UN-Ctg8035275
UN-Ctg8128298
UN-Ctg8227050
UN-Ctg8325138
UN-Ctg8423475
-
+
chunk - 3943 sequences + 4254 sequences - -

Other

- - - - - -
FGENESH gene predictions:45,833
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_punctata_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_punctata_IPtop500.html index 85a97aed..856c77cc 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_punctata_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_punctata_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1339 - 2206 + 1390 + 1963 2 - IPR000719
  - 1283 - 14664 + IPR000719
Protein kinase domain + 1328 + 3150 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1237 - 2544 + 1280 + 2113 4 - IPR008271
Serine/threonine-protein kinase, active site - 1011 - 1554 + IPR036047
F-box-like domain superfamily + 558 + 707 5 - IPR032675
  - 978 - 5420 + IPR002885
Pentatricopeptide repeat + 489 + 6645 6 - IPR017441
Protein kinase, ATP binding site - 888 - 1292 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 461 + 853 7 - IPR011990
  - 720 - 10935 + IPR001611
Leucine-rich repeat + 441 + 1425 8 - IPR013083
  - 671 - 2046 + IPR001841
Zinc finger, RING-type + 440 + 882 9 - IPR036047
F-box-like domain superfamily - 503 - 694 + IPR029058
Alpha/Beta hydrolase fold + 388 + 596 10 - IPR002885
  - 493 - 27820 + IPR009057
Homeobox-like domain superfamily + 386 + 500 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 433 - 937 + IPR001810
F-box domain + 385 + 715 12 - IPR001611
  - 430 - 9885 + IPR036291
NAD(P)-binding domain superfamily + 367 + 540 13 - IPR001841
  - 419 - 2776 + IPR016024
Armadillo-type fold + 362 + 587 14 - IPR029058
  - 388 - 2540 + IPR044974
Disease resistance protein, plants + 362 + 588 15 - IPR001810
  - 374 - 3144 + IPR011990
Tetratricopeptide-like helical domain superfamily + 333 + 542 16 - IPR036291
NAD(P)-binding domain superfamily - 367 - 616 + IPR038765
Papain-like cysteine peptidase superfamily + 327 + 432 17 - IPR016024
Armadillo-type fold - 359 - 1291 + IPR002182
NB-ARC + 322 + 404 18 - IPR009057
Homeobox-like domain superfamily - 337 - 499 + IPR012337
Ribonuclease H-like superfamily + 308 + 391 19 - IPR002182
NB-ARC - 322 - 435 + IPR036396
Cytochrome P450 superfamily + 299 + 387 20 - IPR035979
RNA-binding domain superfamily - 294 - 652 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 298 + 363 21 - IPR012677
  - 286 - 1364 + IPR035979
RNA-binding domain superfamily + 295 + 610 22 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 285 - 382 + IPR001128
Cytochrome P450 + 291 + 1380 23 - IPR003593
AAA+ ATPase domain - 284 - 554 + IPR041118
Rx, N-terminal + 274 + 314 24 - IPR036396
  - 281 - 2547 + IPR000504
RNA recognition motif domain + 267 + 1183 25 - IPR001128
Cytochrome P450 - 277 - 1416 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 255 + 416 26 - IPR003591
Leucine-rich repeat, typical subtype - 275 - 2606 + IPR017853
Glycoside hydrolase superfamily + 253 + 397 27 - IPR000504
  - 268 - 5397 + IPR036259
MFS transporter superfamily + 252 + 367 28 - IPR015943
  - 259 - 1836 + IPR002401
Cytochrome P450, E-class, group I + 246 + 1795 29 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 255 - 509 + IPR017930
Myb domain + 243 + 777 30 - IPR038765
Papain-like cysteine peptidase superfamily - 253 - 475 + IPR001005
SANT/Myb domain + 238 + 792 31 - IPR036259
MFS transporter superfamily - 242 - 621 + IPR036322
WD40-repeat-containing domain superfamily + 236 + 412 32 - IPR001680
  - 241 - 11499 + IPR036249
Thioredoxin-like superfamily + 229 + 364 33 - IPR036322
WD40-repeat-containing domain superfamily - 241 - 615 + IPR001680
WD40 repeat + 215 + 1861 34 - IPR017853
Glycoside hydrolase superfamily - 239 - 448 + IPR043502
DNA/RNA polymerase superfamily + 202 + 218 35 - IPR002401
Cytochrome P450, E-class, group I - 237 - 1834 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 192 + 220 36 - IPR011989
  - 236 - 964 + IPR011992
EF-hand domain pair + 190 + 264 37 - IPR036249
Thioredoxin-like superfamily - 236 - 406 + IPR016177
DNA-binding domain superfamily + 182 + 243 38 - IPR001005
SANT/Myb domain - 224 - 1046 + IPR002048
EF-hand domain + 176 + 1012 39 - IPR017972
Cytochrome P450, conserved site - 224 - 310 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 174 + 211 40 - IPR017986
  - 218 - 1146 + IPR001471
AP2/ERF domain + 170 + 951 41 - IPR011992
EF-hand domain pair - 185 - 296 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 165 + 373 42 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 180 - 224 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 164 + 352 43 - IPR020846
  - 173 - 846 + IPR036236
Zinc finger C2H2 superfamily + 163 + 232 44 - IPR002048
  - 171 - 4986 + IPR036412
HAD-like superfamily + 162 + 255 45 - IPR013087
  - 170 - 2523 + IPR036390
Winged helix DNA-binding domain superfamily + 156 + 201 46 - IPR036638
  - 169 - 1194 + IPR021109
Aspartic peptidase domain superfamily + 151 + 181 47 - IPR016177
DNA-binding domain superfamily - 169 - 237 + IPR036875
Zinc finger, CCHC-type superfamily + 150 + 217 48 - IPR036388
  - 169 - 472 + IPR001878
Zinc finger, CCHC-type + 148 + 463 49 - IPR017930
  - 166 - 634 + IPR011333
SKP1/BTB/POZ domain superfamily + 146 + 190 50 - IPR036412
HAD-like superfamily - 163 - 359 + IPR036093
NAC domain superfamily + 146 + 162 51 - IPR011598
  - 160 - 2076 + IPR036770
Ankyrin repeat-containing domain superfamily + 145 + 188 52 - IPR001471
  - 159 - 3261 + IPR001650
Helicase, C-terminal + 142 + 477 53 - IPR036955
  - 159 - 624 + IPR013087
Zinc finger C2H2-type + 142 + 303 54 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 156 - 194 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 140 + 171 55 - IPR036390
Winged helix DNA-binding domain superfamily - 155 - 202 + IPR012340
Nucleic acid-binding, OB-fold + 140 + 259 56 - IPR018247
EF-Hand 1, calcium-binding site - 154 - 487 + IPR029044
Nucleotide-diphospho-sugar transferases + 139 + 202 57 - IPR029044
  - 152 - 1200 + IPR010255
Haem peroxidase superfamily + 139 + 171 58 - IPR023214
  - 150 - 730 + IPR002016
Haem peroxidase + 138 + 977 59 - IPR014001
  - 147 - 982 + IPR003441
NAC domain + 136 + 299 60 - IPR011333
SKP1/BTB/POZ domain superfamily - 144 - 205 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 135 + 233 61 - IPR001650
  - 142 - 1890 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 133 + 168 62 - IPR036236
Zinc finger C2H2 superfamily - 141 - 249 + IPR002110
Ankyrin repeat + 130 + 512 63 - IPR036093
  - 140 - 945 + IPR003439
ABC transporter-like, ATP-binding domain + 127 + 590 64 - IPR019775
WD40 repeat, conserved site - 137 - 355 + IPR036188
FAD/NAD(P)-binding domain superfamily + 126 + 210 65 - IPR003441
  - 136 - 921 + IPR000823
Plant peroxidase + 124 + 1058 66 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 135 - 203 + IPR005174
Domain unknown function DUF295 + 121 + 142 67 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 132 - 169 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 120 + 210 68 - IPR003439
  - 130 - 1710 + IPR036869
Chaperone J-domain superfamily + 117 + 147 69 - IPR020683
  - 129 - 1300 + IPR003959
ATPase, AAA-type, core + 116 + 179 70 - IPR036770
  - 129 - 970 + IPR018289
MULE transposase domain + 115 + 117 71 - IPR036188
  - 128 - 1496 + IPR033905
Secretory peroxidase + 114 + 132 72 - IPR014710
  - 124 - 398 + IPR036426
Bulb-type lectin domain superfamily + 114 + 148 73 - IPR014729
  - 124 - 452 + IPR001623
DnaJ domain + 112 + 712 74 - IPR013026
  - 123 - 810 + IPR007527
Zinc finger, SWIM-type + 111 + 174 75 - IPR035595
UDP-glycosyltransferase family, conserved site - 119 - 143 + IPR001087
GDSL lipase/esterase + 110 + 148 76 - IPR036869
  - 117 - 598 + IPR001480
Bulb-type lectin domain + 110 + 379 77 - IPR023213
  - 116 - 480 + IPR020846
Major facilitator superfamily domain + 109 + 149 78 - IPR036514
  - 116 - 328 + IPR003480
Transferase + 107 + 115 79 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 116 - 230 + IPR000210
BTB/POZ domain + 106 + 270 80 - IPR012340
Nucleic acid-binding, OB-fold - 115 - 220 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 105 + 164 81 - IPR002110
  - 115 - 3729 + IPR011011
Zinc finger, FYVE/PHD-type + 105 + 196 82 - IPR019734
  - 114 - 4599 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 104 + 159 83 - IPR003959
ATPase, AAA-type, core - 114 + IPR035892
C2 domain superfamily + 103 196 84 - IPR021109
  - 112 - 822 + IPR031052
FHY3/FAR1 family + 103 + 182 85 - IPR001623
  - 112 - 1650 + IPR020683
Ankyrin repeat-containing domain + 103 + 192 86 - IPR000210
  - 111 - 1146 + IPR036576
WRKY domain superfamily + 102 + 127 87 - IPR001461
Aspartic peptidase A1 family - 110 - 325 + IPR019734
Tetratricopeptide repeat + 101 + 373 88 - IPR036426
  - 106 - 736 + IPR008972
Cupredoxin + 101 + 209 89 - IPR008972
  - 104 - 894 + IPR029071
Ubiquitin-like domain superfamily + 101 + 175 90 - IPR005123
  - 104 - 933 + IPR003657
WRKY domain + 101 + 250 91 - IPR011011
Zinc finger, FYVE/PHD-type - 104 - 198 + IPR015424
Pyridoxal phosphate-dependent transferase + 101 + 149 92 - IPR033121
  - 103 - 258 + IPR033121
Peptidase family A1 domain + 100 + 134 93 - IPR001087
GDSL lipase/esterase - 102 - 138 + IPR001584
Integrase, catalytic core + 99 + 154 94 - IPR015424
Pyridoxal phosphate-dependent transferase - 102 - 174 + IPR000477
Reverse transcriptase domain + 99 + 151 95 - IPR013785
  - 101 - 618 + IPR044810
WRKY transcription factor, plant + 98 + 108 96 - IPR001480
  - 101 - 822 + IPR035669
GDSL lipase/esterase-like, plant + 97 + 120 97 - IPR003480
Transferase - 101 - 127 + IPR001356
Homeobox domain + 96 + 300 98 - IPR035669
GDSL lipase/esterase-like, plant - 100 - 135 + IPR032861
Xylanase inhibitor, N-terminal + 95 + 123 99 - IPR011051
RmlC-like cupin domain superfamily - 100 - 165 + IPR003609
PAN/Apple domain + 93 + 218 100 - IPR015421
  - 99 - 474 + IPR032799
Xylanase inhibitor, C-terminal + 93 + 120 101 - IPR012337
Ribonuclease H-like superfamily - 99 - 192 + IPR011051
RmlC-like cupin domain superfamily + 93 + 121 102 - IPR032861
Xylanase inhibitor, N-terminal - 99 - 119 + IPR011050
Pectin lyase fold/virulence factor + 92 + 102 103 - IPR005225
Small GTP-binding protein domain - 99 - 129 + IPR011676
Domain of unknown function DUF1618 + 92 + 111 104 - IPR036576
  - 98 - 717 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 91 + 115 105 - IPR032799
Xylanase inhibitor, C-terminal - 98 - 117 + IPR000008
C2 domain + 90 + 393 106 - IPR003657
  - 98 - 1059 + IPR000073
Alpha/beta hydrolase fold-1 + 90 + 278 107 - IPR008974
  - 98 - 804 + IPR025315
Domain of unknown function DUF4220 + 90 + 101 108 - IPR027443
  - 97 - 350 + IPR000858
S-locus glycoprotein domain + 88 + 109 109 - IPR005174
Domain unknown function DUF295 - 96 - 125 + IPR007658
Protein of unknown function DUF594 + 88 + 90 110 - IPR001356
  - 95 - 1290 + IPR004827
Basic-leucine zipper domain + 88 + 213 111 - IPR011050
Pectin lyase fold/virulence factor - 94 - 116 + IPR020472
G-protein beta WD-40 repeat + 87 + 414 112 - IPR032867
DYW domain - 94 - 114 + IPR011545
DEAD/DEAH box helicase domain + 87 + 151 113 - IPR035892
  - 90 - 384 + IPR036457
PPM-type phosphatase domain superfamily + 86 + 137 114 - IPR017871
ABC transporter, conserved site - 90 - 163 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 86 + 132 115 - IPR015422
  - 90 - 654 + IPR001932
PPM-type phosphatase domain + 86 + 422 116 - IPR003609
  - 89 - 636 + IPR002156
Ribonuclease H domain + 85 + 137 117 - IPR020472
G-protein beta WD-40 repeat - 89 - 420 + IPR015300
DNA-binding pseudobarrel domain superfamily + 85 + 157 118 - IPR000073
Alpha/beta hydrolase fold-1 - 89 - 265 + IPR026992
Non-haem dioxygenase N-terminal domain + 84 + 131 119 - IPR011545
DEAD/DEAH box helicase domain - 89 - 155 + IPR002347
Short-chain dehydrogenase/reductase SDR + 83 + 767 120 - IPR015300
  - 89 - 676 + IPR032867
DYW domain + 83 + 93 121 - IPR012334
  - 89 - 208 + IPR003340
B3 DNA binding domain + 82 + 422 122 - IPR000008
  - 88 - 1090 + IPR000109
Proton-dependent oligopeptide transporter family + 82 + 265 123 - IPR006447
Myb domain, plants - 88 - 124 + IPR005828
Major facilitator, sugar transporter-like + 82 + 121 124 - IPR009072
  - 88 - 612 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 82 + 114 125 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 87 - 143 + IPR009072
Histone-fold + 82 + 98 126 - IPR004827
  - 87 - 1371 + IPR005162
Retrotransposon gag domain + 80 + 82 127 - IPR036457
  - 86 - 600 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 80 + 119 128 - IPR029071
Ubiquitin-like domain superfamily - 86 - 142 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 79 + 104 129 - IPR036397
  - 85 - 411 + IPR000270
PB1 domain + 79 + 132 130 - IPR001932
  - 85 - 1611 + IPR002083
MATH/TRAF domain + 78 + 238 131 - IPR001965
Zinc finger, PHD-type - 84 - 193 + IPR001461
Aspartic peptidase A1 family + 78 + 276 132 - IPR003653
  - 83 - 465 + IPR013766
Thioredoxin domain + 77 + 200 133 - IPR011676
Domain of unknown function DUF1618 - 83 - 104 + IPR003613
U box domain + 77 + 178 134 - IPR025315
Domain of unknown function DUF4220 - 83 + IPR036163
Heavy metal-associated domain superfamily + 76 101 135 - IPR002347
Short-chain dehydrogenase/reductase SDR - 82 - 806 + IPR004330
FAR1 DNA binding domain + 75 + 90 136 - IPR003340
  - 81 - 1854 + IPR006121
Heavy metal-associated domain, HMA + 74 + 244 137 - IPR000858
S-locus glycoprotein domain - 80 - 111 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 73 + 76 138 - IPR005828
Major facilitator, sugar transporter-like - 80 - 135 + IPR043129
ATPase, nucleotide binding domain + 72 + 173 139 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 80 - 134 + IPR036879
Transcription factor, MADS-box superfamily + 72 + 95 140 - IPR017907
Zinc finger, RING-type, conserved site - 79 - 114 + IPR004332
Transposase, MuDR, plant + 71 + 72 141 - IPR024171
S-receptor-like serine/threonine-protein kinase - 78 - 101 + IPR002100
Transcription factor, MADS-box + 71 + 446 142 - IPR007658
Protein of unknown function DUF594 - 78 - 82 + IPR004045
Glutathione S-transferase, N-terminal + 71 + 216 143 - IPR015655
Protein phosphatase 2C family - 78 - 113 + IPR036908
RlpA-like domain superfamily + 71 + 83 144 - IPR003613
  - 78 - 768 + IPR016039
Thiolase-like + 69 + 145 145 - IPR006121
  - 77 - 762 + IPR019557
Aminotransferase-like, plant mobile domain + 68 + 78 146 - IPR000109
Proton-dependent oligopeptide transporter family - 77 - 328 + IPR000626
Ubiquitin-like domain + 67 + 221 147 - IPR002083
  - 77 - 915 + IPR001220
Legume lectin domain + 67 + 144 148 - IPR026992
Non-haem dioxygenase N-terminal domain - 77 - 134 + IPR029052
Metallo-dependent phosphatase-like + 67 + 96 149 - IPR036163
Heavy metal-associated domain superfamily - 77 - 103 + IPR000571
Zinc finger, CCCH-type + 67 + 332 150 - IPR013783
  - 75 - 232 + IPR010987
Glutathione S-transferase, C-terminal-like + 66 + 92 151 - IPR013766
  - 75 - 564 + IPR013057
Amino acid transporter, transmembrane domain + 65 + 92 152 - IPR000742
  - 75 - 458 + IPR006501
Pectinesterase inhibitor domain + 65 + 68 153 - IPR016039
  - 74 - 858 + IPR009003
Peptidase S1, PA clan + 64 + 125 154 - IPR004045
  - 72 - 756 + IPR000048
IQ motif, EF-hand binding site + 64 + 346 155 - IPR036908
  - 71 - 332 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 63 + 73 156 - IPR000270
  - 71 - 510 + IPR023395
Mitochondrial carrier domain superfamily + 63 + 78 157 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 70 - 91 + IPR007117
Expansin, cellulose-binding-like domain + 63 + 145 158 - IPR003960
ATPase, AAA-type, conserved site - 70 - 106 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 62 + 105 159 - IPR002100
  - 69 - 1878 + IPR019787
Zinc finger, PHD-finger + 62 + 173 160 - IPR036879
  - 69 - 609 + IPR002902
Gnk2-homologous domain + 62 + 294 161 - IPR000225
  - 69 - 2202 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 435 162 - IPR035513
  - 68 - 282 + IPR013094
Alpha/beta hydrolase fold-3 + 62 + 77 163 - IPR010987
  - 68 - 232 + IPR026961
PGG domain + 61 + 130 164 - IPR001878
  - 67 - 1185 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 61 + 78 165 - IPR036961
  - 66 - 498 + IPR020568
Ribosomal protein S5 domain 2-type fold + 61 + 103 166 - IPR000571
  - 66 - 1734 + IPR001806
Small GTPase + 61 + 145 167 - IPR006045
Cupin 1 - 65 - 187 + IPR044965
Glycoside hydrolase family 17, plant + 60 + 85 168 - IPR001220
Legume lectin domain - 65 - 150 + IPR000490
Glycoside hydrolase family 17 + 60 + 73 169 - IPR036875
Zinc finger, CCHC-type superfamily - 64 - 104 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 59 + 85 170 - IPR013057
Amino acid transporter, transmembrane domain - 63 - 85 + IPR003245
Phytocyanin domain + 59 + 124 171 - IPR023395
  - 63 - 400 + IPR026057
PC-Esterase + 58 + 74 172 - IPR001806
Small GTPase superfamily - 63 - 83 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 58 + 62 173 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 62 - 92 + IPR039391
Phytocyanin + 57 + 61 174 - IPR018108
  - 62 - 976 + IPR006045
Cupin 1 + 57 + 89 175 - IPR000048
  - 62 - 1575 + IPR003663
Sugar/inositol transporter + 57 + 324 176 - IPR003245
  - 61 - 558 + IPR008949
Isoprenoid synthase domain superfamily + 56 + 88 177 - IPR006501
Pectinesterase inhibitor domain - 61 - 174 + IPR013525
ABC-2 type transporter + 56 + 120 178 - IPR009003
Peptidase S1, PA clan - 61 - 132 + IPR029962
Trichome birefringence-like family + 56 + 76 179 - IPR018097
EGF-like calcium-binding, conserved site - 61 - 81 + IPR007112
Expansin/pollen allergen, DPBB domain + 56 + 65 180 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 60 - 66 + IPR002528
Multi antimicrobial extrusion protein + 55 + 131 181 - IPR008979
  - 60 - 376 + IPR004158
Protein of unknown function DUF247, plant + 55 + 136 182 - IPR020568
Ribosomal protein S5 domain 2-type fold - 60 - 120 + IPR036915
Cyclin-like superfamily + 55 + 124 183 - IPR013094
Alpha/beta hydrolase fold-3 - 59 - 71 + IPR008906
HAT, C-terminal dimerisation domain + 54 + 58 184 - IPR026057
PC-Esterase - 58 - 83 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 54 + 63 185 - IPR019787
  - 58 - 342 + IPR005202
Transcription factor GRAS + 54 + 196 186 - IPR016135
  - 58 - 332 + IPR004242
Transposon, En/Spm-like + 54 + 57 187 - IPR001881
EGF-like calcium-binding domain - 57 - 124 + IPR025452
Domain of unknown function DUF4218 + 53 + 53 188 - IPR007112
  - 57 - 262 + IPR003676
Small auxin-up RNA + 53 + 58 189 - IPR019786
Zinc finger, PHD-type, conserved site - 57 - 101 + IPR013103
Reverse transcriptase, RNA-dependent DNA polymerase + 53 + 56 190 - IPR005829
Sugar transporter, conserved site - 57 - 123 + IPR025846
PMR5 N-terminal domain + 52 + 65 191 - IPR029052
  - 57 - 170 + IPR036852
Peptidase S8/S53 domain superfamily + 52 + 59 192 - IPR000490
Glycoside hydrolase family 17 - 57 - 114 + IPR001752
Kinesin motor domain + 52 + 435 193 - IPR015915
  - 57 - 624 + IPR044808
Ethylene-responsive transcription factor + 52 + 60 194 - IPR011993
  - 57 - 202 + IPR000209
Peptidase S8/S53 domain + 52 + 59 195 - IPR036852
  - 56 - 1041 + IPR000225
Armadillo + 52 + 228 196 - IPR006566
FBD domain - 56 - 85 + IPR001563
Peptidase S10, serine carboxypeptidase + 51 + 401 197 - IPR004158
Protein of unknown function DUF247, plant - 56 - 67 + IPR007118
Expansin/Lol pI + 51 + 300 198 - IPR003676
Small auxin-up RNA - 56 - 58 + IPR016159
Cullin repeat-like-containing domain superfamily + 51 + 64 199 - IPR000626
  - 55 - 699 + IPR024788
Malectin-like domain + 51 + 79 200 - IPR029962
Trichome birefringence-like family - 55 - 85 + IPR017884
SANT domain + 50 + 77 201 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 55 - 65 + IPR011032
GroES-like superfamily + 50 + 95 202 - IPR027640
Kinesin-like protein - 55 - 161 + IPR008979
Galactose-binding-like domain superfamily + 50 + 97 203 - IPR000209
Peptidase S8/S53 domain - 55 - 81 + IPR015915
Kelch-type beta propeller + 50 + 74 204 - IPR013525
ABC-2 type transporter - 54 - 128 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 49 + 56 205 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 54 - 67 + IPR016181
Acyl-CoA N-acyltransferase + 49 + 74 206 - IPR014014
  - 54 - 182 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 49 + 53 207 - IPR026961
PGG domain - 54 - 131 + IPR012946
X8 domain + 49 + 69 208 - IPR036749
  - 54 - 254 + IPR036465
von Willebrand factor A-like domain superfamily + 49 + 66 209 - IPR038408
  - 54 - 370 + IPR030184
WAT1-related protein + 49 + 96 210 - IPR002902
  - 54 - 732 + IPR023298
P-type ATPase, transmembrane domain superfamily + 49 + 76 211 - IPR007117
  - 54 - 254 + IPR041569
AAA ATPase, AAA+ lid domain + 49 + 75 212 - IPR036915
Cyclin-like superfamily - 54 - 142 + IPR000620
EamA domain + 49 + 129 213 - IPR001509
NAD-dependent epimerase/dehydratase - 53 - 91 + IPR015500
Peptidase S8, subtilisin-related + 49 + 161 214 - IPR002016
  - 53 - 891 + IPR002921
Fungal lipase-like domain + 48 + 69 215 - IPR010255
Haem peroxidase - 53 - 69 + IPR008978
HSP20-like chaperone + 48 + 54 216 - IPR034090
BPM, C-terminal - 53 - 70 + IPR000608
Ubiquitin-conjugating enzyme E2 + 48 + 175 217 - IPR001752
  - 53 - 1899 + IPR045051
Subtilisin-like protease + 48 + 61 218 - IPR037045
  - 53 - 130 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 48 + 57 219 - IPR007118
Expansin/Lol pI - 52 - 318 + IPR034161
Pepsin-like domain, plant + 48 + 61 220 - IPR034161
Pepsin-like domain, plant - 52 - 57 + IPR004265
Dirigent protein + 48 + 54 221 - IPR002528
Multi antimicrobial extrusion protein - 52 - 222 + IPR036855
Zinc finger, CCCH-type superfamily + 48 + 137 222 - IPR025846
PMR5 N-terminal domain - 52 - 69 + IPR033389
AUX/IAA domain + 47 + 66 223 - IPR030184
WAT1-related protein - 52 - 83 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 47 + 139 224 - IPR003663
Sugar/inositol transporter - 52 - 401 + IPR008250
P-type ATPase, A domain superfamily + 47 + 75 225 - IPR015500
Peptidase S8, subtilisin-related - 52 - 184 + IPR001509
NAD-dependent epimerase/dehydratase + 47 + 85 226 - IPR002921
Fungal lipase-like domain - 51 - 69 + IPR013763
Cyclin-like + 47 + 97 227 - IPR012946
X8 domain - 51 - 134 + IPR022059
Protein of unknown function DUF3615 + 47 + 61 228 - IPR005202
  - 51 - 256 + IPR001214
SET domain + 47 + 134 229 - IPR000620
EamA domain - 51 - 127 + IPR043926
ABC transporter family G domain + 46 + 80 230 - IPR008949
  - 50 - 388 + IPR029055
Nucleophile aminohydrolases, N-terminal + 46 + 67 231 - IPR001563
Peptidase S10, serine carboxypeptidase - 50 - 445 + IPR044824
Protein MAINTENANCE OF MERISTEMS-like + 46 + 66 232 - IPR023393
  - 50 - 168 + IPR034197
Cucumisin-like catalytic domain + 46 + 52 233 - IPR036465
  - 50 - 256 + IPR011527
ABC transporter type 1, transmembrane domain + 46 + 280 234 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 49 - 74 + IPR006566
FBD domain + 46 + 57 235 - IPR001757
P-type ATPase - 49 - 256 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 46 + 103 236 - IPR016159
Cullin repeat-like-containing domain superfamily - 49 - 80 + IPR000873
AMP-dependent synthetase/ligase + 45 + 69 237 - IPR023298
P-type ATPase, transmembrane domain superfamily - 49 - 209 + IPR011006
CheY-like superfamily + 45 + 67 238 - IPR011032
GroES-like superfamily - 48 - 98 + IPR033896
MADS MEF2-like + 44 + 65 239 - IPR016181
Acyl-CoA N-acyltransferase - 48 - 74 + IPR014014
RNA helicase, DEAD-box type, Q motif + 44 + 72 240 - IPR008978
  - 48 - 206 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 44 + 75 241 - IPR036640
  - 48 - 759 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 121 242 - IPR029055
  - 48 - 232 + IPR009000
Translation protein, beta-barrel domain superfamily + 43 + 57 243 - IPR034197
Cucumisin-like catalytic domain - 48 - 67 + IPR003656
Zinc finger, BED-type + 43 + 75 244 - IPR022059
Protein of unknown function DUF3615 - 48 - 74 + IPR008928
Six-hairpin glycosidase superfamily + 43 + 55 245 - IPR011527
  - 48 - 756 + IPR014756
Immunoglobulin E-set + 43 + 65 246 - IPR024788
Malectin-like carbohydrate-binding domain - 48 - 78 + IPR000070
Pectinesterase, catalytic + 43 + 48 247 - IPR036855
Zinc finger, CCCH-type superfamily - 48 - 147 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 43 + 52 248 - IPR008250
P-type ATPase, A domain superfamily - 47 - 87 + IPR006016
UspA + 42 + 54 249 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 47 - 540 + IPR011701
Major facilitator superfamily + 42 + 73 250 - IPR023299
  - 47 - 366 + IPR026960
Reverse transcriptase zinc-binding domain + 42 + 43 251 - IPR001214
  - 47 - 645 + IPR011012
Longin-like domain superfamily + 42 + 65 252 - IPR006016
UspA - 46 - 56 + IPR000668
Peptidase C1A, papain C-terminal + 42 + 166 253 - IPR000608
  - 46 - 372 + IPR001117
Multicopper oxidase, type 1 + 41 + 48 254 - IPR000873
AMP-dependent synthetase/ligase - 46 - 69 + IPR003137
PA domain + 41 + 54 255 - IPR001938
  - 46 - 752 + IPR000742
EGF-like domain + 41 + 51 256 - IPR013763
Cyclin-like - 46 - 215 + IPR011706
Multicopper oxidase, C-terminal + 41 + 48 257 - IPR000222
PPM-type phosphatase, divalent cation binding - 46 - 62 + IPR045087
Multicopper oxidase + 41 + 51 258 - IPR018253
DnaJ domain, conserved site - 46 - 54 + IPR006702
Casparian strip membrane protein domain + 41 + 43 259 - IPR033389
AUX/IAA domain - 45 - 63 + IPR004853
Sugar phosphate transporter domain + 40 + 68 260 - IPR017451
F-box associated interaction domain - 45 - 53 + IPR000330
SNF2, N-terminal + 40 + 69 261 - IPR036890
  - 45 - 320 + IPR004839
Aminotransferase, class I/classII + 40 + 62 262 - IPR004265
Dirigent protein - 45 - 52 + IPR024752
Myb/SANT-like domain + 40 + 41 263 - IPR018303
P-type ATPase, phosphorylation site - 45 - 70 + IPR008889
VQ + 40 + 42 264 - IPR013128
Peptidase C1A - 44 - 122 + IPR011707
Multicopper oxidase, N-termianl + 40 + 48 265 - IPR011701
Major facilitator superfamily - 44 - 78 + IPR010402
CCT domain + 39 + 103 266 - IPR017970
Homeobox, conserved site - 44 - 49 + IPR000182
GNAT domain + 39 + 101 267 - IPR002109
  - 44 - 333 + IPR029466
No apical meristem-associated, C-terminal domain + 39 + 40 268 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 43 - 162 + IPR041577
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain + 39 + 39 269 - IPR008928
Six-hairpin glycosidase superfamily - 43 - 77 + IPR004263
Exostosin-like + 39 + 52 270 - IPR014756
Immunoglobulin E-set - 43 - 72 + IPR029480
Transposase-associated domain + 39 + 39 271 - IPR012341
  - 43 - 198 + IPR000863
Sulfotransferase domain + 39 + 43 272 - IPR017877
  - 43 - 154 + IPR002109
Glutaredoxin + 39 + 45 273 - IPR011012
Longin-like domain superfamily - 42 - 67 + IPR002912
ACT domain + 39 + 100 274 - IPR027923
Hydrophobic seed protein - 42 - 88 + IPR036318
FAD-binding, type PCMH-like superfamily + 38 + 49 275 - IPR020845
AMP-binding, conserved site - 42 - 58 + IPR016461
O-methyltransferase COMT-type + 38 + 81 276 - IPR000070
Pectinesterase, catalytic - 42 - 51 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 38 + 54 277 - IPR001117
Multicopper oxidase, type 1 - 41 - 48 + IPR009060
UBA-like superfamily + 38 + 67 278 - IPR008942
  - 41 - 208 + IPR002068
Alpha crystallin/Hsp20 domain + 38 + 81 279 - IPR010402
  - 41 - 285 + IPR001938
Thaumatin family + 38 + 263 280 - IPR001929
Germin - 41 - 137 + IPR007125
Histone H2A/H2B/H3 + 38 + 43 281 - IPR003137
PA domain - 41 - 54 + IPR006671
Cyclin, N-terminal + 38 + 52 282 - IPR004839
Aminotransferase, class I/classII - 41 - 70 + IPR028889
Ubiquitin specific protease domain + 38 + 60 283 - IPR011006
CheY-like superfamily - 41 - 61 + IPR000743
Glycoside hydrolase, family 28 + 38 + 49 284 - IPR004046
Glutathione S-transferase, C-terminal - 41 - 70 + IPR037176
Osmotin/thaumatin-like superfamily + 38 + 41 285 - IPR011706
Multicopper oxidase, type 2 - 41 - 51 + IPR025659
Tubby-like, C-terminal + 37 + 50 286 - IPR011707
Multicopper oxidase, type 3 - 41 - 49 + IPR007493
Protein of unknown function DUF538 + 37 + 87 287 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 41 - 127 + IPR036612
K Homology domain, type 1 superfamily + 37 + 104 288 - IPR033896
MADS MEF2-like - 40 - 66 + IPR016166
FAD-binding domain, PCMH-type + 37 + 47 289 - IPR011016
  - 40 - 408 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 37 + 121 290 - IPR036691
  - 40 - 448 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 37 + 61 291 - IPR009000
Translation protein, beta-barrel domain superfamily - 40 - 67 + IPR036758
At5g01610-like superfamily + 37 + 43 292 - IPR000668
Peptidase C1A, papain C-terminal - 40 - 210 + IPR027923
Hydrophobic seed protein domain + 37 + 83 293 - IPR002912
  - 40 - 280 + IPR004046
Glutathione S-transferase, C-terminal + 37 + 52 294 - IPR001789
  - 40 - 645 + IPR002487
Transcription factor, K-box + 37 + 106 295 - IPR004853
Sugar phosphate transporter domain - 39 - 66 + IPR015947
PUA-like superfamily + 37 + 50 296 - IPR009060
UBA-like superfamily - 39 - 64 + IPR008942
ENTH/VHS + 36 + 53 297 - IPR029021
  - 39 - 256 + IPR016040
NAD(P)-binding domain + 36 + 58 298 - IPR000330
SNF2-related, N-terminal domain - 39 - 68 + IPR025322
Protein of unknown function DUF4228, plant + 36 + 37 299 - IPR000863
Sulfotransferase domain - 39 - 42 + IPR013149
Alcohol dehydrogenase, C-terminal + 36 + 49 300 - IPR019794
Peroxidase, active site - 39 - 43 + IPR029021
Protein-tyrosine phosphatase-like + 36 + 56 301 - IPR000743
Glycoside hydrolase, family 28 - 39 - 68 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 36 + 45 302 - IPR036612
  - 38 - 684 + IPR039417
Papain-like cysteine endopeptidase + 36 + 40 303 - IPR001077
O-methyltransferase, family 2 - 38 - 44 + IPR002495
Glycosyl transferase, family 8 + 36 + 43 304 - IPR013780
  - 38 - 154 + IPR002067
Mitochondrial carrier protein + 36 + 205 305 - IPR000644
  - 38 - 716 + IPR000644
CBS domain + 36 + 182 306 - IPR015947
PUA-like superfamily - 38 - 67 + IPR001929
Germin + 35 + 121 307 - IPR037176
  - 38 - 176 + IPR008991
Translation protein SH3-like domain superfamily + 35 + 42 308 - IPR006702
Casparian strip membrane protein domain - 38 - 46 + IPR004320
Protein of unknown function DUF241, plant + 35 + 40 309 - IPR000182
  - 37 - 188 + IPR023271
Aquaporin-like + 35 + 37 310 - IPR036318
FAD-binding, type 2-like superfamily - 37 - 61 + IPR004140
Exocyst complex component Exo70 + 35 + 83 311 - IPR001969
Aspartic peptidase, active site - 37 - 60 + IPR001077
O-methyltransferase domain + 35 + 40 312 - IPR006652
Kelch repeat type 1 - 37 - 191 + IPR000425
Major intrinsic protein + 35 + 261 313 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 37 - 66 + IPR004314
Neprosin + 35 + 44 314 - IPR038718
  - 37 - 170 + IPR043519
Nucleotidyltransferase superfamily + 35 + 55 315 - IPR006671
Cyclin, N-terminal - 37 - 90 + IPR011043
Galactose oxidase/kelch, beta-propeller + 35 + 39 316 - IPR007493
Protein of unknown function DUF538 - 36 - 85 + IPR041588
Integrase zinc-binding domain + 35 + 35 317 - IPR002068
  - 36 - 150 + IPR004041
NAF domain + 34 + 53 318 - IPR016166
  - 36 - 171 + IPR025525
hAT-like transposase, RNase-H fold + 34 + 35 319 - IPR003594
Histidine kinase/HSP90-like ATPase - 36 - 121 + IPR027806
Harbinger transposase-derived nuclease domain + 34 + 34 320 - IPR007125
Histone H2A/H2B/H3 - 36 - 38 + IPR018451
NAF/FISL domain + 34 + 53 321 - IPR002495
Glycosyl transferase, family 8 - 36 - 64 + IPR006652
Kelch repeat type 1 + 34 + 77 322 - IPR002067
Mitochondrial carrier protein - 36 - 232 + IPR015655
Protein phosphatase 2C family + 34 + 67 323 - IPR028889
  - 36 - 130 + IPR019378
GDP-fucose protein O-fucosyltransferase + 34 + 45 324 - IPR011042
  - 36 - 138 + IPR033443
Pentacotripeptide-repeat region of PRORP + 34 + 50 325 - IPR002487
  - 36 - 372 + IPR006458
Ovate protein family, C-terminal + 34 + 66 326 - IPR014721
  - 36 - 134 + IPR040911
Exostosin, GT47 domain + 34 + 42 327 - IPR025659
  - 35 - 168 + IPR025312
Domain of unknown function DUF4216 + 33 + 34 328 - IPR016461
  - 35 - 216 + IPR001251
CRAL-TRIO lipid binding domain + 33 + 123 329 - IPR013149
Alcohol dehydrogenase, C-terminal - 35 - 50 + IPR001296
Glycosyl transferase, family 1 + 33 + 41 330 - IPR023271
  - 35 - 170 + IPR005135
Endonuclease/exonuclease/phosphatase + 33 + 60 331 - IPR004140
Exocyst complex component Exo70 - 35 - 88 + IPR002423
Chaperonin Cpn60/TCP-1 family + 33 + 50 332 - IPR034294
Aquaporin transporter - 35 - 45 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 43 333 - IPR036758
  - 35 - 172 + IPR034294
Aquaporin transporter + 33 + 35 334 - IPR029045
ClpP/crotonase-like domain superfamily - 35 - 56 + IPR022742
Serine aminopeptidase, S33 + 33 + 40 335 - IPR019378
GDP-fucose protein O-fucosyltransferase - 35 - 59 + IPR029045
ClpP/crotonase-like domain superfamily + 33 + 57 336 - IPR000425
Major intrinsic protein - 35 - 283 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 33 + 48 337 - IPR006458
  - 35 - 196 + IPR006073
GTP binding domain + 33 + 129 338 - IPR011141
Polyketide synthase, type III - 35 - 70 + IPR032710
NTF2-like domain superfamily + 32 + 42 339 - IPR000823
Plant peroxidase - 35 - 242 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 32 + 38 340 - IPR036865
  - 34 - 190 + IPR000717
Proteasome component (PCI) domain + 32 + 74 341 - IPR022742
Serine aminopeptidase, S33 - 34 - 47 + IPR038933
Ovate protein family + 32 + 33 342 - IPR008266
Tyrosine-protein kinase, active site - 34 - 39 + IPR035940
CAP superfamily + 32 + 38 343 - IPR003311
AUX/IAA protein - 34 - 58 + IPR027356
NPH3 domain + 32 + 72 344 - IPR004314
Neprosin - 34 - 42 + IPR004883
Lateral organ boundaries, LOB + 32 + 66 345 - IPR006073
GTP binding domain - 34 - 111 + IPR008480
Protein of unknown function DUF761, plant + 32 + 32 346 - IPR016040
NAD(P)-binding domain - 33 - 59 + IPR027409
GroEL-like apical domain superfamily + 32 + 42 347 - IPR006626
Parallel beta-helix repeat - 33 - 179 + IPR001906
Terpene synthase, N-terminal domain + 32 + 46 348 - IPR019821
Kinesin motor domain, conserved site - 33 - 52 + IPR003311
AUX/IAA protein + 32 + 44 349 - IPR001251
  - 33 - 342 + IPR011141
Polyketide synthase, type III + 32 + 40 350 - IPR038933
Ovate protein family - 33 - 37 + IPR023210
NADP-dependent oxidoreductase domain + 32 + 51 351 - IPR004263
Exostosin-like - 33 - 47 + IPR036378
FAS1 domain superfamily + 31 + 46 352 - IPR013154
Alcohol dehydrogenase, N-terminal - 33 - 51 + IPR001360
Glycoside hydrolase family 1 + 31 + 422 353 - IPR033131
Pectinesterase, Asp active site - 33 - 38 + IPR044835
Auxin response factor + 31 + 45 354 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 33 - 283 + IPR005630
Terpene synthase, metal-binding domain + 31 + 48 355 - IPR038538
  - 33 - 118 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 31 + 41 356 - IPR008480
Protein of unknown function DUF761, plant - 33 - 34 + IPR013154
Alcohol dehydrogenase, N-terminal + 31 + 41 357 - IPR033443
Pentacotripeptide-repeat region of PRORP - 33 - 57 + IPR003406
Glycosyl transferase, family 14 + 31 + 39 358 - IPR019780
Germin, manganese binding site - 33 - 38 + IPR043454
NPH3/RPT2-like family + 31 + 37 359 - IPR020843
Polyketide synthase, enoylreductase domain - 33 - 45 + IPR014044
CAP domain + 31 + 37 360 - IPR000727
  - 32 - 214 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 31 + 55 361 - IPR025322
Protein of unknown function DUF4228, plant - 32 - 33 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 31 + 69 362 - IPR000717
  - 32 - 202 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 31 + 49 363 - IPR001296
Glycosyl transferase, family 1 - 32 - 50 + IPR001099
Chalcone/stilbene synthase, N-terminal + 31 + 37 364 - IPR002423
Chaperonin Cpn60/TCP-1 family - 32 - 58 + IPR000727
Target SNARE coiled-coil homology domain + 30 + 66 365 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 32 - 46 + IPR018490
Cyclic nucleotide-binding-like + 30 + 48 366 - IPR002963
Expansin - 32 - 273 + IPR000315
B-box-type zinc finger + 30 + 78 367 - IPR022357
Major intrinsic protein, conserved site - 32 - 37 + IPR000795
Translational (tr)-type GTP-binding domain + 30 + 219 368 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 32 - 49 + IPR002963
Expansin + 30 + 259 369 - IPR012328
Chalcone/stilbene synthase, C-terminal - 32 - 35 + IPR001283
Cysteine-rich secretory protein-related + 30 + 137 370 - IPR018490
Cyclic nucleotide-binding-like - 31 - 49 + IPR006094
FAD linked oxidase, N-terminal + 30 + 37 371 - IPR032710
NTF2-like domain superfamily - 31 - 37 + IPR012328
Chalcone/stilbene synthase, C-terminal + 30 + 33 372 - IPR005135
Endonuclease/exonuclease/phosphatase - 31 - 56 + IPR003851
Zinc finger, Dof-type + 30 + 66 373 - IPR035940
  - 31 - 158 + IPR013126
Heat shock protein 70 family + 30 + 65 374 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 31 - 111 + IPR036404
Jacalin-like lectin domain superfamily + 30 + 42 375 - IPR002123
Phospholipid/glycerol acyltransferase - 31 - 63 + IPR039361
Cyclin + 30 + 39 376 - IPR019793
Peroxidases heam-ligand binding site - 31 - 39 + IPR036034
PDZ superfamily + 30 + 53 377 - IPR027409
  - 31 - 210 + IPR036041
Ribosome-inactivating protein superfamily + 30 + 34 378 - IPR004088
K Homology domain, type 1 - 31 - 115 + IPR012967
Plant methyltransferase dimerisation + 30 + 31 379 - IPR004087
K Homology domain - 31 - 117 + IPR001229
Jacalin-like lectin domain + 30 + 81 380 - IPR036404
  - 31 - 248 + IPR010920
LSM domain superfamily + 29 + 37 381 - IPR025661
Cysteine peptidase, asparagine active site - 31 - 35 + IPR002659
Glycosyl transferase, family 31 + 29 + 100 382 - IPR011043
Galactose oxidase/kelch, beta-propeller - 31 + IPR044848
PHR1-like + 29 37 383 - IPR036034
PDZ superfamily - 31 - 51 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 40 384 - IPR012967
Plant methyltransferase dimerisation - 31 - 31 + IPR004813
Oligopeptide transporter, OPT superfamily + 29 + 43 385 - IPR001229
  - 31 - 308 + IPR004088
K Homology domain, type 1 + 29 + 87 386 - IPR004041
NAF domain - 30 - 44 + IPR016197
Chromo-like domain superfamily + 29 + 51 387 - IPR018451
  - 30 - 132 + IPR031127
E3 ubiquitin ligase RBR family + 29 + 39 388 - IPR002659
Glycosyl transferase, family 31 - 30 - 101 + IPR025110
AMP-binding enzyme, C-terminal domain + 28 + 44 389 - IPR007650
  - 30 - 132 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 28 + 218 390 - IPR027356
  - 30 - 152 + IPR029000
Cyclophilin-like domain superfamily + 28 + 37 391 - IPR038770
  - 30 - 74 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 28 + 121 392 - IPR003406
Glycosyl transferase, family 14 - 30 + IPR024709
Putative O-fucosyltransferase, plant + 28 39 393 - IPR004883
  - 30 - 138 + IPR001594
Palmitoyltransferase, DHHC domain + 28 + 49 394 - IPR002035
  - 30 - 202 + IPR007650
Zf-FLZ domain + 28 + 62 395 - IPR006094
FAD linked oxidase, N-terminal - 30 - 41 + IPR004367
Cyclin, C-terminal domain + 28 + 36 396 - IPR013126
Heat shock protein 70 family - 30 - 284 + IPR002123
Phospholipid/glycerol acyltransferase + 28 + 36 397 - IPR000595
  - 30 - 322 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 28 + 47 398 - IPR009091
  - 30 - 300 + IPR005821
Ion transport domain + 28 + 45 399 - IPR008889
VQ - 30 - 30 + IPR000595
Cyclic nucleotide-binding domain + 28 + 118 400 - IPR000679
  - 30 - 411 + IPR015940
Ubiquitin-associated domain + 27 + 90 401 - IPR001099
Chalcone/stilbene synthase, N-terminal - 30 - 36 + IPR006153
Cation/H+ exchanger + 27 + 38 402 - IPR025110
AMP-binding enzyme, C-terminal domain - 29 - 43 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 27 + 68 403 - IPR036378
  - 29 - 142 + IPR013216
Methyltransferase type 11 + 27 + 38 404 - IPR036965
  - 29 - 189 + IPR000408
Regulator of chromosome condensation, RCC1 + 27 + 652 405 - IPR001360
Glycoside hydrolase family 1 - 29 - 486 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 27 + 28 406 - IPR013088
  - 29 - 108 + IPR023299
P-type ATPase, cytoplasmic domain N + 27 + 48 407 - IPR008991
Translation protein SH3-like domain superfamily - 29 - 36 + IPR001757
P-type ATPase + 27 + 126 408 - IPR000315
  - 29 - 432 + IPR044791
Beta-glucanase/XTH + 27 + 35 409 - IPR005630
Terpene synthase, metal-binding domain - 29 - 55 + IPR003855
Potassium transporter + 27 + 79 410 - IPR033124
Serine carboxypeptidases, histidine active site - 29 - 45 + IPR000757
Glycoside hydrolase family 16 + 27 + 67 411 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 29 - 44 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 26 + 33 412 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 29 - 132 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 26 + 126 413 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 62 + IPR017938
Riboflavin synthase-like beta-barrel + 26 + 34 414 - IPR005821
Ion transport domain - 29 - 41 + IPR002867
IBR domain + 26 + 49 415 - IPR014044
CAP domain - 29 - 72 + IPR013581
Plant PDR ABC transporter associated + 26 + 41 416 - IPR031107
Small heat shock protein HSP20 - 29 - 35 + IPR008422
Homeobox KN domain + 26 + 30 417 - IPR001906
Terpene synthase, N-terminal domain - 29 - 55 + IPR027725
Heat shock transcription factor family + 26 + 28 418 - IPR000757
  - 29 - 204 + IPR005150
Cellulose synthase + 26 + 60 419 - IPR010525
Auxin response factor - 29 - 42 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 26 + 33 420 - IPR002130
  - 28 - 900 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 26 + 37 421 - IPR029000
  - 28 - 198 + IPR044839
Protein NDR1-like + 26 + 28 422 - IPR001179
  - 28 - 244 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 26 + 32 423 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 28 - 89 + IPR025724
GAG-pre-integrase domain + 26 + 26 424 - IPR018200
Ubiquitin specific protease, conserved site - 28 - 86 + IPR036392
PLAT/LH2 domain superfamily + 26 + 28 425 - IPR027725
Heat shock transcription factor family - 28 - 33 + IPR000679
Zinc finger, GATA-type + 26 + 88 426 - IPR031052
FHY3/FAR1 family - 28 - 48 + IPR005175
PPC domain + 26 + 81 427 - IPR011013
Galactose mutarotase-like domain superfamily - 28 - 48 + IPR036085
PAZ domain superfamily + 25 + 40 428 - IPR004813
Oligopeptide transporter, OPT superfamily - 28 - 84 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 25 + 45 429 - IPR000169
Cysteine peptidase, cysteine active site - 28 - 31 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 26 430 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 28 - 58 + IPR036420
BRCT domain superfamily + 25 + 61 431 - IPR018202
Serine carboxypeptidase, serine active site - 28 - 44 + IPR023753
FAD/NAD(P)-binding domain + 25 + 32 432 - IPR015940
  - 27 - 234 + IPR029061
Thiamin diphosphate-binding fold + 25 + 66 433 - IPR010920
LSM domain superfamily - 27 - 41 + IPR005333
Transcription factor, TCP + 25 + 27 434 - IPR008422
Homeobox KN domain - 27 - 39 + IPR001353
Proteasome, subunit alpha/beta + 25 + 31 435 - IPR004320
Protein of unknown function DUF241, plant - 27 - 49 + IPR027413
GroEL-like equatorial domain superfamily + 25 + 39 436 - IPR031112
AP2-like ethylene-responsive transcription factor - 27 - 48 + IPR001763
Rhodanese-like domain + 25 + 73 437 - IPR000408
  - 27 - 1544 + IPR003594
Histidine kinase/HSP90-like ATPase + 25 + 37 438 - IPR004367
Cyclin, C-terminal domain - 27 - 78 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 25 + 35 439 - IPR002355
Multicopper oxidase, copper-binding site - 27 - 31 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 25 + 35 440 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 27 - 33 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 25 + 34 441 - IPR005150
Cellulose synthase - 27 - 78 + IPR034285
Laccase, second cupredoxin domain + 25 + 28 442 - IPR036866
  - 27 - 254 + IPR001849
Pleckstrin homology domain + 25 + 64 443 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 27 - 70 + IPR029062
Class I glutamine amidotransferase-like + 25 + 57 444 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 27 + IPR025486
Domain of unknown function DUF4378 + 25 31 445 - IPR003851
  - 27 - 357 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 103 446 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 27 - 164 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 25 + 27 447 - IPR029047
  - 27 - 120 + IPR015797
NUDIX hydrolase-like domain superfamily + 25 + 30 448 - IPR036041
Ribosome-inactivating protein superfamily - 27 - 34 + IPR001574
Ribosome-inactivating protein + 25 + 56 449 - IPR025660
Cysteine peptidase, histidine active site - 27 - 41 + IPR010525
Auxin response factor domain + 25 + 34 450 - IPR005175
  - 27 - 162 + IPR000782
FAS1 domain + 24 + 64 451 - IPR002913
  - 27 - 267 + IPR003106
Leucine zipper, homeobox-associated + 24 + 25 452 - IPR017938
Riboflavin synthase-like beta-barrel - 26 - 40 + IPR001024
PLAT/LH2 domain + 24 + 49 453 - IPR000782
  - 26 - 178 + IPR025753
AAA-type ATPase, N-terminal domain + 24 + 27 454 - IPR006153
Cation/H+ exchanger - 26 - 42 + IPR001357
BRCT domain + 24 + 102 455 - IPR025753
AAA-type ATPase, N-terminal domain - 26 - 29 + IPR005299
SAM dependent carboxyl methyltransferase + 24 + 67 456 - IPR024709
Putative O-fucosyltransferase, plant - 26 + IPR011016
Zinc finger, RING-CH-type + 24 77 457 - IPR036420
  - 26 - 206 + IPR036010
2Fe-2S ferredoxin-like superfamily + 24 + 35 458 - IPR013216
Methyltransferase type 11 - 26 - 33 + IPR002293
Amino acid/polyamine transporter I + 24 + 39 459 - IPR023753
FAD/NAD(P)-binding domain - 26 - 36 + IPR034288
Laccase, first cupredoxin domain + 24 + 27 460 - IPR001594
Palmitoyltransferase, DHHC domain - 26 - 35 + IPR002035
von Willebrand factor, type A + 24 + 55 461 - IPR000795
  - 26 - 804 + IPR029069
HotDog domain superfamily + 24 + 51 462 - IPR012675
  - 26 - 80 + IPR001701
Glycoside hydrolase family 9 + 24 + 26 463 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 26 - 33 + IPR000086
NUDIX hydrolase domain + 24 + 56 464 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 26 - 49 + IPR044066
TRIAD supradomain + 24 + 29 465 - IPR025486
Domain of unknown function DUF4378 - 26 - 36 + IPR002937
Amine oxidase + 24 + 39 466 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 26 - 30 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 24 + 33 467 - IPR003855
Potassium transporter - 26 - 130 + IPR002913
START domain + 24 + 71 468 - IPR027410
  - 26 - 228 + IPR041373
Reverse transcriptase, RNase H-like domain + 24 + 24 469 - IPR017946
  - 25 - 270 + IPR003100
PAZ domain + 23 + 70 470 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 25 - 49 + IPR013601
FAE1/Type III polyketide synthase-like protein + 23 + 24 471 - IPR003106
Leucine zipper, homeobox-associated - 25 - 45 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 23 + 24 472 - IPR001357
  - 25 - 332 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 23 + 25 473 - IPR029061
Thiamin diphosphate-binding fold - 25 - 63 + IPR003347
JmjC domain + 23 + 75 474 - IPR001353
Proteasome, subunit alpha/beta - 25 - 31 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 23 + 33 475 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 25 - 38 + IPR029057
Phosphoribosyltransferase-like + 23 + 39 476 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 25 - 69 + IPR016897
S-phase kinase-associated protein 1 + 23 + 30 477 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 25 - 26 + IPR041679
DNA2/NAM7 helicase-like, C-terminal + 23 + 89 478 - IPR016167
  - 25 - 120 + IPR001876
Zinc finger, RanBP2-type + 23 + 117 479 - IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase - 25 - 34 + IPR036296
SKP1-like, dimerisation domain superfamily + 23 + 29 480 - IPR001876
  - 25 - 478 + IPR006594
LIS1 homology motif + 22 + 54 481 - IPR017937
Thioredoxin, conserved site - 25 - 40 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 51 482 - IPR031127
E3 ubiquitin ligase RBR family - 25 - 41 + IPR002403
Cytochrome P450, E-class, group IV + 22 + 139 483 - IPR024752
Myb/SANT-like domain - 25 - 29 + IPR000387
Tyrosine specific protein phosphatases domain + 22 + 33 484 - IPR002937
Amine oxidase - 25 - 39 + IPR007612
LURP-one-related + 22 + 57 485 - IPR036812
  - 25 - 190 + IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain + 22 + 26 486 - IPR015797
NUDIX hydrolase-like domain superfamily - 25 - 37 + IPR001163
LSM domain, eukaryotic/archaea-type + 22 + 29 487 - IPR017927
  - 24 - 90 + IPR004161
Translation elongation factor EFTu-like, domain 2 + 22 + 24 488 - IPR017884
  - 24 - 76 + IPR007657
Glycosyltransferase 61 + 22 + 55 489 - IPR036085
PAZ domain superfamily - 24 - 63 + IPR017887
Transcription factor TCP subgroup + 22 + 44 490 - IPR013601
FAE1/Type III polyketide synthase-like protein - 24 - 25 + IPR011257
DNA glycosylase + 22 + 37 491 - IPR002867
IBR domain - 24 - 93 + IPR025422
Transcription factor TGA like domain + 22 + 70 492 - IPR003954
RNA recognition motif domain, eukaryote - 24 - 55 + IPR010989
SNARE + 22 + 31 493 - IPR005299
SAM dependent carboxyl methyltransferase - 24 - 79 + IPR003337
Trehalose-phosphatase + 22 + 33 494 - IPR013581
Plant PDR ABC transporter associated - 24 - 44 + IPR016072
SKP1 component, dimerisation + 22 + 26 495 - IPR007657
Glycosyltransferase 61 - 24 - 59 + IPR007592
GLABROUS1 enhancer-binding protein family + 22 + 46 496 - IPR018181
Heat shock protein 70, conserved site - 24 - 64 + IPR039421
Type 1 protein exporter + 22 + 57 497 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 24 - 51 + IPR002939
Chaperone DnaJ, C-terminal + 22 + 26 498 - IPR034288
Laccase, first cupredoxin domain - 24 - 26 + IPR002641
Patatin-like phospholipase domain + 22 + 54 499 - IPR033905
Secretory peroxidase - 24 - 31 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 22 + 33 500 - IPR014722
  - 24 - 82 + IPR006311
Twin-arginine translocation pathway, signal sequence + 22 + 30 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_rufipogon.html b/gramene/htdocs/ssi/species/stats_Oryza_rufipogon.html index 1889feaf..27a581b1 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_rufipogon.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_rufipogon.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.11 + 87.11 Base Pairs: @@ -21,12 +21,12 @@

Summary

Gene counts

- + - - + +
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 37,071
Gene transcriptsHASH(0x68ce400):51,004Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:50,219
@@ -57,7 +57,7 @@

Coordinate Systems

11277855851223561512 -
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_rufipogon_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_rufipogon_IPtop500.html index cde59ba4..1ed6a371 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_rufipogon_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_rufipogon_IPtop500.html @@ -18,3500 +18,3500 @@ 1 IPR011009
Protein kinase-like domain superfamily 1446 - 2542 + 2346 2 - IPR000719
  - 1379 - 16548 + IPR000719
Protein kinase domain + 1375 + 3671 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase 1370 - 2941 + 2524 4 - IPR032675
  - 1224 - 7100 + IPR036047
F-box-like domain superfamily + 659 + 1010 5 - IPR008271
Serine/threonine-protein kinase, active site - 1117 - 1765 + IPR044974
Disease resistance protein, plants + 490 + 1093 6 - IPR017441
Protein kinase, ATP binding site - 960 - 1468 + IPR002885
Pentatricopeptide repeat + 489 + 7786 7 - IPR011990
  - 724 - 11562 + IPR001810
F-box domain + 482 + 1125 8 - IPR013083
  - 675 - 2016 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 462 + 1000 9 - IPR036047
F-box-like domain superfamily - 659 - 1027 + IPR001611
Leucine-rich repeat + 453 + 1586 10 - IPR001810
  - 498 - 5025 + IPR002182
NB-ARC + 447 + 720 11 - IPR002885
  - 489 - 30330 + IPR001841
Zinc finger, RING-type + 426 + 932 12 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 464 - 989 + IPR009057
Homeobox-like domain superfamily + 377 + 499 13 - IPR002182
NB-ARC - 460 - 745 + IPR016024
Armadillo-type fold + 368 + 685 14 - IPR001611
  - 448 - 10506 + IPR029058
Alpha/Beta hydrolase fold + 366 + 565 15 - IPR001841
  - 425 - 2900 + IPR036291
NAD(P)-binding domain superfamily + 357 + 589 16 - IPR009057
Homeobox-like domain superfamily - 377 - 503 + IPR041118
Rx, N-terminal + 353 + 566 17 - IPR016024
Armadillo-type fold - 368 - 1428 + IPR011990
Tetratricopeptide-like helical domain superfamily + 332 + 590 18 - IPR029058
  - 367 - 2388 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 322 + 431 19 - IPR036291
NAD(P)-binding domain superfamily - 357 - 650 + IPR036396
Cytochrome P450 superfamily + 314 + 456 20 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 319 - 428 + IPR001128
Cytochrome P450 + 305 + 1597 21 - IPR036396
  - 316 - 2913 + IPR035979
RNA-binding domain superfamily + 303 + 611 22 - IPR003591
Leucine-rich repeat, typical subtype - 313 - 2978 + IPR017853
Glycoside hydrolase superfamily + 264 + 424 23 - IPR001128
Cytochrome P450 - 305 - 1590 + IPR000504
RNA recognition motif domain + 264 + 1178 24 - IPR035979
RNA-binding domain superfamily - 303 - 652 + IPR002401
Cytochrome P450, E-class, group I + 261 + 2010 25 - IPR012677
  - 296 - 1378 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 257 + 416 26 - IPR003593
AAA+ ATPase domain - 276 - 605 + IPR036259
MFS transporter superfamily + 250 + 447 27 - IPR000504
  - 268 - 5349 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 238 + 362 28 - IPR017853
Glycoside hydrolase superfamily - 264 - 465 + IPR036322
WD40-repeat-containing domain superfamily + 236 + 408 29 - IPR002401
Cytochrome P450, E-class, group I - 261 - 2010 + IPR038765
Papain-like cysteine peptidase superfamily + 236 + 364 30 - IPR001005
SANT/Myb domain - 259 - 1103 + IPR017930
Myb domain + 231 + 710 31 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 257 - 486 + IPR001005
SANT/Myb domain + 223 + 719 32 - IPR036259
MFS transporter superfamily - 250 - 703 + IPR036249
Thioredoxin-like superfamily + 219 + 370 33 - IPR017972
Cytochrome P450, conserved site - 248 - 355 + IPR001680
WD40 repeat + 205 + 1863 34 - IPR011989
  - 246 - 1094 + IPR011992
EF-hand domain pair + 195 + 263 35 - IPR015943
  - 246 - 1881 + IPR002048
EF-hand domain + 178 + 1007 36 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 238 - 362 + IPR016177
DNA-binding domain superfamily + 176 + 277 37 - IPR036322
WD40-repeat-containing domain superfamily - 236 - 637 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 171 + 212 38 - IPR038765
Papain-like cysteine peptidase superfamily - 236 - 433 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 166 + 408 39 - IPR001680
  - 230 - 11418 + IPR036412
HAD-like superfamily + 166 + 266 40 - IPR036249
Thioredoxin-like superfamily - 219 - 376 + IPR036770
Ankyrin repeat-containing domain superfamily + 163 + 240 41 - IPR017986
  - 205 - 1167 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 162 + 353 42 - IPR017930
  - 202 - 678 + IPR001471
AP2/ERF domain + 159 + 899 43 - IPR011992
EF-hand domain pair - 195 - 284 + IPR011333
SKP1/BTB/POZ domain superfamily + 159 + 250 44 - IPR002048
  - 178 - 4824 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 153 + 200 45 - IPR020846
  - 178 - 932 + IPR036390
Winged helix DNA-binding domain superfamily + 150 + 195 46 - IPR016177
DNA-binding domain superfamily - 176 - 277 + IPR002110
Ankyrin repeat + 148 + 658 47 - IPR036638
  - 171 - 1173 + IPR036093
NAC domain superfamily + 143 + 168 48 - IPR036388
  - 171 - 448 + IPR029044
Nucleotide-diphospho-sugar transferases + 141 + 207 49 - IPR013087
  - 166 - 2394 + IPR036236
Zinc finger C2H2 superfamily + 141 + 203 50 - IPR036412
HAD-like superfamily - 166 - 378 + IPR003441
NAC domain + 139 + 325 51 - IPR018247
EF-Hand 1, calcium-binding site - 164 - 449 + IPR001650
Helicase, C-terminal + 138 + 465 52 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 163 - 203 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 137 + 243 53 - IPR011598
  - 163 - 2031 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 135 + 154 54 - IPR036770
  - 163 - 1178 + IPR013087
Zinc finger C2H2-type + 135 + 257 55 - IPR020683
  - 162 - 1730 + IPR036188
FAD/NAD(P)-binding domain superfamily + 132 + 247 56 - IPR001471
  - 161 - 3333 + IPR005174
Domain unknown function DUF295 + 130 + 170 57 - IPR036955
  - 160 - 636 + IPR012340
Nucleic acid-binding, OB-fold + 127 + 250 58 - IPR011333
SKP1/BTB/POZ domain superfamily - 159 - 270 + IPR020683
Ankyrin repeat-containing domain + 124 + 283 59 - IPR029044
  - 154 - 1022 + IPR003439
ABC transporter-like, ATP-binding domain + 124 + 613 60 - IPR002110
  - 154 - 5061 + IPR012337
Ribonuclease H-like superfamily + 119 + 184 61 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 153 - 232 + IPR003480
Transferase + 119 + 154 62 - IPR036390
Winged helix DNA-binding domain superfamily - 150 - 195 + IPR036869
Chaperone J-domain superfamily + 118 + 156 63 - IPR023214
  - 148 - 740 + IPR000210
BTB/POZ domain + 116 + 390 64 - IPR014001
  - 145 - 976 + IPR029071
Ubiquitin-like domain superfamily + 115 + 153 65 - IPR036093
  - 143 - 999 + IPR021109
Aspartic peptidase domain superfamily + 113 + 161 66 - IPR036236
Zinc finger C2H2 superfamily - 141 - 246 + IPR003959
ATPase, AAA-type, core + 113 + 191 67 - IPR003441
  - 139 - 966 + IPR025315
Domain of unknown function DUF4220 + 113 + 122 68 - IPR001650
  - 139 - 1858 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 112 + 200 69 - IPR036188
  - 137 - 1568 + IPR036426
Bulb-type lectin domain superfamily + 111 + 176 70 - IPR023213
  - 137 - 582 + IPR001623
DnaJ domain + 110 + 751 71 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 135 - 155 + IPR001480
Bulb-type lectin domain + 108 + 444 72 - IPR019775
WD40 repeat, conserved site - 133 - 359 + IPR011050
Pectin lyase fold/virulence factor + 105 + 116 73 - IPR014729
  - 130 - 534 + IPR020846
Major facilitator superfamily domain + 105 + 156 74 - IPR013026
  - 128 - 726 + IPR011011
Zinc finger, FYVE/PHD-type + 104 + 167 75 - IPR012340
Nucleic acid-binding, OB-fold - 127 - 266 + IPR035892
C2 domain superfamily + 103 + 203 76 - IPR008974
  - 125 - 1083 + IPR019734
Tetratricopeptide repeat + 103 + 321 77 - IPR003439
  - 124 - 1839 + IPR001087
GDSL lipase/esterase + 102 + 142 78 - IPR019734
  - 123 - 3999 + IPR033121
Peptidase family A1 domain + 102 + 159 79 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 122 - 204 + IPR015424
Pyridoxal phosphate-dependent transferase + 101 + 143 80 - IPR036869
  - 120 - 618 + IPR008972
Cupredoxin + 100 + 236 81 - IPR000210
  - 119 - 1698 + IPR036576
WRKY domain superfamily + 99 + 143 82 - IPR012337
Ribonuclease H-like superfamily - 119 - 214 + IPR003657
WRKY domain + 99 + 283 83 - IPR003480
Transferase - 119 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 98 154 84 - IPR035595
UDP-glycosyltransferase family, conserved site - 118 - 143 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 96 + 192 85 - IPR029071
Ubiquitin-like domain superfamily - 115 - 154 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 96 + 106 86 - IPR021109
  - 114 - 966 + IPR032799
Xylanase inhibitor, C-terminal + 95 + 128 87 - IPR003959
ATPase, AAA-type, core - 114 - 193 + IPR032861
Xylanase inhibitor, N-terminal + 95 + 129 88 - IPR025315
Domain of unknown function DUF4220 - 114 - 122 + IPR044810
WRKY transcription factor, plant + 94 + 121 89 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 113 - 198 + IPR036457
PPM-type phosphatase domain superfamily + 93 + 131 90 - IPR005174
Domain unknown function DUF295 - 111 - 136 + IPR007658
Protein of unknown function DUF594 + 93 + 99 91 - IPR036426
  - 111 - 834 + IPR002083
MATH/TRAF domain + 93 + 338 92 - IPR001623
  - 110 - 1762 + IPR015300
DNA-binding pseudobarrel domain superfamily + 93 + 176 93 - IPR036514
  - 110 - 304 + IPR032867
DYW domain + 92 + 110 94 - IPR014710
  - 109 - 400 + IPR035669
GDSL lipase/esterase-like, plant + 91 + 121 95 - IPR001480
  - 108 - 948 + IPR001356
Homeobox domain + 90 + 293 96 - IPR005123
  - 105 - 942 + IPR001932
PPM-type phosphatase domain + 90 + 371 97 - IPR011050
Pectin lyase fold/virulence factor - 105 - 122 + IPR000008
C2 domain + 89 + 389 98 - IPR011011
Zinc finger, FYVE/PHD-type - 104 - 167 + IPR000109
Proton-dependent oligopeptide transporter family + 88 + 357 99 - IPR001461
Aspartic peptidase A1 family - 103 - 364 + IPR005828
Major facilitator, sugar transporter-like + 88 + 153 100 - IPR013785
  - 102 - 687 + IPR011676
Domain of unknown function DUF1618 + 88 + 128 101 - IPR033121
  - 102 - 318 + IPR011051
RmlC-like cupin domain superfamily + 88 + 124 102 - IPR015421
  - 101 - 429 + IPR003609
PAN/Apple domain + 87 + 256 103 - IPR015424
Pyridoxal phosphate-dependent transferase - 101 - 150 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 87 + 142 104 - IPR008972
  - 100 - 984 + IPR000858
S-locus glycoprotein domain + 86 + 138 105 - IPR012334
  - 100 - 234 + IPR011545
DEAD/DEAH box helicase domain + 86 + 153 106 - IPR036576
  - 99 - 858 + IPR000073
Alpha/beta hydrolase fold-1 + 85 + 245 107 - IPR005225
Small GTP-binding protein domain - 99 - 136 + IPR020472
G-protein beta WD-40 repeat + 81 + 408 108 - IPR003657
  - 99 - 1275 + IPR004827
Basic-leucine zipper domain + 81 + 211 109 - IPR036397
  - 96 - 486 + IPR026992
Non-haem dioxygenase N-terminal domain + 80 + 127 110 - IPR032799
Xylanase inhibitor, C-terminal - 96 - 129 + IPR001461
Aspartic peptidase A1 family + 80 + 310 111 - IPR032861
Xylanase inhibitor, N-terminal - 95 - 129 + IPR003340
B3 DNA binding domain + 79 + 447 112 - IPR032867
DYW domain - 95 - 113 + IPR002347
Short-chain dehydrogenase/reductase SDR + 79 + 845 113 - IPR036457
  - 94 - 600 + IPR026961
PGG domain + 79 + 173 114 - IPR027443
  - 94 - 334 + IPR001220
Legume lectin domain + 79 + 173 115 - IPR015300
  - 94 - 696 + IPR009072
Histone-fold + 79 + 92 116 - IPR035892
  - 93 - 380 + IPR013766
Thioredoxin domain + 78 + 195 117 - IPR001087
GDSL lipase/esterase - 93 - 120 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 75 + 92 118 - IPR007658
Protein of unknown function DUF594 - 93 - 99 + IPR043129
ATPase, nucleotide binding domain + 75 + 198 119 - IPR002083
  - 93 - 1179 + IPR003613
U box domain + 75 + 182 120 - IPR035669
GDSL lipase/esterase-like, plant - 91 - 121 + IPR000270
PB1 domain + 75 + 131 121 - IPR024171
S-receptor-like serine/threonine-protein kinase - 91 - 143 + IPR000626
Ubiquitin-like domain + 73 + 161 122 - IPR001356
  - 91 - 1212 + IPR002100
Transcription factor, MADS-box + 73 + 514 123 - IPR001932
  - 90 - 1587 + IPR036879
Transcription factor, MADS-box superfamily + 73 + 111 124 - IPR000109
Proton-dependent oligopeptide transporter family - 89 - 369 + IPR002902
Gnk2-homologous domain + 72 + 429 125 - IPR000008
  - 88 - 1030 + IPR036163
Heavy metal-associated domain superfamily + 72 + 104 126 - IPR005828
Major facilitator, sugar transporter-like - 88 - 153 + IPR004158
Protein of unknown function DUF247, plant + 72 + 177 127 - IPR011051
RmlC-like cupin domain superfamily - 88 - 156 + IPR016039
Thiolase-like + 71 + 148 128 - IPR000858
S-locus glycoprotein domain - 87 - 139 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 71 + 120 129 - IPR003609
  - 87 - 736 + IPR044965
Glycoside hydrolase family 17, plant + 70 + 127 130 - IPR017871
ABC transporter, conserved site - 87 - 169 + IPR000571
Zinc finger, CCCH-type + 70 + 323 131 - IPR017907
Zinc finger, RING-type, conserved site - 87 - 129 + IPR006121
Heavy metal-associated domain, HMA + 69 + 236 132 - IPR006447
Myb domain, plants - 86 - 106 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 68 + 72 133 - IPR011545
DEAD/DEAH box helicase domain - 86 - 153 + IPR036908
RlpA-like domain superfamily + 66 + 79 134 - IPR011676
Domain of unknown function DUF1618 - 85 - 126 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 66 + 146 135 - IPR015655
Protein phosphatase 2C family - 85 - 132 + IPR016159
Cullin repeat-like-containing domain superfamily + 65 + 81 136 - IPR015422
  - 84 - 534 + IPR000048
IQ motif, EF-hand binding site + 65 + 368 137 - IPR004827
  - 84 - 1212 + IPR008949
Isoprenoid synthase domain superfamily + 64 + 101 138 - IPR000073
Alpha/beta hydrolase fold-1 - 83 - 237 + IPR013057
Amino acid transporter, transmembrane domain + 64 + 87 139 - IPR009072
  - 83 - 561 + IPR029052
Metallo-dependent phosphatase-like + 64 + 106 140 - IPR000742
  - 82 - 596 + IPR020568
Ribosomal protein S5 domain 2-type fold + 63 + 96 141 - IPR020472
G-protein beta WD-40 repeat - 81 - 408 + IPR023395
Mitochondrial carrier domain superfamily + 63 + 84 142 - IPR003340
  - 80 - 1788 + IPR005202
Transcription factor GRAS + 63 + 217 143 - IPR026992
Non-haem dioxygenase N-terminal domain - 80 - 127 + IPR004045
Glutathione S-transferase, N-terminal + 63 + 242 144 - IPR001220
Legume lectin domain - 80 - 175 + IPR001806
Small GTPase + 63 + 154 145 - IPR001965
Zinc finger, PHD-type - 80 - 172 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 460 146 - IPR002347
Short-chain dehydrogenase/reductase SDR - 79 - 845 + IPR000490
Glycoside hydrolase family 17 + 62 + 89 147 - IPR026961
PGG domain - 79 - 173 + IPR026057
PC-Esterase + 60 + 93 148 - IPR017451
F-box associated interaction domain - 77 - 91 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 60 + 67 149 - IPR000270
  - 76 - 525 + IPR010987
Glutathione S-transferase, C-terminal-like + 60 + 107 150 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 75 - 92 + IPR006501
Pectinesterase inhibitor domain + 60 + 63 151 - IPR003613
  - 75 - 819 + IPR007117
Expansin, cellulose-binding-like domain + 60 + 133 152 - IPR000626
  - 73 - 654 + IPR009003
Peptidase S1, PA clan + 60 + 138 153 - IPR013783
  - 73 - 234 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 59 + 99 154 - IPR013766
  - 73 - 570 + IPR003663
Sugar/inositol transporter + 59 + 369 155 - IPR002100
  - 73 - 2046 + IPR045051
Subtilisin-like protease + 58 + 136 156 - IPR036879
  - 73 - 651 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 58 + 82 157 - IPR006121
  - 72 - 726 + IPR019787
Zinc finger, PHD-finger + 57 + 137 158 - IPR002902
  - 72 - 862 + IPR025846
PMR5 N-terminal domain + 57 + 81 159 - IPR036163
Heavy metal-associated domain superfamily - 72 - 104 + IPR036915
Cyclin-like superfamily + 57 + 181 160 - IPR016039
  - 71 - 879 + IPR029962
Trichome birefringence-like family + 56 + 95 161 - IPR038408
  - 71 - 434 + IPR007112
Expansin/pollen allergen, DPBB domain + 56 + 63 162 - IPR004158
Protein of unknown function DUF247, plant - 71 - 86 + IPR024788
Malectin-like domain + 56 + 110 163 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 71 - 123 + IPR001563
Peptidase S10, serine carboxypeptidase + 55 + 477 164 - IPR018097
EGF-like calcium-binding, conserved site - 70 - 104 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 55 + 96 165 - IPR000571
  - 70 - 1590 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 55 + 120 166 - IPR001881
EGF-like calcium-binding domain - 69 - 178 + IPR036852
Peptidase S8/S53 domain superfamily + 55 + 102 167 - IPR035513
  - 68 - 270 + IPR001752
Kinesin motor domain + 54 + 574 168 - IPR000225
  - 68 - 2115 + IPR000209
Peptidase S8/S53 domain + 54 + 100 169 - IPR036961
  - 67 - 588 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 53 + 59 170 - IPR036908
  - 66 - 320 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 53 + 57 171 - IPR006566
FBD domain - 66 - 108 + IPR022059
Protein of unknown function DUF3615 + 53 + 88 172 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 66 - 158 + IPR003245
Phytocyanin domain + 53 + 137 173 - IPR008949
  - 65 - 486 + IPR008979
Galactose-binding-like domain superfamily + 53 + 85 174 - IPR003960
ATPase, AAA-type, conserved site - 65 - 97 + IPR015915
Kelch-type beta propeller + 53 + 70 175 - IPR013057
Amino acid transporter, transmembrane domain - 65 - 88 + IPR010255
Haem peroxidase superfamily + 53 + 86 176 - IPR016159
Cullin repeat-like-containing domain superfamily - 65 - 111 + IPR013094
Alpha/beta hydrolase fold-3 + 53 + 65 177 - IPR000048
  - 65 - 1704 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 52 + 87 178 - IPR005829
Sugar transporter, conserved site - 64 - 137 + IPR011032
GroES-like superfamily + 52 + 84 179 - IPR004045
  - 64 - 735 + IPR039391
Phytocyanin + 52 + 66 180 - IPR020568
Ribosomal protein S5 domain 2-type fold - 63 - 113 + IPR002528
Multi antimicrobial extrusion protein + 52 + 153 181 - IPR023395
  - 63 - 400 + IPR006566
FBD domain + 52 + 81 182 - IPR000490
Glycoside hydrolase family 17 - 63 - 133 + IPR000620
EamA domain + 52 + 142 183 - IPR015915
  - 63 - 549 + IPR003676
Small auxin-up RNA + 52 + 70 184 - IPR034090
BPM, C-terminal - 63 - 114 + IPR000225
Armadillo + 52 + 242 185 - IPR001806
Small GTPase superfamily - 63 - 91 + IPR016181
Acyl-CoA N-acyltransferase + 51 + 70 186 - IPR018108
  - 62 - 940 + IPR013525
ABC-2 type transporter + 51 + 141 187 - IPR006501
Pectinesterase inhibitor domain - 62 - 170 + IPR002016
Haem peroxidase + 51 + 330 188 - IPR005202
  - 61 - 272 + IPR023298
P-type ATPase, transmembrane domain superfamily + 51 + 88 189 - IPR010987
  - 61 - 216 + IPR015500
Peptidase S8, subtilisin-related + 51 + 220 190 - IPR026057
PC-Esterase - 60 - 93 + IPR001878
Zinc finger, CCHC-type + 51 + 181 191 - IPR036749
  - 60 - 266 + IPR012946
X8 domain + 50 + 76 192 - IPR008979
  - 60 - 370 + IPR004265
Dirigent protein + 50 + 51 193 - IPR007117
  - 60 - 266 - - + IPR006045
Cupin 1 + 50 + 89 + + 194 - IPR009003
Peptidase S1, PA clan - 60 - 144 + IPR036465
von Willebrand factor A-like domain superfamily + 50 + 90 195 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 59 - 99 + IPR002921
Fungal lipase-like domain + 49 + 62 196 - IPR016135
  - 59 - 362 + IPR008978
HSP20-like chaperone + 49 + 56 197 - IPR036852
  - 59 - 1287 + IPR000608
Ubiquitin-conjugating enzyme E2 + 49 + 173 198 - IPR003663
Sugar/inositol transporter - 59 - 429 + IPR007118
Expansin/Lol pI + 49 + 285 199 - IPR011993
  - 59 - 178 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 49 + 74 200 - IPR019787
  - 57 - 274 + IPR000742
EGF-like domain + 49 + 63 201 - IPR025846
PMR5 N-terminal domain - 57 - 81 + IPR000668
Peptidase C1A, papain C-terminal + 49 + 209 202 - IPR036915
Cyclin-like superfamily - 57 - 181 + IPR017884
SANT domain + 48 + 70 203 - IPR001563
Peptidase S10, serine carboxypeptidase - 56 - 482 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 48 + 143 204 - IPR013128
Peptidase C1A - 56 - 110 + IPR008250
P-type ATPase, A domain superfamily + 48 + 80 205 - IPR027640
Kinesin-like protein - 56 - 162 + IPR013763
Cyclin-like + 48 + 131 206 - IPR007112
  - 56 - 238 + IPR004140
Exocyst complex component Exo70 + 48 + 130 207 - IPR024788
Malectin-like carbohydrate-binding domain - 56 - 110 + IPR011527
ABC transporter type 1, transmembrane domain + 48 + 288 208 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 55 - 96 + IPR030184
WAT1-related protein + 48 + 122 209 - IPR029962
Trichome birefringence-like family - 55 - 97 + IPR034197
Cucumisin-like catalytic domain + 47 + 81 210 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 55 - 535 + IPR041569
AAA ATPase, AAA+ lid domain + 47 + 79 211 - IPR003653
  - 55 - 360 + IPR036875
Zinc finger, CCHC-type superfamily + 47 + 76 212 - IPR019786
Zinc finger, PHD-type, conserved site - 55 - 80 + IPR044808
Ethylene-responsive transcription factor + 47 + 53 213 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 54 - 58 + IPR036318
FAD-binding, type PCMH-like superfamily + 46 + 53 214 - IPR003245
  - 54 - 606 + IPR009060
UBA-like superfamily + 46 + 57 215 - IPR029052
  - 54 - 198 + IPR034161
Pepsin-like domain, plant + 46 + 60 216 - IPR001752
  - 54 - 2019 + IPR004263
Exostosin-like + 46 + 70 217 - IPR000209
Peptidase S8/S53 domain - 54 - 98 + IPR008928
Six-hairpin glycosidase superfamily + 46 + 63 218 - IPR023393
  - 53 - 166 + IPR000070
Pectinesterase, catalytic + 46 + 55 219 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 53 - 59 + IPR036855
Zinc finger, CCCH-type superfamily + 46 + 121 220 - IPR022059
Protein of unknown function DUF3615 - 53 - 86 + IPR033389
AUX/IAA domain + 45 + 65 221 - IPR036465
  - 53 - 350 + IPR001509
NAD-dependent epimerase/dehydratase + 45 + 96 222 - IPR030184
WAT1-related protein - 53 - 133 + IPR011006
CheY-like superfamily + 45 + 68 223 - IPR010255
Haem peroxidase - 53 - 92 + IPR045087
Multicopper oxidase + 45 + 70 224 - IPR013094
Alpha/beta hydrolase fold-3 - 53 - 65 + IPR001906
Terpene synthase, N-terminal domain + 45 + 70 225 - IPR011032
GroES-like superfamily - 52 - 86 + IPR000743
Glycoside hydrolase, family 28 + 45 + 53 226 - IPR002528
Multi antimicrobial extrusion protein - 52 - 218 + IPR000182
GNAT domain + 44 + 97 227 - IPR000620
EamA domain - 52 - 142 + IPR033896
MADS MEF2-like + 44 + 78 228 - IPR003676
Small auxin-up RNA - 52 - 70 + IPR011701
Major facilitator superfamily + 44 + 98 229 - IPR001878
  - 52 - 870 + IPR014014
RNA helicase, DEAD-box type, Q motif + 44 + 68 230 - IPR037045
  - 52 - 200 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 122 231 - IPR016181
Acyl-CoA N-acyltransferase - 51 - 74 + IPR043926
ABC transporter family G domain + 43 + 93 232 - IPR013525
ABC-2 type transporter - 51 - 142 + IPR006016
UspA + 43 + 48 233 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 51 - 148 + IPR000873
AMP-dependent synthetase/ligase + 43 + 76 234 - IPR014014
  - 51 - 160 + IPR029055
Nucleophile aminohydrolases, N-terminal + 43 + 61 235 - IPR002016
  - 51 - 990 + IPR014756
Immunoglobulin E-set + 43 + 70 236 - IPR023298
P-type ATPase, transmembrane domain superfamily - 51 - 241 + IPR001214
SET domain + 43 + 143 237 - IPR015500
Peptidase S8, subtilisin-related - 51 - 220 + IPR004853
Sugar phosphate transporter domain + 42 + 55 238 - IPR002921
Fungal lipase-like domain - 50 - 63 + IPR000330
SNF2, N-terminal + 42 + 76 239 - IPR008978
  - 50 - 226 + IPR005630
Terpene synthase, metal-binding domain + 42 + 66 240 - IPR012946
X8 domain - 50 - 152 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 42 + 69 241 - IPR004140
Exocyst complex component Exo70 - 50 - 142 + IPR009000
Translation protein, beta-barrel domain superfamily + 41 + 71 242 - IPR000222
PPM-type phosphatase, divalent cation binding - 50 - 64 + IPR011707
Multicopper oxidase, N-termianl + 41 + 54 243 - IPR004265
Dirigent protein - 50 - 52 + IPR001117
Multicopper oxidase, type 1 + 40 + 55 244 - IPR018253
DnaJ domain, conserved site - 50 - 64 + IPR016461
O-methyltransferase COMT-type + 40 + 98 245 - IPR006045
Cupin 1 - 50 - 180 + IPR027356
NPH3 domain + 40 + 80 246 - IPR000668
Peptidase C1A, papain C-terminal - 50 - 279 + IPR016166
FAD-binding domain, PCMH-type + 40 + 45 247 - IPR036640
  - 49 - 888 + IPR011706
Multicopper oxidase, C-terminal + 40 + 53 248 - IPR000608
  - 49 - 350 + IPR011043
Galactose oxidase/kelch, beta-propeller + 40 + 44 249 - IPR007118
Expansin/Lol pI - 49 - 285 + IPR015947
PUA-like superfamily + 40 + 55 250 - IPR013763
Cyclin-like - 49 - 244 + IPR002068
Alpha crystallin/Hsp20 domain + 39 + 79 251 - IPR008250
P-type ATPase, A domain superfamily - 48 - 99 + IPR029021
Protein-tyrosine phosphatase-like + 39 + 80 252 - IPR011527
  - 48 - 864 + IPR036612
K Homology domain, type 1 superfamily + 39 + 132 253 - IPR023299
  - 48 - 405 + IPR011012
Longin-like domain superfamily + 39 + 65 254 - IPR017877
  - 48 - 132 + IPR029045
ClpP/crotonase-like domain superfamily + 39 + 82 255 - IPR034161
Pepsin-like domain, plant - 47 - 61 + IPR036041
Ribosome-inactivating protein superfamily + 39 + 53 256 - IPR034197
Cucumisin-like catalytic domain - 47 - 81 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 39 + 61 257 - IPR036875
Zinc finger, CCHC-type superfamily - 47 - 76 + IPR037176
Osmotin/thaumatin-like superfamily + 39 + 47 258 - IPR006016
UspA - 46 - 53 + IPR010402
CCT domain + 38 + 97 259 - IPR036318
FAD-binding, type 2-like superfamily - 46 - 53 + IPR004041
NAF domain + 38 + 48 260 - IPR009060
UBA-like superfamily - 46 - 57 + IPR018451
NAF/FISL domain + 38 + 47 261 - IPR001509
NAD-dependent epimerase/dehydratase - 46 - 98 + IPR003137
PA domain + 38 + 51 262 - IPR001938
  - 46 - 754 + IPR002495
Glycosyl transferase, family 8 + 38 + 58 263 - IPR008928
Six-hairpin glycosidase superfamily - 46 - 84 + IPR006671
Cyclin, N-terminal + 38 + 78 264 - IPR000070
Pectinesterase, catalytic - 46 - 55 + IPR000644
CBS domain + 38 + 176 265 - IPR036855
Zinc finger, CCCH-type superfamily - 46 - 121 + IPR008889
VQ + 38 + 39 266 - IPR033389
AUX/IAA domain - 45 - 65 + IPR001574
Ribosome-inactivating protein + 38 + 74 267 - IPR036965
  - 45 - 249 + IPR008942
ENTH/VHS + 37 + 52 268 - IPR000873
AMP-dependent synthetase/ligase - 45 - 78 + IPR025322
Protein of unknown function DUF4228, plant + 37 + 38 269 - IPR005630
Terpene synthase, metal-binding domain - 45 - 73 + IPR025659
Tubby-like, C-terminal + 37 + 51 270 - IPR011006
CheY-like superfamily - 45 - 71 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 37 + 75 271 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 45 - 86 + IPR001938
Thaumatin family + 37 + 281 272 - IPR001757
P-type ATPase - 45 - 265 + IPR004839
Aminotransferase, class I/classII + 37 + 55 273 - IPR001906
Terpene synthase, N-terminal domain - 45 - 72 + IPR043454
NPH3/RPT2-like family + 37 + 50 274 - IPR011042
  - 45 - 172 + IPR004883
Lateral organ boundaries, LOB + 37 + 77 275 - IPR000743
Glycoside hydrolase, family 28 - 45 - 74 + IPR001077
O-methyltransferase domain + 37 + 50 276 - IPR001789
  - 45 - 714 + IPR033443
Pentacotripeptide-repeat region of PRORP + 37 + 57 277 - IPR000182
  - 44 - 194 + IPR039417
Papain-like cysteine endopeptidase + 37 + 55 278 - IPR033896
MADS MEF2-like - 44 - 78 + IPR040911
Exostosin, GT47 domain + 37 + 51 279 - IPR011701
Major facilitator superfamily - 44 - 98 + IPR028889
Ubiquitin specific protease domain + 37 + 58 280 - IPR018303
P-type ATPase, phosphorylation site - 44 - 69 + IPR000823
Plant peroxidase + 37 + 264 281 - IPR012341
  - 44 - 183 + IPR006702
Casparian strip membrane protein domain + 37 + 38 282 - IPR029055
  - 43 - 242 + IPR015655
Protein phosphatase 2C family + 36 + 64 283 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 43 - 64 + IPR002109
Glutaredoxin + 36 + 44 284 - IPR017970
Homeobox, conserved site - 43 - 47 + IPR013126
Heat shock protein 70 family + 36 + 110 285 - IPR014756
Immunoglobulin E-set - 43 - 73 + IPR004314
Neprosin + 36 + 47 286 - IPR001214
  - 43 - 597 + IPR002487
Transcription factor, K-box + 36 + 134 287 - IPR004853
Sugar phosphate transporter domain - 42 - 55 + IPR002156
Ribonuclease H domain + 35 + 56 288 - IPR000330
SNF2-related, N-terminal domain - 42 - 76 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 35 + 36 289 - IPR036890
  - 42 - 290 + IPR013154
Alcohol dehydrogenase, N-terminal + 35 + 38 290 - IPR002109
  - 42 - 288 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 35 + 56 291 - IPR008942
  - 41 - 218 + IPR019378
GDP-fucose protein O-fucosyltransferase + 35 + 57 292 - IPR009000
Translation protein, beta-barrel domain superfamily - 41 - 72 + IPR006094
FAD linked oxidase, N-terminal + 35 + 40 293 - IPR027356
  - 41 - 162 + IPR006458
Ovate protein family, C-terminal + 35 + 68 294 - IPR038718
  - 41 - 192 + IPR043519
Nucleotidyltransferase superfamily + 35 + 57 295 - IPR011707
Multicopper oxidase, type 3 - 41 - 54 + IPR002912
ACT domain + 35 + 108 296 - IPR001117
Multicopper oxidase, type 1 - 40 - 55 + IPR012967
Plant methyltransferase dimerisation + 35 + 38 297 - IPR029021
  - 40 - 332 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 34 + 58 298 - IPR036612
  - 40 - 717 + IPR038933
Ovate protein family + 34 + 35 299 - IPR016166
  - 40 - 135 + IPR023271
Aquaporin-like + 34 + 46 300 - IPR020845
AMP-binding, conserved site - 40 - 63 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 34 + 129 301 - IPR011706
Multicopper oxidase, type 2 - 40 - 53 + IPR007125
Histone H2A/H2B/H3 + 34 + 39 302 - IPR011043
Galactose oxidase/kelch, beta-propeller - 40 - 53 + IPR000425
Major intrinsic protein + 34 + 292 303 - IPR014721
  - 40 - 158 + IPR002067
Mitochondrial carrier protein + 34 + 210 304 - IPR015947
PUA-like superfamily - 40 - 58 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 34 + 76 305 - IPR002068
  - 39 - 158 + IPR013149
Alcohol dehydrogenase, C-terminal + 33 + 45 306 - IPR004263
Exostosin-like - 39 - 54 + IPR007493
Protein of unknown function DUF538 + 33 + 79 307 - IPR011012
Longin-like domain superfamily - 39 - 65 + IPR001296
Glycosyl transferase, family 1 + 33 + 51 308 - IPR029045
ClpP/crotonase-like domain superfamily - 39 - 107 + IPR000863
Sulfotransferase domain + 33 + 48 309 - IPR006671
Cyclin, N-terminal - 39 - 118 + IPR039361
Cyclin + 33 + 83 310 - IPR000644
  - 39 - 646 + IPR001251
CRAL-TRIO lipid binding domain + 32 + 130 311 - IPR036041
Ribosome-inactivating protein superfamily - 39 - 62 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 32 + 84 312 - IPR037176
  - 39 - 194 + IPR001881
EGF-like calcium-binding domain + 32 + 53 313 - IPR010402
  - 38 - 291 + IPR034294
Aquaporin transporter + 32 + 46 314 - IPR025322
Protein of unknown function DUF4228, plant - 38 - 40 + IPR022742
Serine aminopeptidase, S33 + 32 + 48 315 - IPR004041
NAF domain - 38 - 48 + IPR036758
At5g01610-like superfamily + 32 + 40 316 - IPR016461
  - 38 - 258 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 32 + 62 317 - IPR018451
  - 38 - 141 + IPR011141
Polyketide synthase, type III + 32 + 43 318 - IPR003137
PA domain - 38 - 50 + IPR006073
GTP binding domain + 32 + 107 319 - IPR001077
O-methyltransferase, family 2 - 38 - 50 + IPR016040
NAD(P)-binding domain + 31 + 48 320 - IPR002495
Glycosyl transferase, family 8 - 38 - 58 + IPR015940
Ubiquitin-associated domain + 31 + 73 321 - IPR013780
  - 38 - 144 + IPR018490
Cyclic nucleotide-binding-like + 31 + 49 322 - IPR008889
VQ - 38 - 39 + IPR001360
Glycoside hydrolase family 1 + 31 + 520 323 - IPR025659
  - 37 - 174 + IPR005135
Endonuclease/exonuclease/phosphatase + 31 + 59 324 - IPR036691
  - 37 - 438 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 31 + 44 325 - IPR001969
Aspartic peptidase, active site - 37 - 73 + IPR004046
Glutathione S-transferase, C-terminal + 31 + 59 326 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 37 - 56 + IPR004088
K Homology domain, type 1 + 31 + 113 327 - IPR004839
Aminotransferase, class I/classII - 37 - 55 + IPR000595
Cyclic nucleotide-binding domain + 31 + 126 328 - IPR004883
  - 37 - 154 + IPR006311
Twin-arginine translocation pathway, signal sequence + 31 + 32 329 - IPR028889
  - 37 - 116 + IPR032710
NTF2-like domain superfamily + 30 + 44 330 - IPR004314
Neprosin - 37 - 48 - + IPR005333
Transcription factor, TCP + 30 + 40 + 331 - IPR000823
Plant peroxidase - 37 - 264 + IPR002423
Chaperonin Cpn60/TCP-1 family + 30 + 52 332 - IPR001574
Ribosome-inactivating protein - 37 - 49 + IPR000795
Translational (tr)-type GTP-binding domain + 30 + 286 333 - IPR006702
Casparian strip membrane protein domain - 37 - 38 + IPR006652
Kelch repeat type 1 + 30 + 65 334 - IPR006626
Parallel beta-helix repeat - 36 - 194 + IPR003406
Glycosyl transferase, family 14 + 30 + 42 335 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 36 - 58 + IPR016897
S-phase kinase-associated protein 1 + 30 + 36 336 - IPR019378
GDP-fucose protein O-fucosyltransferase - 36 - 58 + IPR027409
GroEL-like apical domain superfamily + 30 + 50 337 - IPR013126
Heat shock protein 70 family - 36 - 343 + IPR027923
Hydrophobic seed protein domain + 30 + 66 338 - IPR002487
  - 36 - 420 + IPR003311
AUX/IAA protein + 30 + 43 339 - IPR013154
Alcohol dehydrogenase, N-terminal - 35 - 38 + IPR001099
Chalcone/stilbene synthase, N-terminal + 30 + 36 340 - IPR003594
Histidine kinase/HSP90-like ATPase - 35 - 116 + IPR001929
Germin + 29 + 94 341 - IPR006652
Kelch repeat type 1 - 35 - 167 + IPR005299
SAM dependent carboxyl methyltransferase + 29 + 121 342 - IPR019794
Peroxidase, active site - 35 - 54 + IPR008991
Translation protein SH3-like domain superfamily + 29 + 30 343 - IPR006094
FAD linked oxidase, N-terminal - 35 - 40 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 29 + 36 344 - IPR006458
  - 35 - 198 + IPR044848
PHR1-like + 29 + 36 345 - IPR002912
  - 35 - 248 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 41 346 - IPR012967
Plant methyltransferase dimerisation - 35 - 38 + IPR002963
Expansin + 29 + 249 347 - IPR007493
Protein of unknown function DUF538 - 34 - 82 + IPR008480
Protein of unknown function DUF761, plant + 29 + 29 348 - IPR011016
  - 34 - 312 + IPR003851
Zinc finger, Dof-type + 29 + 60 349 - IPR038933
Ovate protein family - 34 - 42 + IPR036296
SKP1-like, dimerisation domain superfamily + 29 + 33 350 - IPR001296
Glycosyl transferase, family 1 - 34 - 52 + IPR044791
Beta-glucanase/XTH + 29 + 39 351 - IPR023271
  - 34 - 186 + IPR036404
Jacalin-like lectin domain superfamily + 29 + 60 352 - IPR034294
Aquaporin transporter - 34 - 49 + IPR000727
Target SNARE coiled-coil homology domain + 28 + 72 353 - IPR022742
Serine aminopeptidase, S33 - 34 - 51 + IPR006153
Cation/H+ exchanger + 28 + 39 354 - IPR008266
Tyrosine-protein kinase, active site - 34 - 54 + IPR024709
Putative O-fucosyltransferase, plant + 28 + 53 355 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 34 - 35 + IPR044835
Auxin response factor + 28 + 52 356 - IPR000425
Major intrinsic protein - 34 - 312 + IPR000717
Proteasome component (PCI) domain + 28 + 58 357 - IPR002067
Mitochondrial carrier protein - 34 - 210 + IPR002659
Glycosyl transferase, family 31 + 28 + 93 358 - IPR016138
  - 34 - 84 + IPR007657
Glycosyltransferase 61 + 28 + 69 359 - IPR025661
Cysteine peptidase, asparagine active site - 34 - 48 + IPR007650
Zf-FLZ domain + 28 + 67 360 - IPR013149
Alcohol dehydrogenase, C-terminal - 33 - 45 + IPR044814
Terpene cyclases, class 1, plant + 28 + 47 361 - IPR000863
Sulfotransferase domain - 33 - 48 + IPR005150
Cellulose synthase + 28 + 54 362 - IPR004046
Glutathione S-transferase, C-terminal - 33 - 63 + IPR023299
P-type ATPase, cytoplasmic domain N + 28 + 47 363 - IPR004088
K Homology domain, type 1 - 33 - 117 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 28 + 49 364 - IPR004087
K Homology domain - 33 - 121 + IPR003855
Potassium transporter + 28 + 97 365 - IPR020843
Polyketide synthase, enoylreductase domain - 33 - 40 + IPR000679
Zinc finger, GATA-type + 28 + 99 366 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 33 - 37 + IPR000757
Glycoside hydrolase family 16 + 28 + 74 367 - IPR015940
  - 32 - 214 + IPR001229
Jacalin-like lectin domain + 28 + 113 368 - IPR019821
Kinesin motor domain, conserved site - 32 - 55 + IPR025110
AMP-binding enzyme, C-terminal domain + 27 + 41 369 - IPR001251
  - 32 - 344 + IPR013601
FAE1/Type III polyketide synthase-like protein + 27 + 28 370 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 32 - 87 + IPR036378
FAS1 domain superfamily + 27 + 38 371 - IPR000315
  - 32 - 531 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 27 + 31 372 - IPR036865
  - 32 - 180 + IPR029000
Cyclophilin-like domain superfamily + 27 + 41 373 - IPR033131
Pectinesterase, Asp active site - 32 - 34 + IPR021790
PTBP1, RNA recognition motif 2-like + 27 + 29 374 - IPR038538
  - 32 - 118 + IPR000315
B-box-type zinc finger + 27 + 74 375 - IPR036758
  - 32 - 160 + IPR023753
FAD/NAD(P)-binding domain + 27 + 38 376 - IPR009091
  - 32 - 360 + IPR029061
Thiamin diphosphate-binding fold + 27 + 62 377 - IPR011141
Polyketide synthase, type III - 32 - 66 + IPR017887
Transcription factor TCP subgroup + 27 + 50 378 - IPR006073
GTP binding domain - 32 - 107 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 27 + 41 379 - IPR018490
Cyclic nucleotide-binding-like - 31 - 49 + IPR035940
CAP superfamily + 27 + 33 380 - IPR001360
Glycoside hydrolase family 1 - 31 - 532 + IPR000408
Regulator of chromosome condensation, RCC1 + 27 + 679 381 - IPR018200
Ubiquitin specific protease, conserved site - 31 - 83 + IPR004367
Cyclin, C-terminal domain + 27 + 45 382 - IPR005135
Endonuclease/exonuclease/phosphatase - 31 - 55 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 27 + 34 383 - IPR038770
  - 31 - 80 + IPR005821
Ion transport domain + 27 + 37 384 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 31 - 317 + IPR012328
Chalcone/stilbene synthase, C-terminal + 27 + 31 385 - IPR027409
  - 31 - 206 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 27 + 34 386 - IPR027923
Hydrophobic seed protein - 31 - 67 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 27 + 50 387 - IPR002035
  - 31 - 230 + IPR005175
PPC domain + 27 + 86 388 - IPR022357
Major intrinsic protein, conserved site - 31 + IPR017938
Riboflavin synthase-like beta-barrel + 26 37 389 - IPR000169
Cysteine peptidase, cysteine active site - 31 - 51 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 26 + 225 390 - IPR000595
  - 31 - 336 + IPR013187
F-box associated domain, type 3 + 26 + 29 391 - IPR025660
Cysteine peptidase, histidine active site - 31 - 48 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 26 + 103 392 - IPR006311
  - 31 - 64 + IPR010920
LSM domain superfamily + 26 + 31 393 - IPR016040
NAD(P)-binding domain - 30 - 48 + IPR036420
BRCT domain superfamily + 26 + 84 394 - IPR032710
NTF2-like domain superfamily - 30 - 44 + IPR027725
Heat shock transcription factor family + 26 + 31 395 - IPR002423
Chaperonin Cpn60/TCP-1 family - 30 - 52 + IPR001594
Palmitoyltransferase, DHHC domain + 26 + 37 396 - IPR000795
  - 30 - 861 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 26 + 43 397 - IPR003406
Glycosyl transferase, family 14 - 30 - 42 + IPR002123
Phospholipid/glycerol acyltransferase + 26 + 30 398 - IPR019793
Peroxidases heam-ligand binding site - 30 - 51 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 26 + 36 399 - IPR031107
Small heat shock protein HSP20 - 30 - 31 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 26 + 32 400 - IPR003311
AUX/IAA protein - 30 - 46 + IPR014044
CAP domain + 26 + 32 401 - IPR003855
Potassium transporter - 30 - 136 + IPR029062
Class I glutamine amidotransferase-like + 26 + 45 402 - IPR001099
Chalcone/stilbene synthase, N-terminal - 30 - 36 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 26 + 33 403 - IPR001929
Germin - 29 - 94 + IPR031127
E3 ubiquitin ligase RBR family + 26 + 61 404 - IPR005299
SAM dependent carboxyl methyltransferase - 29 - 124 + IPR023210
NADP-dependent oxidoreductase domain + 26 + 55 405 - IPR008991
Translation protein SH3-like domain superfamily - 29 - 30 + IPR002913
START domain + 26 + 80 406 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 29 - 38 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 25 + 34 407 - IPR011013
Galactose mutarotase-like domain superfamily - 29 - 48 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 25 + 123 408 - IPR002963
Expansin - 29 - 249 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 29 409 - IPR007125
Histone H2A/H2B/H3 - 29 - 33 + IPR013216
Methyltransferase type 11 + 25 + 31 410 - IPR008480
Protein of unknown function DUF761, plant - 29 - 29 + IPR019557
Aminotransferase-like, plant mobile domain + 25 + 40 411 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 45 + IPR001763
Rhodanese-like domain + 25 + 60 412 - IPR003851
  - 29 - 357 + IPR045048
F-box only protein 31/39 + 25 + 93 413 - IPR036296
SKP1-like, dimerisation domain superfamily - 29 - 33 + IPR016072
SKP1 component, dimerisation + 25 + 29 414 - IPR036404
  - 29 - 240 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 25 + 55 415 - IPR018202
Serine carboxypeptidase, serine active site - 29 - 35 + IPR001283
Cysteine-rich secretory protein-related + 25 + 124 416 - IPR000757
  - 29 - 225 + IPR044839
Protein NDR1-like + 25 + 27 417 - IPR000727
  - 28 - 248 + IPR002035
von Willebrand factor, type A + 25 + 74 418 - IPR006153
Cation/H+ exchanger - 28 - 39 + IPR004813
Oligopeptide transporter, OPT superfamily + 25 + 48 419 - IPR024709
Putative O-fucosyltransferase, plant - 28 - 79 + IPR029069
HotDog domain superfamily + 25 + 50 420 - IPR013088
  - 28 - 105 + IPR001757
P-type ATPase + 25 + 135 421 - IPR000717
  - 28 - 162 + IPR001701
Glycoside hydrolase family 9 + 25 + 31 422 - IPR002659
Glycosyl transferase, family 31 - 28 - 97 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 102 423 - IPR007657
Glycosyltransferase 61 - 28 - 74 + IPR036034
PDZ superfamily + 25 + 37 424 - IPR007650
  - 28 - 134 + IPR010525
Auxin response factor domain + 25 + 37 425 - IPR031112
AP2-like ethylene-responsive transcription factor - 28 - 54 + IPR033734
Jacalin-like lectin domain, plant + 25 + 51 426 - IPR002123
Phospholipid/glycerol acyltransferase - 28 + IPR036085
PAZ domain superfamily + 24 61 427 - IPR005150
Cellulose synthase - 28 - 54 + IPR000782
FAS1 domain + 24 + 61 428 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 28 - 49 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 24 + 25 429 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 28 - 57 + IPR001357
BRCT domain + 24 + 135 430 - IPR029047
  - 28 - 148 + IPR011016
Zinc finger, RING-CH-type + 24 + 61 431 - IPR000679
  - 28 - 387 + IPR008422
Homeobox KN domain + 24 + 32 432 - IPR001229
  - 28 - 326 + IPR012416
CALMODULIN-BINDING PROTEIN60 + 24 + 72 433 - IPR025110
AMP-binding enzyme, C-terminal domain - 27 - 41 + IPR003337
Trehalose-phosphatase + 24 + 35 434 - IPR013601
FAE1/Type III polyketide synthase-like protein - 27 - 28 + IPR003594
Histidine kinase/HSP90-like ATPase + 24 + 30 435 - IPR036378
  - 27 - 136 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 24 + 35 436 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 27 - 55 + IPR036427
Bromodomain-like superfamily + 24 + 39 437 - IPR029000
  - 27 - 180 + IPR025486
Domain of unknown function DUF4378 + 24 + 36 438 - IPR023753
FAD/NAD(P)-binding domain - 27 - 39 + IPR015797
NUDIX hydrolase-like domain superfamily + 24 + 30 439 - IPR029061
Thiamin diphosphate-binding fold - 27 - 66 + IPR003100
PAZ domain + 23 + 107 440 - IPR005333
Transcription factor, TCP - 27 - 27 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 23 + 45 441 - IPR009030
Growth factor receptor cysteine-rich domain superfamily - 27 - 49 + IPR016073
SKP1 component, POZ domain + 23 + 27 442 - IPR035940
  - 27 - 132 + IPR002867
IBR domain + 23 + 60 443 - IPR033124
Serine carboxypeptidases, histidine active site - 27 - 40 + IPR025753
AAA-type ATPase, N-terminal domain + 23 + 26 444 - IPR000408
  - 27 - 1494 + IPR036010
2Fe-2S ferredoxin-like superfamily + 23 + 27 445 - IPR004367
Cyclin, C-terminal domain - 27 - 89 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 23 + 26 446 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 46 + IPR033905
Secretory peroxidase + 23 + 44 447 - IPR005821
Ion transport domain - 27 - 37 + IPR001849
Pleckstrin homology domain + 23 + 59 448 - IPR012328
Chalcone/stilbene synthase, C-terminal - 27 - 31 + IPR039421
Type 1 protein exporter + 23 + 54 449 - IPR036812
  - 27 - 206 + IPR044730
Ribonuclease H-like domain, plant type + 23 + 25 450 - IPR005175
  - 27 - 172 + IPR044066
TRIAD supradomain + 23 + 38 451 - IPR010525
Auxin response factor - 27 - 40 + IPR036392
PLAT/LH2 domain superfamily + 23 + 27 452 - IPR017938
Riboflavin synthase-like beta-barrel - 26 - 43 + IPR001487
Bromodomain + 23 + 156 453 - IPR002130
  - 26 - 675 + IPR006867
Domain of unknown function DUF632 + 23 + 27 454 - IPR013187
F-box associated domain, type 3 - 26 - 29 + IPR008971
HSP40/DnaJ peptide-binding + 22 + 62 455 - IPR001179
  - 26 - 206 + IPR003106
Leucine zipper, homeobox-associated + 22 + 23 456 - IPR010920
LSM domain superfamily - 26 - 32 + IPR006593
Cytochrome b561/ferric reductase transmembrane + 22 + 44 457 - IPR036420
  - 26 - 350 + IPR004316
SWEET sugar transporter + 22 + 49 458 - IPR001594
Palmitoyltransferase, DHHC domain - 26 - 37 + IPR025422
Transcription factor TGA like domain + 22 + 95 459 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 26 - 100 + IPR020103
Pseudouridine synthase, catalytic domain superfamily + 22 + 42 460 - IPR002355
Multicopper oxidase, copper-binding site - 26 - 33 + IPR034285
Laccase, second cupredoxin domain + 22 + 26 461 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 26 - 29 + IPR004776
Membrane transport protein + 22 + 39 462 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 26 - 59 + IPR002939
Chaperone DnaJ, C-terminal + 22 + 37 463 - IPR016072
SKP1 component, dimerisation - 26 - 30 + IPR000086
NUDIX hydrolase domain + 22 + 54 464 - IPR016167
  - 26 - 117 + IPR002937
Amine oxidase + 22 + 31 465 - IPR014044
CAP domain - 26 - 63 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 22 + 37 466 - IPR001849
  - 26 - 190 + IPR029033
Histidine phosphatase superfamily + 22 + 39 467 - IPR001232
S-phase kinase-associated protein 1-like - 26 - 30 + IPR036443
Zinc finger, RanBP2-type superfamily + 22 + 63 468 - IPR033443
Pentacotripeptide-repeat region of PRORP - 26 - 44 + IPR006689
Small GTPase superfamily, ARF/SAR type + 21 + 120 469 - IPR029062
  - 26 - 184 + IPR010666
Zinc finger, GRF-type + 21 + 27 470 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 26 - 33 + IPR002403
Cytochrome P450, E-class, group IV + 21 + 109 471 - IPR031127
E3 ubiquitin ligase RBR family - 26 - 65 + IPR000387
Tyrosine specific protein phosphatases domain + 21 + 36 472 - IPR023210
NADP-dependent oxidoreductase domain - 26 - 107 + IPR007612
LURP-one-related + 21 + 63 473 - IPR002913
  - 26 - 333 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 21 + 28 474 - IPR017927
  - 25 - 102 + IPR001440
Tetratricopeptide repeat 1 + 21 + 37 475 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 25 - 26 + IPR013581
Plant PDR ABC transporter associated + 21 + 43 476 - IPR001357
  - 25 - 562 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 21 + 32 477 - IPR027725
Heat shock transcription factor family - 25 - 32 + IPR000340
Dual specificity phosphatase, catalytic domain + 21 + 35 478 - IPR036866
  - 25 - 302 + IPR018392
LysM domain + 21 + 83 479 - IPR006379
HAD-superfamily hydrolase, subfamily IIB - 25 - 38 + IPR005516
Remorin, C-terminal + 21 + 21 480 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 25 - 126 + IPR014977
WRC domain + 21 + 48 481 - IPR014722
  - 25 - 68 + IPR001353
Proteasome, subunit alpha/beta + 21 + 30 482 - IPR001876
  - 25 - 422 + IPR027413
GroEL-like equatorial domain superfamily + 21 + 30 483 - IPR004813
Oligopeptide transporter, OPT superfamily - 25 - 89 + IPR010989
SNARE + 21 + 27 484 - IPR029069
HotDog domain superfamily - 25 - 51 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 21 + 23 485 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 25 - 70 + IPR007592
GLABROUS1 enhancer-binding protein family + 21 + 48 486 - IPR001701
Glycoside hydrolase family 9 - 25 - 31 + IPR034288
Laccase, first cupredoxin domain + 21 + 23 487 - IPR036427
  - 25 - 240 + IPR036610
PEBP-like superfamily + 21 + 24 488 - IPR025486
Domain of unknown function DUF4378 - 25 - 37 + IPR022796
Chlorophyll A-B binding protein + 21 + 24 489 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 25 - 152 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 21 + 24 490 - IPR036034
PDZ superfamily - 25 - 37 + IPR001876
Zinc finger, RanBP2-type + 21 + 92 491 - IPR033734
Jacalin-like lectin domain, plant - 25 - 51 + IPR016161
Aldehyde/histidinol dehydrogenase + 21 + 27 492 - IPR000528
Plant lipid transfer protein/Par allergen - 24 - 115 + IPR035441
TFIIS/LEDGF domain superfamily + 21 + 33 493 - IPR036085
PAZ domain superfamily - 24 - 78 + IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain + 21 + 55 494 - IPR000782
  - 24 - 178 + IPR008962
PapD-like superfamily + 20 + 32 495 - IPR003954
RNA recognition motif domain, eukaryote - 24 - 69 + IPR006195
Aminoacyl-tRNA synthetase, class II + 20 + 31 496 - IPR004162
E3 ubiquitin-protein ligase SIN-like - 24 - 37 + IPR035952
Rhomboid-like superfamily + 20 + 24 497 - IPR008422
Homeobox KN domain - 24 - 32 + IPR001107
Band 7 domain + 20 + 27 498 - IPR013216
Methyltransferase type 11 - 24 - 30 + IPR008984
SMAD/FHA domain superfamily + 20 + 31 499 - IPR012416
CALMODULIN-BINDING PROTEIN60 - 24 - 33 + IPR036186
Serpin superfamily + 20 + 27 500 - IPR019557
Aminotransferase-like, plant mobile domain - 24 - 35 + IPR001163
LSM domain, eukaryotic/archaea-type + 20 + 22 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa.html index bf498017..013c0487 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_sativa.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa.html @@ -4,11 +4,11 @@

Summary

- + - + @@ -17,20 +17,20 @@

Summary

-
Assembly:IRGSP-1.0, IRGSP-1.0, Oct 2015
Database version:93.787.7
Base Pairs: Golden Path Length: 375,049,285
Genebuild by: IRGSP
Genebuild method: Imported from RAP-DB
Genebuild started: Apr 2013
Genebuild version: IRGSP-1.0
+ Genebuild by: RAPDB Genebuild method: Import Genebuild started: Sep 2022 Genebuild last updated/patched: Jun 2019

Gene counts

- - + + - - + + - - + +
Coding genesHASH(0x68bff40):35,825Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		35,806
PseudogenesHASH(0x68c43f8):9Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		7
Gene transcriptsHASH(0x68ce400):96,715Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:45,973
@@ -63,7 +63,7 @@

Coordinate Systems

11290211061227531856 -
+
@@ -126,7 +126,7 @@

Coordinate Systems

Syng_TIGR_0496261Syng_TIGR_0508529 -
+
@@ -142,7 +142,7 @@

Other

Short Variants (SNPs, indels, somatic mutations): - 28,179,246 + 46,889,355 Structural variants: diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa117425.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa117425.html new file mode 100644 index 00000000..e57353a1 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa117425.html @@ -0,0 +1,117 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os117425RS1, Jan 2020
Database version:87.1
Base Pairs:380,354,188
Golden Path Length:380,354,188
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,442
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:43,741
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
143678955
235923432
338376620
434329365
530566713
631837697
729525146
829509711
924223890
1024626213
1129239054
1226627073
+
+
scaffold
+
29 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg55164080
UN-Ctg56154790
UN-Ctg57135286
UN-Ctg5886954
UN-Ctg5986604
UN-Ctg6085268
UN-Ctg6173422
UN-Ctg6272421
UN-Ctg6369131
UN-Ctg6467633
UN-Ctg6566963
UN-Ctg6664055
UN-Ctg6761917
UN-Ctg6861817
UN-Ctg6958589
UN-Ctg7057522
UN-Ctg7154430
UN-Ctg7252430
UN-Ctg7351297
UN-Ctg7451042
UN-Ctg7544568
UN-Ctg7640724
UN-Ctg7738900
UN-Ctg7835943
UN-Ctg7934788
UN-Ctg8034017
UN-Ctg8133934
UN-Ctg8225954
UN-Ctg8325840
+
+
chunk3824 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):19,010,064
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14572010
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14032109
3IPR000719
Protein kinase domain		13703145
4IPR036047
F-box-like domain superfamily		672836
5IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		509858
6IPR044974
Disease resistance protein, plants		501867
7IPR002885
Pentatricopeptide repeat		4976203
8IPR001810
F-box domain		474866
9IPR001611
Leucine-rich repeat		4691531
10IPR002182
NB-ARC		459540
11IPR001841
Zinc finger, RING-type		438901
12IPR036291
NAD(P)-binding domain superfamily		376565
13IPR016024
Armadillo-type fold		376603
14IPR009057
Homeobox-like domain superfamily		375476
15IPR041118
Rx, N-terminal		366408
16IPR029058
Alpha/Beta hydrolase fold		366518
17IPR011990
Tetratricopeptide-like helical domain superfamily		338503
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		316397
19IPR036396
Cytochrome P450 superfamily		311409
20IPR001128
Cytochrome P450		3061487
21IPR035979
RNA-binding domain superfamily		300600
22IPR001005
SANT/Myb domain		2731344
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		271405
24IPR000504
RNA recognition motif domain		2701164
25IPR002401
Cytochrome P450, E-class, group I		2651819
26IPR036259
MFS transporter superfamily		262409
27IPR017853
Glycoside hydrolase superfamily		261368
28IPR038005
Virus X resistance protein-like, coiled-coil domain		254279
29IPR036322
WD40-repeat-containing domain superfamily		236359
30IPR017930
Myb domain		235347
31IPR038765
Papain-like cysteine peptidase superfamily		232291
32IPR036249
Thioredoxin-like superfamily		231344
33IPR001680
WD40 repeat		2101695
34IPR011992
EF-hand domain pair		191244
35IPR036770
Ankyrin repeat-containing domain superfamily		182256
36IPR002048
EF-hand domain		181928
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		173396
38IPR036412
HAD-like superfamily		170219
39IPR036638
Helix-loop-helix DNA-binding domain superfamily		168194
40IPR016177
DNA-binding domain superfamily		167243
41IPR012337
Ribonuclease H-like superfamily		164205
42IPR002110
Ankyrin repeat		164689
43IPR011333
SKP1/BTB/POZ domain superfamily		162240
44IPR036390
Winged helix DNA-binding domain superfamily		161204
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		156328
46IPR001471
AP2/ERF domain		150850
47IPR003441
NAC domain		147330
48IPR036093
NAC domain superfamily		147169
49IPR029044
Nucleotide-diphospho-sugar transferases		144179
50IPR036236
Zinc finger C2H2 superfamily		143204
51IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		142170
52IPR010255
Haem peroxidase superfamily		142179
53IPR001650
Helicase, C-terminal		139404
54IPR012340
Nucleic acid-binding, OB-fold		139286
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		139210
56IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		137180
57IPR005174
Domain unknown function DUF295		137159
58IPR020683
Ankyrin repeat-containing domain		136305
59IPR002016
Haem peroxidase		135600
60IPR013087
Zinc finger C2H2-type		133243
61IPR036188
FAD/NAD(P)-binding domain superfamily		133227
62IPR003439
ABC transporter-like, ATP-binding domain		130504
63IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		123174
64IPR021109
Aspartic peptidase domain superfamily		123157
65IPR003480
Transferase		123152
66IPR000210
BTB/POZ domain		122369
67IPR036869
Chaperone J-domain superfamily		118162
68IPR003959
ATPase, AAA-type, core		117175
69IPR036426
Bulb-type lectin domain superfamily		114167
70IPR001623
DnaJ domain		113797
71IPR020846
Major facilitator superfamily domain		112156
72IPR025315
Domain of unknown function DUF4220		112120
73IPR033121
Peptidase family A1 domain		110152
74IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		110130
75IPR007658
Protein of unknown function DUF594		109114
76IPR001480
Bulb-type lectin domain		109421
77IPR015424
Pyridoxal phosphate-dependent transferase		109140
78IPR008972
Cupredoxin		108210
79IPR005123
Oxoglutarate/iron-dependent dioxygenase		108371
80IPR019734
Tetratricopeptide repeat		105305
81IPR001087
GDSL lipase/esterase		105135
82IPR011011
Zinc finger, FYVE/PHD-type		105150
83IPR032861
Xylanase inhibitor, N-terminal		103127
84IPR032799
Xylanase inhibitor, C-terminal		102127
85IPR011676
Domain of unknown function DUF1618		102136
86IPR035892
C2 domain superfamily		101196
87IPR036576
WRKY domain superfamily		100134
88IPR003657
WRKY domain		100265
89IPR029071
Ubiquitin-like domain superfamily		99153
90IPR015300
DNA-binding pseudobarrel domain superfamily		99168
91IPR011050
Pectin lyase fold/virulence factor		97109
92IPR036457
PPM-type phosphatase domain superfamily		95135
93IPR045005
BTB/POZ and MATH domain-containing protein 1-6		95158
94IPR044810
WRKY transcription factor, plant		95124
95IPR009072
Histone-fold		93103
96IPR001932
PPM-type phosphatase domain		93385
97IPR005828
Major facilitator, sugar transporter-like		92145
98IPR000823
Plant peroxidase		92368
99IPR000008
C2 domain		90420
100IPR011545
DEAD/DEAH box helicase domain		90136
101IPR011051
RmlC-like cupin domain superfamily		90115
102IPR002347
Short-chain dehydrogenase/reductase SDR		89776
103IPR000858
S-locus glycoprotein domain		88129
104IPR003609
PAN/Apple domain		88238
105IPR020472
G-protein beta WD-40 repeat		87393
106IPR002083
MATH/TRAF domain		87301
107IPR001356
Homeobox domain		87271
108IPR000073
Alpha/beta hydrolase fold-1		85248
109IPR001461
Aspartic peptidase A1 family		85269
110IPR003340
B3 DNA binding domain		84402
111IPR035669
GDSL lipase/esterase-like, plant		84105
112IPR000109
Proton-dependent oligopeptide transporter family		83328
113IPR026961
PGG domain		83183
114IPR004827
Basic-leucine zipper domain		83210
115IPR026992
Non-haem dioxygenase N-terminal domain		81101
116IPR013766
Thioredoxin domain		79184
117IPR043129
ATPase, nucleotide binding domain		79201
118IPR036282
Glutathione S-transferase, C-terminal domain superfamily		76104
119IPR036875
Zinc finger, CCHC-type superfamily		7693
120IPR012871
Protein of unknown function DUF1677, Oryza sativa		7589
121IPR031052
FHY3/FAR1 family		73140
122IPR002100
Transcription factor, MADS-box		71392
123IPR004158
Protein of unknown function DUF247, plant		71173
124IPR003613
U box domain		71164
125IPR001878
Zinc finger, CCHC-type		71155
126IPR036879
Transcription factor, MADS-box superfamily		7087
127IPR036163
Heavy metal-associated domain superfamily		6992
128IPR016039
Thiolase-like		68148
129IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6871
130IPR036749
Expansin, cellulose-binding-like domain superfamily		6881
131IPR002902
Gnk2-homologous domain		68375
132IPR004045
Glutathione S-transferase, N-terminal		68196
133IPR006121
Heavy metal-associated domain, HMA		67219
134IPR013057
Amino acid transporter, transmembrane domain		6794
135IPR001220
Legume lectin domain		67164
136IPR007117
Expansin, cellulose-binding-like domain		67157
137IPR000270
PB1 domain		67116
138IPR008949
Isoprenoid synthase domain superfamily		6681
139IPR016159
Cullin repeat-like-containing domain superfamily		6681
140IPR036908
RlpA-like domain superfamily		6579
141IPR044965
Glycoside hydrolase family 17, plant		65106
142IPR000048
IQ motif, EF-hand binding site		65336
143IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		6599
144IPR003653
Ulp1 protease family, C-terminal catalytic domain		64120
145IPR036915
Cyclin-like superfamily		64156
146IPR018108
Mitochondrial substrate/solute carrier		63468
147IPR023395
Mitochondrial carrier domain superfamily		6384
148IPR029052
Metallo-dependent phosphatase-like		6394
149IPR007527
Zinc finger, SWIM-type		63111
150IPR019787
Zinc finger, PHD-finger		62147
151IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6288
152IPR020568
Ribosomal protein S5 domain 2-type fold		62106
153IPR010987
Glutathione S-transferase, C-terminal-like		6288
154IPR009003
Peptidase S1, PA clan		62109
155IPR004330
FAR1 DNA binding domain		6271
156IPR000626
Ubiquitin-like domain		60153
157IPR002156
Ribonuclease H domain		6077
158IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6070
159IPR036852
Peptidase S8/S53 domain superfamily		6088
160IPR006501
Pectinesterase inhibitor domain		6063
161IPR024788
Malectin-like domain		6082
162IPR001806
Small GTPase		60138
163IPR003245
Phytocyanin domain		59125
164IPR005202
Transcription factor GRAS		59224
165IPR000490
Glycoside hydrolase family 17		5980
166IPR003663
Sugar/inositol transporter		59339
167IPR000209
Peptidase S8/S53 domain		5986
168IPR039391
Phytocyanin		5869
169IPR026057
PC-Esterase		5779
170IPR006566
FBD domain		5774
171IPR000571
Zinc finger, CCCH-type		57301
172IPR041469
Subtilisin-like protease, fibronectin type-III domain		5679
173IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5685
174IPR045051
Subtilisin-like protease		56107
175IPR007112
Expansin/pollen allergen, DPBB domain		5666
176IPR022059
Protein of unknown function DUF3615		5671
177IPR029962
Trichome birefringence-like family		5580
178IPR002921
Fungal lipase-like domain		5466
179IPR011032
GroES-like superfamily		5473
180IPR001563
Peptidase S10, serine carboxypeptidase		54400
181IPR025846
PMR5 N-terminal domain		5471
182IPR003676
Small auxin-up RNA		5465
183IPR000608
Ubiquitin-conjugating enzyme E2		53202
184IPR009009
RlpA-like protein, double-psi beta-barrel domain		5363
185IPR013763
Cyclin-like		53119
186IPR006045
Cupin 1		5392
187IPR036465
von Willebrand factor A-like domain superfamily		5372
188IPR015915
Kelch-type beta propeller		5378
189IPR001752
Kinesin motor domain		53455
190IPR000225
Armadillo		53239
191IPR013525
ABC-2 type transporter		52109
192IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5263
193IPR023298
P-type ATPase, transmembrane domain superfamily		5266
194IPR015500
Peptidase S8, subtilisin-related		52172
195IPR016181
Acyl-CoA N-acyltransferase		5160
196IPR008978
HSP20-like chaperone		5061
197IPR007118
Expansin/Lol pI		50300
198IPR008250
P-type ATPase, A domain superfamily		5060
199IPR034161
Pepsin-like domain, plant		5063
200IPR002528
Multi antimicrobial extrusion protein		50123
201IPR017884
SANT domain		4963
202IPR008979
Galactose-binding-like domain superfamily		4881
203IPR007125
Histone H2A/H2B/H3		4850
204IPR044808
Ethylene-responsive transcription factor		4860
205IPR036640
ABC transporter type 1, transmembrane domain superfamily		47103
206IPR013201
Cathepsin propeptide inhibitor domain (I29)		4760
207IPR034197
Cucumisin-like catalytic domain		4764
208IPR011527
ABC transporter type 1, transmembrane domain		47204
209IPR014756
Immunoglobulin E-set		4765
210IPR041569
AAA ATPase, AAA+ lid domain		4766
211IPR036318
FAD-binding, type PCMH-like superfamily		4656
212IPR029055
Nucleophile aminohydrolases, N-terminal		4662
213IPR005630
Terpene synthase, metal-binding domain		4652
214IPR014014
RNA helicase, DEAD-box type, Q motif		4663
215IPR004140
Exocyst complex component Exo70		46129
216IPR006671
Cyclin, N-terminal		4671
217IPR030184
WAT1-related protein		4692
218IPR013094
Alpha/beta hydrolase fold-3		4670
219IPR000620
EamA domain		46105
220IPR011701
Major facilitator superfamily		4574
221IPR000873
AMP-dependent synthetase/ligase		4567
222IPR012946
X8 domain		4567
223IPR004265
Dirigent protein		4553
224IPR008928
Six-hairpin glycosidase superfamily		4556
225IPR000742
EGF-like domain		4550
226IPR045087
Multicopper oxidase		4559
227IPR011043
Galactose oxidase/kelch, beta-propeller		4550
228IPR044730
Ribonuclease H-like domain, plant type		4546
229IPR001117
Multicopper oxidase, type 1		4448
230IPR004853
Sugar phosphate transporter domain		4483
231IPR009060
UBA-like superfamily		4471
232IPR009000
Translation protein, beta-barrel domain superfamily		4463
233IPR001906
Terpene synthase, N-terminal domain		4454
234IPR000182
GNAT domain		4387
235IPR016461
O-methyltransferase COMT-type		4399
236IPR036612
K Homology domain, type 1 superfamily		43120
237IPR004263
Exostosin-like		4350
238IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4363
239IPR011006
CheY-like superfamily		4358
240IPR011706
Multicopper oxidase, C-terminal		4348
241IPR000668
Peptidase C1A, papain C-terminal		43168
242IPR036855
Zinc finger, CCCH-type superfamily		43120
243IPR001214
SET domain		43110
244IPR011707
Multicopper oxidase, N-termianl		4347
245IPR000743
Glycoside hydrolase, family 28		4351
246IPR006016
UspA		4251
247IPR001509
NAD-dependent epimerase/dehydratase		4262
248IPR011012
Longin-like domain superfamily		4267
249IPR032867
DYW domain		4244
250IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4250
251IPR008889
VQ		4244
252IPR033389
AUX/IAA domain		4155
253IPR010402
CCT domain		41115
254IPR004041
NAF domain		4149
255IPR033896
MADS MEF2-like		4157
256IPR018451
NAF/FISL domain		4148
257IPR001077
O-methyltransferase domain		4151
258IPR000070
Pectinesterase, catalytic		4149
259IPR015947
PUA-like superfamily		4156
260IPR006702
Casparian strip membrane protein domain		4142
261IPR000330
SNF2, N-terminal		4068
262IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4057
263IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		4052
264IPR029045
ClpP/crotonase-like domain superfamily		4058
265IPR028889
Ubiquitin specific protease domain		4049
266IPR024752
Myb/SANT-like domain		4042
267IPR001789
Signal transduction response regulator, receiver domain		4091
268IPR016040
NAD(P)-binding domain		3964
269IPR002068
Alpha crystallin/Hsp20 domain		3991
270IPR016166
FAD-binding domain, PCMH-type		3948
271IPR033905
Secretory peroxidase		3942
272IPR000644
CBS domain		39181
273IPR043926
ABC transporter family G domain		3871
274IPR025659
Tubby-like, C-terminal		3849
275IPR007493
Protein of unknown function DUF538		3880
276IPR029021
Protein-tyrosine phosphatase-like		3861
277IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3842
278IPR003137
PA domain		3847
279IPR004839
Aminotransferase, class I/classII		3853
280IPR043454
NPH3/RPT2-like family		3862
281IPR036758
At5g01610-like superfamily		3841
282IPR002495
Glycosyl transferase, family 8		3846
283IPR040911
Exostosin, GT47 domain		3841
284IPR002109
Glutaredoxin		3847
285IPR013126
Heat shock protein 70 family		38113
286IPR039361
Cyclin		3857
287IPR002912
ACT domain		38101
288IPR008942
ENTH/VHS		3745
289IPR025322
Protein of unknown function DUF4228, plant		3739
290IPR015655
Protein phosphatase 2C family		3766
291IPR039417
Papain-like cysteine endopeptidase		3751
292IPR012967
Plant methyltransferase dimerisation		3737
293IPR023271
Aquaporin-like		3647
294IPR027356
NPH3 domain		3698
295IPR004883
Lateral organ boundaries, LOB		3675
296IPR000425
Major intrinsic protein		36296
297IPR033443
Pentacotripeptide-repeat region of PRORP		3645
298IPR002067
Mitochondrial carrier protein		36233
299IPR004367
Cyclin, C-terminal domain		3540
300IPR022742
Serine aminopeptidase, S33		3544
301IPR006652
Kelch repeat type 1		3581
302IPR019378
GDP-fucose protein O-fucosyltransferase		3546
303IPR004046
Glutathione S-transferase, C-terminal		3545
304IPR004088
K Homology domain, type 1		35103
305IPR004314
Neprosin		3553
306IPR002487
Transcription factor, K-box		35102
307IPR006311
Twin-arginine translocation pathway, signal sequence		3537
308IPR037176
Osmotin/thaumatin-like superfamily		3542
309IPR001360
Glycoside hydrolase family 1		34352
310IPR013149
Alcohol dehydrogenase, C-terminal		3440
311IPR001938
Thaumatin family		34235
312IPR013154
Alcohol dehydrogenase, N-terminal		3440
313IPR006094
FAD linked oxidase, N-terminal		3442
314IPR038933
Ovate protein family		3334
315IPR000795
Translational (tr)-type GTP-binding domain		33251
316IPR034294
Aquaporin transporter		3349
317IPR006458
Ovate protein family, C-terminal		3364
318IPR043519
Nucleotidyltransferase superfamily		3350
319IPR001251
CRAL-TRIO lipid binding domain		32132
320IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3248
321IPR044822
Myb/SANT-like DNA-binding domain 4		3241
322IPR001594
Palmitoyltransferase, DHHC domain		3255
323IPR001223
Glycoside hydrolase family 18, catalytic domain		3273
324IPR006073
GTP binding domain		32120
325IPR018490
Cyclic nucleotide-binding-like		3139
326IPR032710
NTF2-like domain superfamily		3139
327IPR005299
SAM dependent carboxyl methyltransferase		31100
328IPR008991
Translation protein SH3-like domain superfamily		3142
329IPR000717
Proteasome component (PCI) domain		3169
330IPR029061
Thiamin diphosphate-binding fold		3176
331IPR001296
Glycosyl transferase, family 1		3153
332IPR005135
Endonuclease/exonuclease/phosphatase		3142
333IPR036865
CRAL-TRIO lipid binding domain superfamily		3146
334IPR003406
Glycosyl transferase, family 14		3137
335IPR002963
Expansin		31259
336IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3160
337IPR036041
Ribosome-inactivating protein superfamily		3135
338IPR001574
Ribosome-inactivating protein		3165
339IPR015940
Ubiquitin-associated domain		3095
340IPR044835
Auxin response factor		3054
341IPR002423
Chaperonin Cpn60/TCP-1 family		3044
342IPR011013
Galactose mutarotase-like domain superfamily		3045
343IPR004813
Oligopeptide transporter, OPT superfamily		3058
344IPR023299
P-type ATPase, cytoplasmic domain N		3039
345IPR003851
Zinc finger, Dof-type		3066
346IPR000595
Cyclic nucleotide-binding domain		3095
347IPR001929
Germin		29101
348IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		29233
349IPR029000
Cyclophilin-like domain superfamily		2942
350IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		29114
351IPR000315
B-box-type zinc finger		2980
352IPR002659
Glycosyl transferase, family 31		2989
353IPR005150
Cellulose synthase		2967
354IPR027409
GroEL-like apical domain superfamily		2936
355IPR003855
Potassium transporter		29117
356IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2937
357IPR011141
Polyketide synthase, type III		2940
358IPR036812
NADP-dependent oxidoreductase domain superfamily		2945
359IPR001099
Chalcone/stilbene synthase, N-terminal		2937
360IPR000727
Target SNARE coiled-coil homology domain		2852
361IPR000528
Plant non-specific lipid-transfer protein/Par allergen		28136
362IPR036378
FAS1 domain superfamily		2840
363IPR006153
Cation/H+ exchanger		2838
364IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		28100
365IPR024709
Putative O-fucosyltransferase, plant		2842
366IPR044848
PHR1-like		2840
367IPR000863
Sulfotransferase domain		2839
368IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2833
369IPR008480
Protein of unknown function DUF761, plant		2828
370IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2847
371IPR044791
Beta-glucanase/XTH		2843
372IPR036404
Jacalin-like lectin domain superfamily		2839
373IPR025110
AMP-binding enzyme, C-terminal domain		2737
374IPR010920
LSM domain superfamily		2737
375IPR040417
Glycine-rich cell wall structural protein 1/2		2739
376IPR005333
Transcription factor, TCP		2730
377IPR007650
Zf-FLZ domain		2772
378IPR003690
Transcription termination factor, mitochondrial/chloroplastic		27101
379IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2736
380IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2739
381IPR029062
Class I glutamine amidotransferase-like		2747
382IPR012328
Chalcone/stilbene synthase, C-terminal		2730
383IPR003311
AUX/IAA protein		2741
384IPR000757
Glycoside hydrolase family 16		2775
385IPR005175
PPC domain		2783
386IPR002913
START domain		2776
387IPR017938
Riboflavin synthase-like beta-barrel		2639
388IPR013601
FAE1/Type III polyketide synthase-like protein		2634
389IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2636
390IPR025753
AAA-type ATPase, N-terminal domain		2630
391IPR001357
BRCT domain		2688
392IPR036420
BRCT domain superfamily		2656
393IPR027725
Heat shock transcription factor family		2631
394IPR000408
Regulator of chromosome condensation, RCC1		26669
395IPR002123
Phospholipid/glycerol acyltransferase		2629
396IPR016897
S-phase kinase-associated protein 1		2635
397IPR002035
von Willebrand factor, type A		2660
398IPR001757
P-type ATPase		26108
399IPR036296
SKP1-like, dimerisation domain superfamily		2634
400IPR001701
Glycoside hydrolase family 9		2632
401IPR000232
Heat shock factor (HSF)-type, DNA-binding		26110
402IPR036034
PDZ superfamily		2633
403IPR023210
NADP-dependent oxidoreductase domain		2645
404IPR015797
NUDIX hydrolase-like domain superfamily		2631
405IPR036085
PAZ domain superfamily		2539
406IPR000782
FAS1 domain		2563
407IPR008971
HSP40/DnaJ peptide-binding		2570
408IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2531
409IPR029466
No apical meristem-associated, C-terminal domain		2525
410IPR044778
Sugar transport protein STP/MST-like, plant		2530
411IPR026960
Reverse transcriptase zinc-binding domain		2525
412IPR035940
CAP superfamily		2536
413IPR001763
Rhodanese-like domain		2557
414IPR003337
Trehalose-phosphatase		2534
415IPR036273
CRAL/TRIO, N-terminal domain superfamily		2534
416IPR004014
Cation-transporting P-type ATPase, N-terminal		2527
417IPR027923
Hydrophobic seed protein domain		2567
418IPR002939
Chaperone DnaJ, C-terminal		2538
419IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2534
420IPR000679
Zinc finger, GATA-type		2599
421IPR001229
Jacalin-like lectin domain		2566
422IPR017927
FAD-binding domain, ferredoxin reductase-type		2433
423IPR004316
SWEET sugar transporter		2445
424IPR023753
FAD/NAD(P)-binding domain		2434
425IPR007657
Glycosyltransferase 61		2467
426IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2430
427IPR044675
E3 ubiquitin-protein ligase RING1-like		2428
428IPR011332
Zinc-binding ribosomal protein		2427
429IPR016072
SKP1 component, dimerisation		2431
430IPR006461
PLAC8 motif-containing protein		2449
431IPR044839
Protein NDR1-like		2425
432IPR005821
Ion transport domain		2431
433IPR034285
Laccase, second cupredoxin domain		2427
434IPR001849
Pleckstrin homology domain		2450
435IPR039421
Type 1 protein exporter		2436
436IPR029069
HotDog domain superfamily		2449
437IPR041677
DNA2/NAM7 helicase, helicase domain		2450
438IPR025486
Domain of unknown function DUF4378		2439
439IPR002937
Amine oxidase		2438
440IPR010525
Auxin response factor domain		2437
441IPR003100
PAZ domain		2373
442IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2340
443IPR002867
IBR domain		2353
444IPR013187
F-box associated domain, type 3		2328
445IPR011016
Zinc finger, RING-CH-type		2370
446IPR001163
LSM domain, eukaryotic/archaea-type		2330
447IPR012416
CALMODULIN-BINDING PROTEIN60		2368
448IPR019557
Aminotransferase-like, plant mobile domain		2326
449IPR003656
Zinc finger, BED-type		2343
450IPR001353
Proteasome, subunit alpha/beta		2330
451IPR025422
Transcription factor TGA like domain		2353
452IPR045048
F-box only protein 31/39		2362
453IPR001283
Cysteine-rich secretory protein-related		2386
454IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2336
455IPR020946
Flavin monooxygenase-like		2336
456IPR014044
CAP domain		2330
457IPR041679
DNA2/NAM7 helicase-like, C-terminal		2363
458IPR004146
DC1		2335
459IPR000086
NUDIX hydrolase domain		2354
460IPR029033
Histidine phosphatase superfamily		2330
461IPR036443
Zinc finger, RanBP2-type superfamily		2360
462IPR003106
Leucine zipper, homeobox-associated		2222
463IPR000387
Tyrosine specific protein phosphatases domain		2239
464IPR013581
Plant PDR ABC transporter associated		2235
465IPR008422
Homeobox KN domain		2230
466IPR001881
EGF-like calcium-binding domain		2233
467IPR017887
Transcription factor TCP subgroup		2246
468IPR009030
Growth factor receptor cysteine-rich domain superfamily		2228
469IPR036010
2Fe-2S ferredoxin-like superfamily		2225
470IPR010989
SNARE		2224
471IPR003594
Histidine kinase/HSP90-like ATPase		2233
472IPR020103
Pseudouridine synthase, catalytic domain superfamily		2231
473IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2226
474IPR036427
Bromodomain-like superfamily		2236
475IPR045055
DNA2/NAM7-like helicase		2250
476IPR031127
E3 ubiquitin ligase RBR family		2249
477IPR006868
Domain of unknown function DUF630		2227
478IPR044066
TRIAD supradomain		2232
479IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2231
480IPR000535
Major sperm protein (MSP) domain		2155
481IPR008962
PapD-like superfamily		2130
482IPR022149
Protein of unknown function DUF3681		2145
483IPR035952
Rhomboid-like superfamily		2125
484IPR007612
LURP-one-related		2153
485IPR003347
JmjC domain		2141
486IPR013216
Methyltransferase type 11		2129
487IPR018392
LysM domain		2177
488IPR005516
Remorin, C-terminal		2126
489IPR027413
GroEL-like equatorial domain superfamily		2130
490IPR020422
Dual specificity protein phosphatase domain		2135
491IPR007592
GLABROUS1 enhancer-binding protein family		2146
492IPR022796
Chlorophyll A-B binding protein		2130
493IPR001876
Zinc finger, RanBP2-type		2194
494IPR016161
Aldehyde/histidinol dehydrogenase		2131
495IPR014720
Double-stranded RNA-binding domain		2181
496IPR001487
Bromodomain		21165
497IPR013809
ENTH domain		2132
498IPR006867
Domain of unknown function DUF632		2127
499IPR004274
FCP1 homology domain		2160
500IPR033133
Pumilio homology domain		2023
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa125619.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa125619.html new file mode 100644 index 00000000..4c12defb --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa125619.html @@ -0,0 +1,110 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os125619RS1, Jan 2020
Database version:87.1
Base Pairs:391,869,645
Golden Path Length:391,869,645
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,316
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:43,203
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144857821
236826335
339135551
436683579
530747645
632756457
730435284
829615634
924428863
1025260475
1132107744
1227340555
+
+
scaffold
+
30 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg17118397
UN-Ctg18103525
UN-Ctg1984176
UN-Ctg2084157
UN-Ctg2181735
UN-Ctg2273549
UN-Ctg2373460
UN-Ctg2469414
UN-Ctg2564870
UN-Ctg2660399
UN-Ctg2759659
UN-Ctg2854528
UN-Ctg2953458
UN-Ctg3053396
UN-Ctg3153050
UN-Ctg3253406
UN-Ctg3351148
UN-Ctg3450590
UN-Ctg3546031
UN-Ctg3645228
UN-Ctg3744186
UN-Ctg3843930
UN-Ctg3942059
UN-Ctg4040696
UN-Ctg4139423
UN-Ctg4239067
UN-Ctg4336085
UN-Ctg4428006
UN-Ctg4520418
UN-Ctg465656
+
+
chunk3941 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa125619_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa125619_IPtop500.html new file mode 100644 index 00000000..5f435c72 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa125619_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14782043
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14372083
3IPR000719
Protein kinase domain		13723165
4IPR036047
F-box-like domain superfamily		659823
5IPR044974
Disease resistance protein, plants		534892
6IPR002885
Pentatricopeptide repeat		5046277
7IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		500867
8IPR002182
NB-ARC		495583
9IPR001810
F-box domain		473856
10IPR001611
Leucine-rich repeat		4711573
11IPR001841
Zinc finger, RING-type		424872
12IPR041118
Rx, N-terminal		385426
13IPR009057
Homeobox-like domain superfamily		380478
14IPR036291
NAD(P)-binding domain superfamily		379553
15IPR016024
Armadillo-type fold		379561
16IPR029058
Alpha/Beta hydrolase fold		367499
17IPR011990
Tetratricopeptide-like helical domain superfamily		333501
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		321414
19IPR036396
Cytochrome P450 superfamily		317405
20IPR001128
Cytochrome P450		3091472
21IPR035979
RNA-binding domain superfamily		299606
22IPR001005
SANT/Myb domain		2741361
23IPR038005
Virus X resistance protein-like, coiled-coil domain		269294
24IPR002401
Cytochrome P450, E-class, group I		2681793
25IPR000504
RNA recognition motif domain		2661124
26IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		266394
27IPR036259
MFS transporter superfamily		258411
28IPR017853
Glycoside hydrolase superfamily		256360
29IPR036249
Thioredoxin-like superfamily		241339
30IPR017930
Myb domain		238356
31IPR036322
WD40-repeat-containing domain superfamily		236348
32IPR038765
Papain-like cysteine peptidase superfamily		222277
33IPR001680
WD40 repeat		2091643
34IPR011992
EF-hand domain pair		188236
35IPR002048
EF-hand domain		177902
36IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		173405
37IPR036770
Ankyrin repeat-containing domain superfamily		173240
38IPR016177
DNA-binding domain superfamily		171236
39IPR036412
HAD-like superfamily		170220
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		163197
41IPR002110
Ankyrin repeat		159660
42IPR011333
SKP1/BTB/POZ domain superfamily		156241
43IPR001471
AP2/ERF domain		154847
44IPR036390
Winged helix DNA-binding domain superfamily		153200
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		150326
46IPR036093
NAC domain superfamily		148171
47IPR012337
Ribonuclease H-like superfamily		146183
48IPR003441
NAC domain		145328
49IPR029044
Nucleotide-diphospho-sugar transferases		143173
50IPR036236
Zinc finger C2H2 superfamily		140196
51IPR012340
Nucleic acid-binding, OB-fold		139244
52IPR001650
Helicase, C-terminal		138388
53IPR010255
Haem peroxidase superfamily		138176
54IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		135178
55IPR013087
Zinc finger C2H2-type		135246
56IPR002016
Haem peroxidase		135608
57IPR014001
Helicase superfamily 1/2, ATP-binding domain		135196
58IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		134160
59IPR036188
FAD/NAD(P)-binding domain superfamily		133213
60IPR005174
Domain unknown function DUF295		133159
61IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		131188
62IPR003439
ABC transporter-like, ATP-binding domain		129482
63IPR020683
Ankyrin repeat-containing domain		126271
64IPR003480
Transferase		121142
65IPR000210
BTB/POZ domain		118371
66IPR036426
Bulb-type lectin domain superfamily		118158
67IPR003959
ATPase, AAA-type, core		117173
68IPR001480
Bulb-type lectin domain		115396
69IPR020846
Major facilitator superfamily domain		114158
70IPR007658
Protein of unknown function DUF594		111116
71IPR015424
Pyridoxal phosphate-dependent transferase		110145
72IPR001087
GDSL lipase/esterase		109145
73IPR005123
Oxoglutarate/iron-dependent dioxygenase		109390
74IPR021109
Aspartic peptidase domain superfamily		109145
75IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		109126
76IPR036869
Chaperone J-domain superfamily		109150
77IPR025315
Domain of unknown function DUF4220		107118
78IPR008972
Cupredoxin		106215
79IPR011011
Zinc finger, FYVE/PHD-type		104145
80IPR011676
Domain of unknown function DUF1618		103130
81IPR019734
Tetratricopeptide repeat		102309
82IPR001623
DnaJ domain		102732
83IPR003657
WRKY domain		101247
84IPR036576
WRKY domain superfamily		100124
85IPR029071
Ubiquitin-like domain superfamily		100153
86IPR011050
Pectin lyase fold/virulence factor		99113
87IPR035892
C2 domain superfamily		98193
88IPR033121
Peptidase family A1 domain		95142
89IPR044810
WRKY transcription factor, plant		94123
90IPR036457
PPM-type phosphatase domain superfamily		93129
91IPR011051
RmlC-like cupin domain superfamily		93119
92IPR032861
Xylanase inhibitor, N-terminal		92120
93IPR001356
Homeobox domain		92278
94IPR009072
Histone-fold		92103
95IPR015300
DNA-binding pseudobarrel domain superfamily		92153
96IPR000858
S-locus glycoprotein domain		91120
97IPR003609
PAN/Apple domain		91219
98IPR045005
BTB/POZ and MATH domain-containing protein 1-6		91165
99IPR001932
PPM-type phosphatase domain		91370
100IPR032799
Xylanase inhibitor, C-terminal		90115
101IPR011545
DEAD/DEAH box helicase domain		90130
102IPR002347
Short-chain dehydrogenase/reductase SDR		89768
103IPR000008
C2 domain		88405
104IPR000823
Plant peroxidase		88366
105IPR005828
Major facilitator, sugar transporter-like		87138
106IPR035669
GDSL lipase/esterase-like, plant		86107
107IPR003340
B3 DNA binding domain		85401
108IPR000073
Alpha/beta hydrolase fold-1		84216
109IPR002083
MATH/TRAF domain		82304
110IPR000109
Proton-dependent oligopeptide transporter family		81304
111IPR026961
PGG domain		81169
112IPR013766
Thioredoxin domain		81181
113IPR036282
Glutathione S-transferase, C-terminal domain superfamily		81105
114IPR004827
Basic-leucine zipper domain		81200
115IPR026992
Non-haem dioxygenase N-terminal domain		80107
116IPR043129
ATPase, nucleotide binding domain		80204
117IPR036875
Zinc finger, CCHC-type superfamily		8099
118IPR020472
G-protein beta WD-40 repeat		79360
119IPR001461
Aspartic peptidase A1 family		79279
120IPR012871
Protein of unknown function DUF1677, Oryza sativa		7897
121IPR031052
FHY3/FAR1 family		76144
122IPR002100
Transcription factor, MADS-box		76432
123IPR036879
Transcription factor, MADS-box superfamily		7697
124IPR004158
Protein of unknown function DUF247, plant		75185
125IPR008949
Isoprenoid synthase domain superfamily		7486
126IPR002902
Gnk2-homologous domain		74375
127IPR001878
Zinc finger, CCHC-type		74177
128IPR004045
Glutathione S-transferase, N-terminal		73195
129IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		73119
130IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7276
131IPR016039
Thiolase-like		71156
132IPR003613
U box domain		71160
133IPR004330
FAR1 DNA binding domain		7077
134IPR036163
Heavy metal-associated domain superfamily		6989
135IPR006121
Heavy metal-associated domain, HMA		68212
136IPR001220
Legume lectin domain		68170
137IPR016159
Cullin repeat-like-containing domain superfamily		6882
138IPR000270
PB1 domain		68111
139IPR010987
Glutathione S-transferase, C-terminal-like		6688
140IPR044965
Glycoside hydrolase family 17, plant		6694
141IPR036749
Expansin, cellulose-binding-like domain superfamily		6581
142IPR013057
Amino acid transporter, transmembrane domain		6586
143IPR036908
RlpA-like domain superfamily		6583
144IPR019787
Zinc finger, PHD-finger		64142
145IPR006501
Pectinesterase inhibitor domain		6467
146IPR007117
Expansin, cellulose-binding-like domain		64155
147IPR036915
Cyclin-like superfamily		64142
148IPR001806
Small GTPase		64142
149IPR003653
Ulp1 protease family, C-terminal catalytic domain		63122
150IPR020568
Ribosomal protein S5 domain 2-type fold		63103
151IPR023395
Mitochondrial carrier domain superfamily		6385
152IPR009003
Peptidase S1, PA clan		6393
153IPR018108
Mitochondrial substrate/solute carrier		62469
154IPR029052
Metallo-dependent phosphatase-like		6288
155IPR000048
IQ motif, EF-hand binding site		62291
156IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6182
157IPR007527
Zinc finger, SWIM-type		61103
158IPR003663
Sugar/inositol transporter		61350
159IPR000571
Zinc finger, CCCH-type		61263
160IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6066
161IPR000490
Glycoside hydrolase family 17		6079
162IPR024788
Malectin-like domain		6077
163IPR000626
Ubiquitin-like domain		59154
164IPR003245
Phytocyanin domain		59126
165IPR005202
Transcription factor GRAS		59219
166IPR022059
Protein of unknown function DUF3615		5875
167IPR036852
Peptidase S8/S53 domain superfamily		5885
168IPR000209
Peptidase S8/S53 domain		5883
169IPR011032
GroES-like superfamily		5783
170IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5783
171IPR039391
Phytocyanin		5767
172IPR041469
Subtilisin-like protease, fibronectin type-III domain		5678
173IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5667
174IPR045051
Subtilisin-like protease		56104
175IPR006045
Cupin 1		5692
176IPR001563
Peptidase S10, serine carboxypeptidase		55407
177IPR001752
Kinesin motor domain		55409
178IPR015915
Kelch-type beta propeller		5482
179IPR026057
PC-Esterase		5376
180IPR007112
Expansin/pollen allergen, DPBB domain		5367
181IPR000225
Armadillo		53229
182IPR013525
ABC-2 type transporter		52101
183IPR002156
Ribonuclease H domain		5270
184IPR005630
Terpene synthase, metal-binding domain		5263
185IPR013763
Cyclin-like		52106
186IPR015500
Peptidase S8, subtilisin-related		52167
187IPR002921
Fungal lipase-like domain		5162
188IPR016181
Acyl-CoA N-acyltransferase		5159
189IPR000608
Ubiquitin-conjugating enzyme E2		51187
190IPR029962
Trichome birefringence-like family		5176
191IPR009009
RlpA-like protein, double-psi beta-barrel domain		5165
192IPR036465
von Willebrand factor A-like domain superfamily		5166
193IPR023298
P-type ATPase, transmembrane domain superfamily		5166
194IPR002528
Multi antimicrobial extrusion protein		50129
195IPR025846
PMR5 N-terminal domain		5068
196IPR036640
ABC transporter type 1, transmembrane domain superfamily		49105
197IPR008250
P-type ATPase, A domain superfamily		4963
198IPR004140
Exocyst complex component Exo70		49128
199IPR008979
Galactose-binding-like domain superfamily		4977
200IPR011527
ABC transporter type 1, transmembrane domain		49213
201IPR006566
FBD domain		4959
202IPR001906
Terpene synthase, N-terminal domain		4959
203IPR003676
Small auxin-up RNA		4960
204IPR044808
Ethylene-responsive transcription factor		4956
205IPR008978
HSP20-like chaperone		4863
206IPR007118
Expansin/Lol pI		48275
207IPR013201
Cathepsin propeptide inhibitor domain (I29)		4852
208IPR033905
Secretory peroxidase		4851
209IPR007125
Histone H2A/H2B/H3		4848
210IPR013094
Alpha/beta hydrolase fold-3		4868
211IPR017884
SANT domain		4762
212IPR001509
NAD-dependent epimerase/dehydratase		4765
213IPR029055
Nucleophile aminohydrolases, N-terminal		4768
214IPR034197
Cucumisin-like catalytic domain		4764
215IPR032867
DYW domain		4751
216IPR041569
AAA ATPase, AAA+ lid domain		4767
217IPR000620
EamA domain		47100
218IPR036318
FAD-binding, type PCMH-like superfamily		4656
219IPR011701
Major facilitator superfamily		4685
220IPR008928
Six-hairpin glycosidase superfamily		4657
221IPR012946
X8 domain		4557
222IPR045087
Multicopper oxidase		4566
223IPR030184
WAT1-related protein		4578
224IPR036855
Zinc finger, CCCH-type superfamily		45103
225IPR004853
Sugar phosphate transporter domain		4478
226IPR009000
Translation protein, beta-barrel domain superfamily		4465
227IPR004263
Exostosin-like		4455
228IPR014014
RNA helicase, DEAD-box type, Q motif		4462
229IPR011006
CheY-like superfamily		4458
230IPR006671
Cyclin, N-terminal		4461
231IPR014756
Immunoglobulin E-set		4458
232IPR001214
SET domain		4499
233IPR008889
VQ		4445
234IPR001117
Multicopper oxidase, type 1		4349
235IPR000182
GNAT domain		4389
236IPR033896
MADS MEF2-like		4364
237IPR000873
AMP-dependent synthetase/ligase		4370
238IPR034161
Pepsin-like domain, plant		4355
239IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4358
240IPR004265
Dirigent protein		4352
241IPR000668
Peptidase C1A, papain C-terminal		43156
242IPR000070
Pectinesterase, catalytic		4353
243IPR000743
Glycoside hydrolase, family 28		4350
244IPR001789
Signal transduction response regulator, receiver domain		4397
245IPR010402
CCT domain		42114
246IPR011012
Longin-like domain superfamily		4262
247IPR011706
Multicopper oxidase, C-terminal		4249
248IPR011043
Galactose oxidase/kelch, beta-propeller		4249
249IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4251
250IPR011707
Multicopper oxidase, N-termianl		4248
251IPR006702
Casparian strip membrane protein domain		4243
252IPR033389
AUX/IAA domain		4153
253IPR043926
ABC transporter family G domain		4169
254IPR009060
UBA-like superfamily		4167
255IPR000330
SNF2, N-terminal		4164
256IPR000742
EGF-like domain		4143
257IPR013126
Heat shock protein 70 family		41114
258IPR044730
Ribonuclease H-like domain, plant type		4143
259IPR015947
PUA-like superfamily		4156
260IPR006016
UspA		4049
261IPR016461
O-methyltransferase COMT-type		4099
262IPR036612
K Homology domain, type 1 superfamily		40100
263IPR001077
O-methyltransferase domain		4053
264IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3955
265IPR023271
Aquaporin-like		3947
266IPR016166
FAD-binding domain, PCMH-type		3949
267IPR029045
ClpP/crotonase-like domain superfamily		3960
268IPR000425
Major intrinsic protein		39294
269IPR002495
Glycosyl transferase, family 8		3943
270IPR039361
Cyclin		3961
271IPR025322
Protein of unknown function DUF4228, plant		3840
272IPR025659
Tubby-like, C-terminal		3848
273IPR013149
Alcohol dehydrogenase, C-terminal		3845
274IPR029021
Protein-tyrosine phosphatase-like		3860
275IPR003137
PA domain		3846
276IPR039417
Papain-like cysteine endopeptidase		3843
277IPR040911
Exostosin, GT47 domain		3842
278IPR000644
CBS domain		38159
279IPR002109
Glutaredoxin		3846
280IPR002912
ACT domain		38113
281IPR008942
ENTH/VHS		3744
282IPR016040
NAD(P)-binding domain		3760
283IPR004041
NAF domain		3746
284IPR007493
Protein of unknown function DUF538		3779
285IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3751
286IPR018451
NAF/FISL domain		3746
287IPR004839
Aminotransferase, class I/classII		3755
288IPR004883
Lateral organ boundaries, LOB		3779
289IPR036758
At5g01610-like superfamily		3741
290IPR015655
Protein phosphatase 2C family		3760
291IPR004046
Glutathione S-transferase, C-terminal		3747
292IPR007811
DNA-directed RNA polymerase III subunit RPC4		3783
293IPR002068
Alpha crystallin/Hsp20 domain		3690
294IPR034294
Aquaporin transporter		3648
295IPR019378
GDP-fucose protein O-fucosyltransferase		3649
296IPR002067
Mitochondrial carrier protein		36223
297IPR037176
Osmotin/thaumatin-like superfamily		3643
298IPR001360
Glycoside hydrolase family 1		35352
299IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3539
300IPR013154
Alcohol dehydrogenase, N-terminal		3543
301IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3554
302IPR033443
Pentacotripeptide-repeat region of PRORP		3540
303IPR028889
Ubiquitin specific protease domain		3550
304IPR002487
Transcription factor, K-box		35112
305IPR043454
NPH3/RPT2-like family		3459
306IPR006094
FAD linked oxidase, N-terminal		3443
307IPR043519
Nucleotidyltransferase superfamily		3453
308IPR001251
CRAL-TRIO lipid binding domain		33121
309IPR038933
Ovate protein family		3335
310IPR001938
Thaumatin family		33237
311IPR036865
CRAL-TRIO lipid binding domain superfamily		3342
312IPR006652
Kelch repeat type 1		3382
313IPR006458
Ovate protein family, C-terminal		3364
314IPR004314
Neprosin		3345
315IPR024752
Myb/SANT-like domain		3333
316IPR006073
GTP binding domain		33116
317IPR008991
Translation protein SH3-like domain superfamily		3243
318IPR000795
Translational (tr)-type GTP-binding domain		32264
319IPR004367
Cyclin, C-terminal domain		3238
320IPR022742
Serine aminopeptidase, S33		3239
321IPR005150
Cellulose synthase		3269
322IPR003406
Glycosyl transferase, family 14		3237
323IPR000863
Sulfotransferase domain		3248
324IPR004088
K Homology domain, type 1		3286
325IPR011141
Polyketide synthase, type III		3243
326IPR012967
Plant methyltransferase dimerisation		3233
327IPR001099
Chalcone/stilbene synthase, N-terminal		3239
328IPR018490
Cyclic nucleotide-binding-like		3144
329IPR001929
Germin		3195
330IPR032710
NTF2-like domain superfamily		3139
331IPR029061
Thiamin diphosphate-binding fold		3180
332IPR003855
Potassium transporter		31118
333IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3157
334IPR036041
Ribosome-inactivating protein superfamily		3134
335IPR000528
Plant non-specific lipid-transfer protein/Par allergen		30136
336IPR029000
Cyclophilin-like domain superfamily		3040
337IPR005299
SAM dependent carboxyl methyltransferase		3086
338IPR044822
Myb/SANT-like DNA-binding domain 4		3038
339IPR000315
B-box-type zinc finger		3075
340IPR000717
Proteasome component (PCI) domain		3069
341IPR001296
Glycosyl transferase, family 1		3055
342IPR001594
Palmitoyltransferase, DHHC domain		3046
343IPR005135
Endonuclease/exonuclease/phosphatase		3038
344IPR035940
CAP superfamily		3039
345IPR002423
Chaperonin Cpn60/TCP-1 family		3048
346IPR027356
NPH3 domain		3095
347IPR003690
Transcription termination factor, mitochondrial/chloroplastic		30102
348IPR003851
Zinc finger, Dof-type		3061
349IPR006311
Twin-arginine translocation pathway, signal sequence		3030
350IPR001574
Ribosome-inactivating protein		3063
351IPR045048
F-box only protein 31/39		2948
352IPR002963
Expansin		29243
353IPR001283
Cysteine-rich secretory protein-related		29115
354IPR008480
Protein of unknown function DUF761, plant		2929
355IPR027409
GroEL-like apical domain superfamily		2941
356IPR023299
P-type ATPase, cytoplasmic domain N		2938
357IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2942
358IPR012328
Chalcone/stilbene synthase, C-terminal		2932
359IPR000595
Cyclic nucleotide-binding domain		2996
360IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2936
361IPR015940
Ubiquitin-associated domain		2891
362IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28208
363IPR006153
Cation/H+ exchanger		2841
364IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28102
365IPR024709
Putative O-fucosyltransferase, plant		2841
366IPR010920
LSM domain superfamily		2837
367IPR044835
Auxin response factor		2861
368IPR044848
PHR1-like		2840
369IPR005333
Transcription factor, TCP		2830
370IPR004320
Protein of unknown function DUF241, plant		2837
371IPR007650
Zf-FLZ domain		2867
372IPR002123
Phospholipid/glycerol acyltransferase		2832
373IPR011013
Galactose mutarotase-like domain superfamily		2842
374IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2835
375IPR004813
Oligopeptide transporter, OPT superfamily		2858
376IPR001223
Glycoside hydrolase family 18, catalytic domain		2869
377IPR036812
NADP-dependent oxidoreductase domain superfamily		2843
378IPR000757
Glycoside hydrolase family 16		2870
379IPR000727
Target SNARE coiled-coil homology domain		2748
380IPR013601
FAE1/Type III polyketide synthase-like protein		2734
381IPR036378
FAS1 domain superfamily		2740
382IPR025753
AAA-type ATPase, N-terminal domain		2731
383IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2790
384IPR036420
BRCT domain superfamily		2742
385IPR002659
Glycosyl transferase, family 31		2787
386IPR003337
Trehalose-phosphatase		2738
387IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2734
388IPR014044
CAP domain		2735
389IPR001701
Glycoside hydrolase family 9		2734
390IPR044791
Beta-glucanase/XTH		2739
391IPR003311
AUX/IAA protein		2741
392IPR015797
NUDIX hydrolase-like domain superfamily		2732
393IPR036085
PAZ domain superfamily		2640
394IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2635
395IPR001357
BRCT domain		2667
396IPR040417
Glycine-rich cell wall structural protein 1/2		2638
397IPR026960
Reverse transcriptase zinc-binding domain		2626
398IPR027725
Heat shock transcription factor family		2632
399IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2638
400IPR000408
Regulator of chromosome condensation, RCC1		26607
401IPR036273
CRAL/TRIO, N-terminal domain superfamily		2632
402IPR004014
Cation-transporting P-type ATPase, N-terminal		2634
403IPR016897
S-phase kinase-associated protein 1		2633
404IPR005821
Ion transport domain		2636
405IPR039421
Type 1 protein exporter		2646
406IPR029062
Class I glutamine amidotransferase-like		2650
407IPR036296
SKP1-like, dimerisation domain superfamily		2632
408IPR000232
Heat shock factor (HSF)-type, DNA-binding		26110
409IPR023210
NADP-dependent oxidoreductase domain		2645
410IPR000679
Zinc finger, GATA-type		26102
411IPR005175
PPC domain		2676
412IPR002913
START domain		2671
413IPR003100
PAZ domain		2576
414IPR025110
AMP-binding enzyme, C-terminal domain		2536
415IPR017938
Riboflavin synthase-like beta-barrel		2534
416IPR004316
SWEET sugar transporter		2544
417IPR044778
Sugar transport protein STP/MST-like, plant		2531
418IPR009030
Growth factor receptor cysteine-rich domain superfamily		2533
419IPR001763
Rhodanese-like domain		2555
420IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2539
421IPR027923
Hydrophobic seed protein domain		2571
422IPR002035
von Willebrand factor, type A		2559
423IPR036404
Jacalin-like lectin domain superfamily		2537
424IPR036034
PDZ superfamily		2530
425IPR017927
FAD-binding domain, ferredoxin reductase-type		2433
426IPR000782
FAS1 domain		2463
427IPR013187
F-box associated domain, type 3		2428
428IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2429
429IPR008422
Homeobox KN domain		2431
430IPR023753
FAD/NAD(P)-binding domain		2436
431IPR018392
LysM domain		2481
432IPR019557
Aminotransferase-like, plant mobile domain		2429
433IPR016072
SKP1 component, dimerisation		2429
434IPR034285
Laccase, second cupredoxin domain		2428
435IPR001849
Pleckstrin homology domain		2451
436IPR029069
HotDog domain superfamily		2450
437IPR001757
P-type ATPase		24107
438IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2431
439IPR000086
NUDIX hydrolase domain		2456
440IPR029033
Histidine phosphatase superfamily		2430
441IPR036443
Zinc finger, RanBP2-type superfamily		2462
442IPR010525
Auxin response factor domain		2437
443IPR008971
HSP40/DnaJ peptide-binding		2364
444IPR011016
Zinc finger, RING-CH-type		2372
445IPR001163
LSM domain, eukaryotic/archaea-type		2328
446IPR007657
Glycosyltransferase 61		2366
447IPR017887
Transcription factor TCP subgroup		2346
448IPR001353
Proteasome, subunit alpha/beta		2333
449IPR010989
SNARE		2327
450IPR003594
Histidine kinase/HSP90-like ATPase		2331
451IPR044675
E3 ubiquitin-protein ligase RING1-like		2327
452IPR020103
Pseudouridine synthase, catalytic domain superfamily		2329
453IPR044839
Protein NDR1-like		2324
454IPR002939
Chaperone DnaJ, C-terminal		2335
455IPR025486
Domain of unknown function DUF4378		2337
456IPR002937
Amine oxidase		2329
457IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2334
458IPR001229
Jacalin-like lectin domain		2363
459IPR006689
Small GTPase superfamily, ARF/SAR type		22129
460IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2239
461IPR002867
IBR domain		2242
462IPR000387
Tyrosine specific protein phosphatases domain		2240
463IPR021790
PTBP1, RNA recognition motif 2-like		2230
464IPR013581
Plant PDR ABC transporter associated		2229
465IPR012416
CALMODULIN-BINDING PROTEIN60		2274
466IPR001881
EGF-like calcium-binding domain		2228
467IPR036010
2Fe-2S ferredoxin-like superfamily		2226
468IPR011257
DNA glycosylase		2228
469IPR025422
Transcription factor TGA like domain		2254
470IPR021720
Malectin domain		2242
471IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2226
472IPR020946
Flavin monooxygenase-like		2236
473IPR036427
Bromodomain-like superfamily		2237
474IPR031127
E3 ubiquitin ligase RBR family		2241
475IPR006868
Domain of unknown function DUF630		2225
476IPR003106
Leucine zipper, homeobox-associated		2121
477IPR022149
Protein of unknown function DUF3681		2149
478IPR007612
LURP-one-related		2156
479IPR001440
Tetratricopeptide repeat 1		2130
480IPR008999
Actin-crosslinking		2126
481IPR013216
Methyltransferase type 11		2130
482IPR005516
Remorin, C-terminal		2126
483IPR027413
GroEL-like equatorial domain superfamily		2132
484IPR000215
Serpin family		2134
485IPR013078
Histidine phosphatase superfamily, clade-1		2148
486IPR007592
GLABROUS1 enhancer-binding protein family		2147
487IPR022796
Chlorophyll A-B binding protein		2130
488IPR004776
Membrane transport protein		2137
489IPR001876
Zinc finger, RanBP2-type		2193
490IPR041677
DNA2/NAM7 helicase, helicase domain		2148
491IPR016161
Aldehyde/histidinol dehydrogenase		2131
492IPR032474
Protein argonaute, N-terminal		2132
493IPR029993
Plant galacturonosyltransferase GAUT		2130
494IPR001313
Pumilio RNA-binding repeat		21250
495IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2		2130
496IPR044066
TRIAD supradomain		2127
497IPR001487
Bromodomain		21167
498IPR013809
ENTH domain		2131
499IPR006867
Domain of unknown function DUF632		2125
500IPR033133
Pumilio homology domain		2022
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa125827.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa125827.html new file mode 100644 index 00000000..2ea8dbe7 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa125827.html @@ -0,0 +1,651 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os125827RS1, Jan 2020
Database version:87.1
Base Pairs:490,154,521
Golden Path Length:490,154,521
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		43,893
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:52,422
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144746243
237642977
339283915
437887228
530936521
632345421
729704550
830913760
924008571
1025458101
1132301089
1226804887
+
+
scaffold
+
563 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg26226979
UN-Ctg27101110
UN-Ctg28222998
UN-Ctg2940359
UN-Ctg30256021
UN-Ctg3193777
UN-Ctg3264992
UN-Ctg3376528
UN-Ctg34127432
UN-Ctg35251212
UN-Ctg3692765
UN-Ctg37175731
UN-Ctg38136140
UN-Ctg3992694
UN-Ctg40134729
UN-Ctg41256350
UN-Ctg42135926
UN-Ctg43101332
UN-Ctg4497842
UN-Ctg4585700
UN-Ctg4698654
UN-Ctg47140217
UN-Ctg48194807
UN-Ctg49230882
UN-Ctg50657594
UN-Ctg5193673
UN-Ctg52164271
UN-Ctg53146000
UN-Ctg5480131
UN-Ctg5595148
UN-Ctg5673396
UN-Ctg57167660
UN-Ctg58101756
UN-Ctg59113289
UN-Ctg6076820
UN-Ctg6194844
UN-Ctg62154492
UN-Ctg6393042
UN-Ctg64112008
UN-Ctg6576880
UN-Ctg6682417
UN-Ctg67168643
UN-Ctg68118658
UN-Ctg69129497
UN-Ctg7095800
UN-Ctg7199466
UN-Ctg7284307
UN-Ctg73124977
UN-Ctg7488118
UN-Ctg7589322
UN-Ctg7699872
UN-Ctg77102498
UN-Ctg78107266
UN-Ctg7982188
UN-Ctg80104905
UN-Ctg81286927
UN-Ctg8294160
UN-Ctg83235646
UN-Ctg84343402
UN-Ctg85241040
UN-Ctg8697166
UN-Ctg87186577
UN-Ctg88159027
UN-Ctg8983965
UN-Ctg90109729
UN-Ctg91111898
UN-Ctg9286169
UN-Ctg93343883
UN-Ctg94758236
UN-Ctg95143279
UN-Ctg96138534
UN-Ctg97156803
UN-Ctg98229908
UN-Ctg9999654
UN-Ctg10099770
UN-Ctg10156385
UN-Ctg102196694
UN-Ctg103114443
UN-Ctg104113533
UN-Ctg105186632
UN-Ctg106105044
UN-Ctg10762802
UN-Ctg108169235
UN-Ctg109121982
UN-Ctg110130368
UN-Ctg11193251
UN-Ctg11298587
UN-Ctg113157053
UN-Ctg114121715
UN-Ctg115101939
UN-Ctg116146291
UN-Ctg117433698
UN-Ctg11868624
UN-Ctg119286633
UN-Ctg12064082
UN-Ctg12199770
UN-Ctg122121509
UN-Ctg123114556
UN-Ctg124793824
UN-Ctg12581595
UN-Ctg126123156
UN-Ctg12793189
UN-Ctg128577170
UN-Ctg129404474
UN-Ctg130104994
UN-Ctg13184302
UN-Ctg132102689
UN-Ctg133340348
UN-Ctg13488340
UN-Ctg135279783
UN-Ctg136185319
UN-Ctg137116015
UN-Ctg138179570
UN-Ctg13979993
UN-Ctg14090847
UN-Ctg141205178
UN-Ctg142182475
UN-Ctg143404102
UN-Ctg144144109
UN-Ctg145102041
UN-Ctg146674128
UN-Ctg14784630
UN-Ctg14885356
UN-Ctg149232543
UN-Ctg150485761
UN-Ctg151100231
UN-Ctg152311455
UN-Ctg153140746
UN-Ctg154102057
UN-Ctg155301084
UN-Ctg156231050
UN-Ctg157132689
UN-Ctg158209417
UN-Ctg159213686
UN-Ctg160122977
UN-Ctg16190017
UN-Ctg16298852
UN-Ctg163106227
UN-Ctg164234126
UN-Ctg16560278
UN-Ctg166125855
UN-Ctg167105620
UN-Ctg16891081
UN-Ctg169765214
UN-Ctg170133710
UN-Ctg17186351
UN-Ctg172172804
UN-Ctg17394949
UN-Ctg174130609
UN-Ctg17578652
UN-Ctg176258667
UN-Ctg177150060
UN-Ctg17882010
UN-Ctg179151829
UN-Ctg180132402
UN-Ctg18181867
UN-Ctg18294309
UN-Ctg18371139
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UN-Ctg448530759
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UN-Ctg478197059
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UN-Ctg483114739
UN-Ctg484550080
UN-Ctg485317855
UN-Ctg48694092
UN-Ctg487156547
UN-Ctg488161457
UN-Ctg489183633
UN-Ctg490144089
UN-Ctg491126718
UN-Ctg49276966
UN-Ctg493145749
UN-Ctg49478358
UN-Ctg495514305
UN-Ctg496151810
UN-Ctg497308084
UN-Ctg498724558
UN-Ctg49991492
UN-Ctg500115868
UN-Ctg50183738
UN-Ctg50273937
UN-Ctg50365222
UN-Ctg50488803
UN-Ctg50594346
UN-Ctg506619523
UN-Ctg50794455
UN-Ctg508191623
UN-Ctg509272828
UN-Ctg51062950
UN-Ctg511162390
UN-Ctg512435694
UN-Ctg51371407
UN-Ctg51472996
UN-Ctg515143884
UN-Ctg5161065626
UN-Ctg517130712
UN-Ctg518143800
UN-Ctg519618958
UN-Ctg520240658
UN-Ctg521441538
UN-Ctg52281719
UN-Ctg523441414
UN-Ctg524114224
UN-Ctg525192350
UN-Ctg526371255
UN-Ctg527150036
UN-Ctg528296205
UN-Ctg529365369
UN-Ctg530159953
UN-Ctg531172724
UN-Ctg532217568
UN-Ctg53388420
UN-Ctg534352419
UN-Ctg535230184
UN-Ctg53679755
UN-Ctg537249850
UN-Ctg538112837
UN-Ctg53985003
UN-Ctg54092781
UN-Ctg54192930
UN-Ctg542106484
UN-Ctg54370613
UN-Ctg544313462
UN-Ctg545181066
UN-Ctg54673302
UN-Ctg54789257
UN-Ctg548100963
UN-Ctg54952109
UN-Ctg550124348
UN-Ctg551787093
UN-Ctg552460964
UN-Ctg553417637
UN-Ctg554284005
UN-Ctg555220183
UN-Ctg556172461
UN-Ctg557164299
UN-Ctg558158398
UN-Ctg559138791
UN-Ctg560137738
UN-Ctg561133700
UN-Ctg562124189
UN-Ctg563120629
UN-Ctg564110408
UN-Ctg565107773
UN-Ctg566107532
UN-Ctg567106650
UN-Ctg568105653
UN-Ctg569103933
UN-Ctg570100899
UN-Ctg57197676
UN-Ctg57293596
UN-Ctg57392047
UN-Ctg57490435
UN-Ctg57590045
UN-Ctg57685562
UN-Ctg57784998
UN-Ctg57880444
UN-Ctg57980058
UN-Ctg58078564
UN-Ctg58177852
UN-Ctg58267869
UN-Ctg58363212
UN-Ctg58460326
UN-Ctg58559701
UN-Ctg58656675
UN-Ctg58751962
UN-Ctg58831057
+
+
chunk5162 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):19,435,202
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No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		18262506
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		17232589
3IPR000719
Protein kinase domain		16863879
4IPR036047
F-box-like domain superfamily		7891022
5IPR044974
Disease resistance protein, plants		6581149
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		627989
7IPR001611
Leucine-rich repeat		6071950
8IPR002182
NB-ARC		602736
9IPR002885
Pentatricopeptide repeat		5877308
10IPR001810
F-box domain		5731097
11IPR001841
Zinc finger, RING-type		486998
12IPR041118
Rx, N-terminal		474547
13IPR016024
Armadillo-type fold		456706
14IPR036291
NAD(P)-binding domain superfamily		455685
15IPR009057
Homeobox-like domain superfamily		439555
16IPR029058
Alpha/Beta hydrolase fold		421594
17IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		411528
18IPR011990
Tetratricopeptide-like helical domain superfamily		389606
19IPR036396
Cytochrome P450 superfamily		380492
20IPR001128
Cytochrome P450		3721796
21IPR035979
RNA-binding domain superfamily		352680
22IPR038005
Virus X resistance protein-like, coiled-coil domain		335377
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		325475
24IPR002401
Cytochrome P450, E-class, group I		3212156
25IPR000504
RNA recognition motif domain		3131282
26IPR017853
Glycoside hydrolase superfamily		312451
27IPR036259
MFS transporter superfamily		301455
28IPR038765
Papain-like cysteine peptidase superfamily		281342
29IPR036322
WD40-repeat-containing domain superfamily		279426
30IPR036249
Thioredoxin-like superfamily		267389
31IPR017930
Myb domain		267763
32IPR001005
SANT/Myb domain		265769
33IPR001680
WD40 repeat		2451880
34IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		229528
35IPR036770
Ankyrin repeat-containing domain superfamily		222306
36IPR011992
EF-hand domain pair		204266
37IPR036412
HAD-like superfamily		202267
38IPR016177
DNA-binding domain superfamily		199274
39IPR002110
Ankyrin repeat		199804
40IPR002048
EF-hand domain		1971078
41IPR036638
Helix-loop-helix DNA-binding domain superfamily		193222
42IPR012337
Ribonuclease H-like superfamily		185232
43IPR001471
AP2/ERF domain		182980
44IPR036390
Winged helix DNA-binding domain superfamily		181235
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		179373
46IPR011333
SKP1/BTB/POZ domain superfamily		174244
47IPR020683
Ankyrin repeat-containing domain		168360
48IPR003439
ABC transporter-like, ATP-binding domain		167640
49IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		166219
50IPR036093
NAC domain superfamily		163183
51IPR010255
Haem peroxidase superfamily		163209
52IPR001650
Helicase, C-terminal		161470
53IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		158224
54IPR003441
NAC domain		158347
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		158236
56IPR036236
Zinc finger C2H2 superfamily		158219
57IPR029044
Nucleotide-diphospho-sugar transferases		157199
58IPR005174
Domain unknown function DUF295		157185
59IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		155186
60IPR002016
Haem peroxidase		155735
61IPR036188
FAD/NAD(P)-binding domain superfamily		153250
62IPR012340
Nucleic acid-binding, OB-fold		152272
63IPR013087
Zinc finger C2H2-type		151271
64IPR036426
Bulb-type lectin domain superfamily		149206
65IPR003480
Transferase		148185
66IPR001480
Bulb-type lectin domain		145513
67IPR021109
Aspartic peptidase domain superfamily		136172
68IPR007658
Protein of unknown function DUF594		135143
69IPR000210
BTB/POZ domain		134376
70IPR025315
Domain of unknown function DUF4220		134153
71IPR036869
Chaperone J-domain superfamily		131174
72IPR003959
ATPase, AAA-type, core		130209
73IPR015424
Pyridoxal phosphate-dependent transferase		128168
74IPR020846
Major facilitator superfamily domain		126175
75IPR001087
GDSL lipase/esterase		125158
76IPR008972
Cupredoxin		125262
77IPR001623
DnaJ domain		125851
78IPR026961
PGG domain		124286
79IPR002347
Short-chain dehydrogenase/reductase SDR		1231064
80IPR011011
Zinc finger, FYVE/PHD-type		123186
81IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		120138
82IPR019734
Tetratricopeptide repeat		119353
83IPR033121
Peptidase family A1 domain		119165
84IPR032861
Xylanase inhibitor, N-terminal		117145
85IPR011676
Domain of unknown function DUF1618		117148
86IPR003657
WRKY domain		116296
87IPR036576
WRKY domain superfamily		115151
88IPR011050
Pectin lyase fold/virulence factor		114127
89IPR009072
Histone-fold		114124
90IPR032799
Xylanase inhibitor, C-terminal		113137
91IPR005123
Oxoglutarate/iron-dependent dioxygenase		111149
92IPR029071
Ubiquitin-like domain superfamily		111157
93IPR000858
S-locus glycoprotein domain		110148
94IPR045005
BTB/POZ and MATH domain-containing protein 1-6		110189
95IPR001356
Homeobox domain		110350
96IPR044810
WRKY transcription factor, plant		108136
97IPR000823
Plant peroxidase		108476
98IPR015300
DNA-binding pseudobarrel domain superfamily		108180
99IPR003609
PAN/Apple domain		107269
100IPR035892
C2 domain superfamily		106202
101IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		106141
102IPR001461
Aspartic peptidase A1 family		104322
103IPR005828
Major facilitator, sugar transporter-like		103159
104IPR000109
Proton-dependent oligopeptide transporter family		102329
105IPR011051
RmlC-like cupin domain superfamily		102137
106IPR036875
Zinc finger, CCHC-type superfamily		101117
107IPR036457
PPM-type phosphatase domain superfamily		100138
108IPR011545
DEAD/DEAH box helicase domain		100151
109IPR043129
ATPase, nucleotide binding domain		98234
110IPR001932
PPM-type phosphatase domain		97391
111IPR003340
B3 DNA binding domain		96452
112IPR002083
MATH/TRAF domain		95329
113IPR001878
Zinc finger, CCHC-type		95186
114IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		95162
115IPR000073
Alpha/beta hydrolase fold-1		94258
116IPR020472
G-protein beta WD-40 repeat		93414
117IPR026992
Non-haem dioxygenase N-terminal domain		92123
118IPR004158
Protein of unknown function DUF247, plant		92210
119IPR035669
GDSL lipase/esterase-like, plant		91108
120IPR000008
C2 domain		91409
121IPR012871
Protein of unknown function DUF1677, Oryza sativa		91110
122IPR013766
Thioredoxin domain		90208
123IPR003613
U box domain		90194
124IPR004827
Basic-leucine zipper domain		88219
125IPR036282
Glutathione S-transferase, C-terminal domain superfamily		86117
126IPR008949
Isoprenoid synthase domain superfamily		85101
127IPR024788
Malectin-like domain		84109
128IPR001220
Legume lectin domain		82198
129IPR016039
Thiolase-like		81172
130IPR000270
PB1 domain		81136
131IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		8084
132IPR031052
FHY3/FAR1 family		80163
133IPR002902
Gnk2-homologous domain		80416
134IPR002100
Transcription factor, MADS-box		80456
135IPR036163
Heavy metal-associated domain superfamily		80108
136IPR036879
Transcription factor, MADS-box superfamily		80102
137IPR006121
Heavy metal-associated domain, HMA		78246
138IPR019787
Zinc finger, PHD-finger		77181
139IPR004045
Glutathione S-transferase, N-terminal		77217
140IPR004330
FAR1 DNA binding domain		7786
141IPR001806
Small GTPase		75166
142IPR003653
Ulp1 protease family, C-terminal catalytic domain		73144
143IPR016159
Cullin repeat-like-containing domain superfamily		7381
144IPR000571
Zinc finger, CCCH-type		73299
145IPR013057
Amino acid transporter, transmembrane domain		72105
146IPR020568
Ribosomal protein S5 domain 2-type fold		72117
147IPR007527
Zinc finger, SWIM-type		72125
148IPR036908
RlpA-like domain superfamily		7188
149IPR006501
Pectinesterase inhibitor domain		7174
150IPR029052
Metallo-dependent phosphatase-like		7195
151IPR003663
Sugar/inositol transporter		71393
152IPR044965
Glycoside hydrolase family 17, plant		70107
153IPR000048
IQ motif, EF-hand binding site		70368
154IPR022059
Protein of unknown function DUF3615		6985
155IPR005202
Transcription factor GRAS		69245
156IPR010987
Glutathione S-transferase, C-terminal-like		6998
157IPR026057
PC-Esterase		6899
158IPR036749
Expansin, cellulose-binding-like domain superfamily		6884
159IPR018108
Mitochondrial substrate/solute carrier		68543
160IPR023395
Mitochondrial carrier domain superfamily		6896
161IPR007117
Expansin, cellulose-binding-like domain		67166
162IPR036915
Cyclin-like superfamily		67153
163IPR011032
GroES-like superfamily		66101
164IPR029962
Trichome birefringence-like family		66102
165IPR009003
Peptidase S1, PA clan		66109
166IPR000225
Armadillo		66242
167IPR000626
Ubiquitin-like domain		65150
168IPR001563
Peptidase S10, serine carboxypeptidase		65465
169IPR003245
Phytocyanin domain		65137
170IPR000490
Glycoside hydrolase family 17		6589
171IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		6488
172IPR013525
ABC-2 type transporter		64139
173IPR005630
Terpene synthase, metal-binding domain		6479
174IPR039391
Phytocyanin		6477
175IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6473
176IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6493
177IPR023298
P-type ATPase, transmembrane domain superfamily		6488
178IPR002156
Ribonuclease H domain		6382
179IPR036640
ABC transporter type 1, transmembrane domain superfamily		63134
180IPR011527
ABC transporter type 1, transmembrane domain		63274
181IPR015915
Kelch-type beta propeller		6394
182IPR007125
Histone H2A/H2B/H3		6264
183IPR036852
Peptidase S8/S53 domain superfamily		6282
184IPR001906
Terpene synthase, N-terminal domain		6274
185IPR030184
WAT1-related protein		62106
186IPR001752
Kinesin motor domain		62452
187IPR000620
EamA domain		62128
188IPR006566
FBD domain		6175
189IPR036465
von Willebrand factor A-like domain superfamily		6179
190IPR000209
Peptidase S8/S53 domain		6179
191IPR045051
Subtilisin-like protease		6096
192IPR008250
P-type ATPase, A domain superfamily		6080
193IPR008979
Galactose-binding-like domain superfamily		60104
194IPR004265
Dirigent protein		5973
195IPR002528
Multi antimicrobial extrusion protein		59140
196IPR025846
PMR5 N-terminal domain		5981
197IPR041469
Subtilisin-like protease, fibronectin type-III domain		5872
198IPR016181
Acyl-CoA N-acyltransferase		5872
199IPR013201
Cathepsin propeptide inhibitor domain (I29)		5864
200IPR006045
Cupin 1		58102
201IPR013126
Heat shock protein 70 family		58163
202IPR007811
DNA-directed RNA polymerase III subunit RPC4		58118
203IPR002921
Fungal lipase-like domain		5768
204IPR017884
SANT domain		5771
205IPR004853
Sugar phosphate transporter domain		5792
206IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5767
207IPR007112
Expansin/pollen allergen, DPBB domain		5771
208IPR013094
Alpha/beta hydrolase fold-3		5786
209IPR045087
Multicopper oxidase		5688
210IPR029055
Nucleophile aminohydrolases, N-terminal		5573
211IPR009009
RlpA-like protein, double-psi beta-barrel domain		5567
212IPR013763
Cyclin-like		55115
213IPR011006
CheY-like superfamily		5571
214IPR001117
Multicopper oxidase, type 1		5462
215IPR000608
Ubiquitin-conjugating enzyme E2		54212
216IPR001509
NAD-dependent epimerase/dehydratase		5476
217IPR015500
Peptidase S8, subtilisin-related		54173
218IPR044808
Ethylene-responsive transcription factor		5463
219IPR001789
Signal transduction response regulator, receiver domain		54121
220IPR036318
FAD-binding, type PCMH-like superfamily		5368
221IPR016461
O-methyltransferase COMT-type		53122
222IPR008978
HSP20-like chaperone		5367
223IPR000873
AMP-dependent synthetase/ligase		5377
224IPR004140
Exocyst complex component Exo70		53130
225IPR033905
Secretory peroxidase		5360
226IPR041569
AAA ATPase, AAA+ lid domain		5378
227IPR036855
Zinc finger, CCCH-type superfamily		53121
228IPR007118
Expansin/Lol pI		52303
229IPR009000
Translation protein, beta-barrel domain superfamily		5276
230IPR008928
Six-hairpin glycosidase superfamily		5264
231IPR014756
Immunoglobulin E-set		5278
232IPR011707
Multicopper oxidase, N-termianl		5259
233IPR043926
ABC transporter family G domain		5189
234IPR011701
Major facilitator superfamily		51100
235IPR000330
SNF2, N-terminal		5193
236IPR001077
O-methyltransferase domain		5168
237IPR011706
Multicopper oxidase, C-terminal		5161
238IPR032867
DYW domain		5152
239IPR000070
Pectinesterase, catalytic		5163
240IPR008889
VQ		5153
241IPR009060
UBA-like superfamily		5075
242IPR036890
Histidine kinase/HSP90-like ATPase superfamily		5068
243IPR011012
Longin-like domain superfamily		5065
244IPR033389
AUX/IAA domain		4959
245IPR000182
GNAT domain		49106
246IPR006016
UspA		4960
247IPR014014
RNA helicase, DEAD-box type, Q motif		4969
248IPR034197
Cucumisin-like catalytic domain		4960
249IPR044730
Ribonuclease H-like domain, plant type		4950
250IPR001214
SET domain		49115
251IPR033896
MADS MEF2-like		4868
252IPR034161
Pepsin-like domain, plant		4862
253IPR012946
X8 domain		4868
254IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		4871
255IPR029045
ClpP/crotonase-like domain superfamily		4864
256IPR006671
Cyclin, N-terminal		4867
257IPR003676
Small auxin-up RNA		4859
258IPR004263
Exostosin-like		4755
259IPR000668
Peptidase C1A, papain C-terminal		47180
260IPR000743
Glycoside hydrolase, family 28		4754
261IPR015947
PUA-like superfamily		4766
262IPR035940
CAP superfamily		4665
263IPR016166
FAD-binding domain, PCMH-type		4661
264IPR000742
EGF-like domain		4653
265IPR028889
Ubiquitin specific protease domain		4658
266IPR011043
Galactose oxidase/kelch, beta-propeller		4655
267IPR024752
Myb/SANT-like domain		4547
268IPR006702
Casparian strip membrane protein domain		4546
269IPR016040
NAD(P)-binding domain		4475
270IPR010402
CCT domain		44116
271IPR008991
Translation protein SH3-like domain superfamily		4458
272IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4461
273IPR036612
K Homology domain, type 1 superfamily		44126
274IPR039417
Papain-like cysteine endopeptidase		4451
275IPR004314
Neprosin		4465
276IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4451
277IPR037176
Osmotin/thaumatin-like superfamily		4448
278IPR004839
Aminotransferase, class I/classII		4360
279IPR019378
GDP-fucose protein O-fucosyltransferase		4364
280IPR025659
Tubby-like, C-terminal		4254
281IPR002068
Alpha crystallin/Hsp20 domain		42102
282IPR029021
Protein-tyrosine phosphatase-like		4267
283IPR023271
Aquaporin-like		4256
284IPR000863
Sulfotransferase domain		4261
285IPR001283
Cysteine-rich secretory protein-related		42154
286IPR000425
Major intrinsic protein		42351
287IPR033443
Pentacotripeptide-repeat region of PRORP		4256
288IPR002495
Glycosyl transferase, family 8		4251
289IPR000644
CBS domain		42198
290IPR025322
Protein of unknown function DUF4228, plant		4143
291IPR001360
Glycoside hydrolase family 1		41407
292IPR007493
Protein of unknown function DUF538		4198
293IPR018451
NAF/FISL domain		4154
294IPR003137
PA domain		4152
295IPR040417
Glycine-rich cell wall structural protein 1/2		4155
296IPR013154
Alcohol dehydrogenase, N-terminal		4152
297IPR036758
At5g01610-like superfamily		4152
298IPR004046
Glutathione S-transferase, C-terminal		4153
299IPR040911
Exostosin, GT47 domain		4146
300IPR002109
Glutaredoxin		4151
301IPR043519
Nucleotidyltransferase superfamily		4162
302IPR004041
NAF domain		4054
303IPR013149
Alcohol dehydrogenase, C-terminal		4051
304IPR001938
Thaumatin family		40257
305IPR022742
Serine aminopeptidase, S33		4052
306IPR003690
Transcription termination factor, mitochondrial/chloroplastic		40144
307IPR043454
NPH3/RPT2-like family		4067
308IPR004883
Lateral organ boundaries, LOB		4086
309IPR006094
FAD linked oxidase, N-terminal		4052
310IPR002067
Mitochondrial carrier protein		40257
311IPR039361
Cyclin		4053
312IPR001223
Glycoside hydrolase family 18, catalytic domain		4090
313IPR002912
ACT domain		40112
314IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3958
315IPR029061
Thiamin diphosphate-binding fold		3993
316IPR003406
Glycosyl transferase, family 14		3944
317IPR014044
CAP domain		3953
318IPR002487
Transcription factor, K-box		39118
319IPR008942
ENTH/VHS		3852
320IPR032710
NTF2-like domain superfamily		3849
321IPR006652
Kelch repeat type 1		3899
322IPR015655
Protein phosphatase 2C family		3863
323IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		3846
324IPR036041
Ribosome-inactivating protein superfamily		3842
325IPR001574
Ribosome-inactivating protein		3873
326IPR005299
SAM dependent carboxyl methyltransferase		37104
327IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3742
328IPR000795
Translational (tr)-type GTP-binding domain		37307
329IPR034294
Aquaporin transporter		3757
330IPR023299
P-type ATPase, cytoplasmic domain N		3754
331IPR012967
Plant methyltransferase dimerisation		3737
332IPR036812
NADP-dependent oxidoreductase domain superfamily		3761
333IPR006311
Twin-arginine translocation pathway, signal sequence		3737
334IPR006073
GTP binding domain		37123
335IPR018490
Cyclic nucleotide-binding-like		3649
336IPR001251
CRAL-TRIO lipid binding domain		36142
337IPR008999
Actin-crosslinking		3642
338IPR005135
Endonuclease/exonuclease/phosphatase		3647
339IPR027356
NPH3 domain		36100
340IPR011013
Galactose mutarotase-like domain superfamily		3656
341IPR004088
K Homology domain, type 1		36110
342IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3665
343IPR000757
Glycoside hydrolase family 16		3689
344IPR007657
Glycosyltransferase 61		3599
345IPR001296
Glycosyl transferase, family 1		3558
346IPR005333
Transcription factor, TCP		3535
347IPR002423
Chaperonin Cpn60/TCP-1 family		3555
348IPR036865
CRAL-TRIO lipid binding domain superfamily		3549
349IPR044791
Beta-glucanase/XTH		3550
350IPR003311
AUX/IAA protein		3547
351IPR000595
Cyclic nucleotide-binding domain		35116
352IPR015797
NUDIX hydrolase-like domain superfamily		3541
353IPR000727
Target SNARE coiled-coil homology domain		3465
354IPR036378
FAS1 domain superfamily		3449
355IPR001929
Germin		34118
356IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		34123
357IPR010920
LSM domain superfamily		3447
358IPR038933
Ovate protein family		3435
359IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3438
360IPR021720
Malectin domain		3458
361IPR005150
Cellulose synthase		3460
362IPR006458
Ovate protein family, C-terminal		3466
363IPR003851
Zinc finger, Dof-type		3470
364IPR011141
Polyketide synthase, type III		3447
365IPR001099
Chalcone/stilbene synthase, N-terminal		3441
366IPR025110
AMP-binding enzyme, C-terminal domain		3337
367IPR001594
Palmitoyltransferase, DHHC domain		3360
368IPR004367
Cyclin, C-terminal domain		3337
369IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		3341
370IPR027409
GroEL-like apical domain superfamily		3343
371IPR001757
P-type ATPase		33149
372IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		3346
373IPR001701
Glycoside hydrolase family 9		3340
374IPR013601
FAE1/Type III polyketide synthase-like protein		3237
375IPR006153
Cation/H+ exchanger		3243
376IPR029000
Cyclophilin-like domain superfamily		3247
377IPR000315
B-box-type zinc finger		3290
378IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		3244
379IPR004014
Cation-transporting P-type ATPase, N-terminal		3243
380IPR000086
NUDIX hydrolase domain		3274
381IPR036404
Jacalin-like lectin domain superfamily		3248
382IPR003855
Potassium transporter		32125
383IPR023210
NADP-dependent oxidoreductase domain		3265
384IPR002913
START domain		32114
385IPR015940
Ubiquitin-associated domain		31104
386IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		31257
387IPR024709
Putative O-fucosyltransferase, plant		3153
388IPR044822
Myb/SANT-like DNA-binding domain 4		3141
389IPR000717
Proteasome component (PCI) domain		3174
390IPR019557
Aminotransferase-like, plant mobile domain		3135
391IPR007650
Zf-FLZ domain		3174
392IPR003337
Trehalose-phosphatase		3142
393IPR012328
Chalcone/stilbene synthase, C-terminal		3134
394IPR007679
Domain of unknown function DUF569		3131
395IPR000782
FAS1 domain		3079
396IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3037
397IPR003106
Leucine zipper, homeobox-associated		3031
398IPR004316
SWEET sugar transporter		3055
399IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		30116
400IPR013581
Plant PDR ABC transporter associated		3046
401IPR044778
Sugar transport protein STP/MST-like, plant		3032
402IPR002659
Glycosyl transferase, family 31		30107
403IPR027725
Heat shock transcription factor family		3042
404IPR001763
Rhodanese-like domain		3064
405IPR008480
Protein of unknown function DUF761, plant		3030
406IPR027923
Hydrophobic seed protein domain		3081
407IPR002035
von Willebrand factor, type A		3068
408IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3038
409IPR000528
Plant non-specific lipid-transfer protein/Par allergen		29136
410IPR017938
Riboflavin synthase-like beta-barrel		2940
411IPR013187
F-box associated domain, type 3		2935
412IPR036186
Serpin superfamily		2939
413IPR036420
BRCT domain superfamily		2972
414IPR010989
SNARE		2933
415IPR000408
Regulator of chromosome condensation, RCC1		29689
416IPR045048
F-box only protein 31/39		2988
417IPR000215
Serpin family		2943
418IPR002963
Expansin		29246
419IPR004813
Oligopeptide transporter, OPT superfamily		2967
420IPR023796
Serpin domain		2944
421IPR022149
Protein of unknown function DUF3681		2865
422IPR001357
BRCT domain		28109
423IPR044835
Auxin response factor		2862
424IPR001163
LSM domain, eukaryotic/archaea-type		2836
425IPR008422
Homeobox KN domain		2836
426IPR013216
Methyltransferase type 11		2839
427IPR044848
PHR1-like		2839
428IPR001881
EGF-like calcium-binding domain		2838
429IPR017887
Transcription factor TCP subgroup		2856
430IPR009030
Growth factor receptor cysteine-rich domain superfamily		2838
431IPR001353
Proteasome, subunit alpha/beta		2835
432IPR011257
DNA glycosylase		2836
433IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2841
434IPR013010
Zinc finger, SIAH-type		2834
435IPR036273
CRAL/TRIO, N-terminal domain superfamily		2836
436IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2845
437IPR016897
S-phase kinase-associated protein 1		2835
438IPR005821
Ion transport domain		2837
439IPR001849
Pleckstrin homology domain		2859
440IPR039421
Type 1 protein exporter		2850
441IPR029062
Class I glutamine amidotransferase-like		2848
442IPR036296
SKP1-like, dimerisation domain superfamily		2834
443IPR025486
Domain of unknown function DUF4378		2843
444IPR000232
Heat shock factor (HSF)-type, DNA-binding		28113
445IPR002937
Amine oxidase		2837
446IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2836
447IPR000679
Zinc finger, GATA-type		28107
448IPR005175
PPC domain		2886
449IPR001229
Jacalin-like lectin domain		2875
450IPR017927
FAD-binding domain, ferredoxin reductase-type		2738
451IPR036085
PAZ domain superfamily		2739
452IPR008971
HSP40/DnaJ peptide-binding		2768
453IPR023753
FAD/NAD(P)-binding domain		2738
454IPR003594
Histidine kinase/HSP90-like ATPase		2737
455IPR002123
Phospholipid/glycerol acyltransferase		2730
456IPR044814
Terpene cyclases, class 1, plant		2728
457IPR016072
SKP1 component, dimerisation		2732
458IPR006461
PLAC8 motif-containing protein		2763
459IPR007592
GLABROUS1 enhancer-binding protein family		2758
460IPR020946
Flavin monooxygenase-like		2747
461IPR036928
Amidase signature (AS) superfamily		2736
462IPR041677
DNA2/NAM7 helicase, helicase domain		2766
463IPR016161
Aldehyde/histidinol dehydrogenase		2738
464IPR002939
Chaperone DnaJ, C-terminal		2738
465IPR017923
Transcription factor IIS, N-terminal		2754
466IPR035441
TFIIS/LEDGF domain superfamily		2729
467IPR003100
PAZ domain		2674
468IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2629
469IPR011016
Zinc finger, RING-CH-type		2679
470IPR026960
Reverse transcriptase zinc-binding domain		2627
471IPR004320
Protein of unknown function DUF241, plant		2636
472IPR036010
2Fe-2S ferredoxin-like superfamily		2631
473IPR027413
GroEL-like equatorial domain superfamily		2636
474IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2632
475IPR041679
DNA2/NAM7 helicase-like, C-terminal		2687
476IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2		2642
477IPR009080
Aminoacyl-tRNA synthetase, class Ia, anticodon-binding		2640
478IPR019587
Polyketide cyclase/dehydrase		2627
479IPR036443
Zinc finger, RanBP2-type superfamily		2670
480IPR004294
Carotenoid oxygenase		2593
481IPR006689
Small GTPase superfamily, ARF/SAR type		25140
482IPR007612
LURP-one-related		2562
483IPR025753
AAA-type ATPase, N-terminal domain		2530
484IPR003347
JmjC domain		2548
485IPR044746
ABC transporter C family, six-transmembrane helical domain 1		2529
486IPR044675
E3 ubiquitin-protein ligase RING1-like		2529
487IPR011053
Single hybrid motif		2536
488IPR029069
HotDog domain superfamily		2548
489IPR045055
DNA2/NAM7-like helicase		2568
490IPR036034
PDZ superfamily		2529
491IPR015590
Aldehyde dehydrogenase domain		2541
492IPR010525
Auxin response factor domain		2541
493IPR045040
PORR family		2429
494IPR006594
LIS1 homology motif		2445
495IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2442
496IPR016064
NAD kinase/diacylglycerol kinase-like domain superfamily		2433
497IPR000387
Tyrosine specific protein phosphatases domain		2444
498IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		2425
499IPR036873
Rhodanese-like domain superfamily		2432
500IPR012416
CALMODULIN-BINDING PROTEIN60		2469
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127518.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127518.html new file mode 100644 index 00000000..066fba84 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127518.html @@ -0,0 +1,114 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os127518RS1, Jan 2020
Database version:87.1
Base Pairs:399,249,348
Golden Path Length:399,249,348
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,476
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:43,423
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144762005
237531860
340367348
436893333
531266701
632080718
730265487
829253686
925340617
1025441380
1132703027
1227831558
+
+
scaffold
+
34 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg281211332
UN-Ctg29306613
UN-Ctg30271051
UN-Ctg31244053
UN-Ctg32204062
UN-Ctg33185161
UN-Ctg34180222
UN-Ctg35162420
UN-Ctg36160205
UN-Ctg37154748
UN-Ctg38153005
UN-Ctg39146920
UN-Ctg40142094
UN-Ctg41137575
UN-Ctg42121688
UN-Ctg43120287
UN-Ctg44119471
UN-Ctg45118518
UN-Ctg46117243
UN-Ctg47109586
UN-Ctg48108298
UN-Ctg49106517
UN-Ctg50103959
UN-Ctg5199045
UN-Ctg5279685
UN-Ctg5382860
UN-Ctg5479532
UN-Ctg5577168
UN-Ctg5675336
UN-Ctg5772839
UN-Ctg5870939
UN-Ctg5964385
UN-Ctg6062529
UN-Ctg6162282
+
+
chunk4016 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127518_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127518_IPtop500.html new file mode 100644 index 00000000..c9c38012 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127518_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		15092090
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14422108
3IPR000719
Protein kinase domain		14123233
4IPR036047
F-box-like domain superfamily		663816
5IPR044974
Disease resistance protein, plants		550908
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		523877
7IPR002885
Pentatricopeptide repeat		5076319
8IPR002182
NB-ARC		499596
9IPR001810
F-box domain		486860
10IPR001611
Leucine-rich repeat		4841564
11IPR001841
Zinc finger, RING-type		432886
12IPR041118
Rx, N-terminal		397441
13IPR016024
Armadillo-type fold		390585
14IPR009057
Homeobox-like domain superfamily		382478
15IPR036291
NAD(P)-binding domain superfamily		376560
16IPR029058
Alpha/Beta hydrolase fold		372517
17IPR011990
Tetratricopeptide-like helical domain superfamily		335514
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		332414
19IPR036396
Cytochrome P450 superfamily		319409
20IPR001128
Cytochrome P450		3121495
21IPR035979
RNA-binding domain superfamily		303612
22IPR002401
Cytochrome P450, E-class, group I		2751833
23IPR038005
Virus X resistance protein-like, coiled-coil domain		274305
24IPR001005
SANT/Myb domain		2741350
25IPR000504
RNA recognition motif domain		2721146
26IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		262375
27IPR036259
MFS transporter superfamily		261392
28IPR017853
Glycoside hydrolase superfamily		259369
29IPR036249
Thioredoxin-like superfamily		237351
30IPR036322
WD40-repeat-containing domain superfamily		235338
31IPR017930
Myb domain		233347
32IPR038765
Papain-like cysteine peptidase superfamily		224275
33IPR001680
WD40 repeat		2071606
34IPR011992
EF-hand domain pair		188234
35IPR002048
EF-hand domain		178905
36IPR036770
Ankyrin repeat-containing domain superfamily		177253
37IPR016177
DNA-binding domain superfamily		175233
38IPR036412
HAD-like superfamily		174232
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		169390
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		168198
41IPR011333
SKP1/BTB/POZ domain superfamily		161234
42IPR036390
Winged helix DNA-binding domain superfamily		161214
43IPR002110
Ankyrin repeat		161663
44IPR001471
AP2/ERF domain		158845
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		157340
46IPR036093
NAC domain superfamily		148169
47IPR029044
Nucleotide-diphospho-sugar transferases		146182
48IPR012337
Ribonuclease H-like superfamily		146181
49IPR003441
NAC domain		145322
50IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		143190
51IPR001650
Helicase, C-terminal		141409
52IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		139169
53IPR013087
Zinc finger C2H2-type		138259
54IPR036236
Zinc finger C2H2 superfamily		137201
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		136202
56IPR010255
Haem peroxidase superfamily		135170
57IPR005174
Domain unknown function DUF295		134162
58IPR020683
Ankyrin repeat-containing domain		132283
59IPR036188
FAD/NAD(P)-binding domain superfamily		131214
60IPR012340
Nucleic acid-binding, OB-fold		130240
61IPR003439
ABC transporter-like, ATP-binding domain		129479
62IPR002016
Haem peroxidase		127615
63IPR021109
Aspartic peptidase domain superfamily		126156
64IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		122179
65IPR003480
Transferase		122144
66IPR000210
BTB/POZ domain		119357
67IPR036426
Bulb-type lectin domain superfamily		119178
68IPR036869
Chaperone J-domain superfamily		118155
69IPR003959
ATPase, AAA-type, core		117177
70IPR001480
Bulb-type lectin domain		116441
71IPR007658
Protein of unknown function DUF594		114120
72IPR020846
Major facilitator superfamily domain		114159
73IPR001623
DnaJ domain		112774
74IPR033121
Peptidase family A1 domain		112153
75IPR025315
Domain of unknown function DUF4220		110122
76IPR011676
Domain of unknown function DUF1618		109142
77IPR032799
Xylanase inhibitor, C-terminal		108129
78IPR032861
Xylanase inhibitor, N-terminal		108132
79IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		108127
80IPR019734
Tetratricopeptide repeat		107303
81IPR036576
WRKY domain superfamily		107133
82IPR005123
Oxoglutarate/iron-dependent dioxygenase		107350
83IPR003657
WRKY domain		107264
84IPR001087
GDSL lipase/esterase		106133
85IPR015424
Pyridoxal phosphate-dependent transferase		105144
86IPR011011
Zinc finger, FYVE/PHD-type		104144
87IPR008972
Cupredoxin		103209
88IPR029071
Ubiquitin-like domain superfamily		101152
89IPR044810
WRKY transcription factor, plant		99125
90IPR035892
C2 domain superfamily		98183
91IPR036457
PPM-type phosphatase domain superfamily		98137
92IPR011050
Pectin lyase fold/virulence factor		98112
93IPR001932
PPM-type phosphatase domain		96390
94IPR009072
Histone-fold		95105
95IPR000858
S-locus glycoprotein domain		94136
96IPR045005
BTB/POZ and MATH domain-containing protein 1-6		93168
97IPR003609
PAN/Apple domain		92244
98IPR011051
RmlC-like cupin domain superfamily		91123
99IPR005828
Major facilitator, sugar transporter-like		90140
100IPR011545
DEAD/DEAH box helicase domain		90134
101IPR001356
Homeobox domain		90274
102IPR015300
DNA-binding pseudobarrel domain superfamily		90151
103IPR002347
Short-chain dehydrogenase/reductase SDR		88745
104IPR000823
Plant peroxidase		88394
105IPR000008
C2 domain		87383
106IPR000073
Alpha/beta hydrolase fold-1		86238
107IPR035669
GDSL lipase/esterase-like, plant		84103
108IPR000109
Proton-dependent oligopeptide transporter family		84254
109IPR026961
PGG domain		84175
110IPR002083
MATH/TRAF domain		84307
111IPR013766
Thioredoxin domain		83188
112IPR001461
Aspartic peptidase A1 family		83275
113IPR043129
ATPase, nucleotide binding domain		82208
114IPR003340
B3 DNA binding domain		81396
115IPR020472
G-protein beta WD-40 repeat		81357
116IPR004158
Protein of unknown function DUF247, plant		81206
117IPR036875
Zinc finger, CCHC-type superfamily		8192
118IPR004827
Basic-leucine zipper domain		79187
119IPR036282
Glutathione S-transferase, C-terminal domain superfamily		78110
120IPR026992
Non-haem dioxygenase N-terminal domain		7791
121IPR002902
Gnk2-homologous domain		75377
122IPR003613
U box domain		74162
123IPR001878
Zinc finger, CCHC-type		74144
124IPR012871
Protein of unknown function DUF1677, Oryza sativa		7389
125IPR002100
Transcription factor, MADS-box		72425
126IPR001220
Legume lectin domain		72186
127IPR036879
Transcription factor, MADS-box superfamily		7292
128IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7175
129IPR036163
Heavy metal-associated domain superfamily		71100
130IPR008949
Isoprenoid synthase domain superfamily		7080
131IPR031052
FHY3/FAR1 family		70142
132IPR006121
Heavy metal-associated domain, HMA		69230
133IPR016159
Cullin repeat-like-containing domain superfamily		6983
134IPR000270
PB1 domain		69109
135IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		69108
136IPR016039
Thiolase-like		68146
137IPR004045
Glutathione S-transferase, N-terminal		67195
138IPR036908
RlpA-like domain superfamily		6783
139IPR013057
Amino acid transporter, transmembrane domain		6692
140IPR044965
Glycoside hydrolase family 17, plant		6695
141IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6573
142IPR000626
Ubiquitin-like domain		64156
143IPR036749
Expansin, cellulose-binding-like domain superfamily		6480
144IPR010987
Glutathione S-transferase, C-terminal-like		6493
145IPR007527
Zinc finger, SWIM-type		64111
146IPR036915
Cyclin-like superfamily		64144
147IPR004330
FAR1 DNA binding domain		6474
148IPR000048
IQ motif, EF-hand binding site		64306
149IPR018108
Mitochondrial substrate/solute carrier		63490
150IPR020568
Ribosomal protein S5 domain 2-type fold		63105
151IPR023395
Mitochondrial carrier domain superfamily		6387
152IPR029052
Metallo-dependent phosphatase-like		6383
153IPR007117
Expansin, cellulose-binding-like domain		63155
154IPR009003
Peptidase S1, PA clan		6394
155IPR003663
Sugar/inositol transporter		63347
156IPR000571
Zinc finger, CCCH-type		63308
157IPR001806
Small GTPase		63143
158IPR006501
Pectinesterase inhibitor domain		6265
159IPR024788
Malectin-like domain		6280
160IPR045051
Subtilisin-like protease		6192
161IPR022059
Protein of unknown function DUF3615		6176
162IPR019787
Zinc finger, PHD-finger		60136
163IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6079
164IPR036852
Peptidase S8/S53 domain superfamily		6076
165IPR000209
Peptidase S8/S53 domain		6073
166IPR003653
Ulp1 protease family, C-terminal catalytic domain		59117
167IPR000490
Glycoside hydrolase family 17		5978
168IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5878
169IPR003245
Phytocyanin domain		57121
170IPR005202
Transcription factor GRAS		57213
171IPR041469
Subtilisin-like protease, fibronectin type-III domain		5665
172IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5666
173IPR026057
PC-Esterase		5679
174IPR039391
Phytocyanin		5667
175IPR007112
Expansin/pollen allergen, DPBB domain		5669
176IPR011032
GroES-like superfamily		5582
177IPR015915
Kelch-type beta propeller		5577
178IPR000225
Armadillo		55240
179IPR001563
Peptidase S10, serine carboxypeptidase		54399
180IPR016181
Acyl-CoA N-acyltransferase		5462
181IPR029962
Trichome birefringence-like family		5480
182IPR034161
Pepsin-like domain, plant		5465
183IPR013763
Cyclin-like		54111
184IPR001752
Kinesin motor domain		54383
185IPR013525
ABC-2 type transporter		5397
186IPR002528
Multi antimicrobial extrusion protein		53124
187IPR015500
Peptidase S8, subtilisin-related		53163
188IPR002921
Fungal lipase-like domain		5265
189IPR002156
Ribonuclease H domain		5270
190IPR009009
RlpA-like protein, double-psi beta-barrel domain		5264
191IPR008979
Galactose-binding-like domain superfamily		5190
192IPR006045
Cupin 1		5195
193IPR025846
PMR5 N-terminal domain		5168
194IPR006566
FBD domain		5156
195IPR036465
von Willebrand factor A-like domain superfamily		5165
196IPR000608
Ubiquitin-conjugating enzyme E2		50183
197IPR008250
P-type ATPase, A domain superfamily		5063
198IPR005630
Terpene synthase, metal-binding domain		5057
199IPR004140
Exocyst complex component Exo70		50131
200IPR030184
WAT1-related protein		5091
201IPR023298
P-type ATPase, transmembrane domain superfamily		5066
202IPR017884
SANT domain		4961
203IPR007118
Expansin/Lol pI		49298
204IPR000620
EamA domain		49108
205IPR044808
Ethylene-responsive transcription factor		4957
206IPR008978
HSP20-like chaperone		4861
207IPR013201
Cathepsin propeptide inhibitor domain (I29)		4853
208IPR034197
Cucumisin-like catalytic domain		4857
209IPR041569
AAA ATPase, AAA+ lid domain		4865
210IPR036855
Zinc finger, CCCH-type superfamily		48122
211IPR003676
Small auxin-up RNA		4859
212IPR033905
Secretory peroxidase		4753
213IPR013094
Alpha/beta hydrolase fold-3		4769
214IPR036640
ABC transporter type 1, transmembrane domain superfamily		46104
215IPR000873
AMP-dependent synthetase/ligase		4667
216IPR014014
RNA helicase, DEAD-box type, Q motif		4666
217IPR012946
X8 domain		4660
218IPR008928
Six-hairpin glycosidase superfamily		4655
219IPR011527
ABC transporter type 1, transmembrane domain		46210
220IPR006671
Cyclin, N-terminal		4663
221IPR001906
Terpene synthase, N-terminal domain		4654
222IPR001214
SET domain		46102
223IPR033896
MADS MEF2-like		4565
224IPR036318
FAD-binding, type PCMH-like superfamily		4557
225IPR004853
Sugar phosphate transporter domain		4582
226IPR011701
Major facilitator superfamily		4584
227IPR029055
Nucleophile aminohydrolases, N-terminal		4564
228IPR009000
Translation protein, beta-barrel domain superfamily		4566
229IPR004265
Dirigent protein		4553
230IPR007125
Histone H2A/H2B/H3		4547
231IPR014756
Immunoglobulin E-set		4560
232IPR009060
UBA-like superfamily		4472
233IPR011006
CheY-like superfamily		4461
234IPR032867
DYW domain		4447
235IPR010402
CCT domain		43115
236IPR000182
GNAT domain		4385
237IPR001509
NAD-dependent epimerase/dehydratase		4364
238IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4361
239IPR000742
EGF-like domain		4348
240IPR045087
Multicopper oxidase		4362
241IPR008889
VQ		4344
242IPR000743
Glycoside hydrolase, family 28		4354
243IPR001117
Multicopper oxidase, type 1		4248
244IPR016461
O-methyltransferase COMT-type		4293
245IPR004263
Exostosin-like		4252
246IPR000070
Pectinesterase, catalytic		4250
247IPR015947
PUA-like superfamily		4256
248IPR001789
Signal transduction response regulator, receiver domain		42100
249IPR033389
AUX/IAA domain		4151
250IPR016040
NAD(P)-binding domain		4165
251IPR043926
ABC transporter family G domain		4164
252IPR036612
K Homology domain, type 1 superfamily		41110
253IPR011012
Longin-like domain superfamily		4163
254IPR011706
Multicopper oxidase, C-terminal		4148
255IPR000668
Peptidase C1A, papain C-terminal		41155
256IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4148
257IPR011707
Multicopper oxidase, N-termianl		4147
258IPR006016
UspA		4050
259IPR000330
SNF2, N-terminal		4066
260IPR029045
ClpP/crotonase-like domain superfamily		4060
261IPR015655
Protein phosphatase 2C family		4060
262IPR013126
Heat shock protein 70 family		40117
263IPR011043
Galactose oxidase/kelch, beta-propeller		4049
264IPR044730
Ribonuclease H-like domain, plant type		4042
265IPR025659
Tubby-like, C-terminal		3949
266IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3953
267IPR001077
O-methyltransferase domain		3953
268IPR002495
Glycosyl transferase, family 8		3944
269IPR002109
Glutaredoxin		3947
270IPR039361
Cyclin		3955
271IPR002912
ACT domain		39109
272IPR006702
Casparian strip membrane protein domain		3941
273IPR025322
Protein of unknown function DUF4228, plant		3840
274IPR029021
Protein-tyrosine phosphatase-like		3863
275IPR023271
Aquaporin-like		3847
276IPR016166
FAD-binding domain, PCMH-type		3850
277IPR004839
Aminotransferase, class I/classII		3855
278IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3852
279IPR000425
Major intrinsic protein		38304
280IPR000644
CBS domain		38154
281IPR008942
ENTH/VHS		3745
282IPR003137
PA domain		3749
283IPR019378
GDP-fucose protein O-fucosyltransferase		3754
284IPR004046
Glutathione S-transferase, C-terminal		3748
285IPR040911
Exostosin, GT47 domain		3743
286IPR028889
Ubiquitin specific protease domain		3748
287IPR001360
Glycoside hydrolase family 1		36339
288IPR013149
Alcohol dehydrogenase, C-terminal		3642
289IPR007493
Protein of unknown function DUF538		3678
290IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3656
291IPR002068
Alpha crystallin/Hsp20 domain		3688
292IPR036758
At5g01610-like superfamily		3640
293IPR002067
Mitochondrial carrier protein		36241
294IPR002487
Transcription factor, K-box		36114
295IPR037176
Osmotin/thaumatin-like superfamily		3641
296IPR004041
NAF domain		3549
297IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3539
298IPR001938
Thaumatin family		35232
299IPR034294
Aquaporin transporter		3547
300IPR022742
Serine aminopeptidase, S33		3542
301IPR004883
Lateral organ boundaries, LOB		3580
302IPR039417
Papain-like cysteine endopeptidase		3542
303IPR024752
Myb/SANT-like domain		3535
304IPR018451
NAF/FISL domain		3447
305IPR038933
Ovate protein family		3435
306IPR000795
Translational (tr)-type GTP-binding domain		34283
307IPR004367
Cyclin, C-terminal domain		3440
308IPR043454
NPH3/RPT2-like family		3463
309IPR033443
Pentacotripeptide-repeat region of PRORP		3442
310IPR006458
Ovate protein family, C-terminal		3466
311IPR004314
Neprosin		3446
312IPR043519
Nucleotidyltransferase superfamily		3451
313IPR013154
Alcohol dehydrogenase, N-terminal		3341
314IPR006652
Kelch repeat type 1		3378
315IPR000863
Sulfotransferase domain		3346
316IPR006094
FAD linked oxidase, N-terminal		3343
317IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3359
318IPR036041
Ribosome-inactivating protein superfamily		3336
319IPR012967
Plant methyltransferase dimerisation		3333
320IPR006311
Twin-arginine translocation pathway, signal sequence		3334
321IPR001574
Ribosome-inactivating protein		3364
322IPR001251
CRAL-TRIO lipid binding domain		32124
323IPR005333
Transcription factor, TCP		3234
324IPR005135
Endonuclease/exonuclease/phosphatase		3241
325IPR036865
CRAL-TRIO lipid binding domain superfamily		3244
326IPR018490
Cyclic nucleotide-binding-like		3141
327IPR032710
NTF2-like domain superfamily		3135
328IPR044822
Myb/SANT-like DNA-binding domain 4		3139
329IPR000315
B-box-type zinc finger		3180
330IPR001296
Glycosyl transferase, family 1		3153
331IPR035940
CAP superfamily		3141
332IPR027356
NPH3 domain		3192
333IPR005150
Cellulose synthase		3162
334IPR003406
Glycosyl transferase, family 14		3138
335IPR004088
K Homology domain, type 1		3193
336IPR000595
Cyclic nucleotide-binding domain		31104
337IPR001223
Glycoside hydrolase family 18, catalytic domain		3171
338IPR007811
DNA-directed RNA polymerase III subunit RPC4		3171
339IPR006073
GTP binding domain		31118
340IPR029000
Cyclophilin-like domain superfamily		3040
341IPR008991
Translation protein SH3-like domain superfamily		3040
342IPR000717
Proteasome component (PCI) domain		3067
343IPR029061
Thiamin diphosphate-binding fold		3074
344IPR001594
Palmitoyltransferase, DHHC domain		3046
345IPR002423
Chaperonin Cpn60/TCP-1 family		3051
346IPR011013
Galactose mutarotase-like domain superfamily		3046
347IPR003690
Transcription termination factor, mitochondrial/chloroplastic		30100
348IPR001283
Cysteine-rich secretory protein-related		30116
349IPR027409
GroEL-like apical domain superfamily		3041
350IPR003851
Zinc finger, Dof-type		3064
351IPR003855
Potassium transporter		30121
352IPR011141
Polyketide synthase, type III		3041
353IPR000727
Target SNARE coiled-coil homology domain		2951
354IPR000528
Plant non-specific lipid-transfer protein/Par allergen		29142
355IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		29222
356IPR006153
Cation/H+ exchanger		2934
357IPR010920
LSM domain superfamily		2936
358IPR044835
Auxin response factor		2958
359IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2936
360IPR002963
Expansin		29252
361IPR016897
S-phase kinase-associated protein 1		2933
362IPR023299
P-type ATPase, cytoplasmic domain N		2938
363IPR036296
SKP1-like, dimerisation domain superfamily		2932
364IPR001099
Chalcone/stilbene synthase, N-terminal		2934
365IPR025110
AMP-binding enzyme, C-terminal domain		2834
366IPR015940
Ubiquitin-associated domain		2893
367IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28110
368IPR024709
Putative O-fucosyltransferase, plant		2843
369IPR002659
Glycosyl transferase, family 31		2888
370IPR044848
PHR1-like		2839
371IPR003337
Trehalose-phosphatase		2842
372IPR016072
SKP1 component, dimerisation		2830
373IPR008480
Protein of unknown function DUF761, plant		2828
374IPR014044
CAP domain		2837
375IPR004813
Oligopeptide transporter, OPT superfamily		2860
376IPR029062
Class I glutamine amidotransferase-like		2848
377IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2842
378IPR012328
Chalcone/stilbene synthase, C-terminal		2831
379IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2836
380IPR005175
PPC domain		2884
381IPR036378
FAS1 domain superfamily		2740
382IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		27100
383IPR005299
SAM dependent carboxyl methyltransferase		2774
384IPR044778
Sugar transport protein STP/MST-like, plant		2731
385IPR040417
Glycine-rich cell wall structural protein 1/2		2738
386IPR007650
Zf-FLZ domain		2766
387IPR000408
Regulator of chromosome condensation, RCC1		27649
388IPR002123
Phospholipid/glycerol acyltransferase		2728
389IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2737
390IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2733
391IPR001757
P-type ATPase		27119
392IPR001701
Glycoside hydrolase family 9		2732
393IPR044791
Beta-glucanase/XTH		2741
394IPR003311
AUX/IAA protein		2741
395IPR036404
Jacalin-like lectin domain superfamily		2742
396IPR000757
Glycoside hydrolase family 16		2770
397IPR002913
START domain		2768
398IPR015797
NUDIX hydrolase-like domain superfamily		2731
399IPR013601
FAE1/Type III polyketide synthase-like protein		2632
400IPR001929
Germin		2690
401IPR004316
SWEET sugar transporter		2646
402IPR027725
Heat shock transcription factor family		2632
403IPR001881
EGF-like calcium-binding domain		2637
404IPR001763
Rhodanese-like domain		2671
405IPR045048
F-box only protein 31/39		2654
406IPR004014
Cation-transporting P-type ATPase, N-terminal		2630
407IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2641
408IPR027923
Hydrophobic seed protein domain		2670
409IPR002035
von Willebrand factor, type A		2663
410IPR001849
Pleckstrin homology domain		2659
411IPR000232
Heat shock factor (HSF)-type, DNA-binding		26110
412IPR000679
Zinc finger, GATA-type		26104
413IPR001229
Jacalin-like lectin domain		2676
414IPR036085
PAZ domain superfamily		2534
415IPR017938
Riboflavin synthase-like beta-barrel		2536
416IPR008971
HSP40/DnaJ peptide-binding		2561
417IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2533
418IPR025753
AAA-type ATPase, N-terminal domain		2530
419IPR036420
BRCT domain superfamily		2554
420IPR004320
Protein of unknown function DUF241, plant		2534
421IPR036273
CRAL/TRIO, N-terminal domain superfamily		2533
422IPR044839
Protein NDR1-like		2526
423IPR005821
Ion transport domain		2534
424IPR002939
Chaperone DnaJ, C-terminal		2537
425IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2532
426IPR017927
FAD-binding domain, ferredoxin reductase-type		2436
427IPR003100
PAZ domain		2465
428IPR000782
FAS1 domain		2463
429IPR001357
BRCT domain		2485
430IPR011016
Zinc finger, RING-CH-type		2484
431IPR001163
LSM domain, eukaryotic/archaea-type		2429
432IPR013216
Methyltransferase type 11		2430
433IPR012416
CALMODULIN-BINDING PROTEIN60		2473
434IPR023753
FAD/NAD(P)-binding domain		2432
435IPR007657
Glycosyltransferase 61		2464
436IPR019557
Aminotransferase-like, plant mobile domain		2428
437IPR003594
Histidine kinase/HSP90-like ATPase		2435
438IPR029069
HotDog domain superfamily		2448
439IPR000086
NUDIX hydrolase domain		2454
440IPR002937
Amine oxidase		2434
441IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2435
442IPR029033
Histidine phosphatase superfamily		2430
443IPR036812
NADP-dependent oxidoreductase domain superfamily		2442
444IPR036443
Zinc finger, RanBP2-type superfamily		2467
445IPR010525
Auxin response factor domain		2437
446IPR003106
Leucine zipper, homeobox-associated		2323
447IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2327
448IPR029466
No apical meristem-associated, C-terminal domain		2323
449IPR008999
Actin-crosslinking		2327
450IPR008422
Homeobox KN domain		2330
451IPR017887
Transcription factor TCP subgroup		2346
452IPR036010
2Fe-2S ferredoxin-like superfamily		2328
453IPR011257
DNA glycosylase		2328
454IPR010989
SNARE		2325
455IPR020103
Pseudouridine synthase, catalytic domain superfamily		2332
456IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2332
457IPR034285
Laccase, second cupredoxin domain		2327
458IPR039421
Type 1 protein exporter		2342
459IPR041677
DNA2/NAM7 helicase, helicase domain		2351
460IPR025486
Domain of unknown function DUF4378		2336
461IPR036034
PDZ superfamily		2327
462IPR006689
Small GTPase superfamily, ARF/SAR type		22143
463IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2236
464IPR016073
SKP1 component, POZ domain		2224
465IPR002867
IBR domain		2245
466IPR000387
Tyrosine specific protein phosphatases domain		2242
467IPR007612
LURP-one-related		2253
468IPR013187
F-box associated domain, type 3		2224
469IPR036186
Serpin superfamily		2231
470IPR018392
LysM domain		2276
471IPR009030
Growth factor receptor cysteine-rich domain superfamily		2229
472IPR001353
Proteasome, subunit alpha/beta		2229
473IPR025422
Transcription factor TGA like domain		2252
474IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2230
475IPR044675
E3 ubiquitin-protein ligase RING1-like		2226
476IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2227
477IPR044814
Terpene cyclases, class 1, plant		2223
478IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2224
479IPR004776
Membrane transport protein		2236
480IPR001876
Zinc finger, RanBP2-type		22103
481IPR016161
Aldehyde/histidinol dehydrogenase		2235
482IPR036427
Bromodomain-like superfamily		2236
483IPR031127
E3 ubiquitin ligase RBR family		2244
484IPR006868
Domain of unknown function DUF630		2226
485IPR023210
NADP-dependent oxidoreductase domain		2245
486IPR023796
Serpin domain		2234
487IPR033133
Pumilio homology domain		2122
488IPR004000
Actin family		21195
489IPR035952
Rhomboid-like superfamily		2129
490IPR036873
Rhodanese-like domain superfamily		2135
491IPR013581
Plant PDR ABC transporter associated		2128
492IPR005516
Remorin, C-terminal		2126
493IPR027413
GroEL-like equatorial domain superfamily		2135
494IPR022812
Dynamin		21168
495IPR000215
Serpin family		2133
496IPR006461
PLAC8 motif-containing protein		2151
497IPR007592
GLABROUS1 enhancer-binding protein family		2146
498IPR036610
PEBP-like superfamily		2122
499IPR022796
Chlorophyll A-B binding protein		2132
500IPR020946
Flavin monooxygenase-like		2134
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127564.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127564.html new file mode 100644 index 00000000..b8aaae98 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127564.html @@ -0,0 +1,161 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os127564RS1, Jan 2020
Database version:87.1
Base Pairs:405,399,143
Golden Path Length:405,399,143
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		37,044
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:43,787
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144959450
237901196
339451588
436936500
531248194
632484336
730742511
829289589
924047418
1025773493
1132421942
1227369091
+
+
scaffold
+
81 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg31859396
UN-Ctg32423004
UN-Ctg33378719
UN-Ctg34344904
UN-Ctg35302159
UN-Ctg36296945
UN-Ctg37265702
UN-Ctg38265307
UN-Ctg39239042
UN-Ctg40238511
UN-Ctg41238405
UN-Ctg42234649
UN-Ctg43233963
UN-Ctg44233527
UN-Ctg45230460
UN-Ctg46212683
UN-Ctg47205121
UN-Ctg48197756
UN-Ctg49195788
UN-Ctg50194945
UN-Ctg51183173
UN-Ctg52163692
UN-Ctg53160496
UN-Ctg54159154
UN-Ctg55158732
UN-Ctg56157112
UN-Ctg57155975
UN-Ctg58156014
UN-Ctg59152683
UN-Ctg60148572
UN-Ctg61147066
UN-Ctg62145353
UN-Ctg63144367
UN-Ctg64143928
UN-Ctg65142203
UN-Ctg66141676
UN-Ctg67138727
UN-Ctg68136956
UN-Ctg69135089
UN-Ctg70132926
UN-Ctg71130762
UN-Ctg72126456
UN-Ctg73126202
UN-Ctg74120140
UN-Ctg75119908
UN-Ctg76119127
UN-Ctg77118247
UN-Ctg78116211
UN-Ctg79115737
UN-Ctg80114934
UN-Ctg81108472
UN-Ctg82107998
UN-Ctg83107873
UN-Ctg84107085
UN-Ctg85105535
UN-Ctg86105458
UN-Ctg87104346
UN-Ctg88101298
UN-Ctg8997799
UN-Ctg9097592
UN-Ctg9197573
UN-Ctg9295559
UN-Ctg9393167
UN-Ctg9493391
UN-Ctg9593197
UN-Ctg9692996
UN-Ctg9791928
UN-Ctg9891010
UN-Ctg9987994
UN-Ctg10087082
UN-Ctg10186339
UN-Ctg10286322
UN-Ctg10383944
UN-Ctg10481629
UN-Ctg10574559
UN-Ctg10668523
UN-Ctg10768502
UN-Ctg10867795
UN-Ctg10963030
UN-Ctg11062871
UN-Ctg11160364
+
+
chunk4099 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127564_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127564_IPtop500.html new file mode 100644 index 00000000..4b5fffc6 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127564_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14881982
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14302036
3IPR000719
Protein kinase domain		13893064
4IPR036047
F-box-like domain superfamily		659834
5IPR044974
Disease resistance protein, plants		542924
6IPR002182
NB-ARC		512587
7IPR002885
Pentatricopeptide repeat		4966146
8IPR001611
Leucine-rich repeat		4941577
9IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		492827
10IPR001810
F-box domain		481881
11IPR001841
Zinc finger, RING-type		424872
12IPR041118
Rx, N-terminal		400438
13IPR009057
Homeobox-like domain superfamily		379478
14IPR036291
NAD(P)-binding domain superfamily		378548
15IPR016024
Armadillo-type fold		373574
16IPR029058
Alpha/Beta hydrolase fold		367504
17IPR036396
Cytochrome P450 superfamily		333428
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		331416
19IPR011990
Tetratricopeptide-like helical domain superfamily		326497
20IPR001128
Cytochrome P450		3251526
21IPR035979
RNA-binding domain superfamily		298566
22IPR038005
Virus X resistance protein-like, coiled-coil domain		287311
23IPR002401
Cytochrome P450, E-class, group I		2771836
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		273383
25IPR000504
RNA recognition motif domain		2631055
26IPR017853
Glycoside hydrolase superfamily		259359
27IPR036259
MFS transporter superfamily		258395
28IPR017930
Myb domain		241695
29IPR001005
SANT/Myb domain		233677
30IPR036249
Thioredoxin-like superfamily		232333
31IPR038765
Papain-like cysteine peptidase superfamily		232278
32IPR036322
WD40-repeat-containing domain superfamily		231332
33IPR001680
WD40 repeat		2091570
34IPR011992
EF-hand domain pair		185227
35IPR036412
HAD-like superfamily		177229
36IPR002048
EF-hand domain		173871
37IPR016177
DNA-binding domain superfamily		173241
38IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		171397
39IPR036770
Ankyrin repeat-containing domain superfamily		169237
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		167192
41IPR001471
AP2/ERF domain		159861
42IPR012337
Ribonuclease H-like superfamily		156190
43IPR011333
SKP1/BTB/POZ domain superfamily		156235
44IPR002110
Ankyrin repeat		156656
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		155325
46IPR036390
Winged helix DNA-binding domain superfamily		152192
47IPR036093
NAC domain superfamily		149168
48IPR003441
NAC domain		145321
49IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		138163
50IPR029044
Nucleotide-diphospho-sugar transferases		137168
51IPR001650
Helicase, C-terminal		137389
52IPR036188
FAD/NAD(P)-binding domain superfamily		137224
53IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		136173
54IPR012340
Nucleic acid-binding, OB-fold		136264
55IPR005174
Domain unknown function DUF295		133156
56IPR014001
Helicase superfamily 1/2, ATP-binding domain		132188
57IPR036236
Zinc finger C2H2 superfamily		132185
58IPR010255
Haem peroxidase superfamily		131181
59IPR013087
Zinc finger C2H2-type		130232
60IPR020683
Ankyrin repeat-containing domain		127274
61IPR036426
Bulb-type lectin domain superfamily		126164
62IPR002016
Haem peroxidase		125620
63IPR001480
Bulb-type lectin domain		123407
64IPR003439
ABC transporter-like, ATP-binding domain		123452
65IPR025315
Domain of unknown function DUF4220		119124
66IPR021109
Aspartic peptidase domain superfamily		118153
67IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		117165
68IPR000210
BTB/POZ domain		116359
69IPR007658
Protein of unknown function DUF594		116119
70IPR003959
ATPase, AAA-type, core		115172
71IPR001087
GDSL lipase/esterase		112139
72IPR003480
Transferase		112130
73IPR020846
Major facilitator superfamily domain		110155
74IPR036869
Chaperone J-domain superfamily		109145
75IPR033121
Peptidase family A1 domain		107148
76IPR015424
Pyridoxal phosphate-dependent transferase		107140
77IPR008972
Cupredoxin		106213
78IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		106119
79IPR011011
Zinc finger, FYVE/PHD-type		105146
80IPR019734
Tetratricopeptide repeat		104306
81IPR001623
DnaJ domain		103722
82IPR011676
Domain of unknown function DUF1618		102135
83IPR003657
WRKY domain		102272
84IPR036576
WRKY domain superfamily		101137
85IPR032861
Xylanase inhibitor, N-terminal		101126
86IPR011050
Pectin lyase fold/virulence factor		99115
87IPR032799
Xylanase inhibitor, C-terminal		99124
88IPR035892
C2 domain superfamily		98180
89IPR000858
S-locus glycoprotein domain		98123
90IPR003609
PAN/Apple domain		96222
91IPR036457
PPM-type phosphatase domain superfamily		95136
92IPR044810
WRKY transcription factor, plant		95121
93IPR005123
Oxoglutarate/iron-dependent dioxygenase		94115
94IPR029071
Ubiquitin-like domain superfamily		94148
95IPR009072
Histone-fold		93101
96IPR011051
RmlC-like cupin domain superfamily		92119
97IPR004158
Protein of unknown function DUF247, plant		92250
98IPR001932
PPM-type phosphatase domain		91384
99IPR015300
DNA-binding pseudobarrel domain superfamily		89150
100IPR000008
C2 domain		88375
101IPR002347
Short-chain dehydrogenase/reductase SDR		88737
102IPR005828
Major facilitator, sugar transporter-like		88135
103IPR011545
DEAD/DEAH box helicase domain		87124
104IPR001356
Homeobox domain		87277
105IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		86105
106IPR045005
BTB/POZ and MATH domain-containing protein 1-6		85162
107IPR001461
Aspartic peptidase A1 family		85278
108IPR035669
GDSL lipase/esterase-like, plant		8499
109IPR000109
Proton-dependent oligopeptide transporter family		83282
110IPR000823
Plant peroxidase		82376
111IPR003340
B3 DNA binding domain		81389
112IPR013766
Thioredoxin domain		81177
113IPR002083
MATH/TRAF domain		81301
114IPR026961
PGG domain		80169
115IPR020472
G-protein beta WD-40 repeat		79324
116IPR000073
Alpha/beta hydrolase fold-1		78213
117IPR004827
Basic-leucine zipper domain		78183
118IPR036875
Zinc finger, CCHC-type superfamily		7895
119IPR012871
Protein of unknown function DUF1677, Oryza sativa		7798
120IPR031052
FHY3/FAR1 family		76139
121IPR026992
Non-haem dioxygenase N-terminal domain		7696
122IPR043129
ATPase, nucleotide binding domain		75184
123IPR036163
Heavy metal-associated domain superfamily		73100
124IPR036282
Glutathione S-transferase, C-terminal domain superfamily		73103
125IPR001878
Zinc finger, CCHC-type		72160
126IPR006121
Heavy metal-associated domain, HMA		71230
127IPR002100
Transcription factor, MADS-box		71376
128IPR044965
Glycoside hydrolase family 17, plant		71104
129IPR036879
Transcription factor, MADS-box superfamily		7184
130IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		71112
131IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7074
132IPR002902
Gnk2-homologous domain		70371
133IPR004330
FAR1 DNA binding domain		7076
134IPR008949
Isoprenoid synthase domain superfamily		6983
135IPR016039
Thiolase-like		69153
136IPR001220
Legume lectin domain		69163
137IPR003613
U box domain		69154
138IPR000270
PB1 domain		69115
139IPR013057
Amino acid transporter, transmembrane domain		6888
140IPR036749
Expansin, cellulose-binding-like domain superfamily		6784
141IPR003653
Ulp1 protease family, C-terminal catalytic domain		67126
142IPR004045
Glutathione S-transferase, N-terminal		67200
143IPR036908
RlpA-like domain superfamily		6584
144IPR016159
Cullin repeat-like-containing domain superfamily		6578
145IPR007117
Expansin, cellulose-binding-like domain		65161
146IPR020568
Ribosomal protein S5 domain 2-type fold		64110
147IPR029052
Metallo-dependent phosphatase-like		6390
148IPR007527
Zinc finger, SWIM-type		63103
149IPR024788
Malectin-like domain		6382
150IPR000626
Ubiquitin-like domain		62161
151IPR019787
Zinc finger, PHD-finger		62140
152IPR000490
Glycoside hydrolase family 17		6280
153IPR036915
Cyclin-like superfamily		62133
154IPR000048
IQ motif, EF-hand binding site		62275
155IPR018108
Mitochondrial substrate/solute carrier		61450
156IPR023395
Mitochondrial carrier domain superfamily		6182
157IPR009003
Peptidase S1, PA clan		6194
158IPR003663
Sugar/inositol transporter		61333
159IPR000571
Zinc finger, CCCH-type		61288
160IPR001806
Small GTPase		61136
161IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6066
162IPR005202
Transcription factor GRAS		60222
163IPR036852
Peptidase S8/S53 domain superfamily		6075
164IPR006501
Pectinesterase inhibitor domain		6063
165IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5981
166IPR010987
Glutathione S-transferase, C-terminal-like		5987
167IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5885
168IPR000209
Peptidase S8/S53 domain		5873
169IPR045051
Subtilisin-like protease		5788
170IPR022059
Protein of unknown function DUF3615		5776
171IPR015915
Kelch-type beta propeller		5783
172IPR041469
Subtilisin-like protease, fibronectin type-III domain		5667
173IPR007112
Expansin/pollen allergen, DPBB domain		5671
174IPR003245
Phytocyanin domain		56120
175IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5564
176IPR039391
Phytocyanin		5565
177IPR006045
Cupin 1		5589
178IPR001563
Peptidase S10, serine carboxypeptidase		54424
179IPR002156
Ribonuclease H domain		5472
180IPR009009
RlpA-like protein, double-psi beta-barrel domain		5467
181IPR023298
P-type ATPase, transmembrane domain superfamily		5470
182IPR011032
GroES-like superfamily		5381
183IPR026057
PC-Esterase		5373
184IPR002528
Multi antimicrobial extrusion protein		53132
185IPR036465
von Willebrand factor A-like domain superfamily		5369
186IPR002921
Fungal lipase-like domain		5262
187IPR013094
Alpha/beta hydrolase fold-3		5274
188IPR001752
Kinesin motor domain		52379
189IPR008250
P-type ATPase, A domain superfamily		5163
190IPR015500
Peptidase S8, subtilisin-related		51162
191IPR017884
SANT domain		5064
192IPR016181
Acyl-CoA N-acyltransferase		5058
193IPR000608
Ubiquitin-conjugating enzyme E2		50194
194IPR029962
Trichome birefringence-like family		5077
195IPR013763
Cyclin-like		5099
196IPR044808
Ethylene-responsive transcription factor		5057
197IPR000225
Armadillo		50217
198IPR013525
ABC-2 type transporter		4990
199IPR007118
Expansin/Lol pI		49291
200IPR005630
Terpene synthase, metal-binding domain		4959
201IPR008979
Galactose-binding-like domain superfamily		4978
202IPR025846
PMR5 N-terminal domain		4965
203IPR045087
Multicopper oxidase		4968
204IPR041569
AAA ATPase, AAA+ lid domain		4966
205IPR034161
Pepsin-like domain, plant		4861
206IPR001906
Terpene synthase, N-terminal domain		4857
207IPR008978
HSP20-like chaperone		4762
208IPR013201
Cathepsin propeptide inhibitor domain (I29)		4752
209IPR004140
Exocyst complex component Exo70		47119
210IPR034197
Cucumisin-like catalytic domain		4755
211IPR008928
Six-hairpin glycosidase superfamily		4756
212IPR003676
Small auxin-up RNA		4758
213IPR036640
ABC transporter type 1, transmembrane domain superfamily		4699
214IPR007125
Histone H2A/H2B/H3		4646
215IPR011527
ABC transporter type 1, transmembrane domain		46199
216IPR006566
FBD domain		4653
217IPR036855
Zinc finger, CCCH-type superfamily		46115
218IPR001117
Multicopper oxidase, type 1		4549
219IPR036318
FAD-binding, type PCMH-like superfamily		4556
220IPR011701
Major facilitator superfamily		4585
221IPR001509
NAD-dependent epimerase/dehydratase		4570
222IPR029055
Nucleophile aminohydrolases, N-terminal		4563
223IPR009000
Translation protein, beta-barrel domain superfamily		4561
224IPR012946
X8 domain		4557
225IPR011706
Multicopper oxidase, C-terminal		4551
226IPR030184
WAT1-related protein		4581
227IPR014756
Immunoglobulin E-set		4567
228IPR000620
EamA domain		4596
229IPR004853
Sugar phosphate transporter domain		4473
230IPR000742
EGF-like domain		4447
231IPR033389
AUX/IAA domain		4352
232IPR033896
MADS MEF2-like		4356
233IPR000873
AMP-dependent synthetase/ligase		4360
234IPR004263
Exostosin-like		4352
235IPR014014
RNA helicase, DEAD-box type, Q motif		4361
236IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4357
237IPR004265
Dirigent protein		4352
238IPR011006
CheY-like superfamily		4352
239IPR011043
Galactose oxidase/kelch, beta-propeller		4349
240IPR001214
SET domain		4398
241IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4352
242IPR000743
Glycoside hydrolase, family 28		4353
243IPR000182
GNAT domain		4286
244IPR009060
UBA-like superfamily		4266
245IPR011012
Longin-like domain superfamily		4262
246IPR006671
Cyclin, N-terminal		4257
247IPR000070
Pectinesterase, catalytic		4251
248IPR008889
VQ		4244
249IPR011707
Multicopper oxidase, N-termianl		4246
250IPR001789
Signal transduction response regulator, receiver domain		4287
251IPR016461
O-methyltransferase COMT-type		4197
252IPR000330
SNF2, N-terminal		4168
253IPR037176
Osmotin/thaumatin-like superfamily		4147
254IPR006702
Casparian strip membrane protein domain		4143
255IPR036612
K Homology domain, type 1 superfamily		40108
256IPR001938
Thaumatin family		40278
257IPR033905
Secretory peroxidase		4050
258IPR001077
O-methyltransferase domain		4053
259IPR029045
ClpP/crotonase-like domain superfamily		4055
260IPR000668
Peptidase C1A, papain C-terminal		40148
261IPR044730
Ribonuclease H-like domain, plant type		4042
262IPR010402
CCT domain		3996
263IPR043926
ABC transporter family G domain		3961
264IPR007493
Protein of unknown function DUF538		3990
265IPR036758
At5g01610-like superfamily		3946
266IPR015655
Protein phosphatase 2C family		3969
267IPR025322
Protein of unknown function DUF4228, plant		3840
268IPR004041
NAF domain		3849
269IPR018451
NAF/FISL domain		3848
270IPR016166
FAD-binding domain, PCMH-type		3849
271IPR004839
Aminotransferase, class I/classII		3850
272IPR032867
DYW domain		3843
273IPR040911
Exostosin, GT47 domain		3843
274IPR000644
CBS domain		38171
275IPR013126
Heat shock protein 70 family		38111
276IPR039361
Cyclin		3855
277IPR002912
ACT domain		38103
278IPR015947
PUA-like superfamily		3852
279IPR006016
UspA		3747
280IPR025659
Tubby-like, C-terminal		3747
281IPR013149
Alcohol dehydrogenase, C-terminal		3746
282IPR029021
Protein-tyrosine phosphatase-like		3766
283IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3751
284IPR003137
PA domain		3747
285IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3754
286IPR002495
Glycosyl transferase, family 8		3745
287IPR008942
ENTH/VHS		3648
288IPR016040
NAD(P)-binding domain		3657
289IPR001360
Glycoside hydrolase family 1		36328
290IPR002068
Alpha crystallin/Hsp20 domain		3693
291IPR006652
Kelch repeat type 1		3685
292IPR039417
Papain-like cysteine endopeptidase		3643
293IPR002067
Mitochondrial carrier protein		36216
294IPR028889
Ubiquitin specific protease domain		3649
295IPR002109
Glutaredoxin		3645
296IPR004314
Neprosin		3651
297IPR005299
SAM dependent carboxyl methyltransferase		3595
298IPR023271
Aquaporin-like		3547
299IPR022742
Serine aminopeptidase, S33		3542
300IPR004883
Lateral organ boundaries, LOB		3577
301IPR019378
GDP-fucose protein O-fucosyltransferase		3548
302IPR000425
Major intrinsic protein		35294
303IPR004046
Glutathione S-transferase, C-terminal		3546
304IPR033443
Pentacotripeptide-repeat region of PRORP		3541
305IPR024752
Myb/SANT-like domain		3535
306IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3452
307IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3438
308IPR013154
Alcohol dehydrogenase, N-terminal		3443
309IPR006094
FAD linked oxidase, N-terminal		3444
310IPR002487
Transcription factor, K-box		3496
311IPR006073
GTP binding domain		34118
312IPR001251
CRAL-TRIO lipid binding domain		33118
313IPR038933
Ovate protein family		3336
314IPR000795
Translational (tr)-type GTP-binding domain		33257
315IPR036865
CRAL-TRIO lipid binding domain superfamily		3342
316IPR043454
NPH3/RPT2-like family		3361
317IPR006458
Ovate protein family, C-terminal		3364
318IPR043519
Nucleotidyltransferase superfamily		3350
319IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3356
320IPR034294
Aquaporin transporter		3249
321IPR018490
Cyclic nucleotide-binding-like		3143
322IPR001929
Germin		31101
323IPR032710
NTF2-like domain superfamily		3138
324IPR006153
Cation/H+ exchanger		3143
325IPR008991
Translation protein SH3-like domain superfamily		3140
326IPR004367
Cyclin, C-terminal domain		3135
327IPR000863
Sulfotransferase domain		3145
328IPR023299
P-type ATPase, cytoplasmic domain N		3138
329IPR003855
Potassium transporter		31114
330IPR036041
Ribosome-inactivating protein superfamily		3134
331IPR012967
Plant methyltransferase dimerisation		3131
332IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		30228
333IPR029000
Cyclophilin-like domain superfamily		3041
334IPR029466
No apical meristem-associated, C-terminal domain		3030
335IPR044822
Myb/SANT-like DNA-binding domain 4		3037
336IPR000315
B-box-type zinc finger		3085
337IPR029061
Thiamin diphosphate-binding fold		3071
338IPR001296
Glycosyl transferase, family 1		3050
339IPR001594
Palmitoyltransferase, DHHC domain		3045
340IPR002423
Chaperonin Cpn60/TCP-1 family		3049
341IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3034
342IPR027356
NPH3 domain		3094
343IPR011013
Galactose mutarotase-like domain superfamily		3042
344IPR003406
Glycosyl transferase, family 14		3038
345IPR027409
GroEL-like apical domain superfamily		3042
346IPR004088
K Homology domain, type 1		3090
347IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		3044
348IPR003851
Zinc finger, Dof-type		3068
349IPR000595
Cyclic nucleotide-binding domain		30102
350IPR001223
Glycoside hydrolase family 18, catalytic domain		3069
351IPR011141
Polyketide synthase, type III		3039
352IPR001099
Chalcone/stilbene synthase, N-terminal		3036
353IPR001574
Ribosome-inactivating protein		3063
354IPR000727
Target SNARE coiled-coil homology domain		2953
355IPR000528
Plant non-specific lipid-transfer protein/Par allergen		29127
356IPR000717
Proteasome component (PCI) domain		2962
357IPR044848
PHR1-like		2942
358IPR003690
Transcription termination factor, mitochondrial/chloroplastic		29100
359IPR008480
Protein of unknown function DUF761, plant		2929
360IPR003311
AUX/IAA protein		2942
361IPR036812
NADP-dependent oxidoreductase domain superfamily		2947
362IPR013601
FAE1/Type III polyketide synthase-like protein		2836
363IPR010920
LSM domain superfamily		2837
364IPR044835
Auxin response factor		2856
365IPR027725
Heat shock transcription factor family		2834
366IPR005135
Endonuclease/exonuclease/phosphatase		2837
367IPR003337
Trehalose-phosphatase		2837
368IPR005150
Cellulose synthase		2852
369IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2833
370IPR016897
S-phase kinase-associated protein 1		2834
371IPR036296
SKP1-like, dimerisation domain superfamily		2832
372IPR000232
Heat shock factor (HSF)-type, DNA-binding		28117
373IPR006311
Twin-arginine translocation pathway, signal sequence		2828
374IPR015797
NUDIX hydrolase-like domain superfamily		2835
375IPR015940
Ubiquitin-associated domain		2787
376IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2738
377IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		2794
378IPR024709
Putative O-fucosyltransferase, plant		2741
379IPR036186
Serpin superfamily		2737
380IPR005333
Transcription factor, TCP		2729
381IPR009030
Growth factor receptor cysteine-rich domain superfamily		2728
382IPR035940
CAP superfamily		2731
383IPR016072
SKP1 component, dimerisation		2730
384IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2734
385IPR002963
Expansin		27228
386IPR027923
Hydrophobic seed protein domain		2773
387IPR004813
Oligopeptide transporter, OPT superfamily		2761
388IPR029062
Class I glutamine amidotransferase-like		2747
389IPR001757
P-type ATPase		27124
390IPR012328
Chalcone/stilbene synthase, C-terminal		2730
391IPR001701
Glycoside hydrolase family 9		2733
392IPR044791
Beta-glucanase/XTH		2740
393IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2735
394IPR000757
Glycoside hydrolase family 16		2768
395IPR005175
PPC domain		2783
396IPR023796
Serpin domain		2740
397IPR025110
AMP-binding enzyme, C-terminal domain		2631
398IPR036378
FAS1 domain superfamily		2639
399IPR004316
SWEET sugar transporter		2646
400IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2690
401IPR044778
Sugar transport protein STP/MST-like, plant		2630
402IPR036420
BRCT domain superfamily		2645
403IPR040417
Glycine-rich cell wall structural protein 1/2		2636
404IPR002659
Glycosyl transferase, family 31		2686
405IPR007650
Zf-FLZ domain		2670
406IPR001763
Rhodanese-like domain		2656
407IPR002123
Phospholipid/glycerol acyltransferase		2628
408IPR000215
Serpin family		2638
409IPR004014
Cation-transporting P-type ATPase, N-terminal		2630
410IPR001283
Cysteine-rich secretory protein-related		2698
411IPR044839
Protein NDR1-like		2627
412IPR036404
Jacalin-like lectin domain superfamily		2634
413IPR036034
PDZ superfamily		2630
414IPR023210
NADP-dependent oxidoreductase domain		2650
415IPR002913
START domain		2673
416IPR036085
PAZ domain superfamily		2536
417IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2531
418IPR001357
BRCT domain		2569
419IPR004320
Protein of unknown function DUF241, plant		2535
420IPR000408
Regulator of chromosome condensation, RCC1		25581
421IPR005821
Ion transport domain		2533
422IPR014044
CAP domain		2529
423IPR002035
von Willebrand factor, type A		2559
424IPR000086
NUDIX hydrolase domain		2562
425IPR000679
Zinc finger, GATA-type		2596
426IPR003100
PAZ domain		2469
427IPR017938
Riboflavin synthase-like beta-barrel		2432
428IPR011016
Zinc finger, RING-CH-type		2472
429IPR001163
LSM domain, eukaryotic/archaea-type		2430
430IPR019557
Aminotransferase-like, plant mobile domain		2428
431IPR044675
E3 ubiquitin-protein ligase RING1-like		2426
432IPR045048
F-box only protein 31/39		2455
433IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2433
434IPR004776
Membrane transport protein		2443
435IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2438
436IPR010525
Auxin response factor domain		2436
437IPR017927
FAD-binding domain, ferredoxin reductase-type		2330
438IPR006689
Small GTPase superfamily, ARF/SAR type		23116
439IPR000782
FAS1 domain		2361
440IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2339
441IPR003106
Leucine zipper, homeobox-associated		2324
442IPR013187
F-box associated domain, type 3		2326
443IPR008422
Homeobox KN domain		2330
444IPR012416
CALMODULIN-BINDING PROTEIN60		2372
445IPR023753
FAD/NAD(P)-binding domain		2332
446IPR007657
Glycosyltransferase 61		2366
447IPR026960
Reverse transcriptase zinc-binding domain		2323
448IPR001353
Proteasome, subunit alpha/beta		2331
449IPR010989
SNARE		2324
450IPR003594
Histidine kinase/HSP90-like ATPase		2331
451IPR036273
CRAL/TRIO, N-terminal domain superfamily		2328
452IPR001849
Pleckstrin homology domain		2353
453IPR029069
HotDog domain superfamily		2346
454IPR016161
Aldehyde/histidinol dehydrogenase		2336
455IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2328
456IPR036427
Bromodomain-like superfamily		2336
457IPR025486
Domain of unknown function DUF4378		2336
458IPR029033
Histidine phosphatase superfamily		2326
459IPR008971
HSP40/DnaJ peptide-binding		2253
460IPR000387
Tyrosine specific protein phosphatases domain		2246
461IPR008999
Actin-crosslinking		2226
462IPR013216
Methyltransferase type 11		2228
463IPR017887
Transcription factor TCP subgroup		2244
464IPR027413
GroEL-like equatorial domain superfamily		2233
465IPR020946
Flavin monooxygenase-like		2238
466IPR034285
Laccase, second cupredoxin domain		2225
467IPR039421
Type 1 protein exporter		2234
468IPR036928
Amidase signature (AS) superfamily		2233
469IPR040361
Tapetum determinant 1		2222
470IPR002939
Chaperone DnaJ, C-terminal		2229
471IPR006868
Domain of unknown function DUF630		2224
472IPR007811
DNA-directed RNA polymerase III subunit RPC4		2250
473IPR015590
Aldehyde dehydrogenase domain		2240
474IPR001229
Jacalin-like lectin domain		2251
475IPR016073
SKP1 component, POZ domain		2124
476IPR002867
IBR domain		2150
477IPR036873
Rhodanese-like domain superfamily		2127
478IPR025753
AAA-type ATPase, N-terminal domain		2124
479IPR001440
Tetratricopeptide repeat 1		2129
480IPR005516
Remorin, C-terminal		2126
481IPR014977
WRC domain		2147
482IPR036010
2Fe-2S ferredoxin-like superfamily		2125
483IPR011257
DNA glycosylase		2127
484IPR025422
Transcription factor TGA like domain		2152
485IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2131
486IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2127
487IPR020103
Pseudouridine synthase, catalytic domain superfamily		2127
488IPR007592
GLABROUS1 enhancer-binding protein family		2146
489IPR036610
PEBP-like superfamily		2121
490IPR022796
Chlorophyll A-B binding protein		2127
491IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2125
492IPR041677
DNA2/NAM7 helicase, helicase domain		2133
493IPR031127
E3 ubiquitin ligase RBR family		2143
494IPR013809
ENTH domain		2132
495IPR002937
Amine oxidase		2129
496IPR019587
Polyketide cyclase/dehydrase		2122
497IPR006867
Domain of unknown function DUF632		2125
498IPR004274
FCP1 homology domain		2158
499IPR045040
PORR family		2024
500IPR006593
Cytochrome b561/ferric reductase transmembrane		2039
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127652.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127652.html new file mode 100644 index 00000000..83df1124 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127652.html @@ -0,0 +1,87 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os127652RS1, Jan 2020
Database version:87.1
Base Pairs:384,203,823
Golden Path Length:384,203,823
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

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Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,196
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:43,471
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
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+ + + +
SequenceLength (bp)
143642146
237782930
338826486
435328705
531007770
631934329
729233059
829945256
923589837
1025103795
1131305988
1226020635
+
+
scaffold
+
7 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg20113797
UN-Ctg2185018
UN-Ctg2272541
UN-Ctg2365355
UN-Ctg2457790
UN-Ctg2545497
UN-Ctg2642889
+
+
chunk3853 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127652_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127652_IPtop500.html new file mode 100644 index 00000000..124e9098 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127652_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14852023
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14292106
3IPR000719
Protein kinase domain		13813122
4IPR036047
F-box-like domain superfamily		651811
5IPR044974
Disease resistance protein, plants		523936
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		520866
7IPR002885
Pentatricopeptide repeat		5056376
8IPR002182
NB-ARC		484574
9IPR001611
Leucine-rich repeat		4811471
10IPR001810
F-box domain		476855
11IPR001841
Zinc finger, RING-type		426879
12IPR041118
Rx, N-terminal		383429
13IPR016024
Armadillo-type fold		382611
14IPR036291
NAD(P)-binding domain superfamily		379542
15IPR009057
Homeobox-like domain superfamily		379479
16IPR029058
Alpha/Beta hydrolase fold		365521
17IPR011990
Tetratricopeptide-like helical domain superfamily		340513
18IPR036396
Cytochrome P450 superfamily		317422
19IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		313388
20IPR001128
Cytochrome P450		3111488
21IPR035979
RNA-binding domain superfamily		301595
22IPR000504
RNA recognition motif domain		2651100
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		265399
24IPR002401
Cytochrome P450, E-class, group I		2641758
25IPR038005
Virus X resistance protein-like, coiled-coil domain		258286
26IPR017853
Glycoside hydrolase superfamily		253381
27IPR036259
MFS transporter superfamily		249406
28IPR001005
SANT/Myb domain		237707
29IPR017930
Myb domain		236698
30IPR036249
Thioredoxin-like superfamily		233338
31IPR038765
Papain-like cysteine peptidase superfamily		233291
32IPR036322
WD40-repeat-containing domain superfamily		227342
33IPR001680
WD40 repeat		2071669
34IPR011992
EF-hand domain pair		189235
35IPR036770
Ankyrin repeat-containing domain superfamily		180245
36IPR002048
EF-hand domain		179895
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		174404
38IPR036412
HAD-like superfamily		174230
39IPR036638
Helix-loop-helix DNA-binding domain superfamily		166197
40IPR016177
DNA-binding domain superfamily		164234
41IPR002110
Ankyrin repeat		163634
42IPR011333
SKP1/BTB/POZ domain superfamily		159232
43IPR012337
Ribonuclease H-like superfamily		158194
44IPR036390
Winged helix DNA-binding domain superfamily		157207
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		151326
46IPR001471
AP2/ERF domain		150820
47IPR036093
NAC domain superfamily		150164
48IPR003441
NAC domain		146313
49IPR036236
Zinc finger C2H2 superfamily		142199
50IPR001650
Helicase, C-terminal		140403
51IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		138175
52IPR010255
Haem peroxidase superfamily		138180
53IPR029044
Nucleotide-diphospho-sugar transferases		137173
54IPR014001
Helicase superfamily 1/2, ATP-binding domain		137202
55IPR012340
Nucleic acid-binding, OB-fold		136277
56IPR002016
Haem peroxidase		135599
57IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		133163
58IPR036188
FAD/NAD(P)-binding domain superfamily		132238
59IPR013087
Zinc finger C2H2-type		131240
60IPR005174
Domain unknown function DUF295		131157
61IPR020683
Ankyrin repeat-containing domain		128265
62IPR003439
ABC transporter-like, ATP-binding domain		125490
63IPR000210
BTB/POZ domain		124358
64IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		120170
65IPR021109
Aspartic peptidase domain superfamily		117154
66IPR036426
Bulb-type lectin domain superfamily		117168
67IPR003959
ATPase, AAA-type, core		115170
68IPR003480
Transferase		115141
69IPR001480
Bulb-type lectin domain		113420
70IPR007658
Protein of unknown function DUF594		112118
71IPR025315
Domain of unknown function DUF4220		109120
72IPR033121
Peptidase family A1 domain		108153
73IPR011011
Zinc finger, FYVE/PHD-type		108158
74IPR036869
Chaperone J-domain superfamily		108143
75IPR019734
Tetratricopeptide repeat		107328
76IPR020846
Major facilitator superfamily domain		107146
77IPR001087
GDSL lipase/esterase		106134
78IPR008972
Cupredoxin		105211
79IPR003657
WRKY domain		104265
80IPR036576
WRKY domain superfamily		103134
81IPR001623
DnaJ domain		103716
82IPR015424
Pyridoxal phosphate-dependent transferase		101139
83IPR029071
Ubiquitin-like domain superfamily		100147
84IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		100124
85IPR035892
C2 domain superfamily		99192
86IPR044810
WRKY transcription factor, plant		99125
87IPR032799
Xylanase inhibitor, C-terminal		98123
88IPR011050
Pectin lyase fold/virulence factor		97112
89IPR032861
Xylanase inhibitor, N-terminal		97125
90IPR045005
BTB/POZ and MATH domain-containing protein 1-6		94168
91IPR036457
PPM-type phosphatase domain superfamily		93138
92IPR011051
RmlC-like cupin domain superfamily		93123
93IPR001356
Homeobox domain		92277
94IPR000823
Plant peroxidase		92378
95IPR005123
Oxoglutarate/iron-dependent dioxygenase		91122
96IPR003609
PAN/Apple domain		91234
97IPR011676
Domain of unknown function DUF1618		91120
98IPR009072
Histone-fold		91102
99IPR005828
Major facilitator, sugar transporter-like		90138
100IPR015300
DNA-binding pseudobarrel domain superfamily		90155
101IPR001932
PPM-type phosphatase domain		90399
102IPR002083
MATH/TRAF domain		88292
103IPR011545
DEAD/DEAH box helicase domain		88128
104IPR000858
S-locus glycoprotein domain		87122
105IPR000008
C2 domain		87401
106IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		86113
107IPR000073
Alpha/beta hydrolase fold-1		85245
108IPR035669
GDSL lipase/esterase-like, plant		8499
109IPR002347
Short-chain dehydrogenase/reductase SDR		83698
110IPR026961
PGG domain		81165
111IPR001461
Aspartic peptidase A1 family		80284
112IPR036875
Zinc finger, CCHC-type superfamily		8096
113IPR043129
ATPase, nucleotide binding domain		79194
114IPR003340
B3 DNA binding domain		78380
115IPR012871
Protein of unknown function DUF1677, Oryza sativa		7896
116IPR020472
G-protein beta WD-40 repeat		78360
117IPR013766
Thioredoxin domain		78179
118IPR026992
Non-haem dioxygenase N-terminal domain		7899
119IPR004158
Protein of unknown function DUF247, plant		78190
120IPR000109
Proton-dependent oligopeptide transporter family		77318
121IPR036282
Glutathione S-transferase, C-terminal domain superfamily		77111
122IPR004827
Basic-leucine zipper domain		77191
123IPR031052
FHY3/FAR1 family		75139
124IPR002902
Gnk2-homologous domain		72347
125IPR003613
U box domain		72164
126IPR001878
Zinc finger, CCHC-type		72152
127IPR006121
Heavy metal-associated domain, HMA		71234
128IPR036163
Heavy metal-associated domain superfamily		7199
129IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7075
130IPR004045
Glutathione S-transferase, N-terminal		70202
131IPR016039
Thiolase-like		68144
132IPR002100
Transcription factor, MADS-box		68369
133IPR016159
Cullin repeat-like-containing domain superfamily		6884
134IPR036879
Transcription factor, MADS-box superfamily		6882
135IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		68143
136IPR008949
Isoprenoid synthase domain superfamily		6790
137IPR000270
PB1 domain		67122
138IPR001220
Legume lectin domain		66151
139IPR036915
Cyclin-like superfamily		66136
140IPR044965
Glycoside hydrolase family 17, plant		65116
141IPR029052
Metallo-dependent phosphatase-like		6585
142IPR000048
IQ motif, EF-hand binding site		65349
143IPR019787
Zinc finger, PHD-finger		64152
144IPR003653
Ulp1 protease family, C-terminal catalytic domain		64128
145IPR013057
Amino acid transporter, transmembrane domain		6490
146IPR024788
Malectin-like domain		6485
147IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6369
148IPR020568
Ribosomal protein S5 domain 2-type fold		63107
149IPR010987
Glutathione S-transferase, C-terminal-like		6392
150IPR006501
Pectinesterase inhibitor domain		6366
151IPR009003
Peptidase S1, PA clan		6399
152IPR018108
Mitochondrial substrate/solute carrier		62472
153IPR023395
Mitochondrial carrier domain superfamily		6284
154IPR036852
Peptidase S8/S53 domain superfamily		6281
155IPR001806
Small GTPase		62136
156IPR045051
Subtilisin-like protease		61100
157IPR036908
RlpA-like domain superfamily		6177
158IPR000490
Glycoside hydrolase family 17		6188
159IPR000209
Peptidase S8/S53 domain		6183
160IPR005202
Transcription factor GRAS		60229
161IPR003663
Sugar/inositol transporter		60330
162IPR000626
Ubiquitin-like domain		59140
163IPR026057
PC-Esterase		5980
164IPR036749
Expansin, cellulose-binding-like domain superfamily		5972
165IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5977
166IPR000571
Zinc finger, CCCH-type		59268
167IPR029962
Trichome birefringence-like family		5883
168IPR022059
Protein of unknown function DUF3615		5873
169IPR007117
Expansin, cellulose-binding-like domain		58139
170IPR011032
GroES-like superfamily		5782
171IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5776
172IPR002156
Ribonuclease H domain		5778
173IPR013763
Cyclin-like		56104
174IPR039391
Phytocyanin		5666
175IPR003245
Phytocyanin domain		56120
176IPR006045
Cupin 1		5689
177IPR041469
Subtilisin-like protease, fibronectin type-III domain		5570
178IPR004330
FAR1 DNA binding domain		5562
179IPR015915
Kelch-type beta propeller		5481
180IPR007527
Zinc finger, SWIM-type		5492
181IPR001563
Peptidase S10, serine carboxypeptidase		53405
182IPR016181
Acyl-CoA N-acyltransferase		5367
183IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5360
184IPR007112
Expansin/pollen allergen, DPBB domain		5363
185IPR015500
Peptidase S8, subtilisin-related		53174
186IPR000225
Armadillo		53227
187IPR013525
ABC-2 type transporter		5299
188IPR025846
PMR5 N-terminal domain		5268
189IPR036465
von Willebrand factor A-like domain superfamily		5264
190IPR013094
Alpha/beta hydrolase fold-3		5270
191IPR001752
Kinesin motor domain		52399
192IPR002921
Fungal lipase-like domain		5161
193IPR009009
RlpA-like protein, double-psi beta-barrel domain		5159
194IPR008979
Galactose-binding-like domain superfamily		5191
195IPR002528
Multi antimicrobial extrusion protein		51123
196IPR006566
FBD domain		5160
197IPR000608
Ubiquitin-conjugating enzyme E2		50186
198IPR034161
Pepsin-like domain, plant		5063
199IPR030184
WAT1-related protein		5091
200IPR023298
P-type ATPase, transmembrane domain superfamily		5069
201IPR013201
Cathepsin propeptide inhibitor domain (I29)		4954
202IPR005630
Terpene synthase, metal-binding domain		4969
203IPR004140
Exocyst complex component Exo70		49130
204IPR000620
EamA domain		49101
205IPR036640
ABC transporter type 1, transmembrane domain superfamily		48110
206IPR008250
P-type ATPase, A domain superfamily		4864
207IPR004265
Dirigent protein		4857
208IPR034197
Cucumisin-like catalytic domain		4860
209IPR011527
ABC transporter type 1, transmembrane domain		48221
210IPR006671
Cyclin, N-terminal		4861
211IPR044808
Ethylene-responsive transcription factor		4855
212IPR008978
HSP20-like chaperone		4756
213IPR007118
Expansin/Lol pI		47261
214IPR008928
Six-hairpin glycosidase superfamily		4758
215IPR041569
AAA ATPase, AAA+ lid domain		4765
216IPR003676
Small auxin-up RNA		4760
217IPR001509
NAD-dependent epimerase/dehydratase		4666
218IPR009000
Translation protein, beta-barrel domain superfamily		4661
219IPR014014
RNA helicase, DEAD-box type, Q motif		4663
220IPR045087
Multicopper oxidase		4664
221IPR017884
SANT domain		4559
222IPR016461
O-methyltransferase COMT-type		4598
223IPR004853
Sugar phosphate transporter domain		4580
224IPR011701
Major facilitator superfamily		4581
225IPR029055
Nucleophile aminohydrolases, N-terminal		4570
226IPR007125
Histone H2A/H2B/H3		4548
227IPR000070
Pectinesterase, catalytic		4554
228IPR036318
FAD-binding, type PCMH-like superfamily		4454
229IPR000873
AMP-dependent synthetase/ligase		4466
230IPR012946
X8 domain		4468
231IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4461
232IPR000668
Peptidase C1A, papain C-terminal		44156
233IPR001906
Terpene synthase, N-terminal domain		4465
234IPR036855
Zinc finger, CCCH-type superfamily		44105
235IPR001117
Multicopper oxidase, type 1		4348
236IPR000182
GNAT domain		4394
237IPR009060
UBA-like superfamily		4365
238IPR033905
Secretory peroxidase		4348
239IPR011706
Multicopper oxidase, C-terminal		4349
240IPR014756
Immunoglobulin E-set		4361
241IPR001214
SET domain		43104
242IPR008889
VQ		4344
243IPR033896
MADS MEF2-like		4255
244IPR036612
K Homology domain, type 1 superfamily		42122
245IPR004263
Exostosin-like		4253
246IPR011006
CheY-like superfamily		4255
247IPR000742
EGF-like domain		4247
248IPR032867
DYW domain		4245
249IPR006016
UspA		4154
250IPR000330
SNF2, N-terminal		4168
251IPR001077
O-methyltransferase domain		4152
252IPR044730
Ribonuclease H-like domain, plant type		4143
253IPR011707
Multicopper oxidase, N-termianl		4145
254IPR000743
Glycoside hydrolase, family 28		4151
255IPR001789
Signal transduction response regulator, receiver domain		4190
256IPR010402
CCT domain		40107
257IPR043926
ABC transporter family G domain		4069
258IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4057
259IPR011012
Longin-like domain superfamily		4062
260IPR029045
ClpP/crotonase-like domain superfamily		4065
261IPR039361
Cyclin		4053
262IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4047
263IPR033389
AUX/IAA domain		3949
264IPR016040
NAD(P)-binding domain		3955
265IPR011043
Galactose oxidase/kelch, beta-propeller		3942
266IPR037176
Osmotin/thaumatin-like superfamily		3945
267IPR006702
Casparian strip membrane protein domain		3941
268IPR025322
Protein of unknown function DUF4228, plant		3840
269IPR003137
PA domain		3847
270IPR001938
Thaumatin family		38262
271IPR015655
Protein phosphatase 2C family		3874
272IPR002495
Glycosyl transferase, family 8		3844
273IPR015947
PUA-like superfamily		3851
274IPR025659
Tubby-like, C-terminal		3747
275IPR029021
Protein-tyrosine phosphatase-like		3757
276IPR004839
Aminotransferase, class I/classII		3753
277IPR019378
GDP-fucose protein O-fucosyltransferase		3757
278IPR039417
Papain-like cysteine endopeptidase		3742
279IPR040911
Exostosin, GT47 domain		3744
280IPR002109
Glutaredoxin		3746
281IPR013126
Heat shock protein 70 family		37106
282IPR008942
ENTH/VHS		3647
283IPR007493
Protein of unknown function DUF538		3680
284IPR013154
Alcohol dehydrogenase, N-terminal		3641
285IPR016166
FAD-binding domain, PCMH-type		3646
286IPR004883
Lateral organ boundaries, LOB		3679
287IPR036758
At5g01610-like superfamily		3641
288IPR002067
Mitochondrial carrier protein		36223
289IPR000644
CBS domain		36186
290IPR012967
Plant methyltransferase dimerisation		3636
291IPR002068
Alpha crystallin/Hsp20 domain		3576
292IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3539
293IPR023271
Aquaporin-like		3546
294IPR043454
NPH3/RPT2-like family		3562
295IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3556
296IPR000425
Major intrinsic protein		35291
297IPR004046
Glutathione S-transferase, C-terminal		3549
298IPR004088
K Homology domain, type 1		35109
299IPR028889
Ubiquitin specific protease domain		3550
300IPR002912
ACT domain		35102
301IPR004041
NAF domain		3447
302IPR018451
NAF/FISL domain		3444
303IPR000795
Translational (tr)-type GTP-binding domain		34257
304IPR043519
Nucleotidyltransferase superfamily		3453
305IPR002487
Transcription factor, K-box		3489
306IPR013149
Alcohol dehydrogenase, C-terminal		3340
307IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3350
308IPR008991
Translation protein SH3-like domain superfamily		3344
309IPR038933
Ovate protein family		3335
310IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3341
311IPR004367
Cyclin, C-terminal domain		3336
312IPR022742
Serine aminopeptidase, S33		3343
313IPR000863
Sulfotransferase domain		3346
314IPR006094
FAD linked oxidase, N-terminal		3342
315IPR006458
Ovate protein family, C-terminal		3364
316IPR004314
Neprosin		3344
317IPR005333
Transcription factor, TCP		3236
318IPR036865
CRAL-TRIO lipid binding domain superfamily		3248
319IPR034294
Aquaporin transporter		3248
320IPR006652
Kelch repeat type 1		3271
321IPR033443
Pentacotripeptide-repeat region of PRORP		3237
322IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3258
323IPR018490
Cyclic nucleotide-binding-like		3141
324IPR032710
NTF2-like domain superfamily		3137
325IPR001360
Glycoside hydrolase family 1		31341
326IPR001251
CRAL-TRIO lipid binding domain		31131
327IPR005299
SAM dependent carboxyl methyltransferase		3190
328IPR001296
Glycosyl transferase, family 1		3158
329IPR003406
Glycosyl transferase, family 14		3138
330IPR003690
Transcription termination factor, mitochondrial/chloroplastic		31101
331IPR000595
Cyclic nucleotide-binding domain		3198
332IPR006073
GTP binding domain		3197
333IPR000528
Plant non-specific lipid-transfer protein/Par allergen		30146
334IPR001929
Germin		30108
335IPR044835
Auxin response factor		3057
336IPR044822
Myb/SANT-like DNA-binding domain 4		3037
337IPR000315
B-box-type zinc finger		3077
338IPR029061
Thiamin diphosphate-binding fold		3075
339IPR001594
Palmitoyltransferase, DHHC domain		3046
340IPR005135
Endonuclease/exonuclease/phosphatase		3041
341IPR002423
Chaperonin Cpn60/TCP-1 family		3049
342IPR027356
NPH3 domain		3088
343IPR023299
P-type ATPase, cytoplasmic domain N		3040
344IPR003851
Zinc finger, Dof-type		3066
345IPR001223
Glycoside hydrolase family 18, catalytic domain		3074
346IPR036041
Ribosome-inactivating protein superfamily		3033
347IPR007811
DNA-directed RNA polymerase III subunit RPC4		3076
348IPR000727
Target SNARE coiled-coil homology domain		2952
349IPR015940
Ubiquitin-associated domain		2987
350IPR006153
Cation/H+ exchanger		2936
351IPR011013
Galactose mutarotase-like domain superfamily		2939
352IPR005150
Cellulose synthase		2968
353IPR027409
GroEL-like apical domain superfamily		2941
354IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2941
355IPR003855
Potassium transporter		29119
356IPR011141
Polyketide synthase, type III		2938
357IPR024752
Myb/SANT-like domain		2930
358IPR006311
Twin-arginine translocation pathway, signal sequence		2930
359IPR001099
Chalcone/stilbene synthase, N-terminal		2937
360IPR001574
Ribosome-inactivating protein		2959
361IPR013601
FAE1/Type III polyketide synthase-like protein		2836
362IPR036378
FAS1 domain superfamily		2837
363IPR029000
Cyclophilin-like domain superfamily		2843
364IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28102
365IPR024709
Putative O-fucosyltransferase, plant		2846
366IPR000717
Proteasome component (PCI) domain		2863
367IPR044848
PHR1-like		2837
368IPR008480
Protein of unknown function DUF761, plant		2828
369IPR001701
Glycoside hydrolase family 9		2833
370IPR044791
Beta-glucanase/XTH		2845
371IPR000757
Glycoside hydrolase family 16		2873
372IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		27237
373IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2796
374IPR010920
LSM domain superfamily		2737
375IPR044778
Sugar transport protein STP/MST-like, plant		2729
376IPR002659
Glycosyl transferase, family 31		2790
377IPR007650
Zf-FLZ domain		2773
378IPR003337
Trehalose-phosphatase		2736
379IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2742
380IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2734
381IPR002963
Expansin		27224
382IPR004813
Oligopeptide transporter, OPT superfamily		2758
383IPR029062
Class I glutamine amidotransferase-like		2747
384IPR012328
Chalcone/stilbene synthase, C-terminal		2728
385IPR003311
AUX/IAA protein		2741
386IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2735
387IPR002913
START domain		2775
388IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2634
389IPR029466
No apical meristem-associated, C-terminal domain		2627
390IPR036420
BRCT domain superfamily		2662
391IPR027725
Heat shock transcription factor family		2634
392IPR001763
Rhodanese-like domain		2658
393IPR000408
Regulator of chromosome condensation, RCC1		26610
394IPR002123
Phospholipid/glycerol acyltransferase		2628
395IPR045048
F-box only protein 31/39		2656
396IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2634
397IPR044839
Protein NDR1-like		2627
398IPR027923
Hydrophobic seed protein domain		2669
399IPR002035
von Willebrand factor, type A		2654
400IPR001757
P-type ATPase		26117
401IPR000232
Heat shock factor (HSF)-type, DNA-binding		26118
402IPR005175
PPC domain		2680
403IPR025110
AMP-binding enzyme, C-terminal domain		2534
404IPR000782
FAS1 domain		2559
405IPR001357
BRCT domain		25105
406IPR007657
Glycosyltransferase 61		2557
407IPR036273
CRAL/TRIO, N-terminal domain superfamily		2536
408IPR005821
Ion transport domain		2531
409IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2533
410IPR036034
PDZ superfamily		2534
411IPR000679
Zinc finger, GATA-type		25104
412IPR015797
NUDIX hydrolase-like domain superfamily		2529
413IPR036085
PAZ domain superfamily		2440
414IPR017938
Riboflavin synthase-like beta-barrel		2434
415IPR013187
F-box associated domain, type 3		2428
416IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2428
417IPR008422
Homeobox KN domain		2427
418IPR023753
FAD/NAD(P)-binding domain		2435
419IPR017887
Transcription factor TCP subgroup		2446
420IPR035940
CAP superfamily		2437
421IPR004320
Protein of unknown function DUF241, plant		2433
422IPR004014
Cation-transporting P-type ATPase, N-terminal		2433
423IPR016897
S-phase kinase-associated protein 1		2433
424IPR001849
Pleckstrin homology domain		2452
425IPR029069
HotDog domain superfamily		2452
426IPR036296
SKP1-like, dimerisation domain superfamily		2432
427IPR025486
Domain of unknown function DUF4378		2436
428IPR002937
Amine oxidase		2434
429IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2438
430IPR010525
Auxin response factor domain		2437
431IPR017927
FAD-binding domain, ferredoxin reductase-type		2333
432IPR003100
PAZ domain		2377
433IPR008971
HSP40/DnaJ peptide-binding		2356
434IPR003106
Leucine zipper, homeobox-associated		2323
435IPR004316
SWEET sugar transporter		2342
436IPR013581
Plant PDR ABC transporter associated		2332
437IPR011016
Zinc finger, RING-CH-type		2370
438IPR001163
LSM domain, eukaryotic/archaea-type		2328
439IPR040417
Glycine-rich cell wall structural protein 1/2		2332
440IPR026960
Reverse transcriptase zinc-binding domain		2323
441IPR003656
Zinc finger, BED-type		2339
442IPR001353
Proteasome, subunit alpha/beta		2330
443IPR016072
SKP1 component, dimerisation		2330
444IPR001283
Cysteine-rich secretory protein-related		23100
445IPR034285
Laccase, second cupredoxin domain		2326
446IPR039421
Type 1 protein exporter		2335
447IPR002939
Chaperone DnaJ, C-terminal		2331
448IPR036427
Bromodomain-like superfamily		2332
449IPR023210
NADP-dependent oxidoreductase domain		2349
450IPR029033
Histidine phosphatase superfamily		2327
451IPR036812
NADP-dependent oxidoreductase domain superfamily		2342
452IPR036443
Zinc finger, RanBP2-type superfamily		2370
453IPR006689
Small GTPase superfamily, ARF/SAR type		22119
454IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2236
455IPR000387
Tyrosine specific protein phosphatases domain		2234
456IPR025753
AAA-type ATPase, N-terminal domain		2225
457IPR018392
LysM domain		2272
458IPR036010
2Fe-2S ferredoxin-like superfamily		2225
459IPR011257
DNA glycosylase		2229
460IPR025422
Transcription factor TGA like domain		2256
461IPR010989
SNARE		2227
462IPR044675
E3 ubiquitin-protein ligase RING1-like		2228
463IPR021720
Malectin domain		2251
464IPR011053
Single hybrid motif		2225
465IPR020103
Pseudouridine synthase, catalytic domain superfamily		2228
466IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2224
467IPR014044
CAP domain		2233
468IPR016161
Aldehyde/histidinol dehydrogenase		2236
469IPR000086
NUDIX hydrolase domain		2250
470IPR036392
PLAT/LH2 domain superfamily		2225
471IPR001487
Bromodomain		22143
472IPR002403
Cytochrome P450, E-class, group IV		21114
473IPR001440
Tetratricopeptide repeat 1		2134
474IPR008999
Actin-crosslinking		2125
475IPR003347
JmjC domain		2143
476IPR021790
PTBP1, RNA recognition motif 2-like		2130
477IPR013216
Methyltransferase type 11		2127
478IPR019557
Aminotransferase-like, plant mobile domain		2125
479IPR009030
Growth factor receptor cysteine-rich domain superfamily		2125
480IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2127
481IPR003594
Histidine kinase/HSP90-like ATPase		2134
482IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2128
483IPR007592
GLABROUS1 enhancer-binding protein family		2147
484IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2129
485IPR041679
DNA2/NAM7 helicase-like, C-terminal		2161
486IPR041677
DNA2/NAM7 helicase, helicase domain		2140
487IPR017923
Transcription factor IIS, N-terminal		2148
488IPR036404
Jacalin-like lectin domain superfamily		2135
489IPR006868
Domain of unknown function DUF630		2123
490IPR015590
Aldehyde dehydrogenase domain		2139
491IPR006867
Domain of unknown function DUF632		2125
492IPR004274
FCP1 homology domain		2160
493IPR009606
Modifying wall lignin-1/2		2029
494IPR004000
Actin family		20163
495IPR006593
Cytochrome b561/ferric reductase transmembrane		2040
496IPR022149
Protein of unknown function DUF3681		2043
497IPR002867
IBR domain		2042
498IPR006195
Aminoacyl-tRNA synthetase, class II		2031
499IPR035952
Rhomboid-like superfamily		2024
500IPR007612
LURP-one-related		2053
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127742.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127742.html new file mode 100644 index 00000000..22bfad38 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127742.html @@ -0,0 +1,108 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os127742RS1, Jan 2020
Database version:87.1
Base Pairs:394,601,903
Golden Path Length:394,601,903
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,436
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,616
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144389110
238145511
339183656
436994916
530835662
632214687
730657547
830034931
924975197
1025709007
1132028703
1226007178
+
+
scaffold
+
28 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg31252157
UN-Ctg32244419
UN-Ctg33173434
UN-Ctg34170323
UN-Ctg35162676
UN-Ctg36157855
UN-Ctg37141363
UN-Ctg38136137
UN-Ctg39135217
UN-Ctg40125429
UN-Ctg41122386
UN-Ctg42121044
UN-Ctg43118451
UN-Ctg44111849
UN-Ctg45110519
UN-Ctg46106572
UN-Ctg47105902
UN-Ctg48105085
UN-Ctg49100285
UN-Ctg5093655
UN-Ctg5187427
UN-Ctg5285277
UN-Ctg5383826
UN-Ctg5481192
UN-Ctg5580418
UN-Ctg5679351
UN-Ctg5771372
UN-Ctg5862177
+
+
chunk3967 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa127742_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa127742_IPtop500.html new file mode 100644 index 00000000..13c2123e --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa127742_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14822132
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14482260
3IPR000719
Protein kinase domain		13793296
4IPR036047
F-box-like domain superfamily		668835
5IPR044974
Disease resistance protein, plants		555985
6IPR002885
Pentatricopeptide repeat		5076344
7IPR002182
NB-ARC		506626
8IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		506927
9IPR001810
F-box domain		484883
10IPR001611
Leucine-rich repeat		4661505
11IPR001841
Zinc finger, RING-type		424885
12IPR041118
Rx, N-terminal		399461
13IPR009057
Homeobox-like domain superfamily		387496
14IPR016024
Armadillo-type fold		385642
15IPR036291
NAD(P)-binding domain superfamily		380575
16IPR029058
Alpha/Beta hydrolase fold		372547
17IPR011990
Tetratricopeptide-like helical domain superfamily		342531
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		311396
19IPR036396
Cytochrome P450 superfamily		310411
20IPR001128
Cytochrome P450		3031499
21IPR035979
RNA-binding domain superfamily		303630
22IPR038005
Virus X resistance protein-like, coiled-coil domain		286332
23IPR000504
RNA recognition motif domain		2711179
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		267411
25IPR002401
Cytochrome P450, E-class, group I		2601795
26IPR017853
Glycoside hydrolase superfamily		260371
27IPR036259
MFS transporter superfamily		254403
28IPR036249
Thioredoxin-like superfamily		239357
29IPR036322
WD40-repeat-containing domain superfamily		239360
30IPR017930
Myb domain		238720
31IPR038765
Papain-like cysteine peptidase superfamily		237303
32IPR001005
SANT/Myb domain		237722
33IPR001680
WD40 repeat		2101682
34IPR011992
EF-hand domain pair		185235
35IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		177413
36IPR002048
EF-hand domain		175909
37IPR036770
Ankyrin repeat-containing domain superfamily		175249
38IPR016177
DNA-binding domain superfamily		170234
39IPR036412
HAD-like superfamily		168234
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		162200
41IPR002110
Ankyrin repeat		162670
42IPR011333
SKP1/BTB/POZ domain superfamily		158235
43IPR036390
Winged helix DNA-binding domain superfamily		156208
44IPR001471
AP2/ERF domain		155845
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		152343
46IPR012337
Ribonuclease H-like superfamily		151188
47IPR036093
NAC domain superfamily		147170
48IPR010255
Haem peroxidase superfamily		147186
49IPR003441
NAC domain		145327
50IPR029044
Nucleotide-diphospho-sugar transferases		142175
51IPR001650
Helicase, C-terminal		142420
52IPR005174
Domain unknown function DUF295		141163
53IPR012340
Nucleic acid-binding, OB-fold		139311
54IPR036236
Zinc finger C2H2 superfamily		139201
55IPR002016
Haem peroxidase		138623
56IPR014001
Helicase superfamily 1/2, ATP-binding domain		137212
57IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		136160
58IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		134176
59IPR013087
Zinc finger C2H2-type		133246
60IPR020683
Ankyrin repeat-containing domain		132291
61IPR036188
FAD/NAD(P)-binding domain superfamily		131230
62IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		129193
63IPR003439
ABC transporter-like, ATP-binding domain		126526
64IPR003480
Transferase		124150
65IPR003959
ATPase, AAA-type, core		121182
66IPR021109
Aspartic peptidase domain superfamily		119155
67IPR036426
Bulb-type lectin domain superfamily		119169
68IPR000210
BTB/POZ domain		118361
69IPR001480
Bulb-type lectin domain		114415
70IPR036869
Chaperone J-domain superfamily		112154
71IPR007658
Protein of unknown function DUF594		111116
72IPR020846
Major facilitator superfamily domain		111159
73IPR015424
Pyridoxal phosphate-dependent transferase		110155
74IPR011676
Domain of unknown function DUF1618		109144
75IPR025315
Domain of unknown function DUF4220		109120
76IPR001623
DnaJ domain		108771
77IPR019734
Tetratricopeptide repeat		107340
78IPR001087
GDSL lipase/esterase		107135
79IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		107122
80IPR011011
Zinc finger, FYVE/PHD-type		106157
81IPR003657
WRKY domain		105271
82IPR036576
WRKY domain superfamily		104136
83IPR008972
Cupredoxin		104208
84IPR029071
Ubiquitin-like domain superfamily		103161
85IPR032799
Xylanase inhibitor, C-terminal		102127
86IPR033121
Peptidase family A1 domain		102149
87IPR032861
Xylanase inhibitor, N-terminal		99125
88IPR011051
RmlC-like cupin domain superfamily		98121
89IPR035892
C2 domain superfamily		97197
90IPR044810
WRKY transcription factor, plant		97123
91IPR000858
S-locus glycoprotein domain		96131
92IPR036457
PPM-type phosphatase domain superfamily		94148
93IPR005123
Oxoglutarate/iron-dependent dioxygenase		94120
94IPR011050
Pectin lyase fold/virulence factor		94103
95IPR009072
Histone-fold		94104
96IPR015300
DNA-binding pseudobarrel domain superfamily		94172
97IPR003609
PAN/Apple domain		92232
98IPR000823
Plant peroxidase		92373
99IPR001932
PPM-type phosphatase domain		92410
100IPR001356
Homeobox domain		91284
101IPR002347
Short-chain dehydrogenase/reductase SDR		90825
102IPR011545
DEAD/DEAH box helicase domain		90141
103IPR045005
BTB/POZ and MATH domain-containing protein 1-6		89169
104IPR000008
C2 domain		86412
105IPR005828
Major facilitator, sugar transporter-like		86135
106IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		86112
107IPR000109
Proton-dependent oligopeptide transporter family		85278
108IPR003340
B3 DNA binding domain		84440
109IPR035669
GDSL lipase/esterase-like, plant		84102
110IPR002083
MATH/TRAF domain		84310
111IPR013766
Thioredoxin domain		83198
112IPR020472
G-protein beta WD-40 repeat		82375
113IPR001461
Aspartic peptidase A1 family		82293
114IPR000073
Alpha/beta hydrolase fold-1		81243
115IPR043129
ATPase, nucleotide binding domain		81204
116IPR004158
Protein of unknown function DUF247, plant		81191
117IPR004827
Basic-leucine zipper domain		80193
118IPR026961
PGG domain		78166
119IPR026992
Non-haem dioxygenase N-terminal domain		78100
120IPR036282
Glutathione S-transferase, C-terminal domain superfamily		78112
121IPR012871
Protein of unknown function DUF1677, Oryza sativa		7692
122IPR002902
Gnk2-homologous domain		76366
123IPR036875
Zinc finger, CCHC-type superfamily		7692
124IPR031052
FHY3/FAR1 family		75129
125IPR003613
U box domain		73157
126IPR003653
Ulp1 protease family, C-terminal catalytic domain		72139
127IPR004330
FAR1 DNA binding domain		7277
128IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		72125
129IPR008949
Isoprenoid synthase domain superfamily		7190
130IPR004045
Glutathione S-transferase, N-terminal		71204
131IPR016039
Thiolase-like		70157
132IPR002100
Transcription factor, MADS-box		70395
133IPR036879
Transcription factor, MADS-box superfamily		7088
134IPR001878
Zinc finger, CCHC-type		70143
135IPR036163
Heavy metal-associated domain superfamily		6994
136IPR044965
Glycoside hydrolase family 17, plant		69100
137IPR000270
PB1 domain		69124
138IPR006121
Heavy metal-associated domain, HMA		67222
139IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6772
140IPR001220
Legume lectin domain		67165
141IPR007527
Zinc finger, SWIM-type		67113
142IPR013057
Amino acid transporter, transmembrane domain		6588
143IPR016159
Cullin repeat-like-containing domain superfamily		6579
144IPR000571
Zinc finger, CCCH-type		65295
145IPR000048
IQ motif, EF-hand binding site		65345
146IPR000626
Ubiquitin-like domain		64162
147IPR036749
Expansin, cellulose-binding-like domain superfamily		6480
148IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6474
149IPR036908
RlpA-like domain superfamily		6480
150IPR010987
Glutathione S-transferase, C-terminal-like		6495
151IPR029052
Metallo-dependent phosphatase-like		6489
152IPR001806
Small GTPase		64147
153IPR019787
Zinc finger, PHD-finger		63146
154IPR007117
Expansin, cellulose-binding-like domain		63153
155IPR018108
Mitochondrial substrate/solute carrier		62497
156IPR020568
Ribosomal protein S5 domain 2-type fold		62102
157IPR023395
Mitochondrial carrier domain superfamily		6287
158IPR005202
Transcription factor GRAS		62226
159IPR036915
Cyclin-like superfamily		62131
160IPR024788
Malectin-like domain		6279
161IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6186
162IPR000490
Glycoside hydrolase family 17		6179
163IPR009003
Peptidase S1, PA clan		6197
164IPR026057
PC-Esterase		6083
165IPR006045
Cupin 1		6094
166IPR036852
Peptidase S8/S53 domain superfamily		6072
167IPR000209
Peptidase S8/S53 domain		6069
168IPR003663
Sugar/inositol transporter		59331
169IPR045051
Subtilisin-like protease		5886
170IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5780
171IPR029962
Trichome birefringence-like family		5783
172IPR022059
Protein of unknown function DUF3615		5772
173IPR003245
Phytocyanin domain		57121
174IPR006501
Pectinesterase inhibitor domain		5761
175IPR041469
Subtilisin-like protease, fibronectin type-III domain		5663
176IPR011032
GroES-like superfamily		5685
177IPR039391
Phytocyanin		5668
178IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5461
179IPR036465
von Willebrand factor A-like domain superfamily		5468
180IPR001563
Peptidase S10, serine carboxypeptidase		53400
181IPR002156
Ribonuclease H domain		5373
182IPR002528
Multi antimicrobial extrusion protein		53129
183IPR015915
Kelch-type beta propeller		5382
184IPR001752
Kinesin motor domain		53488
185IPR000225
Armadillo		53241
186IPR002921
Fungal lipase-like domain		5264
187IPR013525
ABC-2 type transporter		52115
188IPR007112
Expansin/pollen allergen, DPBB domain		5264
189IPR025846
PMR5 N-terminal domain		5268
190IPR015500
Peptidase S8, subtilisin-related		52165
191IPR016181
Acyl-CoA N-acyltransferase		5160
192IPR013201
Cathepsin propeptide inhibitor domain (I29)		5157
193IPR005630
Terpene synthase, metal-binding domain		5166
194IPR013763
Cyclin-like		5196
195IPR023298
P-type ATPase, transmembrane domain superfamily		5169
196IPR013094
Alpha/beta hydrolase fold-3		5171
197IPR000608
Ubiquitin-conjugating enzyme E2		50198
198IPR008250
P-type ATPase, A domain superfamily		4965
199IPR009009
RlpA-like protein, double-psi beta-barrel domain		4959
200IPR034197
Cucumisin-like catalytic domain		4956
201IPR008979
Galactose-binding-like domain superfamily		4983
202IPR036318
FAD-binding, type PCMH-like superfamily		4858
203IPR008978
HSP20-like chaperone		4861
204IPR007125
Histone H2A/H2B/H3		4851
205IPR006566
FBD domain		4858
206IPR001906
Terpene synthase, N-terminal domain		4861
207IPR030184
WAT1-related protein		4883
208IPR003676
Small auxin-up RNA		4859
209IPR007118
Expansin/Lol pI		47278
210IPR000620
EamA domain		47109
211IPR044808
Ethylene-responsive transcription factor		4755
212IPR017884
SANT domain		4656
213IPR036640
ABC transporter type 1, transmembrane domain superfamily		46112
214IPR034161
Pepsin-like domain, plant		4658
215IPR009000
Translation protein, beta-barrel domain superfamily		4664
216IPR004140
Exocyst complex component Exo70		46125
217IPR008928
Six-hairpin glycosidase superfamily		4660
218IPR011527
ABC transporter type 1, transmembrane domain		46225
219IPR041569
AAA ATPase, AAA+ lid domain		4668
220IPR036855
Zinc finger, CCCH-type superfamily		46113
221IPR004853
Sugar phosphate transporter domain		4579
222IPR001509
NAD-dependent epimerase/dehydratase		4570
223IPR029055
Nucleophile aminohydrolases, N-terminal		4566
224IPR004263
Exostosin-like		4553
225IPR012946
X8 domain		4560
226IPR011006
CheY-like superfamily		4566
227IPR000742
EGF-like domain		4550
228IPR009060
UBA-like superfamily		4468
229IPR011701
Major facilitator superfamily		4487
230IPR000873
AMP-dependent synthetase/ligase		4478
231IPR014014
RNA helicase, DEAD-box type, Q motif		4464
232IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4467
233IPR004265
Dirigent protein		4453
234IPR032867
DYW domain		4449
235IPR006702
Casparian strip membrane protein domain		4445
236IPR001117
Multicopper oxidase, type 1		4348
237IPR000182
GNAT domain		4389
238IPR045087
Multicopper oxidase		4357
239IPR006671
Cyclin, N-terminal		4356
240IPR014756
Immunoglobulin E-set		4364
241IPR001214
SET domain		43110
242IPR011707
Multicopper oxidase, N-termianl		4347
243IPR015947
PUA-like superfamily		4357
244IPR001789
Signal transduction response regulator, receiver domain		43109
245IPR011706
Multicopper oxidase, C-terminal		4247
246IPR011043
Galactose oxidase/kelch, beta-propeller		4252
247IPR044730
Ribonuclease H-like domain, plant type		4244
248IPR008889
VQ		4243
249IPR010402
CCT domain		41117
250IPR043926
ABC transporter family G domain		4179
251IPR016461
O-methyltransferase COMT-type		4193
252IPR000330
SNF2, N-terminal		4170
253IPR016166
FAD-binding domain, PCMH-type		4151
254IPR033905
Secretory peroxidase		4144
255IPR011012
Longin-like domain superfamily		4161
256IPR000070
Pectinesterase, catalytic		4148
257IPR000743
Glycoside hydrolase, family 28		4150
258IPR033389
AUX/IAA domain		4064
259IPR001077
O-methyltransferase domain		4053
260IPR013126
Heat shock protein 70 family		40110
261IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4047
262IPR007811
DNA-directed RNA polymerase III subunit RPC4		4094
263IPR006016
UspA		3947
264IPR033896
MADS MEF2-like		3957
265IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3955
266IPR036612
K Homology domain, type 1 superfamily		39115
267IPR029045
ClpP/crotonase-like domain superfamily		3960
268IPR000668
Peptidase C1A, papain C-terminal		39163
269IPR040911
Exostosin, GT47 domain		3944
270IPR008942
ENTH/VHS		3843
271IPR016040
NAD(P)-binding domain		3860
272IPR025322
Protein of unknown function DUF4228, plant		3841
273IPR025659
Tubby-like, C-terminal		3852
274IPR003137
PA domain		3849
275IPR002495
Glycosyl transferase, family 8		3845
276IPR000644
CBS domain		38175
277IPR039361
Cyclin		3850
278IPR007493
Protein of unknown function DUF538		3782
279IPR002068
Alpha crystallin/Hsp20 domain		3791
280IPR004839
Aminotransferase, class I/classII		3754
281IPR036758
At5g01610-like superfamily		3742
282IPR015655
Protein phosphatase 2C family		3769
283IPR019378
GDP-fucose protein O-fucosyltransferase		3756
284IPR002109
Glutaredoxin		3746
285IPR001929
Germin		36109
286IPR013149
Alcohol dehydrogenase, C-terminal		3643
287IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3653
288IPR043454
NPH3/RPT2-like family		3660
289IPR004883
Lateral organ boundaries, LOB		3680
290IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3658
291IPR004046
Glutathione S-transferase, C-terminal		3649
292IPR002067
Mitochondrial carrier protein		36243
293IPR028889
Ubiquitin specific protease domain		3653
294IPR037176
Osmotin/thaumatin-like superfamily		3643
295IPR001360
Glycoside hydrolase family 1		35316
296IPR008991
Translation protein SH3-like domain superfamily		3545
297IPR029021
Protein-tyrosine phosphatase-like		3562
298IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3539
299IPR023271
Aquaporin-like		3548
300IPR001938
Thaumatin family		35251
301IPR000425
Major intrinsic protein		35305
302IPR039417
Papain-like cysteine endopeptidase		3543
303IPR002912
ACT domain		35102
304IPR002487
Transcription factor, K-box		35110
305IPR004041
NAF domain		3446
306IPR018451
NAF/FISL domain		3446
307IPR000795
Translational (tr)-type GTP-binding domain		34277
308IPR022742
Serine aminopeptidase, S33		3441
309IPR006094
FAD linked oxidase, N-terminal		3443
310IPR043519
Nucleotidyltransferase superfamily		3456
311IPR024752
Myb/SANT-like domain		3435
312IPR038933
Ovate protein family		3334
313IPR013154
Alcohol dehydrogenase, N-terminal		3342
314IPR004367
Cyclin, C-terminal domain		3336
315IPR006458
Ovate protein family, C-terminal		3364
316IPR012967
Plant methyltransferase dimerisation		3333
317IPR001251
CRAL-TRIO lipid binding domain		32136
318IPR029061
Thiamin diphosphate-binding fold		3280
319IPR036865
CRAL-TRIO lipid binding domain superfamily		3248
320IPR027356
NPH3 domain		3288
321IPR034294
Aquaporin transporter		3250
322IPR004088
K Homology domain, type 1		3298
323IPR033443
Pentacotripeptide-repeat region of PRORP		3240
324IPR004314
Neprosin		3251
325IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3262
326IPR000528
Plant non-specific lipid-transfer protein/Par allergen		31135
327IPR018490
Cyclic nucleotide-binding-like		3137
328IPR032710
NTF2-like domain superfamily		3138
329IPR001296
Glycosyl transferase, family 1		3155
330IPR035940
CAP superfamily		3138
331IPR006652
Kelch repeat type 1		3177
332IPR005150
Cellulose synthase		3168
333IPR003690
Transcription termination factor, mitochondrial/chloroplastic		31108
334IPR000863
Sulfotransferase domain		3140
335IPR003855
Potassium transporter		31118
336IPR036041
Ribosome-inactivating protein superfamily		3134
337IPR006311
Twin-arginine translocation pathway, signal sequence		3132
338IPR006073
GTP binding domain		31112
339IPR029000
Cyclophilin-like domain superfamily		3045
340IPR025753
AAA-type ATPase, N-terminal domain		3033
341IPR044822
Myb/SANT-like DNA-binding domain 4		3039
342IPR000315
B-box-type zinc finger		3081
343IPR005135
Endonuclease/exonuclease/phosphatase		3040
344IPR002423
Chaperonin Cpn60/TCP-1 family		3046
345IPR003406
Glycosyl transferase, family 14		3039
346IPR027409
GroEL-like apical domain superfamily		3040
347IPR003851
Zinc finger, Dof-type		3066
348IPR000595
Cyclic nucleotide-binding domain		3087
349IPR001574
Ribosome-inactivating protein		3061
350IPR013601
FAE1/Type III polyketide synthase-like protein		2936
351IPR006153
Cation/H+ exchanger		2938
352IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		29112
353IPR005299
SAM dependent carboxyl methyltransferase		2983
354IPR000717
Proteasome component (PCI) domain		2962
355IPR001594
Palmitoyltransferase, DHHC domain		2950
356IPR007650
Zf-FLZ domain		2969
357IPR011013
Galactose mutarotase-like domain superfamily		2944
358IPR002963
Expansin		29235
359IPR001283
Cysteine-rich secretory protein-related		29105
360IPR002035
von Willebrand factor, type A		2964
361IPR023299
P-type ATPase, cytoplasmic domain N		2941
362IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2941
363IPR001223
Glycoside hydrolase family 18, catalytic domain		2973
364IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2936
365IPR011141
Polyketide synthase, type III		2939
366IPR001099
Chalcone/stilbene synthase, N-terminal		2935
367IPR000727
Target SNARE coiled-coil homology domain		2853
368IPR015940
Ubiquitin-associated domain		2896
369IPR036378
FAS1 domain superfamily		2842
370IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2836
371IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28245
372IPR024709
Putative O-fucosyltransferase, plant		2844
373IPR010920
LSM domain superfamily		2837
374IPR044835
Auxin response factor		2872
375IPR002659
Glycosyl transferase, family 31		28101
376IPR044848
PHR1-like		2843
377IPR005333
Transcription factor, TCP		2830
378IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2834
379IPR008480
Protein of unknown function DUF761, plant		2828
380IPR016897
S-phase kinase-associated protein 1		2835
381IPR014044
CAP domain		2833
382IPR036296
SKP1-like, dimerisation domain superfamily		2833
383IPR036812
NADP-dependent oxidoreductase domain superfamily		2842
384IPR002913
START domain		2888
385IPR036085
PAZ domain superfamily		2739
386IPR025110
AMP-binding enzyme, C-terminal domain		2733
387IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		27104
388IPR007657
Glycosyltransferase 61		2771
389IPR026960
Reverse transcriptase zinc-binding domain		2727
390IPR003337
Trehalose-phosphatase		2741
391IPR016072
SKP1 component, dimerisation		2731
392IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2734
393IPR001701
Glycoside hydrolase family 9		2734
394IPR003311
AUX/IAA protein		2742
395IPR036404
Jacalin-like lectin domain superfamily		2740
396IPR000757
Glycoside hydrolase family 16		2771
397IPR015797
NUDIX hydrolase-like domain superfamily		2733
398IPR003100
PAZ domain		2674
399IPR044778
Sugar transport protein STP/MST-like, plant		2629
400IPR036420
BRCT domain superfamily		2648
401IPR040417
Glycine-rich cell wall structural protein 1/2		2636
402IPR027725
Heat shock transcription factor family		2633
403IPR009030
Growth factor receptor cysteine-rich domain superfamily		2631
404IPR001763
Rhodanese-like domain		2658
405IPR000408
Regulator of chromosome condensation, RCC1		26692
406IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2636
407IPR005821
Ion transport domain		2632
408IPR004813
Oligopeptide transporter, OPT superfamily		2660
409IPR001849
Pleckstrin homology domain		2656
410IPR029062
Class I glutamine amidotransferase-like		2647
411IPR012328
Chalcone/stilbene synthase, C-terminal		2629
412IPR044791
Beta-glucanase/XTH		2640
413IPR000679
Zinc finger, GATA-type		26103
414IPR005175
PPC domain		2677
415IPR001229
Jacalin-like lectin domain		2674
416IPR017938
Riboflavin synthase-like beta-barrel		2540
417IPR008971
HSP40/DnaJ peptide-binding		2559
418IPR004316
SWEET sugar transporter		2544
419IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2532
420IPR001357
BRCT domain		2577
421IPR019557
Aminotransferase-like, plant mobile domain		2529
422IPR001881
EGF-like calcium-binding domain		2531
423IPR004320
Protein of unknown function DUF241, plant		2534
424IPR002123
Phospholipid/glycerol acyltransferase		2527
425IPR036273
CRAL/TRIO, N-terminal domain superfamily		2535
426IPR004014
Cation-transporting P-type ATPase, N-terminal		2534
427IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2542
428IPR027923
Hydrophobic seed protein domain		2569
429IPR001757
P-type ATPase		25118
430IPR002939
Chaperone DnaJ, C-terminal		2532
431IPR000232
Heat shock factor (HSF)-type, DNA-binding		25106
432IPR023210
NADP-dependent oxidoreductase domain		2542
433IPR000782
FAS1 domain		2465
434IPR002867
IBR domain		2447
435IPR013187
F-box associated domain, type 3		2426
436IPR008422
Homeobox KN domain		2427
437IPR023753
FAD/NAD(P)-binding domain		2434
438IPR003594
Histidine kinase/HSP90-like ATPase		2436
439IPR044675
E3 ubiquitin-protein ligase RING1-like		2427
440IPR045048
F-box only protein 31/39		2456
441IPR044839
Protein NDR1-like		2425
442IPR034285
Laccase, second cupredoxin domain		2427
443IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2432
444IPR036427
Bromodomain-like superfamily		2441
445IPR000086
NUDIX hydrolase domain		2458
446IPR036034
PDZ superfamily		2428
447IPR029033
Histidine phosphatase superfamily		2427
448IPR010525
Auxin response factor domain		2448
449IPR017927
FAD-binding domain, ferredoxin reductase-type		2336
450IPR003106
Leucine zipper, homeobox-associated		2323
451IPR008999
Actin-crosslinking		2327
452IPR011016
Zinc finger, RING-CH-type		2380
453IPR001163
LSM domain, eukaryotic/archaea-type		2328
454IPR036010
2Fe-2S ferredoxin-like superfamily		2325
455IPR039421
Type 1 protein exporter		2344
456IPR041677
DNA2/NAM7 helicase, helicase domain		2351
457IPR025486
Domain of unknown function DUF4378		2337
458IPR031127
E3 ubiquitin ligase RBR family		2342
459IPR044066
TRIAD supradomain		2330
460IPR001487
Bromodomain		23201
461IPR002937
Amine oxidase		2337
462IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2331
463IPR006689
Small GTPase superfamily, ARF/SAR type		22141
464IPR004000
Actin family		22173
465IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2237
466IPR013216
Methyltransferase type 11		2231
467IPR017887
Transcription factor TCP subgroup		2244
468IPR001353
Proteasome, subunit alpha/beta		2229
469IPR011257
DNA glycosylase		2228
470IPR025422
Transcription factor TGA like domain		2256
471IPR010989
SNARE		2225
472IPR021720
Malectin domain		2240
473IPR020103
Pseudouridine synthase, catalytic domain superfamily		2234
474IPR007592
GLABROUS1 enhancer-binding protein family		2248
475IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2230
476IPR022796
Chlorophyll A-B binding protein		2225
477IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2225
478IPR041679
DNA2/NAM7 helicase-like, C-terminal		2274
479IPR029069
HotDog domain superfamily		2248
480IPR016161
Aldehyde/histidinol dehydrogenase		2234
481IPR006868
Domain of unknown function DUF630		2225
482IPR013809
ENTH domain		2232
483IPR033734
Jacalin-like lectin domain, plant		2231
484IPR033133
Pumilio homology domain		2123
485IPR016073
SKP1 component, POZ domain		2124
486IPR035952
Rhomboid-like superfamily		2131
487IPR000387
Tyrosine specific protein phosphatases domain		2144
488IPR007612
LURP-one-related		2154
489IPR001440
Tetratricopeptide repeat 1		2131
490IPR029466
No apical meristem-associated, C-terminal domain		2121
491IPR003347
JmjC domain		2146
492IPR013581
Plant PDR ABC transporter associated		2132
493IPR036186
Serpin superfamily		2127
494IPR018392
LysM domain		2174
495IPR005516
Remorin, C-terminal		2126
496IPR027413
GroEL-like equatorial domain superfamily		2130
497IPR002293
Amino acid/polyamine transporter I		2129
498IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2126
499IPR044814
Terpene cyclases, class 1, plant		2129
500IPR011053
Single hybrid motif		2127
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa128077.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa128077.html new file mode 100644 index 00000000..7d6f28d2 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa128077.html @@ -0,0 +1,93 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os128077RS1, Jan 2020
Database version:87.1
Base Pairs:382,007,384
Golden Path Length:382,007,384
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,612
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,321
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
143443826
236365133
337488606
434281816
530414546
631738027
730624898
829554190
923544870
1025901498
1130696581
1226705100
+
+
scaffold
+
13 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg29183249
UN-Ctg30177201
UN-Ctg31137752
UN-Ctg32114397
UN-Ctg33103714
UN-Ctg3497451
UN-Ctg3589468
UN-Ctg3678798
UN-Ctg3765778
UN-Ctg3863727
UN-Ctg3953308
UN-Ctg4050227
UN-Ctg4133223
+
+
chunk3832 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa128077_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa128077_IPtop500.html new file mode 100644 index 00000000..7ab7a083 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa128077_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14832096
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14062148
3IPR000719
Protein kinase domain		13863246
4IPR036047
F-box-like domain superfamily		649834
5IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		523879
6IPR044974
Disease resistance protein, plants		512883
7IPR002885
Pentatricopeptide repeat		5006224
8IPR001611
Leucine-rich repeat		4661517
9IPR002182
NB-ARC		461560
10IPR001810
F-box domain		458870
11IPR001841
Zinc finger, RING-type		443916
12IPR016024
Armadillo-type fold		388620
13IPR029058
Alpha/Beta hydrolase fold		378512
14IPR036291
NAD(P)-binding domain superfamily		377551
15IPR009057
Homeobox-like domain superfamily		376484
16IPR041118
Rx, N-terminal		368416
17IPR011990
Tetratricopeptide-like helical domain superfamily		335531
18IPR036396
Cytochrome P450 superfamily		315421
19IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		312405
20IPR001128
Cytochrome P450		3071516
21IPR035979
RNA-binding domain superfamily		305608
22IPR000504
RNA recognition motif domain		2721151
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		269414
24IPR001005
SANT/Myb domain		2691360
25IPR002401
Cytochrome P450, E-class, group I		2631859
26IPR036259
MFS transporter superfamily		253402
27IPR017853
Glycoside hydrolase superfamily		252373
28IPR038005
Virus X resistance protein-like, coiled-coil domain		249279
29IPR038765
Papain-like cysteine peptidase superfamily		242319
30IPR017930
Myb domain		234351
31IPR036249
Thioredoxin-like superfamily		233332
32IPR036322
WD40-repeat-containing domain superfamily		231352
33IPR001680
WD40 repeat		2071693
34IPR011992
EF-hand domain pair		194251
35IPR002048
EF-hand domain		182945
36IPR036770
Ankyrin repeat-containing domain superfamily		175246
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		174403
38IPR012337
Ribonuclease H-like superfamily		170224
39IPR011333
SKP1/BTB/POZ domain superfamily		170248
40IPR016177
DNA-binding domain superfamily		169234
41IPR036412
HAD-like superfamily		169226
42IPR002110
Ankyrin repeat		163680
43IPR036390
Winged helix DNA-binding domain superfamily		162216
44IPR036638
Helix-loop-helix DNA-binding domain superfamily		158189
45IPR001471
AP2/ERF domain		151818
46IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		149328
47IPR036093
NAC domain superfamily		148170
48IPR003441
NAC domain		145328
49IPR029044
Nucleotide-diphospho-sugar transferases		143178
50IPR036236
Zinc finger C2H2 superfamily		141203
51IPR001650
Helicase, C-terminal		140415
52IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		140186
53IPR010255
Haem peroxidase superfamily		138174
54IPR014001
Helicase superfamily 1/2, ATP-binding domain		137207
55IPR012340
Nucleic acid-binding, OB-fold		136279
56IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		135161
57IPR036188
FAD/NAD(P)-binding domain superfamily		135232
58IPR002016
Haem peroxidase		134610
59IPR013087
Zinc finger C2H2-type		133247
60IPR020683
Ankyrin repeat-containing domain		130282
61IPR000210
BTB/POZ domain		129374
62IPR003480
Transferase		129153
63IPR003439
ABC transporter-like, ATP-binding domain		128488
64IPR005174
Domain unknown function DUF295		127148
65IPR036426
Bulb-type lectin domain superfamily		124168
66IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		120194
67IPR021109
Aspartic peptidase domain superfamily		120166
68IPR001480
Bulb-type lectin domain		119414
69IPR003959
ATPase, AAA-type, core		119184
70IPR025315
Domain of unknown function DUF4220		117125
71IPR015424
Pyridoxal phosphate-dependent transferase		112160
72IPR036869
Chaperone J-domain superfamily		112151
73IPR007658
Protein of unknown function DUF594		111117
74IPR005123
Oxoglutarate/iron-dependent dioxygenase		110367
75IPR019734
Tetratricopeptide repeat		108339
76IPR011011
Zinc finger, FYVE/PHD-type		108162
77IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		108129
78IPR020846
Major facilitator superfamily domain		108155
79IPR001623
DnaJ domain		107736
80IPR033121
Peptidase family A1 domain		106160
81IPR011676
Domain of unknown function DUF1618		104137
82IPR008972
Cupredoxin		103207
83IPR001087
GDSL lipase/esterase		102132
84IPR036576
WRKY domain superfamily		102137
85IPR011050
Pectin lyase fold/virulence factor		102113
86IPR003657
WRKY domain		102268
87IPR045005
BTB/POZ and MATH domain-containing protein 1-6		101168
88IPR029071
Ubiquitin-like domain superfamily		101160
89IPR035892
C2 domain superfamily		99195
90IPR003609
PAN/Apple domain		99235
91IPR000858
S-locus glycoprotein domain		98127
92IPR036457
PPM-type phosphatase domain superfamily		97140
93IPR032799
Xylanase inhibitor, C-terminal		97131
94IPR015300
DNA-binding pseudobarrel domain superfamily		96170
95IPR044810
WRKY transcription factor, plant		95122
96IPR032861
Xylanase inhibitor, N-terminal		94127
97IPR001932
PPM-type phosphatase domain		94397
98IPR002083
MATH/TRAF domain		92309
99IPR000823
Plant peroxidase		92386
100IPR009072
Histone-fold		91101
101IPR011545
DEAD/DEAH box helicase domain		90135
102IPR011051
RmlC-like cupin domain superfamily		89120
103IPR001356
Homeobox domain		89269
104IPR000008
C2 domain		87407
105IPR000109
Proton-dependent oligopeptide transporter family		87308
106IPR002347
Short-chain dehydrogenase/reductase SDR		86797
107IPR005828
Major facilitator, sugar transporter-like		86136
108IPR000073
Alpha/beta hydrolase fold-1		86248
109IPR020472
G-protein beta WD-40 repeat		84381
110IPR035669
GDSL lipase/esterase-like, plant		83103
111IPR036875
Zinc finger, CCHC-type superfamily		83106
112IPR003340
B3 DNA binding domain		82414
113IPR004827
Basic-leucine zipper domain		82200
114IPR043129
ATPase, nucleotide binding domain		81206
115IPR012871
Protein of unknown function DUF1677, Oryza sativa		8095
116IPR013766
Thioredoxin domain		80183
117IPR026992
Non-haem dioxygenase N-terminal domain		7995
118IPR001461
Aspartic peptidase A1 family		79264
119IPR026961
PGG domain		78176
120IPR031052
FHY3/FAR1 family		78149
121IPR002902
Gnk2-homologous domain		77345
122IPR001878
Zinc finger, CCHC-type		76171
123IPR036282
Glutathione S-transferase, C-terminal domain superfamily		7599
124IPR003653
Ulp1 protease family, C-terminal catalytic domain		74142
125IPR003613
U box domain		73163
126IPR001220
Legume lectin domain		71176
127IPR008949
Isoprenoid synthase domain superfamily		7083
128IPR002100
Transcription factor, MADS-box		70401
129IPR004158
Protein of unknown function DUF247, plant		70169
130IPR007527
Zinc finger, SWIM-type		70123
131IPR000270
PB1 domain		70118
132IPR036879
Transcription factor, MADS-box superfamily		7087
133IPR004330
FAR1 DNA binding domain		7078
134IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		70122
135IPR016039
Thiolase-like		69147
136IPR036163
Heavy metal-associated domain superfamily		6996
137IPR004045
Glutathione S-transferase, N-terminal		68185
138IPR016159
Cullin repeat-like-containing domain superfamily		6783
139IPR006121
Heavy metal-associated domain, HMA		66228
140IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		6668
141IPR013057
Amino acid transporter, transmembrane domain		6690
142IPR036908
RlpA-like domain superfamily		6680
143IPR044965
Glycoside hydrolase family 17, plant		66107
144IPR036749
Expansin, cellulose-binding-like domain superfamily		6576
145IPR019787
Zinc finger, PHD-finger		65160
146IPR000048
IQ motif, EF-hand binding site		65328
147IPR000626
Ubiquitin-like domain		64162
148IPR022059
Protein of unknown function DUF3615		6482
149IPR010987
Glutathione S-transferase, C-terminal-like		6483
150IPR007117
Expansin, cellulose-binding-like domain		64150
151IPR018108
Mitochondrial substrate/solute carrier		63498
152IPR023395
Mitochondrial carrier domain superfamily		6390
153IPR029052
Metallo-dependent phosphatase-like		6389
154IPR009003
Peptidase S1, PA clan		63111
155IPR036915
Cyclin-like superfamily		63141
156IPR020568
Ribosomal protein S5 domain 2-type fold		6299
157IPR036852
Peptidase S8/S53 domain superfamily		6185
158IPR000209
Peptidase S8/S53 domain		6183
159IPR026057
PC-Esterase		6083
160IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6070
161IPR000571
Zinc finger, CCCH-type		60277
162IPR001806
Small GTPase		60135
163IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5988
164IPR005202
Transcription factor GRAS		59226
165IPR000490
Glycoside hydrolase family 17		5979
166IPR045051
Subtilisin-like protease		5896
167IPR029962
Trichome birefringence-like family		5885
168IPR006501
Pectinesterase inhibitor domain		5860
169IPR003663
Sugar/inositol transporter		58334
170IPR024788
Malectin-like domain		5877
171IPR001563
Peptidase S10, serine carboxypeptidase		57388
172IPR041469
Subtilisin-like protease, fibronectin type-III domain		5675
173IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5681
174IPR002156
Ribonuclease H domain		5674
175IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5669
176IPR003245
Phytocyanin domain		56120
177IPR039391
Phytocyanin		5565
178IPR007112
Expansin/pollen allergen, DPBB domain		5564
179IPR002921
Fungal lipase-like domain		5464
180IPR002528
Multi antimicrobial extrusion protein		54139
181IPR001752
Kinesin motor domain		54461
182IPR000225
Armadillo		54239
183IPR011032
GroES-like superfamily		5379
184IPR013763
Cyclin-like		53106
185IPR006045
Cupin 1		5395
186IPR025846
PMR5 N-terminal domain		5369
187IPR036465
von Willebrand factor A-like domain superfamily		5367
188IPR015500
Peptidase S8, subtilisin-related		53180
189IPR016181
Acyl-CoA N-acyltransferase		5263
190IPR013525
ABC-2 type transporter		52114
191IPR009009
RlpA-like protein, double-psi beta-barrel domain		5261
192IPR015915
Kelch-type beta propeller		5276
193IPR013201
Cathepsin propeptide inhibitor domain (I29)		5165
194IPR006566
FBD domain		5163
195IPR023298
P-type ATPase, transmembrane domain superfamily		5174
196IPR000608
Ubiquitin-conjugating enzyme E2		50199
197IPR008250
P-type ATPase, A domain superfamily		5068
198IPR034197
Cucumisin-like catalytic domain		5068
199IPR013094
Alpha/beta hydrolase fold-3		5068
200IPR008978
HSP20-like chaperone		4960
201IPR007118
Expansin/Lol pI		49283
202IPR005630
Terpene synthase, metal-binding domain		4960
203IPR003676
Small auxin-up RNA		4960
204IPR012946
X8 domain		4869
205IPR004140
Exocyst complex component Exo70		48130
206IPR007125
Histone H2A/H2B/H3		4850
207IPR014014
RNA helicase, DEAD-box type, Q motif		4768
208IPR008979
Galactose-binding-like domain superfamily		4787
209IPR000743
Glycoside hydrolase, family 28		4753
210IPR000873
AMP-dependent synthetase/ligase		4667
211IPR029055
Nucleophile aminohydrolases, N-terminal		4663
212IPR009000
Translation protein, beta-barrel domain superfamily		4665
213IPR001906
Terpene synthase, N-terminal domain		4660
214IPR041569
AAA ATPase, AAA+ lid domain		4669
215IPR036855
Zinc finger, CCCH-type superfamily		46113
216IPR017884
SANT domain		4569
217IPR036640
ABC transporter type 1, transmembrane domain superfamily		45102
218IPR009060
UBA-like superfamily		4572
219IPR001509
NAD-dependent epimerase/dehydratase		4563
220IPR011006
CheY-like superfamily		4555
221IPR008928
Six-hairpin glycosidase superfamily		4554
222IPR011527
ABC transporter type 1, transmembrane domain		45204
223IPR000668
Peptidase C1A, papain C-terminal		45180
224IPR006671
Cyclin, N-terminal		4562
225IPR000620
EamA domain		4598
226IPR044808
Ethylene-responsive transcription factor		4554
227IPR001117
Multicopper oxidase, type 1		4448
228IPR036318
FAD-binding, type PCMH-like superfamily		4455
229IPR016461
O-methyltransferase COMT-type		44105
230IPR011701
Major facilitator superfamily		4476
231IPR034161
Pepsin-like domain, plant		4459
232IPR011706
Multicopper oxidase, C-terminal		4449
233IPR045087
Multicopper oxidase		4461
234IPR030184
WAT1-related protein		4479
235IPR014756
Immunoglobulin E-set		4466
236IPR000070
Pectinesterase, catalytic		4452
237IPR000182
GNAT domain		4389
238IPR033896
MADS MEF2-like		4360
239IPR004265
Dirigent protein		4350
240IPR001077
O-methyltransferase domain		4350
241IPR032867
DYW domain		4345
242IPR011043
Galactose oxidase/kelch, beta-propeller		4350
243IPR044730
Ribonuclease H-like domain, plant type		4345
244IPR008889
VQ		4345
245IPR001789
Signal transduction response regulator, receiver domain		4389
246IPR004853
Sugar phosphate transporter domain		4276
247IPR004263
Exostosin-like		4254
248IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4257
249IPR033905
Secretory peroxidase		4245
250IPR011012
Longin-like domain superfamily		4273
251IPR000742
EGF-like domain		4246
252IPR001214
SET domain		42104
253IPR011707
Multicopper oxidase, N-termianl		4247
254IPR006702
Casparian strip membrane protein domain		4244
255IPR033389
AUX/IAA domain		4159
256IPR010402
CCT domain		41111
257IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4153
258IPR006016
UspA		4051
259IPR000330
SNF2, N-terminal		4069
260IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4055
261IPR029045
ClpP/crotonase-like domain superfamily		4061
262IPR004046
Glutathione S-transferase, C-terminal		4051
263IPR039417
Papain-like cysteine endopeptidase		4056
264IPR043926
ABC transporter family G domain		3973
265IPR025322
Protein of unknown function DUF4228, plant		3941
266IPR036612
K Homology domain, type 1 superfamily		39114
267IPR003137
PA domain		3948
268IPR002495
Glycosyl transferase, family 8		3946
269IPR024752
Myb/SANT-like domain		3940
270IPR015947
PUA-like superfamily		3950
271IPR025659
Tubby-like, C-terminal		3848
272IPR002068
Alpha crystallin/Hsp20 domain		3890
273IPR043454
NPH3/RPT2-like family		3867
274IPR015655
Protein phosphatase 2C family		3867
275IPR000644
CBS domain		38183
276IPR002109
Glutaredoxin		3846
277IPR013126
Heat shock protein 70 family		38121
278IPR012967
Plant methyltransferase dimerisation		3838
279IPR008942
ENTH/VHS		3746
280IPR016040
NAD(P)-binding domain		3761
281IPR027356
NPH3 domain		37103
282IPR016166
FAD-binding domain, PCMH-type		3748
283IPR004839
Aminotransferase, class I/classII		3754
284IPR039361
Cyclin		3751
285IPR002912
ACT domain		37100
286IPR004041
NAF domain		3651
287IPR018451
NAF/FISL domain		3649
288IPR029021
Protein-tyrosine phosphatase-like		3662
289IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3640
290IPR013154
Alcohol dehydrogenase, N-terminal		3642
291IPR004883
Lateral organ boundaries, LOB		3674
292IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3660
293IPR019378
GDP-fucose protein O-fucosyltransferase		3650
294IPR033443
Pentacotripeptide-repeat region of PRORP		3647
295IPR040911
Exostosin, GT47 domain		3643
296IPR028889
Ubiquitin specific protease domain		3655
297IPR002487
Transcription factor, K-box		36105
298IPR001360
Glycoside hydrolase family 1		35324
299IPR007493
Protein of unknown function DUF538		3579
300IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3547
301IPR008991
Translation protein SH3-like domain superfamily		3545
302IPR023271
Aquaporin-like		3543
303IPR006652
Kelch repeat type 1		3580
304IPR036758
At5g01610-like superfamily		3540
305IPR000425
Major intrinsic protein		35285
306IPR002067
Mitochondrial carrier protein		35229
307IPR013149
Alcohol dehydrogenase, C-terminal		3441
308IPR000795
Translational (tr)-type GTP-binding domain		34258
309IPR004314
Neprosin		3453
310IPR006311
Twin-arginine translocation pathway, signal sequence		3437
311IPR038933
Ovate protein family		3334
312IPR001296
Glycosyl transferase, family 1		3356
313IPR022742
Serine aminopeptidase, S33		3342
314IPR006094
FAD linked oxidase, N-terminal		3341
315IPR006458
Ovate protein family, C-terminal		3364
316IPR043519
Nucleotidyltransferase superfamily		3352
317IPR037176
Osmotin/thaumatin-like superfamily		3339
318IPR001251
CRAL-TRIO lipid binding domain		32123
319IPR001938
Thaumatin family		32215
320IPR034294
Aquaporin transporter		3245
321IPR004088
K Homology domain, type 1		32102
322IPR018490
Cyclic nucleotide-binding-like		3143
323IPR032710
NTF2-like domain superfamily		3137
324IPR029061
Thiamin diphosphate-binding fold		3178
325IPR026960
Reverse transcriptase zinc-binding domain		3131
326IPR036865
CRAL-TRIO lipid binding domain superfamily		3142
327IPR004367
Cyclin, C-terminal domain		3138
328IPR000863
Sulfotransferase domain		3146
329IPR023299
P-type ATPase, cytoplasmic domain N		3143
330IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3164
331IPR036041
Ribosome-inactivating protein superfamily		3134
332IPR006073
GTP binding domain		31118
333IPR001574
Ribosome-inactivating protein		3160
334IPR015940
Ubiquitin-associated domain		3091
335IPR005299
SAM dependent carboxyl methyltransferase		3099
336IPR044835
Auxin response factor		3065
337IPR044822
Myb/SANT-like DNA-binding domain 4		3039
338IPR000315
B-box-type zinc finger		3086
339IPR000717
Proteasome component (PCI) domain		3067
340IPR001594
Palmitoyltransferase, DHHC domain		3045
341IPR005135
Endonuclease/exonuclease/phosphatase		3039
342IPR002423
Chaperonin Cpn60/TCP-1 family		3044
343IPR003406
Glycosyl transferase, family 14		3037
344IPR002963
Expansin		30240
345IPR003851
Zinc finger, Dof-type		3066
346IPR000595
Cyclic nucleotide-binding domain		30103
347IPR011141
Polyketide synthase, type III		3041
348IPR001099
Chalcone/stilbene synthase, N-terminal		3038
349IPR001929
Germin		2992
350IPR002659
Glycosyl transferase, family 31		2987
351IPR007650
Zf-FLZ domain		2971
352IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2934
353IPR005150
Cellulose synthase		2959
354IPR027409
GroEL-like apical domain superfamily		2938
355IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2947
356IPR012328
Chalcone/stilbene synthase, C-terminal		2931
357IPR001223
Glycoside hydrolase family 18, catalytic domain		2975
358IPR000727
Target SNARE coiled-coil homology domain		2848
359IPR036378
FAS1 domain superfamily		2838
360IPR006153
Cation/H+ exchanger		2835
361IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28114
362IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2895
363IPR024709
Putative O-fucosyltransferase, plant		2843
364IPR010920
LSM domain superfamily		2839
365IPR040417
Glycine-rich cell wall structural protein 1/2		2839
366IPR005333
Transcription factor, TCP		2830
367IPR035940
CAP superfamily		2838
368IPR003337
Trehalose-phosphatase		2838
369IPR011013
Galactose mutarotase-like domain superfamily		2841
370IPR003690
Transcription termination factor, mitochondrial/chloroplastic		2896
371IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2833
372IPR008480
Protein of unknown function DUF761, plant		2828
373IPR003855
Potassium transporter		28115
374IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2837
375IPR036812
NADP-dependent oxidoreductase domain superfamily		2847
376IPR002913
START domain		2875
377IPR025110
AMP-binding enzyme, C-terminal domain		2733
378IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		27220
379IPR029000
Cyclophilin-like domain superfamily		2739
380IPR025753
AAA-type ATPase, N-terminal domain		2730
381IPR007657
Glycosyltransferase 61		2768
382IPR044848
PHR1-like		2739
383IPR027725
Heat shock transcription factor family		2733
384IPR019557
Aminotransferase-like, plant mobile domain		2732
385IPR002123
Phospholipid/glycerol acyltransferase		2729
386IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2737
387IPR001283
Cysteine-rich secretory protein-related		2789
388IPR002035
von Willebrand factor, type A		2763
389IPR004813
Oligopeptide transporter, OPT superfamily		2760
390IPR029062
Class I glutamine amidotransferase-like		2750
391IPR044791
Beta-glucanase/XTH		2742
392IPR003311
AUX/IAA protein		2741
393IPR000757
Glycoside hydrolase family 16		2774
394IPR000528
Plant non-specific lipid-transfer protein/Par allergen		26138
395IPR029466
No apical meristem-associated, C-terminal domain		2626
396IPR044778
Sugar transport protein STP/MST-like, plant		2628
397IPR036420
BRCT domain superfamily		2660
398IPR009030
Growth factor receptor cysteine-rich domain superfamily		2637
399IPR000408
Regulator of chromosome condensation, RCC1		26682
400IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2647
401IPR016897
S-phase kinase-associated protein 1		2637
402IPR001849
Pleckstrin homology domain		2657
403IPR036296
SKP1-like, dimerisation domain superfamily		2637
404IPR001701
Glycoside hydrolase family 9		2631
405IPR000232
Heat shock factor (HSF)-type, DNA-binding		26110
406IPR036034
PDZ superfamily		2637
407IPR000679
Zinc finger, GATA-type		26102
408IPR005175
PPC domain		2677
409IPR017938
Riboflavin synthase-like beta-barrel		2540
410IPR000782
FAS1 domain		2559
411IPR013601
FAE1/Type III polyketide synthase-like protein		2529
412IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2531
413IPR004316
SWEET sugar transporter		2545
414IPR013187
F-box associated domain, type 3		2528
415IPR001357
BRCT domain		2596
416IPR001881
EGF-like calcium-binding domain		2537
417IPR004320
Protein of unknown function DUF241, plant		2533
418IPR001763
Rhodanese-like domain		2565
419IPR036273
CRAL/TRIO, N-terminal domain superfamily		2530
420IPR004014
Cation-transporting P-type ATPase, N-terminal		2533
421IPR005821
Ion transport domain		2531
422IPR034285
Laccase, second cupredoxin domain		2528
423IPR029069
HotDog domain superfamily		2544
424IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2533
425IPR023210
NADP-dependent oxidoreductase domain		2548
426IPR015797
NUDIX hydrolase-like domain superfamily		2533
427IPR017927
FAD-binding domain, ferredoxin reductase-type		2437
428IPR003100
PAZ domain		2483
429IPR036085
PAZ domain superfamily		2442
430IPR008971
HSP40/DnaJ peptide-binding		2455
431IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2427
432IPR023753
FAD/NAD(P)-binding domain		2434
433IPR016072
SKP1 component, dimerisation		2435
434IPR044839
Protein NDR1-like		2425
435IPR001757
P-type ATPase		24120
436IPR041677
DNA2/NAM7 helicase, helicase domain		2446
437IPR002939
Chaperone DnaJ, C-terminal		2430
438IPR025486
Domain of unknown function DUF4378		2437
439IPR036404
Jacalin-like lectin domain superfamily		2438
440IPR002937
Amine oxidase		2437
441IPR010525
Auxin response factor domain		2441
442IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2340
443IPR022149
Protein of unknown function DUF3681		2349
444IPR021790
PTBP1, RNA recognition motif 2-like		2330
445IPR001163
LSM domain, eukaryotic/archaea-type		2331
446IPR008422
Homeobox KN domain		2330
447IPR018392
LysM domain		2375
448IPR017887
Transcription factor TCP subgroup		2346
449IPR003656
Zinc finger, BED-type		2339
450IPR001353
Proteasome, subunit alpha/beta		2330
451IPR025422
Transcription factor TGA like domain		2365
452IPR044675
E3 ubiquitin-protein ligase RING1-like		2326
453IPR006461
PLAC8 motif-containing protein		2349
454IPR007592
GLABROUS1 enhancer-binding protein family		2351
455IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2325
456IPR020946
Flavin monooxygenase-like		2338
457IPR041679
DNA2/NAM7 helicase-like, C-terminal		2365
458IPR036427
Bromodomain-like superfamily		2332
459IPR000086
NUDIX hydrolase domain		2360
460IPR031127
E3 ubiquitin ligase RBR family		2349
461IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2335
462IPR029033
Histidine phosphatase superfamily		2331
463IPR036443
Zinc finger, RanBP2-type superfamily		2358
464IPR004000
Actin family		22154
465IPR003106
Leucine zipper, homeobox-associated		2222
466IPR002867
IBR domain		2252
467IPR000387
Tyrosine specific protein phosphatases domain		2243
468IPR001440
Tetratricopeptide repeat 1		2239
469IPR011016
Zinc finger, RING-CH-type		2268
470IPR013216
Methyltransferase type 11		2232
471IPR039637
CCR4-NOT transcription complex subunit 7/8/Pop2		2224
472IPR036010
2Fe-2S ferredoxin-like superfamily		2227
473IPR010989
SNARE		2224
474IPR003594
Histidine kinase/HSP90-like ATPase		2232
475IPR020103
Pseudouridine synthase, catalytic domain superfamily		2231
476IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2228
477IPR022796
Chlorophyll A-B binding protein		2230
478IPR014044
CAP domain		2230
479IPR039421
Type 1 protein exporter		2235
480IPR016161
Aldehyde/histidinol dehydrogenase		2238
481IPR045055
DNA2/NAM7-like helicase		2243
482IPR006868
Domain of unknown function DUF630		2225
483IPR002641
Patatin-like phospholipase domain		2245
484IPR021864
Domain of unknown function DUF3475		2228
485IPR044066
TRIAD supradomain		2231
486IPR001487
Bromodomain		22149
487IPR001229
Jacalin-like lectin domain		2268
488IPR033133
Pumilio homology domain		2122
489IPR006689
Small GTPase superfamily, ARF/SAR type		21147
490IPR002403
Cytochrome P450, E-class, group IV		21113
491IPR035952
Rhomboid-like superfamily		2127
492IPR007612
LURP-one-related		2152
493IPR036873
Rhodanese-like domain superfamily		2134
494IPR003347
JmjC domain		2143
495IPR013581
Plant PDR ABC transporter associated		2130
496IPR004161
Translation elongation factor EFTu-like, domain 2		2130
497IPR012416
CALMODULIN-BINDING PROTEIN60		2168
498IPR005516
Remorin, C-terminal		2125
499IPR027413
GroEL-like equatorial domain superfamily		2130
500IPR045048
F-box only protein 31/39		2161
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa132278.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa132278.html new file mode 100644 index 00000000..7191fcde --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa132278.html @@ -0,0 +1,149 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os132278RS1, Jan 2020
Database version:87.1
Base Pairs:383,243,376
Golden Path Length:383,243,376
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,999
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:45,326
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144309235
236543595
337868050
435476227
530350168
630913884
729253422
828522915
923059464
1023736288
1128801513
1228022142
+
+
scaffold
+
69 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg68319402
UN-Ctg69273944
UN-Ctg70232362
UN-Ctg71231136
UN-Ctg72188153
UN-Ctg73184041
UN-Ctg74181308
UN-Ctg75166415
UN-Ctg76154601
UN-Ctg77142496
UN-Ctg78137357
UN-Ctg79135059
UN-Ctg80133902
UN-Ctg81124341
UN-Ctg82119510
UN-Ctg83111646
UN-Ctg84107704
UN-Ctg85104613
UN-Ctg86104176
UN-Ctg87102459
UN-Ctg88101965
UN-Ctg89100805
UN-Ctg9097191
UN-Ctg9195828
UN-Ctg9291213
UN-Ctg9389961
UN-Ctg9481876
UN-Ctg9581490
UN-Ctg9680209
UN-Ctg9777400
UN-Ctg9874926
UN-Ctg9974527
UN-Ctg10074225
UN-Ctg10173987
UN-Ctg10270935
UN-Ctg10370454
UN-Ctg10469326
UN-Ctg10568662
UN-Ctg10668651
UN-Ctg10767838
UN-Ctg10867629
UN-Ctg10967535
UN-Ctg11067378
UN-Ctg11167185
UN-Ctg11267070
UN-Ctg11365338
UN-Ctg11464367
UN-Ctg11563829
UN-Ctg11662624
UN-Ctg11761110
UN-Ctg11860755
UN-Ctg11958268
UN-Ctg12058141
UN-Ctg12156585
UN-Ctg12253710
UN-Ctg12352721
UN-Ctg12452416
UN-Ctg12546162
UN-Ctg12645759
UN-Ctg12745491
UN-Ctg12844926
UN-Ctg12941092
UN-Ctg13039280
UN-Ctg13139047
UN-Ctg13237477
UN-Ctg13335416
UN-Ctg13434540
UN-Ctg13533281
UN-Ctg13631247
+
+
chunk3872 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa132278_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa132278_IPtop500.html new file mode 100644 index 00000000..de55957a --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa132278_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR027417
P-loop containing nucleoside triphosphate hydrolase		14872288
2IPR011009
Protein kinase-like domain superfamily		14392041
3IPR000719
Protein kinase domain		13533201
4IPR036047
F-box-like domain superfamily		660842
5IPR044974
Disease resistance protein, plants		515914
6IPR002885
Pentatricopeptide repeat		5036309
7IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		494884
8IPR002182
NB-ARC		470576
9IPR001810
F-box domain		465891
10IPR001611
Leucine-rich repeat		4511560
11IPR001841
Zinc finger, RING-type		438917
12IPR036291
NAD(P)-binding domain superfamily		408606
13IPR016024
Armadillo-type fold		389657
14IPR009057
Homeobox-like domain superfamily		382477
15IPR029058
Alpha/Beta hydrolase fold		376540
16IPR041118
Rx, N-terminal		369428
17IPR011990
Tetratricopeptide-like helical domain superfamily		348541
18IPR036396
Cytochrome P450 superfamily		326429
19IPR001128
Cytochrome P450		3191580
20IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		306402
21IPR035979
RNA-binding domain superfamily		302610
22IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		277423
23IPR002401
Cytochrome P450, E-class, group I		2761940
24IPR000504
RNA recognition motif domain		2721154
25IPR017853
Glycoside hydrolase superfamily		263383
26IPR038005
Virus X resistance protein-like, coiled-coil domain		255289
27IPR036259
MFS transporter superfamily		255413
28IPR001005
SANT/Myb domain		237696
29IPR036249
Thioredoxin-like superfamily		235338
30IPR017930
Myb domain		235692
31IPR038765
Papain-like cysteine peptidase superfamily		234293
32IPR036322
WD40-repeat-containing domain superfamily		232353
33IPR001680
WD40 repeat		2071719
34IPR011992
EF-hand domain pair		191249
35IPR002048
EF-hand domain		181954
36IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		178409
37IPR036770
Ankyrin repeat-containing domain superfamily		177257
38IPR036412
HAD-like superfamily		172238
39IPR012337
Ribonuclease H-like superfamily		171227
40IPR016177
DNA-binding domain superfamily		169241
41IPR011333
SKP1/BTB/POZ domain superfamily		169247
42IPR003439
ABC transporter-like, ATP-binding domain		163598
43IPR002110
Ankyrin repeat		163689
44IPR036638
Helix-loop-helix DNA-binding domain superfamily		161185
45IPR036390
Winged helix DNA-binding domain superfamily		161210
46IPR001471
AP2/ERF domain		153871
47IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		150316
48IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		147174
49IPR036093
NAC domain superfamily		147168
50IPR001650
Helicase, C-terminal		145425
51IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		145189
52IPR003441
NAC domain		144326
53IPR029044
Nucleotide-diphospho-sugar transferases		142182
54IPR036188
FAD/NAD(P)-binding domain superfamily		142242
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		142220
56IPR012340
Nucleic acid-binding, OB-fold		139286
57IPR036236
Zinc finger C2H2 superfamily		138206
58IPR010255
Haem peroxidase superfamily		134175
59IPR013087
Zinc finger C2H2-type		132257
60IPR002016
Haem peroxidase		131621
61IPR020683
Ankyrin repeat-containing domain		128286
62IPR000210
BTB/POZ domain		127375
63IPR005174
Domain unknown function DUF295		125148
64IPR003480
Transferase		124155
65IPR015424
Pyridoxal phosphate-dependent transferase		120166
66IPR003959
ATPase, AAA-type, core		119185
67IPR021109
Aspartic peptidase domain superfamily		118160
68IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		114164
69IPR036426
Bulb-type lectin domain superfamily		113155
70IPR036869
Chaperone J-domain superfamily		112152
71IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		110125
72IPR020846
Major facilitator superfamily domain		110159
73IPR019734
Tetratricopeptide repeat		109350
74IPR001480
Bulb-type lectin domain		109395
75IPR008972
Cupredoxin		108211
76IPR033121
Peptidase family A1 domain		108156
77IPR001087
GDSL lipase/esterase		107136
78IPR001623
DnaJ domain		107753
79IPR011011
Zinc finger, FYVE/PHD-type		107169
80IPR002347
Short-chain dehydrogenase/reductase SDR		105931
81IPR025315
Domain of unknown function DUF4220		105113
82IPR036576
WRKY domain superfamily		103133
83IPR007658
Protein of unknown function DUF594		103108
84IPR011676
Domain of unknown function DUF1618		103140
85IPR003657
WRKY domain		103263
86IPR029071
Ubiquitin-like domain superfamily		101156
87IPR035892
C2 domain superfamily		100194
88IPR032799
Xylanase inhibitor, C-terminal		100130
89IPR045005
BTB/POZ and MATH domain-containing protein 1-6		100169
90IPR011050
Pectin lyase fold/virulence factor		99111
91IPR032861
Xylanase inhibitor, N-terminal		98128
92IPR036457
PPM-type phosphatase domain superfamily		96144
93IPR002083
MATH/TRAF domain		96310
94IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		94120
95IPR011051
RmlC-like cupin domain superfamily		94121
96IPR044810
WRKY transcription factor, plant		94115
97IPR001932
PPM-type phosphatase domain		94425
98IPR011545
DEAD/DEAH box helicase domain		93147
99IPR009072
Histone-fold		93108
100IPR005123
Oxoglutarate/iron-dependent dioxygenase		92122
101IPR000823
Plant peroxidase		92396
102IPR015300
DNA-binding pseudobarrel domain superfamily		91161
103IPR003609
PAN/Apple domain		90221
104IPR005828
Major facilitator, sugar transporter-like		90140
105IPR000858
S-locus glycoprotein domain		89118
106IPR001356
Homeobox domain		89277
107IPR000008
C2 domain		88405
108IPR020472
G-protein beta WD-40 repeat		86402
109IPR000109
Proton-dependent oligopeptide transporter family		85323
110IPR035669
GDSL lipase/esterase-like, plant		84101
111IPR012871
Protein of unknown function DUF1677, Oryza sativa		84100
112IPR000073
Alpha/beta hydrolase fold-1		84246
113IPR026961
PGG domain		83172
114IPR026992
Non-haem dioxygenase N-terminal domain		83106
115IPR013766
Thioredoxin domain		81184
116IPR003340
B3 DNA binding domain		80402
117IPR043129
ATPase, nucleotide binding domain		80213
118IPR001461
Aspartic peptidase A1 family		80284
119IPR031052
FHY3/FAR1 family		79149
120IPR004827
Basic-leucine zipper domain		79205
121IPR003653
Ulp1 protease family, C-terminal catalytic domain		76133
122IPR036282
Glutathione S-transferase, C-terminal domain superfamily		75105
123IPR016039
Thiolase-like		74156
124IPR003613
U box domain		74167
125IPR002902
Gnk2-homologous domain		73346
126IPR001220
Legume lectin domain		73171
127IPR007527
Zinc finger, SWIM-type		73126
128IPR004158
Protein of unknown function DUF247, plant		72177
129IPR002100
Transcription factor, MADS-box		71417
130IPR036908
RlpA-like domain superfamily		7184
131IPR036163
Heavy metal-associated domain superfamily		71102
132IPR044965
Glycoside hydrolase family 17, plant		71121
133IPR000270
PB1 domain		71133
134IPR036879
Transcription factor, MADS-box superfamily		7191
135IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7074
136IPR002156
Ribonuclease H domain		6988
137IPR004045
Glutathione S-transferase, N-terminal		69194
138IPR008949
Isoprenoid synthase domain superfamily		6886
139IPR006121
Heavy metal-associated domain, HMA		68241
140IPR004330
FAR1 DNA binding domain		6876
141IPR036749
Expansin, cellulose-binding-like domain superfamily		6776
142IPR036915
Cyclin-like superfamily		67140
143IPR016159
Cullin repeat-like-containing domain superfamily		6683
144IPR007117
Expansin, cellulose-binding-like domain		66150
145IPR019787
Zinc finger, PHD-finger		65164
146IPR013057
Amino acid transporter, transmembrane domain		6586
147IPR020568
Ribosomal protein S5 domain 2-type fold		65108
148IPR000048
IQ motif, EF-hand binding site		65343
149IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		65132
150IPR009003
Peptidase S1, PA clan		64116
151IPR018108
Mitochondrial substrate/solute carrier		63508
152IPR023395
Mitochondrial carrier domain superfamily		6390
153IPR010987
Glutathione S-transferase, C-terminal-like		6388
154IPR029052
Metallo-dependent phosphatase-like		6387
155IPR036875
Zinc finger, CCHC-type superfamily		6384
156IPR005202
Transcription factor GRAS		62238
157IPR006501
Pectinesterase inhibitor domain		6266
158IPR000626
Ubiquitin-like domain		61154
159IPR000490
Glycoside hydrolase family 17		6188
160IPR000571
Zinc finger, CCCH-type		61297
161IPR001806
Small GTPase		61140
162IPR026057
PC-Esterase		6084
163IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6070
164IPR003663
Sugar/inositol transporter		60356
165IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5986
166IPR036852
Peptidase S8/S53 domain superfamily		5988
167IPR001878
Zinc finger, CCHC-type		59159
168IPR003245
Phytocyanin domain		58124
169IPR000209
Peptidase S8/S53 domain		5885
170IPR029962
Trichome birefringence-like family		5785
171IPR013763
Cyclin-like		57108
172IPR039391
Phytocyanin		5768
173IPR007112
Expansin/pollen allergen, DPBB domain		5763
174IPR022059
Protein of unknown function DUF3615		5775
175IPR024788
Malectin-like domain		5773
176IPR009009
RlpA-like protein, double-psi beta-barrel domain		5662
177IPR006045
Cupin 1		5693
178IPR041469
Subtilisin-like protease, fibronectin type-III domain		5579
179IPR016181
Acyl-CoA N-acyltransferase		5569
180IPR015915
Kelch-type beta propeller		5585
181IPR001752
Kinesin motor domain		55440
182IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5477
183IPR045051
Subtilisin-like protease		54100
184IPR002528
Multi antimicrobial extrusion protein		54152
185IPR025846
PMR5 N-terminal domain		5471
186IPR000225
Armadillo		54240
187IPR002921
Fungal lipase-like domain		5365
188IPR001563
Peptidase S10, serine carboxypeptidase		53402
189IPR013525
ABC-2 type transporter		53117
190IPR000873
AMP-dependent synthetase/ligase		5370
191IPR008250
P-type ATPase, A domain superfamily		5374
192IPR006566
FBD domain		5364
193IPR036465
von Willebrand factor A-like domain superfamily		5366
194IPR023298
P-type ATPase, transmembrane domain superfamily		5382
195IPR044730
Ribonuclease H-like domain, plant type		5355
196IPR011032
GroES-like superfamily		5281
197IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5265
198IPR007118
Expansin/Lol pI		52303
199IPR000608
Ubiquitin-conjugating enzyme E2		51194
200IPR009000
Translation protein, beta-barrel domain superfamily		5172
201IPR015500
Peptidase S8, subtilisin-related		51167
202IPR036640
ABC transporter type 1, transmembrane domain superfamily		50122
203IPR013201
Cathepsin propeptide inhibitor domain (I29)		5057
204IPR008979
Galactose-binding-like domain superfamily		5091
205IPR011527
ABC transporter type 1, transmembrane domain		50240
206IPR003676
Small auxin-up RNA		5061
207IPR017884
SANT domain		4963
208IPR007125
Histone H2A/H2B/H3		4953
209IPR006671
Cyclin, N-terminal		4962
210IPR030184
WAT1-related protein		49100
211IPR000620
EamA domain		49111
212IPR044808
Ethylene-responsive transcription factor		4961
213IPR008978
HSP20-like chaperone		4857
214IPR012946
X8 domain		4872
215IPR013094
Alpha/beta hydrolase fold-3		4873
216IPR034161
Pepsin-like domain, plant		4759
217IPR029055
Nucleophile aminohydrolases, N-terminal		4772
218IPR011006
CheY-like superfamily		4766
219IPR041569
AAA ATPase, AAA+ lid domain		4769
220IPR036318
FAD-binding, type PCMH-like superfamily		4656
221IPR005630
Terpene synthase, metal-binding domain		4660
222IPR014014
RNA helicase, DEAD-box type, Q motif		4665
223IPR004140
Exocyst complex component Exo70		46146
224IPR034197
Cucumisin-like catalytic domain		4663
225IPR000668
Peptidase C1A, papain C-terminal		46169
226IPR032867
DYW domain		4647
227IPR014756
Immunoglobulin E-set		4673
228IPR000182
GNAT domain		4596
229IPR001509
NAD-dependent epimerase/dehydratase		4569
230IPR008928
Six-hairpin glycosidase superfamily		4559
231IPR000742
EGF-like domain		4551
232IPR029045
ClpP/crotonase-like domain superfamily		4572
233IPR036855
Zinc finger, CCCH-type superfamily		45120
234IPR001214
SET domain		45107
235IPR001789
Signal transduction response regulator, receiver domain		45105
236IPR009060
UBA-like superfamily		4470
237IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4461
238IPR001906
Terpene synthase, N-terminal domain		4460
239IPR011043
Galactose oxidase/kelch, beta-propeller		4451
240IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4459
241IPR000743
Glycoside hydrolase, family 28		4452
242IPR001117
Multicopper oxidase, type 1		4347
243IPR004853
Sugar phosphate transporter domain		4385
244IPR011701
Major facilitator superfamily		4381
245IPR004263
Exostosin-like		4350
246IPR011706
Multicopper oxidase, C-terminal		4348
247IPR045087
Multicopper oxidase		4359
248IPR000070
Pectinesterase, catalytic		4350
249IPR008889
VQ		4345
250IPR016040
NAD(P)-binding domain		4269
251IPR043926
ABC transporter family G domain		4272
252IPR033896
MADS MEF2-like		4261
253IPR004265
Dirigent protein		4251
254IPR033905
Secretory peroxidase		4248
255IPR011012
Longin-like domain superfamily		4270
256IPR024752
Myb/SANT-like domain		4245
257IPR011707
Multicopper oxidase, N-termianl		4246
258IPR033389
AUX/IAA domain		4159
259IPR010402
CCT domain		41108
260IPR016461
O-methyltransferase COMT-type		4197
261IPR004839
Aminotransferase, class I/classII		4161
262IPR039417
Papain-like cysteine endopeptidase		4150
263IPR039361
Cyclin		4154
264IPR015947
PUA-like superfamily		4157
265IPR006016
UspA		4047
266IPR000330
SNF2, N-terminal		4068
267IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4060
268IPR036612
K Homology domain, type 1 superfamily		40105
269IPR016166
FAD-binding domain, PCMH-type		4050
270IPR001077
O-methyltransferase domain		4049
271IPR004046
Glutathione S-transferase, C-terminal		4051
272IPR006702
Casparian strip membrane protein domain		4042
273IPR025659
Tubby-like, C-terminal		3950
274IPR029061
Thiamin diphosphate-binding fold		3988
275IPR015655
Protein phosphatase 2C family		3966
276IPR002495
Glycosyl transferase, family 8		3949
277IPR016161
Aldehyde/histidinol dehydrogenase		3953
278IPR000644
CBS domain		39195
279IPR013126
Heat shock protein 70 family		39114
280IPR025322
Protein of unknown function DUF4228, plant		3841
281IPR008991
Translation protein SH3-like domain superfamily		3847
282IPR029021
Protein-tyrosine phosphatase-like		3868
283IPR003137
PA domain		3850
284IPR000795
Translational (tr)-type GTP-binding domain		38281
285IPR040911
Exostosin, GT47 domain		3843
286IPR036041
Ribosome-inactivating protein superfamily		3842
287IPR015590
Aldehyde dehydrogenase domain		3856
288IPR001574
Ribosome-inactivating protein		3874
289IPR008942
ENTH/VHS		3755
290IPR004041
NAF domain		3751
291IPR018451
NAF/FISL domain		3749
292IPR002068
Alpha crystallin/Hsp20 domain		3787
293IPR004883
Lateral organ boundaries, LOB		3779
294IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3750
295IPR028889
Ubiquitin specific protease domain		3747
296IPR002109
Glutaredoxin		3746
297IPR002912
ACT domain		37116
298IPR012967
Plant methyltransferase dimerisation		3737
299IPR001360
Glycoside hydrolase family 1		36388
300IPR022742
Serine aminopeptidase, S33		3645
301IPR043454
NPH3/RPT2-like family		3662
302IPR019378
GDP-fucose protein O-fucosyltransferase		3649
303IPR033443
Pentacotripeptide-repeat region of PRORP		3645
304IPR002067
Mitochondrial carrier protein		36237
305IPR004314
Neprosin		3652
306IPR006073
GTP binding domain		36138
307IPR007493
Protein of unknown function DUF538		3576
308IPR023271
Aquaporin-like		3544
309IPR027356
NPH3 domain		3596
310IPR004367
Cyclin, C-terminal domain		3540
311IPR036758
At5g01610-like superfamily		3540
312IPR000425
Major intrinsic protein		35290
313IPR002487
Transcription factor, K-box		35112
314IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3451
315IPR005299
SAM dependent carboxyl methyltransferase		34106
316IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3438
317IPR006652
Kelch repeat type 1		3488
318IPR023299
P-type ATPase, cytoplasmic domain N		3452
319IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		3452
320IPR025110
AMP-binding enzyme, C-terminal domain		3337
321IPR001251
CRAL-TRIO lipid binding domain		33132
322IPR001296
Glycosyl transferase, family 1		3356
323IPR005135
Endonuclease/exonuclease/phosphatase		3345
324IPR006094
FAD linked oxidase, N-terminal		3342
325IPR043519
Nucleotidyltransferase superfamily		3356
326IPR003855
Potassium transporter		33133
327IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3366
328IPR006311
Twin-arginine translocation pathway, signal sequence		3334
329IPR001929
Germin		32101
330IPR013149
Alcohol dehydrogenase, C-terminal		3239
331IPR026960
Reverse transcriptase zinc-binding domain		3232
332IPR001594
Palmitoyltransferase, DHHC domain		3251
333IPR002423
Chaperonin Cpn60/TCP-1 family		3244
334IPR036865
CRAL-TRIO lipid binding domain superfamily		3244
335IPR013154
Alcohol dehydrogenase, N-terminal		3243
336IPR034294
Aquaporin transporter		3245
337IPR003406
Glycosyl transferase, family 14		3240
338IPR002963
Expansin		32262
339IPR004088
K Homology domain, type 1		3291
340IPR029062
Class I glutamine amidotransferase-like		3255
341IPR037176
Osmotin/thaumatin-like superfamily		3239
342IPR032710
NTF2-like domain superfamily		3138
343IPR038933
Ovate protein family		3132
344IPR001938
Thaumatin family		31218
345IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3140
346IPR027409
GroEL-like apical domain superfamily		3142
347IPR006458
Ovate protein family, C-terminal		3160
348IPR011141
Polyketide synthase, type III		3132
349IPR036812
NADP-dependent oxidoreductase domain superfamily		3153
350IPR015940
Ubiquitin-associated domain		3094
351IPR018490
Cyclic nucleotide-binding-like		3042
352IPR029000
Cyclophilin-like domain superfamily		3046
353IPR000717
Proteasome component (PCI) domain		3069
354IPR035940
CAP superfamily		3038
355IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		3038
356IPR003851
Zinc finger, Dof-type		3068
357IPR001223
Glycoside hydrolase family 18, catalytic domain		3071
358IPR001099
Chalcone/stilbene synthase, N-terminal		3031
359IPR000528
Plant non-specific lipid-transfer protein/Par allergen		29142
360IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		29256
361IPR006153
Cation/H+ exchanger		2939
362IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		29101
363IPR029466
No apical meristem-associated, C-terminal domain		2929
364IPR010920
LSM domain superfamily		2938
365IPR044835
Auxin response factor		2965
366IPR044822
Myb/SANT-like DNA-binding domain 4		2939
367IPR000315
B-box-type zinc finger		2987
368IPR002659
Glycosyl transferase, family 31		2997
369IPR005333
Transcription factor, TCP		2931
370IPR007650
Zf-FLZ domain		2976
371IPR005150
Cellulose synthase		2974
372IPR000863
Sulfotransferase domain		2944
373IPR012328
Chalcone/stilbene synthase, C-terminal		2929
374IPR000595
Cyclic nucleotide-binding domain		29106
375IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2936
376IPR000727
Target SNARE coiled-coil homology domain		2852
377IPR036378
FAS1 domain superfamily		2838
378IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28118
379IPR024709
Putative O-fucosyltransferase, plant		2844
380IPR044848
PHR1-like		2839
381IPR011013
Galactose mutarotase-like domain superfamily		2841
382IPR003690
Transcription termination factor, mitochondrial/chloroplastic		28103
383IPR001283
Cysteine-rich secretory protein-related		28104
384IPR027923
Hydrophobic seed protein domain		2870
385IPR039421
Type 1 protein exporter		2842
386IPR044791
Beta-glucanase/XTH		2844
387IPR023210
NADP-dependent oxidoreductase domain		2856
388IPR002913
START domain		2884
389IPR015797
NUDIX hydrolase-like domain superfamily		2835
390IPR036420
BRCT domain superfamily		2753
391IPR023753
FAD/NAD(P)-binding domain		2738
392IPR019557
Aminotransferase-like, plant mobile domain		2731
393IPR000408
Regulator of chromosome condensation, RCC1		27700
394IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2739
395IPR008480
Protein of unknown function DUF761, plant		2727
396IPR016897
S-phase kinase-associated protein 1		2737
397IPR014044
CAP domain		2733
398IPR002035
von Willebrand factor, type A		2762
399IPR001757
P-type ATPase		27132
400IPR036296
SKP1-like, dimerisation domain superfamily		2737
401IPR003311
AUX/IAA protein		2739
402IPR000757
Glycoside hydrolase family 16		2771
403IPR013601
FAE1/Type III polyketide synthase-like protein		2633
404IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2635
405IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2633
406IPR044778
Sugar transport protein STP/MST-like, plant		2630
407IPR040417
Glycine-rich cell wall structural protein 1/2		2635
408IPR001763
Rhodanese-like domain		2664
409IPR003337
Trehalose-phosphatase		2639
410IPR002123
Phospholipid/glycerol acyltransferase		2630
411IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2633
412IPR004813
Oligopeptide transporter, OPT superfamily		2663
413IPR001701
Glycoside hydrolase family 9		2633
414IPR036034
PDZ superfamily		2634
415IPR000679
Zinc finger, GATA-type		26103
416IPR005175
PPC domain		2683
417IPR000782
FAS1 domain		2560
418IPR008971
HSP40/DnaJ peptide-binding		2564
419IPR004316
SWEET sugar transporter		2545
420IPR001357
BRCT domain		2579
421IPR007657
Glycosyltransferase 61		2572
422IPR027725
Heat shock transcription factor family		2531
423IPR004320
Protein of unknown function DUF241, plant		2533
424IPR003594
Histidine kinase/HSP90-like ATPase		2537
425IPR044675
E3 ubiquitin-protein ligase RING1-like		2528
426IPR036273
CRAL/TRIO, N-terminal domain superfamily		2531
427IPR004014
Cation-transporting P-type ATPase, N-terminal		2536
428IPR029069
HotDog domain superfamily		2556
429IPR002939
Chaperone DnaJ, C-terminal		2535
430IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2537
431IPR010525
Auxin response factor domain		2542
432IPR003100
PAZ domain		2479
433IPR036085
PAZ domain superfamily		2440
434IPR017938
Riboflavin synthase-like beta-barrel		2434
435IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		2426
436IPR001440
Tetratricopeptide repeat 1		2445
437IPR013581
Plant PDR ABC transporter associated		2437
438IPR011053
Single hybrid motif		2431
439IPR020103
Pseudouridine synthase, catalytic domain superfamily		2433
440IPR016072
SKP1 component, dimerisation		2434
441IPR044839
Protein NDR1-like		2426
442IPR005821
Ion transport domain		2430
443IPR001849
Pleckstrin homology domain		2458
444IPR041677
DNA2/NAM7 helicase, helicase domain		2450
445IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2432
446IPR000086
NUDIX hydrolase domain		2459
447IPR000232
Heat shock factor (HSF)-type, DNA-binding		24104
448IPR029033
Histidine phosphatase superfamily		2433
449IPR017927
FAD-binding domain, ferredoxin reductase-type		2332
450IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2338
451IPR002867
IBR domain		2353
452IPR025753
AAA-type ATPase, N-terminal domain		2327
453IPR011016
Zinc finger, RING-CH-type		2386
454IPR001163
LSM domain, eukaryotic/archaea-type		2329
455IPR004161
Translation elongation factor EFTu-like, domain 2		2332
456IPR001353
Proteasome, subunit alpha/beta		2331
457IPR025422
Transcription factor TGA like domain		2361
458IPR006461
PLAC8 motif-containing protein		2351
459IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2325
460IPR041679
DNA2/NAM7 helicase-like, C-terminal		2366
461IPR034285
Laccase, second cupredoxin domain		2326
462IPR004146
DC1		2334
463IPR036427
Bromodomain-like superfamily		2340
464IPR025486
Domain of unknown function DUF4378		2335
465IPR036404
Jacalin-like lectin domain superfamily		2334
466IPR003106
Leucine zipper, homeobox-associated		2223
467IPR022149
Protein of unknown function DUF3681		2242
468IPR000387
Tyrosine specific protein phosphatases domain		2244
469IPR007612
LURP-one-related		2256
470IPR013187
F-box associated domain, type 3		2224
471IPR021790
PTBP1, RNA recognition motif 2-like		2230
472IPR000089
Biotin/lipoyl attachment		2253
473IPR008422
Homeobox KN domain		2227
474IPR001881
EGF-like calcium-binding domain		2231
475IPR017887
Transcription factor TCP subgroup		2244
476IPR036010
2Fe-2S ferredoxin-like superfamily		2227
477IPR027413
GroEL-like equatorial domain superfamily		2231
478IPR010989
SNARE		2225
479IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme		2230
480IPR045048
F-box only protein 31/39		2260
481IPR007592
GLABROUS1 enhancer-binding protein family		2248
482IPR020946
Flavin monooxygenase-like		2239
483IPR036928
Amidase signature (AS) superfamily		2229
484IPR031127
E3 ubiquitin ligase RBR family		2249
485IPR006868
Domain of unknown function DUF630		2224
486IPR002641
Patatin-like phospholipase domain		2244
487IPR044066
TRIAD supradomain		2232
488IPR001487
Bromodomain		22202
489IPR002937
Amine oxidase		2233
490IPR036443
Zinc finger, RanBP2-type superfamily		2260
491IPR001229
Jacalin-like lectin domain		2267
492IPR006689
Small GTPase superfamily, ARF/SAR type		21150
493IPR006593
Cytochrome b561/ferric reductase transmembrane		2140
494IPR035952
Rhomboid-like superfamily		2129
495IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		2125
496IPR036873
Rhodanese-like domain superfamily		2132
497IPR003347
JmjC domain		2143
498IPR036186
Serpin superfamily		2127
499IPR013216
Methyltransferase type 11		2130
500IPR018392
LysM domain		2179
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa132424.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa132424.html new file mode 100644 index 00000000..c1a117af --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa132424.html @@ -0,0 +1,93 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Os132424RS1, Jan 2020
Database version:87.1
Base Pairs:392,847,014
Golden Path Length:392,847,014
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,237
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:42,627
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144395019
237061605
339504282
437684947
530842205
632490609
730315321
829604901
924952073
1025670804
1131753752
1227497477
+
+
scaffold
+
13 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg37282625
UN-Ctg38170691
UN-Ctg39160477
UN-Ctg4075104
UN-Ctg4162237
UN-Ctg4256779
UN-Ctg4354175
UN-Ctg4450804
UN-Ctg4548928
UN-Ctg4640282
UN-Ctg4735429
UN-Ctg4827773
UN-Ctg498715
+
+
chunk3940 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa132424_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa132424_IPtop500.html new file mode 100644 index 00000000..48f5ecf4 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa132424_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14921976
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		13992022
3IPR000719
Protein kinase domain		13873051
4IPR036047
F-box-like domain superfamily		646825
5IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		510843
6IPR044974
Disease resistance protein, plants		506871
7IPR002885
Pentatricopeptide repeat		4976219
8IPR001611
Leucine-rich repeat		4891559
9IPR001810
F-box domain		474876
10IPR002182
NB-ARC		473564
11IPR001841
Zinc finger, RING-type		439880
12IPR016024
Armadillo-type fold		384571
13IPR009057
Homeobox-like domain superfamily		380475
14IPR041118
Rx, N-terminal		378417
15IPR036291
NAD(P)-binding domain superfamily		374542
16IPR029058
Alpha/Beta hydrolase fold		367500
17IPR011990
Tetratricopeptide-like helical domain superfamily		338513
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		331402
19IPR036396
Cytochrome P450 superfamily		316404
20IPR001128
Cytochrome P450		3071495
21IPR035979
RNA-binding domain superfamily		305586
22IPR002401
Cytochrome P450, E-class, group I		2711817
23IPR038005
Virus X resistance protein-like, coiled-coil domain		268295
24IPR000504
RNA recognition motif domain		2681076
25IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		264385
26IPR017853
Glycoside hydrolase superfamily		254372
27IPR036259
MFS transporter superfamily		254409
28IPR001005
SANT/Myb domain		238685
29IPR017930
Myb domain		237684
30IPR036249
Thioredoxin-like superfamily		232341
31IPR036322
WD40-repeat-containing domain superfamily		232338
32IPR038765
Papain-like cysteine peptidase superfamily		231277
33IPR001680
WD40 repeat		2091586
34IPR011992
EF-hand domain pair		188240
35IPR002048
EF-hand domain		175904
36IPR016177
DNA-binding domain superfamily		173238
37IPR036770
Ankyrin repeat-containing domain superfamily		173245
38IPR036412
HAD-like superfamily		172219
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		170406
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		164191
41IPR011333
SKP1/BTB/POZ domain superfamily		159238
42IPR001471
AP2/ERF domain		157849
43IPR002110
Ankyrin repeat		156648
44IPR036390
Winged helix DNA-binding domain superfamily		155201
45IPR012337
Ribonuclease H-like superfamily		154182
46IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		154327
47IPR036093
NAC domain superfamily		150171
48IPR003441
NAC domain		147328
49IPR029044
Nucleotide-diphospho-sugar transferases		143170
50IPR010255
Haem peroxidase superfamily		142183
51IPR001650
Helicase, C-terminal		140397
52IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		139182
53IPR005174
Domain unknown function DUF295		137164
54IPR014001
Helicase superfamily 1/2, ATP-binding domain		137198
55IPR013087
Zinc finger C2H2-type		136255
56IPR036236
Zinc finger C2H2 superfamily		136195
57IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		135161
58IPR012340
Nucleic acid-binding, OB-fold		135269
59IPR036188
FAD/NAD(P)-binding domain superfamily		134216
60IPR002016
Haem peroxidase		134614
61IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		131177
62IPR020683
Ankyrin repeat-containing domain		129289
63IPR003439
ABC transporter-like, ATP-binding domain		125454
64IPR007658
Protein of unknown function DUF594		120124
65IPR003480
Transferase		120144
66IPR000210
BTB/POZ domain		119367
67IPR025315
Domain of unknown function DUF4220		119129
68IPR021109
Aspartic peptidase domain superfamily		116148
69IPR011676
Domain of unknown function DUF1618		115150
70IPR036426
Bulb-type lectin domain superfamily		115156
71IPR003959
ATPase, AAA-type, core		113170
72IPR036869
Chaperone J-domain superfamily		112142
73IPR001480
Bulb-type lectin domain		111388
74IPR020846
Major facilitator superfamily domain		108152
75IPR011011
Zinc finger, FYVE/PHD-type		107142
76IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		107121
77IPR001623
DnaJ domain		106672
78IPR015424
Pyridoxal phosphate-dependent transferase		106137
79IPR001087
GDSL lipase/esterase		105136
80IPR019734
Tetratricopeptide repeat		104295
81IPR008972
Cupredoxin		104214
82IPR003657
WRKY domain		103259
83IPR029071
Ubiquitin-like domain superfamily		102151
84IPR033121
Peptidase family A1 domain		102143
85IPR036576
WRKY domain superfamily		101131
86IPR035892
C2 domain superfamily		100183
87IPR032799
Xylanase inhibitor, C-terminal		99123
88IPR032861
Xylanase inhibitor, N-terminal		99123
89IPR036457
PPM-type phosphatase domain superfamily		96133
90IPR044810
WRKY transcription factor, plant		96123
91IPR005123
Oxoglutarate/iron-dependent dioxygenase		95119
92IPR011050
Pectin lyase fold/virulence factor		95111
93IPR011051
RmlC-like cupin domain superfamily		94121
94IPR001932
PPM-type phosphatase domain		94374
95IPR015300
DNA-binding pseudobarrel domain superfamily		92151
96IPR000858
S-locus glycoprotein domain		91120
97IPR001356
Homeobox domain		91282
98IPR009072
Histone-fold		91100
99IPR045005
BTB/POZ and MATH domain-containing protein 1-6		90168
100IPR011545
DEAD/DEAH box helicase domain		90131
101IPR002347
Short-chain dehydrogenase/reductase SDR		89799
102IPR003609
PAN/Apple domain		89215
103IPR000008
C2 domain		88380
104IPR005828
Major facilitator, sugar transporter-like		88133
105IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		88109
106IPR000823
Plant peroxidase		88356
107IPR000073
Alpha/beta hydrolase fold-1		85231
108IPR000109
Proton-dependent oligopeptide transporter family		84300
109IPR003340
B3 DNA binding domain		83393
110IPR020472
G-protein beta WD-40 repeat		83351
111IPR002083
MATH/TRAF domain		83298
112IPR001461
Aspartic peptidase A1 family		83280
113IPR035669
GDSL lipase/esterase-like, plant		8299
114IPR004827
Basic-leucine zipper domain		82191
115IPR013766
Thioredoxin domain		81188
116IPR036875
Zinc finger, CCHC-type superfamily		8090
117IPR026992
Non-haem dioxygenase N-terminal domain		7898
118IPR043129
ATPase, nucleotide binding domain		78189
119IPR001878
Zinc finger, CCHC-type		78149
120IPR012871
Protein of unknown function DUF1677, Oryza sativa		7795
121IPR026961
PGG domain		77168
122IPR004158
Protein of unknown function DUF247, plant		76172
123IPR036282
Glutathione S-transferase, C-terminal domain superfamily		76108
124IPR031052
FHY3/FAR1 family		75140
125IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7276
126IPR003613
U box domain		72160
127IPR036163
Heavy metal-associated domain superfamily		7198
128IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		71123
129IPR016039
Thiolase-like		70150
130IPR003653
Ulp1 protease family, C-terminal catalytic domain		70133
131IPR002902
Gnk2-homologous domain		70377
132IPR000270
PB1 domain		70110
133IPR006121
Heavy metal-associated domain, HMA		69224
134IPR002100
Transcription factor, MADS-box		69394
135IPR001220
Legume lectin domain		69173
136IPR036879
Transcription factor, MADS-box superfamily		6987
137IPR008949
Isoprenoid synthase domain superfamily		6882
138IPR016159
Cullin repeat-like-containing domain superfamily		6879
139IPR007527
Zinc finger, SWIM-type		68112
140IPR004330
FAR1 DNA binding domain		6875
141IPR004045
Glutathione S-transferase, N-terminal		66190
142IPR013057
Amino acid transporter, transmembrane domain		6588
143IPR044965
Glycoside hydrolase family 17, plant		6595
144IPR000626
Ubiquitin-like domain		64151
145IPR036908
RlpA-like domain superfamily		6479
146IPR000048
IQ motif, EF-hand binding site		64302
147IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6367
148IPR006501
Pectinesterase inhibitor domain		6366
149IPR000571
Zinc finger, CCCH-type		63279
150IPR019787
Zinc finger, PHD-finger		62129
151IPR018108
Mitochondrial substrate/solute carrier		62467
152IPR020568
Ribosomal protein S5 domain 2-type fold		62101
153IPR023395
Mitochondrial carrier domain superfamily		6282
154IPR010987
Glutathione S-transferase, C-terminal-like		6292
155IPR029052
Metallo-dependent phosphatase-like		6284
156IPR001806
Small GTPase		62134
157IPR005202
Transcription factor GRAS		61221
158IPR009003
Peptidase S1, PA clan		6189
159IPR036915
Cyclin-like superfamily		61137
160IPR003663
Sugar/inositol transporter		61332
161IPR022059
Protein of unknown function DUF3615		6074
162IPR000490
Glycoside hydrolase family 17		6079
163IPR024788
Malectin-like domain		6074
164IPR041469
Subtilisin-like protease, fibronectin type-III domain		5970
165IPR036749
Expansin, cellulose-binding-like domain superfamily		5974
166IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5974
167IPR036852
Peptidase S8/S53 domain superfamily		5977
168IPR007117
Expansin, cellulose-binding-like domain		59145
169IPR000209
Peptidase S8/S53 domain		5976
170IPR011032
GroES-like superfamily		5884
171IPR045051
Subtilisin-like protease		5889
172IPR003245
Phytocyanin domain		58124
173IPR026057
PC-Esterase		5776
174IPR039391
Phytocyanin		5768
175IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5665
176IPR006045
Cupin 1		5697
177IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5577
178IPR029962
Trichome birefringence-like family		5580
179IPR001752
Kinesin motor domain		55374
180IPR036465
von Willebrand factor A-like domain superfamily		5466
181IPR015915
Kelch-type beta propeller		5479
182IPR015500
Peptidase S8, subtilisin-related		54174
183IPR002921
Fungal lipase-like domain		5362
184IPR001563
Peptidase S10, serine carboxypeptidase		53396
185IPR002156
Ribonuclease H domain		5370
186IPR025846
PMR5 N-terminal domain		5368
187IPR000225
Armadillo		53226
188IPR013525
ABC-2 type transporter		5293
189IPR013763
Cyclin-like		52104
190IPR007112
Expansin/pollen allergen, DPBB domain		5264
191IPR002528
Multi antimicrobial extrusion protein		51122
192IPR016181
Acyl-CoA N-acyltransferase		5058
193IPR000608
Ubiquitin-conjugating enzyme E2		50172
194IPR008250
P-type ATPase, A domain superfamily		5061
195IPR009009
RlpA-like protein, double-psi beta-barrel domain		5060
196IPR034197
Cucumisin-like catalytic domain		5059
197IPR006566
FBD domain		5057
198IPR023298
P-type ATPase, transmembrane domain superfamily		5063
199IPR017884
SANT domain		4959
200IPR008978
HSP20-like chaperone		4962
201IPR005630
Terpene synthase, metal-binding domain		4964
202IPR004140
Exocyst complex component Exo70		49120
203IPR008979
Galactose-binding-like domain superfamily		4987
204IPR034161
Pepsin-like domain, plant		4860
205IPR003676
Small auxin-up RNA		4858
206IPR044808
Ethylene-responsive transcription factor		4855
207IPR007118
Expansin/Lol pI		47280
208IPR013201
Cathepsin propeptide inhibitor domain (I29)		4751
209IPR014014
RNA helicase, DEAD-box type, Q motif		4767
210IPR001906
Terpene synthase, N-terminal domain		4762
211IPR041569
AAA ATPase, AAA+ lid domain		4763
212IPR013094
Alpha/beta hydrolase fold-3		4770
213IPR008928
Six-hairpin glycosidase superfamily		4656
214IPR007125
Histone H2A/H2B/H3		4646
215IPR036318
FAD-binding, type PCMH-like superfamily		4556
216IPR036640
ABC transporter type 1, transmembrane domain superfamily		4597
217IPR011701
Major facilitator superfamily		4591
218IPR029055
Nucleophile aminohydrolases, N-terminal		4560
219IPR012946
X8 domain		4559
220IPR000742
EGF-like domain		4548
221IPR011527
ABC transporter type 1, transmembrane domain		45194
222IPR000620
EamA domain		4593
223IPR036855
Zinc finger, CCCH-type superfamily		45111
224IPR009060
UBA-like superfamily		4467
225IPR000873
AMP-dependent synthetase/ligase		4463
226IPR001509
NAD-dependent epimerase/dehydratase		4459
227IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4459
228IPR004265
Dirigent protein		4452
229IPR011006
CheY-like superfamily		4460
230IPR006671
Cyclin, N-terminal		4458
231IPR032867
DYW domain		4445
232IPR030184
WAT1-related protein		4475
233IPR014756
Immunoglobulin E-set		4458
234IPR011043
Galactose oxidase/kelch, beta-propeller		4451
235IPR001214
SET domain		4498
236IPR000182
GNAT domain		4386
237IPR033896
MADS MEF2-like		4358
238IPR004853
Sugar phosphate transporter domain		4373
239IPR009000
Translation protein, beta-barrel domain superfamily		4355
240IPR004263
Exostosin-like		4351
241IPR045087
Multicopper oxidase		4360
242IPR001117
Multicopper oxidase, type 1		4249
243IPR033905
Secretory peroxidase		4248
244IPR000070
Pectinesterase, catalytic		4253
245IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4250
246IPR008889
VQ		4243
247IPR011707
Multicopper oxidase, N-termianl		4248
248IPR033389
AUX/IAA domain		4149
249IPR016040
NAD(P)-binding domain		4166
250IPR043926
ABC transporter family G domain		4166
251IPR000330
SNF2, N-terminal		4168
252IPR011012
Longin-like domain superfamily		4160
253IPR000743
Glycoside hydrolase, family 28		4150
254IPR015947
PUA-like superfamily		4157
255IPR001789
Signal transduction response regulator, receiver domain		4194
256IPR010402
CCT domain		40103
257IPR006016
UspA		4047
258IPR029045
ClpP/crotonase-like domain superfamily		4057
259IPR011706
Multicopper oxidase, C-terminal		4048
260IPR000644
CBS domain		40157
261IPR013126
Heat shock protein 70 family		40115
262IPR044730
Ribonuclease H-like domain, plant type		4042
263IPR016461
O-methyltransferase COMT-type		3989
264IPR036612
K Homology domain, type 1 superfamily		39111
265IPR000668
Peptidase C1A, papain C-terminal		39153
266IPR002495
Glycosyl transferase, family 8		3945
267IPR007811
DNA-directed RNA polymerase III subunit RPC4		3993
268IPR008942
ENTH/VHS		3844
269IPR002068
Alpha crystallin/Hsp20 domain		3892
270IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3851
271IPR003137
PA domain		3850
272IPR016166
FAD-binding domain, PCMH-type		3849
273IPR001077
O-methyltransferase domain		3850
274IPR015655
Protein phosphatase 2C family		3862
275IPR040911
Exostosin, GT47 domain		3842
276IPR039361
Cyclin		3850
277IPR006702
Casparian strip membrane protein domain		3840
278IPR025322
Protein of unknown function DUF4228, plant		3740
279IPR023271
Aquaporin-like		3748
280IPR004839
Aminotransferase, class I/classII		3753
281IPR000425
Major intrinsic protein		37310
282IPR004046
Glutathione S-transferase, C-terminal		3748
283IPR002067
Mitochondrial carrier protein		37228
284IPR002109
Glutaredoxin		3747
285IPR037176
Osmotin/thaumatin-like superfamily		3745
286IPR025659
Tubby-like, C-terminal		3652
287IPR013149
Alcohol dehydrogenase, C-terminal		3644
288IPR029021
Protein-tyrosine phosphatase-like		3651
289IPR013154
Alcohol dehydrogenase, N-terminal		3645
290IPR004883
Lateral organ boundaries, LOB		3677
291IPR019378
GDP-fucose protein O-fucosyltransferase		3651
292IPR039417
Papain-like cysteine endopeptidase		3643
293IPR024752
Myb/SANT-like domain		3637
294IPR004041
NAF domain		3542
295IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3555
296IPR018451
NAF/FISL domain		3542
297IPR033443
Pentacotripeptide-repeat region of PRORP		3542
298IPR043519
Nucleotidyltransferase superfamily		3555
299IPR007493
Protein of unknown function DUF538		3480
300IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3438
301IPR001938
Thaumatin family		34242
302IPR034294
Aquaporin transporter		3452
303IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3452
304IPR036758
At5g01610-like superfamily		3441
305IPR028889
Ubiquitin specific protease domain		3447
306IPR002912
ACT domain		3498
307IPR002487
Transcription factor, K-box		34102
308IPR001360
Glycoside hydrolase family 1		33327
309IPR038933
Ovate protein family		3334
310IPR000795
Translational (tr)-type GTP-binding domain		33240
311IPR004367
Cyclin, C-terminal domain		3337
312IPR022742
Serine aminopeptidase, S33		3340
313IPR006652
Kelch repeat type 1		3385
314IPR043454
NPH3/RPT2-like family		3358
315IPR006094
FAD linked oxidase, N-terminal		3342
316IPR006458
Ovate protein family, C-terminal		3364
317IPR004314
Neprosin		3354
318IPR001251
CRAL-TRIO lipid binding domain		32119
319IPR005299
SAM dependent carboxyl methyltransferase		3293
320IPR008991
Translation protein SH3-like domain superfamily		3242
321IPR044822
Myb/SANT-like DNA-binding domain 4		3240
322IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3239
323IPR036865
CRAL-TRIO lipid binding domain superfamily		3244
324IPR004088
K Homology domain, type 1		3296
325IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3259
326IPR011141
Polyketide synthase, type III		3242
327IPR018490
Cyclic nucleotide-binding-like		3138
328IPR001929
Germin		31106
329IPR032710
NTF2-like domain superfamily		3135
330IPR029061
Thiamin diphosphate-binding fold		3176
331IPR001296
Glycosyl transferase, family 1		3157
332IPR000863
Sulfotransferase domain		3143
333IPR006073
GTP binding domain		31106
334IPR001099
Chalcone/stilbene synthase, N-terminal		3137
335IPR000528
Plant non-specific lipid-transfer protein/Par allergen		30134
336IPR000315
B-box-type zinc finger		3085
337IPR000717
Proteasome component (PCI) domain		3074
338IPR005135
Endonuclease/exonuclease/phosphatase		3039
339IPR002423
Chaperonin Cpn60/TCP-1 family		3048
340IPR011013
Galactose mutarotase-like domain superfamily		3043
341IPR003406
Glycosyl transferase, family 14		3036
342IPR027409
GroEL-like apical domain superfamily		3039
343IPR023299
P-type ATPase, cytoplasmic domain N		3037
344IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		3040
345IPR003851
Zinc finger, Dof-type		3062
346IPR001223
Glycoside hydrolase family 18, catalytic domain		3075
347IPR003855
Potassium transporter		30118
348IPR012967
Plant methyltransferase dimerisation		3030
349IPR015940
Ubiquitin-associated domain		2983
350IPR029000
Cyclophilin-like domain superfamily		2939
351IPR001594
Palmitoyltransferase, DHHC domain		2944
352IPR005333
Transcription factor, TCP		2931
353IPR027356
NPH3 domain		2987
354IPR005150
Cellulose synthase		2961
355IPR008480
Protein of unknown function DUF761, plant		2930
356IPR002035
von Willebrand factor, type A		2963
357IPR000595
Cyclic nucleotide-binding domain		2988
358IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2936
359IPR006311
Twin-arginine translocation pathway, signal sequence		2931
360IPR000727
Target SNARE coiled-coil homology domain		2848
361IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28213
362IPR006153
Cation/H+ exchanger		2834
363IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28100
364IPR024709
Putative O-fucosyltransferase, plant		2841
365IPR029466
No apical meristem-associated, C-terminal domain		2828
366IPR010920
LSM domain superfamily		2835
367IPR044835
Auxin response factor		2854
368IPR044848
PHR1-like		2840
369IPR035940
CAP superfamily		2839
370IPR003337
Trehalose-phosphatase		2837
371IPR003690
Transcription termination factor, mitochondrial/chloroplastic		2896
372IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2835
373IPR002963
Expansin		28244
374IPR016897
S-phase kinase-associated protein 1		2833
375IPR012328
Chalcone/stilbene synthase, C-terminal		2831
376IPR036296
SKP1-like, dimerisation domain superfamily		2832
377IPR036041
Ribosome-inactivating protein superfamily		2831
378IPR025110
AMP-binding enzyme, C-terminal domain		2732
379IPR036378
FAS1 domain superfamily		2740
380IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2798
381IPR002659
Glycosyl transferase, family 31		2788
382IPR009030
Growth factor receptor cysteine-rich domain superfamily		2731
383IPR001763
Rhodanese-like domain		2756
384IPR045048
F-box only protein 31/39		2755
385IPR016072
SKP1 component, dimerisation		2730
386IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2731
387IPR001283
Cysteine-rich secretory protein-related		27105
388IPR027923
Hydrophobic seed protein domain		2771
389IPR004813
Oligopeptide transporter, OPT superfamily		2764
390IPR001757
P-type ATPase		27120
391IPR001701
Glycoside hydrolase family 9		2732
392IPR044791
Beta-glucanase/XTH		2738
393IPR003311
AUX/IAA protein		2738
394IPR000679
Zinc finger, GATA-type		27107
395IPR000757
Glycoside hydrolase family 16		2766
396IPR015797
NUDIX hydrolase-like domain superfamily		2733
397IPR036085
PAZ domain superfamily		2636
398IPR013601
FAE1/Type III polyketide synthase-like protein		2631
399IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2633
400IPR040417
Glycine-rich cell wall structural protein 1/2		2634
401IPR027725
Heat shock transcription factor family		2630
402IPR007650
Zf-FLZ domain		2670
403IPR000408
Regulator of chromosome condensation, RCC1		26645
404IPR002123
Phospholipid/glycerol acyltransferase		2628
405IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2640
406IPR005821
Ion transport domain		2632
407IPR014044
CAP domain		2632
408IPR029062
Class I glutamine amidotransferase-like		2645
409IPR000232
Heat shock factor (HSF)-type, DNA-binding		26102
410IPR002913
START domain		2672
411IPR001574
Ribosome-inactivating protein		2655
412IPR003100
PAZ domain		2568
413IPR044778
Sugar transport protein STP/MST-like, plant		2528
414IPR036186
Serpin superfamily		2530
415IPR036420
BRCT domain superfamily		2542
416IPR004320
Protein of unknown function DUF241, plant		2534
417IPR036273
CRAL/TRIO, N-terminal domain superfamily		2531
418IPR004014
Cation-transporting P-type ATPase, N-terminal		2530
419IPR036404
Jacalin-like lectin domain superfamily		2539
420IPR036034
PDZ superfamily		2527
421IPR005175
PPC domain		2578
422IPR017938
Riboflavin synthase-like beta-barrel		2433
423IPR000782
FAS1 domain		2462
424IPR004316
SWEET sugar transporter		2442
425IPR001357
BRCT domain		2466
426IPR008422
Homeobox KN domain		2430
427IPR023753
FAD/NAD(P)-binding domain		2433
428IPR003594
Histidine kinase/HSP90-like ATPase		2434
429IPR044839
Protein NDR1-like		2425
430IPR029069
HotDog domain superfamily		2449
431IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2430
432IPR000086
NUDIX hydrolase domain		2458
433IPR029033
Histidine phosphatase superfamily		2428
434IPR036812
NADP-dependent oxidoreductase domain superfamily		2444
435IPR023796
Serpin domain		2432
436IPR010525
Auxin response factor domain		2435
437IPR017927
FAD-binding domain, ferredoxin reductase-type		2332
438IPR008971
HSP40/DnaJ peptide-binding		2354
439IPR003106
Leucine zipper, homeobox-associated		2324
440IPR013187
F-box associated domain, type 3		2326
441IPR008999
Actin-crosslinking		2327
442IPR021790
PTBP1, RNA recognition motif 2-like		2331
443IPR011016
Zinc finger, RING-CH-type		2366
444IPR001163
LSM domain, eukaryotic/archaea-type		2327
445IPR007657
Glycosyltransferase 61		2365
446IPR017887
Transcription factor TCP subgroup		2346
447IPR000215
Serpin family		2331
448IPR020103
Pseudouridine synthase, catalytic domain superfamily		2326
449IPR034285
Laccase, second cupredoxin domain		2327
450IPR001849
Pleckstrin homology domain		2349
451IPR039421
Type 1 protein exporter		2343
452IPR041677
DNA2/NAM7 helicase, helicase domain		2345
453IPR002939
Chaperone DnaJ, C-terminal		2330
454IPR025486
Domain of unknown function DUF4378		2336
455IPR002937
Amine oxidase		2332
456IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2333
457IPR036443
Zinc finger, RanBP2-type superfamily		2363
458IPR001229
Jacalin-like lectin domain		2373
459IPR006689
Small GTPase superfamily, ARF/SAR type		22116
460IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2235
461IPR000387
Tyrosine specific protein phosphatases domain		2232
462IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2224
463IPR013581
Plant PDR ABC transporter associated		2227
464IPR019557
Aminotransferase-like, plant mobile domain		2225
465IPR001881
EGF-like calcium-binding domain		2226
466IPR036010
2Fe-2S ferredoxin-like superfamily		2226
467IPR001353
Proteasome, subunit alpha/beta		2229
468IPR011257
DNA glycosylase		2227
469IPR010989
SNARE		2224
470IPR044675
E3 ubiquitin-protein ligase RING1-like		2227
471IPR011053
Single hybrid motif		2228
472IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2225
473IPR004776
Membrane transport protein		2239
474IPR016161
Aldehyde/histidinol dehydrogenase		2232
475IPR036427
Bromodomain-like superfamily		2236
476IPR006868
Domain of unknown function DUF630		2224
477IPR023210
NADP-dependent oxidoreductase domain		2247
478IPR016073
SKP1 component, POZ domain		2124
479IPR002867
IBR domain		2151
480IPR025753
AAA-type ATPase, N-terminal domain		2126
481IPR000089
Biotin/lipoyl attachment		2148
482IPR014977
WRC domain		2148
483IPR044824
Protein MAINTENANCE OF MERISTEMS-like		2127
484IPR027413
GroEL-like equatorial domain superfamily		2132
485IPR025422
Transcription factor TGA like domain		2153
486IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2129
487IPR021720
Malectin domain		2138
488IPR001025
Bromo adjacent homology (BAH) domain		2153
489IPR013078
Histidine phosphatase superfamily, clade-1		2148
490IPR041679
DNA2/NAM7 helicase-like, C-terminal		2165
491IPR001876
Zinc finger, RanBP2-type		21103
492IPR011004
Trimeric LpxA-like superfamily		2130
493IPR017923
Transcription factor IIS, N-terminal		2143
494IPR003388
Reticulon		2152
495IPR010399
Tify domain		2153
496IPR001487
Bromodomain		21167
497IPR013809
ENTH domain		2129
498IPR035441
TFIIS/LEDGF domain superfamily		2122
499IPR006867
Domain of unknown function DUF632		2127
500IPR004274
FCP1 homology domain		2156
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativa_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativa_IPtop500.html index e69a9728..4ef856b2 100644 --- a/gramene/htdocs/ssi/species/stats_Oryza_sativa_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativa_IPtop500.html @@ -17,3501 +17,3501 @@ 1 IPR011009
Protein kinase-like domain superfamily - 1337 - 1724 + 1352 + 1653 2 - IPR000719
  - 1258 - 11232 + IPR000719
Protein kinase domain + 1270 + 2616 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1227 - 1847 + 1239 + 1666 4 - IPR008271
Serine/threonine-protein kinase, active site - 1001 - 1174 + IPR036047
F-box-like domain superfamily + 510 + 576 5 - IPR032675
  - 995 - 4274 + IPR002885
Pentatricopeptide repeat + 462 + 6008 6 - IPR017441
Protein kinase, ATP binding site - 891 - 1049 + IPR001611
Leucine-rich repeat + 424 + 1286 7 - IPR011990
  - 682 - 8445 + IPR044974
Disease resistance protein, plants + 420 + 536 8 - IPR013083
  - 636 - 1588 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 415 + 684 9 - IPR036047
F-box-like domain superfamily - 507 - 581 + IPR001841
Zinc finger, RING-type + 409 + 765 10 - IPR002885
  - 462 - 22880 + IPR036291
NAD(P)-binding domain superfamily + 399 + 535 11 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 422 - 693 + IPR001810
F-box domain + 372 + 624 12 - IPR001611
  - 415 - 7257 + IPR029058
Alpha/Beta hydrolase fold + 370 + 445 13 - IPR001841
  - 404 - 2284 + IPR036396
Cytochrome P450 superfamily + 344 + 386 14 - IPR036291
NAD(P)-binding domain superfamily - 399 - 574 + IPR001128
Cytochrome P450 + 339 + 1424 15 - IPR001810
  - 379 - 2427 + IPR016024
Armadillo-type fold + 336 + 482 16 - IPR029058
  - 371 - 1848 + IPR009057
Homeobox-like domain superfamily + 335 + 435 17 - IPR036396
  - 343 - 2313 + IPR002182
NB-ARC + 328 + 376 18 - IPR001128
Cytochrome P450 - 338 - 1386 + IPR011990
Tetratricopeptide-like helical domain superfamily + 315 + 445 19 - IPR002182
NB-ARC - 336 - 386 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 282 + 315 20 - IPR016024
Armadillo-type fold - 330 - 747 + IPR002401
Cytochrome P450, E-class, group I + 277 + 1864 21 - IPR009057
Homeobox-like domain superfamily - 329 - 412 + IPR036259
MFS transporter superfamily + 276 + 363 22 - IPR036259
MFS transporter superfamily - 276 - 530 + IPR041118
Rx, N-terminal + 266 + 290 23 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 273 - 304 + IPR035979
RNA-binding domain superfamily + 266 + 489 24 - IPR002401
Cytochrome P450, E-class, group I - 272 - 1810 + IPR017853
Glycoside hydrolase superfamily + 258 + 339 25 - IPR035979
RNA-binding domain superfamily - 265 - 516 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 250 + 330 26 - IPR012677
  - 262 - 1078 + IPR000504
RNA recognition motif domain + 244 + 967 27 - IPR003591
Leucine-rich repeat, typical subtype - 258 - 1959 + IPR001005
SANT/Myb domain + 239 + 1253 28 - IPR017853
Glycoside hydrolase superfamily - 257 - 360 + IPR036249
Thioredoxin-like superfamily + 231 + 314 29 - IPR017972
Cytochrome P450, conserved site - 251 - 266 + IPR017930
Myb domain + 209 + 330 30 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 249 - 385 + IPR036322
WD40-repeat-containing domain superfamily + 208 + 270 31 - IPR000504
  - 243 - 4317 + IPR001680
WD40 repeat + 192 + 1290 32 - IPR003593
AAA+ ATPase domain - 237 - 348 + IPR011992
EF-hand domain pair + 184 + 223 33 - IPR011989
  - 231 - 754 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 170 + 185 34 - IPR036249
Thioredoxin-like superfamily - 230 - 319 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 169 + 380 35 - IPR001005
SANT/Myb domain - 225 - 861 + IPR002048
EF-hand domain + 168 + 843 36 - IPR015943
  - 224 - 1200 + IPR012337
Ribonuclease H-like superfamily + 157 + 187 37 - IPR001680
  - 207 - 7752 + IPR036412
HAD-like superfamily + 157 + 200 38 - IPR036322
WD40-repeat-containing domain superfamily - 206 - 372 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 154 + 177 39 - IPR017986
  - 189 - 777 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 153 + 162 40 - IPR020846
  - 188 - 748 + IPR016177
DNA-binding domain superfamily + 152 + 213 41 - IPR011992
EF-hand domain pair - 184 - 233 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 149 + 309 42 - IPR017930
  - 173 - 584 + IPR010255
Haem peroxidase superfamily + 146 + 175 43 - IPR002048
  - 168 - 4083 + IPR002016
Haem peroxidase + 144 + 1053 44 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 168 - 183 + IPR036770
Ankyrin repeat-containing domain superfamily + 144 + 184 45 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 166 - 189 + IPR036188
FAD/NAD(P)-binding domain superfamily + 143 + 218 46 - IPR036388
  - 159 - 410 + IPR036390
Winged helix DNA-binding domain superfamily + 143 + 178 47 - IPR012337
Ribonuclease H-like superfamily - 157 - 198 + IPR038765
Papain-like cysteine peptidase superfamily + 143 + 173 48 - IPR036412
HAD-like superfamily - 155 - 258 + IPR002110
Ankyrin repeat + 139 + 875 49 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 153 - 162 + IPR001471
AP2/ERF domain + 138 + 818 50 - IPR036638
  - 152 - 948 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 135 + 155 51 - IPR029044
  - 148 - 808 + IPR011333
SKP1/BTB/POZ domain superfamily + 135 + 149 52 - IPR018247
EF-Hand 1, calcium-binding site - 148 - 398 + IPR036236
Zinc finger C2H2 superfamily + 132 + 189 53 - IPR011598
  - 148 - 1662 + IPR029044
Nucleotide-diphospho-sugar transferases + 131 + 169 54 - IPR010255
Haem peroxidase - 146 - 176 + IPR001650
Helicase, C-terminal + 131 + 320 55 - IPR036770
  - 146 - 892 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 129 + 159 56 - IPR016177
DNA-binding domain superfamily - 144 - 198 + IPR000823
Plant peroxidase + 128 + 1182 57 - IPR013087
  - 144 - 2067 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 125 + 136 58 - IPR036188
  - 144 - 1274 + IPR012340
Nucleic acid-binding, OB-fold + 124 + 193 59 - IPR020683
  - 144 - 1248 + IPR003439
ABC transporter-like, ATP-binding domain + 122 + 377 60 - IPR002016
  - 144 - 3165 + IPR013087
Zinc finger C2H2-type + 118 + 221 61 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 143 - 218 + IPR020846
Major facilitator superfamily domain + 118 + 145 62 - IPR023214
  - 142 - 548 + IPR001087
GDSL lipase/esterase + 117 + 136 63 - IPR036390
Winged helix DNA-binding domain superfamily - 142 - 177 + IPR036426
Bulb-type lectin domain superfamily + 117 + 129 64 - IPR038765
Papain-like cysteine peptidase superfamily - 141 - 185 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 115 + 122 65 - IPR002110
  - 138 - 3543 + IPR001480
Bulb-type lectin domain + 114 + 332 66 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 135 - 180 + IPR021109
Aspartic peptidase domain superfamily + 113 + 135 67 - IPR014001
  - 134 - 604 + IPR033905
Secretory peroxidase + 113 + 131 68 - IPR035595
UDP-glycosyltransferase family, conserved site - 133 - 153 + IPR008972
Cupredoxin + 111 + 209 69 - IPR011333
SKP1/BTB/POZ domain superfamily - 133 - 157 + IPR003959
ATPase, AAA-type, core + 108 + 160 70 - IPR036955
  - 131 - 507 + IPR003480
Transferase + 107 + 121 71 - IPR001471
  - 130 - 2760 + IPR003441
NAC domain + 104 + 235 72 - IPR001650
  - 129 - 1248 + IPR015424
Pyridoxal phosphate-dependent transferase + 104 + 132 73 - IPR000823
Plant peroxidase - 128 - 1182 + IPR000858
S-locus glycoprotein domain + 103 + 109 74 - IPR036236
Zinc finger C2H2 superfamily - 128 - 231 + IPR036093
NAC domain superfamily + 103 + 118 75 - IPR023213
  - 127 - 478 + IPR002347
Short-chain dehydrogenase/reductase SDR + 102 + 841 76 - IPR013026
  - 125 - 543 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 102 + 115 77 - IPR012340
Nucleic acid-binding, OB-fold - 123 - 194 + IPR000210
BTB/POZ domain + 102 + 224 78 - IPR036514
  - 123 - 286 + IPR036869
Chaperone J-domain superfamily + 102 + 128 79 - IPR014710
  - 122 - 322 + IPR019734
Tetratricopeptide repeat + 101 + 240 80 - IPR019775
WD40 repeat, conserved site - 122 - 250 + IPR000109
Proton-dependent oligopeptide transporter family + 101 + 245 81 - IPR003439
  - 121 - 1077 + IPR011051
RmlC-like cupin domain superfamily + 101 + 109 82 - IPR019793
Peroxidases heam-ligand binding site - 118 - 138 + IPR033121
Peptidase family A1 domain + 99 + 131 83 - IPR019734
  - 117 - 2775 + IPR011050
Pectin lyase fold/virulence factor + 97 + 107 84 - IPR014729
  - 117 - 332 + IPR003609
PAN/Apple domain + 96 + 183 85 - IPR021109
  - 114 - 786 + IPR001623
DnaJ domain + 96 + 628 86 - IPR033905
Secretory peroxidase - 113 - 131 + IPR015300
DNA-binding pseudobarrel domain superfamily + 96 + 132 87 - IPR036426
  - 113 - 612 + IPR029071
Ubiquitin-like domain superfamily + 95 + 146 88 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 112 - 126 + IPR035892
C2 domain superfamily + 94 + 166 89 - IPR008972
  - 112 - 872 + IPR032861
Xylanase inhibitor, N-terminal + 94 + 105 90 - IPR001480
  - 111 - 690 + IPR032799
Xylanase inhibitor, C-terminal + 93 + 104 91 - IPR005123
  - 108 - 690 + IPR011011
Zinc finger, FYVE/PHD-type + 93 + 127 92 - IPR003480
Transferase - 107 - 120 + IPR005828
Major facilitator, sugar transporter-like + 92 + 126 93 - IPR027443
  - 106 - 252 + IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain + 92 + 106 94 - IPR019794
Peroxidase, active site - 106 - 115 + IPR036457
PPM-type phosphatase domain superfamily + 91 + 124 95 - IPR001461
Aspartic peptidase A1 family - 106 - 308 + IPR009072
Histone-fold + 91 + 96 96 - IPR003959
ATPase, AAA-type, core - 106 - 156 + IPR035669
GDSL lipase/esterase-like, plant + 90 + 100 97 - IPR000210
  - 104 - 948 + IPR003340
B3 DNA binding domain + 88 + 344 98 - IPR015424
Pyridoxal phosphate-dependent transferase - 104 - 138 + IPR003657
WRKY domain + 88 + 221 99 - IPR036869
  - 104 - 504 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 88 + 104 100 - IPR013785
  - 103 - 441 + IPR044810
WRKY transcription factor, plant + 88 + 104 101 - IPR003441
  - 103 - 675 + IPR001932
PPM-type phosphatase domain + 88 + 347 102 - IPR015421
  - 103 - 378 + IPR036576
WRKY domain superfamily + 86 + 110 103 - IPR036093
  - 103 - 687 + IPR000073
Alpha/beta hydrolase fold-1 + 86 + 202 104 - IPR002347
Short-chain dehydrogenase/reductase SDR - 102 - 840 + IPR001356
Homeobox domain + 86 + 306 105 - IPR000109
Proton-dependent oligopeptide transporter family - 101 - 240 + IPR026992
Non-haem dioxygenase N-terminal domain + 85 + 98 106 - IPR011051
RmlC-like cupin domain superfamily - 101 - 135 + IPR011545
DEAD/DEAH box helicase domain + 85 + 103 107 - IPR033121
  - 100 - 264 + IPR001461
Aspartic peptidase A1 family + 85 + 268 108 - IPR000858
S-locus glycoprotein domain - 98 - 104 + IPR000008
C2 domain + 84 + 330 109 - IPR008974
  - 98 - 552 + IPR032867
DYW domain + 83 + 88 110 - IPR011050
Pectin lyase fold/virulence factor - 97 - 107 + IPR004827
Basic-leucine zipper domain + 80 + 191 111 - IPR015300
  - 97 - 506 + IPR020472
G-protein beta WD-40 repeat + 79 + 279 112 - IPR001623
  - 96 - 1460 + IPR025315
Domain of unknown function DUF4220 + 78 + 83 113 - IPR005225
Small GTP-binding protein domain - 96 - 118 + IPR010987
Glutathione S-transferase, C-terminal-like + 76 + 90 114 - IPR012334
  - 96 - 214 + IPR002902
Gnk2-homologous domain + 75 + 291 115 - IPR003609
  - 94 - 496 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 75 + 82 116 - IPR009072
  - 94 - 594 + IPR000270
PB1 domain + 75 + 115 117 - IPR032861
Xylanase inhibitor, N-terminal - 93 - 104 + IPR013766
Thioredoxin domain + 74 + 178 118 - IPR005828
Major facilitator, sugar transporter-like - 92 - 126 + IPR036908
RlpA-like domain superfamily + 74 + 80 119 - IPR032799
Xylanase inhibitor, C-terminal - 92 - 103 + IPR000571
Zinc finger, CCCH-type + 73 + 320 120 - IPR029071
Ubiquitin-like domain superfamily - 92 - 142 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 72 + 77 121 - IPR001087
GDSL lipase/esterase - 91 - 102 + IPR007117
Expansin, cellulose-binding-like domain + 72 + 154 122 - IPR036457
  - 91 - 556 + IPR011676
Domain of unknown function DUF1618 + 71 + 75 123 - IPR011011
Zinc finger, FYVE/PHD-type - 90 - 121 + IPR043129
ATPase, nucleotide binding domain + 71 + 157 124 - IPR003340
  - 89 - 1350 + IPR004045
Glutathione S-transferase, N-terminal + 71 + 163 125 - IPR015655
Protein phosphatase 2C family - 88 - 123 + IPR003613
U-box domain + 70 + 157 126 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 88 - 107 + IPR002083
MATH/TRAF domain + 69 + 159 127 - IPR001932
  - 88 - 1440 + IPR001220
Legume lectin domain + 68 + 129 128 - IPR035669
GDSL lipase/esterase-like, plant - 87 - 97 + IPR005174
Domain unknown function DUF295 + 67 + 70 129 - IPR024171
S-receptor-like serine/threonine-protein kinase - 87 - 103 + IPR025846
Trichome birefringence-like, N-terminal domain + 67 + 73 130 - IPR032867
DYW domain - 87 - 93 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 66 + 67 131 - IPR015422
  - 87 - 525 + IPR029052
Metallo-dependent phosphatase-like + 65 + 88 132 - IPR000073
Alpha/beta hydrolase fold-1 - 86 - 198 + IPR026057
PC-Esterase + 64 + 75 133 - IPR001356
  - 86 - 1167 + IPR029962
Trichome birefringence-like family + 64 + 77 134 - IPR036397
  - 85 - 306 + IPR006045
Cupin 1 + 64 + 84 135 - IPR011545
DEAD/DEAH box helicase domain - 85 - 102 + IPR044965
Glycoside hydrolase family 17, plant + 64 + 107 136 - IPR035892
  - 84 - 304 + IPR036915
Cyclin-like superfamily + 64 + 120 137 - IPR026992
Non-haem dioxygenase N-terminal domain - 84 - 96 + IPR006121
Heavy metal-associated domain, HMA + 63 + 213 138 - IPR003657
  - 84 - 948 + IPR016039
Thiolase-like + 63 + 118 139 - IPR036576
  - 83 - 639 + IPR007658
Protein of unknown function DUF594 + 63 + 65 140 - IPR017871
ABC transporter, conserved site - 82 - 120 + IPR007112
Expansin/pollen allergen, DPBB domain + 63 + 69 141 - IPR000008
  - 80 - 848 + IPR036852
Peptidase S8/S53 domain superfamily + 63 + 73 142 - IPR004827
  - 80 - 987 + IPR036163
Heavy metal-associated domain superfamily + 63 + 87 143 - IPR020472
G-protein beta WD-40 repeat - 79 - 276 + IPR000626
Ubiquitin-like domain + 62 + 188 144 - IPR000742
  - 78 - 366 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 62 + 81 145 - IPR010987
  - 77 - 182 + IPR023395
Mitochondrial carrier domain superfamily + 62 + 83 146 - IPR025315
Domain of unknown function DUF4220 - 76 - 81 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 61 + 66 147 - IPR002902
  - 75 - 590 + IPR006501
Pectinesterase inhibitor domain + 61 + 62 148 - IPR017907
Zinc finger, RING-type, conserved site - 75 - 94 + IPR001806
Small GTPase + 61 + 142 149 - IPR038408
  - 74 - 292 + IPR000209
Peptidase S8/S53 domain + 61 + 71 150 - IPR006447
Myb domain, plants - 74 - 94 + IPR045051
Subtilisin-like protease + 60 + 69 151 - IPR036908
  - 74 - 320 + IPR039391
Phytocyanin + 60 + 64 152 - IPR000270
  - 74 - 447 + IPR018108
Mitochondrial substrate/solute carrier + 60 + 415 153 - IPR000571
  - 73 - 1554 + IPR013057
Amino acid transporter, transmembrane domain + 60 + 79 154 - IPR036749
  - 72 - 308 + IPR003245
Phytocyanin domain + 60 + 123 155 - IPR004045
  - 72 - 486 + IPR000490
Glycoside hydrolase family 17 + 60 + 83 156 - IPR007117
  - 72 - 308 + IPR003663
Sugar/inositol transporter + 60 + 318 157 - IPR011676
Domain of unknown function DUF1618 - 71 - 75 + IPR007118
Expansin/Lol pI + 58 + 351 158 - IPR013766
  - 70 - 522 + IPR001509
NAD-dependent epimerase/dehydratase + 58 + 64 159 - IPR002083
  - 70 - 558 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 58 + 70 160 - IPR013783
  - 69 - 192 + IPR020568
Ribosomal protein S5 domain 2-type fold + 58 + 86 161 - IPR003613
  - 69 - 699 + IPR026961
PGG domain + 57 + 127 162 - IPR001881
EGF-like calcium-binding domain - 68 - 99 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 56 + 61 163 - IPR001220
Legume lectin domain - 68 - 129 + IPR001563
Peptidase S10, serine carboxypeptidase + 56 + 390 164 - IPR018097
EGF-like calcium-binding, conserved site - 67 - 73 + IPR002100
Transcription factor, MADS-box + 56 + 296 165 - IPR001965
Zinc finger, PHD-type - 67 - 110 + IPR024788
Malectin-like domain + 56 + 66 166 - IPR035513
  - 66 - 258 + IPR036879
Transcription factor, MADS-box superfamily + 56 + 63 167 - IPR000225
  - 66 - 1725 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 56 + 88 168 - IPR006121
  - 65 - 651 + IPR011032
GroES-like superfamily + 55 + 93 169 - IPR003960
ATPase, AAA-type, conserved site - 65 - 83 + IPR013763
Cyclin-like + 55 + 89 170 - IPR025846
PMR5 N-terminal domain - 65 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 55 71 171 - IPR036852
  - 65 - 828 + IPR005202
Transcription factor GRAS + 55 + 189 172 - IPR006045
Cupin 1 - 64 - 168 + IPR000048
IQ motif, EF-hand binding site + 55 + 266 173 - IPR036915
Cyclin-like superfamily - 64 - 117 + IPR008949
Isoprenoid synthase domain superfamily + 54 + 68 174 - IPR016039
  - 63 - 696 + IPR015915
Kelch-type beta propeller + 54 + 79 175 - IPR007112
  - 63 - 266 + IPR016159
Cullin repeat-like-containing domain superfamily + 53 + 64 176 - IPR036163
Heavy metal-associated domain superfamily - 63 - 87 + IPR030184
WAT1-related protein + 53 + 66 177 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 62 - 80 + IPR004158
Protein of unknown function DUF247, plant + 53 + 118 178 - IPR026057
PC-Esterase - 62 - 73 + IPR000620
EamA domain + 53 + 103 179 - IPR023395
  - 62 - 364 + IPR036875
Zinc finger, CCHC-type superfamily + 53 + 76 180 - IPR006501
Pectinesterase inhibitor domain - 62 - 161 + IPR019787
Zinc finger, PHD-finger + 52 + 119 181 - IPR029962
Trichome birefringence-like family - 61 - 76 + IPR007527
Zinc finger, SWIM-type + 52 + 115 182 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 61 - 66 + IPR001878
Zinc finger, CCHC-type + 52 + 168 183 - IPR007658
Protein of unknown function DUF594 - 61 - 63 + IPR036855
Zinc finger, CCCH-type superfamily + 51 + 129 184 - IPR013057
Amino acid transporter, transmembrane domain - 61 - 80 + IPR000225
Armadillo + 51 + 201 185 - IPR015915
  - 61 - 531 + IPR002528
Multi antimicrobial extrusion protein + 50 + 102 186 - IPR001806
Small GTPase superfamily - 61 - 78 + IPR000742
EGF-like domain + 50 + 51 187 - IPR000209
Peptidase S8/S53 domain - 61 - 71 + IPR013094
Alpha/beta hydrolase fold-3 + 50 + 55 188 - IPR000626
  - 60 - 765 + IPR015500
Peptidase S8, subtilisin-related + 50 + 163 189 - IPR005829
Sugar transporter, conserved site - 60 - 120 + IPR008978
HSP20-like chaperone + 49 + 57 190 - IPR018108
  - 60 - 824 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 49 + 53 191 - IPR003245
  - 60 - 540 + IPR045087
Multicopper oxidase + 49 + 54 192 - IPR003663
Sugar/inositol transporter - 60 - 373 + IPR036465
von Willebrand factor A-like domain superfamily + 49 + 62 193 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 59 - 71 + IPR016181
Acyl-CoA N-acyltransferase + 48 + 54 194 - IPR000490
Glycoside hydrolase family 17 - 59 - 125 + IPR034197
Cucumisin-like catalytic domain + 48 + 54 195 - IPR011993
  - 59 - 148 + IPR023298
P-type ATPase, transmembrane domain superfamily + 48 + 67 196 - IPR007118
Expansin/Lol pI - 58 - 351 + IPR036318
FAD-binding, type PCMH-like superfamily + 47 + 56 197 - IPR005174
Domain unknown function DUF295 - 58 - 61 + IPR013525
ABC-2 type transporter + 47 + 73 198 - IPR029052
  - 58 - 162 + IPR000608
Ubiquitin-conjugating enzyme E2 + 47 + 172 199 - IPR001509
NAD-dependent epimerase/dehydratase - 57 - 65 + IPR012946
X8 domain + 47 + 72 200 - IPR001938
  - 57 - 724 + IPR004265
Dirigent protein + 47 + 47 201 - IPR026961
PGG domain - 57 - 127 + IPR009003
Peptidase S1, PA clan + 47 + 64 202 - IPR016135
  - 57 - 292 + IPR001752
Kinesin motor domain + 47 + 294 203 - IPR008979
  - 57 - 340 + IPR001117
Multicopper oxidase, type 1 + 46 + 49 204 - IPR020568
Ribosomal protein S5 domain 2-type fold - 57 - 97 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 46 + 86 205 - IPR030184
WAT1-related protein - 57 - 72 + IPR008979
Galactose-binding-like domain superfamily + 46 + 85 206 - IPR001563
Peptidase S10, serine carboxypeptidase - 56 - 390 + IPR006671
Cyclin, N-terminal + 46 + 50 207 - IPR002100
  - 56 - 1185 + IPR041569
AAA ATPase, AAA+ lid domain + 46 + 72 208 - IPR036879
  - 56 - 375 + IPR011707
Multicopper oxidase, N-terminal + 46 + 48 209 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 56 - 91 + IPR011701
Major facilitator superfamily + 45 + 58 210 - IPR011032
GroES-like superfamily - 55 - 93 + IPR014014
RNA helicase, DEAD-box type, Q motif + 45 + 52 211 - IPR013763
Cyclin-like - 55 - 168 + IPR003676
Small auxin-up RNA + 45 + 46 212 - IPR036961
  - 55 - 264 + IPR033389
AUX/IAA domain + 44 + 64 213 - IPR034090
BPM, C-terminal - 55 - 58 + IPR017884
SANT domain + 44 + 53 214 - IPR024788
Malectin-like carbohydrate-binding domain - 55 - 65 + IPR000873
AMP-dependent synthetase/ligase + 44 + 52 215 - IPR000048
  - 55 - 1161 + IPR034161
Pepsin-like domain, plant + 44 + 49 216 - IPR008949
  - 54 - 270 + IPR029055
Nucleophile aminohydrolases, N-terminal + 44 + 55 217 - IPR027640
Kinesin-like protein - 54 - 78 + IPR018289
MULE transposase domain + 44 + 54 218 - IPR001878
  - 54 - 789 + IPR011527
ABC transporter type 1, transmembrane domain + 44 + 167 219 - IPR000620
EamA domain - 53 - 103 + IPR037176
Osmotin/thaumatin-like superfamily + 44 + 45 220 - IPR036875
Zinc finger, CCHC-type superfamily - 53 - 76 + IPR002921
Fungal lipase-like domain + 43 + 47 221 - IPR023393
  - 52 - 128 + IPR033896
MADS MEF2-like + 43 + 49 222 - IPR014014
  - 52 - 120 + IPR004853
Sugar phosphate transporter domain + 43 + 57 223 - IPR019787
  - 52 - 230 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 43 + 46 224 - IPR019786
Zinc finger, PHD-type, conserved site - 52 - 64 + IPR011012
Longin-like domain superfamily + 43 + 55 225 - IPR005202
  - 52 - 246 + IPR011706
Multicopper oxidase, C-terminal + 43 + 46 226 - IPR016159
Cullin repeat-like-containing domain superfamily - 52 - 84 + IPR000070
Pectinesterase, catalytic + 43 + 47 227 - IPR004158
Protein of unknown function DUF247, plant - 52 - 58 + IPR044808
Ethylene-responsive transcription factor + 43 + 55 228 - IPR007527
  - 52 - 345 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 42 + 51 229 - IPR036855
Zinc finger, CCCH-type superfamily - 51 - 129 + IPR004263
Exostosin-like + 42 + 55 230 - IPR008978
  - 50 - 228 + IPR001938
Thaumatin family + 42 + 259 231 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 50 - 53 + IPR016166
FAD-binding domain, PCMH-type + 42 + 49 232 - IPR000222
PPM-type phosphatase, divalent cation binding - 50 - 61 + IPR008928
Six-hairpin glycosidase superfamily + 42 + 54 233 - IPR002528
Multi antimicrobial extrusion protein - 50 - 145 + IPR001929
Germin + 41 + 125 234 - IPR036465
  - 50 - 228 + IPR009000
Translation protein, beta-barrel domain superfamily + 41 + 61 235 - IPR013094
Alpha/beta hydrolase fold-3 - 50 - 55 + IPR007125
Histone H2A/H2B/H3 + 41 + 43 236 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 49 - 55 + IPR002109
Glutaredoxin + 41 + 50 237 - IPR015500
Peptidase S8, subtilisin-related - 49 - 160 + IPR001214
SET domain + 41 + 94 238 - IPR037045
  - 49 - 104 + IPR000743
Glycoside hydrolase, family 28 + 41 + 48 239 - IPR016181
Acyl-CoA N-acyltransferase - 48 - 57 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 40 + 48 240 - IPR036640
  - 48 - 507 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 40 + 58 241 - IPR034197
Cucumisin-like catalytic domain - 48 - 53 + IPR004140
Exocyst complex component Exo70 + 40 + 132 242 - IPR018253
DnaJ domain, conserved site - 48 + IPR031052
FHY3/FAR1 family + 40 63 243 - IPR023298
P-type ATPase, transmembrane domain superfamily - 48 - 157 + IPR011006
CheY-like superfamily + 40 + 65 244 - IPR013525
ABC-2 type transporter - 47 - 65 + IPR015655
Protein phosphatase 2C family + 40 + 50 245 - IPR000608
  - 47 - 344 + IPR004046
Glutathione S-transferase, C-terminal + 40 + 50 246 - IPR012946
X8 domain - 47 - 145 + IPR001789
Signal transduction response regulator, receiver domain + 40 + 122 247 - IPR004265
Dirigent protein - 47 + IPR043926
ABC transporter family G domain + 39 47 248 - IPR031052
FHY3/FAR1 family - 47 - 68 + IPR023271
Aquaporin-like + 39 + 49 249 - IPR009003
Peptidase S1, PA clan - 47 - 70 + IPR004839
Aminotransferase, class I/classII + 39 + 49 250 - IPR003676
Small auxin-up RNA - 47 - 48 + IPR000425
Major intrinsic protein + 39 + 318 251 - IPR001117
Multicopper oxidase, type 1 - 46 - 49 + IPR014756
Immunoglobulin E-set + 39 + 55 252 - IPR017451
F-box associated interaction domain - 46 - 57 + IPR039361
Cyclin + 39 + 44 253 - IPR006671
Cyclin, N-terminal - 46 - 73 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 39 + 42 254 - IPR002109
  - 46 - 309 + IPR010402
CCT domain + 38 + 92 255 - IPR001752
  - 46 - 981 + IPR000182
GNAT domain + 38 + 75 256 - IPR011707
Multicopper oxidase, type 3 - 46 - 48 + IPR001360
Glycoside hydrolase family 1 + 38 + 291 257 - IPR036318
FAD-binding, type 2-like superfamily - 45 - 50 + IPR001906
Terpene synthase, N-terminal domain + 38 + 43 258 - IPR011701
Major facilitator superfamily - 45 - 58 + IPR024752
Myb/SANT-like domain + 38 + 39 259 - IPR036691
  - 45 - 272 + IPR006702
Casparian strip membrane protein domain + 38 + 45 260 - IPR000873
AMP-dependent synthetase/ligase - 45 - 53 + IPR013149
Alcohol dehydrogenase-like, C-terminal + 37 + 49 261 - IPR018289
MULE transposase domain - 45 - 55 + IPR009060
UBA-like superfamily + 37 + 63 262 - IPR002921
Fungal lipase-like domain - 44 - 48 + IPR002068
Alpha crystallin/Hsp20 domain + 37 + 82 263 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 44 - 369 + IPR000330
SNF2, N-terminal + 37 + 47 264 - IPR011527
  - 44 - 501 + IPR036612
K Homology domain, type 1 superfamily + 37 + 86 265 - IPR012341
  - 44 - 177 + IPR003137
PA domain + 37 + 48 266 - IPR037176
  - 44 - 184 + IPR008250
P-type ATPase, A domain superfamily + 37 + 46 267 - IPR033896
MADS MEF2-like - 43 - 49 + IPR003656
Zinc finger, BED-type + 37 + 66 268 - IPR004853
Sugar phosphate transporter domain - 43 - 57 + IPR013154
Alcohol dehydrogenase, N-terminal + 37 + 50 269 - IPR034161
Pepsin-like domain, plant - 43 + IPR034294
Aquaporin transporter + 37 48 270 - IPR029055
  - 43 - 208 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 37 + 40 271 - IPR011012
Longin-like domain superfamily - 43 - 55 + IPR040911
Exostosin, GT47 domain + 37 + 48 272 - IPR011706
Multicopper oxidase, type 2 - 43 - 46 + IPR002912
ACT domain + 37 + 97 273 - IPR000070
Pectinesterase, catalytic - 43 - 47 + IPR025322
PADRE domain + 36 + 37 274 - IPR033389
AUX/IAA domain - 42 - 63 + IPR004041
NAF domain + 36 + 49 275 - IPR013128
Peptidase C1A - 42 - 54 + IPR006016
UspA + 36 + 44 276 - IPR001969
Aspartic peptidase, active site - 42 - 67 + IPR007493
Protein of unknown function DUF538 + 36 + 82 277 - IPR004140
Exocyst complex component Exo70 - 42 - 94 + IPR018451
NAF/FISL domain + 36 + 48 278 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 42 - 43 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 36 + 40 279 - IPR008928
Six-hairpin glycosidase superfamily - 42 - 68 + IPR008906
HAT, C-terminal dimerisation domain + 36 + 41 280 - IPR004046
Glutathione S-transferase, C-terminal - 42 - 52 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 36 + 100 281 - IPR006566
FBD domain - 42 - 45 + IPR036758
At5g01610-like superfamily + 36 + 41 282 - IPR001929
Germin - 41 - 125 + IPR029045
ClpP/crotonase-like domain superfamily + 36 + 46 283 - IPR009000
Translation protein, beta-barrel domain superfamily - 41 - 62 + IPR006094
FAD linked oxidase, N-terminal + 36 + 41 284 - IPR003656
  - 41 - 321 - + IPR002487
Transcription factor, K-box + 36 + 76 + 285 - IPR023299
  - 41 - 258 + IPR008889
VQ + 36 + 36 286 - IPR000743
Glycoside hydrolase, family 28 - 41 - 65 + IPR022059
Protein of unknown function DUF3615 + 35 + 42 287 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 40 - 48 + IPR028889
Ubiquitin specific protease domain + 35 + 38 288 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 40 - 47 + IPR008942
ENTH/VHS + 34 + 43 289 - IPR001214
  - 40 - 366 + IPR016461
O-methyltransferase COMT-type + 34 + 70 290 - IPR008942
  - 39 - 184 + IPR029021
Protein-tyrosine phosphatase-like + 34 + 51 291 - IPR006016
UspA - 39 - 47 + IPR035940
CAP superfamily + 34 + 36 292 - IPR036612
  - 39 - 450 + IPR002963
Expansin + 34 + 302 293 - IPR006564
Zinc finger, PMZ-type - 39 - 50 + IPR000668
Peptidase C1A, papain C-terminal + 34 + 126 294 - IPR023271
  - 39 - 198 + IPR002495
Glycosyl transferase, family 8 + 34 + 43 295 - IPR034294
Aquaporin transporter - 39 - 51 + IPR002067
Mitochondrial carrier protein + 34 + 209 296 - IPR016166
  - 39 - 129 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 34 + 45 297 - IPR004839
Aminotransferase, class I/classII - 39 - 49 + IPR015947
PUA-like superfamily + 34 + 40 298 - IPR011006
CheY-like superfamily - 39 - 63 + IPR016040
NAD(P)-binding domain + 33 + 58 299 - IPR000425
Major intrinsic protein - 39 - 338 + IPR000528
Plant non-specific lipid-transfer protein/Par allergen + 33 + 152 300 - IPR001757
P-type ATPase - 39 - 235 + IPR025659
Tubby-like, C-terminal + 33 + 44 301 - IPR001789
  - 39 - 690 + IPR027806
Harbinger transposase-derived nuclease domain + 33 + 35 302 - IPR000182
  - 38 - 150 + IPR005630
Terpene synthase, metal-binding domain + 33 + 35 303 - IPR001360
Glycoside hydrolase family 1 - 38 - 272 + IPR001283
Cysteine-rich secretory protein-related + 33 + 164 304 - IPR036890
  - 38 - 228 + IPR014044
CAP domain + 33 + 34 305 - IPR017970
Homeobox, conserved site - 38 - 44 + IPR019378
GDP-fucose protein O-fucosyltransferase + 33 + 37 306 - IPR029045
ClpP/crotonase-like domain superfamily - 38 - 57 + IPR039417
Papain-like cysteine endopeptidase + 33 + 35 307 - IPR020845
AMP-binding, conserved site - 38 - 44 + IPR006566
FBD domain + 33 + 33 308 - IPR014756
Immunoglobulin E-set - 38 - 56 + IPR044791
Beta-glucanase/XTH + 33 + 44 309 - IPR024752
Myb/SANT-like domain - 38 - 39 + IPR023210
NADP-dependent oxidoreductase domain + 33 + 45 310 - IPR025322
Protein of unknown function DUF4228, plant - 37 - 38 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 32 + 36 311 - IPR036965
  - 37 - 147 + IPR001296
Glycosyl transferase, family 1 + 32 + 56 312 - IPR013149
Alcohol dehydrogenase, C-terminal - 37 - 49 + IPR004367
Cyclin, C-terminal domain + 32 + 35 313 - IPR007493
Protein of unknown function DUF538 - 37 - 83 + IPR022742
Serine aminopeptidase, S33 + 32 + 35 314 - IPR002068
  - 37 - 164 + IPR006652
Kelch repeat type 1 + 32 + 68 315 - IPR003137
PA domain - 37 - 49 + IPR003406
Glycosyl transferase, family 14 + 32 + 38 316 - IPR004263
Exostosin-like - 37 - 48 + IPR027923
Hydrophobic seed protein domain + 32 + 62 317 - IPR013154
Alcohol dehydrogenase, N-terminal - 37 - 50 + IPR001077
O-methyltransferase domain + 32 + 33 318 - IPR002912
  - 37 - 222 + IPR033443
Pentacotripeptide-repeat region of PRORP + 32 + 42 319 - IPR017877
  - 37 - 80 + IPR006458
Ovate protein family, C-terminal + 32 + 62 320 - IPR006702
Casparian strip membrane protein domain - 37 - 44 + IPR013126
Heat shock protein 70 family + 32 + 78 321 - IPR010402
  - 36 - 258 + IPR038933
Ovate protein family + 31 + 31 322 - IPR004041
NAF domain - 36 - 49 + IPR002659
Glycosyl transferase, family 31 + 31 + 73 323 - IPR009060
UBA-like superfamily - 36 - 62 + IPR001594
Palmitoyltransferase, DHHC domain + 31 + 39 324 - IPR018451
  - 36 - 144 + IPR005150
Cellulose synthase + 31 + 75 325 - IPR008250
P-type ATPase, A domain superfamily - 36 - 52 + IPR004883
Lateral organ boundaries, LOB + 31 + 63 326 - IPR008906
HAT, C-terminal dimerisation domain - 36 - 41 + IPR004088
K Homology domain, type 1 + 31 + 78 327 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 36 - 39 + IPR000644
CBS domain + 31 + 129 328 - IPR036758
  - 36 - 164 + IPR043519
Nucleotidyltransferase superfamily + 31 + 38 329 - IPR019780
Germin, manganese binding site - 36 - 37 + IPR011043
Galactose oxidase/kelch, beta-propeller + 31 + 36 330 - IPR001906
Terpene synthase, N-terminal domain - 36 - 39 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 31 + 69 331 - IPR002487
  - 36 - 228 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 31 + 43 332 - IPR029021
  - 35 - 202 + IPR000757
Glycoside hydrolase family 16 + 31 + 68 333 - IPR011016
  - 35 - 342 + IPR006073
GTP binding domain + 31 + 94 334 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 35 - 76 + IPR001251
CRAL-TRIO lipid binding domain + 30 + 105 335 - IPR035940
  - 35 - 148 + IPR044835
Auxin response factor + 30 + 45 336 - IPR006652
Kelch repeat type 1 - 35 - 170 + IPR005135
Endonuclease/exonuclease/phosphatase + 30 + 36 337 - IPR022059
Protein of unknown function DUF3615 - 35 - 42 + IPR004320
Protein BPS1, chloroplastic + 30 + 30 338 - IPR007125
Histone H2A/H2B/H3 - 35 - 37 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 30 + 36 339 - IPR018303
P-type ATPase, phosphorylation site - 35 - 46 + IPR027356
NPH3 domain + 30 + 65 340 - IPR019378
GDP-fucose protein O-fucosyltransferase - 35 - 40 + IPR000863
Sulfotransferase domain + 30 + 31 341 - IPR006094
FAD linked oxidase, N-terminal - 35 - 36 + IPR003311
AUX/IAA protein + 30 + 43 342 - IPR013780
  - 35 - 124 + IPR018490
Cyclic nucleotide-binding-like + 29 + 36 343 - IPR020843
Polyketide synthase, enoylreductase domain - 35 - 47 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 29 + 77 344 - IPR008889
VQ - 35 - 35 + IPR000795
Translational (tr)-type GTP-binding domain + 29 + 221 345 - IPR014721
  - 35 - 136 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 29 + 30 346 - IPR016461
  - 34 - 183 + IPR043502
DNA/RNA polymerase superfamily + 29 + 38 347 - IPR006626
Parallel beta-helix repeat - 34 - 192 + IPR011013
Galactose mutarotase-like domain superfamily + 29 + 40 348 - IPR000330
SNF2-related, N-terminal domain - 34 - 43 + IPR043454
NPH3/RPT2-like family + 29 + 33 349 - IPR003594
Histidine kinase/HSP90-like ATPase - 34 - 105 + IPR000595
Cyclic nucleotide-binding domain + 29 + 90 350 - IPR002963
Expansin - 34 - 302 + IPR011141
Polyketide synthase, type III + 29 + 29 351 - IPR001283
Cysteine-rich secretory protein, allergen V5/Tpx-1-related - 34 - 170 + IPR004330
FAR1 DNA binding domain + 29 + 42 352 - IPR014044
CAP domain - 34 - 69 + IPR012967
Plant methyltransferase dimerisation + 29 + 30 353 - IPR000668
Peptidase C1A, papain C-terminal - 34 - 161 + IPR000727
Target SNARE coiled-coil homology domain + 28 + 47 354 - IPR002495
Glycosyl transferase, family 8 - 34 - 42 + IPR025110
AMP-binding enzyme, C-terminal domain + 28 + 30 355 - IPR002067
Mitochondrial carrier protein - 34 - 209 + IPR036378
FAS1 domain superfamily + 28 + 45 356 - IPR028889
  - 34 - 74 + IPR007657
Glycosyltransferase 61 + 28 + 66 357 - IPR023210
NADP-dependent oxidoreductase domain - 34 - 87 + IPR002423
Chaperonin Cpn60/GroEL/TCP-1 family + 28 + 37 358 - IPR036812
  - 34 - 186 + IPR045048
F-box only protein 31/39 + 28 + 37 359 - IPR025659
  - 33 - 166 + IPR004813
Oligopeptide transporter, OPT superfamily + 28 + 37 360 - IPR027806
Harbinger transposase-derived nuclease domain - 33 - 35 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 28 + 44 361 - IPR005630
Terpene synthase, metal-binding domain - 33 - 33 + IPR003855
Potassium transporter + 28 + 75 362 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 33 - 245 + IPR001954
Gliadin/LMW glutenin + 28 + 51 363 - IPR038538
  - 33 - 94 + IPR017938
Riboflavin synthase-like beta-barrel + 27 + 41 364 - IPR027923
Hydrophobic seed protein - 33 - 61 + IPR032710
NTF2-like domain superfamily + 27 + 29 365 - IPR002035
  - 33 - 168 + IPR010920
LSM domain superfamily + 27 + 33 366 - IPR022357
Major intrinsic protein, conserved site - 33 - 39 + IPR005299
SAM dependent carboxyl methyltransferase + 27 + 56 367 - IPR004088
K Homology domain, type 1 - 33 - 81 + IPR000315
B-box-type zinc finger + 27 + 74 368 - IPR038718
  - 33 - 110 + IPR044848
PHR1-like + 27 + 37 369 - IPR000644
  - 33 - 458 + IPR007650
Zf-FLZ domain + 27 + 60 370 - IPR013126
Heat shock protein 70 family - 33 - 349 + IPR000408
Regulator of chromosome condensation, RCC1 + 27 + 461 371 - IPR015947
PUA-like superfamily - 33 - 45 + IPR008480
Protein of unknown function DUF761, plant + 27 + 28 372 - IPR016040
NAD(P)-binding domain - 32 - 54 + IPR027409
GroEL-like apical domain superfamily + 27 + 35 373 - IPR018200
Ubiquitin specific protease, conserved site - 32 - 53 + IPR031127
E3 ubiquitin ligase RBR family + 27 + 32 374 - IPR038933
Ovate protein family - 32 - 40 + IPR006311
Twin-arginine translocation pathway, signal sequence + 27 + 28 375 - IPR002659
Glycosyl transferase, family 31 - 32 - 74 + IPR005175
PPC domain + 27 + 96 376 - IPR001296
Glycosyl transferase, family 1 - 32 - 52 + IPR001099
Chalcone/stilbene synthase, N-terminal + 27 + 29 377 - IPR036865
  - 32 - 156 + IPR006153
Cation/H+ exchanger + 26 + 32 378 - IPR004367
Cyclin, C-terminal domain - 32 - 62 + IPR025525
hAT-like transposase, RNase-H fold + 26 + 31 379 - IPR002355
Multicopper oxidase, copper-binding site - 32 - 35 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 26 + 102 380 - IPR022742
Serine aminopeptidase, S33 - 32 - 35 + IPR000717
Proteasome component (PCI) domain + 26 + 77 381 - IPR003406
Glycosyl transferase, family 14 - 32 - 38 + IPR008422
Homeobox KN domain + 26 + 40 382 - IPR001077
O-methyltransferase, family 2 - 32 - 33 + IPR029061
Thiamin diphosphate-binding fold + 26 + 61 383 - IPR006458
  - 32 - 180 + IPR027725
Heat shock transcription factor family + 26 + 36 384 - IPR000315
  - 31 - 492 + IPR005333
Transcription factor, TCP + 26 + 28 385 - IPR001594
Palmitoyltransferase, DHHC domain - 31 - 39 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 26 + 33 386 - IPR005135
Endonuclease/exonuclease/phosphatase - 31 - 35 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 26 + 39 387 - IPR004883
  - 31 - 126 + IPR034288
Laccase, first cupredoxin domain + 26 + 28 388 - IPR003311
AUX/IAA protein - 31 - 43 + IPR005821
Ion transport domain + 26 + 33 389 - IPR011043
Galactose oxidase/kelch, beta-propeller - 31 - 44 + IPR034285
Laccase, second cupredoxin domain + 26 + 27 390 - IPR009091
  - 31 - 212 + IPR001757
P-type ATPase + 26 + 139 391 - IPR011042
  - 31 - 106 + IPR012328
Chalcone/stilbene synthase, C-terminal + 26 + 26 392 - IPR000757
  - 31 - 204 + IPR003851
Zinc finger, Dof-type + 26 + 56 393 - IPR000528
Plant lipid transfer protein/Par allergen - 30 - 144 + IPR036404
Jacalin-like lectin domain superfamily + 26 + 34 394 - IPR025525
hAT-like transposase, RNase-H fold - 30 - 35 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 26 + 33 395 - IPR001251
  - 30 - 278 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 25 + 39 396 - IPR020636
Calcium/calmodulin-dependent/calcium-dependent protein kinase - 30 - 43 + IPR000782
FAS1 domain + 25 + 69 397 - IPR004320
Protein of unknown function DUF241, plant - 30 - 31 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 25 + 178 398 - IPR027356
  - 30 - 130 + IPR004316
SWEET sugar transporter + 25 + 42 399 - IPR033131
Pectinesterase, Asp active site - 30 - 32 + IPR029000
Cyclophilin-like domain superfamily + 25 + 33 400 - IPR038770
  - 30 - 74 + IPR044778
Sugar transport protein STP/MST-like, plant + 25 + 29 401 - IPR000863
Sulfotransferase domain - 30 + IPR013216
Methyltransferase type 11 + 25 31 402 - IPR031107
Small heat shock protein HSP20 - 30 - 36 + IPR023753
FAD/NAD(P)-binding domain + 25 + 33 403 - IPR018202
Serine carboxypeptidase, serine active site - 30 - 42 + IPR011332
Zinc-binding ribosomal protein + 25 + 29 404 - IPR006073
GTP binding domain - 30 - 91 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 25 + 29 405 - IPR018490
Cyclic nucleotide-binding-like - 29 - 35 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 25 + 45 - - 406 - IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase - 29 - 74 + + 406 + IPR002035
von Willebrand factor, type A + 25 + 51 407 - IPR002423
Chaperonin Cpn60/TCP-1 family - 29 - 38 + IPR001849
Pleckstrin homology domain + 25 + 41 408 - IPR000795
  - 29 - 663 + IPR029062
Class I glutamine amidotransferase-like + 25 + 39 409 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 29 - 56 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 25 + 27 410 - IPR031112
AP2-like ethylene-responsive transcription factor - 29 - 34 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 25 + 120 411 - IPR011013
Galactose mutarotase-like domain superfamily - 29 - 43 + IPR029033
Histidine phosphatase superfamily + 25 + 33 412 - IPR005150
Cellulose synthase - 29 - 72 + IPR000679
Zinc finger, GATA-type + 25 + 83 413 - IPR019825
Legume lectin, beta chain, Mn/Ca-binding site - 29 - 32 + IPR001229
Jacalin-like lectin domain + 25 + 65 414 - IPR008480
Protein of unknown function DUF761, plant - 29 - 30 + IPR010525
Auxin response factor domain + 25 + 32 415 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 29 - 37 + IPR015940
Ubiquitin-associated domain + 24 + 84 416 - IPR004087
K Homology domain - 29 - 76 + IPR008991
Translation protein SH3-like domain superfamily + 24 + 24 417 - IPR000595
  - 29 - 228 + IPR036420
BRCT domain superfamily + 24 + 44 418 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 29 - 33 + IPR011016
Zinc finger, RING-CH-type + 24 + 69 419 - IPR031127
E3 ubiquitin ligase RBR family - 29 - 36 + IPR001763
Rhodanese-like domain + 24 + 71 420 - IPR011141
Polyketide synthase, type III - 29 - 50 + IPR003594
Histidine kinase/HSP90-like ATPase + 24 + 31 421 - IPR004330
FAR1 DNA binding domain - 29 - 42 + IPR020946
Flavin monooxygenase-like + 24 + 40 422 - IPR012967
Plant methyltransferase dimerisation - 29 - 30 + IPR023299
P-type ATPase, cytoplasmic domain N + 24 + 28 423 - IPR025110
AMP-binding enzyme, C-terminal domain - 28 - 30 + IPR001701
Glycoside hydrolase family 9 + 24 + 26 424 - IPR036378
  - 28 - 158 + IPR002913
START domain + 24 + 70 425 - IPR018244
Allergen V5/Tpx-1-related, conserved site - 28 - 46 + IPR015797
NUDIX hydrolase-like domain superfamily + 24 + 28 426 - IPR007657
Glycosyltransferase 61 - 28 - 65 + IPR036085
PAZ domain superfamily + 23 + 34 427 - IPR034111
Pathogenesis-related protein 1-like, SCP domain - 28 - 29 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 23 + 36 428 - IPR027409
  - 28 - 142 + IPR001357
BRCT domain + 23 + 74 429 - IPR004813
Oligopeptide transporter, OPT superfamily - 28 - 71 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 23 + 26 430 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 28 - 44 + IPR017887
Transcription factor TCP subgroup + 23 + 46 431 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 28 - 48 + IPR001353
Proteasome, subunit alpha/beta + 23 + 29 432 - IPR025661
Cysteine peptidase, asparagine active site - 28 - 30 + IPR025422
Transcription factor TGA like domain + 23 + 50 433 - IPR003855
Potassium transporter - 28 - 105 + IPR003337
Trehalose-phosphatase + 23 + 27 434 - IPR000727
  - 27 - 148 + IPR002293
Amino acid/polyamine transporter I + 23 + 32 435 - IPR017938
Riboflavin synthase-like beta-barrel - 27 - 47 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 23 + 56 436 - IPR010920
LSM domain superfamily - 27 - 33 + IPR006461
PLAC8 motif-containing protein + 23 + 49 437 - IPR005299
SAM dependent carboxyl methyltransferase - 27 - 57 + IPR039421
Type 1 protein exporter + 23 + 37 438 - IPR007650
  - 27 - 120 + IPR029069
HotDog domain superfamily + 23 + 33 439 - IPR033124
Serine carboxypeptidases, histidine active site - 27 - 40 + IPR016161
Aldehyde/histidinol dehydrogenase + 23 + 34 440 - IPR000408
  - 27 - 1004 + IPR004314
Neprosin + 23 + 26 441 - IPR011332
Zinc-binding ribosomal protein - 27 - 31 + IPR036034
PDZ superfamily + 23 + 29 442 - IPR029047
  - 27 - 140 + IPR036443
Zinc finger, RanBP2-type superfamily + 23 + 49 443 - IPR006311
  - 27 - 56 + IPR003100
PAZ domain + 22 + 63 444 - IPR005175
  - 27 - 192 + IPR006594
LIS1 homology motif + 22 + 41 445 - IPR001099
Chalcone/stilbene synthase, N-terminal - 27 - 29 + IPR013601
FAE1/Type III polyketide synthase-like protein + 22 + 23 446 - IPR010525
Auxin response factor - 27 - 33 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 22 + 25 447 - IPR032710
NTF2-like domain superfamily - 26 + IPR003106
Leucine zipper, homeobox-associated + 22 28 448 - IPR006153
Cation/H+ exchanger - 26 - 32 + IPR002403
Cytochrome P450, E-class, group IV + 22 + 121 449 - IPR001179
  - 26 - 204 + IPR025753
AAA-type ATPase, N-terminal domain + 22 + 22 450 - IPR008991
Translation protein SH3-like domain superfamily - 26 - 26 + IPR036010
2Fe-2S ferredoxin-like superfamily + 22 + 31 451 - IPR000717
  - 26 - 220 + IPR027413
GroEL-like equatorial domain superfamily + 22 + 31 452 - IPR008422
Homeobox KN domain - 26 - 33 + IPR010989
SNARE + 22 + 24 453 - IPR029061
Thiamin diphosphate-binding fold - 26 - 62 + IPR002123
Phospholipid/glycerol acyltransferase + 22 + 27 454 - IPR027725
Heat shock transcription factor family - 26 - 38 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 22 + 22 455 - IPR000960
Flavin monooxygenase FMO - 26 - 82 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 22 + 27 456 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 26 - 37 + IPR022796
Chlorophyll A-B binding protein + 22 + 29 457 - IPR034288
Laccase, first cupredoxin domain - 26 - 28 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 22 + 23 458 - IPR034285
Laccase, second cupredoxin domain - 26 - 27 + IPR008963
Purple acid phosphatase-like, N-terminal + 22 + 28 459 - IPR014722
  - 26 - 52 + IPR034289
Laccase, third cupredoxin domain + 22 + 25 460 - IPR017937
Thioredoxin, conserved site - 26 - 47 + IPR025486
Domain of unknown function DUF4378 + 22 + 29 461 - IPR012328
Chalcone/stilbene synthase, C-terminal - 26 - 26 + IPR015914
Purple acid phosphatase, N-terminal + 22 + 28 462 - IPR003851
  - 26 - 333 + IPR036392
PLAT/LH2 domain superfamily + 22 + 25 463 - IPR036404
  - 26 - 134 + IPR002937
Amine oxidase + 22 + 31 464 - IPR017927
  - 25 - 114 + IPR006867
Domain of unknown function DUF632 + 22 + 25 465 - IPR000782
  - 25 - 202 + IPR033734
Jacalin-like lectin domain, plant + 22 + 27 466 - IPR002130
  - 25 - 534 + IPR006689
Small GTPase superfamily, ARF/SAR type + 21 + 123 467 - IPR004316
SWEET sugar transporter - 25 - 40 + IPR008971
HSP40/DnaJ peptide-binding + 21 + 57 468 - IPR029000
  - 25 - 142 + IPR035952
Rhomboid-like superfamily + 21 + 25 469 - IPR033138
Multicopper oxidases, conserved site - 25 - 28 + IPR000387
Tyrosine-specific protein phosphatases domain + 21 + 33 470 - IPR013088
  - 25 - 87 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 21 + 22 471 - IPR013216
Methyltransferase type 11 - 25 - 31 + IPR036873
Rhodanese-like domain superfamily + 21 + 35 472 - IPR018181
Heat shock protein 70, conserved site - 25 - 76 + IPR024709
Putative O-fucosyltransferase, plant + 21 + 23 473 - IPR033275
E3 ubiquitin-protein ligase MARCH-like - 25 - 34 + IPR044837
B3 domain-containing protein REM16-like + 21 + 33 474 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 25 - 28 + IPR001163
LSM domain, eukaryotic/archaea-type + 21 + 26 475 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 25 - 59 + IPR012416
CALMODULIN-BINDING PROTEIN60 + 21 + 74 476 - IPR005821
Ion transport domain - 25 - 31 + IPR004252
Probable transposase, Ptta/En/Spm, plant + 21 + 22 477 - IPR005746
Thioredoxin - 25 - 46 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 21 + 24 478 - IPR001876
  - 25 - 330 + IPR013078
Histidine phosphatase superfamily, clade-1 + 21 + 52 479 - IPR029062
  - 25 - 160 + IPR029057
Phosphoribosyltransferase-like + 21 + 37 480 - IPR000169
Cysteine peptidase, cysteine active site - 25 - 27 + IPR016897
S-phase kinase-associated protein 1 + 21 + 22 481 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 25 - 27 + IPR001876
Zinc finger, RanBP2-type + 21 + 80 482 - IPR000232
Heat shock factor (HSF)-type, DNA-binding - 25 - 178 + IPR036928
Amidase signature (AS) superfamily + 21 + 22 483 - IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site - 25 - 31 + IPR002939
Chaperone DnaJ, C-terminal + 21 + 29 484 - IPR025660
Cysteine peptidase, histidine active site - 25 - 27 + IPR036041
Ribosome-inactivating protein superfamily + 21 + 21 485 - IPR029033
  - 25 - 144 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 21 + 28 486 - IPR000679
  - 25 - 321 + IPR015590
Aldehyde dehydrogenase domain + 21 + 31 487 - IPR001229
  - 25 - 186 + IPR006593
Cytochrome b561/ferric reductase transmembrane + 20 + 43 488 - IPR036420
  - 24 - 180 + IPR013187
F-box associated domain, type 3 + 20 + 26 489 - IPR023753
FAD/NAD(P)-binding domain - 24 - 31 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 20 + 24 490 - IPR011074
CRAL/TRIO, N-terminal domain - 24 - 54 + IPR029466
No apical meristem-associated, C-terminal domain + 20 + 20 491 - IPR036866
  - 24 - 134 + IPR020471
Aldo-keto reductase + 20 + 105 492 - IPR023313
Ubiquitin-conjugating enzyme, active site - 24 - 33 + IPR044174
Glycosyltransferase BC10-like + 20 + 22 493 - IPR020946
Flavin monooxygenase-like - 24 - 40 + IPR005516
Remorin, C-terminal + 20 + 24 494 - IPR001849
  - 24 - 120 + IPR001881
EGF-like calcium-binding domain + 20 + 20 495 - IPR033443
Pentacotripeptide-repeat region of PRORP - 24 - 30 + IPR006694
Fatty acid hydroxylase + 20 + 25 496 - IPR001701
Glycoside hydrolase family 9 - 24 - 26 + IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme + 20 + 27 497 - IPR029006
  - 24 - 136 + IPR000639
Epoxide hydrolase-like + 20 + 102 498 - IPR015797
NUDIX hydrolase-like domain superfamily - 24 - 28 + IPR044814
Terpene cyclases, class 1, plant + 20 + 21 499 - IPR036085
PAZ domain superfamily - 23 - 44 + IPR020103
Pseudouridine synthase, catalytic domain superfamily + 20 + 23 500 - IPR015940
  - 23 - 234 + IPR016072
SKP1 component, dimerisation + 20 + 21 diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena.html b/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena.html new file mode 100644 index 00000000..8e6245de --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena.html @@ -0,0 +1,113 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AzucenaRS1, Jan 2020
Database version:87.1
Base Pairs:381,570,127
Golden Path Length:381,570,127
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,626
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,670
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144011168
236468344
338425022
434192892
530954872
631189045
729327599
829168739
923125300
1025095745
1130181525
1227487302
+
+
scaffold
+
25 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg29381761
UN-Ctg30233832
UN-Ctg31132762
UN-Ctg32110596
UN-Ctg3377876
UN-Ctg3475881
UN-Ctg3571076
UN-Ctg3668078
UN-Ctg3767077
UN-Ctg3866648
UN-Ctg3963692
UN-Ctg4061389
UN-Ctg4160908
UN-Ctg4260136
UN-Ctg4350348
UN-Ctg4449169
UN-Ctg4549121
UN-Ctg4639858
UN-Ctg4735926
UN-Ctg4835590
UN-Ctg4933260
UN-Ctg5031184
UN-Ctg5129756
UN-Ctg5228377
UN-Ctg5328273
+
+
chunk3833 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):19,179,181
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena_IPtop500.html new file mode 100644 index 00000000..bc173aac --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativaazucena_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14682085
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14212168
3IPR000719
Protein kinase domain		13783275
4IPR036047
F-box-like domain superfamily		675850
5IPR044974
Disease resistance protein, plants		528934
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		501879
7IPR002885
Pentatricopeptide repeat		4956331
8IPR001810
F-box domain		482903
9IPR002182
NB-ARC		480595
10IPR001611
Leucine-rich repeat		4621515
11IPR001841
Zinc finger, RING-type		432919
12IPR016024
Armadillo-type fold		386613
13IPR041118
Rx, N-terminal		380440
14IPR009057
Homeobox-like domain superfamily		378493
15IPR036291
NAD(P)-binding domain superfamily		371554
16IPR029058
Alpha/Beta hydrolase fold		363535
17IPR011990
Tetratricopeptide-like helical domain superfamily		336529
18IPR036396
Cytochrome P450 superfamily		317412
19IPR001128
Cytochrome P450		3131551
20IPR035979
RNA-binding domain superfamily		309628
21IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		306401
22IPR002401
Cytochrome P450, E-class, group I		2761901
23IPR001005
SANT/Myb domain		2741412
24IPR000504
RNA recognition motif domain		2721174
25IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		270431
26IPR036259
MFS transporter superfamily		260414
27IPR038005
Virus X resistance protein-like, coiled-coil domain		257300
28IPR017853
Glycoside hydrolase superfamily		256382
29IPR038765
Papain-like cysteine peptidase superfamily		246317
30IPR017930
Myb domain		235365
31IPR036322
WD40-repeat-containing domain superfamily		232369
32IPR036249
Thioredoxin-like superfamily		227339
33IPR001680
WD40 repeat		2091790
34IPR011992
EF-hand domain pair		191242
35IPR002048
EF-hand domain		180929
36IPR011333
SKP1/BTB/POZ domain superfamily		179251
37IPR036770
Ankyrin repeat-containing domain superfamily		176259
38IPR036412
HAD-like superfamily		171229
39IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		168398
40IPR012337
Ribonuclease H-like superfamily		165211
41IPR036638
Helix-loop-helix DNA-binding domain superfamily		164195
42IPR016177
DNA-binding domain superfamily		162230
43IPR002110
Ankyrin repeat		160686
44IPR036390
Winged helix DNA-binding domain superfamily		159207
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		157334
46IPR036093
NAC domain superfamily		146171
47IPR001471
AP2/ERF domain		145817
48IPR003441
NAC domain		144331
49IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		144172
50IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		141190
51IPR036236
Zinc finger C2H2 superfamily		141195
52IPR001650
Helicase, C-terminal		140413
53IPR029044
Nucleotide-diphospho-sugar transferases		139174
54IPR010255
Haem peroxidase superfamily		139181
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		137208
56IPR012340
Nucleic acid-binding, OB-fold		136287
57IPR000210
BTB/POZ domain		135387
58IPR036188
FAD/NAD(P)-binding domain superfamily		135234
59IPR002016
Haem peroxidase		135651
60IPR013087
Zinc finger C2H2-type		130242
61IPR020683
Ankyrin repeat-containing domain		130293
62IPR003480
Transferase		128153
63IPR003439
ABC transporter-like, ATP-binding domain		126499
64IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		125177
65IPR005174
Domain unknown function DUF295		124141
66IPR025315
Domain of unknown function DUF4220		122127
67IPR021109
Aspartic peptidase domain superfamily		121158
68IPR007658
Protein of unknown function DUF594		119123
69IPR003959
ATPase, AAA-type, core		116182
70IPR036426
Bulb-type lectin domain superfamily		114163
71IPR020846
Major facilitator superfamily domain		114159
72IPR036869
Chaperone J-domain superfamily		114156
73IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		113133
74IPR033121
Peptidase family A1 domain		111158
75IPR005123
Oxoglutarate/iron-dependent dioxygenase		109382
76IPR045005
BTB/POZ and MATH domain-containing protein 1-6		109182
77IPR001480
Bulb-type lectin domain		109418
78IPR015424
Pyridoxal phosphate-dependent transferase		109151
79IPR019734
Tetratricopeptide repeat		108342
80IPR001623
DnaJ domain		108765
81IPR011011
Zinc finger, FYVE/PHD-type		108162
82IPR001087
GDSL lipase/esterase		107136
83IPR008972
Cupredoxin		104207
84IPR029071
Ubiquitin-like domain superfamily		103163
85IPR036576
WRKY domain superfamily		101130
86IPR003657
WRKY domain		101257
87IPR011050
Pectin lyase fold/virulence factor		100114
88IPR032799
Xylanase inhibitor, C-terminal		99125
89IPR011676
Domain of unknown function DUF1618		99129
90IPR035892
C2 domain superfamily		98197
91IPR002083
MATH/TRAF domain		98325
92IPR032861
Xylanase inhibitor, N-terminal		97122
93IPR000823
Plant peroxidase		95423
94IPR015300
DNA-binding pseudobarrel domain superfamily		95170
95IPR003609
PAN/Apple domain		94240
96IPR044810
WRKY transcription factor, plant		94119
97IPR036457
PPM-type phosphatase domain superfamily		93135
98IPR009072
Histone-fold		93103
99IPR011051
RmlC-like cupin domain superfamily		92119
100IPR000858
S-locus glycoprotein domain		91126
101IPR005828
Major facilitator, sugar transporter-like		91141
102IPR001932
PPM-type phosphatase domain		91388
103IPR011545
DEAD/DEAH box helicase domain		89136
104IPR001356
Homeobox domain		89281
105IPR003340
B3 DNA binding domain		86417
106IPR035669
GDSL lipase/esterase-like, plant		86103
107IPR000008
C2 domain		86411
108IPR002347
Short-chain dehydrogenase/reductase SDR		86812
109IPR020472
G-protein beta WD-40 repeat		85411
110IPR000109
Proton-dependent oligopeptide transporter family		84319
111IPR031052
FHY3/FAR1 family		84157
112IPR003653
Ulp1 protease family, C-terminal catalytic domain		83154
113IPR026992
Non-haem dioxygenase N-terminal domain		83106
114IPR012871
Protein of unknown function DUF1677, Oryza sativa		8197
115IPR004827
Basic-leucine zipper domain		81207
116IPR000073
Alpha/beta hydrolase fold-1		80238
117IPR001461
Aspartic peptidase A1 family		80269
118IPR026961
PGG domain		79175
119IPR013766
Thioredoxin domain		79181
120IPR043129
ATPase, nucleotide binding domain		77194
121IPR004158
Protein of unknown function DUF247, plant		76179
122IPR036282
Glutathione S-transferase, C-terminal domain superfamily		74105
123IPR003613
U box domain		74174
124IPR002902
Gnk2-homologous domain		72378
125IPR002100
Transcription factor, MADS-box		72418
126IPR036879
Transcription factor, MADS-box superfamily		7291
127IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7174
128IPR001220
Legume lectin domain		71174
129IPR004330
FAR1 DNA binding domain		7178
130IPR036163
Heavy metal-associated domain superfamily		70100
131IPR000270
PB1 domain		69119
132IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		69142
133IPR007527
Zinc finger, SWIM-type		68125
134IPR036915
Cyclin-like superfamily		68154
135IPR006121
Heavy metal-associated domain, HMA		67234
136IPR016039
Thiolase-like		67143
137IPR036908
RlpA-like domain superfamily		6781
138IPR001878
Zinc finger, CCHC-type		67151
139IPR008949
Isoprenoid synthase domain superfamily		6685
140IPR036749
Expansin, cellulose-binding-like domain superfamily		6679
141IPR044965
Glycoside hydrolase family 17, plant		66102
142IPR000626
Ubiquitin-like domain		65166
143IPR019787
Zinc finger, PHD-finger		65152
144IPR013057
Amino acid transporter, transmembrane domain		6586
145IPR016159
Cullin repeat-like-containing domain superfamily		6580
146IPR007117
Expansin, cellulose-binding-like domain		65154
147IPR036875
Zinc finger, CCHC-type superfamily		6586
148IPR004045
Glutathione S-transferase, N-terminal		64189
149IPR000048
IQ motif, EF-hand binding site		64364
150IPR018108
Mitochondrial substrate/solute carrier		63505
151IPR022059
Protein of unknown function DUF3615		6372
152IPR023395
Mitochondrial carrier domain superfamily		6391
153IPR006501
Pectinesterase inhibitor domain		6366
154IPR029052
Metallo-dependent phosphatase-like		6385
155IPR000571
Zinc finger, CCCH-type		63314
156IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6271
157IPR020568
Ribosomal protein S5 domain 2-type fold		62106
158IPR010987
Glutathione S-transferase, C-terminal-like		6289
159IPR009003
Peptidase S1, PA clan		62107
160IPR003663
Sugar/inositol transporter		60355
161IPR005202
Transcription factor GRAS		59235
162IPR000490
Glycoside hydrolase family 17		5980
163IPR001806
Small GTPase		59136
164IPR026057
PC-Esterase		5880
165IPR013763
Cyclin-like		58123
166IPR036852
Peptidase S8/S53 domain superfamily		5890
167IPR024788
Malectin-like domain		5878
168IPR000209
Peptidase S8/S53 domain		5887
169IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5787
170IPR003245
Phytocyanin domain		57122
171IPR029962
Trichome birefringence-like family		5682
172IPR039391
Phytocyanin		5667
173IPR007112
Expansin/pollen allergen, DPBB domain		5666
174IPR015915
Kelch-type beta propeller		5688
175IPR041469
Subtilisin-like protease, fibronectin type-III domain		5581
176IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5577
177IPR002921
Fungal lipase-like domain		5467
178IPR045051
Subtilisin-like protease		54106
179IPR006045
Cupin 1		5495
180IPR001752
Kinesin motor domain		54452
181IPR001563
Peptidase S10, serine carboxypeptidase		53406
182IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5368
183IPR009009
RlpA-like protein, double-psi beta-barrel domain		5363
184IPR002528
Multi antimicrobial extrusion protein		53136
185IPR006566
FBD domain		5363
186IPR000225
Armadillo		53240
187IPR016181
Acyl-CoA N-acyltransferase		5264
188IPR025846
PMR5 N-terminal domain		5268
189IPR023298
P-type ATPase, transmembrane domain superfamily		5278
190IPR015500
Peptidase S8, subtilisin-related		52170
191IPR013525
ABC-2 type transporter		51106
192IPR002156
Ribonuclease H domain		5168
193IPR036465
von Willebrand factor A-like domain superfamily		5167
194IPR007118
Expansin/Lol pI		50305
195IPR008250
P-type ATPase, A domain superfamily		5067
196IPR007125
Histone H2A/H2B/H3		5053
197IPR006671
Cyclin, N-terminal		5072
198IPR000608
Ubiquitin-conjugating enzyme E2		49204
199IPR003676
Small auxin-up RNA		4959
200IPR008978
HSP20-like chaperone		4860
201IPR034161
Pepsin-like domain, plant		4860
202IPR008979
Galactose-binding-like domain superfamily		4883
203IPR036855
Zinc finger, CCCH-type superfamily		48124
204IPR044808
Ethylene-responsive transcription factor		4858
205IPR017884
SANT domain		4763
206IPR000873
AMP-dependent synthetase/ligase		4765
207IPR013201
Cathepsin propeptide inhibitor domain (I29)		4760
208IPR030184
WAT1-related protein		4794
209IPR041569
AAA ATPase, AAA+ lid domain		4766
210IPR000620
EamA domain		47109
211IPR029055
Nucleophile aminohydrolases, N-terminal		4669
212IPR014014
RNA helicase, DEAD-box type, Q motif		4668
213IPR004140
Exocyst complex component Exo70		46128
214IPR004265
Dirigent protein		4655
215IPR034197
Cucumisin-like catalytic domain		4666
216IPR033905
Secretory peroxidase		4650
217IPR032867
DYW domain		4649
218IPR001906
Terpene synthase, N-terminal domain		4664
219IPR013094
Alpha/beta hydrolase fold-3		4670
220IPR011032
GroES-like superfamily		4574
221IPR033896
MADS MEF2-like		4564
222IPR036318
FAD-binding, type PCMH-like superfamily		4554
223IPR036640
ABC transporter type 1, transmembrane domain superfamily		45105
224IPR011701
Major facilitator superfamily		4577
225IPR005630
Terpene synthase, metal-binding domain		4558
226IPR008928
Six-hairpin glycosidase superfamily		4558
227IPR011527
ABC transporter type 1, transmembrane domain		45211
228IPR014756
Immunoglobulin E-set		4568
229IPR001117
Multicopper oxidase, type 1		4448
230IPR004853
Sugar phosphate transporter domain		4479
231IPR009000
Translation protein, beta-barrel domain superfamily		4457
232IPR012946
X8 domain		4460
233IPR011006
CheY-like superfamily		4464
234IPR000668
Peptidase C1A, papain C-terminal		44171
235IPR045087
Multicopper oxidase		4459
236IPR000070
Pectinesterase, catalytic		4452
237IPR000743
Glycoside hydrolase, family 28		4453
238IPR000182
GNAT domain		4391
239IPR009060
UBA-like superfamily		4371
240IPR001509
NAD-dependent epimerase/dehydratase		4364
241IPR000742
EGF-like domain		4348
242IPR011706
Multicopper oxidase, C-terminal		4347
243IPR001214
SET domain		43103
244IPR008889
VQ		4345
245IPR011707
Multicopper oxidase, N-termianl		4347
246IPR006702
Casparian strip membrane protein domain		4344
247IPR001789
Signal transduction response regulator, receiver domain		43107
248IPR004263
Exostosin-like		4252
249IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4261
250IPR011012
Longin-like domain superfamily		4267
251IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4253
252IPR033389
AUX/IAA domain		4153
253IPR016040
NAD(P)-binding domain		4165
254IPR010402
CCT domain		41117
255IPR006016
UspA		4153
256IPR016461
O-methyltransferase COMT-type		4097
257IPR000330
SNF2, N-terminal		4069
258IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4056
259IPR036612
K Homology domain, type 1 superfamily		40120
260IPR004046
Glutathione S-transferase, C-terminal		4051
261IPR044730
Ribonuclease H-like domain, plant type		4043
262IPR043926
ABC transporter family G domain		3965
263IPR025322
Protein of unknown function DUF4228, plant		3943
264IPR016166
FAD-binding domain, PCMH-type		3948
265IPR001077
O-methyltransferase domain		3947
266IPR029045
ClpP/crotonase-like domain superfamily		3962
267IPR000644
CBS domain		39194
268IPR011043
Galactose oxidase/kelch, beta-propeller		3945
269IPR039361
Cyclin		3950
270IPR015947
PUA-like superfamily		3955
271IPR025659
Tubby-like, C-terminal		3847
272IPR003137
PA domain		3849
273IPR004839
Aminotransferase, class I/classII		3856
274IPR019378
GDP-fucose protein O-fucosyltransferase		3854
275IPR039417
Papain-like cysteine endopeptidase		3853
276IPR002495
Glycosyl transferase, family 8		3846
277IPR013126
Heat shock protein 70 family		38111
278IPR024752
Myb/SANT-like domain		3840
279IPR008942
ENTH/VHS		3748
280IPR007493
Protein of unknown function DUF538		3775
281IPR002068
Alpha crystallin/Hsp20 domain		3788
282IPR029021
Protein-tyrosine phosphatase-like		3761
283IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3741
284IPR015655
Protein phosphatase 2C family		3764
285IPR033443
Pentacotripeptide-repeat region of PRORP		3745
286IPR040911
Exostosin, GT47 domain		3743
287IPR002912
ACT domain		37108
288IPR012967
Plant methyltransferase dimerisation		3737
289IPR004041
NAF domain		3649
290IPR018451
NAF/FISL domain		3645
291IPR023271
Aquaporin-like		3645
292IPR006652
Kelch repeat type 1		3691
293IPR036758
At5g01610-like superfamily		3638
294IPR000425
Major intrinsic protein		36297
295IPR002067
Mitochondrial carrier protein		36244
296IPR002109
Glutaredoxin		3647
297IPR036041
Ribosome-inactivating protein superfamily		3639
298IPR002487
Transcription factor, K-box		36105
299IPR001574
Ribosome-inactivating protein		3670
300IPR008991
Translation protein SH3-like domain superfamily		3546
301IPR004367
Cyclin, C-terminal domain		3541
302IPR043454
NPH3/RPT2-like family		3560
303IPR004883
Lateral organ boundaries, LOB		3573
304IPR004314
Neprosin		3551
305IPR001360
Glycoside hydrolase family 1		34384
306IPR005299
SAM dependent carboxyl methyltransferase		34108
307IPR027356
NPH3 domain		3496
308IPR022742
Serine aminopeptidase, S33		3443
309IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3455
310IPR028889
Ubiquitin specific protease domain		3449
311IPR001251
CRAL-TRIO lipid binding domain		33137
312IPR038933
Ovate protein family		3334
313IPR005135
Endonuclease/exonuclease/phosphatase		3342
314IPR034294
Aquaporin transporter		3347
315IPR006094
FAD linked oxidase, N-terminal		3341
316IPR043519
Nucleotidyltransferase superfamily		3352
317IPR006311
Twin-arginine translocation pathway, signal sequence		3333
318IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3248
319IPR001296
Glycosyl transferase, family 1		3256
320IPR000795
Translational (tr)-type GTP-binding domain		32227
321IPR036865
CRAL-TRIO lipid binding domain superfamily		3247
322IPR004088
K Homology domain, type 1		32104
323IPR006458
Ovate protein family, C-terminal		3262
324IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3263
325IPR037176
Osmotin/thaumatin-like superfamily		3238
326IPR018490
Cyclic nucleotide-binding-like		3142
327IPR032710
NTF2-like domain superfamily		3138
328IPR029466
No apical meristem-associated, C-terminal domain		3131
329IPR029061
Thiamin diphosphate-binding fold		3176
330IPR001594
Palmitoyltransferase, DHHC domain		3154
331IPR001938
Thaumatin family		31213
332IPR003406
Glycosyl transferase, family 14		3138
333IPR023299
P-type ATPase, cytoplasmic domain N		3145
334IPR006073
GTP binding domain		31118
335IPR015940
Ubiquitin-associated domain		3098
336IPR001929
Germin		3095
337IPR013149
Alcohol dehydrogenase, C-terminal		3037
338IPR044835
Auxin response factor		3056
339IPR044822
Myb/SANT-like DNA-binding domain 4		3041
340IPR000315
B-box-type zinc finger		3086
341IPR000717
Proteasome component (PCI) domain		3065
342IPR002659
Glycosyl transferase, family 31		3094
343IPR035940
CAP superfamily		3037
344IPR002423
Chaperonin Cpn60/TCP-1 family		3045
345IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3036
346IPR013154
Alcohol dehydrogenase, N-terminal		3038
347IPR002963
Expansin		30253
348IPR003851
Zinc finger, Dof-type		3070
349IPR001223
Glycoside hydrolase family 18, catalytic domain		3077
350IPR011141
Polyketide synthase, type III		3041
351IPR025110
AMP-binding enzyme, C-terminal domain		2933
352IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		29120
353IPR019557
Aminotransferase-like, plant mobile domain		2933
354IPR007650
Zf-FLZ domain		2975
355IPR000863
Sulfotransferase domain		2943
356IPR004813
Oligopeptide transporter, OPT superfamily		2957
357IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2943
358IPR012328
Chalcone/stilbene synthase, C-terminal		2931
359IPR000595
Cyclic nucleotide-binding domain		2997
360IPR003855
Potassium transporter		29111
361IPR001099
Chalcone/stilbene synthase, N-terminal		2936
362IPR036378
FAS1 domain superfamily		2838
363IPR006153
Cation/H+ exchanger		2835
364IPR029000
Cyclophilin-like domain superfamily		2841
365IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2899
366IPR024709
Putative O-fucosyltransferase, plant		2844
367IPR010920
LSM domain superfamily		2838
368IPR040417
Glycine-rich cell wall structural protein 1/2		2839
369IPR044848
PHR1-like		2839
370IPR005150
Cellulose synthase		2864
371IPR003690
Transcription termination factor, mitochondrial/chloroplastic		28102
372IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2834
373IPR001283
Cysteine-rich secretory protein-related		28100
374IPR008480
Protein of unknown function DUF761, plant		2828
375IPR016897
S-phase kinase-associated protein 1		2834
376IPR027409
GroEL-like apical domain superfamily		2838
377IPR036296
SKP1-like, dimerisation domain superfamily		2833
378IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2835
379IPR000727
Target SNARE coiled-coil homology domain		2752
380IPR036420
BRCT domain superfamily		2749
381IPR027725
Heat shock transcription factor family		2734
382IPR005333
Transcription factor, TCP		2729
383IPR003337
Trehalose-phosphatase		2737
384IPR000408
Regulator of chromosome condensation, RCC1		27674
385IPR011013
Galactose mutarotase-like domain superfamily		2741
386IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2735
387IPR014044
CAP domain		2733
388IPR029062
Class I glutamine amidotransferase-like		2750
389IPR003311
AUX/IAA protein		2740
390IPR036812
NADP-dependent oxidoreductase domain superfamily		2745
391IPR000679
Zinc finger, GATA-type		27115
392IPR000757
Glycoside hydrolase family 16		2777
393IPR002913
START domain		2781
394IPR000528
Plant non-specific lipid-transfer protein/Par allergen		26140
395IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		26225
396IPR001357
BRCT domain		2675
397IPR044778
Sugar transport protein STP/MST-like, plant		2630
398IPR007657
Glycosyltransferase 61		2674
399IPR002123
Phospholipid/glycerol acyltransferase		2629
400IPR036273
CRAL/TRIO, N-terminal domain superfamily		2635
401IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2640
402IPR027923
Hydrophobic seed protein domain		2669
403IPR001701
Glycoside hydrolase family 9		2634
404IPR044791
Beta-glucanase/XTH		2641
405IPR000232
Heat shock factor (HSF)-type, DNA-binding		26114
406IPR036034
PDZ superfamily		2637
407IPR005175
PPC domain		2683
408IPR015797
NUDIX hydrolase-like domain superfamily		2630
409IPR036085
PAZ domain superfamily		2542
410IPR017938
Riboflavin synthase-like beta-barrel		2536
411IPR000782
FAS1 domain		2560
412IPR004316
SWEET sugar transporter		2544
413IPR013187
F-box associated domain, type 3		2530
414IPR025753
AAA-type ATPase, N-terminal domain		2528
415IPR021790
PTBP1, RNA recognition motif 2-like		2534
416IPR012416
CALMODULIN-BINDING PROTEIN60		2579
417IPR009030
Growth factor receptor cysteine-rich domain superfamily		2533
418IPR004320
Protein of unknown function DUF241, plant		2534
419IPR004014
Cation-transporting P-type ATPase, N-terminal		2534
420IPR016072
SKP1 component, dimerisation		2530
421IPR005821
Ion transport domain		2532
422IPR001849
Pleckstrin homology domain		2559
423IPR001757
P-type ATPase		25122
424IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2535
425IPR002937
Amine oxidase		2539
426IPR017927
FAD-binding domain, ferredoxin reductase-type		2434
427IPR003100
PAZ domain		2481
428IPR013601
FAE1/Type III polyketide synthase-like protein		2429
429IPR008971
HSP40/DnaJ peptide-binding		2459
430IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2430
431IPR022149
Protein of unknown function DUF3681		2450
432IPR023753
FAD/NAD(P)-binding domain		2436
433IPR026960
Reverse transcriptase zinc-binding domain		2424
434IPR001881
EGF-like calcium-binding domain		2435
435IPR001763
Rhodanese-like domain		2460
436IPR006461
PLAC8 motif-containing protein		2453
437IPR034285
Laccase, second cupredoxin domain		2427
438IPR002035
von Willebrand factor, type A		2460
439IPR029069
HotDog domain superfamily		2447
440IPR002939
Chaperone DnaJ, C-terminal		2432
441IPR000086
NUDIX hydrolase domain		2454
442IPR036404
Jacalin-like lectin domain superfamily		2437
443IPR023210
NADP-dependent oxidoreductase domain		2450
444IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2436
445IPR029033
Histidine phosphatase superfamily		2432
446IPR010525
Auxin response factor domain		2437
447IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2335
448IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2326
449IPR011016
Zinc finger, RING-CH-type		2382
450IPR001163
LSM domain, eukaryotic/archaea-type		2328
451IPR008422
Homeobox KN domain		2332
452IPR001353
Proteasome, subunit alpha/beta		2329
453IPR025422
Transcription factor TGA like domain		2357
454IPR007592
GLABROUS1 enhancer-binding protein family		2350
455IPR044839
Protein NDR1-like		2324
456IPR041677
DNA2/NAM7 helicase, helicase domain		2339
457IPR025486
Domain of unknown function DUF4378		2336
458IPR036443
Zinc finger, RanBP2-type superfamily		2354
459IPR016073
SKP1 component, POZ domain		2225
460IPR000387
Tyrosine specific protein phosphatases domain		2239
461IPR001440
Tetratricopeptide repeat 1		2236
462IPR013581
Plant PDR ABC transporter associated		2232
463IPR013216
Methyltransferase type 11		2234
464IPR017887
Transcription factor TCP subgroup		2244
465IPR003656
Zinc finger, BED-type		2240
466IPR010989
SNARE		2224
467IPR003594
Histidine kinase/HSP90-like ATPase		2233
468IPR044675
E3 ubiquitin-protein ligase RING1-like		2225
469IPR020103
Pseudouridine synthase, catalytic domain superfamily		2228
470IPR020946
Flavin monooxygenase-like		2240
471IPR041679
DNA2/NAM7 helicase-like, C-terminal		2253
472IPR039421
Type 1 protein exporter		2241
473IPR036427
Bromodomain-like superfamily		2232
474IPR031127
E3 ubiquitin ligase RBR family		2244
475IPR006868
Domain of unknown function DUF630		2225
476IPR001229
Jacalin-like lectin domain		2270
477IPR004274
FCP1 homology domain		2271
478IPR033133
Pumilio homology domain		2124
479IPR003106
Leucine zipper, homeobox-associated		2121
480IPR007612
LURP-one-related		2152
481IPR003347
JmjC domain		2145
482IPR018392
LysM domain		2172
483IPR005516
Remorin, C-terminal		2127
484IPR036010
2Fe-2S ferredoxin-like superfamily		2124
485IPR027413
GroEL-like equatorial domain superfamily		2130
486IPR045048
F-box only protein 31/39		2162
487IPR020422
Dual specificity protein phosphatase domain		2133
488IPR021720
Malectin domain		2142
489IPR029057
Phosphoribosyltransferase-like		2135
490IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		2130
491IPR022796
Chlorophyll A-B binding protein		2127
492IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2125
493IPR001876
Zinc finger, RanBP2-type		2185
494IPR016161
Aldehyde/histidinol dehydrogenase		2133
495IPR001487
Bromodomain		21145
496IPR013809
ENTH domain		2131
497IPR006867
Domain of unknown function DUF632		2126
498IPR006689
Small GTPase superfamily, ARF/SAR type		20125
499IPR006593
Cytochrome b561/ferric reductase transmembrane		2041
500IPR002867
IBR domain		2047
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativair64.html b/gramene/htdocs/ssi/species/stats_Oryza_sativair64.html new file mode 100644 index 00000000..006de840 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativair64.html @@ -0,0 +1,96 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:OsIR64RS1, Jan 2020
Database version:87.1
Base Pairs:387,434,309
Golden Path Length:387,434,309
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		36,102
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:44,230
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144350042
237111999
338826278
435281998
531013547
632151555
731201142
830180556
924266242
1025557007
1131218896
1225539636
+
+
scaffold
+
8 sequences
+
+ +
+ + + +
SequenceLength (bp)
UN-Ctg121175574
UN-Ctg122150475
UN-Ctg12390242
UN-Ctg12480695
UN-Ctg12566796
UN-Ctg12664747
UN-Ctg12755084
UN-Ctg12851798
+
+
chunk3884 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):18,998,256
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14762076
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14272219
3IPR000719
Protein kinase domain		13783243
4IPR036047
F-box-like domain superfamily		667845
5IPR044974
Disease resistance protein, plants		531896
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		506862
7IPR002885
Pentatricopeptide repeat		5006302
8IPR002182
NB-ARC		490590
9IPR001611
Leucine-rich repeat		4741552
10IPR001810
F-box domain		473880
11IPR001841
Zinc finger, RING-type		427886
12IPR041118
Rx, N-terminal		393442
13IPR016024
Armadillo-type fold		389640
14IPR009057
Homeobox-like domain superfamily		385497
15IPR036291
NAD(P)-binding domain superfamily		382579
16IPR029058
Alpha/Beta hydrolase fold		370536
17IPR011990
Tetratricopeptide-like helical domain superfamily		339535
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		319411
19IPR036396
Cytochrome P450 superfamily		307407
20IPR035979
RNA-binding domain superfamily		300615
21IPR001128
Cytochrome P450		2991494
22IPR038005
Virus X resistance protein-like, coiled-coil domain		271305
23IPR000504
RNA recognition motif domain		2691143
24IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		264395
25IPR017853
Glycoside hydrolase superfamily		262379
26IPR002401
Cytochrome P450, E-class, group I		2591800
27IPR036259
MFS transporter superfamily		251396
28IPR017930
Myb domain		240725
29IPR001005
SANT/Myb domain		237720
30IPR036322
WD40-repeat-containing domain superfamily		236360
31IPR036249
Thioredoxin-like superfamily		235349
32IPR038765
Papain-like cysteine peptidase superfamily		232289
33IPR001680
WD40 repeat		2091714
34IPR011992
EF-hand domain pair		186241
35IPR002048
EF-hand domain		177929
36IPR036770
Ankyrin repeat-containing domain superfamily		173244
37IPR016177
DNA-binding domain superfamily		168237
38IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		168392
39IPR036412
HAD-like superfamily		168234
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		164192
41IPR011333
SKP1/BTB/POZ domain superfamily		163240
42IPR002110
Ankyrin repeat		160682
43IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		155330
44IPR036390
Winged helix DNA-binding domain superfamily		154205
45IPR001471
AP2/ERF domain		151838
46IPR012337
Ribonuclease H-like superfamily		151187
47IPR005174
Domain unknown function DUF295		151178
48IPR036093
NAC domain superfamily		148172
49IPR003441
NAC domain		145332
50IPR029044
Nucleotide-diphospho-sugar transferases		144177
51IPR001650
Helicase, C-terminal		142447
52IPR014001
Helicase superfamily 1/2, ATP-binding domain		139222
53IPR036236
Zinc finger C2H2 superfamily		138199
54IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		137167
55IPR010255
Haem peroxidase superfamily		137175
56IPR012340
Nucleic acid-binding, OB-fold		136268
57IPR013087
Zinc finger C2H2-type		134246
58IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		133176
59IPR036188
FAD/NAD(P)-binding domain superfamily		132231
60IPR002016
Haem peroxidase		128609
61IPR020683
Ankyrin repeat-containing domain		127285
62IPR003439
ABC transporter-like, ATP-binding domain		127505
63IPR000210
BTB/POZ domain		123373
64IPR003959
ATPase, AAA-type, core		121184
65IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		120170
66IPR021109
Aspartic peptidase domain superfamily		118157
67IPR036426
Bulb-type lectin domain superfamily		116160
68IPR007658
Protein of unknown function DUF594		114117
69IPR020846
Major facilitator superfamily domain		114161
70IPR025315
Domain of unknown function DUF4220		113123
71IPR003480
Transferase		113134
72IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		112131
73IPR001480
Bulb-type lectin domain		111398
74IPR015424
Pyridoxal phosphate-dependent transferase		109145
75IPR036869
Chaperone J-domain superfamily		109149
76IPR008972
Cupredoxin		107208
77IPR011011
Zinc finger, FYVE/PHD-type		107161
78IPR019734
Tetratricopeptide repeat		106334
79IPR001087
GDSL lipase/esterase		106137
80IPR033121
Peptidase family A1 domain		105154
81IPR003657
WRKY domain		105259
82IPR036576
WRKY domain superfamily		104130
83IPR001623
DnaJ domain		103710
84IPR032861
Xylanase inhibitor, N-terminal		103130
85IPR011676
Domain of unknown function DUF1618		103140
86IPR029071
Ubiquitin-like domain superfamily		102153
87IPR032799
Xylanase inhibitor, C-terminal		100127
88IPR036457
PPM-type phosphatase domain superfamily		97143
89IPR011050
Pectin lyase fold/virulence factor		97109
90IPR035892
C2 domain superfamily		96193
91IPR044810
WRKY transcription factor, plant		96121
92IPR001932
PPM-type phosphatase domain		95399
93IPR005123
Oxoglutarate/iron-dependent dioxygenase		94131
94IPR045005
BTB/POZ and MATH domain-containing protein 1-6		93169
95IPR000858
S-locus glycoprotein domain		92124
96IPR009072
Histone-fold		92104
97IPR003609
PAN/Apple domain		91221
98IPR011545
DEAD/DEAH box helicase domain		91144
99IPR002347
Short-chain dehydrogenase/reductase SDR		90826
100IPR001356
Homeobox domain		90291
101IPR015300
DNA-binding pseudobarrel domain superfamily		89164
102IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		88126
103IPR011051
RmlC-like cupin domain superfamily		88119
104IPR005828
Major facilitator, sugar transporter-like		86134
105IPR002083
MATH/TRAF domain		86306
106IPR000823
Plant peroxidase		86365
107IPR035669
GDSL lipase/esterase-like, plant		85104
108IPR000008
C2 domain		85403
109IPR000109
Proton-dependent oligopeptide transporter family		85289
110IPR026961
PGG domain		85178
111IPR004158
Protein of unknown function DUF247, plant		85208
112IPR020472
G-protein beta WD-40 repeat		84387
113IPR013766
Thioredoxin domain		84195
114IPR000073
Alpha/beta hydrolase fold-1		84238
115IPR003340
B3 DNA binding domain		81432
116IPR043129
ATPase, nucleotide binding domain		81199
117IPR001461
Aspartic peptidase A1 family		80278
118IPR004827
Basic-leucine zipper domain		80203
119IPR026992
Non-haem dioxygenase N-terminal domain		79115
120IPR036875
Zinc finger, CCHC-type superfamily		7997
121IPR004330
FAR1 DNA binding domain		7886
122IPR002902
Gnk2-homologous domain		77383
123IPR031052
FHY3/FAR1 family		76142
124IPR001878
Zinc finger, CCHC-type		76154
125IPR012871
Protein of unknown function DUF1677, Oryza sativa		7590
126IPR036282
Glutathione S-transferase, C-terminal domain superfamily		75107
127IPR003613
U box domain		73167
128IPR008949
Isoprenoid synthase domain superfamily		7286
129IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		72128
130IPR003653
Ulp1 protease family, C-terminal catalytic domain		71133
131IPR016039
Thiolase-like		70153
132IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7074
133IPR036163
Heavy metal-associated domain superfamily		70101
134IPR007527
Zinc finger, SWIM-type		70121
135IPR006121
Heavy metal-associated domain, HMA		68239
136IPR036908
RlpA-like domain superfamily		6884
137IPR016159
Cullin repeat-like-containing domain superfamily		6883
138IPR004045
Glutathione S-transferase, N-terminal		67202
139IPR000270
PB1 domain		67123
140IPR044965
Glycoside hydrolase family 17, plant		66104
141IPR002100
Transcription factor, MADS-box		65402
142IPR036879
Transcription factor, MADS-box superfamily		6586
143IPR000571
Zinc finger, CCCH-type		65319
144IPR019787
Zinc finger, PHD-finger		64150
145IPR013057
Amino acid transporter, transmembrane domain		6487
146IPR029052
Metallo-dependent phosphatase-like		6495
147IPR036915
Cyclin-like superfamily		64139
148IPR022059
Protein of unknown function DUF3615		6378
149IPR020568
Ribosomal protein S5 domain 2-type fold		63101
150IPR001220
Legume lectin domain		63159
151IPR000048
IQ motif, EF-hand binding site		63359
152IPR000626
Ubiquitin-like domain		62152
153IPR036749
Expansin, cellulose-binding-like domain superfamily		6274
154IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6272
155IPR036852
Peptidase S8/S53 domain superfamily		6280
156IPR010987
Glutathione S-transferase, C-terminal-like		6291
157IPR007117
Expansin, cellulose-binding-like domain		62145
158IPR009003
Peptidase S1, PA clan		62100
159IPR000209
Peptidase S8/S53 domain		6279
160IPR018108
Mitochondrial substrate/solute carrier		61485
161IPR023395
Mitochondrial carrier domain superfamily		6186
162IPR001806
Small GTPase		61144
163IPR005202
Transcription factor GRAS		60214
164IPR006501
Pectinesterase inhibitor domain		6063
165IPR003663
Sugar/inositol transporter		60332
166IPR026057
PC-Esterase		5981
167IPR003245
Phytocyanin domain		59125
168IPR000490
Glycoside hydrolase family 17		5982
169IPR041469
Subtilisin-like protease, fibronectin type-III domain		5870
170IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5888
171IPR045051
Subtilisin-like protease		5898
172IPR039391
Phytocyanin		5870
173IPR016135
Ubiquitin-conjugating enzyme/RWD-like		5876
174IPR024788
Malectin-like domain		5775
175IPR011032
GroES-like superfamily		5687
176IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5667
177IPR029962
Trichome birefringence-like family		5683
178IPR001752
Kinesin motor domain		55431
179IPR015500
Peptidase S8, subtilisin-related		55175
180IPR001563
Peptidase S10, serine carboxypeptidase		54406
181IPR015915
Kelch-type beta propeller		5482
182IPR000225
Armadillo		54233
183IPR013763
Cyclin-like		53108
184IPR007112
Expansin/pollen allergen, DPBB domain		5363
185IPR025846
PMR5 N-terminal domain		5370
186IPR036465
von Willebrand factor A-like domain superfamily		5372
187IPR013525
ABC-2 type transporter		52111
188IPR002156
Ribonuclease H domain		5268
189IPR006045
Cupin 1		5295
190IPR013201
Cathepsin propeptide inhibitor domain (I29)		5156
191IPR002528
Multi antimicrobial extrusion protein		51131
192IPR032867
DYW domain		5156
193IPR023298
P-type ATPase, transmembrane domain superfamily		5169
194IPR002921
Fungal lipase-like domain		5065
195IPR034161
Pepsin-like domain, plant		5065
196IPR009009
RlpA-like protein, double-psi beta-barrel domain		5059
197IPR005630
Terpene synthase, metal-binding domain		5062
198IPR004140
Exocyst complex component Exo70		50131
199IPR034197
Cucumisin-like catalytic domain		5061
200IPR000608
Ubiquitin-conjugating enzyme E2		49178
201IPR008250
P-type ATPase, A domain superfamily		4967
202IPR008979
Galactose-binding-like domain superfamily		4989
203IPR003676
Small auxin-up RNA		4960
204IPR017884
SANT domain		4860
205IPR016181
Acyl-CoA N-acyltransferase		4856
206IPR030184
WAT1-related protein		4880
207IPR000620
EamA domain		48100
208IPR044808
Ethylene-responsive transcription factor		4857
209IPR008978
HSP20-like chaperone		4760
210IPR007118
Expansin/Lol pI		47275
211IPR008928
Six-hairpin glycosidase superfamily		4758
212IPR007125
Histone H2A/H2B/H3		4748
213IPR006566
FBD domain		4758
214IPR001906
Terpene synthase, N-terminal domain		4759
215IPR041569
AAA ATPase, AAA+ lid domain		4767
216IPR036640
ABC transporter type 1, transmembrane domain superfamily		46100
217IPR009060
UBA-like superfamily		4675
218IPR009000
Translation protein, beta-barrel domain superfamily		4668
219IPR014014
RNA helicase, DEAD-box type, Q motif		4664
220IPR000742
EGF-like domain		4647
221IPR011527
ABC transporter type 1, transmembrane domain		46200
222IPR006671
Cyclin, N-terminal		4660
223IPR014756
Immunoglobulin E-set		4667
224IPR013094
Alpha/beta hydrolase fold-3		4670
225IPR036318
FAD-binding, type PCMH-like superfamily		4556
226IPR004853
Sugar phosphate transporter domain		4579
227IPR011701
Major facilitator superfamily		4583
228IPR000873
AMP-dependent synthetase/ligase		4566
229IPR036855
Zinc finger, CCCH-type superfamily		45119
230IPR001117
Multicopper oxidase, type 1		4447
231IPR001509
NAD-dependent epimerase/dehydratase		4465
232IPR029055
Nucleophile aminohydrolases, N-terminal		4460
233IPR004263
Exostosin-like		4451
234IPR012946
X8 domain		4462
235IPR011006
CheY-like superfamily		4464
236IPR045087
Multicopper oxidase		4456
237IPR001214
SET domain		44107
238IPR011707
Multicopper oxidase, N-termianl		4447
239IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4362
240IPR004265
Dirigent protein		4352
241IPR011706
Multicopper oxidase, C-terminal		4347
242IPR044730
Ribonuclease H-like domain, plant type		4345
243IPR000070
Pectinesterase, catalytic		4352
244IPR008889
VQ		4344
245IPR015947
PUA-like superfamily		4254
246IPR006702
Casparian strip membrane protein domain		4243
247IPR001789
Signal transduction response regulator, receiver domain		42107
248IPR000182
GNAT domain		4185
249IPR006016
UspA		4149
250IPR033896
MADS MEF2-like		4162
251IPR007493
Protein of unknown function DUF538		4188
252IPR000330
SNF2, N-terminal		4175
253IPR033905
Secretory peroxidase		4148
254IPR011012
Longin-like domain superfamily		4161
255IPR036758
At5g01610-like superfamily		4145
256IPR000668
Peptidase C1A, papain C-terminal		41160
257IPR011043
Galactose oxidase/kelch, beta-propeller		4150
258IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4151
259IPR000743
Glycoside hydrolase, family 28		4149
260IPR033389
AUX/IAA domain		4059
261IPR016040
NAD(P)-binding domain		4064
262IPR043926
ABC transporter family G domain		4075
263IPR036612
K Homology domain, type 1 superfamily		40127
264IPR016461
O-methyltransferase COMT-type		3988
265IPR015655
Protein phosphatase 2C family		3962
266IPR002495
Glycosyl transferase, family 8		3950
267IPR013126
Heat shock protein 70 family		39104
268IPR008942
ENTH/VHS		3852
269IPR010402
CCT domain		38100
270IPR025322
Protein of unknown function DUF4228, plant		3841
271IPR025659
Tubby-like, C-terminal		3851
272IPR029021
Protein-tyrosine phosphatase-like		3862
273IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3856
274IPR003137
PA domain		3849
275IPR016166
FAD-binding domain, PCMH-type		3849
276IPR029045
ClpP/crotonase-like domain superfamily		3861
277IPR040911
Exostosin, GT47 domain		3842
278IPR000644
CBS domain		38161
279IPR039361
Cyclin		3853
280IPR002912
ACT domain		38113
281IPR013149
Alcohol dehydrogenase, C-terminal		3747
282IPR013154
Alcohol dehydrogenase, N-terminal		3746
283IPR004839
Aminotransferase, class I/classII		3752
284IPR001077
O-methyltransferase domain		3746
285IPR019378
GDP-fucose protein O-fucosyltransferase		3753
286IPR001360
Glycoside hydrolase family 1		36344
287IPR002068
Alpha crystallin/Hsp20 domain		3688
288IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3640
289IPR004883
Lateral organ boundaries, LOB		3678
290IPR039417
Papain-like cysteine endopeptidase		3641
291IPR002109
Glutaredoxin		3644
292IPR024752
Myb/SANT-like domain		3636
293IPR002487
Transcription factor, K-box		36111
294IPR037176
Osmotin/thaumatin-like superfamily		3642
295IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3553
296IPR001938
Thaumatin family		35248
297IPR022742
Serine aminopeptidase, S33		3548
298IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3556
299IPR004046
Glutathione S-transferase, C-terminal		3547
300IPR002067
Mitochondrial carrier protein		35234
301IPR004041
NAF domain		3445
302IPR018451
NAF/FISL domain		3445
303IPR000795
Translational (tr)-type GTP-binding domain		34310
304IPR023271
Aquaporin-like		3448
305IPR004367
Cyclin, C-terminal domain		3439
306IPR043454
NPH3/RPT2-like family		3461
307IPR000425
Major intrinsic protein		34314
308IPR033443
Pentacotripeptide-repeat region of PRORP		3446
309IPR028889
Ubiquitin specific protease domain		3450
310IPR006311
Twin-arginine translocation pathway, signal sequence		3437
311IPR001251
CRAL-TRIO lipid binding domain		33150
312IPR036865
CRAL-TRIO lipid binding domain superfamily		3353
313IPR004088
K Homology domain, type 1		33111
314IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3361
315IPR032710
NTF2-like domain superfamily		3243
316IPR008991
Translation protein SH3-like domain superfamily		3244
317IPR038933
Ovate protein family		3233
318IPR034294
Aquaporin transporter		3252
319IPR000863
Sulfotransferase domain		3242
320IPR006094
FAD linked oxidase, N-terminal		3241
321IPR006458
Ovate protein family, C-terminal		3262
322IPR004314
Neprosin		3241
323IPR043519
Nucleotidyltransferase superfamily		3253
324IPR036041
Ribosome-inactivating protein superfamily		3233
325IPR012967
Plant methyltransferase dimerisation		3232
326IPR000528
Plant non-specific lipid-transfer protein/Par allergen		31145
327IPR018490
Cyclic nucleotide-binding-like		3139
328IPR005299
SAM dependent carboxyl methyltransferase		3188
329IPR001296
Glycosyl transferase, family 1		3158
330IPR001594
Palmitoyltransferase, DHHC domain		3152
331IPR005135
Endonuclease/exonuclease/phosphatase		3142
332IPR027356
NPH3 domain		3191
333IPR006652
Kelch repeat type 1		3182
334IPR011013
Galactose mutarotase-like domain superfamily		3146
335IPR000595
Cyclic nucleotide-binding domain		3196
336IPR001223
Glycoside hydrolase family 18, catalytic domain		3177
337IPR006073
GTP binding domain		31112
338IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		30119
339IPR044822
Myb/SANT-like DNA-binding domain 4		3037
340IPR000315
B-box-type zinc finger		3080
341IPR029061
Thiamin diphosphate-binding fold		3078
342IPR035940
CAP superfamily		3038
343IPR002423
Chaperonin Cpn60/TCP-1 family		3047
344IPR027409
GroEL-like apical domain superfamily		3040
345IPR023299
P-type ATPase, cytoplasmic domain N		3045
346IPR003851
Zinc finger, Dof-type		3070
347IPR003855
Potassium transporter		30127
348IPR011141
Polyketide synthase, type III		3036
349IPR001099
Chalcone/stilbene synthase, N-terminal		3035
350IPR001574
Ribosome-inactivating protein		3060
351IPR013601
FAE1/Type III polyketide synthase-like protein		2938
352IPR000717
Proteasome component (PCI) domain		2970
353IPR005150
Cellulose synthase		2969
354IPR003406
Glycosyl transferase, family 14		2936
355IPR003690
Transcription termination factor, mitochondrial/chloroplastic		29104
356IPR001283
Cysteine-rich secretory protein-related		29106
357IPR008480
Protein of unknown function DUF761, plant		2930
358IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2935
359IPR025110
AMP-binding enzyme, C-terminal domain		2832
360IPR015940
Ubiquitin-associated domain		2899
361IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2839
362IPR006153
Cation/H+ exchanger		2834
363IPR025753
AAA-type ATPase, N-terminal domain		2832
364IPR024709
Putative O-fucosyltransferase, plant		2845
365IPR010920
LSM domain superfamily		2836
366IPR002659
Glycosyl transferase, family 31		2889
367IPR005333
Transcription factor, TCP		2830
368IPR007650
Zf-FLZ domain		2870
369IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2833
370IPR016897
S-phase kinase-associated protein 1		2833
371IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2842
372IPR012328
Chalcone/stilbene synthase, C-terminal		2828
373IPR036296
SKP1-like, dimerisation domain superfamily		2832
374IPR001701
Glycoside hydrolase family 9		2833
375IPR044791
Beta-glucanase/XTH		2840
376IPR000757
Glycoside hydrolase family 16		2868
377IPR002913
START domain		2889
378IPR000727
Target SNARE coiled-coil homology domain		2751
379IPR036085
PAZ domain superfamily		2741
380IPR036378
FAS1 domain superfamily		2740
381IPR001929
Germin		2794
382IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		27221
383IPR029000
Cyclophilin-like domain superfamily		2739
384IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2793
385IPR044835
Auxin response factor		2766
386IPR044848
PHR1-like		2738
387IPR003337
Trehalose-phosphatase		2741
388IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2738
389IPR016072
SKP1 component, dimerisation		2730
390IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2734
391IPR002963
Expansin		27230
392IPR005821
Ion transport domain		2736
393IPR029062
Class I glutamine amidotransferase-like		2754
394IPR003311
AUX/IAA protein		2740
395IPR015797
NUDIX hydrolase-like domain superfamily		2734
396IPR017927
FAD-binding domain, ferredoxin reductase-type		2639
397IPR003100
PAZ domain		2678
398IPR017938
Riboflavin synthase-like beta-barrel		2639
399IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2633
400IPR040417
Glycine-rich cell wall structural protein 1/2		2636
401IPR000408
Regulator of chromosome condensation, RCC1		26654
402IPR036273
CRAL/TRIO, N-terminal domain superfamily		2637
403IPR004014
Cation-transporting P-type ATPase, N-terminal		2632
404IPR014044
CAP domain		2632
405IPR002035
von Willebrand factor, type A		2661
406IPR001757
P-type ATPase		26125
407IPR036404
Jacalin-like lectin domain superfamily		2637
408IPR036812
NADP-dependent oxidoreductase domain superfamily		2647
409IPR005175
PPC domain		2683
410IPR036420
BRCT domain superfamily		2554
411IPR027725
Heat shock transcription factor family		2532
412IPR001881
EGF-like calcium-binding domain		2534
413IPR001763
Rhodanese-like domain		2555
414IPR002123
Phospholipid/glycerol acyltransferase		2528
415IPR045048
F-box only protein 31/39		2565
416IPR004813
Oligopeptide transporter, OPT superfamily		2554
417IPR001849
Pleckstrin homology domain		2556
418IPR029069
HotDog domain superfamily		2553
419IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2530
420IPR036034
PDZ superfamily		2534
421IPR000679
Zinc finger, GATA-type		25102
422IPR001229
Jacalin-like lectin domain		2567
423IPR000782
FAS1 domain		2463
424IPR022149
Protein of unknown function DUF3681		2453
425IPR013187
F-box associated domain, type 3		2427
426IPR001357
BRCT domain		2486
427IPR044778
Sugar transport protein STP/MST-like, plant		2428
428IPR011016
Zinc finger, RING-CH-type		2480
429IPR008422
Homeobox KN domain		2431
430IPR007657
Glycosyltransferase 61		2472
431IPR019557
Aminotransferase-like, plant mobile domain		2428
432IPR003594
Histidine kinase/HSP90-like ATPase		2434
433IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2445
434IPR041677
DNA2/NAM7 helicase, helicase domain		2455
435IPR000086
NUDIX hydrolase domain		2460
436IPR000232
Heat shock factor (HSF)-type, DNA-binding		24105
437IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2433
438IPR008971
HSP40/DnaJ peptide-binding		2350
439IPR003106
Leucine zipper, homeobox-associated		2323
440IPR002867
IBR domain		2344
441IPR029466
No apical meristem-associated, C-terminal domain		2323
442IPR001163
LSM domain, eukaryotic/archaea-type		2327
443IPR013216
Methyltransferase type 11		2330
444IPR023753
FAD/NAD(P)-binding domain		2332
445IPR018392
LysM domain		2382
446IPR044675
E3 ubiquitin-protein ligase RING1-like		2326
447IPR020103
Pseudouridine synthase, catalytic domain superfamily		2332
448IPR027923
Hydrophobic seed protein domain		2367
449IPR034285
Laccase, second cupredoxin domain		2326
450IPR002939
Chaperone DnaJ, C-terminal		2328
451IPR025486
Domain of unknown function DUF4378		2335
452IPR031127
E3 ubiquitin ligase RBR family		2342
453IPR023210
NADP-dependent oxidoreductase domain		2351
454IPR007811
DNA-directed RNA polymerase III subunit RPC4		2345
455IPR002937
Amine oxidase		2337
456IPR029033
Histidine phosphatase superfamily		2330
457IPR036443
Zinc finger, RanBP2-type superfamily		2367
458IPR010525
Auxin response factor domain		2345
459IPR006689
Small GTPase superfamily, ARF/SAR type		22160
460IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2237
461IPR004316
SWEET sugar transporter		2246
462IPR000387
Tyrosine specific protein phosphatases domain		2241
463IPR008999
Actin-crosslinking		2226
464IPR013581
Plant PDR ABC transporter associated		2233
465IPR017887
Transcription factor TCP subgroup		2244
466IPR036010
2Fe-2S ferredoxin-like superfamily		2226
467IPR011257
DNA glycosylase		2227
468IPR025422
Transcription factor TGA like domain		2259
469IPR010989
SNARE		2223
470IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2227
471IPR041679
DNA2/NAM7 helicase-like, C-terminal		2281
472IPR039421
Type 1 protein exporter		2237
473IPR016161
Aldehyde/histidinol dehydrogenase		2234
474IPR036427
Bromodomain-like superfamily		2235
475IPR044066
TRIAD supradomain		2228
476IPR033133
Pumilio homology domain		2122
477IPR004000
Actin family		21159
478IPR016073
SKP1 component, POZ domain		2124
479IPR007612
LURP-one-related		2154
480IPR001440
Tetratricopeptide repeat 1		2132
481IPR003347
JmjC domain		2141
482IPR021790
PTBP1, RNA recognition motif 2-like		2130
483IPR036186
Serpin superfamily		2129
484IPR009030
Growth factor receptor cysteine-rich domain superfamily		2126
485IPR004320
Protein of unknown function DUF241, plant		2127
486IPR001353
Proteasome, subunit alpha/beta		2128
487IPR027413
GroEL-like equatorial domain superfamily		2130
488IPR020422
Dual specificity protein phosphatase domain		2132
489IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2128
490IPR021720
Malectin domain		2141
491IPR011053
Single hybrid motif		2129
492IPR007592
GLABROUS1 enhancer-binding protein family		2145
493IPR044839
Protein NDR1-like		2122
494IPR022796
Chlorophyll A-B binding protein		2131
495IPR004776
Membrane transport protein		2140
496IPR001876
Zinc finger, RanBP2-type		21103
497IPR034289
Laccase, third cupredoxin domain		2122
498IPR029993
Plant galacturonosyltransferase GAUT		2134
499IPR017923
Transcription factor IIS, N-terminal		2144
500IPR045055
DNA2/NAM7-like helicase		2159
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake.html b/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake.html new file mode 100644 index 00000000..e4c8b896 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake.html @@ -0,0 +1,97 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Osativa_Kitaake_v2.0, Feb 2020
Database version:87.1
Base Pairs:381,570,803
Golden Path Length:381,570,803
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:48,494
+ + +

Coordinate Systems

+ + + + + + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144294598
237184994
337804764
436974593
530273398
631052574
729683244
829331338
922792385
1024066873
1129738898
1227153574
+
+
scaffold
+
21 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaffold_13272984
scaffold_14210043
scaffold_17117596
scaffold_2282375
scaffold_3154374
scaffold_3351991
scaffold_3451651
scaffold_3747314
scaffold_4145813
scaffold_4343946
scaffold_4938891
scaffold_6430677
scaffold_6530562
scaffold_7229257
scaffold_7329231
scaffold_9124107
scaffold_10020771
scaffold_10420149
scaffold_13115036
scaffold_1481709
scaffold_1491093
+
+
chunk3834 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake_IPtop500.html new file mode 100644 index 00000000..5bbdf344 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativakitaake_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		15042237
2IPR000719
Protein kinase domain		14513612
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		14162393
4IPR036047
F-box-like domain superfamily		703936
5IPR044974
Disease resistance protein, plants		515847
6IPR001810
F-box domain		5041016
7IPR001611
Leucine-rich repeat		4931879
8IPR002885
Pentatricopeptide repeat		4728000
9IPR001841
Zinc finger, RING-type		471988
10IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		4681008
11IPR002182
NB-ARC		460666
12IPR029058
Alpha/Beta hydrolase fold		397617
13IPR036291
NAD(P)-binding domain superfamily		391597
14IPR009057
Homeobox-like domain superfamily		384589
15IPR016024
Armadillo-type fold		383651
16IPR041118
Rx, N-terminal		351484
17IPR036396
Cytochrome P450 superfamily		342408
18IPR011990
Tetratricopeptide-like helical domain superfamily		341658
19IPR001128
Cytochrome P450		3401740
20IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		335423
21IPR002401
Cytochrome P450, E-class, group I		3142427
22IPR035979
RNA-binding domain superfamily		293669
23IPR017853
Glycoside hydrolase superfamily		272410
24IPR000504
RNA recognition motif domain		2701347
25IPR036259
MFS transporter superfamily		269452
26IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		266503
27IPR036249
Thioredoxin-like superfamily		243361
28IPR017930
Myb domain		243909
29IPR001005
SANT/Myb domain		242866
30IPR038005
Virus X resistance protein-like, coiled-coil domain		241326
31IPR036322
WD40-repeat-containing domain superfamily		228417
32IPR001680
WD40 repeat		2111983
33IPR038765
Papain-like cysteine peptidase superfamily		202303
34IPR011992
EF-hand domain pair		192275
35IPR011333
SKP1/BTB/POZ domain superfamily		181216
36IPR002048
EF-hand domain		1791074
37IPR036638
Helix-loop-helix DNA-binding domain superfamily		177289
38IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		176369
39IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		173511
40IPR016177
DNA-binding domain superfamily		172254
41IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		166184
42IPR036770
Ankyrin repeat-containing domain superfamily		165299
43IPR036412
HAD-like superfamily		160246
44IPR001471
AP2/ERF domain		157948
45IPR005174
Domain unknown function DUF295		154171
46IPR036390
Winged helix DNA-binding domain superfamily		154231
47IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		153173
48IPR002110
Ankyrin repeat		151765
49IPR012340
Nucleic acid-binding, OB-fold		149289
50IPR010255
Haem peroxidase superfamily		148175
51IPR002016
Haem peroxidase		1471155
52IPR001650
Helicase, C-terminal		144462
53IPR003441
NAC domain		143372
54IPR014001
Helicase superfamily 1/2, ATP-binding domain		143238
55IPR036093
NAC domain superfamily		142189
56IPR000210
BTB/POZ domain		140324
57IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		137172
58IPR000823
Plant peroxidase		1361243
59IPR029044
Nucleotide-diphospho-sugar transferases		135173
60IPR036188
FAD/NAD(P)-binding domain superfamily		134253
61IPR033905
Secretory peroxidase		134144
62IPR013087
Zinc finger C2H2-type		133264
63IPR036236
Zinc finger C2H2 superfamily		133210
64IPR003439
ABC transporter-like, ATP-binding domain		127585
65IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		123137
66IPR001087
GDSL lipase/esterase		122158
67IPR021109
Aspartic peptidase domain superfamily		121142
68IPR020846
Major facilitator superfamily domain		120187
69IPR020683
Ankyrin repeat-containing domain		119327
70IPR019734
Tetratricopeptide repeat		118427
71IPR011676
Domain of unknown function DUF1618		118150
72IPR036869
Chaperone J-domain superfamily		117174
73IPR003480
Transferase		116126
74IPR002083
MATH/TRAF domain		115297
75IPR045005
BTB/POZ and MATH domain-containing protein 1-6		115131
76IPR003959
ATPase, AAA-type, core		115183
77IPR029071
Ubiquitin-like domain superfamily		113302
78IPR033121
Peptidase family A1 domain		113148
79IPR036426
Bulb-type lectin domain superfamily		113146
80IPR008972
Cupredoxin		112230
81IPR012337
Ribonuclease H-like superfamily		112154
82IPR001623
DnaJ domain		111835
83IPR032861
Xylanase inhibitor, N-terminal		111124
84IPR001480
Bulb-type lectin domain		110374
85IPR005123
Oxoglutarate/iron-dependent dioxygenase		109140
86IPR035669
GDSL lipase/esterase-like, plant		107130
87IPR032799
Xylanase inhibitor, C-terminal		107119
88IPR011011
Zinc finger, FYVE/PHD-type		107210
89IPR003609
PAN/Apple domain		104237
90IPR011051
RmlC-like cupin domain superfamily		104131
91IPR035892
C2 domain superfamily		103208
92IPR015424
Pyridoxal phosphate-dependent transferase		103161
93IPR002347
Short-chain dehydrogenase/reductase SDR		1021165
94IPR003657
WRKY domain		101358
95IPR036576
WRKY domain superfamily		100180
96IPR025315
Domain of unknown function DUF4220		100115
97IPR011050
Pectin lyase fold/virulence factor		99122
98IPR015300
DNA-binding pseudobarrel domain superfamily		99221
99IPR000858
S-locus glycoprotein domain		98123
100IPR044810
WRKY transcription factor, plant		96149
101IPR031052
FHY3/FAR1 family		95145
102IPR036457
PPM-type phosphatase domain superfamily		94146
103IPR036282
Glutathione S-transferase, C-terminal domain superfamily		94111
104IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		93121
105IPR007658
Protein of unknown function DUF594		93101
106IPR001932
PPM-type phosphatase domain		93427
107IPR000073
Alpha/beta hydrolase fold-1		92353
108IPR011545
DEAD/DEAH box helicase domain		92148
109IPR001461
Aspartic peptidase A1 family		92303
110IPR003340
B3 DNA binding domain		91596
111IPR000008
C2 domain		91461
112IPR001356
Homeobox domain		91353
113IPR026992
Non-haem dioxygenase N-terminal domain		90116
114IPR020472
G-protein beta WD-40 repeat		89411
115IPR000109
Proton-dependent oligopeptide transporter family		88308
116IPR004827
Basic-leucine zipper domain		87284
117IPR009072
Histone-fold		87112
118IPR004045
Glutathione S-transferase, N-terminal		86198
119IPR032867
DYW domain		86114
120IPR005828
Major facilitator, sugar transporter-like		84125
121IPR001220
Legume lectin domain		84172
122IPR010987
Glutathione S-transferase, C-terminal-like		8497
123IPR002902
Gnk2-homologous domain		83409
124IPR012871
Protein of unknown function DUF1677, Oryza sativa		8188
125IPR000626
Ubiquitin-like domain		80459
126IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7777
127IPR036908
RlpA-like domain superfamily		7784
128IPR007527
Zinc finger, SWIM-type		77160
129IPR000270
PB1 domain		77175
130IPR013766
Thioredoxin domain		76188
131IPR003613
U box domain		76215
132IPR002100
Transcription factor, MADS-box		74502
133IPR036879
Transcription factor, MADS-box superfamily		74108
134IPR004330
FAR1 DNA binding domain		7497
135IPR001878
Zinc finger, CCHC-type		74268
136IPR036749
Expansin, cellulose-binding-like domain superfamily		7278
137IPR018289
MULE transposase domain		7288
138IPR007117
Expansin, cellulose-binding-like domain		72156
139IPR006121
Heavy metal-associated domain, HMA		71264
140IPR026961
PGG domain		71182
141IPR036163
Heavy metal-associated domain superfamily		71109
142IPR000571
Zinc finger, CCCH-type		71403
143IPR036875
Zinc finger, CCHC-type superfamily		71125
144IPR043129
ATPase, nucleotide binding domain		70191
145IPR006501
Pectinesterase inhibitor domain		6969
146IPR026057
PC-Esterase		68100
147IPR006045
Cupin 1		68103
148IPR044965
Glycoside hydrolase family 17, plant		67120
149IPR016039
Thiolase-like		65150
150IPR000490
Glycoside hydrolase family 17		6596
151IPR009003
Peptidase S1, PA clan		65135
152IPR029962
Trichome birefringence-like family		6491
153IPR019787
Zinc finger, PHD-finger		64173
154IPR025846
PMR5 N-terminal domain		6487
155IPR029052
Metallo-dependent phosphatase-like		64110
156IPR004158
Protein of unknown function DUF247, plant		64159
157IPR036915
Cyclin-like superfamily		64148
158IPR024752
Myb/SANT-like domain		6466
159IPR007112
Expansin/pollen allergen, DPBB domain		6370
160IPR018108
Mitochondrial substrate/solute carrier		63503
161IPR023395
Mitochondrial carrier domain superfamily		6392
162IPR016159
Cullin repeat-like-containing domain superfamily		6392
163IPR008949
Isoprenoid synthase domain superfamily		62116
164IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6273
165IPR003245
Phytocyanin domain		62126
166IPR001806
Small GTPase		62152
167IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		61102
168IPR039391
Phytocyanin		6162
169IPR001509
NAD-dependent epimerase/dehydratase		6085
170IPR009009
RlpA-like protein, double-psi beta-barrel domain		6067
171IPR016135
Ubiquitin-conjugating enzyme/RWD-like		6094
172IPR013094
Alpha/beta hydrolase fold-3		6065
173IPR000048
IQ motif, EF-hand binding site		60403
174IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		60150
175IPR013057
Amino acid transporter, transmembrane domain		5987
176IPR020568
Ribosomal protein S5 domain 2-type fold		5995
177IPR003663
Sugar/inositol transporter		59350
178IPR024788
Malectin-like domain		5999
179IPR007118
Expansin/Lol pI		58361
180IPR000742
EGF-like domain		5766
181IPR004265
Dirigent protein		5661
182IPR022059
Protein of unknown function DUF3615		5679
183IPR002528
Multi antimicrobial extrusion protein		56140
184IPR036852
Peptidase S8/S53 domain superfamily		5670
185IPR000620
EamA domain		56145
186IPR000209
Peptidase S8/S53 domain		5670
187IPR030184
WAT1-related protein		5588
188IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5467
189IPR013763
Cyclin-like		54119
190IPR005202
Transcription factor GRAS		54194
191IPR003676
Small auxin-up RNA		5454
192IPR000225
Armadillo		54294
193IPR041469
Subtilisin-like protease, fibronectin type-III domain		5366
194IPR011032
GroES-like superfamily		5390
195IPR001563
Peptidase S10, serine carboxypeptidase		53630
196IPR034161
Pepsin-like domain, plant		5361
197IPR008979
Galactose-binding-like domain superfamily		5399
198IPR001752
Kinesin motor domain		53570
199IPR015500
Peptidase S8, subtilisin-related		53194
200IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		5256
201IPR000608
Ubiquitin-conjugating enzyme E2		52240
202IPR045051
Subtilisin-like protease		5265
203IPR013201
Cathepsin propeptide inhibitor domain (I29)		5261
204IPR017884
SANT domain		5169
205IPR008978
HSP20-like chaperone		5159
206IPR036691
Endonuclease/exonuclease/phosphatase superfamily		5189
207IPR034197
Cucumisin-like catalytic domain		5162
208IPR006566
FBD domain		5178
209IPR015915
Kelch-type beta propeller		5189
210IPR016181
Acyl-CoA N-acyltransferase		5064
211IPR013525
ABC-2 type transporter		50110
212IPR011043
Galactose oxidase/kelch, beta-propeller		5065
213IPR044808
Ethylene-responsive transcription factor		5058
214IPR002921
Fungal lipase-like domain		4967
215IPR011701
Major facilitator superfamily		49108
216IPR045087
Multicopper oxidase		4959
217IPR036640
ABC transporter type 1, transmembrane domain superfamily		48132
218IPR007125
Histone H2A/H2B/H3		4857
219IPR011527
ABC transporter type 1, transmembrane domain		48264
220IPR036465
von Willebrand factor A-like domain superfamily		4869
221IPR041569
AAA ATPase, AAA+ lid domain		4869
222IPR008250
P-type ATPase, A domain superfamily		4777
223IPR014014
RNA helicase, DEAD-box type, Q motif		4766
224IPR012946
X8 domain		4782
225IPR006671
Cyclin, N-terminal		4763
226IPR011707
Multicopper oxidase, N-termianl		4756
227IPR001117
Multicopper oxidase, type 1		4655
228IPR043926
ABC transporter family G domain		4685
229IPR000873
AMP-dependent synthetase/ligase		4681
230IPR004140
Exocyst complex component Exo70		46140
231IPR003653
Ulp1 protease family, C-terminal catalytic domain		46112
232IPR011706
Multicopper oxidase, C-terminal		4653
233IPR023298
P-type ATPase, transmembrane domain superfamily		4676
234IPR036855
Zinc finger, CCCH-type superfamily		46165
235IPR001214
SET domain		46125
236IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4658
237IPR033389
AUX/IAA domain		4588
238IPR033896
MADS MEF2-like		4575
239IPR009000
Translation protein, beta-barrel domain superfamily		4562
240IPR000668
Peptidase C1A, papain C-terminal		45209
241IPR011006
CheY-like superfamily		4474
242IPR008928
Six-hairpin glycosidase superfamily		4461
243IPR004046
Glutathione S-transferase, C-terminal		4449
244IPR000743
Glycoside hydrolase, family 28		4458
245IPR006016
UspA		4359
246IPR004853
Sugar phosphate transporter domain		4377
247IPR000330
SNF2, N-terminal		4370
248IPR005630
Terpene synthase, metal-binding domain		4378
249IPR000070
Pectinesterase, catalytic		4350
250IPR008889
VQ		4343
251IPR000182
GNAT domain		4294
252IPR001929
Germin		42137
253IPR029055
Nucleophile aminohydrolases, N-terminal		4262
254IPR004263
Exostosin-like		4251
255IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4270
256IPR039417
Papain-like cysteine endopeptidase		4249
257IPR014756
Immunoglobulin E-set		4262
258IPR006702
Casparian strip membrane protein domain		4244
259IPR001789
Signal transduction response regulator, receiver domain		42135
260IPR011012
Longin-like domain superfamily		4150
261IPR029045
ClpP/crotonase-like domain superfamily		4158
262IPR001906
Terpene synthase, N-terminal domain		4177
263IPR036318
FAD-binding, type PCMH-like superfamily		4053
264IPR009060
UBA-like superfamily		4081
265IPR002068
Alpha crystallin/Hsp20 domain		4087
266IPR005135
Endonuclease/exonuclease/phosphatase		4070
267IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		4052
268IPR015655
Protein phosphatase 2C family		4069
269IPR028889
Ubiquitin specific protease domain		4054
270IPR010402
CCT domain		39128
271IPR016461
O-methyltransferase COMT-type		39108
272IPR007493
Protein of unknown function DUF538		3978
273IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3944
274IPR036612
K Homology domain, type 1 superfamily		39177
275IPR016166
FAD-binding domain, PCMH-type		3951
276IPR004839
Aminotransferase, class I/classII		3971
277IPR036758
At5g01610-like superfamily		3939
278IPR002912
ACT domain		39133
279IPR015947
PUA-like superfamily		3959
280IPR025322
Protein of unknown function DUF4228, plant		3840
281IPR025659
Tubby-like, C-terminal		3856
282IPR001360
Glycoside hydrolase family 1		38388
283IPR029466
No apical meristem-associated, C-terminal domain		3841
284IPR033443
Pentacotripeptide-repeat region of PRORP		3866
285IPR040911
Exostosin, GT47 domain		3847
286IPR002109
Glutaredoxin		3849
287IPR039361
Cyclin		3851
288IPR008942
ENTH/VHS		3748
289IPR013149
Alcohol dehydrogenase, C-terminal		3755
290IPR029021
Protein-tyrosine phosphatase-like		3757
291IPR003137
PA domain		3752
292IPR035940
CAP superfamily		3739
293IPR023271
Aquaporin-like		3751
294IPR013154
Alcohol dehydrogenase, N-terminal		3751
295IPR027923
Hydrophobic seed protein domain		3772
296IPR001077
O-methyltransferase domain		3752
297IPR000425
Major intrinsic protein		37361
298IPR000644
CBS domain		37245
299IPR002487
Transcription factor, K-box		37132
300IPR005299
SAM dependent carboxyl methyltransferase		36138
301IPR004367
Cyclin, C-terminal domain		3646
302IPR045048
F-box only protein 31/39		3661
303IPR000863
Sulfotransferase domain		3638
304IPR001283
Cysteine-rich secretory protein-related		36167
305IPR014044
CAP domain		3638
306IPR002495
Glycosyl transferase, family 8		3652
307IPR000528
Plant non-specific lipid-transfer protein/Par allergen		35174
308IPR043502
DNA/RNA polymerase superfamily		3551
309IPR034294
Aquaporin transporter		3550
310IPR022742
Serine aminopeptidase, S33		3548
311IPR003690
Transcription termination factor, mitochondrial/chloroplastic		35126
312IPR002067
Mitochondrial carrier protein		35238
313IPR012967
Plant methyltransferase dimerisation		3549
314IPR037176
Osmotin/thaumatin-like superfamily		3540
315IPR004041
NAF domain		3448
316IPR018451
NAF/FISL domain		3448
317IPR001296
Glycosyl transferase, family 1		3466
318IPR009030
Growth factor receptor cysteine-rich domain superfamily		3443
319IPR001938
Thaumatin family		34251
320IPR002963
Expansin		34282
321IPR043519
Nucleotidyltransferase superfamily		3461
322IPR036041
Ribosome-inactivating protein superfamily		3440
323IPR001251
CRAL-TRIO lipid binding domain		33167
324IPR008991
Translation protein SH3-like domain superfamily		3339
325IPR006652
Kelch repeat type 1		3382
326IPR019378
GDP-fucose protein O-fucosyltransferase		3369
327IPR006094
FAD linked oxidase, N-terminal		3343
328IPR006458
Ovate protein family, C-terminal		3366
329IPR004314
Neprosin		3345
330IPR001223
Glycoside hydrolase family 18, catalytic domain		3372
331IPR006073
GTP binding domain		33124
332IPR001574
Ribosome-inactivating protein		3368
333IPR002659
Glycosyl transferase, family 31		3281
334IPR001881
EGF-like calcium-binding domain		3240
335IPR036865
CRAL-TRIO lipid binding domain superfamily		3256
336IPR036404
Jacalin-like lectin domain superfamily		3270
337IPR001229
Jacalin-like lectin domain		32131
338IPR032710
NTF2-like domain superfamily		3144
339IPR044822
Myb/SANT-like DNA-binding domain 4		3156
340IPR038933
Ovate protein family		3133
341IPR001594
Palmitoyltransferase, DHHC domain		3152
342IPR000795
Translational (tr)-type GTP-binding domain		31257
343IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		3143
344IPR003406
Glycosyl transferase, family 14		3138
345IPR004883
Lateral organ boundaries, LOB		3169
346IPR004088
K Homology domain, type 1		31159
347IPR013126
Heat shock protein 70 family		3187
348IPR044791
Beta-glucanase/XTH		3132
349IPR003311
AUX/IAA protein		3157
350IPR000757
Glycoside hydrolase family 16		3164
351IPR000727
Target SNARE coiled-coil homology domain		3059
352IPR016040
NAD(P)-binding domain		3044
353IPR025110
AMP-binding enzyme, C-terminal domain		3039
354IPR018490
Cyclic nucleotide-binding-like		3041
355IPR044848
PHR1-like		3066
356IPR011332
Zinc-binding ribosomal protein		3035
357IPR011013
Galactose mutarotase-like domain superfamily		3054
358IPR005150
Cellulose synthase		3054
359IPR000595
Cyclic nucleotide-binding domain		30103
360IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3071
361IPR000679
Zinc finger, GATA-type		30123
362IPR036378
FAS1 domain superfamily		2954
363IPR010920
LSM domain superfamily		2932
364IPR013216
Methyltransferase type 11		2940
365IPR007650
Zf-FLZ domain		2966
366IPR044675
E3 ubiquitin-protein ligase RING1-like		2929
367IPR001849
Pleckstrin homology domain		2980
368IPR023299
P-type ATPase, cytoplasmic domain N		2943
369IPR023210
NADP-dependent oxidoreductase domain		2950
370IPR036812
NADP-dependent oxidoreductase domain superfamily		2950
371IPR015940
Ubiquitin-associated domain		28105
372IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28239
373IPR029000
Cyclophilin-like domain superfamily		2842
374IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		28186
375IPR000315
B-box-type zinc finger		2873
376IPR000717
Proteasome component (PCI) domain		2881
377IPR036420
BRCT domain superfamily		2884
378IPR002423
Chaperonin Cpn60/TCP-1 family		2839
379IPR027356
NPH3 domain		28104
380IPR044814
Terpene cyclases, class 1, plant		2840
381IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2850
382IPR043454
NPH3/RPT2-like family		2853
383IPR008480
Protein of unknown function DUF761, plant		2830
384IPR027409
GroEL-like apical domain superfamily		2838
385IPR034285
Laccase, second cupredoxin domain		2832
386IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2843
387IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2829
388IPR003851
Zinc finger, Dof-type		2868
389IPR044066
TRIAD supradomain		2837
390IPR017938
Riboflavin synthase-like beta-barrel		2745
391IPR002867
IBR domain		2762
392IPR006153
Cation/H+ exchanger		2737
393IPR013187
F-box associated domain, type 3		2738
394IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		2796
395IPR001357
BRCT domain		27139
396IPR024709
Putative O-fucosyltransferase, plant		2762
397IPR044835
Auxin response factor		2758
398IPR008422
Homeobox KN domain		2743
399IPR023753
FAD/NAD(P)-binding domain		2739
400IPR029061
Thiamin diphosphate-binding fold		2767
401IPR034288
Laccase, first cupredoxin domain		2730
402IPR005821
Ion transport domain		2739
403IPR031127
E3 ubiquitin ligase RBR family		2739
404IPR003855
Potassium transporter		2798
405IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2739
406IPR006311
Twin-arginine translocation pathway, signal sequence		2736
407IPR005175
PPC domain		27107
408IPR002913
START domain		27103
409IPR015797
NUDIX hydrolase-like domain superfamily		2736
410IPR033734
Jacalin-like lectin domain, plant		2761
411IPR017927
FAD-binding domain, ferredoxin reductase-type		2641
412IPR000782
FAS1 domain		2685
413IPR013601
FAE1/Type III polyketide synthase-like protein		2633
414IPR019956
Ubiquitin domain		26161
415IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2633
416IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2632
417IPR007657
Glycosyltransferase 61		26100
418IPR027725
Heat shock transcription factor family		2637
419IPR004320
Protein of unknown function DUF241, plant		2627
420IPR001763
Rhodanese-like domain		2663
421IPR002123
Phospholipid/glycerol acyltransferase		2632
422IPR036273
CRAL/TRIO, N-terminal domain superfamily		2647
423IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2639
424IPR002035
von Willebrand factor, type A		2654
425IPR004813
Oligopeptide transporter, OPT superfamily		2634
426IPR029069
HotDog domain superfamily		2639
427IPR029062
Class I glutamine amidotransferase-like		2658
428IPR001757
P-type ATPase		26179
429IPR012328
Chalcone/stilbene synthase, C-terminal		2628
430IPR000232
Heat shock factor (HSF)-type, DNA-binding		26130
431IPR036034
PDZ superfamily		2640
432IPR011141
Polyketide synthase, type III		2629
433IPR001099
Chalcone/stilbene synthase, N-terminal		2627
434IPR036085
PAZ domain superfamily		2544
435IPR044778
Sugar transport protein STP/MST-like, plant		2527
436IPR000408
Regulator of chromosome condensation, RCC1		25903
437IPR004014
Cation-transporting P-type ATPase, N-terminal		2541
438IPR006461
PLAC8 motif-containing protein		2553
439IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2539
440IPR039421
Type 1 protein exporter		2539
441IPR013581
Plant PDR ABC transporter associated		2436
442IPR011016
Zinc finger, RING-CH-type		24114
443IPR002293
Amino acid/polyamine transporter I		2445
444IPR003594
Histidine kinase/HSP90-like ATPase		2443
445IPR044839
Protein NDR1-like		2424
446IPR001320
Ionotropic glutamate receptor		2435
447IPR016897
S-phase kinase-associated protein 1		2424
448IPR044997
F-box protein, plant		2430
449IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2432
450IPR034289
Laccase, third cupredoxin domain		2425
451IPR036296
SKP1-like, dimerisation domain superfamily		2424
452IPR001701
Glycoside hydrolase family 9		2428
453IPR025486
Domain of unknown function DUF4378		2464
454IPR000086
NUDIX hydrolase domain		2461
455IPR001638
Solute-binding protein family 3/N-terminal domain of MltF		2438
456IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2		2436
457IPR003100
PAZ domain		2383
458IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2347
459IPR004316
SWEET sugar transporter		2353
460IPR000387
Tyrosine specific protein phosphatases domain		2334
461IPR025753
AAA-type ATPase, N-terminal domain		2324
462IPR001440
Tetratricopeptide repeat 1		2335
463IPR032872
Wall-associated receptor kinase, C-terminal		2327
464IPR013010
Zinc finger, SIAH-type		2329
465IPR016072
SKP1 component, dimerisation		2323
466IPR001876
Zinc finger, RanBP2-type		23144
467IPR003616
Post-SET domain		2333
468IPR002937
Amine oxidase		2336
469IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2333
470IPR036443
Zinc finger, RanBP2-type superfamily		2389
471IPR010525
Auxin response factor domain		2351
472IPR006594
LIS1 homology motif		2259
473IPR008971
HSP40/DnaJ peptide-binding		2275
474IPR003106
Leucine zipper, homeobox-associated		2228
475IPR001750
NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit		2227
476IPR007612
LURP-one-related		2259
477IPR004161
Translation elongation factor EFTu-like, domain 2		2230
478IPR005333
Transcription factor, TCP		2234
479IPR036010
2Fe-2S ferredoxin-like superfamily		2228
480IPR001353
Proteasome, subunit alpha/beta		2230
481IPR025422
Transcription factor TGA like domain		22108
482IPR010989
SNARE		2223
483IPR006694
Fatty acid hydroxylase		2234
484IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2233
485IPR006015
Universal stress protein A family		2277
486IPR004776
Membrane transport protein		2237
487IPR041677
DNA2/NAM7 helicase, helicase domain		2246
488IPR002939
Chaperone DnaJ, C-terminal		2241
489IPR029993
Plant galacturonosyltransferase GAUT		2231
490IPR036427
Bromodomain-like superfamily		2242
491IPR002641
Patatin-like phospholipase domain		2253
492IPR036392
PLAT/LH2 domain superfamily		2227
493IPR006689
Small GTPase superfamily, ARF/SAR type		21178
494IPR009606
Modifying wall lignin-1/2		2126
495IPR006593
Cytochrome b561/ferric reductase transmembrane		2144
496IPR006195
Aminoacyl-tRNA synthetase, class II		2132
497IPR002403
Cytochrome P450, E-class, group IV		21120
498IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain		2135
499IPR003347
JmjC domain		2183
500IPR001163
LSM domain, eukaryotic/archaea-type		2122
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativamh63.html b/gramene/htdocs/ssi/species/stats_Oryza_sativamh63.html new file mode 100644 index 00000000..435ae79f --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativamh63.html @@ -0,0 +1,62 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:MH63RS2, Oct 2018
Database version:87.1
Base Pairs:395,765,488
Golden Path Length:395,765,488
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:52,943
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
145027022
237301368
339893253
437319239
531307418
631921180
730877072
830492302
924892599
1025690566
1134100580
1226942889
+
+
chunk3964 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativamh63_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativamh63_IPtop500.html new file mode 100644 index 00000000..9e00adf9 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativamh63_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14912519
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14612766
3IPR000719
Protein kinase domain		13833785
4IPR036047
F-box-like domain superfamily		676991
5IPR044974
Disease resistance protein, plants		5631118
6IPR002182
NB-ARC		518742
7IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		5131049
8IPR002885
Pentatricopeptide repeat		5037734
9IPR001810
F-box domain		4861061
10IPR001611
Leucine-rich repeat		4681667
11IPR001841
Zinc finger, RING-type		431970
12IPR041118
Rx, N-terminal		404556
13IPR029058
Alpha/Beta hydrolase fold		387662
14IPR009057
Homeobox-like domain superfamily		386585
15IPR016024
Armadillo-type fold		383746
16IPR036291
NAD(P)-binding domain superfamily		374626
17IPR011990
Tetratricopeptide-like helical domain superfamily		344677
18IPR036396
Cytochrome P450 superfamily		323431
19IPR001128
Cytochrome P450		3141545
20IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		311459
21IPR035979
RNA-binding domain superfamily		305778
22IPR038005
Virus X resistance protein-like, coiled-coil domain		280391
23IPR000504
RNA recognition motif domain		2751418
24IPR002401
Cytochrome P450, E-class, group I		2691894
25IPR017853
Glycoside hydrolase superfamily		263456
26IPR036259
MFS transporter superfamily		258501
27IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		257474
28IPR038765
Papain-like cysteine peptidase superfamily		242359
29IPR017930
Myb domain		240868
30IPR001005
SANT/Myb domain		239850
31IPR036322
WD40-repeat-containing domain superfamily		234482
32IPR036249
Thioredoxin-like superfamily		233407
33IPR001680
WD40 repeat		2092217
34IPR011992
EF-hand domain pair		187277
35IPR002048
EF-hand domain		1771035
36IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		176407
37IPR036770
Ankyrin repeat-containing domain superfamily		173314
38IPR036412
HAD-like superfamily		172318
39IPR016177
DNA-binding domain superfamily		170274
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		163239
41IPR011333
SKP1/BTB/POZ domain superfamily		160260
42IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		155407
43IPR036093
NAC domain superfamily		154183
44IPR002110
Ankyrin repeat		154848
45IPR001471
AP2/ERF domain		153955
46IPR036390
Winged helix DNA-binding domain superfamily		151208
47IPR003441
NAC domain		150347
48IPR012337
Ribonuclease H-like superfamily		147220
49IPR036236
Zinc finger C2H2 superfamily		144229
50IPR010255
Haem peroxidase superfamily		142181
51IPR001650
Helicase, C-terminal		141494
52IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		141193
53IPR029044
Nucleotide-diphospho-sugar transferases		139219
54IPR012340
Nucleic acid-binding, OB-fold		137319
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		136252
56IPR002016
Haem peroxidase		135623
57IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		133164
58IPR036188
FAD/NAD(P)-binding domain superfamily		131259
59IPR003439
ABC transporter-like, ATP-binding domain		130706
60IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		128207
61IPR013087
Zinc finger C2H2-type		128261
62IPR020683
Ankyrin repeat-containing domain		128388
63IPR005174
Domain unknown function DUF295		128160
64IPR021109
Aspartic peptidase domain superfamily		126172
65IPR036426
Bulb-type lectin domain superfamily		124164
66IPR001480
Bulb-type lectin domain		120410
67IPR000210
BTB/POZ domain		118394
68IPR003959
ATPase, AAA-type, core		116204
69IPR003480
Transferase		116142
70IPR033121
Peptidase family A1 domain		113164
71IPR036869
Chaperone J-domain superfamily		111181
72IPR032799
Xylanase inhibitor, C-terminal		110137
73IPR001087
GDSL lipase/esterase		109152
74IPR032861
Xylanase inhibitor, N-terminal		109140
75IPR025315
Domain of unknown function DUF4220		108127
76IPR008972
Cupredoxin		107228
77IPR001623
DnaJ domain		107930
78IPR020846
Major facilitator superfamily domain		107194
79IPR007658
Protein of unknown function DUF594		106114
80IPR011011
Zinc finger, FYVE/PHD-type		106224
81IPR029071
Ubiquitin-like domain superfamily		105180
82IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		105123
83IPR003657
WRKY domain		104284
84IPR015424
Pyridoxal phosphate-dependent transferase		104174
85IPR036576
WRKY domain superfamily		103147
86IPR019734
Tetratricopeptide repeat		102419
87IPR011676
Domain of unknown function DUF1618		101148
88IPR000858
S-locus glycoprotein domain		100133
89IPR003609
PAN/Apple domain		100241
90IPR036457
PPM-type phosphatase domain superfamily		97164
91IPR044810
WRKY transcription factor, plant		97127
92IPR035892
C2 domain superfamily		96237
93IPR011050
Pectin lyase fold/virulence factor		96124
94IPR015300
DNA-binding pseudobarrel domain superfamily		95201
95IPR001356
Homeobox domain		94327
96IPR001932
PPM-type phosphatase domain		94464
97IPR009072
Histone-fold		93110
98IPR005123
Oxoglutarate/iron-dependent dioxygenase		92137
99IPR000823
Plant peroxidase		91375
100IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		90129
101IPR011545
DEAD/DEAH box helicase domain		90164
102IPR002347
Short-chain dehydrogenase/reductase SDR		89855
103IPR045005
BTB/POZ and MATH domain-containing protein 1-6		89180
104IPR035669
GDSL lipase/esterase-like, plant		88116
105IPR000109
Proton-dependent oligopeptide transporter family		88354
106IPR002083
MATH/TRAF domain		86325
107IPR011051
RmlC-like cupin domain superfamily		86146
108IPR000008
C2 domain		85492
109IPR005828
Major facilitator, sugar transporter-like		85181
110IPR003340
B3 DNA binding domain		84485
111IPR020472
G-protein beta WD-40 repeat		84510
112IPR000073
Alpha/beta hydrolase fold-1		83294
113IPR001461
Aspartic peptidase A1 family		83297
114IPR013766
Thioredoxin domain		82211
115IPR004827
Basic-leucine zipper domain		82218
116IPR004158
Protein of unknown function DUF247, plant		81204
117IPR026961
PGG domain		80178
118IPR043129
ATPase, nucleotide binding domain		80230
119IPR026992
Non-haem dioxygenase N-terminal domain		79116
120IPR003613
U box domain		76207
121IPR036875
Zinc finger, CCHC-type superfamily		7695
122IPR012871
Protein of unknown function DUF1677, Oryza sativa		7593
123IPR002100
Transcription factor, MADS-box		75476
124IPR036282
Glutathione S-transferase, C-terminal domain superfamily		75119
125IPR036879
Transcription factor, MADS-box superfamily		74104
126IPR002902
Gnk2-homologous domain		72401
127IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7174
128IPR004045
Glutathione S-transferase, N-terminal		70231
129IPR036908
RlpA-like domain superfamily		7087
130IPR016159
Cullin repeat-like-containing domain superfamily		7093
131IPR016039
Thiolase-like		69162
132IPR003653
Ulp1 protease family, C-terminal catalytic domain		69158
133IPR036163
Heavy metal-associated domain superfamily		69103
134IPR001220
Legume lectin domain		69166
135IPR044965
Glycoside hydrolase family 17, plant		69112
136IPR000270
PB1 domain		69153
137IPR036749
Expansin, cellulose-binding-like domain superfamily		6781
138IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		67138
139IPR000626
Ubiquitin-like domain		66171
140IPR008949
Isoprenoid synthase domain superfamily		66105
141IPR006121
Heavy metal-associated domain, HMA		66236
142IPR007117
Expansin, cellulose-binding-like domain		66156
143IPR036915
Cyclin-like superfamily		66180
144IPR001878
Zinc finger, CCHC-type		66138
145IPR013057
Amino acid transporter, transmembrane domain		6599
146IPR009003
Peptidase S1, PA clan		65158
147IPR024788
Malectin-like domain		6596
148IPR000048
IQ motif, EF-hand binding site		64440
149IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6368
150IPR018108
Mitochondrial substrate/solute carrier		62673
151IPR020568
Ribosomal protein S5 domain 2-type fold		62135
152IPR023395
Mitochondrial carrier domain superfamily		62123
153IPR010987
Glutathione S-transferase, C-terminal-like		62101
154IPR006501
Pectinesterase inhibitor domain		6264
155IPR029052
Metallo-dependent phosphatase-like		62106
156IPR000490
Glycoside hydrolase family 17		6290
157IPR000571
Zinc finger, CCCH-type		62418
158IPR001806
Small GTPase		62166
159IPR019787
Zinc finger, PHD-finger		61194
160IPR036852
Peptidase S8/S53 domain superfamily		6085
161IPR000209
Peptidase S8/S53 domain		6084
162IPR026057
PC-Esterase		5987
163IPR016135
Ubiquitin-conjugating enzyme/RWD-like		59103
164IPR005202
Transcription factor GRAS		59209
165IPR031052
FHY3/FAR1 family		57109
166IPR003245
Phytocyanin domain		57116
167IPR015915
Kelch-type beta propeller		57106
168IPR003663
Sugar/inositol transporter		57413
169IPR003676
Small auxin-up RNA		5762
170IPR041469
Subtilisin-like protease, fibronectin type-III domain		5675
171IPR011032
GroES-like superfamily		5687
172IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		5698
173IPR045051
Subtilisin-like protease		56100
174IPR013763
Cyclin-like		56141
175IPR039391
Phytocyanin		5670
176IPR007112
Expansin/pollen allergen, DPBB domain		5670
177IPR022059
Protein of unknown function DUF3615		5675
178IPR025846
PMR5 N-terminal domain		5676
179IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5570
180IPR029962
Trichome birefringence-like family		5587
181IPR034161
Pepsin-like domain, plant		5567
182IPR013094
Alpha/beta hydrolase fold-3		5575
183IPR000225
Armadillo		55272
184IPR001752
Kinesin motor domain		54621
185IPR013525
ABC-2 type transporter		53137
186IPR009009
RlpA-like protein, double-psi beta-barrel domain		5366
187IPR002921
Fungal lipase-like domain		5276
188IPR016181
Acyl-CoA N-acyltransferase		5283
189IPR004140
Exocyst complex component Exo70		52157
190IPR008979
Galactose-binding-like domain superfamily		52111
191IPR002528
Multi antimicrobial extrusion protein		52179
192IPR006566
FBD domain		5270
193IPR036465
von Willebrand factor A-like domain superfamily		5277
194IPR006045
Cupin 1		51100
195IPR032867
DYW domain		5157
196IPR023298
P-type ATPase, transmembrane domain superfamily		51103
197IPR015500
Peptidase S8, subtilisin-related		51187
198IPR004330
FAR1 DNA binding domain		5161
199IPR008978
HSP20-like chaperone		5066
200IPR000608
Ubiquitin-conjugating enzyme E2		50233
201IPR007118
Expansin/Lol pI		50320
202IPR008250
P-type ATPase, A domain superfamily		50100
203IPR001563
Peptidase S10, serine carboxypeptidase		49460
204IPR002156
Ribonuclease H domain		4970
205IPR012946
X8 domain		4973
206IPR007527
Zinc finger, SWIM-type		4992
207IPR000620
EamA domain		49128
208IPR005630
Terpene synthase, metal-binding domain		4869
209IPR034197
Cucumisin-like catalytic domain		4864
210IPR006671
Cyclin, N-terminal		4879
211IPR030184
WAT1-related protein		48100
212IPR017884
SANT domain		4787
213IPR036640
ABC transporter type 1, transmembrane domain superfamily		47173
214IPR013201
Cathepsin propeptide inhibitor domain (I29)		4752
215IPR008928
Six-hairpin glycosidase superfamily		4773
216IPR011527
ABC transporter type 1, transmembrane domain		47339
217IPR045087
Multicopper oxidase		4766
218IPR041569
AAA ATPase, AAA+ lid domain		4772
219IPR044808
Ethylene-responsive transcription factor		4760
220IPR001117
Multicopper oxidase, type 1		4655
221IPR001509
NAD-dependent epimerase/dehydratase		4674
222IPR014014
RNA helicase, DEAD-box type, Q motif		4673
223IPR004265
Dirigent protein		4654
224IPR011006
CheY-like superfamily		4672
225IPR033896
MADS MEF2-like		4574
226IPR004853
Sugar phosphate transporter domain		45103
227IPR011701
Major facilitator superfamily		45102
228IPR029055
Nucleophile aminohydrolases, N-terminal		4577
229IPR009000
Translation protein, beta-barrel domain superfamily		4577
230IPR011706
Multicopper oxidase, C-terminal		4554
231IPR001906
Terpene synthase, N-terminal domain		4566
232IPR014756
Immunoglobulin E-set		4585
233IPR001214
SET domain		45146
234IPR036318
FAD-binding, type PCMH-like superfamily		4454
235IPR009060
UBA-like superfamily		4482
236IPR033905
Secretory peroxidase		4449
237IPR007125
Histone H2A/H2B/H3		4446
238IPR008889
VQ		4444
239IPR011707
Multicopper oxidase, N-termianl		4453
240IPR000182
GNAT domain		43111
241IPR000873
AMP-dependent synthetase/ligase		4381
242IPR004263
Exostosin-like		4368
243IPR011043
Galactose oxidase/kelch, beta-propeller		4353
244IPR006702
Casparian strip membrane protein domain		4346
245IPR010402
CCT domain		42144
246IPR043926
ABC transporter family G domain		4290
247IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4286
248IPR000668
Peptidase C1A, papain C-terminal		42159
249IPR000070
Pectinesterase, catalytic		4257
250IPR036855
Zinc finger, CCCH-type superfamily		42169
251IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4260
252IPR001789
Signal transduction response regulator, receiver domain		42115
253IPR033389
AUX/IAA domain		4170
254IPR016040
NAD(P)-binding domain		4168
255IPR000330
SNF2, N-terminal		4183
256IPR011012
Longin-like domain superfamily		4171
257IPR015655
Protein phosphatase 2C family		4194
258IPR000743
Glycoside hydrolase, family 28		4162
259IPR015947
PUA-like superfamily		4167
260IPR037176
Osmotin/thaumatin-like superfamily		4145
261IPR039361
Cyclin		4076
262IPR006016
UspA		3955
263IPR025659
Tubby-like, C-terminal		3956
264IPR036612
K Homology domain, type 1 superfamily		39144
265IPR003137
PA domain		3954
266IPR000742
EGF-like domain		3943
267IPR029045
ClpP/crotonase-like domain superfamily		3979
268IPR000644
CBS domain		39211
269IPR044730
Ribonuclease H-like domain, plant type		3941
270IPR025322
Protein of unknown function DUF4228, plant		3839
271IPR002068
Alpha crystallin/Hsp20 domain		3899
272IPR029021
Protein-tyrosine phosphatase-like		3894
273IPR023271
Aquaporin-like		3851
274IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3865
275IPR000425
Major intrinsic protein		38311
276IPR004046
Glutathione S-transferase, C-terminal		3847
277IPR039417
Papain-like cysteine endopeptidase		3843
278IPR002495
Glycosyl transferase, family 8		3860
279IPR002912
ACT domain		38126
280IPR008942
ENTH/VHS		3756
281IPR007493
Protein of unknown function DUF538		3785
282IPR001938
Thaumatin family		37253
283IPR016166
FAD-binding domain, PCMH-type		3746
284IPR004883
Lateral organ boundaries, LOB		3782
285IPR036758
At5g01610-like superfamily		3743
286IPR019378
GDP-fucose protein O-fucosyltransferase		3788
287IPR040911
Exostosin, GT47 domain		3756
288IPR028889
Ubiquitin specific protease domain		3758
289IPR002109
Glutaredoxin		3749
290IPR013126
Heat shock protein 70 family		37117
291IPR013149
Alcohol dehydrogenase, C-terminal		3646
292IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3680
293IPR013154
Alcohol dehydrogenase, N-terminal		3645
294IPR004367
Cyclin, C-terminal domain		3652
295IPR006652
Kelch repeat type 1		36110
296IPR004839
Aminotransferase, class I/classII		3662
297IPR002067
Mitochondrial carrier protein		36302
298IPR002487
Transcription factor, K-box		36121
299IPR004041
NAF domain		3551
300IPR016461
O-methyltransferase COMT-type		3583
301IPR001360
Glycoside hydrolase family 1		35524
302IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3560
303IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3542
304IPR034294
Aquaporin transporter		3551
305IPR043454
NPH3/RPT2-like family		3575
306IPR024752
Myb/SANT-like domain		3539
307IPR022742
Serine aminopeptidase, S33		3451
308IPR001077
O-methyltransferase domain		3443
309IPR001251
CRAL-TRIO lipid binding domain		33174
310IPR038933
Ovate protein family		3334
311IPR000795
Translational (tr)-type GTP-binding domain		33302
312IPR036865
CRAL-TRIO lipid binding domain superfamily		3369
313IPR027356
NPH3 domain		33108
314IPR004088
K Homology domain, type 1		33127
315IPR006094
FAD linked oxidase, N-terminal		3342
316IPR006458
Ovate protein family, C-terminal		3363
317IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3373
318IPR007811
DNA-directed RNA polymerase III subunit RPC4		3371
319IPR018451
NAF/FISL domain		3248
320IPR006311
Twin-arginine translocation pathway, signal sequence		3236
321IPR018490
Cyclic nucleotide-binding-like		3161
322IPR032710
NTF2-like domain superfamily		3141
323IPR029061
Thiamin diphosphate-binding fold		3181
324IPR001296
Glycosyl transferase, family 1		3158
325IPR001594
Palmitoyltransferase, DHHC domain		3169
326IPR004320
Protein of unknown function DUF241, plant		3136
327IPR003690
Transcription termination factor, mitochondrial/chloroplastic		31138
328IPR033443
Pentacotripeptide-repeat region of PRORP		3158
329IPR043519
Nucleotidyltransferase superfamily		3177
330IPR006073
GTP binding domain		31114
331IPR000528
Plant non-specific lipid-transfer protein/Par allergen		30156
332IPR000315
B-box-type zinc finger		3087
333IPR035940
CAP superfamily		3040
334IPR002423
Chaperonin Cpn60/TCP-1 family		3049
335IPR007650
Zf-FLZ domain		3065
336IPR005150
Cellulose synthase		3081
337IPR003406
Glycosyl transferase, family 14		3046
338IPR000863
Sulfotransferase domain		3043
339IPR027409
GroEL-like apical domain superfamily		3043
340IPR023299
P-type ATPase, cytoplasmic domain N		3066
341IPR003851
Zinc finger, Dof-type		3069
342IPR004314
Neprosin		3039
343IPR000595
Cyclic nucleotide-binding domain		30144
344IPR003855
Potassium transporter		30143
345IPR011141
Polyketide synthase, type III		3041
346IPR001574
Ribosome-inactivating protein		3065
347IPR006153
Cation/H+ exchanger		2956
348IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		29158
349IPR008991
Translation protein SH3-like domain superfamily		2939
350IPR044822
Myb/SANT-like DNA-binding domain 4		2939
351IPR000717
Proteasome component (PCI) domain		2976
352IPR044848
PHR1-like		2961
353IPR005333
Transcription factor, TCP		2934
354IPR005135
Endonuclease/exonuclease/phosphatase		2958
355IPR011013
Galactose mutarotase-like domain superfamily		2951
356IPR002963
Expansin		29264
357IPR008480
Protein of unknown function DUF761, plant		2929
358IPR044791
Beta-glucanase/XTH		2943
359IPR036404
Jacalin-like lectin domain superfamily		2949
360IPR001223
Glycoside hydrolase family 18, catalytic domain		2981
361IPR036041
Ribosome-inactivating protein superfamily		2936
362IPR012967
Plant methyltransferase dimerisation		2929
363IPR000757
Glycoside hydrolase family 16		2978
364IPR001099
Chalcone/stilbene synthase, N-terminal		2936
365IPR000727
Target SNARE coiled-coil homology domain		2860
366IPR015940
Ubiquitin-associated domain		28101
367IPR036378
FAS1 domain superfamily		2841
368IPR024709
Putative O-fucosyltransferase, plant		2873
369IPR044835
Auxin response factor		2874
370IPR002659
Glycosyl transferase, family 31		28112
371IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2847
372IPR003337
Trehalose-phosphatase		2847
373IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2841
374IPR001283
Cysteine-rich secretory protein-related		2891
375IPR044839
Protein NDR1-like		2828
376IPR016897
S-phase kinase-associated protein 1		2833
377IPR001849
Pleckstrin homology domain		2871
378IPR036296
SKP1-like, dimerisation domain superfamily		2833
379IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2839
380IPR036812
NADP-dependent oxidoreductase domain superfamily		2863
381IPR002913
START domain		28108
382IPR015797
NUDIX hydrolase-like domain superfamily		2844
383IPR013601
FAE1/Type III polyketide synthase-like protein		2735
384IPR001929
Germin		27110
385IPR022149
Protein of unknown function DUF3681		2755
386IPR025753
AAA-type ATPase, N-terminal domain		2732
387IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		27131
388IPR029466
No apical meristem-associated, C-terminal domain		2727
389IPR010920
LSM domain superfamily		2742
390IPR000408
Regulator of chromosome condensation, RCC1		27818
391IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2738
392IPR005821
Ion transport domain		2752
393IPR004813
Oligopeptide transporter, OPT superfamily		2765
394IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2757
395IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2734
396IPR001701
Glycoside hydrolase family 9		2739
397IPR003311
AUX/IAA protein		2743
398IPR005175
PPC domain		2792
399IPR001229
Jacalin-like lectin domain		2782
400IPR025110
AMP-binding enzyme, C-terminal domain		2638
401IPR017938
Riboflavin synthase-like beta-barrel		2642
402IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2636
403IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		26282
404IPR029000
Cyclophilin-like domain superfamily		2652
405IPR005299
SAM dependent carboxyl methyltransferase		2685
406IPR016072
SKP1 component, dimerisation		2631
407IPR027923
Hydrophobic seed protein domain		2667
408IPR014044
CAP domain		2634
409IPR002035
von Willebrand factor, type A		2662
410IPR039421
Type 1 protein exporter		2673
411IPR029062
Class I glutamine amidotransferase-like		2660
412IPR012328
Chalcone/stilbene synthase, C-terminal		2629
413IPR000679
Zinc finger, GATA-type		26114
414IPR017927
FAD-binding domain, ferredoxin reductase-type		2540
415IPR036085
PAZ domain superfamily		2545
416IPR004316
SWEET sugar transporter		2547
417IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2532
418IPR001357
BRCT domain		25108
419IPR044778
Sugar transport protein STP/MST-like, plant		2532
420IPR036420
BRCT domain superfamily		2569
421IPR008422
Homeobox KN domain		2542
422IPR007657
Glycosyltransferase 61		2583
423IPR027725
Heat shock transcription factor family		2533
424IPR002123
Phospholipid/glycerol acyltransferase		2533
425IPR036273
CRAL/TRIO, N-terminal domain superfamily		2547
426IPR004014
Cation-transporting P-type ATPase, N-terminal		2542
427IPR001757
P-type ATPase		25147
428IPR000232
Heat shock factor (HSF)-type, DNA-binding		25121
429IPR036034
PDZ superfamily		2546
430IPR023210
NADP-dependent oxidoreductase domain		2568
431IPR000782
FAS1 domain		2463
432IPR011016
Zinc finger, RING-CH-type		2492
433IPR040417
Glycine-rich cell wall structural protein 1/2		2433
434IPR019557
Aminotransferase-like, plant mobile domain		2432
435IPR036010
2Fe-2S ferredoxin-like superfamily		2431
436IPR001763
Rhodanese-like domain		2482
437IPR044675
E3 ubiquitin-protein ligase RING1-like		2426
438IPR034285
Laccase, second cupredoxin domain		2429
439IPR029069
HotDog domain superfamily		2474
440IPR041677
DNA2/NAM7 helicase, helicase domain		2459
441IPR016161
Aldehyde/histidinol dehydrogenase		2443
442IPR025486
Domain of unknown function DUF4378		2441
443IPR000086
NUDIX hydrolase domain		2474
444IPR029033
Histidine phosphatase superfamily		2439
445IPR010525
Auxin response factor domain		2452
446IPR003100
PAZ domain		2384
447IPR006594
LIS1 homology motif		2354
448IPR008971
HSP40/DnaJ peptide-binding		2366
449IPR003106
Leucine zipper, homeobox-associated		2326
450IPR002867
IBR domain		2351
451IPR001163
LSM domain, eukaryotic/archaea-type		2332
452IPR012416
CALMODULIN-BINDING PROTEIN60		23102
453IPR023753
FAD/NAD(P)-binding domain		2347
454IPR017887
Transcription factor TCP subgroup		2345
455IPR045048
F-box only protein 31/39		2353
456IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2334
457IPR007592
GLABROUS1 enhancer-binding protein family		2349
458IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2374
459IPR002939
Chaperone DnaJ, C-terminal		2337
460IPR036427
Bromodomain-like superfamily		2343
461IPR036392
PLAT/LH2 domain superfamily		2325
462IPR006689
Small GTPase superfamily, ARF/SAR type		22132
463IPR004000
Actin family		22201
464IPR007612
LURP-one-related		2251
465IPR013216
Methyltransferase type 11		2233
466IPR018392
LysM domain		2272
467IPR001353
Proteasome, subunit alpha/beta		2235
468IPR011257
DNA glycosylase		2233
469IPR002293
Amino acid/polyamine transporter I		2240
470IPR003594
Histidine kinase/HSP90-like ATPase		2236
471IPR021720
Malectin domain		2262
472IPR041679
DNA2/NAM7 helicase-like, C-terminal		2283
473IPR004776
Membrane transport protein		2241
474IPR011004
Trimeric LpxA-like superfamily		2242
475IPR045055
DNA2/NAM7-like helicase		2264
476IPR031127
E3 ubiquitin ligase RBR family		2245
477IPR006868
Domain of unknown function DUF630		2228
478IPR001487
Bromodomain		22193
479IPR002937
Amine oxidase		2239
480IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2230
481IPR002925
Dienelactone hydrolase		2227
482IPR036443
Zinc finger, RanBP2-type superfamily		2275
483IPR015590
Aldehyde dehydrogenase domain		2242
484IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2142
485IPR016073
SKP1 component, POZ domain		2124
486IPR006593
Cytochrome b561/ferric reductase transmembrane		2145
487IPR035952
Rhomboid-like superfamily		2140
488IPR000387
Tyrosine specific protein phosphatases domain		2158
489IPR013187
F-box associated domain, type 3		2130
490IPR008999
Actin-crosslinking		2127
491IPR003347
JmjC domain		2151
492IPR021790
PTBP1, RNA recognition motif 2-like		2141
493IPR013581
Plant PDR ABC transporter associated		2142
494IPR014977
WRC domain		2151
495IPR003656
Zinc finger, BED-type		2142
496IPR027413
GroEL-like equatorial domain superfamily		2129
497IPR010989
SNARE		2128
498IPR011053
Single hybrid motif		2133
499IPR020103
Pseudouridine synthase, catalytic domain superfamily		2164
500IPR022796
Chlorophyll A-B binding protein		2128
+
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativazs97.html b/gramene/htdocs/ssi/species/stats_Oryza_sativazs97.html new file mode 100644 index 00000000..b7500687 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativazs97.html @@ -0,0 +1,62 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:ZS97RS3, Dec 2020
Database version:87.1
Base Pairs:391,561,630
Golden Path Length:391,561,630
Genebuild method: Ware-lab
Genebuild started: Dec 2020
Genebuild released: Dec 2020
Genebuild last updated/patched: Dec 2020
Genebuild version: 2020-12
+

Gene counts

+ + + + + + +
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:51,628
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
144754788
237267338
339636162
437248126
530786153
632119910
730840550
830264782
922989350
1025797731
1132624309
1227232431
+
+
chunk3921 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Oryza_sativazs97_IPtop500.html b/gramene/htdocs/ssi/species/stats_Oryza_sativazs97_IPtop500.html new file mode 100644 index 00000000..f2c59125 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Oryza_sativazs97_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		14802539
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		14042660
3IPR000719
Protein kinase domain		13763913
4IPR036047
F-box-like domain superfamily		664940
5IPR044974
Disease resistance protein, plants		512991
6IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		5011030
7IPR002885
Pentatricopeptide repeat		4927582
8IPR002182
NB-ARC		480660
9IPR001810
F-box domain		472988
10IPR001611
Leucine-rich repeat		4681723
11IPR001841
Zinc finger, RING-type		431969
12IPR009057
Homeobox-like domain superfamily		390571
13IPR016024
Armadillo-type fold		381763
14IPR036291
NAD(P)-binding domain superfamily		378672
15IPR041118
Rx, N-terminal		378518
16IPR029058
Alpha/Beta hydrolase fold		364627
17IPR011990
Tetratricopeptide-like helical domain superfamily		348678
18IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		312454
19IPR036396
Cytochrome P450 superfamily		309451
20IPR035979
RNA-binding domain superfamily		304729
21IPR001128
Cytochrome P450		3021622
22IPR000504
RNA recognition motif domain		2741346
23IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		262480
24IPR017853
Glycoside hydrolase superfamily		261466
25IPR002401
Cytochrome P450, E-class, group I		2591934
26IPR036259
MFS transporter superfamily		256489
27IPR038005
Virus X resistance protein-like, coiled-coil domain		252336
28IPR017930
Myb domain		246831
29IPR001005
SANT/Myb domain		243803
30IPR036322
WD40-repeat-containing domain superfamily		237479
31IPR036249
Thioredoxin-like superfamily		232386
32IPR038765
Papain-like cysteine peptidase superfamily		231362
33IPR001680
WD40 repeat		2072155
34IPR011992
EF-hand domain pair		186284
35IPR036770
Ankyrin repeat-containing domain superfamily		176275
36IPR002048
EF-hand domain		1751051
37IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		174406
38IPR016177
DNA-binding domain superfamily		173257
39IPR036412
HAD-like superfamily		166288
40IPR036638
Helix-loop-helix DNA-binding domain superfamily		165214
41IPR002110
Ankyrin repeat		163762
42IPR011333
SKP1/BTB/POZ domain superfamily		161257
43IPR001471
AP2/ERF domain		157909
44IPR036390
Winged helix DNA-binding domain superfamily		153222
45IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		153361
46IPR012337
Ribonuclease H-like superfamily		148226
47IPR036093
NAC domain superfamily		146186
48IPR003441
NAC domain		142355
49IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		142191
50IPR029044
Nucleotide-diphospho-sugar transferases		139217
51IPR001650
Helicase, C-terminal		139518
52IPR012340
Nucleic acid-binding, OB-fold		139338
53IPR036236
Zinc finger C2H2 superfamily		139220
54IPR010255
Haem peroxidase superfamily		138175
55IPR014001
Helicase superfamily 1/2, ATP-binding domain		136254
56IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		135161
57IPR013087
Zinc finger C2H2-type		134283
58IPR020683
Ankyrin repeat-containing domain		132307
59IPR002016
Haem peroxidase		132609
60IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		131247
61IPR036188
FAD/NAD(P)-binding domain superfamily		128264
62IPR036426
Bulb-type lectin domain superfamily		128187
63IPR001480
Bulb-type lectin domain		125467
64IPR005174
Domain unknown function DUF295		124157
65IPR003439
ABC transporter-like, ATP-binding domain		124668
66IPR000210
BTB/POZ domain		120394
67IPR007658
Protein of unknown function DUF594		119124
68IPR003959
ATPase, AAA-type, core		118216
69IPR025315
Domain of unknown function DUF4220		117127
70IPR021109
Aspartic peptidase domain superfamily		114156
71IPR020846
Major facilitator superfamily domain		113191
72IPR003480
Transferase		112133
73IPR036869
Chaperone J-domain superfamily		110167
74IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		109123
75IPR008972
Cupredoxin		108236
76IPR011676
Domain of unknown function DUF1618		107140
77IPR011011
Zinc finger, FYVE/PHD-type		107205
78IPR019734
Tetratricopeptide repeat		106440
79IPR029071
Ubiquitin-like domain superfamily		106181
80IPR001623
DnaJ domain		105835
81IPR003657
WRKY domain		104274
82IPR001087
GDSL lipase/esterase		103164
83IPR036576
WRKY domain superfamily		103138
84IPR015424
Pyridoxal phosphate-dependent transferase		103160
85IPR003609
PAN/Apple domain		101277
86IPR000858
S-locus glycoprotein domain		100151
87IPR032799
Xylanase inhibitor, C-terminal		100127
88IPR033121
Peptidase family A1 domain		100150
89IPR035892
C2 domain superfamily		99221
90IPR032861
Xylanase inhibitor, N-terminal		97131
91IPR036457
PPM-type phosphatase domain superfamily		96176
92IPR005123
Oxoglutarate/iron-dependent dioxygenase		96138
93IPR044810
WRKY transcription factor, plant		95123
94IPR011050
Pectin lyase fold/virulence factor		94117
95IPR002347
Short-chain dehydrogenase/reductase SDR		93927
96IPR001932
PPM-type phosphatase domain		93503
97IPR005828
Major facilitator, sugar transporter-like		92174
98IPR044861
Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain		92129
99IPR045005
BTB/POZ and MATH domain-containing protein 1-6		92170
100IPR009072
Histone-fold		92108
101IPR015300
DNA-binding pseudobarrel domain superfamily		92179
102IPR001356
Homeobox domain		91332
103IPR000823
Plant peroxidase		91388
104IPR011545
DEAD/DEAH box helicase domain		90173
105IPR011051
RmlC-like cupin domain superfamily		88133
106IPR035669
GDSL lipase/esterase-like, plant		87120
107IPR000008
C2 domain		87462
108IPR026992
Non-haem dioxygenase N-terminal domain		85118
109IPR002083
MATH/TRAF domain		84317
110IPR020472
G-protein beta WD-40 repeat		83480
111IPR000073
Alpha/beta hydrolase fold-1		83299
112IPR043129
ATPase, nucleotide binding domain		83246
113IPR013766
Thioredoxin domain		82223
114IPR003340
B3 DNA binding domain		81429
115IPR001461
Aspartic peptidase A1 family		81288
116IPR000109
Proton-dependent oligopeptide transporter family		80328
117IPR004827
Basic-leucine zipper domain		80210
118IPR012871
Protein of unknown function DUF1677, Oryza sativa		79100
119IPR026961
PGG domain		79169
120IPR004158
Protein of unknown function DUF247, plant		75187
121IPR036875
Zinc finger, CCHC-type superfamily		7590
122IPR036282
Glutathione S-transferase, C-terminal domain superfamily		74112
123IPR003613
U box domain		73215
124IPR031052
FHY3/FAR1 family		72138
125IPR002100
Transcription factor, MADS-box		72454
126IPR001220
Legume lectin domain		72168
127IPR036879
Transcription factor, MADS-box superfamily		72100
128IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		7074
129IPR000270
PB1 domain		70164
130IPR016039
Thiolase-like		69169
131IPR016159
Cullin repeat-like-containing domain superfamily		6995
132IPR044965
Glycoside hydrolase family 17, plant		69114
133IPR001878
Zinc finger, CCHC-type		69148
134IPR000626
Ubiquitin-like domain		68191
135IPR003653
Ulp1 protease family, C-terminal catalytic domain		68164
136IPR004045
Glutathione S-transferase, N-terminal		68208
137IPR004330
FAR1 DNA binding domain		6878
138IPR013057
Amino acid transporter, transmembrane domain		67105
139IPR036163
Heavy metal-associated domain superfamily		67107
140IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		67124
141IPR008949
Isoprenoid synthase domain superfamily		6693
142IPR036749
Expansin, cellulose-binding-like domain superfamily		6681
143IPR036908
RlpA-like domain superfamily		6681
144IPR006121
Heavy metal-associated domain, HMA		65245
145IPR007117
Expansin, cellulose-binding-like domain		65155
146IPR000048
IQ motif, EF-hand binding site		65461
147IPR019787
Zinc finger, PHD-finger		64184
148IPR002902
Gnk2-homologous domain		64378
149IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6474
150IPR020568
Ribosomal protein S5 domain 2-type fold		64128
151IPR007527
Zinc finger, SWIM-type		64109
152IPR036915
Cyclin-like superfamily		64186
153IPR018108
Mitochondrial substrate/solute carrier		62572
154IPR023395
Mitochondrial carrier domain superfamily		62102
155IPR010987
Glutathione S-transferase, C-terminal-like		6295
156IPR029052
Metallo-dependent phosphatase-like		62111
157IPR000571
Zinc finger, CCCH-type		62396
158IPR003663
Sugar/inositol transporter		61388
159IPR001806
Small GTPase		61163
160IPR006501
Pectinesterase inhibitor domain		6063
161IPR000490
Glycoside hydrolase family 17		6086
162IPR009003
Peptidase S1, PA clan		60109
163IPR026057
PC-Esterase		5988
164IPR036852
Peptidase S8/S53 domain superfamily		59108
165IPR000209
Peptidase S8/S53 domain		59103
166IPR016135
Ubiquitin-conjugating enzyme/RWD-like		58104
167IPR022059
Protein of unknown function DUF3615		5892
168IPR003245
Phytocyanin domain		58120
169IPR005202
Transcription factor GRAS		58211
170IPR024788
Malectin-like domain		58103
171IPR041469
Subtilisin-like protease, fibronectin type-III domain		5795
172IPR011032
GroES-like superfamily		5791
173IPR039391
Phytocyanin		5766
174IPR002921
Fungal lipase-like domain		5684
175IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		56103
176IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5675
177IPR007112
Expansin/pollen allergen, DPBB domain		5667
178IPR015915
Kelch-type beta propeller		5694
179IPR045051
Subtilisin-like protease		55125
180IPR001752
Kinesin motor domain		55541
181IPR029962
Trichome birefringence-like family		5483
182IPR009009
RlpA-like protein, double-psi beta-barrel domain		5463
183IPR013763
Cyclin-like		54143
184IPR025846
PMR5 N-terminal domain		5476
185IPR015500
Peptidase S8, subtilisin-related		54209
186IPR000225
Armadillo		54261
187IPR000742
EGF-like domain		5362
188IPR036465
von Willebrand factor A-like domain superfamily		5380
189IPR013525
ABC-2 type transporter		52145
190IPR006045
Cupin 1		5288
191IPR001563
Peptidase S10, serine carboxypeptidase		51437
192IPR016181
Acyl-CoA N-acyltransferase		5176
193IPR004140
Exocyst complex component Exo70		51144
194IPR002528
Multi antimicrobial extrusion protein		51162
195IPR006566
FBD domain		5167
196IPR030184
WAT1-related protein		51110
197IPR023298
P-type ATPase, transmembrane domain superfamily		51107
198IPR007118
Expansin/Lol pI		50304
199IPR008250
P-type ATPase, A domain superfamily		50101
200IPR008979
Galactose-binding-like domain superfamily		50107
201IPR003676
Small auxin-up RNA		5059
202IPR000608
Ubiquitin-conjugating enzyme E2		49227
203IPR000620
EamA domain		49137
204IPR044808
Ethylene-responsive transcription factor		4958
205IPR017884
SANT domain		4871
206IPR008978
HSP20-like chaperone		4865
207IPR005630
Terpene synthase, metal-binding domain		4861
208IPR034197
Cucumisin-like catalytic domain		4877
209IPR002156
Ribonuclease H domain		4768
210IPR029055
Nucleophile aminohydrolases, N-terminal		4776
211IPR014014
RNA helicase, DEAD-box type, Q motif		4779
212IPR041569
AAA ATPase, AAA+ lid domain		4783
213IPR013094
Alpha/beta hydrolase fold-3		4770
214IPR001117
Multicopper oxidase, type 1		4657
215IPR036318
FAD-binding, type PCMH-like superfamily		4665
216IPR011701
Major facilitator superfamily		46103
217IPR012946
X8 domain		4669
218IPR008928
Six-hairpin glycosidase superfamily		4668
219IPR007125
Histone H2A/H2B/H3		4650
220IPR011706
Multicopper oxidase, C-terminal		4657
221IPR045087
Multicopper oxidase		4671
222IPR011707
Multicopper oxidase, N-termianl		4657
223IPR000873
AMP-dependent synthetase/ligase		4577
224IPR001509
NAD-dependent epimerase/dehydratase		4581
225IPR034161
Pepsin-like domain, plant		4560
226IPR006671
Cyclin, N-terminal		4583
227IPR032867
DYW domain		4552
228IPR001906
Terpene synthase, N-terminal domain		4558
229IPR001214
SET domain		45139
230IPR033896
MADS MEF2-like		4471
231IPR036640
ABC transporter type 1, transmembrane domain superfamily		44145
232IPR009060
UBA-like superfamily		4482
233IPR013201
Cathepsin propeptide inhibitor domain (I29)		4451
234IPR009000
Translation protein, beta-barrel domain superfamily		4478
235IPR011006
CheY-like superfamily		4462
236IPR011527
ABC transporter type 1, transmembrane domain		44290
237IPR014756
Immunoglobulin E-set		4474
238IPR036855
Zinc finger, CCCH-type superfamily		44160
239IPR000182
GNAT domain		43111
240IPR043926
ABC transporter family G domain		4393
241IPR004263
Exostosin-like		4360
242IPR036890
Histidine kinase/HSP90-like ATPase superfamily		4386
243IPR004265
Dirigent protein		4352
244IPR011043
Galactose oxidase/kelch, beta-propeller		4353
245IPR006702
Casparian strip membrane protein domain		4346
246IPR006016
UspA		4259
247IPR004853
Sugar phosphate transporter domain		4294
248IPR011012
Longin-like domain superfamily		4284
249IPR013126
Heat shock protein 70 family		42113
250IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4258
251IPR008889
VQ		4244
252IPR000743
Glycoside hydrolase, family 28		4261
253IPR015655
Protein phosphatase 2C family		4188
254IPR001789
Signal transduction response regulator, receiver domain		41103
255IPR033389
AUX/IAA domain		4066
256IPR000330
SNF2, N-terminal		4077
257IPR033905
Secretory peroxidase		4046
258IPR000668
Peptidase C1A, papain C-terminal		40175
259IPR015947
PUA-like superfamily		4067
260IPR016040
NAD(P)-binding domain		3968
261IPR010402
CCT domain		39116
262IPR016166
FAD-binding domain, PCMH-type		3958
263IPR000644
CBS domain		39234
264IPR002912
ACT domain		39126
265IPR000070
Pectinesterase, catalytic		3951
266IPR024752
Myb/SANT-like domain		3940
267IPR025659
Tubby-like, C-terminal		3851
268IPR016461
O-methyltransferase COMT-type		3885
269IPR029021
Protein-tyrosine phosphatase-like		3889
270IPR036612
K Homology domain, type 1 superfamily		38153
271IPR003137
PA domain		3858
272IPR002495
Glycosyl transferase, family 8		3859
273IPR044730
Ribonuclease H-like domain, plant type		3841
274IPR008942
ENTH/VHS		3757
275IPR025322
Protein of unknown function DUF4228, plant		3740
276IPR013149
Alcohol dehydrogenase, C-terminal		3750
277IPR002068
Alpha crystallin/Hsp20 domain		3793
278IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3741
279IPR036691
Endonuclease/exonuclease/phosphatase superfamily		3776
280IPR004839
Aminotransferase, class I/classII		3760
281IPR004883
Lateral organ boundaries, LOB		3780
282IPR029045
ClpP/crotonase-like domain superfamily		3769
283IPR019378
GDP-fucose protein O-fucosyltransferase		3787
284IPR040911
Exostosin, GT47 domain		3749
285IPR002109
Glutaredoxin		3747
286IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3655
287IPR013154
Alcohol dehydrogenase, N-terminal		3647
288IPR001077
O-methyltransferase domain		3646
289IPR002067
Mitochondrial carrier protein		36265
290IPR039361
Cyclin		3677
291IPR007811
DNA-directed RNA polymerase III subunit RPC4		3688
292IPR004041
NAF domain		3553
293IPR018451
NAF/FISL domain		3552
294IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		3573
295IPR004046
Glutathione S-transferase, C-terminal		3546
296IPR039417
Papain-like cysteine endopeptidase		3547
297IPR028889
Ubiquitin specific protease domain		3564
298IPR002487
Transcription factor, K-box		35124
299IPR037176
Osmotin/thaumatin-like superfamily		3541
300IPR023271
Aquaporin-like		3448
301IPR004367
Cyclin, C-terminal domain		3451
302IPR043454
NPH3/RPT2-like family		3472
303IPR000425
Major intrinsic protein		34308
304IPR006458
Ovate protein family, C-terminal		3466
305IPR001360
Glycoside hydrolase family 1		33555
306IPR001251
CRAL-TRIO lipid binding domain		33159
307IPR008991
Translation protein SH3-like domain superfamily		3347
308IPR038933
Ovate protein family		3334
309IPR000795
Translational (tr)-type GTP-binding domain		33325
310IPR001938
Thaumatin family		33219
311IPR036865
CRAL-TRIO lipid binding domain superfamily		3356
312IPR022742
Serine aminopeptidase, S33		3345
313IPR006652
Kelch repeat type 1		33102
314IPR000863
Sulfotransferase domain		3342
315IPR033443
Pentacotripeptide-repeat region of PRORP		3352
316IPR006094
FAD linked oxidase, N-terminal		3352
317IPR007493
Protein of unknown function DUF538		3277
318IPR036758
At5g01610-like superfamily		3240
319IPR043519
Nucleotidyltransferase superfamily		3264
320IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		3271
321IPR006311
Twin-arginine translocation pathway, signal sequence		3238
322IPR000528
Plant non-specific lipid-transfer protein/Par allergen		31162
323IPR018490
Cyclic nucleotide-binding-like		3157
324IPR032710
NTF2-like domain superfamily		3147
325IPR005299
SAM dependent carboxyl methyltransferase		3197
326IPR001296
Glycosyl transferase, family 1		3165
327IPR001594
Palmitoyltransferase, DHHC domain		3168
328IPR005333
Transcription factor, TCP		3134
329IPR027356
NPH3 domain		31100
330IPR034294
Aquaporin transporter		3151
331IPR003406
Glycosyl transferase, family 14		3139
332IPR004088
K Homology domain, type 1		31134
333IPR023299
P-type ATPase, cytoplasmic domain N		3165
334IPR003855
Potassium transporter		31141
335IPR012967
Plant methyltransferase dimerisation		3131
336IPR006073
GTP binding domain		31125
337IPR029000
Cyclophilin-like domain superfamily		3047
338IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain		30136
339IPR044822
Myb/SANT-like DNA-binding domain 4		3045
340IPR000315
B-box-type zinc finger		3082
341IPR029061
Thiamin diphosphate-binding fold		3086
342IPR044848
PHR1-like		3059
343IPR005135
Endonuclease/exonuclease/phosphatase		3057
344IPR035940
CAP superfamily		3042
345IPR011013
Galactose mutarotase-like domain superfamily		3059
346IPR005150
Cellulose synthase		3088
347IPR002963
Expansin		30241
348IPR003851
Zinc finger, Dof-type		3072
349IPR004314
Neprosin		3042
350IPR000595
Cyclic nucleotide-binding domain		30134
351IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		3037
352IPR036041
Ribosome-inactivating protein superfamily		3036
353IPR000717
Proteasome component (PCI) domain		2975
354IPR002423
Chaperonin Cpn60/TCP-1 family		2946
355IPR003690
Transcription termination factor, mitochondrial/chloroplastic		29109
356IPR001283
Cysteine-rich secretory protein-related		29118
357IPR016897
S-phase kinase-associated protein 1		2933
358IPR027409
GroEL-like apical domain superfamily		2940
359IPR036296
SKP1-like, dimerisation domain superfamily		2932
360IPR001223
Glycoside hydrolase family 18, catalytic domain		2979
361IPR011141
Polyketide synthase, type III		2940
362IPR002913
START domain		29120
363IPR001099
Chalcone/stilbene synthase, N-terminal		2938
364IPR001574
Ribosome-inactivating protein		2962
365IPR015940
Ubiquitin-associated domain		28109
366IPR013601
FAE1/Type III polyketide synthase-like protein		2836
367IPR001929
Germin		28107
368IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		28256
369IPR006153
Cation/H+ exchanger		2848
370IPR024709
Putative O-fucosyltransferase, plant		2870
371IPR010920
LSM domain superfamily		2839
372IPR044835
Auxin response factor		2862
373IPR002659
Glycosyl transferase, family 31		28120
374IPR016072
SKP1 component, dimerisation		2830
375IPR008480
Protein of unknown function DUF761, plant		2828
376IPR004813
Oligopeptide transporter, OPT superfamily		2867
377IPR000727
Target SNARE coiled-coil homology domain		2758
378IPR025110
AMP-binding enzyme, C-terminal domain		2734
379IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		2737
380IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		27114
381IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		2743
382IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		2741
383IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		2737
384IPR005821
Ion transport domain		2744
385IPR014044
CAP domain		2737
386IPR001849
Pleckstrin homology domain		2787
387IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2756
388IPR012328
Chalcone/stilbene synthase, C-terminal		2731
389IPR001701
Glycoside hydrolase family 9		2734
390IPR044791
Beta-glucanase/XTH		2741
391IPR003311
AUX/IAA protein		2751
392IPR000757
Glycoside hydrolase family 16		2770
393IPR005175
PPC domain		2792
394IPR015797
NUDIX hydrolase-like domain superfamily		2740
395IPR036378
FAS1 domain superfamily		2644
396IPR044778
Sugar transport protein STP/MST-like, plant		2630
397IPR011016
Zinc finger, RING-CH-type		26102
398IPR027725
Heat shock transcription factor family		2636
399IPR001881
EGF-like calcium-binding domain		2633
400IPR007650
Zf-FLZ domain		2666
401IPR001763
Rhodanese-like domain		2681
402IPR003337
Trehalose-phosphatase		2646
403IPR000408
Regulator of chromosome condensation, RCC1		26822
404IPR045048
F-box only protein 31/39		2660
405IPR036273
CRAL/TRIO, N-terminal domain superfamily		2641
406IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		2666
407IPR027923
Hydrophobic seed protein domain		2668
408IPR002035
von Willebrand factor, type A		2666
409IPR029062
Class I glutamine amidotransferase-like		2656
410IPR001757
P-type ATPase		26184
411IPR000232
Heat shock factor (HSF)-type, DNA-binding		26114
412IPR036812
NADP-dependent oxidoreductase domain superfamily		2659
413IPR000679
Zinc finger, GATA-type		26104
414IPR036085
PAZ domain superfamily		2544
415IPR017938
Riboflavin synthase-like beta-barrel		2541
416IPR004316
SWEET sugar transporter		2547
417IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2533
418IPR025753
AAA-type ATPase, N-terminal domain		2531
419IPR001357
BRCT domain		2594
420IPR029466
No apical meristem-associated, C-terminal domain		2525
421IPR036420
BRCT domain superfamily		2562
422IPR008422
Homeobox KN domain		2535
423IPR002123
Phospholipid/glycerol acyltransferase		2532
424IPR034285
Laccase, second cupredoxin domain		2534
425IPR010713
Xyloglucan endo-transglycosylase, C-terminal		2532
426IPR025486
Domain of unknown function DUF4378		2539
427IPR017927
FAD-binding domain, ferredoxin reductase-type		2440
428IPR003100
PAZ domain		2485
429IPR013216
Methyltransferase type 11		2442
430IPR007657
Glycosyltransferase 61		2473
431IPR009030
Growth factor receptor cysteine-rich domain superfamily		2431
432IPR003594
Histidine kinase/HSP90-like ATPase		2433
433IPR044675
E3 ubiquitin-protein ligase RING1-like		2428
434IPR004014
Cation-transporting P-type ATPase, N-terminal		2439
435IPR044839
Protein NDR1-like		2425
436IPR016161
Aldehyde/histidinol dehydrogenase		2442
437IPR036427
Bromodomain-like superfamily		2444
438IPR000086
NUDIX hydrolase domain		2472
439IPR036404
Jacalin-like lectin domain superfamily		2440
440IPR027410
TCP-1-like chaperonin intermediate domain superfamily		2434
441IPR010525
Auxin response factor domain		2440
442IPR000782
FAS1 domain		2371
443IPR008971
HSP40/DnaJ peptide-binding		2359
444IPR003106
Leucine zipper, homeobox-associated		2324
445IPR001163
LSM domain, eukaryotic/archaea-type		2330
446IPR040417
Glycine-rich cell wall structural protein 1/2		2338
447IPR023753
FAD/NAD(P)-binding domain		2349
448IPR018392
LysM domain		2389
449IPR019557
Aminotransferase-like, plant mobile domain		2329
450IPR017887
Transcription factor TCP subgroup		2348
451IPR001353
Proteasome, subunit alpha/beta		2332
452IPR020103
Pseudouridine synthase, catalytic domain superfamily		2349
453IPR029069
HotDog domain superfamily		2376
454IPR002939
Chaperone DnaJ, C-terminal		2332
455IPR023210
NADP-dependent oxidoreductase domain		2359
456IPR001487
Bromodomain		23208
457IPR002937
Amine oxidase		2341
458IPR029033
Histidine phosphatase superfamily		2344
459IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2246
460IPR016073
SKP1 component, POZ domain		2224
461IPR022149
Protein of unknown function DUF3681		2243
462IPR002867
IBR domain		2261
463IPR013581
Plant PDR ABC transporter associated		2248
464IPR012416
CALMODULIN-BINDING PROTEIN60		2297
465IPR026960
Reverse transcriptase zinc-binding domain		2225
466IPR036010
2Fe-2S ferredoxin-like superfamily		2230
467IPR011257
DNA glycosylase		2235
468IPR010989
SNARE		2229
469IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		2233
470IPR021720
Malectin domain		2265
471IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		2223
472IPR039421
Type 1 protein exporter		2257
473IPR031127
E3 ubiquitin ligase RBR family		2251
474IPR006868
Domain of unknown function DUF630		2229
475IPR036034
PDZ superfamily		2237
476IPR035441
TFIIS/LEDGF domain superfamily		2230
477IPR036443
Zinc finger, RanBP2-type superfamily		2260
478IPR015590
Aldehyde dehydrogenase domain		2242
479IPR001229
Jacalin-like lectin domain		2274
480IPR006689
Small GTPase superfamily, ARF/SAR type		21158
481IPR004000
Actin family		21197
482IPR006593
Cytochrome b561/ferric reductase transmembrane		2147
483IPR035952
Rhomboid-like superfamily		2135
484IPR007612
LURP-one-related		2153
485IPR013187
F-box associated domain, type 3		2124
486IPR036525
Tubulin/FtsZ, GTPase domain superfamily		2132
487IPR036873
Rhodanese-like domain superfamily		2136
488IPR001440
Tetratricopeptide repeat 1		2140
489IPR008999
Actin-crosslinking		2126
490IPR003347
JmjC domain		2152
491IPR005516
Remorin, C-terminal		2133
492IPR004320
Protein of unknown function DUF241, plant		2133
493IPR027413
GroEL-like equatorial domain superfamily		2133
494IPR025422
Transcription factor TGA like domain		2163
495IPR025756
MYB-CC type transcription factor, LHEQLE-containing domain		2145
496IPR002293
Amino acid/polyamine transporter I		2137
497IPR011053
Single hybrid motif		2133
498IPR007592
GLABROUS1 enhancer-binding protein family		2146
499IPR029057
Phosphoribosyltransferase-like		2140
500IPR022796
Chlorophyll A-B binding protein		2126
+
diff --git a/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii.html b/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii.html index 6ae27b45..7c374530 100644 --- a/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii.html +++ b/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.1 + 87.1 Base Pairs: @@ -21,16 +21,16 @@

Summary

Gene counts

- + - + - - + +
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 34,799
PseudogenesHASH(0x68c43f8):Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:		 66
Gene transcriptsHASH(0x68ce400):36,226Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:34,914
@@ -805,10 +805,10 @@

Coordinate Systems

GL378319464GL378320455GL378321437GL378322399Pt143775 +GL378322399HM173080143775 -
+
@@ -1581,6 +1581,6 @@

Coordinate Systems

GL378322.1399HM173080.1143775 -
+
diff --git a/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii_IPtop500.html b/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii_IPtop500.html index 01ea66f7..5a4d080a 100644 --- a/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Selaginella_moellendorffii_IPtop500.html @@ -16,527 +16,527 @@ 1 - IPR011990
  - 2271 - 23205 + IPR002885
Pentatricopeptide repeat + 1846 + 23447 2 - IPR002885
  - 1846 - 62288 + IPR027417
P-loop containing nucleoside triphosphate hydrolase + 1628 + 4191 3 - IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1575 - 2297 + IPR011990
Tetratricopeptide-like helical domain superfamily + 1583 + 4602 4 IPR011009
Protein kinase-like domain superfamily 1376 - 1504 + 1387 5 - IPR000719
  - 1171 - 8694 + IPR000719
Protein kinase domain + 1162 + 2031 6 - IPR008271
Serine/threonine-protein kinase, active site - 797 - 801 + IPR008271
  + 793 + 797 7 IPR013083
  - 632 - 1372 + 651 + 701 8 - IPR032675
  - 563 - 2546 + IPR016040
NAD(P)-binding domain + 609 + 750 9 - IPR017441
Protein kinase, ATP binding site - 562 - 565 + IPR032675
  + 571 + 1089 10 - IPR036291
NAD(P)-binding domain superfamily - 546 - 588 + IPR017441
  + 562 + 566 11 - IPR016024
Armadillo-type fold - 525 - 1258 + IPR036291
NAD(P)-binding domain superfamily + 546 + 555 12 - IPR029058
  - 463 - 1998 + IPR016024
Armadillo-type fold + 525 + 668 13 - IPR036396
  - 441 - 2715 + IPR029058
Alpha/Beta hydrolase fold + 476 + 1066 14 - IPR003593
AAA+ ATPase domain - 424 - 606 + IPR001128
Cytochrome P450 + 441 + 2081 15 - IPR001128
Cytochrome P450 - 423 - 1615 + IPR036396
Cytochrome P450 superfamily + 440 + 442 16 IPR015943
  - 410 - 2016 + 428 + 669 17 - IPR001611
  - 404 - 6864 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 420 + 559 18 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 390 - 493 + IPR011989
  + 417 + 924 19 - IPR036322
WD40-repeat-containing domain superfamily - 383 - 566 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 407 + 912 20 - IPR001680
  - 368 - 11937 + IPR001611
Leucine-rich repeat + 405 + 1162 21 - IPR001841
  - 360 - 1618 + IPR036322
WD40-repeat-containing domain superfamily + 383 + 413 22 - IPR002401
Cytochrome P450, E-class, group I - 358 - 2182 + IPR001841
Zinc finger, RING-type + 361 + 523 23 - IPR011989
  - 345 - 1068 + IPR002401
Cytochrome P450, E-class, group I + 358 + 2182 24 - IPR017986
  - 333 - 1140 + IPR001680
WD40 repeat + 341 + 1937 25 IPR036249
Thioredoxin-like superfamily 319 - 370 + 361 26 - IPR017853
Glycoside hydrolase superfamily - 310 - 355 + IPR009057
Homeobox-like domain superfamily + 317 + 711 27 - IPR012677
  - 305 - 974 + IPR012336
Thioredoxin-like fold + 312 + 369 28 - IPR035979
RNA-binding domain superfamily - 303 - 450 + IPR012677
  + 312 + 512 29 - IPR036047
F-box-like domain superfamily - 301 - 309 + IPR017853
Glycoside hydrolase superfamily + 310 + 312 30 - IPR036412
HAD-like superfamily - 286 - 389 + IPR035979
RNA-binding domain superfamily + 303 + 427 31 - IPR017972
Cytochrome P450, conserved site - 286 - 286 + IPR036047
F-box-like domain superfamily + 301 + 303 32 - IPR009057
Homeobox-like domain superfamily - 279 - 308 + IPR017972
  + 286 + 286 33 - IPR000504
  - 277 - 3837 + IPR036412
HAD-like superfamily + 286 + 293 34 - IPR023214
  - 276 - 806 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 283 + 451 35 - IPR036259
MFS transporter superfamily - 274 - 415 + IPR000504
RNA recognition motif domain + 275 + 833 36 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 273 - 442 + IPR036259
MFS transporter superfamily + 274 + 288 37 - IPR001650
  - 269 - 2004 + IPR023214
  + 269 + 448 38 - IPR001810
  - 254 - 1467 + IPR013781
  + 259 + 302 39 - IPR014001
  - 243 - 950 + IPR001650
Helicase, C-terminal + 251 + 492 40 - IPR003439
  - 242 - 2202 + IPR001810
F-box domain + 246 + 348 41 - IPR003591
Leucine-rich repeat, typical subtype - 234 - 1566 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 243 + 247 42 - IPR036426
  - 225 - 962 + IPR003439
ABC transporter-like, ATP-binding domain + 242 + 734 43 - IPR019775
WD40 repeat, conserved site - 220 - 377 + IPR001480
Bulb-type lectin domain + 228 + 518 44 - IPR011992
EF-hand domain pair - 220 - 247 + IPR001005
SANT/Myb domain + 227 + 950 45 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 219 - 227 + IPR036426
Bulb-type lectin domain superfamily + 225 + 230 46 - IPR020846
  - 218 - 674 + IPR011992
EF-hand domain pair + 222 + 546 47 - IPR036188
  - 213 - 1744 + IPR019775
  + 220 + 383 48 - IPR001480
  - 212 - 974 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 218 + 226 49 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 206 - 207 + IPR015915
Kelch-type beta propeller + 212 + 392 50 - IPR001005
SANT/Myb domain - 204 - 573 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 208 + 546 51 - IPR013026
  - 203 - 870 + IPR036188
FAD/NAD(P)-binding domain superfamily + 204 + 227 52 - IPR015915
  - 199 - 1320 + IPR013830
SGNH hydrolase-type esterase domain + 204 + 216 53 - IPR005123
  - 198 - 1092 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 201 + 558 54 - IPR012340
Nucleic acid-binding, OB-fold - 198 - 300 + IPR023753
FAD/NAD(P)-binding domain + 199 + 520 55 - IPR036514
  - 196 - 398 + IPR012340
Nucleic acid-binding, OB-fold + 198 + 291 56 - IPR019734
  - 194 - 4350 + IPR001087
GDSL lipase/esterase + 191 + 192 57 - IPR002048
  + IPR002048
EF-hand domain 188 - 3627 + 753 58 - IPR010255
Haem peroxidase - 181 - 182 + IPR011991
  + 182 + 207 59 - IPR002016
  - 177 - 3471 + IPR010255
Haem peroxidase superfamily + 181 + 181 60 - IPR001087
GDSL lipase/esterase - 175 - 175 + IPR002016
Haem peroxidase + 177 + 1157 61 - IPR032867
DYW domain - 173 - 173 + IPR027443
  + 174 + 177 62 - IPR003959
ATPase, AAA-type, core - 171 - 208 + IPR032867
DYW domain + 171 + 171 63 - IPR027443
  - 170 - 350 + IPR003959
ATPase, AAA-type, core + 171 + 208 64 - IPR017871
ABC transporter, conserved site + IPR017871
  170 215 65 - IPR018247
EF-Hand 1, calcium-binding site - 164 - 335 + IPR019734
Tetratricopeptide repeat + 167 + 352 66 - IPR038765
Papain-like cysteine peptidase superfamily - 163 - 181 + IPR013785
  + 165 + 186 67 - IPR000823
Plant peroxidase - 162 - 1333 + IPR017930
Myb domain + 165 + 207 68 - IPR036388
  - 160 - 354 + IPR038765
Papain-like cysteine peptidase superfamily + 163 + 163 69 - IPR014710
  - 158 - 394 + IPR018247
  + 163 + 357 70 - IPR029044
  - 156 - 688 + IPR000823
Plant peroxidase + 162 + 1333 71 - IPR023213
  - 156 - 564 + IPR014710
  + 160 + 199 72 - IPR013785
  - 155 - 519 + IPR014729
  + 158 + 196 73 - IPR036390
Winged helix DNA-binding domain superfamily - 152 - 162 + IPR023213
  + 154 + 282 74 - IPR011545
DEAD/DEAH box helicase domain - 151 - 156 + IPR036390
Winged helix DNA-binding domain superfamily + 152 + 162 75 - IPR035595
UDP-glycosyltransferase family, conserved site - 146 - 146 + IPR011545
DEAD/DEAH box helicase domain + 151 + 156 @@ -557,1134 +557,1134 @@ 78 IPR015424
Pyridoxal phosphate-dependent transferase 144 - 162 + 146 79 - IPR011051
RmlC-like cupin domain superfamily - 143 - 148 + IPR015421
  + 143 + 149 80 - IPR017930
  - 143 - 384 + IPR011051
RmlC-like cupin domain superfamily + 143 + 144 81 - IPR015421
  - 142 - 438 + IPR029044
Nucleotide-diphospho-sugar transferases + 142 + 275 82 - IPR014729
  - 142 - 336 + IPR003480
Transferase + 141 + 149 83 - IPR003480
Transferase - 142 - 150 + IPR020472
G-protein beta WD-40 repeat + 136 + 408 84 - IPR020472
G-protein beta WD-40 repeat - 136 - 408 + IPR001623
DnaJ domain + 129 + 805 85 - IPR036852
  - 135 - 1482 + IPR026992
Non-haem dioxygenase N-terminal domain + 129 + 130 86 - IPR036869
  - 131 - 504 + IPR036852
Peptidase S8/S53 domain superfamily + 128 + 130 87 - IPR026992
Non-haem dioxygenase N-terminal domain - 129 - 130 + IPR019793
  + 128 + 128 88 - IPR019793
Peroxidases heam-ligand binding site - 128 - 128 + IPR000209
Peptidase S8/S53 domain + 128 + 376 89 - IPR000209
Peptidase S8/S53 domain - 124 - 129 + IPR036869
Chaperone J-domain superfamily + 126 + 126 90 - IPR005225
Small GTP-binding protein domain - 123 - 127 + IPR015500
Peptidase S8, subtilisin-related + 124 + 509 91 - IPR016177
DNA-binding domain superfamily - 120 - 137 + IPR005225
  + 123 + 127 92 - IPR035669
GDSL lipase/esterase-like, plant - 117 - 117 + IPR029052
Metallo-dependent phosphatase-like + 121 + 272 93 - IPR000073
Alpha/beta hydrolase fold-1 - 117 - 219 + IPR016177
DNA-binding domain superfamily + 120 + 137 94 - IPR001623
  - 116 - 1572 + IPR035669
GDSL lipase/esterase-like, plant + 117 + 117 95 - IPR008949
  - 115 - 486 + IPR008949
Isoprenoid synthase domain superfamily + 116 + 249 96 - IPR015422
  - 115 - 528 + IPR020846
Major facilitator superfamily domain + 115 + 115 97 - IPR036770
  - 114 - 516 + IPR000073
Alpha/beta hydrolase fold-1 + 115 + 217 98 - IPR036955
  - 113 - 387 + IPR001471
AP2/ERF domain + 114 + 671 99 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 112 - 137 + IPR036770
Ankyrin repeat-containing domain superfamily + 114 + 115 100 - IPR001471
  - 112 - 2016 + IPR020683
Ankyrin repeat-containing domain + 113 + 220 101 - IPR002347
Short-chain dehydrogenase/reductase SDR - 111 - 818 + IPR035892
C2 domain superfamily + 113 + 147 102 - IPR017907
Zinc finger, RING-type, conserved site - 111 - 114 + IPR000008
C2 domain + 113 + 450 103 - IPR020683
  - 110 - 600 + IPR017907
  + 111 + 114 104 - IPR036961
  - 110 - 387 + IPR002347
Short-chain dehydrogenase/reductase SDR + 111 + 822 105 - IPR001214
  - 110 - 753 + IPR013766
Thioredoxin domain + 110 + 199 106 - IPR035892
  - 109 - 298 + IPR001214
SET domain + 110 + 201 107 - IPR036640
  - 109 - 1071 + IPR020568
Ribosomal protein S5 domain 2-type fold + 109 + 117 108 - IPR020568
Ribosomal protein S5 domain 2-type fold - 109 - 141 + IPR011527
ABC transporter type 1, transmembrane domain + 109 + 366 109 - IPR011527
  - 109 - 1098 + IPR015422
  + 108 + 133 110 - IPR000225
  - 109 - 2640 + IPR011050
Pectin lyase fold/virulence factor + 108 + 109 111 - IPR011050
Pectin lyase fold/virulence factor - 108 - 117 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 107 + 184 112 - IPR018108
  + IPR018108
Mitochondrial substrate/solute carrier 107 - 1216 + 602 113 - IPR023395
  + IPR023395
Mitochondrial carrier domain superfamily 107 - 486 + 219 114 - IPR027640
Kinesin-like protein - 106 - 148 + IPR012334
  + 107 + 111 115 - IPR013766
  - 105 - 582 + IPR007087
  + 104 + 413 116 - IPR013087
  - 104 - 1281 - - - - 117 IPR016161
Aldehyde/histidinol dehydrogenase 104 104 - + + 117 + IPR001752
Kinesin motor domain + 104 + 655 + + + 118 - IPR012334
  - 104 - 208 + IPR004045
Glutathione S-transferase, N-terminal + 102 + 199 119 - IPR001965
Zinc finger, PHD-type - 103 - 129 + IPR001932
PPM-type phosphatase domain + 102 + 411 120 - IPR004045
  - 102 - 594 + IPR036457
PPM-type phosphatase domain superfamily + 101 + 101 121 - IPR001752
  - 102 - 1929 + IPR003960
  + 100 + 112 122 - IPR036457
  - 101 - 430 + IPR019794
  + 100 + 100 123 - IPR001932
  - 101 - 1272 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 99 + 273 124 - IPR003960
ATPase, AAA-type, conserved site - 100 - 112 + IPR011032
GroES-like superfamily + 98 + 197 125 - IPR019794
Peroxidase, active site - 100 - 100 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 97 + 97 126 - IPR002110
  - 99 - 1617 + IPR002110
Ankyrin repeat + 95 + 252 127 - IPR013783
  - 98 - 384 + IPR004274
FCP1 homology domain + 95 + 193 128 - IPR011032
GroES-like superfamily - 97 - 116 + IPR010987
Glutathione S-transferase, C-terminal-like + 95 + 180 129 - IPR029052
  - 97 - 212 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 94 + 95 130 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 97 - 98 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 94 + 95 131 - IPR016163
  - 96 - 303 + IPR015590
Aldehyde dehydrogenase domain + 94 + 99 132 - IPR015500
Peptidase S8, subtilisin-related - 95 - 277 + IPR013057
Amino acid transporter, transmembrane domain + 93 + 95 133 - IPR004274
  - 95 - 560 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 92 + 129 134 - IPR036638
  - 94 - 558 + IPR019787
Zinc finger, PHD-finger + 91 + 138 135 - IPR011598
  - 94 - 1026 + IPR006045
Cupin 1 + 91 + 110 136 - IPR015590
Aldehyde dehydrogenase domain - 94 - 99 + IPR016163
  + 91 + 91 137 - IPR013057
Amino acid transporter, transmembrane domain - 93 - 95 + IPR003594
Histidine kinase/HSP90-like ATPase + 90 + 166 138 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 92 - 92 + IPR012337
Ribonuclease H-like superfamily + 90 + 178 139 - IPR000008
  - 92 - 772 + IPR043129
ATPase, nucleotide binding domain + 90 + 165 140 - IPR006045
Cupin 1 - 92 - 213 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 89 + 89 141 - IPR019787
  - 91 - 278 + IPR023828
  + 89 + 89 142 - IPR037045
  - 91 - 182 + IPR029071
Ubiquitin-like domain superfamily + 89 + 136 143 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 90 - 90 + IPR013525
ABC-2 type transporter + 88 + 129 144 - IPR015655
Protein phosphatase 2C family - 90 + IPR041569
AAA ATPase, AAA+ lid domain + 88 97 145 - IPR000873
AMP-dependent synthetase/ligase - 89 - 89 + IPR019786
  + 88 + 90 146 - IPR012337
Ribonuclease H-like superfamily - 89 - 108 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 87 + 89 147 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 89 - 89 + IPR036236
Zinc finger C2H2 superfamily + 87 + 117 148 - IPR029071
Ubiquitin-like domain superfamily - 89 - 136 + IPR036318
FAD-binding, type PCMH-like superfamily + 86 + 86 149 - IPR010987
  - 89 - 178 + IPR005202
Transcription factor GRAS + 85 + 254 150 - IPR013525
ABC-2 type transporter - 88 - 129 + IPR034197
Cucumisin-like catalytic domain + 84 + 84 151 - IPR019786
Zinc finger, PHD-type, conserved site - 88 - 89 + IPR011333
SKP1/BTB/POZ domain superfamily + 84 + 87 152 - IPR008979
  - 88 - 352 + IPR023393
  + 83 + 86 153 - IPR036890
  - 87 - 372 + IPR006652
Kelch repeat type 1 + 83 + 137 154 - IPR036236
Zinc finger C2H2 superfamily - 87 - 127 + IPR029021
Protein-tyrosine phosphatase-like + 81 + 190 155 - IPR036318
FAD-binding, type 2-like superfamily - 86 - 86 + IPR000225
Armadillo + 80 + 319 156 - IPR034197
Cucumisin-like catalytic domain - 85 - 85 + IPR016166
FAD-binding domain, PCMH-type + 80 + 80 157 - IPR005202
  - 85 - 342 + IPR008979
Galactose-binding-like domain superfamily + 80 + 166 158 - IPR023393
  - 84 - 174 + IPR000571
Zinc finger, CCCH-type + 80 + 272 159 - IPR014014
  - 84 - 168 + IPR016169
  + 79 + 79 160 - IPR011333
SKP1/BTB/POZ domain superfamily - 84 - 96 + IPR000873
AMP-dependent synthetase/ligase + 78 + 78 161 - IPR006652
Kelch repeat type 1 - 83 - 281 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 78 + 151 162 - IPR029021
  - 81 - 364 + IPR013087
Zinc finger C2H2-type + 77 + 141 163 - IPR016166
  - 80 - 240 + IPR009072
Histone-fold + 77 + 160 164 - IPR000571
  - 80 - 1053 + IPR036908
RlpA-like domain superfamily + 77 + 77 165 - IPR021109
  - 79 - 480 + IPR021109
Aspartic peptidase domain superfamily + 76 + 224 166 - IPR036908
  - 79 - 310 + IPR000109
Proton-dependent oligopeptide transporter family + 76 + 173 167 - IPR009072
  - 79 - 489 + IPR005828
Major facilitator, sugar transporter-like + 76 + 92 168 - IPR008978
  - 76 - 322 + IPR016181
Acyl-CoA N-acyltransferase + 75 + 157 169 - IPR000109
Proton-dependent oligopeptide transporter family - 76 - 171 + IPR019821
  + 75 + 75 170 - IPR005828
Major facilitator, sugar transporter-like - 76 - 92 + IPR002921
Fungal lipase-like domain + 75 + 75 171 - IPR002921
Fungal lipase-like domain - 75 - 75 + IPR029055
Nucleophile aminohydrolases, N-terminal + 75 + 141 172 - IPR019821
Kinesin motor domain, conserved site - 75 + IPR008280
Tubulin/FtsZ, C-terminal + 75 75 173 - IPR029055
  - 75 - 304 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 75 + 128 174 - IPR008280
Tubulin/FtsZ, C-terminal - 75 - 75 + IPR003008
Tubulin/FtsZ, GTPase domain + 74 + 171 175 - IPR016135
  - 75 - 296 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 74 + 74 176 - IPR036525
  - 74 - 298 + IPR008972
Cupredoxin + 74 + 266 177 - IPR008972
  - 74 - 544 + IPR013154
Alcohol dehydrogenase, N-terminal + 74 + 75 178 - IPR013154
Alcohol dehydrogenase, N-terminal - 74 - 75 + IPR014756
Immunoglobulin E-set + 74 + 98 179 - IPR014756
Immunoglobulin E-set - 74 - 100 + IPR000330
SNF2, N-terminal + 73 + 73 180 - IPR016181
Acyl-CoA N-acyltransferase - 73 - 81 + IPR001279
Metallo-beta-lactamase + 73 + 125 181 - IPR000330
SNF2-related, N-terminal domain - 73 - 73 + IPR008978
HSP20-like chaperone + 73 + 155 182 - IPR003613
  - 73 - 636 + IPR001356
Homeobox domain + 71 + 206 183 - IPR006094
FAD linked oxidase, N-terminal - 72 - 72 + IPR003613
U box domain + 71 + 140 184 - IPR000217
Tubulin - 71 - 599 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 70 + 76 185 - IPR001509
NAD-dependent epimerase/dehydratase - 71 - 74 + IPR044965
Glycoside hydrolase family 17, plant + 70 + 72 186 - IPR003594
Histidine kinase/HSP90-like ATPase - 71 - 178 + IPR014721
  + 70 + 76 187 - IPR038718
  - 71 - 168 + IPR015916
  + 70 + 87 188 - IPR001356
  - 71 - 831 + IPR043926
ABC transporter family G domain + 70 + 94 189 - IPR036397
  - 70 - 231 + IPR000490
Glycoside hydrolase family 17 + 70 + 114 190 - IPR036866
  - 70 - 346 + IPR006094
FAD linked oxidase, N-terminal + 69 + 69 191 - IPR001461
Aspartic peptidase A1 family - 70 - 182 + IPR001509
NAD-dependent epimerase/dehydratase + 69 + 72 192 - IPR000490
Glycoside hydrolase family 17 - 70 - 114 + IPR014014
RNA helicase, DEAD-box type, Q motif + 69 + 69 193 - IPR003008
Tubulin/FtsZ, GTPase domain - 69 - 162 + IPR001757
P-type ATPase + 68 + 151 194 - IPR032799
Xylanase inhibitor, C-terminal - 68 - 69 + IPR029045
ClpP/crotonase-like domain superfamily + 68 + 160 195 - IPR001757
P-type ATPase - 68 - 151 + IPR032799
Xylanase inhibitor, C-terminal + 67 + 68 196 - IPR000210
  - 67 - 477 + IPR000217
Tubulin + 67 + 593 197 - IPR023299
  - 67 - 357 + IPR023298
P-type ATPase, transmembrane domain superfamily + 66 + 122 198 - IPR029045
ClpP/crotonase-like domain superfamily - 66 - 92 + IPR005135
Endonuclease/exonuclease/phosphatase + 66 + 126 199 - IPR023123
  - 66 - 132 + IPR023299
P-type ATPase, cytoplasmic domain N + 66 + 127 200 - IPR016162
  - 66 - 306 + IPR018316
Tubulin/FtsZ, 2-layer sandwich domain + 65 + 122 201 - IPR014721
  - 66 - 160 + IPR013149
Alcohol dehydrogenase, C-terminal + 65 + 66 202 - IPR017877
  - 66 - 158 + IPR017975
  + 65 + 65 203 - IPR013149
Alcohol dehydrogenase, C-terminal - 65 - 66 + IPR033121
Peptidase family A1 domain + 65 + 72 204 - IPR017975
Tubulin, conserved site - 65 - 65 + IPR023210
NADP-dependent oxidoreductase domain + 65 + 135 205 - IPR033121
  - 65 - 144 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 65 + 65 206 - IPR023298
P-type ATPase, transmembrane domain superfamily - 65 - 188 + IPR013783
  + 64 + 100 207 - IPR036812
  - 65 - 272 + IPR011993
  + 64 + 69 208 - IPR036691
  - 64 - 302 + IPR008250
P-type ATPase, A domain superfamily + 64 + 145 209 - IPR018253
DnaJ domain, conserved site + IPR018253
  64 64 210 - IPR012341
  - 64 - 204 + IPR023123
  + 64 + 64 211 - IPR000626
  - 63 - 876 + IPR001878
Zinc finger, CCHC-type + 63 + 150 212 - IPR008250
P-type ATPase, A domain superfamily - 63 - 78 + IPR000626
Ubiquitin-like domain + 63 + 202 213 - IPR018316
Tubulin/FtsZ, 2-layer sandwich domain - 63 - 119 + IPR000608
Ubiquitin-conjugating enzyme E2 + 62 + 174 214 - IPR023210
NADP-dependent oxidoreductase domain - 63 - 127 + IPR001929
Germin + 62 + 178 215 - IPR011993
  - 63 - 130 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 62 + 62 216 - IPR001929
Germin - 62 - 178 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 62 + 62 217 - IPR000608
  - 62 - 348 + IPR009000
Translation protein, beta-barrel domain superfamily + 62 + 66 218 - IPR011701
Major facilitator superfamily - 62 - 63 + IPR012946
X8 domain + 62 + 62 219 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 62 + IPR006447
  + 62 62 220 - IPR009000
Translation protein, beta-barrel domain superfamily - 62 - 68 + IPR000182
GNAT domain + 61 + 107 221 - IPR012946
X8 domain - 62 - 124 + IPR011701
Major facilitator superfamily + 61 + 62 222 - IPR006447
Myb domain, plants - 62 - 62 + IPR004263
Exostosin-like + 61 + 173 223 - IPR000182
  - 61 - 214 + IPR011043
Galactose oxidase/kelch, beta-propeller + 61 + 67 224 - IPR003137
PA domain - 61 + IPR018303
  + 61 61 225 - IPR018303
P-type ATPase, phosphorylation site - 61 - 61 + IPR002067
Mitochondrial carrier protein + 60 + 294 226 - IPR011043
Galactose oxidase/kelch, beta-propeller - 61 - 80 + IPR000210
BTB/POZ domain + 59 + 112 227 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 60 - 472 + IPR000668
Peptidase C1A, papain C-terminal + 59 + 147 228 - IPR002067
Mitochondrial carrier protein - 60 - 294 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 59 + 149 229 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 60 - 81 + IPR008928
Six-hairpin glycosidase superfamily + 58 + 58 230 - IPR037103
  - 59 - 118 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 58 + 58 231 - IPR000668
Peptidase C1A, papain C-terminal - 59 - 198 + IPR020845
  + 58 + 58 232 - IPR013780
  - 59 - 130 + IPR019780
  + 58 + 60 233 - IPR009091
  - 59 - 340 + IPR003137
PA domain + 57 + 57 234 - IPR008928
Six-hairpin glycosidase superfamily - 58 - 72 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 57 + 57 235 - IPR020845
AMP-binding, conserved site - 58 - 58 + IPR016162
  + 57 + 59 236 - IPR019780
Germin, manganese binding site - 58 - 60 + IPR003663
Sugar/inositol transporter + 57 + 309 237 - IPR013128
Peptidase C1A - 57 - 63 + IPR012675
  + 56 + 56 238 - IPR020843
Polyketide synthase, enoylreductase domain - 57 - 57 + IPR005829
  + 56 + 95 239 - IPR003663
Sugar/inositol transporter - 57 - 309 + IPR015300
DNA-binding pseudobarrel domain superfamily + 56 + 123 @@ -1696,240 +1696,240 @@ 241 - IPR005829
Sugar transporter, conserved site - 56 + IPR032710
NTF2-like domain superfamily + 56 95 242 - IPR015300
  - 56 - 246 + IPR000387
Tyrosine specific protein phosphatases domain + 56 + 56 243 - IPR001878
  - 55 - 414 + IPR029061
Thiamin diphosphate-binding fold + 55 + 167 244 IPR017938
Riboflavin synthase-like beta-barrel 54 - 61 + 56 245 - IPR006121
  - 54 - 540 + IPR013216
Methyltransferase type 11 + 54 + 55 246 - IPR013216
Methyltransferase type 11 - 54 - 55 + IPR033443
Pentacotripeptide-repeat region of PRORP + 54 + 60 247 - IPR029061
Thiamin diphosphate-binding fold - 54 - 84 + IPR029033
Histidine phosphatase superfamily + 54 + 127 248 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 54 - 54 + IPR001789
Signal transduction response regulator, receiver domain + 54 + 117 249 - IPR007112
  + IPR007112
Expansin/pollen allergen, DPBB domain 54 - 208 + 54 250 IPR011006
CheY-like superfamily 54 - 68 + 65 251 - IPR000644
  - 54 - 634 + IPR001806
Small GTPase + 53 + 100 252 - IPR029033
  - 54 - 246 + IPR016039
Thiolase-like + 53 + 223 253 - IPR001789
  - 54 - 699 + IPR036163
Heavy metal-associated domain superfamily + 53 + 67 254 - IPR032710
NTF2-like domain superfamily - 53 - 53 + IPR006121
Heavy metal-associated domain, HMA + 52 + 173 255 - IPR016039
  - 53 - 624 + IPR011012
Longin-like domain superfamily + 52 + 52 256 - IPR004263
Exostosin-like - 53 - 55 + IPR029062
Class I glutamine amidotransferase-like + 52 + 110 257 - IPR036163
Heavy metal-associated domain superfamily - 53 - 67 + IPR036465
von Willebrand factor A-like domain superfamily + 52 + 53 258 - IPR036465
  - 53 - 194 + IPR001461
Aspartic peptidase A1 family + 52 + 140 259 - IPR001806
Small GTPase superfamily - 53 - 53 + IPR003340
B3 DNA binding domain + 51 + 162 260 - IPR003340
  - 52 - 657 + IPR015655
Protein phosphatase 2C family + 51 + 53 261 - IPR000387
  - 52 - 156 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 51 + 51 262 - IPR011012
Longin-like domain superfamily - 52 - 52 + IPR002068
Alpha crystallin/Hsp20 domain + 51 + 104 263 - IPR029062
  - 52 - 222 + IPR006073
GTP binding domain + 51 + 141 264 - IPR017927
  - 51 - 153 + IPR036915
Cyclin-like superfamily + 50 + 80 265 - IPR002068
  - 51 - 212 + IPR013763
Cyclin-like + 50 + 144 266 - IPR006073
GTP binding domain - 51 - 141 + IPR000270
PB1 domain + 50 + 64 267 - IPR036915
Cyclin-like superfamily - 50 - 82 + IPR004853
Sugar phosphate transporter domain + 49 + 49 268 - IPR000270
  - 50 - 264 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 49 + 49 269 - IPR016040
NAD(P)-binding domain - 49 - 53 + IPR004265
Dirigent protein + 49 + 49 - 270 - IPR004853
Sugar phosphate transporter domain - 49 - 49 + 270 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 49 + 55 271 - IPR004265
Dirigent protein - 49 - 49 + IPR032861
Xylanase inhibitor, N-terminal + 49 + 51 272 - IPR002123
Phospholipid/glycerol acyltransferase - 49 - 92 + IPR011042
  + 49 + 59 273 - IPR032861
Xylanase inhibitor, N-terminal - 49 - 52 + IPR000048
IQ motif, EF-hand binding site + 49 + 264 274 - IPR000048
  - 49 - 1251 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 48 + 48 @@ -1941,50 +1941,50 @@ 276 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 48 - 48 + IPR003851
Zinc finger, Dof-type + 48 + 136 277 - IPR003851
  - 48 - 411 + IPR028889
Ubiquitin specific protease domain + 48 + 48 278 - IPR028889
  - 48 - 96 + IPR039417
Papain-like cysteine endopeptidase + 47 + 47 279 - IPR002130
  + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain 47 - 792 + 264 280 - IPR029000
  + IPR029000
Cyclophilin-like domain superfamily 47 - 198 + 94 281 - IPR012675
  - 47 - 102 + IPR000629
  + 47 + 47 282 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 47 + IPR013780
  + 47 47 @@ -1997,63 +1997,63 @@ 284 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 46 - 71 + IPR013078
Histidine phosphatase superfamily, clade-1 + 45 + 95 285 - IPR005467
  + IPR005467
Histidine kinase domain 45 - 90 + 45 286 - IPR013078
Histidine phosphatase superfamily, clade-1 - 45 - 134 + IPR000644
CBS domain + 45 + 167 287 - IPR033443
Pentacotripeptide-repeat region of PRORP - 45 - 50 + IPR019378
GDP-fucose protein O-fucosyltransferase + 44 + 44 288 - IPR011042
  - 45 - 110 + IPR036855
Zinc finger, CCCH-type superfamily + 44 + 71 289 - IPR029510
Aldehyde dehydrogenase, glutamic acid active site + IPR029510
  44 44 290 - IPR000795
  + IPR000795
Translational (tr)-type GTP-binding domain 44 - 834 + 278 291 - IPR019378
GDP-fucose protein O-fucosyltransferase - 44 + IPR020422
Dual specificity protein phosphatase domain + 44 44 292 - IPR016130
Protein-tyrosine phosphatase, active site + IPR016130
  44 44 @@ -2067,191 +2067,191 @@ 294 - IPR036855
Zinc finger, CCCH-type superfamily - 44 - 71 + IPR036875
Zinc finger, CCHC-type superfamily + 44 + 48 295 - IPR036875
Zinc finger, CCHC-type superfamily - 44 - 48 + IPR002123
Phospholipid/glycerol acyltransferase + 43 + 43 296 - IPR000727
  - 43 - 222 + IPR024880
COPII coat assembly protein, Sec16 + 43 + 67 297 - IPR000222
PPM-type phosphatase, divalent cation binding - 43 - 43 + IPR043472
Macro domain-like + 43 + 45 298 - IPR020422
  - 43 - 312 + IPR018200
  + 42 + 71 299 - IPR001360
Glycoside hydrolase family 1 - 42 - 280 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 42 + 46 300 - IPR018200
Ubiquitin specific protease, conserved site - 42 - 71 + IPR000222
  + 42 + 42 301 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 42 - 76 + IPR036392
PLAT/LH2 domain superfamily + 42 + 42 302 - IPR023346
Lysozyme-like domain superfamily - 42 - 45 + IPR001360
Glycoside hydrolase family 1 + 42 + 278 303 - IPR023566
Peptidyl-prolyl cis-trans isomerase, FKBP-type - 42 - 56 + IPR003661
Signal transduction histidine kinase, dimerisation/phosphoacceptor domain + 42 + 120 304 - IPR002912
  - 42 - 198 + IPR023346
Lysozyme-like domain superfamily + 42 + 45 305 - IPR036392
PLAT/LH2 domain superfamily - 42 - 42 + IPR002912
ACT domain + 42 + 88 306 - IPR003661
Signal transduction histidine kinase, dimerisation/phosphoacceptor domain - 41 - 121 + IPR000727
Target SNARE coiled-coil homology domain + 41 + 68 307 - IPR020471
Aldo/keto reductase - 41 - 208 + IPR000408
Regulator of chromosome condensation, RCC1 + 41 + 618 308 - IPR001279
Metallo-beta-lactamase - 41 - 67 + IPR029069
HotDog domain superfamily + 41 + 131 309 - IPR013763
Cyclin-like - 41 - 118 + IPR015947
PUA-like superfamily + 41 + 52 310 - IPR000408
  - 41 - 1202 + IPR001024
PLAT/LH2 domain + 41 + 106 311 - IPR002528
Multi antimicrobial extrusion protein - 41 - 108 + IPR020471
Aldo-keto reductase + 41 + 181 312 - IPR029069
HotDog domain superfamily - 41 - 63 + IPR002528
Multi antimicrobial extrusion protein + 41 + 108 313 - IPR002109
  - 41 - 240 + IPR013094
Alpha/beta hydrolase fold-3 + 41 + 42 314 - IPR013094
Alpha/beta hydrolase fold-3 - 41 - 42 + IPR004827
Basic-leucine zipper domain + 41 + 103 315 - IPR004827
  - 41 - 429 + IPR036612
K Homology domain, type 1 superfamily + 40 + 70 316 - IPR008942
  - 40 - 146 + IPR036010
2Fe-2S ferredoxin-like superfamily + 40 + 40 317 - IPR003441
  - 40 - 240 + IPR044726
ABC transporter C family, six-transmembrane helical domain 2 + 40 + 40 318 - IPR024298
Ancestral coatomer element 1, Sec16/Sec31 - 40 - 46 + IPR017937
  + 40 + 48 319 - IPR036612
  - 40 - 366 + IPR003029
S1 domain + 40 + 134 320 - IPR036010
2Fe-2S ferredoxin-like superfamily - 40 - 40 + IPR003441
NAC domain + 40 + 162 @@ -2265,553 +2265,553 @@ 322 IPR020103
Pseudouridine synthase, catalytic domain superfamily 40 - 67 + 40 323 - IPR017937
Thioredoxin, conserved site - 40 - 45 + IPR002035
von Willebrand factor, type A + 40 + 79 324 - IPR036093
  - 40 - 246 + IPR004088
K Homology domain, type 1 + 40 + 132 325 - IPR002937
Amine oxidase - 40 - 41 + IPR043519
Nucleotidyltransferase superfamily + 40 + 40 326 - IPR015947
PUA-like superfamily - 40 - 46 + IPR002937
Amine oxidase + 40 + 41 327 - IPR003029
  - 40 - 402 + IPR006195
Aminoacyl-tRNA synthetase, class II + 39 + 40 328 - IPR006195
  - 39 - 80 + IPR000717
Proteasome component (PCI) domain + 39 + 67 329 - IPR001024
  - 39 - 258 + IPR008914
Phosphatidylethanolamine-binding protein + 39 + 62 330 - IPR001179
  - 39 - 218 + IPR002100
Transcription factor, MADS-box + 39 + 183 331 - IPR013581
Plant PDR ABC transporter associated - 39 - 39 + IPR036879
Transcription factor, MADS-box superfamily + 39 + 40 332 - IPR000717
  - 39 - 190 + IPR001179
FKBP-type peptidyl-prolyl cis-trans isomerase domain + 39 + 109 333 - IPR036673
Cyanovirin-N superfamily - 39 - 78 + IPR013581
Plant PDR ABC transporter associated + 39 + 39 334 - IPR024950
Dual specificity phosphatase - 39 - 43 + IPR024298
Ancestral coatomer element 1, Sec16/Sec31 + 39 + 45 335 - IPR034294
Aquaporin transporter - 39 - 40 + IPR036673
Cyanovirin-N superfamily + 39 + 39 336 - IPR036610
  - 39 - 160 + IPR011058
Cyanovirin-N + 39 + 80 337 - IPR002100
  - 39 - 657 + IPR002589
Macro domain + 39 + 74 338 - IPR011058
Cyanovirin-N - 39 - 71 + IPR002109
Glutaredoxin + 38 + 39 339 - IPR025661
Cysteine peptidase, asparagine active site - 39 - 39 + IPR044791
Beta-glucanase/XTH + 38 + 44 340 - IPR002589
  - 39 - 200 + IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain + 38 + 93 341 - IPR036879
  - 39 - 219 + IPR001563
Peptidase S10, serine carboxypeptidase + 38 + 196 342 - IPR001563
Peptidase S10, serine carboxypeptidase - 38 - 200 + IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain + 38 + 38 343 - IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain - 38 + IPR002328
  + 38 38 344 - IPR002328
Alcohol dehydrogenase, zinc-type, conserved site - 38 - 38 + IPR023271
Aquaporin-like + 38 + 76 345 - IPR023271
  - 38 - 152 + IPR004839
Aminotransferase, class I/classII + 38 + 39 346 - IPR004839
Aminotransferase, class I/classII - 38 - 39 + IPR000425
Major intrinsic protein + 38 + 291 347 - IPR022967
RNA-binding domain, S1 - 38 - 93 + IPR004993
GH3 family + 38 + 78 348 - IPR022796
Chlorophyll A-B binding protein - 38 + IPR004147
UbiB domain + 38 38 - 349 - IPR000425
Major intrinsic protein - 38 - 281 + 349 + IPR014720
Double-stranded RNA-binding domain + 38 + 93 350 - IPR004993
GH3 family - 38 - 79 + IPR025661
  + 38 + 38 351 - IPR004147
UbiB domain - 38 - 38 + IPR000757
Glycoside hydrolase family 16 + 38 + 78 352 - IPR000757
  - 38 - 234 + IPR001478
PDZ domain + 37 + 72 353 - IPR001041
  - 38 - 279 + IPR001763
Rhodanese-like domain + 37 + 96 354 IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase 37 - 72 + 67 355 - IPR011016
  - 37 - 297 + IPR007197
Radical SAM + 37 + 65 356 - IPR034686
Terpene cyclase like 2 - 37 - 37 + IPR000172
Glucose-methanol-choline oxidoreductase, N-terminal + 37 + 76 357 - IPR005630
Terpene synthase, metal-binding domain - 37 - 38 + IPR003245
Phytocyanin domain + 37 + 112 358 - IPR005135
Endonuclease/exonuclease/phosphatase - 37 - 37 + IPR036610
PEBP-like superfamily + 37 + 39 359 - IPR000172
Glucose-methanol-choline oxidoreductase, N-terminal - 37 - 76 + IPR035810
Phosphatidylethanolamine-binding protein, eukaryotic + 37 + 55 360 - IPR003245
  - 37 - 336 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 37 + 37 361 - IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 - 37 - 37 + IPR028992
  + 36 + 36 362 - IPR024709
Putative O-fucosyltransferase, plant - 36 - 73 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 36 + 36 363 - IPR036749
  - 36 - 144 + IPR013121
Ferric reductase, NAD binding domain + 36 + 36 364 - IPR017392
AP2/ERF transcription factor ERF/PTI6 - 36 - 47 + IPR003657
WRKY domain + 36 + 211 365 - IPR002902
  - 36 - 156 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 36 + 97 366 - IPR023313
Ubiquitin-conjugating enzyme, active site - 36 - 36 + IPR008942
ENTH/VHS + 36 + 69 367 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 36 - 54 + IPR044746
ABC transporter C family, six-transmembrane helical domain 1 + 36 + 36 368 - IPR013121
Ferric reductase, NAD binding domain - 36 - 36 + IPR007817
Pyoverdine/dityrosine biosynthesis protein + 36 + 77 369 - IPR005746
Thioredoxin - 36 - 61 + IPR023313
  + 36 + 36 370 - IPR004088
K Homology domain, type 1 - 36 - 66 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 36 + 77 371 - IPR003657
  - 36 - 381 + IPR007117
Expansin, cellulose-binding-like domain + 36 + 108 372 - IPR007117
  - 36 - 144 + IPR000620
EamA domain + 36 + 69 373 - IPR036872
  - 36 - 166 + IPR016461
O-methyltransferase COMT-type + 35 + 91 374 - IPR000620
EamA domain - 36 - 69 + IPR001305
Heat shock protein DnaJ, cysteine-rich domain + 35 + 85 375 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 36 - 75 + IPR001353
Proteasome, subunit alpha/beta + 35 + 36 376 - IPR036576
  - 35 - 252 + IPR029056
Ribokinase-like + 35 + 71 377 - IPR000726
Glycoside hydrolase, family 19, catalytic - 35 - 68 + IPR001876
Zinc finger, RanBP2-type + 35 + 168 378 - IPR001251
  - 35 - 274 + IPR039421
Type 1 protein exporter + 35 + 54 379 - IPR007118
Expansin/Lol pI - 35 - 203 + IPR000726
Glycoside hydrolase, family 19, catalytic + 35 + 45 380 - IPR008991
Translation protein SH3-like domain superfamily - 35 - 39 + IPR001251
CRAL-TRIO lipid binding domain + 35 + 137 381 - IPR007817
Pyoverdine biosynthesis - 35 - 71 + IPR001357
BRCT domain + 35 + 117 382 - IPR036865
  - 35 - 138 + IPR024709
Putative O-fucosyltransferase, plant + 35 + 69 383 - IPR029056
  - 35 - 150 + IPR007118
Expansin/Lol pI + 35 + 203 384 - IPR038408
  - 35 - 80 + IPR008991
Translation protein SH3-like domain superfamily + 35 + 39 385 - IPR008266
Tyrosine-protein kinase, active site - 35 - 35 + IPR002902
Gnk2-homologous domain + 35 + 77 386 - IPR007125
Histone H2A/H2B/H3 - 35 + IPR008266
  + 35 35 387 - IPR029481
ABC-transporter N-terminal domain - 35 + IPR007125
Histone H2A/H2B/H3 + 35 35 388 - IPR001876
  - 35 - 352 + IPR001715
Calponin homology domain + 35 + 129 389 - IPR013112
FAD-binding 8 - 34 - 34 + IPR044810
WRKY transcription factor, plant + 35 + 45 390 - IPR036420
  - 34 - 190 + IPR029060
PIN-like domain superfamily + 34 + 59 391 - IPR002423
Chaperonin Cpn60/TCP-1 family - 34 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 34 34 392 - IPR001353
Proteasome, subunit alpha/beta - 34 - 35 + IPR004358
Signal transduction histidine kinase-related protein, C-terminal + 34 + 120 393 - IPR007867
Glucose-methanol-choline oxidoreductase, C-terminal - 34 - 34 + IPR027409
GroEL-like apical domain superfamily + 34 + 68 394 - IPR004358
Signal transduction histidine kinase-related protein, C-terminal - 34 - 120 + IPR036844
Hint domain superfamily + 34 + 34 395 - IPR027409
  - 34 - 136 + IPR015797
NUDIX hydrolase-like domain superfamily + 34 + 72 396 - IPR001077
O-methyltransferase, family 2 - 34 - 35 + IPR017884
SANT domain + 34 + 34 397 - IPR036844
Hint domain superfamily - 34 + IPR013112
FAD-binding 8 + 34 34 398 - IPR004087
K Homology domain - 34 - 64 + IPR002423
Chaperonin Cpn60/TCP-1 family + 34 + 34 399 - IPR030184
WAT1-related protein - 34 - 36 + IPR029481
ABC-transporter, N-terminal domain + 34 + 34 400 IPR009003
Peptidase S1, PA clan 34 - 40 + 36 @@ -2837,317 +2837,317 @@ 404 - IPR015797
NUDIX hydrolase-like domain superfamily - 34 - 34 + IPR032466
Metal-dependent hydrolase + 33 + 33 405 - IPR004316
SWEET sugar transporter - 33 - 62 + IPR020904
  + 33 + 35 406 - IPR003954
RNA recognition motif domain, eukaryote - 33 - 62 + IPR045087
Multicopper oxidase + 33 + 33 407 - IPR009060
UBA-like superfamily - 33 - 40 + IPR000086
NUDIX hydrolase domain + 33 + 64 408 - IPR004161
Translation elongation factor EFTu-like, domain 2 - 33 + IPR036872
CH domain superfamily + 33 33 409 - IPR023753
FAD/NAD(P)-binding domain - 33 - 34 + IPR009060
UBA-like superfamily + 33 + 40 410 - IPR032466
Metal-dependent hydrolase - 33 - 40 + IPR036420
BRCT domain superfamily + 33 + 44 411 - IPR010989
SNARE - 33 + IPR004161
Translation elongation factor EFTu-like, domain 2 + 33 33 412 - IPR011013
Galactose mutarotase-like domain superfamily - 33 - 35 + IPR010989
SNARE + 33 + 33 413 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 33 - 35 + IPR039391
Phytocyanin + 33 + 34 414 - IPR031107
Small heat shock protein HSP20 - 33 - 44 + IPR011013
Galactose mutarotase-like domain superfamily + 33 + 33 415 - IPR014722
  - 33 - 76 + IPR007867
Glucose-methanol-choline oxidoreductase, C-terminal + 33 + 33 416 - IPR013126
Heat shock protein 70 family - 33 - 271 + IPR040249
Ricin B-like lectin EULS3-like + 33 + 58 417 - IPR016461
  - 32 - 156 + IPR025875
Leucine rich repeat 4 + 33 + 35 418 - IPR004331
  - 32 - 170 + IPR013126
Heat shock protein 70 family + 33 + 56 419 - IPR036873
  - 32 - 142 + IPR001412
  + 32 + 32 420 - IPR001412
Aminoacyl-tRNA synthetase, class I, conserved site - 32 - 32 + IPR003347
JmjC domain + 32 + 48 421 - IPR003347
  - 32 - 152 + IPR002293
Amino acid/polyamine transporter I + 32 + 54 422 - IPR027413
  - 32 - 256 + IPR043454
NPH3/RPT2-like family + 32 + 33 423 - IPR027356
  - 32 - 128 + IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily + 32 + 32 424 - IPR002293
Amino acid/polyamine transporter I - 32 - 68 + IPR022796
Chlorophyll A-B binding protein + 32 + 32 425 - IPR022742
Serine aminopeptidase, S33 - 32 + IPR001077
O-methyltransferase domain + 32 32 426 - IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily - 32 - 32 + IPR011059
Metal-dependent hydrolase, composite domain superfamily + 32 + 62 427 - IPR025875
Leucine rich repeat 4 - 32 - 33 + IPR016160
  + 32 + 32 428 - IPR016160
Aldehyde dehydrogenase, cysteine active site - 32 + IPR001767
Hedgehog protein, Hint domain + 32 32 429 - IPR027410
  - 32 - 218 + IPR004331
SPX domain + 32 + 81 430 - IPR001767
Hedgehog protein, Hint domain - 32 - 32 + IPR027413
GroEL-like equatorial domain superfamily + 32 + 97 431 - IPR001357
  - 31 - 286 + IPR027356
NPH3 domain + 32 + 64 432 - IPR012951
Berberine/berberine-like - 31 - 31 + IPR022742
Serine aminopeptidase, S33 + 32 + 32 433 - IPR026057
PC-Esterase - 31 - 31 + IPR012341
  + 32 + 33 434 - IPR013838
Beta tubulin, autoregulation binding site - 31 - 31 + IPR023329
  + 32 + 34 435 - IPR013130
Ferric reductase transmembrane component-like domain - 31 + IPR012951
Berberine/berberine-like + 31 31 436 - IPR018170
Aldo/keto reductase, conserved site - 31 - 67 + IPR013838
  + 31 + 31 437 - IPR008963
  - 31 - 159 + IPR018170
  + 31 + 67 438 - IPR000169
Cysteine peptidase, cysteine active site - 31 - 31 + IPR034294
Aquaporin transporter + 31 + 27 439 - IPR001715
  - 31 - 330 + IPR013816
  + 31 + 41 440 - IPR000086
  - 31 - 177 + IPR008963
Purple acid phosphatase-like, N-terminal + 31 + 31 441 - IPR004294
Carotenoid oxygenase - 30 - 64 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 31 + 67 442 - IPR021133
  - 30 - 172 + IPR026057
PC-Esterase + 31 + 31 443 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 30 - 60 + IPR013130
Ferric reductase transmembrane component-like domain + 31 + 31 444 - IPR018392
  - 30 - 370 + IPR024977
Anaphase-promoting complex subunit 4, WD40 domain + 31 + 31 445 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 30 - 31 + IPR004294
Carotenoid oxygenase + 30 + 60 446 - IPR037219
Peptidase M41-like - 30 - 30 + IPR006594
LIS1 homology motif + 30 + 38 447 - IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme - 30 - 37 + IPR004316
SWEET sugar transporter + 30 + 59 448 - IPR002453
Beta tubulin - 30 - 342 + IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme + 30 + 30 @@ -3166,16 +3166,16 @@ 451 - IPR001849
  - 30 - 138 + IPR002452
Alpha tubulin + 30 + 331 452 - IPR002452
Alpha tubulin - 30 - 331 + IPR000169
  + 30 + 30 @@ -3187,9 +3187,9 @@ 454 - IPR036779
  + IPR036779
LysM domain superfamily 30 - 108 + 34 @@ -3201,317 +3201,317 @@ 456 - IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site + IPR033132
  30 30 457 - IPR011707
Multicopper oxidase, type 3 - 30 - 30 + IPR021133
HEAT, type 2 + 30 + 86 458 - IPR001163
LSM domain, eukaryotic/archaea-type - 29 - 57 + IPR029962
Trichome birefringence-like family + 30 + 31 459 - IPR006734
Protein of unknown function DUF597 - 29 - 29 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 30 + 30 460 - IPR022812
Dynamin superfamily - 29 - 151 + IPR018392
LysM domain + 30 + 171 461 - IPR006694
Fatty acid hydroxylase - 29 - 29 + IPR037219
Peptidase M41-like + 30 + 30 462 - IPR004883
  - 29 - 116 + IPR000403
Phosphatidylinositol 3-/4-kinase, catalytic domain + 30 + 93 463 - IPR022357
Major intrinsic protein, conserved site - 29 - 29 + IPR015914
Purple acid phosphatase, N-terminal + 30 + 56 464 - IPR002495
Glycosyl transferase, family 8 - 29 - 31 + IPR011707
Multicopper oxidase, N-termianl + 30 + 30 465 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 29 - 29 + IPR045076
DNA mismatch repair MutS family + 30 + 37 466 - IPR006439
HAD hydrolase, subfamily IA - 29 - 71 + IPR036873
Rhodanese-like domain superfamily + 29 + 31 467 - IPR008974
  - 29 - 195 + IPR016455
Xyloglucan endotransglucosylase/hydrolase + 29 + 53 468 - IPR036443
Zinc finger, RanBP2-type superfamily - 29 - 48 + IPR004883
Lateral organ boundaries, LOB + 29 + 58 469 - IPR009078
Ferritin-like superfamily - 28 - 28 + IPR014722
  + 29 + 31 470 - IPR000315
  - 28 - 363 + IPR022357
  + 29 + 29 471 - IPR029962
Trichome birefringence-like family - 28 - 29 + IPR006439
HAD hydrolase, subfamily IA + 29 + 71 472 - IPR007173
D-arabinono-1,4-lactone oxidase - 28 - 28 + IPR001163
LSM domain, eukaryotic/archaea-type + 29 + 29 473 - IPR007197
Radical SAM - 28 - 56 + IPR006734
PLATZ transcription factor + 29 + 29 474 - IPR001938
  - 28 - 488 + IPR022812
Dynamin + 29 + 182 475 - IPR033131
Pectinesterase, Asp active site - 28 - 28 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 29 + 29 476 - IPR038770
  - 28 - 58 + IPR036443
Zinc finger, RanBP2-type superfamily + 29 + 48 477 - IPR001199
  - 28 - 238 + IPR009078
Ferritin-like superfamily + 28 + 28 478 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 28 - 28 + IPR001938
Thaumatin family + 28 + 241 479 - IPR002035
  - 28 - 118 + IPR001199
Cytochrome b5-like heme/steroid binding domain + 28 + 122 480 - IPR036400
  - 28 - 112 + IPR016167
  + 28 + 28 481 - IPR011706
Multicopper oxidase, type 2 - 28 + IPR036400
Cytochrome b5-like heme/steroid binding domain superfamily + 28 28 482 - IPR011948
Dullard phosphatase domain, eukaryotic - 28 - 28 + IPR002495
Glycosyl transferase, family 8 + 28 + 30 483 - IPR031157
Tr-type G domain, conserved site - 28 + IPR036187
DNA mismatch repair protein MutS, core domain superfamily + 28 28 484 - IPR000403
  - 28 - 148 + IPR009080
Aminoacyl-tRNA synthetase, class Ia, anticodon-binding + 28 + 51 485 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 28 - 29 + IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase + 28 + 201 486 - IPR036187
DNA mismatch repair protein MutS, core domain superfamily - 28 + IPR037176
Osmotin/thaumatin-like superfamily + 28 28 487 - IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase - 28 - 227 + IPR011016
Zinc finger, RING-CH-type + 28 + 60 488 - IPR037176
  - 28 - 112 + IPR033131
  + 28 + 28 489 - IPR001117
Multicopper oxidase, type 1 - 27 - 27 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 28 + 28 490 - IPR006594
  - 27 - 150 + IPR011706
Multicopper oxidase, C-terminal + 28 + 28 491 - IPR015940
  - 27 - 170 + IPR031157
  + 28 + 28 492 - IPR008971
HSP40/DnaJ peptide-binding - 27 - 71 + IPR030184
WAT1-related protein + 28 + 28 493 - IPR006016
UspA - 27 - 29 + IPR041792
Purple acid phosphatase, metallophosphatase domain + 28 + 28 494 - IPR034001
ATP-binding cassette transporter, PDR-like subfamily G, domain 1 - 27 - 27 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 28 + 58 495 - IPR000933
Glycoside hydrolase, family 29 - 27 - 68 + IPR003812
Fido domain + 28 + 51 496 - IPR003609
  - 27 - 82 + IPR015940
Ubiquitin-associated domain + 27 + 55 497 - IPR001594
Palmitoyltransferase, DHHC domain - 27 - 27 + IPR008971
HSP40/DnaJ peptide-binding + 27 + 52 498 - IPR001478
  - 27 - 201 + IPR034001
ATP-binding cassette transporter, PDR-like subfamily G, domain 1 + 27 + 27 499 - IPR001763
  - 27 - 166 + IPR003609
PAN/Apple domain + 27 + 39 500 - IPR017926
  - 27 - 96 + IPR007173
D-arabinono-1,4-lactone oxidase + 27 + 27 diff --git a/gramene/htdocs/ssi/species/stats_Sorghum_bicolor.html b/gramene/htdocs/ssi/species/stats_Sorghum_bicolor.html index e1fcd79d..37c930e4 100644 --- a/gramene/htdocs/ssi/species/stats_Sorghum_bicolor.html +++ b/gramene/htdocs/ssi/species/stats_Sorghum_bicolor.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.30 + 87.30 Base Pairs: @@ -21,11 +21,11 @@

Summary

Gene counts

- + - + @@ -55,7 +55,7 @@

Coordinate Systems

9
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 34,118
Gene transcriptsHASH(0x68ce400):Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.: 48,471
59416394
1061233695
-
+
@@ -926,22 +926,10 @@

Coordinate Systems

super_33231039super_33261005 -
+
contig 4773 sequences - -

Other

- - - - - - - - - -
Short Variants (SNPs, indels, somatic mutations):8,179,874
Structural variants:55,773
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Sorghum_bicolor_IPtop500.html b/gramene/htdocs/ssi/species/stats_Sorghum_bicolor_IPtop500.html index 5ebdf19e..711b93c8 100644 --- a/gramene/htdocs/ssi/species/stats_Sorghum_bicolor_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Sorghum_bicolor_IPtop500.html @@ -18,3500 +18,3500 @@ 1 IPR011009
Protein kinase-like domain superfamily 1323 - 2200 + 2048 2 - IPR000719
  + IPR000719
Protein kinase domain 1263 - 14457 + 3267 3 IPR027417
P-loop containing nucleoside triphosphate hydrolase 1257 - 2737 + 2327 4 - IPR008271
Serine/threonine-protein kinase, active site - 1015 - 1517 + IPR036047
F-box-like domain superfamily + 653 + 892 5 - IPR032675
  - 967 - 5250 + IPR001841
Zinc finger, RING-type + 499 + 1031 6 - IPR017441
Protein kinase, ATP binding site - 908 - 1348 + IPR002885
Pentatricopeptide repeat + 492 + 8884 7 - IPR013083
  - 781 - 2536 + IPR001810
F-box domain + 439 + 822 8 - IPR011990
  - 707 - 12768 + IPR001611
Leucine-rich repeat + 422 + 1413 9 - IPR036047
F-box-like domain superfamily - 653 - 917 + IPR036291
NAD(P)-binding domain superfamily + 418 + 621 10 - IPR001841
  - 494 - 3136 + IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain + 414 + 1024 11 - IPR002885
  - 492 - 34228 + IPR029058
Alpha/Beta hydrolase fold + 409 + 584 12 - IPR001810
  - 442 - 3282 + IPR009057
Homeobox-like domain superfamily + 401 + 598 13 - IPR001611
  - 424 - 8223 + IPR016024
Armadillo-type fold + 355 + 614 14 - IPR036291
NAD(P)-binding domain superfamily - 418 - 712 + IPR036396
Cytochrome P450 superfamily + 353 + 441 15 - IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 415 - 1022 + IPR001128
Cytochrome P450 + 351 + 1852 16 - IPR029058
  - 411 - 2500 + IPR011990
Tetratricopeptide-like helical domain superfamily + 324 + 653 17 - IPR009057
Homeobox-like domain superfamily - 401 - 598 + IPR044974
Disease resistance protein, plants + 317 + 686 18 - IPR016024
Armadillo-type fold - 355 - 1240 + IPR002182
NB-ARC + 316 + 564 19 - IPR036396
  - 353 - 2688 + IPR002401
Cytochrome P450, E-class, group I + 313 + 2403 20 - IPR001128
Cytochrome P450 - 350 - 1851 + IPR001005
SANT/Myb domain + 302 + 2325 21 - IPR002182
NB-ARC - 330 - 580 + IPR036875
Zinc finger, CCHC-type superfamily + 294 + 641 22 - IPR002401
Cytochrome P450, E-class, group I - 313 - 2403 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 291 + 359 23 - IPR017972
Cytochrome P450, conserved site - 312 - 370 + IPR001878
Zinc finger, CCHC-type + 283 + 993 24 - IPR003593
AAA+ ATPase domain - 297 - 552 + IPR036259
MFS transporter superfamily + 282 + 504 25 - IPR036875
Zinc finger, CCHC-type superfamily - 294 - 644 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase + 281 + 492 26 - IPR001878
  - 294 - 5703 + IPR035979
RNA-binding domain superfamily + 279 + 756 27 - IPR001005
SANT/Myb domain - 291 - 1419 + IPR036249
Thioredoxin-like superfamily + 267 + 379 28 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 290 - 356 + IPR041118
Rx, N-terminal + 265 + 399 29 - IPR036259
MFS transporter superfamily - 282 - 802 + IPR017930
Myb domain + 264 + 462 30 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 281 - 572 + IPR000504
RNA recognition motif domain + 260 + 1543 31 - IPR035979
RNA-binding domain superfamily - 279 - 809 + IPR017853
Glycoside hydrolase superfamily + 252 + 380 32 - IPR012677
  - 275 - 1706 + IPR036322
WD40-repeat-containing domain superfamily + 228 + 379 33 - IPR003591
Leucine-rich repeat, typical subtype - 273 - 2303 + IPR001680
WD40 repeat + 214 + 1671 34 - IPR036249
Thioredoxin-like superfamily - 267 - 389 + IPR016177
DNA-binding domain superfamily + 203 + 318 35 - IPR000504
  - 260 - 6978 + IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase + 199 + 446 36 - IPR017853
Glycoside hydrolase superfamily - 252 - 416 + IPR038765
Papain-like cysteine peptidase superfamily + 195 + 304 37 - IPR011989
  - 240 - 1032 + IPR011333
SKP1/BTB/POZ domain superfamily + 188 + 262 38 - IPR015943
  - 237 - 1656 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 185 + 315 39 - IPR017930
  - 235 - 890 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 182 + 549 40 - IPR001680
  - 230 - 10530 + IPR001471
AP2/ERF domain + 180 + 1086 41 - IPR036322
WD40-repeat-containing domain superfamily - 228 - 568 + IPR011992
EF-hand domain pair + 175 + 219 42 - IPR020846
  - 216 - 1182 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 174 + 278 43 - IPR016177
DNA-binding domain superfamily - 203 - 318 + IPR036390
Winged helix DNA-binding domain superfamily + 173 + 227 44 - IPR017986
  - 203 - 1026 + IPR036412
HAD-like superfamily + 169 + 320 45 - IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 197 - 223 + IPR002048
EF-hand domain + 161 + 831 46 - IPR038765
Papain-like cysteine peptidase superfamily - 195 - 331 + IPR000210
BTB/POZ domain + 157 + 420 47 - IPR011333
SKP1/BTB/POZ domain superfamily - 188 - 276 + IPR002016
Haem peroxidase + 155 + 1142 48 - IPR036638
  - 185 - 1797 + IPR010255
Haem peroxidase superfamily + 155 + 173 49 - IPR008974
  - 184 - 1410 + IPR036236
Zinc finger C2H2 superfamily + 155 + 289 50 - IPR036388
  - 183 - 550 + IPR036770
Ankyrin repeat-containing domain superfamily + 151 + 227 51 - IPR011598
  - 182 - 3204 + IPR029044
Nucleotide-diphospho-sugar transferases + 149 + 210 52 - IPR013087
  - 181 - 3090 + IPR013087
Zinc finger C2H2-type + 149 + 315 53 - IPR001471
  - 180 - 4020 + IPR001650
Helicase, C-terminal + 147 + 552 54 - IPR036955
  - 180 - 774 + IPR013320
Concanavalin A-like lectin/glucanase domain superfamily + 147 + 181 55 - IPR011992
EF-hand domain pair - 175 - 233 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 144 + 279 56 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 174 - 278 + IPR000823
Plant peroxidase + 141 + 1300 57 - IPR036390
Winged helix DNA-binding domain superfamily - 173 - 227 + IPR036188
FAD/NAD(P)-binding domain superfamily + 139 + 241 58 - IPR036412
HAD-like superfamily - 169 - 476 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 138 + 143 59 - IPR029044
  - 163 - 1028 + IPR033905
Secretory peroxidase + 138 + 150 60 - IPR002048
  - 161 - 4077 + IPR003439
ABC transporter-like, ATP-binding domain + 134 + 602 61 - IPR000210
  - 161 - 1824 + IPR036093
NAC domain superfamily + 133 + 185 62 - IPR023214
  - 155 - 932 + IPR020846
Major facilitator superfamily domain + 133 + 225 63 - IPR002016
  - 155 - 3426 + IPR011011
Zinc finger, FYVE/PHD-type + 132 + 233 64 - IPR010255
Haem peroxidase - 155 - 175 + IPR002110
Ankyrin repeat + 132 + 712 65 - IPR036236
Zinc finger C2H2 superfamily - 155 - 347 + IPR003441
NAC domain + 131 + 364 66 - IPR036770
  - 151 - 1192 + IPR001087
GDSL lipase/esterase + 130 + 159 67 - IPR014001
  - 150 - 1112 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 130 + 529 68 - IPR001650
  - 147 - 2212 + IPR045005
BTB/POZ and MATH domain-containing protein 1-6 + 130 + 187 69 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 147 - 218 + IPR002083
MATH/TRAF domain + 129 + 432 70 - IPR018247
EF-Hand 1, calcium-binding site - 147 - 395 + IPR012340
Nucleic acid-binding, OB-fold + 129 + 254 71 - IPR035595
UDP-glycosyltransferase family, conserved site - 144 - 152 + IPR012337
Ribonuclease H-like superfamily + 125 + 181 72 - IPR036188
  - 144 - 1508 + IPR036869
Chaperone J-domain superfamily + 123 + 172 73 - IPR020683
  - 144 - 1644 + IPR003959
ATPase, AAA-type, core + 120 + 193 74 - IPR000823
Plant peroxidase - 141 - 1300 + IPR035669
GDSL lipase/esterase-like, plant + 117 + 141 75 - IPR036514
  - 139 - 350 + IPR001623
DnaJ domain + 117 + 874 76 - IPR002110
  - 139 - 5070 + IPR008972
Cupredoxin + 116 + 242 77 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 138 - 144 + IPR029071
Ubiquitin-like domain superfamily + 115 + 286 78 - IPR033905
Secretory peroxidase - 138 - 150 + IPR020683
Ankyrin repeat-containing domain + 113 + 265 79 - IPR019775
WD40 repeat, conserved site - 136 - 343 + IPR036908
RlpA-like domain superfamily + 111 + 125 80 - IPR019793
Peroxidases heam-ligand binding site - 134 - 146 + IPR021109
Aspartic peptidase domain superfamily + 108 + 137 81 - IPR003439
  - 134 - 1809 + IPR002347
Short-chain dehydrogenase/reductase SDR + 106 + 1079 82 - IPR036093
  - 133 - 1113 + IPR019734
Tetratricopeptide repeat + 104 + 346 83 - IPR011011
Zinc finger, FYVE/PHD-type - 132 - 233 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 102 + 132 84 - IPR003441
  - 131 - 1080 + IPR026992
Non-haem dioxygenase N-terminal domain + 100 + 137 85 - IPR005123
  - 130 - 1065 + IPR033121
Peptidase family A1 domain + 99 + 142 86 - IPR002083
  - 129 - 1491 + IPR015300
DNA-binding pseudobarrel domain superfamily + 99 + 289 87 - IPR012340
Nucleic acid-binding, OB-fold - 129 - 261 + IPR035892
C2 domain superfamily + 98 + 205 88 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 128 - 180 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 98 + 140 89 - IPR013026
  - 127 - 867 + IPR032799
Xylanase inhibitor, C-terminal + 98 + 115 90 - IPR036869
  - 126 - 684 + IPR036426
Bulb-type lectin domain superfamily + 98 + 120 91 - IPR012337
Ribonuclease H-like superfamily - 125 - 206 + IPR036576
WRKY domain superfamily + 97 + 155 92 - IPR001087
GDSL lipase/esterase - 124 - 150 + IPR003657
WRKY domain + 97 + 308 93 - IPR019734
  - 120 - 4281 + IPR032861
Xylanase inhibitor, N-terminal + 96 + 110 94 - IPR003959
ATPase, AAA-type, core - 120 - 193 + IPR004045
Glutathione S-transferase, N-terminal + 96 + 236 95 - IPR027443
  - 119 - 352 + IPR003480
Transferase + 96 + 130 96 - IPR014729
  - 119 - 410 + IPR011545
DEAD/DEAH box helicase domain + 94 + 180 97 - IPR035669
GDSL lipase/esterase-like, plant - 117 - 141 + IPR011051
RmlC-like cupin domain superfamily + 94 + 116 98 - IPR001623
  - 117 - 2048 + IPR001480
Bulb-type lectin domain + 94 + 316 99 - IPR008972
  - 116 - 1008 + IPR009072
Histone-fold + 94 + 109 100 - IPR014710
  - 115 - 328 + IPR003340
B3 DNA binding domain + 93 + 810 101 - IPR029071
Ubiquitin-like domain superfamily - 115 - 286 + IPR011050
Pectin lyase fold/virulence factor + 93 + 135 102 - IPR013785
  - 111 - 531 + IPR001461
Aspartic peptidase A1 family + 93 + 341 103 - IPR019794
Peroxidase, active site - 111 - 126 + IPR015424
Pyridoxal phosphate-dependent transferase + 93 + 144 104 - IPR036908
  - 111 - 500 + IPR004827
Basic-leucine zipper domain + 93 + 319 105 - IPR036397
  - 109 - 477 + IPR005828
Major facilitator, sugar transporter-like + 92 + 159 106 - IPR021109
  - 108 - 832 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 92 + 104 107 - IPR023213
  - 108 - 512 + IPR000073
Alpha/beta hydrolase fold-1 + 92 + 283 108 - IPR005225
Small GTP-binding protein domain - 108 - 137 + IPR044810
WRKY transcription factor, plant + 92 + 122 109 - IPR034090
BPM, C-terminal - 108 - 138 + IPR036457
PPM-type phosphatase domain superfamily + 91 + 137 110 - IPR002347
Short-chain dehydrogenase/reductase SDR - 106 - 1079 + IPR001932
PPM-type phosphatase domain + 91 + 400 111 - IPR001461
Aspartic peptidase A1 family - 103 - 373 + IPR000008
C2 domain + 90 + 453 112 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 102 - 134 + IPR000626
Ubiquitin-like domain + 89 + 451 113 - IPR026992
Non-haem dioxygenase N-terminal domain - 101 - 138 + IPR000109
Proton-dependent oligopeptide transporter family + 89 + 289 114 - IPR006447
Myb domain, plants - 99 - 132 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 89 + 92 115 - IPR033121
  - 99 - 284 + IPR001356
Homeobox domain + 89 + 340 116 - IPR001965
Zinc finger, PHD-type - 99 - 250 + IPR010987
Glutathione S-transferase, C-terminal-like + 88 + 110 117 - IPR009072
  - 99 - 672 + IPR007117
Expansin, cellulose-binding-like domain + 88 + 197 118 - IPR015300
  - 99 - 1148 + IPR007112
Expansin/pollen allergen, DPBB domain + 86 + 100 119 - IPR032799
Xylanase inhibitor, C-terminal - 98 - 115 + IPR032867
DYW domain + 85 + 126 120 - IPR004045
  - 98 - 711 + IPR036163
Heavy metal-associated domain superfamily + 84 + 123 121 - IPR036426
  - 98 - 572 + IPR016039
Thiolase-like + 83 + 183 122 - IPR036576
  - 97 - 930 + IPR003609
PAN/Apple domain + 83 + 190 123 - IPR003657
  - 97 - 1386 + IPR005174
Domain unknown function DUF295 + 83 + 110 124 - IPR004827
  - 97 - 1851 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 82 + 94 125 - IPR032861
Xylanase inhibitor, N-terminal - 96 - 110 + IPR020472
G-protein beta WD-40 repeat + 82 + 342 126 - IPR003480
Transferase - 96 - 130 + IPR007118
Expansin/Lol pI + 81 + 528 127 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 95 - 141 + IPR005202
Transcription factor GRAS + 81 + 312 128 - IPR015421
  - 94 - 432 + IPR000858
S-locus glycoprotein domain + 79 + 97 129 - IPR011545
DEAD/DEAH box helicase domain - 94 - 180 + IPR013766
Thioredoxin domain + 79 + 188 130 - IPR011051
RmlC-like cupin domain superfamily - 94 - 121 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 78 + 81 131 - IPR001480
  - 94 - 664 + IPR002100
Transcription factor, MADS-box + 78 + 459 132 - IPR003340
  - 93 - 3234 + IPR000270
PB1 domain + 78 + 131 133 - IPR011050
Pectin lyase fold/virulence factor - 93 - 136 + IPR036879
Transcription factor, MADS-box superfamily + 78 + 98 134 - IPR036749
  - 93 - 416 + IPR006121
Heavy metal-associated domain, HMA + 76 + 283 135 - IPR010987
  - 93 - 238 + IPR019787
Zinc finger, PHD-finger + 76 + 226 136 - IPR015424
Pyridoxal phosphate-dependent transferase - 93 - 153 + IPR003676
Small auxin-up RNA + 76 + 77 137 - IPR005828
Major facilitator, sugar transporter-like - 92 - 159 + IPR006501
Pectinesterase inhibitor domain + 74 + 77 138 - IPR017907
Zinc finger, RING-type, conserved site - 92 - 153 + IPR029052
Metallo-dependent phosphatase-like + 73 + 112 139 - IPR012334
  - 92 - 270 + IPR043129
ATPase, nucleotide binding domain + 72 + 180 140 - IPR036457
  - 91 - 620 + IPR003613
U box domain + 72 + 212 141 - IPR000073
Alpha/beta hydrolase fold-1 - 91 - 281 + IPR011676
Domain of unknown function DUF1618 + 71 + 92 142 - IPR017871
ABC transporter, conserved site - 91 - 169 + IPR013057
Amino acid transporter, transmembrane domain + 68 + 92 143 - IPR001932
  - 91 - 1692 + IPR003245
Phytocyanin domain + 68 + 147 144 - IPR035892
  - 90 - 396 + IPR039391
Phytocyanin + 67 + 74 145 - IPR024171
S-receptor-like serine/threonine-protein kinase - 90 - 127 + IPR007658
Protein of unknown function DUF594 + 66 + 83 146 - IPR001356
  - 90 - 1419 + IPR025315
Domain of unknown function DUF4220 + 66 + 85 147 - IPR000626
  - 89 - 1935 + IPR001509
NAD-dependent epimerase/dehydratase + 65 + 86 148 - IPR000109
Proton-dependent oligopeptide transporter family - 89 - 292 + IPR006566
FBD domain + 65 + 80 149 - IPR007117
  - 89 - 400 + IPR000048
IQ motif, EF-hand binding site + 65 + 419 150 - IPR000008
  - 88 - 1184 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 64 + 99 151 - IPR032867
DYW domain - 88 - 131 + IPR003663
Sugar/inositol transporter + 64 + 406 152 - IPR007112
  - 86 - 388 + IPR000571
Zinc finger, CCCH-type + 64 + 385 153 - IPR006121
  - 84 - 885 + IPR013094
Alpha/beta hydrolase fold-3 + 63 + 80 154 - IPR003609
  - 84 - 530 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 63 + 220 155 - IPR036163
Heavy metal-associated domain superfamily - 84 - 123 + IPR018108
Mitochondrial substrate/solute carrier + 62 + 687 156 - IPR016039
  - 83 - 1116 + IPR023395
Mitochondrial carrier domain superfamily + 62 + 129 157 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 82 - 95 + IPR026057
PC-Esterase + 61 + 76 158 - IPR020472
G-protein beta WD-40 repeat - 82 - 342 + IPR029962
Trichome birefringence-like family + 61 + 78 159 - IPR015422
  - 82 - 579 + IPR002902
Gnk2-homologous domain + 61 + 339 160 - IPR007118
Expansin/Lol pI - 81 - 528 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 61 + 86 161 - IPR005202
  - 81 - 404 + IPR020568
Ribosomal protein S5 domain 2-type fold + 61 + 90 162 - IPR000858
S-locus glycoprotein domain - 80 - 98 + IPR006045
Cupin 1 + 61 + 72 163 - IPR035513
  - 80 - 318 + IPR025846
PMR5 N-terminal domain + 61 + 74 164 - IPR015655
Protein phosphatase 2C family - 80 - 141 + IPR001806
Small GTPase + 61 + 142 165 - IPR019786
Zinc finger, PHD-type, conserved site - 78 - 127 + IPR017884
SANT domain + 60 + 92 166 - IPR005829
Sugar transporter, conserved site - 78 - 186 + IPR001563
Peptidase S10, serine carboxypeptidase + 60 + 453 167 - IPR002100
  - 78 - 1794 + IPR016181
Acyl-CoA N-acyltransferase + 60 + 85 168 - IPR006566
FBD domain - 78 - 106 + IPR031052
FHY3/FAR1 family + 60 + 118 169 - IPR000270
  - 78 - 522 + IPR011701
Major facilitator superfamily + 59 + 120 170 - IPR036879
  - 78 - 588 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 59 + 71 171 - IPR003960
ATPase, AAA-type, conserved site - 76 - 102 + IPR036915
Cyclin-like superfamily + 59 + 156 172 - IPR019787
  - 76 - 450 + IPR007527
Zinc finger, SWIM-type + 58 + 166 173 - IPR003676
Small auxin-up RNA - 76 - 77 + IPR002921
Fungal lipase-like domain + 57 + 76 174 - IPR005174
Domain unknown function DUF295 - 75 - 102 + IPR011032
GroES-like superfamily + 57 + 99 175 - IPR006501
Pectinesterase inhibitor domain - 75 - 204 + IPR008949
Isoprenoid synthase domain superfamily + 57 + 95 176 - IPR013783
  - 74 - 284 + IPR008978
HSP20-like chaperone + 57 + 65 177 - IPR013766
  - 74 - 558 + IPR001220
Legume lectin domain + 57 + 115 178 - IPR000742
  - 74 - 520 + IPR030184
WAT1-related protein + 57 + 92 179 - IPR003613
  - 72 - 954 + IPR000620
EamA domain + 57 + 151 180 - IPR011676
Domain of unknown function DUF1618 - 71 - 92 + IPR044808
Ethylene-responsive transcription factor + 57 + 70 181 - IPR001509
NAD-dependent epimerase/dehydratase - 69 - 93 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 56 + 58 182 - IPR031052
FHY3/FAR1 family - 68 - 128 + IPR002528
Multi antimicrobial extrusion protein + 56 + 163 183 - IPR013057
Amino acid transporter, transmembrane domain - 68 - 92 + IPR011043
Galactose oxidase/kelch, beta-propeller + 56 + 65 184 - IPR003245
  - 68 - 648 + IPR012871
Protein of unknown function DUF1677, Oryza sativa + 55 + 71 185 - IPR007658
Protein of unknown function DUF594 - 66 - 83 + IPR026961
PGG domain + 55 + 167 186 - IPR025315
Domain of unknown function DUF4220 - 66 - 85 + IPR008979
Galactose-binding-like domain superfamily + 55 + 100 187 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 65 - 100 + IPR036852
Peptidase S8/S53 domain superfamily + 55 + 63 188 - IPR036961
  - 65 - 411 + IPR000209
Peptidase S8/S53 domain + 55 + 63 189 - IPR003663
Sugar/inositol transporter - 65 - 482 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 54 + 62 190 - IPR000048
  - 65 - 2007 + IPR001929
Germin + 54 + 168 191 - IPR011993
  - 65 - 196 + IPR016461
O-methyltransferase COMT-type + 54 + 113 192 - IPR000571
  - 64 - 1929 + IPR013525
ABC-2 type transporter + 54 + 122 193 - IPR016135
  - 63 - 346 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 54 + 157 194 - IPR029052
  - 63 - 186 + IPR036465
von Willebrand factor A-like domain superfamily + 54 + 74 195 - IPR013094
Alpha/beta hydrolase fold-3 - 63 - 79 + IPR000490
Glycoside hydrolase family 17 + 54 + 83 196 - IPR018097
EGF-like calcium-binding, conserved site - 63 - 94 + IPR007493
Protein of unknown function DUF538 + 53 + 114 197 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 63 - 224 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 53 + 59 198 - IPR000225
  - 63 - 2091 + IPR045051
Subtilisin-like protease + 53 + 66 199 - IPR018108
  - 62 - 1398 + IPR000873
AMP-dependent synthetase/ligase + 53 + 97 200 - IPR008979
  - 62 - 410 + IPR036758
At5g01610-like superfamily + 53 + 56 201 - IPR023395
  - 62 - 592 + IPR044965
Glycoside hydrolase family 17, plant + 53 + 89 202 - IPR001563
Peptidase S10, serine carboxypeptidase - 61 - 454 + IPR015500
Peptidase S8, subtilisin-related + 53 + 182 203 - IPR026057
PC-Esterase - 61 - 76 + IPR001214
SET domain + 53 + 168 204 - IPR002902
  - 61 - 680 + IPR029055
Nucleophile aminohydrolases, N-terminal + 52 + 67 205 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 61 - 73 + IPR004265
Dirigent protein + 52 + 75 206 - IPR020568
Ribosomal protein S5 domain 2-type fold - 61 - 107 + IPR011006
CheY-like superfamily + 52 + 68 207 - IPR006045
Cupin 1 - 61 - 144 + IPR015915
Kelch-type beta propeller + 52 + 98 208 - IPR025846
PMR5 N-terminal domain - 61 - 74 + IPR001752
Kinesin motor domain + 52 + 447 209 - IPR001806
Small GTPase superfamily - 61 - 80 + IPR000608
Ubiquitin-conjugating enzyme E2 + 51 + 199 210 - IPR016181
Acyl-CoA N-acyltransferase - 60 - 87 + IPR008250
P-type ATPase, A domain superfamily + 51 + 99 211 - IPR011701
Major facilitator superfamily - 60 - 122 + IPR016159
Cullin repeat-like-containing domain superfamily + 51 + 64 212 - IPR029962
Trichome birefringence-like family - 60 - 78 + IPR014756
Immunoglobulin E-set + 51 + 94 213 - IPR001881
EGF-like calcium-binding domain - 60 - 141 + IPR023298
P-type ATPase, transmembrane domain superfamily + 51 + 108 214 - IPR038408
  - 60 - 340 + IPR000225
Armadillo + 51 + 217 215 - IPR030184
WAT1-related protein - 60 - 96 + IPR001789
Signal transduction response regulator, receiver domain + 51 + 123 216 - IPR008978
  - 59 - 270 + IPR001077
O-methyltransferase domain + 50 + 54 217 - IPR015915
  - 59 - 729 + IPR041569
AAA ATPase, AAA+ lid domain + 50 + 77 218 - IPR036915
Cyclin-like superfamily - 59 - 156 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 49 + 132 219 - IPR002921
Fungal lipase-like domain - 58 - 77 + IPR014014
RNA helicase, DEAD-box type, Q motif + 49 + 84 220 - IPR008949
  - 58 - 452 + IPR034197
Cucumisin-like catalytic domain + 49 + 57 221 - IPR001938
  - 58 - 1050 + IPR011527
ABC transporter type 1, transmembrane domain + 49 + 262 222 - IPR036465
  - 58 - 276 + IPR000668
Peptidase C1A, papain C-terminal + 49 + 196 223 - IPR007527
  - 58 - 498 + IPR009003
Peptidase S1, PA clan + 49 + 146 224 - IPR011032
GroES-like superfamily - 57 - 99 + IPR000182
GNAT domain + 48 + 110 225 - IPR036852
  - 57 - 807 + IPR018289
MULE transposase domain + 48 + 82 226 - IPR001220
Legume lectin domain - 57 - 115 + IPR000742
EGF-like domain + 48 + 70 227 - IPR000620
EamA domain - 57 - 153 + IPR043926
ABC transporter family G domain + 47 + 93 228 - IPR023393
  - 56 - 136 + IPR013201
Cathepsin propeptide inhibitor domain (I29) + 47 + 53 229 - IPR027640
Kinesin-like protein - 56 - 109 + IPR012946
X8 domain + 47 + 66 230 - IPR002528
Multi antimicrobial extrusion protein - 56 - 240 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 47 + 75 231 - IPR011043
Galactose oxidase/kelch, beta-propeller - 56 - 80 + IPR008928
Six-hairpin glycosidase superfamily + 47 + 55 232 - IPR013525
ABC-2 type transporter - 55 - 123 + IPR045087
Multicopper oxidase + 47 + 62 233 - IPR012871
Protein of unknown function DUF1677, Oryza sativa - 55 - 71 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 47 + 65 234 - IPR014014
  - 55 - 192 + IPR037176
Osmotin/thaumatin-like superfamily + 47 + 54 235 - IPR026961
PGG domain - 55 - 167 + IPR001117
Multicopper oxidase, type 1 + 46 + 56 236 - IPR000209
Peptidase S8/S53 domain - 55 + IPR036318
FAD-binding, type PCMH-like superfamily + 46 63 237 - IPR001929
Germin - 54 - 168 + IPR002068
Alpha crystallin/Hsp20 domain + 46 + 97 238 - IPR017451
F-box associated interaction domain - 54 - 72 + IPR001938
Thaumatin family + 46 + 386 239 - IPR000873
AMP-dependent synthetase/ligase - 54 - 98 + IPR013763
Cyclin-like + 46 + 119 240 - IPR003653
  - 54 - 471 + IPR007125
Histone H2A/H2B/H3 + 46 + 51 241 - IPR018253
DnaJ domain, conserved site - 54 - 77 + IPR011706
Multicopper oxidase, C-terminal + 46 + 57 242 - IPR000490
Glycoside hydrolase family 17 - 54 - 124 + IPR002109
Glutaredoxin + 46 + 57 243 - IPR007493
Protein of unknown function DUF538 - 53 - 115 + IPR036855
Zinc finger, CCCH-type superfamily + 46 + 140 244 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 53 - 59 + IPR009060
UBA-like superfamily + 44 + 76 245 - IPR006564
Zinc finger, PMZ-type - 53 - 86 + IPR009000
Translation protein, beta-barrel domain superfamily + 44 + 63 246 - IPR036758
  - 53 - 224 + IPR016166
FAD-binding domain, PCMH-type + 44 + 60 247 - IPR015500
Peptidase S8, subtilisin-related - 53 - 182 + IPR039417
Papain-like cysteine endopeptidase + 44 + 47 248 - IPR001214
  - 53 - 705 + IPR006702
Casparian strip membrane protein domain + 44 + 46 249 - IPR001789
  - 53 - 750 + IPR033896
MADS MEF2-like + 43 + 62 250 - IPR029055
  - 52 - 270 + IPR025659
Tubby-like, C-terminal + 43 + 58 251 - IPR004265
Dirigent protein - 52 - 75 + IPR004263
Exostosin-like + 43 + 203 252 - IPR011006
CheY-like superfamily - 52 - 73 + IPR000070
Pectinesterase, catalytic + 43 + 61 253 - IPR023299
  - 52 - 522 + IPR004330
FAR1 DNA binding domain + 43 + 94 254 - IPR001752
  - 52 - 1569 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 43 + 55 255 - IPR016461
  - 51 - 291 + IPR011707
Multicopper oxidase, N-termianl + 43 + 53 256 - IPR000608
  - 51 - 400 + IPR033389
AUX/IAA domain + 42 + 65 257 - IPR008250
P-type ATPase, A domain superfamily - 51 - 123 + IPR003137
PA domain + 42 + 47 258 - IPR001757
P-type ATPase - 51 - 340 + IPR005630
Terpene synthase, metal-binding domain + 42 + 73 259 - IPR016159
Cullin repeat-like-containing domain superfamily - 51 - 93 + IPR013010
Zinc finger, SIAH-type + 42 + 68 260 - IPR014756
Immunoglobulin E-set - 51 - 95 + IPR002067
Mitochondrial carrier protein + 42 + 330 261 - IPR023298
P-type ATPase, transmembrane domain superfamily - 51 - 311 + IPR023210
NADP-dependent oxidoreductase domain + 42 + 55 262 - IPR013128
Peptidase C1A - 50 - 69 + IPR006016
UspA + 41 + 57 263 - IPR001077
O-methyltransferase, family 2 - 50 - 54 + IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein + 41 + 46 264 - IPR018303
P-type ATPase, phosphorylation site - 50 - 88 + IPR023271
Aquaporin-like + 41 + 47 265 - IPR002109
  - 50 - 354 + IPR011013
Galactose mutarotase-like domain superfamily + 41 + 63 266 - IPR036640
  - 49 - 696 + IPR002963
Expansin + 41 + 320 267 - IPR004162
E3 ubiquitin-protein ligase SIN-like - 49 - 85 + IPR000425
Major intrinsic protein + 41 + 350 268 - IPR013763
Cyclin-like - 49 - 238 + IPR006671
Cyclin, N-terminal + 41 + 69 269 - IPR034197
Cucumisin-like catalytic domain - 49 - 57 + IPR004158
Protein of unknown function DUF247, plant + 41 + 102 270 - IPR011527
  - 49 - 786 + IPR001360
Glycoside hydrolase family 1 + 40 + 518 271 - IPR000668
Peptidase C1A, papain C-terminal - 49 - 246 + IPR013149
Alcohol dehydrogenase, C-terminal + 40 + 54 272 - IPR019780
Germin, manganese binding site - 49 - 51 + IPR000330
SNF2, N-terminal + 40 + 78 273 - IPR009003
Peptidase S1, PA clan - 49 - 152 + IPR013216
Methyltransferase type 11 + 40 + 54 274 - IPR004330
FAR1 DNA binding domain - 49 - 101 + IPR036691
Endonuclease/exonuclease/phosphatase superfamily + 40 + 73 275 - IPR000182
  - 48 - 220 + IPR036612
K Homology domain, type 1 superfamily + 40 + 122 276 - IPR013201
Cathepsin propeptide inhibitor domain (I29) - 48 - 109 + IPR022742
Serine aminopeptidase, S33 + 40 + 55 277 - IPR036890
  - 48 - 320 + IPR022059
Protein of unknown function DUF3615 + 40 + 57 278 - IPR018289
MULE transposase domain - 48 - 82 + IPR012328
Chalcone/stilbene synthase, C-terminal + 40 + 44 279 - IPR037045
  - 48 - 102 + IPR012967
Plant methyltransferase dimerisation + 40 + 44 280 - IPR012946
X8 domain - 47 - 132 + IPR002913
START domain + 40 + 115 281 - IPR008928
Six-hairpin glycosidase superfamily - 47 - 71 + IPR004320
Protein of unknown function DUF241, plant + 39 + 47 282 - IPR011042
  - 47 - 138 + IPR004046
Glutathione S-transferase, C-terminal + 39 + 49 283 - IPR018202
Serine carboxypeptidase, serine active site - 47 - 58 + IPR001906
Terpene synthase, N-terminal domain + 39 + 68 284 - IPR037176
  - 47 - 228 + IPR008889
VQ + 39 + 46 285 - IPR017877
  - 47 - 188 + IPR015947
PUA-like superfamily + 39 + 90 286 - IPR001117
Multicopper oxidase, type 1 - 46 + IPR008942
ENTH/VHS + 38 56 287 - IPR036318
FAD-binding, type 2-like superfamily - 46 - 63 + IPR016040
NAD(P)-binding domain + 38 + 57 288 - IPR002068
  - 46 - 194 + IPR004853
Sugar phosphate transporter domain + 38 + 58 289 - IPR001969
Aspartic peptidase, active site - 46 - 89 + IPR013154
Alcohol dehydrogenase, N-terminal + 38 + 54 290 - IPR017970
Homeobox, conserved site - 46 - 59 + IPR034294
Aquaporin transporter + 38 + 46 291 - IPR020845
AMP-binding, conserved site - 46 - 82 + IPR011012
Longin-like domain superfamily + 38 + 50 292 - IPR011706
Multicopper oxidase, type 2 - 46 - 57 + IPR027923
Hydrophobic seed protein domain + 38 + 76 293 - IPR036574
  - 46 - 170 + IPR018121
Seven-in-absentia protein, TRAF-like domain + 38 + 59 294 - IPR036855
Zinc finger, CCCH-type superfamily - 46 - 140 + IPR006458
Ovate protein family, C-terminal + 38 + 74 295 - IPR029466
No apical meristem-associated, C-terminal domain - 45 - 51 + IPR036354
Proteinase inhibitor I13, potato inhibitor I superfamily + 38 + 41 296 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 45 - 511 + IPR002912
ACT domain + 38 + 141 297 - IPR007125
Histone H2A/H2B/H3 - 45 - 49 + IPR000743
Glycoside hydrolase, family 28 + 38 + 57 298 - IPR009060
UBA-like superfamily - 44 - 76 + IPR005795
Major pollen allergen Lol pI + 37 + 339 299 - IPR009000
Translation protein, beta-barrel domain superfamily - 44 - 64 + IPR000864
Proteinase inhibitor I13, potato inhibitor I + 37 + 115 300 - IPR016166
  - 44 - 180 + IPR029466
No apical meristem-associated, C-terminal domain + 37 + 43 301 - IPR013780
  - 44 - 164 + IPR038933
Ovate protein family + 37 + 39 302 - IPR012341
  - 44 - 177 + IPR006652
Kelch repeat type 1 + 37 + 129 303 - IPR006702
Casparian strip membrane protein domain - 44 - 46 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 37 + 134 304 - IPR033896
MADS MEF2-like - 43 - 62 + IPR036574
Knottin, scorpion toxin-like superfamily + 37 + 38 305 - IPR025659
  - 43 - 182 + IPR011141
Polyketide synthase, type III + 37 + 43 306 - IPR000070
Pectinesterase, catalytic - 43 - 61 + IPR002487
Transcription factor, K-box + 37 + 129 307 - IPR036812
  - 43 - 228 + IPR025322
Protein of unknown function DUF4228, plant + 36 + 36 308 - IPR011707
Multicopper oxidase, type 3 - 43 - 53 + IPR013187
F-box associated domain, type 3 + 36 + 43 309 - IPR033389
AUX/IAA domain - 42 - 65 + IPR001251
CRAL-TRIO lipid binding domain + 36 + 202 310 - IPR008942
  - 42 - 232 + IPR034161
Pepsin-like domain, plant + 36 + 42 311 - IPR006016
UspA - 42 - 58 + IPR005135
Endonuclease/exonuclease/phosphatase + 36 + 60 312 - IPR003137
PA domain - 42 - 47 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 36 + 70 313 - IPR005630
Terpene synthase, metal-binding domain - 42 - 73 + IPR000644
CBS domain + 36 + 187 314 - IPR000222
PPM-type phosphatase, divalent cation binding - 42 - 67 + IPR001099
Chalcone/stilbene synthase, N-terminal + 36 + 40 315 - IPR013010
  - 42 - 204 + IPR010402
CCT domain + 35 + 100 316 - IPR002067
Mitochondrial carrier protein - 42 - 330 + IPR004140
Exocyst complex component Exo70 + 35 + 95 317 - IPR023210
NADP-dependent oxidoreductase domain - 42 - 107 + IPR005150
Cellulose synthase + 35 + 71 318 - IPR013149
Alcohol dehydrogenase, C-terminal - 41 - 55 + IPR003406
Glycosyl transferase, family 14 + 35 + 45 319 - IPR036612
  - 41 - 633 + IPR008480
Protein of unknown function DUF761, plant + 35 + 38 320 - IPR023271
  - 41 - 190 + IPR029045
ClpP/crotonase-like domain superfamily + 35 + 59 321 - IPR033124
Serine carboxypeptidases, histidine active site - 41 - 43 + IPR006094
FAD linked oxidase, N-terminal + 35 + 44 322 - IPR034294
Aquaporin transporter - 41 - 50 + IPR044791
Beta-glucanase/XTH + 35 + 38 323 - IPR022742
Serine aminopeptidase, S33 - 41 - 56 + IPR024788
Malectin-like domain + 35 + 41 324 - IPR011013
Galactose mutarotase-like domain superfamily - 41 - 74 + IPR000757
Glycoside hydrolase family 16 + 35 + 76 325 - IPR002963
Expansin - 41 - 320 + IPR025110
AMP-binding enzyme, C-terminal domain + 34 + 47 326 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 41 - 49 + IPR019956
Ubiquitin domain + 34 + 167 327 - IPR000425
Major intrinsic protein - 41 - 379 + IPR007650
Zf-FLZ domain + 34 + 83 328 - IPR004158
Protein of unknown function DUF247, plant - 41 - 50 + IPR004839
Aminotransferase, class I/classII + 34 + 62 329 - IPR025660
Cysteine peptidase, histidine active site - 41 - 46 + IPR004883
Lateral organ boundaries, LOB + 34 + 82 330 - IPR001360
Glycoside hydrolase family 1 - 40 - 520 + IPR015655
Protein phosphatase 2C family + 34 + 59 331 - IPR000330
SNF2-related, N-terminal domain - 40 - 78 + IPR019378
GDP-fucose protein O-fucosyltransferase + 34 + 52 332 - IPR013216
Methyltransferase type 11 - 40 - 54 + IPR002495
Glycosyl transferase, family 8 + 34 + 49 333 - IPR036691
  - 40 - 436 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 34 + 37 334 - IPR006652
Kelch repeat type 1 - 40 - 303 + IPR013126
Heat shock protein 70 family + 34 + 74 335 - IPR022059
Protein of unknown function DUF3615 - 40 - 57 + IPR006073
GTP binding domain + 34 + 151 336 - IPR004046
Glutathione S-transferase, C-terminal - 40 - 49 + IPR004041
NAF domain + 33 + 52 337 - IPR038718
  - 40 - 176 + IPR002156
Ribonuclease H domain + 33 + 37 338 - IPR006671
Cyclin, N-terminal - 40 - 97 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 33 + 53 339 - IPR001906
Terpene synthase, N-terminal domain - 40 - 73 + IPR001296
Glycosyl transferase, family 1 + 33 + 53 340 - IPR012328
Chalcone/stilbene synthase, C-terminal - 40 - 44 + IPR029069
HotDog domain superfamily + 33 + 58 341 - IPR025661
Cysteine peptidase, asparagine active site - 40 - 43 + IPR039361
Cyclin + 33 + 57 342 - IPR012967
Plant methyltransferase dimerisation - 40 - 44 + IPR013181
Protein of unknown function DUF1719 + 33 + 39 343 - IPR002913
  - 40 - 474 + IPR013601
FAE1/Type III polyketide synthase-like protein + 32 + 35 344 - IPR000864
Proteinase inhibitor I13, potato inhibitor I - 39 - 166 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 32 + 35 345 - IPR036965
  - 39 - 240 + IPR032710
NTF2-like domain superfamily + 32 + 45 346 - IPR004320
Protein of unknown function DUF241, plant - 39 - 47 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 32 + 268 347 - IPR004263
Exostosin-like - 39 - 65 + IPR029000
Cyclophilin-like domain superfamily + 32 + 46 348 - IPR018121
Seven-in-absentia protein, TRAF-like domain - 39 - 60 + IPR018451
NAF/FISL domain + 32 + 50 349 - IPR008889
VQ - 39 - 46 + IPR029021
Protein-tyrosine phosphatase-like + 32 + 52 350 - IPR015947
PUA-like superfamily - 39 - 95 + IPR001881
EGF-like calcium-binding domain + 32 + 49 351 - IPR006626
Parallel beta-helix repeat - 38 - 277 + IPR000795
Translational (tr)-type GTP-binding domain + 32 + 276 352 - IPR004853
Sugar phosphate transporter domain - 38 - 58 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 32 + 67 353 - IPR013154
Alcohol dehydrogenase, N-terminal - 38 - 54 + IPR004088
K Homology domain, type 1 + 32 + 110 354 - IPR011012
Longin-like domain superfamily - 38 - 51 + IPR033443
Pentacotripeptide-repeat region of PRORP + 32 + 47 355 - IPR027923
Hydrophobic seed protein - 38 - 76 + IPR028889
Ubiquitin specific protease domain + 32 + 67 356 - IPR006458
  - 38 - 220 + IPR043519
Nucleotidyltransferase superfamily + 32 + 56 357 - IPR036354
Proteinase inhibitor I13, potato inhibitor I superfamily - 38 - 41 + IPR000679
Zinc finger, GATA-type + 32 + 144 358 - IPR002912
  - 38 - 308 + IPR001357
BRCT domain + 31 + 165 359 - IPR002487
  - 38 - 390 + IPR010920
LSM domain superfamily + 31 + 43 360 - IPR014721
  - 38 - 126 + IPR018392
LysM domain + 31 + 100 361 - IPR000743
Glycoside hydrolase, family 28 - 38 - 84 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 31 + 61 362 - IPR005795
Major pollen allergen Lol pI - 37 - 339 + IPR000727
Target SNARE coiled-coil homology domain + 30 + 59 363 - IPR038933
Ovate protein family - 37 - 39 + IPR018490
Cyclic nucleotide-binding-like + 30 + 43 364 - IPR005135
Endonuclease/exonuclease/phosphatase - 37 - 57 + IPR000315
B-box-type zinc finger + 30 + 89 365 - IPR003594
Histidine kinase/HSP90-like ATPase - 37 - 116 + IPR036420
BRCT domain superfamily + 30 + 90 366 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 37 - 377 + IPR002659
Glycosyl transferase, family 31 + 30 + 87 367 - IPR038538
  - 37 - 172 + IPR007657
Glycosyltransferase 61 + 30 + 74 368 - IPR000152
EGF-type aspartate/asparagine hydroxylation site - 37 - 55 + IPR006694
Fatty acid hydroxylase + 30 + 42 369 - IPR022357
Major intrinsic protein, conserved site - 37 - 43 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 30 + 58 370 - IPR000169
Cysteine peptidase, cysteine active site - 37 - 43 + IPR043454
NPH3/RPT2-like family + 30 + 61 371 - IPR000644
  - 37 - 646 + IPR004813
Oligopeptide transporter, OPT superfamily + 30 + 39 372 - IPR020843
Polyketide synthase, enoylreductase domain - 37 - 45 + IPR003851
Zinc finger, Dof-type + 30 + 72 373 - IPR011141
Polyketide synthase, type III - 37 - 79 + IPR000595
Cyclic nucleotide-binding domain + 30 + 111 374 - IPR025322
Protein of unknown function DUF4228, plant - 36 - 36 + IPR017938
Riboflavin synthase-like beta-barrel + 29 + 41 375 - IPR013187
F-box associated domain, type 3 - 36 - 43 + IPR036378
FAS1 domain superfamily + 29 + 40 376 - IPR001251
  - 36 - 538 + IPR002403
Cytochrome P450, E-class, group IV + 29 + 321 377 - IPR034161
Pepsin-like domain, plant - 36 - 42 + IPR007612
LURP-one-related + 29 + 69 378 - IPR036865
  - 36 - 282 + IPR044839
Protein NDR1-like + 29 + 30 379 - IPR004140
Exocyst complex component Exo70 - 36 - 97 + IPR001849
Pleckstrin homology domain + 29 + 71 380 - IPR031107
Small heat shock protein HSP20 - 36 - 39 + IPR023299
P-type ATPase, cytoplasmic domain N + 29 + 54 381 - IPR001099
Chalcone/stilbene synthase, N-terminal - 36 - 40 + IPR029062
Class I glutamine amidotransferase-like + 29 + 61 382 - IPR010402
  - 35 - 300 + IPR003855
Potassium transporter + 29 + 89 383 - IPR033131
Pectinesterase, Asp active site - 35 - 50 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 28 + 37 384 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 35 - 51 + IPR015940
Ubiquitin-associated domain + 28 + 107 385 - IPR005150
Cellulose synthase - 35 - 71 + IPR000782
FAS1 domain + 28 + 64 386 - IPR003406
Glycosyl transferase, family 14 - 35 - 45 + IPR008991
Translation protein SH3-like domain superfamily + 28 + 34 387 - IPR008480
Protein of unknown function DUF761, plant - 35 - 38 + IPR000717
Proteasome component (PCI) domain + 28 + 63 388 - IPR029045
ClpP/crotonase-like domain superfamily - 35 - 73 + IPR023753
FAD/NAD(P)-binding domain + 28 + 38 389 - IPR019378
GDP-fucose protein O-fucosyltransferase - 35 - 53 + IPR001594
Palmitoyltransferase, DHHC domain + 28 + 40 390 - IPR006094
FAD linked oxidase, N-terminal - 35 - 44 + IPR002423
Chaperonin Cpn60/TCP-1 family + 28 + 32 391 - IPR024788
Malectin-like carbohydrate-binding domain - 35 - 41 + IPR027356
NPH3 domain + 28 + 108 392 - IPR000757
  - 35 - 228 + IPR004367
Cyclin, C-terminal domain + 28 + 47 393 - IPR016040
NAD(P)-binding domain - 34 - 50 + IPR044675
E3 ubiquitin-protein ligase RING1-like + 28 + 29 394 - IPR025110
AMP-binding enzyme, C-terminal domain - 34 - 47 + IPR011332
Zinc-binding ribosomal protein + 28 + 30 395 - IPR019956
Ubiquitin - 34 - 167 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 28 + 37 396 - IPR029021
  - 34 - 228 + IPR005821
Ion transport domain + 28 + 41 397 - IPR000315
  - 34 - 618 + IPR001757
P-type ATPase + 28 + 186 398 - IPR007650
  - 34 - 166 + IPR003311
AUX/IAA protein + 28 + 43 399 - IPR002355
Multicopper oxidase, copper-binding site - 34 - 40 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 28 + 56 400 - IPR004839
Aminotransferase, class I/classII - 34 - 62 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 28 + 55 401 - IPR004883
  - 34 - 164 + IPR002867
IBR domain + 27 + 80 402 - IPR002035
  - 34 - 206 + IPR006153
Cation/H+ exchanger + 27 + 35 403 - IPR004088
K Homology domain, type 1 - 34 - 112 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 27 + 30 404 - IPR002495
Glycosyl transferase, family 8 - 34 - 49 + IPR024709
Putative O-fucosyltransferase, plant + 27 + 47 405 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 34 - 37 + IPR044835
Auxin response factor + 27 + 61 406 - IPR013126
Heat shock protein 70 family - 34 - 358 + IPR044837
B3 domain-containing protein REM16-like + 27 + 107 407 - IPR006073
GTP binding domain - 34 - 151 + IPR020471
Aldo-keto reductase + 27 + 141 408 - IPR004041
NAF domain - 33 - 52 + IPR029061
Thiamin diphosphate-binding fold + 27 + 59 409 - IPR029000
  - 33 - 202 + IPR044848
PHR1-like + 27 + 46 410 - IPR019821
Kinesin motor domain, conserved site - 33 - 48 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 27 + 41 411 - IPR029069
HotDog domain superfamily - 33 - 58 + IPR002293
Amino acid/polyamine transporter I + 27 + 46 412 - IPR004087
K Homology domain - 33 - 112 + IPR044814
Terpene cyclases, class 1, plant + 27 + 40 413 - IPR013181
Protein of unknown function DUF1719 - 33 - 75 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 27 + 37 414 - IPR013601
FAE1/Type III polyketide synthase-like protein - 32 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 27 35 415 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 32 - 68 + IPR027409
GroEL-like apical domain superfamily + 27 + 31 416 - IPR032710
NTF2-like domain superfamily - 32 - 45 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 27 + 46 417 - IPR002130
  - 32 - 804 + IPR044066
TRIAD supradomain + 27 + 47 418 - IPR001357
  - 32 - 658 + IPR005175
PPC domain + 27 + 109 419 - IPR018451
  - 32 - 150 + IPR010525
Auxin response factor domain + 27 + 48 420 - IPR013088
  - 32 - 147 + IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily + 26 + 55 421 - IPR011016
  - 32 - 486 + IPR013581
Plant PDR ABC transporter associated + 26 + 45 422 - IPR001296
Glycosyl transferase, family 1 - 32 - 52 + IPR009030
Growth factor receptor cysteine-rich domain superfamily + 26 + 33 423 - IPR018392
  - 32 - 276 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 26 + 52 424 - IPR000795
  - 32 - 828 + IPR001701
Glycoside hydrolase family 9 + 26 + 27 425 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 32 - 67 + IPR031127
E3 ubiquitin ligase RBR family + 26 + 48 426 - IPR016167
  - 32 - 147 + IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily + 26 + 30 427 - IPR028889
  - 32 - 134 + IPR002641
Patatin-like phospholipase domain + 26 + 63 428 - IPR000679
  - 32 - 552 + IPR036034
PDZ superfamily + 26 + 49 429 - IPR010920
LSM domain superfamily - 31 - 43 + IPR043363
Transcription factor DIVARICATA-like + 25 + 38 430 - IPR002659
Glycosyl transferase, family 31 - 31 - 89 + IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase + 25 + 95 431 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 31 + IPR036010
2Fe-2S ferredoxin-like superfamily + 25 33 432 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 31 - 65 + IPR001353
Proteasome, subunit alpha/beta + 25 + 25 433 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 31 - 52 + IPR012552
DVL + 25 + 28 434 - IPR001849
  - 31 - 220 + IPR002123
Phospholipid/glycerol acyltransferase + 25 + 37 435 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 31 - 72 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 25 + 31 436 - IPR034741
Terpene cyclase-like 1, C-terminal domain - 31 - 51 + IPR020946
Flavin monooxygenase-like + 25 + 49 437 - IPR033132
Glycosyl hydrolases family 1, N-terminal conserved site - 31 - 57 + IPR034285
Laccase, second cupredoxin domain + 25 + 31 438 - IPR000727
  - 30 - 194 + IPR007608
Senescence regulator S40 + 25 + 26 439 - IPR018490
Cyclic nucleotide-binding-like - 30 - 43 + IPR002035
von Willebrand factor, type A + 25 + 59 440 - IPR033138
Multicopper oxidases, conserved site - 30 - 34 + IPR036427
Bromodomain-like superfamily + 25 + 37 441 - IPR018200
Ubiquitin specific protease, conserved site - 30 - 95 + IPR007679
Domain of unknown function DUF569 + 25 + 27 442 - IPR036420
  - 30 - 382 + IPR015797
NUDIX hydrolase-like domain superfamily + 25 + 40 443 - IPR007657
Glycosyltransferase 61 - 30 - 77 + IPR003100
PAZ domain + 24 + 80 444 - IPR038770
  - 30 - 82 + IPR006689
Small GTPase superfamily, ARF/SAR type + 24 + 150 445 - IPR006694
Fatty acid hydroxylase - 30 - 42 + IPR036085
PAZ domain superfamily + 24 + 39 446 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 30 - 95 + IPR025753
AAA-type ATPase, N-terminal domain + 24 + 26 447 - IPR004813
Oligopeptide transporter, OPT superfamily - 30 - 77 + IPR018957
Zinc finger, C3HC4 RING-type + 24 + 31 448 - IPR003851
  - 30 - 429 + IPR003347
JmjC domain + 24 + 63 449 - IPR000595
  - 30 - 288 + IPR044778
Sugar transport protein STP/MST-like, plant + 24 + 28 450 - IPR017938
Riboflavin synthase-like beta-barrel - 29 - 46 + IPR040417
Glycine-rich cell wall structural protein 1/2 + 24 + 27 451 - IPR036378
  - 29 - 142 + IPR027725
Heat shock transcription factor family + 24 + 31 452 - IPR002403
Cytochrome P450, E-class, group IV - 29 - 321 + IPR025422
Transcription factor TGA like domain + 24 + 114 453 - IPR007612
LURP-one-related - 29 - 70 + IPR001763
Rhodanese-like domain + 24 + 62 454 - IPR011074
CRAL/TRIO, N-terminal domain - 29 - 95 + IPR000408
Regulator of chromosome condensation, RCC1 + 24 + 584 455 - IPR038595
  - 29 - 66 + IPR000639
Epoxide hydrolase-like + 24 + 128 456 - IPR004367
Cyclin, C-terminal domain - 29 - 83 + IPR023214
  + 24 + 72 457 - IPR023313
Ubiquitin-conjugating enzyme, active site - 29 - 40 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 24 + 45 458 - IPR029062
  - 29 - 248 + IPR034288
Laccase, first cupredoxin domain + 24 + 26 459 - IPR036779
  - 29 - 80 + IPR003616
Post-SET domain + 24 + 44 460 - IPR003855
Potassium transporter - 29 - 135 + IPR025486
Domain of unknown function DUF4378 + 24 + 52 461 - IPR017927
  - 28 - 111 + IPR036779
LysM domain superfamily + 24 + 27 462 - IPR015940
  - 28 - 306 + IPR000232
Heat shock factor (HSF)-type, DNA-binding + 24 + 116 463 - IPR000782
  - 28 - 178 + IPR001487
Bromodomain + 24 + 147 464 - IPR008991
Translation protein SH3-like domain superfamily - 28 - 34 + IPR006594
LIS1 homology motif + 23 + 51 465 - IPR000717
  - 28 - 174 + IPR003106
Leucine zipper, homeobox-associated + 23 + 26 466 - IPR023753
FAD/NAD(P)-binding domain - 28 - 38 + IPR035952
Rhomboid-like superfamily + 23 + 31 467 - IPR001594
Palmitoyltransferase, DHHC domain - 28 - 40 + IPR004316
SWEET sugar transporter + 23 + 55 468 - IPR002423
Chaperonin Cpn60/TCP-1 family - 28 - 32 + IPR008984
SMAD/FHA domain superfamily + 23 + 34 469 - IPR027356
  - 28 - 216 + IPR011016
Zinc finger, RING-CH-type + 23 + 100 470 - IPR011332
Zinc-binding ribosomal protein - 28 + IPR001163
LSM domain, eukaryotic/archaea-type + 23 30 471 - IPR000960
Flavin monooxygenase FMO - 28 - 124 + IPR008422
Homeobox KN domain + 23 + 41 472 - IPR005821
Ion transport domain - 28 - 41 + IPR044174
Glycosyltransferase BC10-like + 23 + 30 473 - IPR014722
  - 28 - 76 + IPR010989
SNARE + 23 + 29 474 - IPR003311
AUX/IAA protein - 28 - 43 + IPR003337
Trehalose-phosphatase + 23 + 38 475 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 28 - 28 + IPR003594
Histidine kinase/HSP90-like ATPase + 23 + 30 476 - IPR009091
  - 28 - 290 + IPR001320
Ionotropic glutamate receptor + 23 + 47 477 - IPR002867
IBR domain - 27 - 158 + IPR041679
DNA2/NAM7 helicase-like, C-terminal + 23 + 62 478 - IPR006153
Cation/H+ exchanger - 27 - 35 + IPR001876
Zinc finger, RanBP2-type + 23 + 127 479 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 27 - 30 + IPR039421
Type 1 protein exporter + 23 + 37 480 - IPR003954
RNA recognition motif domain, eukaryote - 27 - 129 + IPR041677
DNA2/NAM7 helicase, helicase domain + 23 + 38 481 - IPR024709
Putative O-fucosyltransferase, plant - 27 - 77 + IPR000086
NUDIX hydrolase domain + 23 + 74 482 - IPR020471
Aldo/keto reductase - 27 - 198 + IPR001638
Solute-binding protein family 3/N-terminal domain of MltF + 23 + 47 483 - IPR029061
Thiamin diphosphate-binding fold - 27 - 63 + IPR010399
Tify domain + 23 + 52 484 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 27 - 56 + IPR044730
Ribonuclease H-like domain, plant type + 23 + 24 485 - IPR002293
Amino acid/polyamine transporter I - 27 - 106 + IPR002530
Zein seed storage protein + 23 + 27 486 - IPR002123
Phospholipid/glycerol acyltransferase - 27 - 76 + IPR002937
Amine oxidase + 23 + 28 487 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 27 - 34 + IPR027410
TCP-1-like chaperonin intermediate domain superfamily + 23 + 24 488 - IPR008266
Tyrosine-protein kinase, active site - 27 - 42 + IPR006311
Twin-arginine translocation pathway, signal sequence + 23 + 29 489 - IPR036866
  - 27 - 248 + IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain + 23 + 69 490 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 27 - 51 + IPR036443
Zinc finger, RanBP2-type superfamily + 23 + 94 491 - IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase - 27 - 39 + IPR009606
Modifying wall lignin-1/2 + 22 + 23 492 - IPR027409
  - 27 - 124 + IPR006195
Aminoacyl-tRNA synthetase, class II + 22 + 31 493 - IPR033443
Pentacotripeptide-repeat region of PRORP - 27 - 47 + IPR025733
Iron/zinc purple acid phosphatase-like C-terminal domain + 22 + 35 494 - IPR029047
  - 27 - 132 + IPR042160
Homeobox-leucine zipper protein GLABRA2/ANL2/PDF2/ATML1-like + 22 + 40 495 - IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 - 27 - 46 + IPR000253
Forkhead-associated (FHA) domain + 22 + 81 496 - IPR005175
  - 27 - 218 + IPR005333
Transcription factor, TCP + 22 + 86 497 - IPR010525
Auxin response factor - 27 - 48 + IPR011074
CRAL/TRIO, N-terminal domain + 22 + 36 498 - IPR017946
  - 26 - 411 + IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily + 22 + 27 499 - IPR019954
Ubiquitin conserved site - 26 - 131 + IPR045035
Metal-nicotianamine transporter YSL-like + 22 + 29 500 - IPR013581
Plant PDR ABC transporter associated - 26 - 45 + IPR022796
Chlorophyll A-B binding protein + 22 + 26 diff --git a/gramene/htdocs/ssi/species/stats_Vitis_vinifera.html b/gramene/htdocs/ssi/species/stats_Vitis_vinifera.html index 358acd57..93c319a2 100644 --- a/gramene/htdocs/ssi/species/stats_Vitis_vinifera.html +++ b/gramene/htdocs/ssi/species/stats_Vitis_vinifera.html @@ -8,7 +8,7 @@

Summary

Database version: - 93.3 + 87.3 Base Pairs: @@ -21,12 +21,12 @@

Summary

Gene counts

- + - - + +
Coding genesHASH(0x68bff40):Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		 29,971
Gene transcriptsHASH(0x68ce400):30,609Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:29,971
@@ -78,7 +78,7 @@

Coordinate Systems

18293600871924021853 -
+
@@ -736,14 +736,6 @@

Coordinate Systems

Un:9800001..9900000100000Un:9900001..10000000100000 -
+
- -

Other

- - - - - -
Short Variants (SNPs, indels, somatic mutations):457,245
\ No newline at end of file diff --git a/gramene/htdocs/ssi/species/stats_Vitis_vinifera_IPtop500.html b/gramene/htdocs/ssi/species/stats_Vitis_vinifera_IPtop500.html index 3dc9a806..0d8b585e 100644 --- a/gramene/htdocs/ssi/species/stats_Vitis_vinifera_IPtop500.html +++ b/gramene/htdocs/ssi/species/stats_Vitis_vinifera_IPtop500.html @@ -18,770 +18,770 @@ 1 IPR011009
Protein kinase-like domain superfamily 1411 - 1531 + 2916 2 IPR027417
P-loop containing nucleoside triphosphate hydrolase - 1338 - 1750 + 1361 + 3258 3 - IPR000719
  + IPR000719
Protein kinase domain 1302 - 9612 + 4408 4 - IPR032675
  - 1005 - 4412 - - - - 5 IPR008271
Serine/threonine-protein kinase, active site 963 985 - - 6 + + 5 IPR017441
Protein kinase, ATP binding site 789 800 + + 6 + IPR013320
Concanavalin A-like lectin/glucanase, subgroup + 745 + 903 + + 7 - IPR011990
  - 777 - 9429 + IPR011990
Tetratricopeptide-like helical + 647 + 1944 8 - IPR002885
  - 567 - 26714 + IPR001611
Leucine-rich repeat + 569 + 3018 9 - IPR001611
  - 556 - 10626 + IPR002885
Pentatricopeptide repeat + 567 + 20494 10 - IPR013083
  - 518 - 1120 + IPR013083
Zinc finger, RING/FYVE/PHD-type + 520 + 561 11 IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain - 485 - 641 + 486 + 1282 12 - IPR036291
NAD(P)-binding domain superfamily - 459 - 495 + IPR016040
NAD(P)-binding domain + 482 + 594 13 - IPR036396
  - 394 - 2475 + IPR036291
NAD(P)-binding domain superfamily + 459 + 469 14 IPR001128
Cytochrome P450 - 387 - 1517 + 395 + 3880 15 - IPR029058
  - 374 - 1658 + IPR036396
Cytochrome P450 superfamily + 394 + 410 16 IPR009057
Homeobox-like domain superfamily - 364 - 388 + 392 + 1848 17 - IPR002182
NB-ARC - 356 - 375 + IPR029058
Alpha/Beta hydrolase fold + 382 + 853 18 - IPR016024
Armadillo-type fold - 353 - 726 + IPR044974
Disease resistance protein, plants + 359 + 546 19 - IPR003591
Leucine-rich repeat, typical subtype - 348 - 2406 + IPR016024
Armadillo-type fold + 353 + 846 20 - IPR002401
Cytochrome P450, E-class, group I - 337 - 2173 + IPR002182
NB-ARC + 348 + 720 21 - IPR001841
  - 323 - 1502 + IPR002401
Cytochrome P450, E-class, group I + 337 + 4346 22 - IPR003593
AAA+ ATPase domain - 317 - 422 + IPR001841
Zinc finger, RING-type + 327 + 1006 23 - IPR029063
S-adenosyl-L-methionine-dependent methyltransferase - 298 - 376 + IPR029063
S-adenosyl-L-methionine-dependent methyltransferase-like + 310 + 730 24 - IPR017972
Cytochrome P450, conserved site - 292 - 303 + IPR011989
Armadillo-like helical + 294 + 555 25 - IPR001005
SANT/Myb domain - 278 - 1105 + IPR017972
Cytochrome P450, conserved site + 292 + 303 26 - IPR015943
  - 272 - 1281 + IPR015943
WD40/YVTN repeat-like-containing domain + 287 + 454 27 - IPR017853
Glycoside hydrolase superfamily - 270 - 315 + IPR001005
SANT/Myb domain + 287 + 3253 28 - IPR036322
WD40-repeat-containing domain superfamily - 267 - 416 + IPR017853
Glycoside hydrolase superfamily + 270 + 562 29 - IPR011989
  - 261 - 738 + IPR036322
WD40-repeat-containing domain superfamily + 267 + 287 30 - IPR036249
Thioredoxin-like superfamily - 253 - 296 + IPR012336
Thioredoxin-like fold + 259 + 924 31 - IPR001680
  - 249 - 8130 + IPR012677
Nucleotide-binding, alpha-beta plait + 253 + 402 32 - IPR035979
RNA-binding domain superfamily - 246 - 364 + IPR036249
Thioredoxin-like superfamily + 253 + 289 33 - IPR012677
  - 245 - 776 + IPR017930
Myb domain + 251 + 722 34 - IPR013210
Leucine-rich repeat-containing N-terminal, plant-type - 233 - 244 + IPR035979
RNA-binding domain superfamily + 246 + 343 35 - IPR017986
  - 227 - 765 + IPR001680
WD40 repeat + 233 + 2630 36 - IPR000504
  - 225 - 3045 + IPR013210
Leucine-rich repeat-containing N-terminal, plant-type + 233 + 488 37 IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase - 224 - 229 + 228 + 1228 38 - IPR036770
  - 222 - 1190 + IPR020683
Ankyrin repeat-containing domain + 225 + 1182 39 - IPR020683
  - 219 - 1592 + IPR000504
RNA recognition motif domain + 224 + 1346 40 - IPR017930
  - 216 - 708 + IPR013781
Glycoside hydrolase, catalytic domain + 221 + 253 41 - IPR036259
MFS transporter superfamily - 210 - 345 + IPR036770
Ankyrin repeat-containing domain superfamily + 218 + 243 42 - IPR036047
F-box-like domain superfamily - 187 - 191 + IPR036259
MFS transporter superfamily + 210 + 226 43 - IPR011992
EF-hand domain pair - 184 - 206 + IPR036047
F-box-like domain superfamily + 187 + 188 44 - IPR002110
  - 180 - 3993 + IPR011992
EF-hand domain pair + 185 + 878 45 - IPR032867
DYW domain - 173 - 173 + IPR005123
Oxoglutarate/iron-dependent dioxygenase + 167 + 805 46 - IPR029044
  - 168 - 828 + IPR003439
ABC transporter-like, ATP-binding domain + 166 + 936 47 - IPR003439
  - 168 - 1410 + IPR027443
Isopenicillin N synthase-like + 165 + 174 48 - IPR005123
  - 167 - 969 + IPR032867
DYW domain + 162 + 162 49 - IPR027443
  - 164 - 342 + IPR036412
HAD-like superfamily + 162 + 166 50 - IPR036412
HAD-like superfamily - 162 - 236 + IPR002048
EF-hand domain + 161 + 1698 51 - IPR002048
  - 161 - 3393 + IPR011991
Winged helix-turn-helix DNA-binding domain + 161 + 182 52 - IPR036388
  - 161 - 358 + IPR036390
Winged helix DNA-binding domain superfamily + 161 + 170 53 - IPR036390
Winged helix DNA-binding domain superfamily - 161 - 170 + IPR008972
Cupredoxin + 161 + 1362 54 - IPR008972
  - 160 - 1382 + IPR029044
Nucleotide-diphospho-sugar transferases + 158 + 277 55 - IPR020846
  - 158 - 512 + IPR019775
WD40 repeat, conserved site + 154 + 253 56 - IPR035595
UDP-glycosyltransferase family, conserved site - 155 - 158 + IPR041118
Rx, N-terminal + 153 + 157 57 - IPR019775
WD40 repeat, conserved site - 154 - 252 + IPR002110
Ankyrin repeat + 152 + 918 58 IPR018247
EF-Hand 1, calcium-binding site 151 - 337 + 344 59 - IPR001810
  - 147 - 855 + IPR016177
DNA-binding domain superfamily + 146 + 330 60 - IPR016177
DNA-binding domain superfamily - 146 - 165 + IPR014710
RmlC-like jelly roll fold + 145 + 168 61 - IPR023214
  - 146 - 480 + IPR001810
F-box domain + 143 + 418 62 - IPR036188
  - 145 - 1094 + IPR011050
Pectin lyase fold/virulence factor + 143 + 300 63 - IPR011050
Pectin lyase fold/virulence factor - 143 - 153 + IPR012334
Pectin lyase fold + 143 + 157 64 - IPR012334
  - 141 - 302 + IPR036188
FAD/NAD(P)-binding domain superfamily + 141 + 180 65 - IPR014710
  - 140 - 334 + IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid + 139 + 530 66 - IPR026961
PGG domain - 138 - 141 + IPR026992
Non-haem dioxygenase N-terminal domain + 138 + 280 67 - IPR026992
Non-haem dioxygenase N-terminal domain - 138 - 140 + IPR038765
Papain-like cysteine peptidase superfamily + 138 + 138 68 - IPR038765
Papain-like cysteine peptidase superfamily - 138 - 154 + IPR026961
PGG domain + 137 + 280 69 - IPR036638
  - 135 - 780 + IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain + 137 + 754 70 - IPR014001
  - 135 - 512 + IPR001471
AP2/ERF domain + 135 + 1688 71 - IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid - 135 - 171 + IPR036638
Helix-loop-helix DNA-binding domain superfamily + 135 + 135 72 - IPR001471
  - 134 - 2529 + IPR012340
Nucleic acid-binding, OB-fold + 131 + 644 73 - IPR036955
  - 134 - 450 + IPR014001
Helicase superfamily 1/2, ATP-binding domain + 131 + 264 74 - IPR011598
  - 133 - 1407 + IPR001650
Helicase, C-terminal + 128 + 500 75 - IPR001650
  - 128 - 1008 + IPR038005
Virus X resistance protein-like, coiled-coil domain + 124 + 129 76 - IPR008949
  - 125 - 580 + IPR023214
HAD-like domain + 124 + 236 77 - IPR038005
Virus X resistance protein-like, coiled-coil domain - 124 - 129 + IPR015424
Pyridoxal phosphate-dependent transferase + 121 + 250 78 - IPR012340
Nucleic acid-binding, OB-fold - 124 - 170 + IPR003959
ATPase, AAA-type, core + 121 + 276 79 - IPR013087
  - 122 - 1455 + IPR014729
Rossmann-like alpha/beta/alpha sandwich fold + 120 + 143 80 - IPR015424
Pyridoxal phosphate-dependent transferase - 121 - 132 + IPR011051
RmlC-like cupin domain superfamily + 119 + 246 81 - IPR003959
ATPase, AAA-type, core - 121 - 138 + IPR036426
Bulb-type lectin domain superfamily + 117 + 128 82 - IPR019734
  - 120 - 2487 + IPR001480
Bulb-type lectin domain + 116 + 884 83 - IPR013026
  - 120 - 450 + IPR015421
Pyridoxal phosphate-dependent transferase, major region, subdomain 1 + 114 + 118 84 - IPR011051
RmlC-like cupin domain superfamily - 119 - 129 + IPR008949
Isoprenoid synthase domain superfamily + 114 + 476 85 - IPR036426
  - 118 - 542 + IPR007087
Zinc finger, C2H2 + 114 + 462 86 - IPR013320
Concanavalin A-like lectin/glucanase domain superfamily - 117 - 136 + IPR010987
Glutathione S-transferase, C-terminal-like + 114 + 416 87 - IPR015421
  - 116 - 363 + IPR045087
Multicopper oxidase + 113 + 132 88 - IPR001480
  - 113 - 642 + IPR036236
Zinc finger C2H2 superfamily + 109 + 154 89 - IPR014729
  - 110 - 256 + IPR036282
Glutathione S-transferase, C-terminal domain superfamily + 106 + 107 90 - IPR036236
Zinc finger C2H2 superfamily - 109 - 182 + IPR016038
Thiolase-like, subgroup + 105 + 206 91 - IPR036282
Glutathione S-transferase, C-terminal domain superfamily - 106 - 107 + IPR013785
Aldolase-type TIM barrel + 104 + 125 92 - IPR016039
  - 105 - 1089 + IPR004045
Glutathione S-transferase, N-terminal + 104 + 416 93 - IPR004045
  - 104 - 618 + IPR016039
Thiolase-like + 103 + 364 94 - IPR002347
Short-chain dehydrogenase/reductase SDR - 102 - 748 + IPR005225
Small GTP-binding protein domain + 102 + 104 95 - IPR005225
Small GTP-binding protein domain - 102 - 104 + IPR002347
Short-chain dehydrogenase/reductase SDR + 102 + 958 96 - IPR020472
G-protein beta WD-40 repeat - 100 - 300 + IPR019734
Tetratricopeptide repeat + 101 + 418 97 - IPR015422
  - 100 - 474 + IPR020472
G-protein beta WD-40 repeat + 100 + 600 98 - IPR036852
  - 98 - 1251 + IPR035892
C2 domain superfamily + 98 + 143 99 - IPR013785
  - 97 - 306 + IPR013830
SGNH hydrolase-type esterase domain + 98 + 109 100 - IPR023213
  - 97 - 316 + IPR015500
Peptidase S8, subtilisin-related + 98 + 788 101 - IPR011706
Multicopper oxidase, type 2 - 97 - 98 + IPR036852
Peptidase S8/S53 domain superfamily + 97 + 108 102 - IPR036514
  - 97 - 204 + IPR011706
Multicopper oxidase, C-terminal + 97 + 196 103 - IPR036869
  - 97 - 386 + IPR000209
Peptidase S8/S53 domain + 97 + 636 104 - IPR003609
  + IPR003609
PAN/Apple domain 96 - 502 + 454 105 - IPR010987
  - 96 - 194 + IPR001623
DnaJ domain + 96 + 1154 106 - IPR010255
Haem peroxidase + IPR010255
Haem peroxidase superfamily 96 - 100 + 198 107 IPR001117
Multicopper oxidase, type 1 95 - 97 + 194 108 - IPR025287
Wall-associated receptor kinase, galacturonan-binding domain - 94 - 97 + IPR000008
C2 domain + 95 + 918 109 - IPR000858
S-locus glycoprotein domain - 94 - 98 + IPR036869
Chaperone J-domain superfamily + 95 + 96 110 - IPR005630
Terpene synthase, metal-binding domain - 94 - 96 + IPR000858
S-locus glycoprotein domain + 94 + 196 @@ -793,219 +793,219 @@ 112 - IPR029071
Ubiquitin-like domain superfamily - 94 - 134 + IPR025287
Wall-associated receptor kinase, galacturonan-binding domain + 94 + 194 113 - IPR000209
Peptidase S8/S53 domain - 94 - 105 + IPR029071
Ubiquitin-related domain + 94 + 134 114 - IPR006045
Cupin 1 - 91 - 208 + IPR013087
Zinc finger C2H2-type/integrase DNA-binding domain + 93 + 79 115 - IPR002016
  - 91 - 1821 + IPR015422
Pyridoxal phosphate-dependent transferase, major region, subdomain 2 + 93 + 104 116 - IPR035892
  - 90 - 274 + IPR020846
Major facilitator superfamily domain + 93 + 186 117 - IPR000008
  - 90 - 836 + IPR001087
GDSL lipase/esterase + 92 + 194 118 - IPR000073
Alpha/beta hydrolase fold-1 - 90 - 202 + IPR005630
Terpene synthase, metal-binding domain + 92 + 190 119 - IPR011011
Zinc finger, FYVE/PHD-type - 89 - 104 + IPR002198
Short-chain dehydrogenase/reductase SDR + 91 + 812 120 - IPR011032
GroES-like superfamily - 88 - 110 + IPR006045
Cupin 1 + 91 + 210 121 - IPR001623
  - 88 - 1116 + IPR002016
Haem peroxidase + 91 + 1214 122 - IPR011707
Multicopper oxidase, type 3 - 88 - 90 + IPR000073
Alpha/beta hydrolase fold-1 + 91 + 406 123 - IPR001087
GDSL lipase/esterase - 87 - 91 + IPR023213
Chloramphenicol acetyltransferase-like domain + 91 + 157 124 - IPR036457
  - 87 - 388 + IPR011032
GroES-like superfamily + 90 + 402 125 - IPR035897
  - 84 - 326 + IPR011011
Zinc finger, FYVE/PHD-type + 89 + 208 126 - IPR021109
  - 84 - 462 + IPR011707
Multicopper oxidase, N-termianl + 88 + 180 127 - IPR011545
DEAD/DEAH box helicase domain - 84 - 85 + IPR001932
PPM-type phosphatase domain + 87 + 678 128 - IPR012337
Ribonuclease H-like superfamily - 83 - 90 + IPR036457
PPM-type phosphatase domain superfamily + 86 + 86 129 - IPR001356
  - 83 - 894 + IPR012337
Ribonuclease H-like superfamily + 84 + 302 130 - IPR009072
  - 83 - 501 + IPR011545
DEAD/DEAH box helicase domain + 84 + 170 131 - IPR001932
  - 82 - 1002 + IPR009072
Histone-fold + 84 + 332 132 - IPR003480
Transferase - 82 - 86 + IPR001356
Homeobox domain + 83 + 438 133 - IPR036965
  - 81 - 273 + IPR003480
Transferase + 82 + 172 134 - IPR019793
Peroxidases heam-ligand binding site - 81 - 83 + IPR041469
Subtilisin-like protease, fibronectin type-III domain + 81 + 89 135 - IPR036961
  - 81 - 312 + IPR001906
Terpene synthase, N-terminal domain + 81 + 330 136 IPR000823
Plant peroxidase 81 - 673 + 1346 137 - IPR000225
  - 81 - 1953 + IPR019793
Peroxidases heam-ligand binding site + 81 + 84 138 - IPR015500
Peptidase S8, subtilisin-related - 79 - 232 + IPR000157
Toll/interleukin-1 receptor homology (TIR) domain + 79 + 446 139 - IPR027640
Kinesin-like protein - 77 - 95 + IPR035897
Toll/interleukin-1 receptor homology (TIR) domain superfamily + 79 + 79 140 - IPR000157
  - 77 - 645 + IPR013766
Thioredoxin domain + 78 + 130 141 - IPR001906
Terpene synthase, N-terminal domain - 77 - 81 + IPR023393
START-like domain + 77 + 79 142 - IPR008978
  - 76 - 298 + IPR021109
Aspartic peptidase domain superfamily + 76 + 424 @@ -1026,7 +1026,7 @@ 145 IPR003676
Small auxin-up RNA 76 - 79 + 158 @@ -1038,1101 +1038,1101 @@ 147 - IPR023828
Peptidase S8, subtilisin, Ser-active site - 75 - 82 + IPR001806
Small GTPase + 75 + 264 148 - IPR000571
  - 75 - 1194 + IPR023828
Peptidase S8, subtilisin, Ser-active site + 75 + 82 149 - IPR001806
Small GTPase superfamily - 75 - 77 + IPR000571
Zinc finger, CCCH-type + 75 + 660 150 IPR013525
ABC-2 type transporter 74 - 104 + 208 151 - IPR003441
  - 74 - 444 + IPR011333
SKP1/BTB/POZ domain superfamily + 74 + 156 152 - IPR013766
  - 74 - 402 + IPR008978
HSP20-like chaperone + 74 + 294 153 - IPR015655
Protein phosphatase 2C family - 74 - 78 + IPR003441
NAC domain + 74 + 518 154 - IPR011333
SKP1/BTB/POZ domain superfamily - 74 - 80 + IPR005150
Cellulose synthase + 73 + 236 155 - IPR036093
  - 74 - 444 + IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 + 72 + 154 156 - IPR023393
  - 73 - 150 + IPR002355
Multicopper oxidase, copper-binding site + 72 + 138 157 - IPR005150
Cellulose synthase - 73 - 118 + IPR006447
Myb domain, plants + 71 + 71 158 - IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9 - 72 - 77 + IPR023395
Mitochondrial carrier domain superfamily + 71 + 292 159 - IPR002355
Multicopper oxidase, copper-binding site - 72 - 73 + IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant + 70 + 71 160 - IPR001461
Aspartic peptidase A1 family - 72 - 159 + IPR003960
ATPase, AAA-type, conserved site + 70 + 74 161 - IPR006447
Myb domain, plants - 71 - 71 + IPR017907
Zinc finger, RING-type, conserved site + 70 + 70 162 - IPR023395
  - 71 - 322 + IPR001929
Germin + 70 + 418 163 - IPR037045
  - 71 - 152 + IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily + 70 + 70 164 - IPR001929
Germin - 70 - 209 + IPR029052
Metallo-dependent phosphatase-like + 69 + 150 165 - IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily - 70 - 70 + IPR005828
Major facilitator, sugar transporter-like + 69 + 154 166 - IPR013783
  - 70 - 154 + IPR000270
PB1 domain + 69 + 158 167 - IPR003960
ATPase, AAA-type, conserved site - 70 - 74 + IPR001752
Kinesin motor domain + 69 + 828 168 - IPR017907
Zinc finger, RING-type, conserved site - 70 - 70 + IPR023298
P-type ATPase, transmembrane domain + 68 + 166 169 - IPR011993
  - 70 - 142 + IPR002528
Multi antimicrobial extrusion protein + 68 + 372 170 - IPR024171
S-receptor-like serine/threonine-protein kinase - 69 - 93 + IPR033121
Peptidase family A1 domain + 68 + 68 171 - IPR005828
Major facilitator, sugar transporter-like - 69 - 77 + IPR000225
Armadillo + 67 + 502 172 - IPR000270
  - 69 - 324 + IPR013149
Alcohol dehydrogenase, C-terminal + 67 + 136 173 - IPR013149
Alcohol dehydrogenase, C-terminal - 68 - 69 + IPR013057
Amino acid transporter, transmembrane domain + 67 + 138 174 - IPR001509
NAD-dependent epimerase/dehydratase - 68 - 69 + IPR043129
ATPase, nucleotide binding domain + 66 + 114 175 - IPR013057
Amino acid transporter, transmembrane domain - 68 - 71 + IPR019794
Peroxidase, active site + 66 + 68 176 - IPR002528
Multi antimicrobial extrusion protein - 68 - 186 + IPR000109
Proton-dependent oligopeptide transporter family + 66 + 280 177 - IPR033121
  - 68 - 152 + IPR034285
Laccase, second cupredoxin domain + 66 + 67 178 - IPR001965
Zinc finger, PHD-type - 68 - 101 + IPR015915
Kelch-type beta propeller + 65 + 102 179 - IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain - 67 - 96 + IPR001878
Zinc finger, CCHC-type + 65 + 566 180 - IPR000109
Proton-dependent oligopeptide transporter family - 66 - 140 + IPR018108
Mitochondrial substrate/solute carrier + 64 + 702 181 - IPR019794
Peroxidase, active site - 66 - 68 + IPR001461
Aspartic peptidase A1 family + 64 + 312 182 - IPR034285
Laccase, second cupredoxin domain - 66 - 67 + IPR001509
NAD-dependent epimerase/dehydratase + 63 + 128 183 - IPR001752
  - 66 - 1206 + IPR019780
Germin, manganese binding site + 63 + 63 184 - IPR033138
Multicopper oxidases, conserved site - 64 - 65 + IPR023299
P-type ATPase, cytoplasmic domain N + 62 + 242 185 - IPR018108
  - 64 - 704 + IPR002100
Transcription factor, MADS-box + 61 + 668 186 - IPR023298
P-type ATPase, transmembrane domain superfamily - 64 - 183 + IPR036879
Transcription factor, MADS-box superfamily + 61 + 61 187 - IPR019780
Germin, manganese binding site - 63 - 63 + IPR034289
Laccase, third cupredoxin domain + 61 + 61 188 - IPR034741
Terpene cyclase-like 1, C-terminal domain - 63 - 63 + IPR036163
Heavy metal-associated domain superfamily + 61 + 77 189 - IPR002100
  - 61 - 1185 + IPR044810
WRKY transcription factor, plant + 61 + 62 190 - IPR034289
Laccase, third cupredoxin domain - 61 - 61 + IPR036640
ABC transporter type 1, transmembrane domain superfamily + 60 + 105 191 - IPR023299
  - 61 - 354 + IPR032799
Xylanase inhibitor, C-terminal + 60 + 61 192 - IPR036163
Heavy metal-associated domain superfamily - 61 - 77 + IPR000626
Ubiquitin-like domain + 60 + 354 193 - IPR036879
  - 61 - 366 + IPR004843
Calcineurin-like phosphoesterase domain, ApaH type + 60 + 124 194 - IPR001878
  - 61 - 882 + IPR011527
ABC transporter type 1, transmembrane domain + 60 + 418 195 - IPR000626
  - 60 - 762 + IPR004046
Glutathione S-transferase, C-terminal + 60 + 122 196 - IPR004843
Calcineurin-like phosphoesterase domain, ApaH type - 60 - 62 + IPR000743
Glycoside hydrolase, family 28 + 60 + 200 197 - IPR001563
Peptidase S10, serine carboxypeptidase - 60 - 335 + IPR019787
Zinc finger, PHD-finger + 59 + 214 198 - IPR036640
  - 60 - 600 + IPR003657
WRKY domain + 59 + 637 199 - IPR002068
  - 60 - 238 + IPR003613
U box domain + 59 + 230 200 - IPR036397
  - 60 - 195 + IPR002068
Alpha crystallin/Hsp20 domain + 59 + 236 201 - IPR032799
Xylanase inhibitor, C-terminal - 60 - 61 + IPR020568
Ribosomal protein S5 domain 2-type fold + 59 + 126 202 - IPR011527
  - 60 - 627 + IPR001757
P-type ATPase + 58 + 480 203 - IPR015915
  - 60 - 408 + IPR043926
ABC transporter family G domain + 58 + 73 204 - IPR000743
Glycoside hydrolase, family 28 - 60 - 100 + IPR001563
Peptidase S10, serine carboxypeptidase + 58 + 660 205 - IPR036576
  - 59 - 423 + IPR014733
Barwin-like endoglucanase + 57 + 58 206 - IPR000210
  - 59 - 456 + IPR011993
Pleckstrin homology-like domain + 57 + 63 207 - IPR019787
  - 59 - 214 + IPR008250
P-type ATPase, A domain superfamily + 57 + 252 208 - IPR020568
Ribosomal protein S5 domain 2-type fold - 59 - 72 - + IPR013154
Alcohol dehydrogenase, N-terminal + 57 + 120 + 209 - IPR003657
  - 59 - 630 + IPR036908
RlpA-like domain superfamily + 57 + 58 210 - IPR003613
  - 59 - 516 + IPR000070
Pectinesterase, catalytic + 56 + 118 211 - IPR001757
P-type ATPase - 58 - 240 + IPR017761
Laccase + 56 + 56 212 - IPR006121
  - 57 - 561 + IPR006121
Heavy metal-associated domain, HMA + 55 + 370 213 - IPR008250
P-type ATPase, A domain superfamily - 57 - 70 + IPR036915
Cyclin-like superfamily + 55 + 93 214 - IPR013154
Alcohol dehydrogenase, N-terminal - 57 - 60 + IPR011141
Polyketide synthase, type III + 55 + 192 215 - IPR036908
  - 57 - 232 + IPR036875
Zinc finger, CCHC-type superfamily + 55 + 73 216 - IPR012341
  - 57 - 171 + IPR011042
Six-bladed beta-propeller, TolB-like + 55 + 71 217 - IPR004046
Glutathione S-transferase, C-terminal - 56 - 57 + IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily + 54 + 54 218 - IPR029052
  - 56 - 118 + IPR044814
Terpene cyclases, class 1, plant + 54 + 54 219 - IPR000070
Pectinesterase, catalytic - 56 - 59 + IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain + 54 + 108 220 - IPR017761
Laccase - 56 - 56 + IPR024788
Malectin-like domain + 54 + 116 221 - IPR020843
Polyketide synthase, enoylreductase domain - 55 - 55 + IPR036855
Zinc finger, CCCH-type superfamily + 54 + 102 222 - IPR036915
Cyclin-like superfamily - 55 - 94 + IPR000210
BTB/POZ domain + 54 + 251 223 - IPR011141
Polyketide synthase, type III - 55 - 100 + IPR013763
Cyclin-like + 54 + 314 224 - IPR036875
Zinc finger, CCHC-type superfamily - 55 - 73 + IPR019786
Zinc finger, PHD-type, conserved site + 54 + 63 225 - IPR035513
  - 54 - 214 + IPR032861
Xylanase inhibitor, N-terminal + 54 + 55 226 - IPR019786
Zinc finger, PHD-type, conserved site - 54 - 57 + IPR006501
Pectinesterase inhibitor domain + 54 + 318 227 - IPR016135
  - 54 - 220 + IPR013094
Alpha/beta hydrolase fold-3 + 54 + 108 228 - IPR032861
Xylanase inhibitor, N-terminal - 54 - 55 + IPR016181
Acyl-CoA N-acyltransferase + 53 + 228 229 - IPR006501
Pectinesterase inhibitor domain - 54 - 155 + IPR005829
Sugar transporter, conserved site + 53 + 80 230 - IPR013094
Alpha/beta hydrolase fold-3 - 54 - 55 + IPR015300
DNA-binding pseudobarrel domain superfamily + 53 + 256 231 - IPR024788
Malectin-like carbohydrate-binding domain - 54 - 57 + IPR024171
S-receptor-like serine/threonine-protein kinase + 53 + 53 232 - IPR004827
  - 54 - 597 + IPR002902
Gnk2-homologous domain + 53 + 402 233 - IPR036855
Zinc finger, CCCH-type superfamily - 54 - 102 + IPR016135
Ubiquitin-conjugating enzyme/RWD-like + 53 + 214 234 - IPR016181
Acyl-CoA N-acyltransferase - 53 - 58 + IPR029045
ClpP/crotonase-like domain + 53 + 112 235 - IPR038408
  - 53 - 202 + IPR004827
Basic-leucine zipper domain + 53 + 290 236 - IPR002902
  - 53 - 402 + IPR003340
B3 DNA binding domain + 52 + 362 237 - IPR005829
Sugar transporter, conserved site - 53 - 80 + IPR018333
Squalene cyclase + 52 + 210 238 - IPR015300
  - 53 - 254 + IPR034288
Laccase, first cupredoxin domain + 52 + 53 239 - IPR003340
  - 52 - 720 + IPR045069
Multidrug and toxic compound extrusion family, eukaryotic + 52 + 52 240 - IPR008266
Tyrosine-protein kinase, active site - 52 - 54 + IPR001099
Chalcone/stilbene synthase, N-terminal + 52 + 106 241 - IPR034288
Laccase, first cupredoxin domain - 52 - 53 + IPR008266
Tyrosine-protein kinase, active site + 52 + 54 242 - IPR008979
  - 52 - 240 + IPR018303
P-type ATPase, phosphorylation site + 52 + 56 243 - IPR018303
P-type ATPase, phosphorylation site - 52 - 56 + IPR003663
Sugar/inositol transporter + 52 + 526 244 - IPR030184
WAT1-related protein - 52 - 54 + IPR023210
NADP-dependent oxidoreductase domain + 52 + 202 245 - IPR003663
Sugar/inositol transporter - 52 - 263 + IPR000620
EamA domain + 51 + 178 246 - IPR036812
  - 52 - 216 + IPR036812
NADP-dependent oxidoreductase domain superfamily + 51 + 52 247 - IPR001099
Chalcone/stilbene synthase, N-terminal - 52 - 53 + IPR036890
Histidine kinase/HSP90-like ATPase superfamily + 50 + 52 248 - IPR036890
  - 51 - 216 + IPR003594
Histidine kinase/HSP90-like ATPase + 50 + 184 249 - IPR029045
ClpP/crotonase-like domain superfamily - 51 - 70 + IPR018253
DnaJ domain, conserved site + 50 + 50 250 - IPR000620
EamA domain - 51 - 89 + IPR000048
IQ motif, EF-hand binding site + 50 + 436 251 - IPR018253
DnaJ domain, conserved site - 50 - 50 + IPR016461
O-methyltransferase COMT-type + 49 + 266 252 - IPR000048
  - 50 - 1014 + IPR030184
WAT1-related protein + 49 + 51 253 - IPR014014
  - 49 - 98 + IPR029061
Thiamin diphosphate-binding fold + 48 + 138 254 - IPR016461
  - 48 - 258 + IPR044965
Glycoside hydrolase family 17, plant + 48 + 49 255 - IPR001077
O-methyltransferase, family 2 - 48 - 50 + IPR005202
Transcription factor GRAS + 48 + 296 256 - IPR031107
Small heat shock protein HSP20 - 48 - 51 + IPR012328
Chalcone/stilbene synthase, C-terminal + 48 + 100 257 - IPR005202
  - 48 - 194 + IPR020904
Short-chain dehydrogenase/reductase, conserved site + 47 + 47 258 - IPR012328
Chalcone/stilbene synthase, C-terminal - 48 - 50 + IPR004883
Lateral organ boundaries, LOB + 47 + 188 259 - IPR000490
Glycoside hydrolase family 17 - 48 - 75 + IPR001077
O-methyltransferase domain + 47 + 98 260 - IPR029061
Thiamin diphosphate-binding fold - 47 - 70 + IPR029055
Nucleophile aminohydrolases, N-terminal + 47 + 87 261 - IPR020904
Short-chain dehydrogenase/reductase, conserved site - 47 - 47 + IPR004839
Aminotransferase, class I/classII + 47 + 98 262 - IPR004839
Aminotransferase, class I/classII - 47 - 49 + IPR008979
Galactose-binding-like domain superfamily + 47 + 218 263 - IPR004883
  - 47 - 188 + IPR000490
Glycoside hydrolase family 17 + 47 + 148 264 - IPR023210
NADP-dependent oxidoreductase domain - 47 - 92 + IPR000608
Ubiquitin-conjugating enzyme E2 + 46 + 266 265 - IPR011042
  - 47 - 110 + IPR008928
Six-hairpin glycosidase superfamily + 46 + 92 266 IPR002921
Fungal lipase-like domain 46 - 48 + 96 267 - IPR000608
  - 46 - 264 + IPR026057
PC-Esterase + 46 + 94 268 - IPR026057
PC-Esterase - 46 - 47 + IPR003137
PA domain + 45 + 96 269 - IPR003137
PA domain - 46 - 49 + IPR041569
AAA ATPase, AAA+ lid domain + 45 + 50 270 - IPR029055
  - 46 - 182 + IPR014014
RNA helicase, DEAD-box type, Q motif + 45 + 90 271 - IPR008928
Six-hairpin glycosidase superfamily - 46 - 57 + IPR003653
Ulp1 protease family, C-terminal catalytic domain + 45 + 148 272 - IPR033131
Pectinesterase, Asp active site - 45 - 46 + IPR011006
CheY-like superfamily + 45 + 100 273 - IPR003653
  - 45 - 222 + IPR018040
Pectinesterase, active site + 45 + 57 274 - IPR011006
CheY-like superfamily - 45 - 52 + IPR001214
SET domain + 45 + 170 275 - IPR001214
  - 45 - 357 - - - - 276 - IPR036318
FAD-binding, type 2-like superfamily + IPR036318
FAD-binding, type PCMH-like superfamily 44 47 - + + 276 + IPR000742
EGF-like domain + 44 + 106 + + + 277 - IPR003245
  - 44 - 387 + IPR001789
Signal transduction response regulator, receiver domain + 44 + 180 278 - IPR000742
  - 44 - 208 + IPR003245
Phytocyanin domain + 44 + 260 279 IPR001220
Legume lectin domain 44 - 83 + 166 280 IPR014756
Immunoglobulin E-set 44 - 46 + 90 281 - IPR001789
  - 44 - 522 + IPR033896
MADS MEF2-like + 43 + 43 282 - IPR033896
MADS MEF2-like - 43 + IPR019821
Kinesin, motor region, conserved site + 43 43 283 - IPR019821
Kinesin motor domain, conserved site - 43 - 43 + IPR004263
Exostosin-like + 43 + 205 284 IPR029962
Trichome birefringence-like family 43 - 46 + 45 285 IPR009000
Translation protein, beta-barrel domain superfamily 43 - 46 + 90 286 - IPR002912
  - 43 - 184 + IPR004088
K Homology domain, type 1 + 43 + 314 287 - IPR036612
  - 42 - 438 + IPR002912
ACT domain + 43 + 168 288 IPR000873
AMP-dependent synthetase/ligase 42 - 44 + 88 289 - IPR013763
Cyclin-like - 42 - 126 + IPR036612
K Homology domain, type 1 superfamily + 42 + 84 290 - IPR000182
  - 41 - 154 + IPR031107
Small heat shock protein HSP20 + 42 + 44 291 - IPR021820
S-locus receptor kinase, C-terminal - 41 - 41 + IPR044791
Beta-glucanase/XTH + 42 + 45 292 - IPR031052
FHY3/FAR1 family - 41 - 43 + IPR000182
GNAT domain + 41 + 154 293 - IPR007112
  - 41 - 142 + IPR017884
SANT domain + 41 + 94 294 - IPR021720
Malectin - 41 - 44 + IPR007112
Expansin/pollen allergen, DPBB domain + 41 + 84 295 - IPR009060
UBA-like superfamily - 40 - 46 + IPR021720
Malectin domain + 41 + 88 296 - IPR000330
SNF2-related, N-terminal domain - 40 - 41 + IPR018202
Peptidase S10, serine carboxypeptidase, active site + 41 + 75 297 - IPR002328
Alcohol dehydrogenase, zinc-type, conserved site - 40 - 42 + IPR000330
SNF2, N-terminal + 40 + 82 298 - IPR009009
RlpA-like protein, double-psi beta-barrel domain - 40 - 41 + IPR025846
PMR5 N-terminal domain + 40 + 82 299 - IPR006553
Leucine-rich repeat, cysteine-containing subtype - 40 - 309 + IPR016169
CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2 + 40 + 41 300 - IPR006652
Kelch repeat type 1 - 40 - 152 + IPR009060
UBA-like superfamily + 40 + 92 301 - IPR025846
PMR5 N-terminal domain - 40 - 41 + IPR002328
Alcohol dehydrogenase, zinc-type, conserved site + 40 + 42 302 - IPR036465
  - 40 - 126 + IPR009009
RlpA-like protein, double-psi beta-barrel domain + 40 + 82 303 - IPR000757
  + IPR000757
Glycoside hydrolase family 16 40 - 234 + 156 @@ -2144,1373 +2144,1373 @@ 305 - IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup - 39 - 40 + IPR036465
von Willebrand factor A-like domain superfamily + 39 + 39 306 - IPR002495
Glycosyl transferase, family 8 - 39 - 40 + IPR015916
Galactose oxidase, beta-propeller + 39 + 43 307 - IPR038718
  - 39 - 100 + IPR021820
S-locus receptor kinase, C-terminal + 39 + 78 308 - IPR033389
AUX/IAA domain - 38 - 43 + IPR003311
AUX/IAA protein + 39 + 175 309 - IPR001360
Glycoside hydrolase family 1 - 38 - 230 + IPR000222
Protein phosphatase 2C, manganese/magnesium aspartate binding site + 38 + 38 310 - IPR004263
Exostosin-like - 38 - 39 + IPR002495
Glycosyl transferase, family 8 + 38 + 78 311 - IPR000222
PPM-type phosphatase, divalent cation binding - 38 - 38 + IPR014721
Ribosomal protein S5 domain 2-type fold, subgroup + 38 + 40 312 - IPR018202
Serine carboxypeptidase, serine active site - 38 - 40 + IPR001360
Glycoside hydrolase family 1 + 38 + 458 313 - IPR017877
  - 38 - 90 + IPR039391
Phytocyanin + 38 + 41 314 - IPR004853
Sugar phosphate transporter domain - 37 - 37 + IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup + 38 + 78 315 - IPR010920
LSM domain superfamily - 37 - 37 + IPR004853
Sugar phosphate transporter domain + 37 + 74 316 - IPR005299
SAM dependent carboxyl methyltransferase - 37 - 83 + IPR010920
LSM domain superfamily + 37 + 74 317 - IPR011016
  - 37 - 255 + IPR005299
SAM dependent carboxyl methyltransferase + 37 + 162 318 - IPR023271
  - 37 - 146 + IPR006671
Cyclin, N-terminal + 37 + 116 319 - IPR034294
Aquaporin transporter - 37 - 37 + IPR023271
Aquaporin-like + 37 + 146 320 - IPR016166
  + IPR016166
FAD-binding domain, PCMH-type 37 - 114 + 76 321 - IPR000425
Major intrinsic protein - 37 - 260 + IPR006652
Kelch repeat type 1 + 37 + 136 322 - IPR002067
Mitochondrial carrier protein - 37 - 179 + IPR000425
Major intrinsic protein + 37 + 520 323 - IPR006671
Cyclin, N-terminal - 37 - 58 + IPR002067
Mitochondrial carrier protein + 37 + 358 324 - IPR032846
Protein accelerated cell death 6 - 37 - 42 + IPR011012
Longin-like domain superfamily + 36 + 72 325 - IPR008974
  - 37 - 267 + IPR004330
FAR1 DNA binding domain + 36 + 74 326 - IPR008942
  - 36 - 136 + IPR015797
NUDIX hydrolase-like domain superfamily + 36 + 144 327 - IPR011012
Longin-like domain superfamily - 36 - 36 + IPR044822
Myb/SANT-like DNA-binding domain 4 + 36 + 42 328 - IPR006094
FAD linked oxidase, N-terminal - 36 - 38 + IPR010713
Xyloglucan endo-transglycosylase, C-terminal + 36 + 74 329 - IPR010713
Xyloglucan endo-transglycosylase, C-terminal - 36 - 37 + IPR012967
Plant methyltransferase dimerisation + 36 + 76 330 - IPR004330
FAR1 DNA binding domain - 36 - 37 + IPR011701
Major facilitator superfamily + 35 + 70 331 - IPR012967
Plant methyltransferase dimerisation - 36 - 38 + IPR018316
Tubulin/FtsZ, 2-layer sandwich domain + 35 + 126 332 - IPR006626
Parallel beta-helix repeat - 35 - 167 + IPR013783
Immunoglobulin-like fold + 35 + 41 333 - IPR000217
Tubulin - 35 - 204 + IPR004014
Cation-transporting P-type ATPase, N-terminal + 35 + 76 334 - IPR011701
Major facilitator superfamily - 35 - 35 + IPR006094
FAD linked oxidase, N-terminal + 35 + 72 335 - IPR012946
X8 domain - 35 - 70 + IPR000217
Tubulin + 35 + 408 336 - IPR003594
Histidine kinase/HSP90-like ATPase - 35 - 82 + IPR012946
X8 domain + 35 + 70 337 - IPR004014
Cation-transporting P-type ATPase, N-terminal - 35 - 71 + IPR013216
Methyltransferase type 11 + 34 + 70 338 - IPR004088
K Homology domain, type 1 - 35 - 76 + IPR016455
Xyloglucan endotransglucosylase/hydrolase + 34 + 122 339 - IPR001849
  - 35 - 134 + IPR008280
Tubulin/FtsZ, C-terminal + 34 + 68 340 - IPR002109
  - 35 - 210 + IPR007125
Histone H2A/H2B/H3 + 34 + 68 341 - IPR004141
Strictosidine synthase - 34 - 38 + IPR017970
Homeobox, conserved site + 34 + 34 342 - IPR013216
Methyltransferase type 11 - 34 - 35 + IPR020845
AMP-binding, conserved site + 34 + 34 343 - IPR008280
Tubulin/FtsZ, C-terminal - 34 - 34 + IPR000916
Bet v I/Major latex protein + 34 + 70 344 - IPR033124
Serine carboxypeptidases, histidine active site - 34 - 35 + IPR036865
CRAL-TRIO lipid binding domain superfamily + 33 + 33 345 - IPR017970
Homeobox, conserved site - 34 - 34 + IPR034294
Aquaporin transporter + 33 + 33 346 - IPR020845
AMP-binding, conserved site - 34 - 34 + IPR004265
Dirigent protein + 33 + 66 347 - IPR019378
GDP-fucose protein O-fucosyltransferase - 34 - 35 + IPR003690
Transcription termination factor, mitochondrial/chloroplastic + 33 + 220 348 - IPR000916
Bet v I/Major latex protein - 34 - 60 + IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase + 33 + 66 349 - IPR004087
K Homology domain - 34 - 76 + IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase + 33 + 66 350 - IPR002487
  - 34 - 201 + IPR019378
GDP-fucose protein O-fucosyltransferase + 33 + 68 351 - IPR006016
UspA - 33 - 34 + IPR002487
Transcription factor, K-box + 33 + 132 352 - IPR001251
  + IPR001251
CRAL-TRIO lipid binding domain 33 - 250 + 258 353 - IPR036691
  + IPR036691
Endonuclease/exonuclease/phosphatase superfamily 33 - 178 + 36 354 - IPR020471
Aldo/keto reductase - 33 - 159 + IPR020946
Flavin monooxygenase-like + 33 + 90 355 - IPR036865
  - 33 - 132 + IPR001849
Pleckstrin homology domain + 33 + 88 356 - IPR038770
  - 33 - 66 + IPR016161
Aldehyde/histidinol dehydrogenase + 33 + 68 357 - IPR004265
Dirigent protein - 33 - 33 + IPR012341
Six-hairpin glycosidase + 33 + 34 358 - IPR003690
Transcription termination factor, mitochondrial/chloroplastic - 33 - 307 + IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily + 32 + 68 359 - IPR038538
  - 33 - 100 + IPR002109
Glutaredoxin + 32 + 68 360 - IPR007125
Histone H2A/H2B/H3 - 33 - 33 + IPR008942
ENTH/VHS + 32 + 128 361 - IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase - 33 - 33 + IPR006016
UspA + 32 + 66 362 - IPR001320
Ionotropic glutamate receptor - 33 + IPR001296
Glycosyl transferase, family 1 + 32 64 363 - IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase - 33 - 38 + IPR016159
Cullin repeat-like-containing domain superfamily + 32 + 66 364 - IPR020946
Flavin monooxygenase-like - 33 - 45 + IPR028889
Ubiquitin carboxyl-terminal hydrolase-like domain + 32 + 32 365 - IPR016161
Aldehyde/histidinol dehydrogenase - 33 - 34 + IPR039361
Cyclin + 32 + 32 366 - IPR014721
  - 33 - 82 + IPR000727
Target SNARE coiled-coil homology domain + 31 + 104 367 - IPR015797
NUDIX hydrolase-like domain superfamily - 33 - 34 + IPR044661
Mediator of RNA polymerase II transcription subunit 15a/b/c-like + 31 + 36 368 - IPR036525
  - 32 - 128 + IPR001969
Peptidase aspartic, active site + 31 + 44 369 - IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily - 32 - 49 + IPR003008
Tubulin/FtsZ, GTPase domain + 31 + 112 370 - IPR037103
  - 32 - 64 + IPR015655
Protein phosphatase 2C + 31 + 33 371 - IPR016159
Cullin repeat-like-containing domain superfamily - 32 - 47 + IPR018502
Annexin repeat + 31 + 428 372 - IPR013780
  - 32 - 74 + IPR036525
Tubulin/FtsZ, GTPase domain superfamily + 31 + 31 373 - IPR028889
  - 32 - 64 + IPR029021
Protein-tyrosine phosphatase-like + 31 + 71 374 - IPR013126
Heat shock protein 70 family - 32 - 214 + IPR013581
Plant PDR ABC transporter associated + 31 + 62 375 - IPR000727
  - 31 - 164 + IPR037104
Annexin superfamily + 31 + 31 376 - IPR029021
  - 31 - 140 + IPR013126
Heat shock protein 70 family + 31 + 114 377 - IPR013581
Plant PDR ABC transporter associated - 31 + IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 + 31 31 378 - IPR001296
Glycosyl transferase, family 1 - 31 - 31 + IPR043502
DNA/RNA polymerase superfamily + 30 + 30 379 - IPR001969
Aspartic peptidase, active site - 31 - 41 + IPR036749
Expansin, cellulose-binding-like domain superfamily + 30 + 30 380 - IPR016455
Xyloglucan endotransglucosylase/hydrolase - 31 - 34 + IPR001320
Ionotropic glutamate receptor + 30 + 64 381 - IPR037104
  - 31 - 231 + IPR015947
PUA-like superfamily + 30 + 78 382 - IPR018502
Annexin repeat - 31 - 146 + IPR018119
Strictosidine synthase, conserved region + 30 + 64 383 - IPR000644
  - 31 - 332 + IPR025110
AMP-binding enzyme, C-terminal domain + 30 + 60 384 - IPR034003
ATP-binding cassette transporter, PDR-like subfamily G, domain 2 - 31 - 31 + IPR032710
NTF2-like domain superfamily + 30 + 30 385 - IPR025110
AMP-binding enzyme, C-terminal domain - 30 - 30 + IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain + 30 + 330 386 - IPR032710
NTF2-like domain superfamily - 30 - 31 + IPR029000
Cyclophilin-like domain + 30 + 60 387 - IPR002130
  - 30 - 495 + IPR005135
Endonuclease/exonuclease/phosphatase + 30 + 136 388 - IPR029000
  - 30 - 126 + IPR011013
Galactose mutarotase-like domain superfamily + 30 + 60 389 - IPR000315
  - 30 - 459 + IPR023313
Ubiquitin-conjugating enzyme, active site + 30 + 30 390 - IPR018316
Tubulin/FtsZ, 2-layer sandwich domain - 30 - 48 + IPR029481
ABC-transporter extracellular N-terminal domain + 30 + 30 391 - IPR036749
  - 30 - 120 + IPR007527
Zinc finger, SWIM-type + 30 + 114 392 - IPR017392
AP2/ERF transcription factor ERF/PTI6 - 30 - 34 + IPR007117
Expansin, cellulose-binding-like domain + 30 + 180 393 - IPR011013
Galactose mutarotase-like domain superfamily - 30 - 32 + IPR001638
Solute-binding protein family 3/N-terminal domain of MltF + 30 + 64 394 - IPR023313
Ubiquitin-conjugating enzyme, active site - 30 - 30 + IPR001223
Glycoside hydrolase family 18, catalytic domain + 30 + 126 395 - IPR016167
  - 30 - 126 + IPR002641
Patatin-like phospholipase domain + 30 + 122 396 - IPR029481
ABC-transporter N-terminal domain - 30 - 30 + IPR006073
GTP binding domain + 30 + 166 397 - IPR007527
  - 30 - 171 + IPR007493
Protein of unknown function DUF538 + 29 + 257 398 - IPR007117
  - 30 - 120 + IPR000315
B-box-type zinc finger + 29 + 150 399 - IPR001638
Solute-binding protein family 3/N-terminal domain of MltF - 30 - 33 + IPR006068
Cation-transporting P-type ATPase, C-terminal + 29 + 62 400 - IPR002641
  - 30 - 183 + IPR001938
Thaumatin family + 29 + 564 401 - IPR016162
  - 30 - 171 + IPR028082
Periplasmic binding protein-like I + 29 + 34 402 - IPR006073
GTP binding domain - 30 - 83 + IPR000086
NUDIX hydrolase domain + 29 + 116 403 - IPR015947
PUA-like superfamily - 30 - 36 + IPR016162
Aldehyde dehydrogenase, N-terminal + 29 + 37 404 - IPR018119
Strictosidine synthase, conserved region - 30 - 32 + IPR037176
Osmotin/thaumatin-like superfamily + 29 + 29 405 IPR006153
Cation/H+ exchanger 29 - 29 + 58 406 IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase 29 - 53 + 106 407 IPR007118
Expansin/Lol pI 29 - 166 + 332 408 - IPR013128
Peptidase C1A - 29 - 30 + IPR008991
Translation protein SH3-like domain superfamily + 29 + 60 409 - IPR008991
Translation protein SH3-like domain superfamily - 29 - 30 + IPR004182
GRAM domain + 29 + 58 410 - IPR006068
Cation-transporting P-type ATPase, C-terminal - 29 - 31 + IPR000668
Peptidase C1A, papain C-terminal + 29 + 200 411 - IPR004182
GRAM domain - 29 - 57 + IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II + 29 + 140 412 - IPR001938
  - 29 - 578 + IPR015590
Aldehyde dehydrogenase domain + 29 + 64 413 - IPR022742
Serine aminopeptidase, S33 - 29 - 29 + IPR010402
CCT domain + 28 + 112 414 - IPR036758
  - 29 - 114 + IPR018200
Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site + 28 + 44 415 - IPR025875
Leucine rich repeat 4 - 29 - 29 + IPR009078
Ferritin-like superfamily + 28 + 56 416 - IPR000668
Peptidase C1A, papain C-terminal - 29 - 125 + IPR018289
MULE transposase domain + 28 + 56 417 - IPR028082
Periplasmic binding protein-like I - 29 - 48 + IPR016167
FAD-binding, type 2, subdomain 1 + 28 + 29 418 - IPR024936
Cyclophilin-type peptidyl-prolyl cis-trans isomerase - 29 - 44 + IPR006689
Small GTPase superfamily, ARF/SAR type + 28 + 210 419 - IPR001223
Glycoside hydrolase family 18, catalytic domain - 29 - 31 + IPR021133
HEAT, type 2 + 28 + 128 420 - IPR009091
  - 29 - 184 + IPR020471
Aldo-keto reductase + 28 + 256 421 - IPR015590
Aldehyde dehydrogenase domain - 29 - 32 + IPR044848
PHR1-like + 28 + 31 422 - IPR037176
  - 29 - 118 + IPR034161
Pepsin-like domain, plant + 28 + 29 423 - IPR010402
  - 28 - 168 + IPR022742
Serine aminopeptidase, S33 + 28 + 56 424 - IPR006689
Small GTPase superfamily, ARF/SAR type - 28 - 105 + IPR001944
Glycoside hydrolase, family 35 + 28 + 400 425 - IPR021133
  - 28 - 128 + IPR000644
CBS domain + 28 + 178 426 - IPR007493
Protein of unknown function DUF538 - 28 - 56 + IPR003855
Potassium transporter + 28 + 144 427 - IPR018200
Ubiquitin specific protease, conserved site - 28 - 44 + IPR016163
Aldehyde dehydrogenase, C-terminal + 28 + 29 428 - IPR009078
Ferritin-like superfamily - 28 - 28 + IPR006702
Casparian strip membrane protein domain + 28 + 56 429 - IPR034161
Pepsin-like domain, plant - 28 - 29 + IPR013601
FAE1/Type III polyketide synthase-like protein + 27 + 54 430 - IPR018289
MULE transposase domain - 28 - 28 + IPR018490
Cyclic nucleotide-binding-like + 27 + 58 431 - IPR005746
Thioredoxin - 28 - 41 + IPR012675
Beta-grasp domain + 27 + 27 432 - IPR001944
Glycoside hydrolase, family 35 - 28 - 169 + IPR029056
Ribokinase-like + 27 + 55 433 - IPR000086
  - 28 - 171 + IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain + 27 + 27 434 - IPR003855
Potassium transporter - 28 - 74 + IPR004813
Oligopeptide transporter, OPT superfamily + 27 + 110 435 - IPR016163
  - 28 - 87 + IPR029069
HotDog domain + 27 + 77 436 - IPR006702
Casparian strip membrane protein domain - 28 + IPR033443
Pentacotripeptide-repeat region of PRORP + 27 28 437 - IPR016040
NAD(P)-binding domain - 27 - 29 + IPR001701
Glycoside hydrolase family 9 + 27 + 54 438 - IPR013601
FAE1/Type III polyketide synthase-like protein - 27 - 27 + IPR000595
Cyclic nucleotide-binding domain + 27 + 156 439 - IPR018490
Cyclic nucleotide-binding-like - 27 - 29 + IPR025660
Cysteine peptidase, histidine active site + 27 + 27 440 - IPR025659
  + IPR025659
Tubby-like, C-terminal 27 - 84 + 54 441 IPR001547
Glycoside hydrolase, family 5 27 - 27 + 54 442 IPR024709
Putative O-fucosyltransferase, plant 27 - 55 + 106 443 - IPR002659
Glycosyl transferase, family 31 - 27 - 49 + IPR000795
Translational (tr)-type GTP-binding domain + 27 + 326 444 - IPR000795
  - 27 - 489 + IPR027356
NPH3 domain + 27 + 106 445 - IPR027356
  - 27 - 106 + IPR002035
von Willebrand factor, type A + 27 + 98 446 - IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain - 27 - 27 + IPR001828
Receptor, ligand binding region + 27 + 64 447 - IPR000960
Flavin monooxygenase FMO - 27 - 94 + IPR037848
GEM-like protein + 27 + 27 448 - IPR014722
  - 27 - 62 + IPR014720
Double-stranded RNA-binding domain + 27 + 83 449 - IPR004813
Oligopeptide transporter, OPT superfamily - 27 - 55 + IPR032697
Squalene cyclase, N-terminal + 27 + 27 450 - IPR029069
HotDog domain superfamily - 27 - 38 + IPR043519
Nucleotidyltransferase superfamily + 27 + 27 451 - IPR036962
  - 27 - 81 + IPR036546
Mediator complex subunit 15, KIX domain + 27 + 28 452 - IPR001701
Glycoside hydrolase family 9 - 27 - 27 + IPR001764
Glycoside hydrolase, family 3, N-terminal + 27 + 252 453 - IPR001828
Receptor, ligand binding region - 27 - 32 + IPR044808
Ethylene-responsive transcription factor + 27 + 29 454 - IPR037848
GEM-like protein - 27 - 31 + IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal + 26 + 52 455 - IPR032697
Squalene cyclase, N-terminal - 27 - 27 + IPR002659
Glycosyl transferase, family 31 + 26 + 96 456 - IPR000595
  - 27 - 208 + IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain + 26 + 52 457 - IPR036546
Mediator complex subunit 15, KIX domain - 27 - 29 + IPR008263
Glycoside hydrolase, family 16, active site + 26 + 26 458 - IPR025660
Cysteine peptidase, histidine active site - 27 - 27 + IPR043454
NPH3/RPT2-like family + 26 + 26 459 - IPR001764
Glycoside hydrolase, family 3, N-terminal - 27 - 99 + IPR027409
GroEL-like apical domain + 26 + 51 460 - IPR017884
  - 26 + IPR005821
Ion transport domain + 26 54 461 - IPR025322
Protein of unknown function DUF4228, plant - 26 + IPR000169
Cysteine peptidase, cysteine active site + 26 26 462 - IPR012392
Very-long-chain 3-ketoacyl-CoA synthase - 26 - 50 + IPR011043
Galactose oxidase/kelch, beta-propeller + 26 + 52 463 - IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal - 26 - 26 + IPR012392
Very-long-chain 3-ketoacyl-CoA synthase + 26 + 98 464 - IPR006564
Zinc finger, PMZ-type - 26 - 26 + IPR004367
Cyclin, C-terminal domain + 26 + 52 465 - IPR005135
Endonuclease/exonuclease/phosphatase - 26 - 26 + IPR003406
Glycosyl transferase, family 14 + 26 + 54 466 - IPR029056
  - 26 - 112 + IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily + 26 + 58 467 - IPR004367
Cyclin, C-terminal domain - 26 - 49 + IPR029047
Heat shock protein 70kD, peptide-binding domain + 26 + 54 468 - IPR003406
Glycosyl transferase, family 14 - 26 - 26 + IPR006594
LIS1 homology motif + 25 + 64 469 - IPR008263
Glycoside hydrolase, family 16, active site - 26 - 26 + IPR015940
Ubiquitin-associated domain + 25 + 60 470 - IPR027409
  - 26 - 102 + IPR025753
AAA-type ATPase, N-terminal domain + 25 + 50 471 - IPR005821
Ion transport domain - 26 - 27 + IPR001594
Palmitoyltransferase, DHHC domain + 25 + 50 472 - IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily - 26 - 29 + IPR000408
Regulator of chromosome condensation, RCC1 + 25 + 822 473 - IPR000169
Cysteine peptidase, cysteine active site - 26 - 26 + IPR031052
FHY3/FAR1 family + 25 + 28 474 - IPR011043
Galactose oxidase/kelch, beta-propeller - 26 - 28 + IPR018120
Glycoside hydrolase, family 1, active site + 25 + 39 475 - IPR029047
  - 26 - 100 + IPR017937
Thioredoxin, conserved site + 25 + 29 476 - IPR017927
  - 25 - 75 + IPR036427
Bromodomain-like superfamily + 25 + 25 477 - IPR015940
  - 25 - 160 + IPR044440
Plant glutamate receptor, periplasmic ligand-binding domain + 25 + 27 478 - IPR025753
AAA-type ATPase, N-terminal domain - 25 - 25 + IPR006439
HAD hydrolase, subfamily IA + 25 + 128 479 - IPR001594
Palmitoyltransferase, DHHC domain - 25 - 25 + IPR032696
Squalene cyclase, C-terminal + 25 + 26 480 - IPR002423
Chaperonin Cpn60/TCP-1 family - 25 - 27 + IPR008948
L-Aspartase-like + 25 + 52 481 - IPR010989
SNARE - 25 - 28 + IPR017927
FAD-binding domain, ferredoxin reductase-type + 25 + 50 482 - IPR000408
  - 25 - 812 + IPR025322
Protein of unknown function DUF4228, plant + 25 + 50 483 - IPR036273
CRAL/TRIO, N-terminal domain superfamily - 25 - 29 + IPR002772
Glycoside hydrolase family 3 C-terminal domain + 25 + 177 484 - IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily - 25 - 40 + IPR002423
Chaperonin Cpn60/TCP-1 family + 25 + 118 485 - IPR000629
ATP-dependent RNA helicase DEAD-box, conserved site - 25 - 25 + IPR010989
SNARE + 25 + 50 486 - IPR036881
  - 25 - 153 + IPR036273
CRAL/TRIO, N-terminal domain superfamily + 25 + 25 487 - IPR002035
  - 25 - 96 + IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily + 25 + 120 488 - IPR017937
Thioredoxin, conserved site - 25 - 29 + IPR000629
RNA helicase, ATP-dependent, DEAD-box, conserved site + 25 + 25 489 - IPR003851
  + IPR003851
Zinc finger, Dof-type 25 - 300 + 200 490 - IPR036427
  - 25 - 150 + IPR001487
Bromodomain + 25 + 260 491 - IPR006439
HAD hydrolase, subfamily IA - 25 - 64 + IPR000782
FAS1 domain + 24 + 172 492 - IPR032696
Squalene cyclase, C-terminal - 25 - 26 + IPR044835
Auxin response factor + 24 + 27 493 - IPR008948
L-Aspartase-like - 25 - 26 + IPR000717
Proteasome component (PCI) domain + 24 + 82 494 - IPR006594
  - 24 - 150 + IPR001279
Metallo-beta-lactamase + 24 + 88 495 - IPR000782
  - 24 - 156 + IPR018170
Aldo/keto reductase, conserved site + 24 + 56 496 - IPR002772
Glycoside hydrolase family 3 C-terminal domain - 24 - 25 + IPR000639
Epoxide hydrolase-like + 24 + 224 497 - IPR036378
  - 24 - 118 + IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like + 24 + 25 498 - IPR000717
  - 24 - 116 + IPR022796
Chlorophyll A-B binding protein + 24 + 48 499 - IPR001163
LSM domain, eukaryotic/archaea-type - 24 - 46 + IPR014722
Ribosomal protein L2 domain 2 + 24 + 24 500 - IPR023753
FAD/NAD(P)-binding domain - 24 + IPR039417
Papain-like cysteine endopeptidase + 24 24 diff --git a/gramene/htdocs/ssi/species/stats_Zea_mays.html.grm b/gramene/htdocs/ssi/species/stats_Zea_mays.html.grm new file mode 100644 index 00000000..abeed339 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Zea_mays.html.grm @@ -0,0 +1,74 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Zm-B73-REFERENCE-GRAMENE-4.0
Database version:86.7
Base Pairs:2,104,350,183
Golden Path Length:2,135,083,061
Genebuild by: CSHL
Genebuild method: MAKER-P
Genebuild started: Dec 2015
Genebuild released: Mar 2016
Genebuild last updated/patched: Mar 2016
Genebuild version: Zm0001d.1
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,498
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:139,122
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
1307041717
2244442276
3235667834
4246994605
5223902240
6174033170
7182381542
8181122637
9159769782
10150982314
Pt140384
Mt569630
+
+
contig3132 sequences
+ +

Other

+ + + + + +
Short Variants (SNPs, indels, somatic mutations):50,114,708
diff --git a/gramene/htdocs/ssi/species/stats_Zea_maysb73.html b/gramene/htdocs/ssi/species/stats_Zea_maysb73.html new file mode 100644 index 00000000..4c0ac114 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Zea_maysb73.html @@ -0,0 +1,769 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:Zm-B73-REFERENCE-NAM-5.0,
Database version:87.1
Base Pairs:2,182,074,994
Golden Path Length:2,182,075,994
Genebuild method: Mikado
Genebuild started: blank 2019
Genebuild version: 2019-cshl
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		41,577
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:77,341
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
10 sequences
+
+ +
+ + + +
SequenceLength (bp)
1308452471
2243675191
3238017767
4250330460
5226353449
6181357234
7185808916
8182411202
9163004744
10152435371
+
+
scaffold
+
695 sequences
+
+ +
+ + + +
SequenceLength (bp)
scaf_1242938814
scaf_2238017767
scaf_3232638519
scaf_4200585289
scaf_5163004744
scaf_6160853524
scaf_7152435371
scaf_8137725724
scaf_9122593601
scaf_10112909852
scaf_11101235347
scaf_1257816695
scaf_1357105421
scaf_1441792357
scaf_1527467948
scaf_1625768060
scaf_1721557578
scaf_1817691841
scaf_1916971076
scaf_20736277
scaf_21712123
scaf_22570058
scaf_23435198
scaf_24387292
scaf_25264983
scaf_26254485
scaf_27247825
scaf_28239868
scaf_29217815
scaf_30207305
scaf_31203238
scaf_32197712
scaf_33196160
scaf_34190448
scaf_35190269
scaf_36187880
scaf_37173911
scaf_38173111
scaf_39172167
scaf_40171701
scaf_41171519
scaf_42169347
scaf_43168052
scaf_44164231
scaf_45164060
scaf_46160926
scaf_47160502
scaf_48159682
scaf_49153763
scaf_50153744
scaf_51152095
scaf_52151820
scaf_53148690
scaf_54144791
scaf_55144328
scaf_56142977
scaf_57142290
scaf_58141577
scaf_59138583
scaf_60137147
scaf_61134092
scaf_62133633
scaf_63132531
scaf_64130230
scaf_65129299
scaf_66128904
scaf_67128482
scaf_68127882
scaf_69127290
scaf_70126443
scaf_71125047
scaf_72124860
scaf_73123043
scaf_74120982
scaf_75120904
scaf_76120818
scaf_77120549
scaf_78120088
scaf_79119143
scaf_80118700
scaf_81118576
scaf_82118500
scaf_83117266
scaf_84117233
scaf_85115765
scaf_86115550
scaf_87114887
scaf_88114023
scaf_89113862
scaf_90113779
scaf_91113002
scaf_92112596
scaf_93112550
scaf_94111637
scaf_95110562
scaf_96110121
scaf_97109951
scaf_98109947
scaf_99109352
scaf_100109197
scaf_101109031
scaf_102108697
scaf_103108378
scaf_104108339
scaf_105107956
scaf_106107526
scaf_107107524
scaf_108106690
scaf_109106305
scaf_110106098
scaf_111105289
scaf_112105250
scaf_113105226
scaf_114105163
scaf_115104537
scaf_116104499
scaf_117103808
scaf_118103806
scaf_119103210
scaf_120102624
scaf_121102406
scaf_122102397
scaf_123102349
scaf_124101678
scaf_125101641
scaf_126100851
scaf_127100600
scaf_128100537
scaf_129100364
scaf_13099893
scaf_13199674
scaf_13298130
scaf_13397996
scaf_13497918
scaf_13596911
scaf_13696690
scaf_13796496
scaf_13896036
scaf_13995934
scaf_14095894
scaf_14195890
scaf_14295521
scaf_14395419
scaf_14495245
scaf_14595129
scaf_14694989
scaf_14794793
scaf_14894647
scaf_14994334
scaf_15094333
scaf_15194036
scaf_15293636
scaf_15393514
scaf_15493405
scaf_15593298
scaf_15693084
scaf_15793056
scaf_15892553
scaf_15991995
scaf_16091958
scaf_16191897
scaf_16291766
scaf_16391439
scaf_16491076
scaf_16591072
scaf_16691034
scaf_16790901
scaf_16890815
scaf_16990613
scaf_17090547
scaf_17189502
scaf_17289377
scaf_17389242
scaf_17489235
scaf_17589155
scaf_17688783
scaf_17788032
scaf_17887897
scaf_17987788
scaf_18087559
scaf_18187401
scaf_18287195
scaf_18386681
scaf_18486649
scaf_18586437
scaf_18686423
scaf_18786029
scaf_18885958
scaf_18985939
scaf_19085707
scaf_19185696
scaf_19285577
scaf_19385542
scaf_19485512
scaf_19584529
scaf_19684483
scaf_19784480
scaf_19884315
scaf_19984283
scaf_20084277
scaf_20183765
scaf_20283195
scaf_20383150
scaf_20483142
scaf_20583098
scaf_20682836
scaf_20782698
scaf_20882580
scaf_20982439
scaf_21082354
scaf_21182347
scaf_21282331
scaf_21381960
scaf_21481777
scaf_21581747
scaf_21681457
scaf_21781340
scaf_21881233
scaf_21980936
scaf_22080837
scaf_22180814
scaf_22280283
scaf_22379710
scaf_22479539
scaf_22579526
scaf_22679449
scaf_22779237
scaf_22878875
scaf_22978242
scaf_23078216
scaf_23178109
scaf_23277884
scaf_23377858
scaf_23477850
scaf_23577518
scaf_23677375
scaf_23777233
scaf_23877062
scaf_23977005
scaf_24076990
scaf_24176896
scaf_24276850
scaf_24376719
scaf_24476711
scaf_24576434
scaf_24676402
scaf_24776349
scaf_24876347
scaf_24976253
scaf_25076174
scaf_25176113
scaf_25276030
scaf_25375901
scaf_25475487
scaf_25575327
scaf_25675278
scaf_25775264
scaf_25875157
scaf_25974994
scaf_26074954
scaf_26174875
scaf_26274862
scaf_26374687
scaf_26474566
scaf_26574453
scaf_26673951
scaf_26773767
scaf_26873692
scaf_26973531
scaf_27073359
scaf_27173251
scaf_27273066
scaf_27373001
scaf_27472796
scaf_27572665
scaf_27672399
scaf_27772053
scaf_27871983
scaf_27971870
scaf_28071434
scaf_28171227
scaf_28271196
scaf_28371104
scaf_28470953
scaf_28570845
scaf_28670600
scaf_28770547
scaf_28870410
scaf_28970226
scaf_29070070
scaf_29169844
scaf_29269796
scaf_29369747
scaf_29469542
scaf_29569529
scaf_29669442
scaf_29769369
scaf_29869364
scaf_29969243
scaf_30069101
scaf_30169023
scaf_30268967
scaf_30368912
scaf_30468810
scaf_30568803
scaf_30668764
scaf_30768750
scaf_30868697
scaf_30968464
scaf_31068461
scaf_31168394
scaf_31268386
scaf_31368340
scaf_31468200
scaf_31568185
scaf_31668157
scaf_31768122
scaf_31867773
scaf_31967715
scaf_32067453
scaf_32167423
scaf_32267253
scaf_32367217
scaf_32467121
scaf_32567094
scaf_32666933
scaf_32766933
scaf_32866728
scaf_32966653
scaf_33066505
scaf_33166412
scaf_33266353
scaf_33366282
scaf_33466272
scaf_33566081
scaf_33666016
scaf_33765790
scaf_33865540
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+
diff --git a/gramene/htdocs/ssi/species/stats_Zea_maysb73_IPtop500.html b/gramene/htdocs/ssi/species/stats_Zea_maysb73_IPtop500.html new file mode 100644 index 00000000..cf5f2f35 --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Zea_maysb73_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		16033323
2IPR000719
Protein kinase domain		14785173
3IPR027417
P-loop containing nucleoside triphosphate hydrolase		14023278
4IPR001841
Zinc finger, RING-type		5651559
5IPR009057
Homeobox-like domain superfamily		5411083
6IPR002885
Pentatricopeptide repeat		54011404
7IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		5021557
8IPR016024
Armadillo-type fold		4821297
9IPR029058
Alpha/Beta hydrolase fold		447935
10IPR036291
NAD(P)-binding domain superfamily		435995
11IPR035979
RNA-binding domain superfamily		4071494
12IPR001005
SANT/Myb domain		3943160
13IPR001611
Leucine-rich repeat		3861552
14IPR000504
RNA recognition motif domain		3712949
15IPR011990
Tetratricopeptide-like helical domain superfamily		363940
16IPR017930
Myb domain		347814
17IPR036322
WD40-repeat-containing domain superfamily		339851
18IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		321805
19IPR036249
Thioredoxin-like superfamily		308631
20IPR036396
Cytochrome P450 superfamily		308469
21IPR036259
MFS transporter superfamily		303691
22IPR036047
F-box-like domain superfamily		301514
23IPR001128
Cytochrome P450		3011806
24IPR001680
WD40 repeat		2973695
25IPR017853
Glycoside hydrolase superfamily		266552
26IPR002401
Cytochrome P450, E-class, group I		2582252
27IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		256410
28IPR011992
EF-hand domain pair		254544
29IPR016177
DNA-binding domain superfamily		251448
30IPR001471
AP2/ERF domain		2321652
31IPR038765
Papain-like cysteine peptidase superfamily		232424
32IPR036638
Helix-loop-helix DNA-binding domain superfamily		229492
33IPR002048
EF-hand domain		2251764
34IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		224871
35IPR036457
PPM-type phosphatase domain superfamily		211398
36IPR012340
Nucleic acid-binding, OB-fold		208530
37IPR029044
Nucleotide-diphospho-sugar transferases		204411
38IPR036390
Winged helix DNA-binding domain superfamily		203422
39IPR001810
F-box domain		202510
40IPR036412
HAD-like superfamily		200503
41IPR001932
PPM-type phosphatase domain		194987
42IPR036236
Zinc finger C2H2 superfamily		185379
43IPR013087
Zinc finger C2H2-type		182514
44IPR003441
NAC domain		175566
45IPR036093
NAC domain superfamily		175282
46IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		171444
47IPR036188
FAD/NAD(P)-binding domain superfamily		168415
48IPR010255
Haem peroxidase superfamily		168249
49IPR002016
Haem peroxidase		1631420
50IPR036869
Chaperone J-domain superfamily		163305
51IPR001650
Helicase, C-terminal		161807
52IPR014001
Helicase superfamily 1/2, ATP-binding domain		159418
53IPR012337
Ribonuclease H-like superfamily		157286
54IPR011011
Zinc finger, FYVE/PHD-type		154435
55IPR015424
Pyridoxal phosphate-dependent transferase		154295
56IPR044974
Disease resistance protein, plants		150313
57IPR003959
ATPase, AAA-type, core		150362
58IPR000048
IQ motif, EF-hand binding site		1491003
59IPR001623
DnaJ domain		1481557
60IPR001356
Homeobox domain		143743
61IPR036770
Ankyrin repeat-containing domain superfamily		143316
62IPR003439
ABC transporter-like, ATP-binding domain		141747
63IPR009072
Histone-fold		140238
64IPR000823
Plant peroxidase		1401445
65IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		138202
66IPR021109
Aspartic peptidase domain superfamily		134200
67IPR011050
Pectin lyase fold/virulence factor		132214
68IPR043129
ATPase, nucleotide binding domain		131414
69IPR020846
Major facilitator superfamily domain		131287
70IPR044810
WRKY transcription factor, plant		130211
71IPR033121
Peptidase family A1 domain		129227
72IPR011333
SKP1/BTB/POZ domain superfamily		128256
73IPR002182
NB-ARC		127251
74IPR003657
WRKY domain		127442
75IPR002110
Ankyrin repeat		127832
76IPR004827
Basic-leucine zipper domain		127561
77IPR036576
WRKY domain superfamily		126224
78IPR033905
Secretory peroxidase		124156
79IPR036908
RlpA-like domain superfamily		118141
80IPR001461
Aspartic peptidase A1 family		118479
81IPR020472
G-protein beta WD-40 repeat		117813
82IPR035892
C2 domain superfamily		115352
83IPR001087
GDSL lipase/esterase		115212
84IPR029071
Ubiquitin-like domain superfamily		114265
85IPR011545
DEAD/DEAH box helicase domain		114292
86IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		111147
87IPR024752
Myb/SANT-like domain		110156
88IPR011051
RmlC-like cupin domain superfamily		109176
89IPR000270
PB1 domain		109315
90IPR036915
Cyclin-like superfamily		108316
91IPR019734
Tetratricopeptide repeat		107617
92IPR005123
Oxoglutarate/iron-dependent dioxygenase		105544
93IPR008972
Cupredoxin		104260
94IPR013766
Thioredoxin domain		104355
95IPR035669
GDSL lipase/esterase-like, plant		101155
96IPR000008
C2 domain		101719
97IPR015300
DNA-binding pseudobarrel domain superfamily		101277
98IPR001806
Small GTPase		99312
99IPR003480
Transferase		98137
100IPR032799
Xylanase inhibitor, C-terminal		97134
101IPR032861
Xylanase inhibitor, N-terminal		96135
102IPR007117
Expansin, cellulose-binding-like domain		95218
103IPR003340
B3 DNA binding domain		94779
104IPR005828
Major facilitator, sugar transporter-like		94245
105IPR036749
Expansin, cellulose-binding-like domain superfamily		93108
106IPR000571
Zinc finger, CCCH-type		93998
107IPR002347
Short-chain dehydrogenase/reductase SDR		921311
108IPR000073
Alpha/beta hydrolase fold-1		92400
109IPR020683
Ankyrin repeat-containing domain		92309
110IPR005202
Transcription factor GRAS		92335
111IPR029052
Metallo-dependent phosphatase-like		92198
112IPR041118
Rx, N-terminal		89154
113IPR036163
Heavy metal-associated domain superfamily		89222
114IPR013763
Cyclin-like		88249
115IPR007112
Expansin/pollen allergen, DPBB domain		88107
116IPR023395
Mitochondrial carrier domain superfamily		88200
117IPR003676
Small auxin-up RNA		8893
118IPR000210
BTB/POZ domain		87324
119IPR019787
Zinc finger, PHD-finger		87387
120IPR018108
Mitochondrial substrate/solute carrier		871015
121IPR020568
Ribosomal protein S5 domain 2-type fold		87208
122IPR016135
Ubiquitin-conjugating enzyme/RWD-like		86217
123IPR006121
Heavy metal-associated domain, HMA		85538
124IPR007118
Expansin/Lol pI		85553
125IPR002100
Transcription factor, MADS-box		85898
126IPR004045
Glutathione S-transferase, N-terminal		85301
127IPR036879
Transcription factor, MADS-box superfamily		85181
128IPR009009
RlpA-like protein, double-psi beta-barrel domain		84101
129IPR032867
DYW domain		84158
130IPR036282
Glutathione S-transferase, C-terminal domain superfamily		84157
131IPR001752
Kinesin motor domain		83969
132IPR000626
Ubiquitin-like domain		81333
133IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		81181
134IPR000109
Proton-dependent oligopeptide transporter family		78327
135IPR003613
U box domain		78267
136IPR023298
P-type ATPase, transmembrane domain superfamily		78156
137IPR000608
Ubiquitin-conjugating enzyme E2		76527
138IPR036890
Histidine kinase/HSP90-like ATPase superfamily		75149
139IPR026992
Non-haem dioxygenase N-terminal domain		75139
140IPR036426
Bulb-type lectin domain superfamily		75105
141IPR016181
Acyl-CoA N-acyltransferase		73141
142IPR029055
Nucleophile aminohydrolases, N-terminal		73143
143IPR013057
Amino acid transporter, transmembrane domain		73170
144IPR033389
AUX/IAA domain		72177
145IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		72101
146IPR016039
Thiolase-like		71208
147IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		71103
148IPR001480
Bulb-type lectin domain		71275
149IPR036612
K Homology domain, type 1 superfamily		70313
150IPR007125
Histone H2A/H2B/H3		70103
151IPR010987
Glutathione S-transferase, C-terminal-like		70116
152IPR006501
Pectinesterase inhibitor domain		7098
153IPR017884
SANT domain		69154
154IPR003609
PAN/Apple domain		69187
155IPR036865
CRAL-TRIO lipid binding domain superfamily		69174
156IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		6992
157IPR036875
Zinc finger, CCHC-type superfamily		69201
158IPR036852
Peptidase S8/S53 domain superfamily		68118
159IPR006671
Cyclin, N-terminal		68137
160IPR014756
Immunoglobulin E-set		68145
161IPR039361
Cyclin		68130
162IPR000743
Glycoside hydrolase, family 28		68110
163IPR026057
PC-Esterase		67127
164IPR029962
Trichome birefringence-like family		67129
165IPR001938
Thaumatin family		67479
166IPR008991
Translation protein SH3-like domain superfamily		6682
167IPR041569
AAA ATPase, AAA+ lid domain		66159
168IPR003663
Sugar/inositol transporter		66645
169IPR000225
Armadillo		66457
170IPR045051
Subtilisin-like protease		65125
171IPR025846
PMR5 N-terminal domain		65111
172IPR000209
Peptidase S8/S53 domain		65115
173IPR001251
CRAL-TRIO lipid binding domain		64484
174IPR000668
Peptidase C1A, papain C-terminal		64259
175IPR033896
MADS MEF2-like		63146
176IPR015915
Kelch-type beta propeller		63191
177IPR013094
Alpha/beta hydrolase fold-3		6383
178IPR008949
Isoprenoid synthase domain superfamily		62124
179IPR000858
S-locus glycoprotein domain		6288
180IPR008250
P-type ATPase, A domain superfamily		62124
181IPR008979
Galactose-binding-like domain superfamily		62189
182IPR036465
von Willebrand factor A-like domain superfamily		62133
183IPR002109
Glutaredoxin		6292
184IPR001878
Zinc finger, CCHC-type		62495
185IPR008978
HSP20-like chaperone		6197
186IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		61217
187IPR011701
Major facilitator superfamily		61132
188IPR016040
NAD(P)-binding domain		60118
189IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		60118
190IPR004263
Exostosin-like		60113
191IPR038005
Virus X resistance protein-like, coiled-coil domain		60102
192IPR003245
Phytocyanin domain		60134
193IPR011006
CheY-like superfamily		60112
194IPR001789
Signal transduction response regulator, receiver domain		60194
195IPR004853
Sugar phosphate transporter domain		59123
196IPR009000
Translation protein, beta-barrel domain superfamily		59150
197IPR039391
Phytocyanin		5966
198IPR004088
K Homology domain, type 1		59291
199IPR044965
Glycoside hydrolase family 17, plant		59119
200IPR000490
Glycoside hydrolase family 17		59109
201IPR004839
Aminotransferase, class I/classII		58118
202IPR029045
ClpP/crotonase-like domain superfamily		58139
203IPR002921
Fungal lipase-like domain		57108
204IPR008942
ENTH/VHS		57129
205IPR001563
Peptidase S10, serine carboxypeptidase		57702
206IPR009060
UBA-like superfamily		57163
207IPR014014
RNA helicase, DEAD-box type, Q motif		57140
208IPR001214
SET domain		57296
209IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5689
210IPR012946
X8 domain		56122
211IPR002528
Multi antimicrobial extrusion protein		56203
212IPR006045
Cupin 1		5689
213IPR015500
Peptidase S8, subtilisin-related		56277
214IPR036855
Zinc finger, CCCH-type superfamily		56384
215IPR008889
VQ		5664
216IPR037176
Osmotin/thaumatin-like superfamily		5677
217IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		56140
218IPR005795
Major pollen allergen Lol pI		55435
219IPR044808
Ethylene-responsive transcription factor		5573
220IPR000182
GNAT domain		54165
221IPR005174
Domain unknown function DUF295		5466
222IPR015655
Protein phosphatase 2C family		54128
223IPR039417
Papain-like cysteine endopeptidase		5469
224IPR016159
Cullin repeat-like-containing domain superfamily		54101
225IPR040911
Exostosin, GT47 domain		5498
226IPR002912
ACT domain		54272
227IPR041469
Subtilisin-like protease, fibronectin type-III domain		5386
228IPR025322
Protein of unknown function DUF4228, plant		5360
229IPR036640
ABC transporter type 1, transmembrane domain superfamily		53187
230IPR000873
AMP-dependent synthetase/ligase		53125
231IPR011527
ABC transporter type 1, transmembrane domain		53368
232IPR013126
Heat shock protein 70 family		53145
233IPR002487
Transcription factor, K-box		53287
234IPR011032
GroES-like superfamily		52158
235IPR010402
CCT domain		52202
236IPR013525
ABC-2 type transporter		52124
237IPR036273
CRAL/TRIO, N-terminal domain superfamily		52128
238IPR000620
EamA domain		52178
239IPR025659
Tubby-like, C-terminal		51100
240IPR004367
Cyclin, C-terminal domain		5181
241IPR002083
MATH/TRAF domain		51303
242IPR019378
GDP-fucose protein O-fucosyltransferase		51135
243IPR004000
Actin family		50525
244IPR000330
SNF2, N-terminal		50115
245IPR013216
Methyltransferase type 11		5090
246IPR003137
PA domain		5093
247IPR011012
Longin-like domain superfamily		50113
248IPR004883
Lateral organ boundaries, LOB		50137
249IPR006702
Casparian strip membrane protein domain		5066
250IPR036318
FAD-binding, type PCMH-like superfamily		4974
251IPR029000
Cyclophilin-like domain superfamily		49105
252IPR044822
Myb/SANT-like DNA-binding domain 4		49109
253IPR001509
NAD-dependent epimerase/dehydratase		49112
254IPR034197
Cucumisin-like catalytic domain		4984
255IPR003594
Histidine kinase/HSP90-like ATPase		4890
256IPR008928
Six-hairpin glycosidase superfamily		48112
257IPR001220
Legume lectin domain		48104
258IPR002067
Mitochondrial carrier protein		48490
259IPR030184
WAT1-related protein		48113
260IPR003311
AUX/IAA protein		48100
261IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		47551
262IPR036525
Tubulin/FtsZ, GTPase domain superfamily		4784
263IPR002068
Alpha crystallin/Hsp20 domain		47114
264IPR013201
Cathepsin propeptide inhibitor domain (I29)		4763
265IPR023271
Aquaporin-like		4778
266IPR002902
Gnk2-homologous domain		47294
267IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		4786
268IPR003165
Piwi domain		47177
269IPR003851
Zinc finger, Dof-type		47148
270IPR043519
Nucleotidyltransferase superfamily		47120
271IPR004041
NAF domain		4699
272IPR018451
NAF/FISL domain		4697
273IPR001296
Glycosyl transferase, family 1		46103
274IPR005333
Transcription factor, TCP		4688
275IPR016166
FAD-binding domain, PCMH-type		4666
276IPR025315
Domain of unknown function DUF4220		4674
277IPR006016
UspA		4577
278IPR000217
Tubulin		45522
279IPR010920
LSM domain superfamily		4570
280IPR002495
Glycosyl transferase, family 8		4591
281IPR000070
Pectinesterase, catalytic		4570
282IPR001929
Germin		44140
283IPR024709
Putative O-fucosyltransferase, plant		44119
284IPR038933
Ovate protein family		4448
285IPR002423
Chaperonin Cpn60/TCP-1 family		4481
286IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		4480
287IPR005150
Cellulose synthase		44100
288IPR000425
Major intrinsic protein		44482
289IPR006458
Ovate protein family, C-terminal		4490
290IPR000644
CBS domain		44329
291IPR015947
PUA-like superfamily		4494
292IPR008971
HSP40/DnaJ peptide-binding		43147
293IPR007493
Protein of unknown function DUF538		4398
294IPR002659
Glycosyl transferase, family 31		43129
295IPR001353
Proteasome, subunit alpha/beta		4384
296IPR022742
Serine aminopeptidase, S33		4393
297IPR006652
Kelch repeat type 1		43238
298IPR003406
Glycosyl transferase, family 14		4391
299IPR043454
NPH3/RPT2-like family		43107
300IPR043926
ABC transporter family G domain		4295
301IPR044835
Auxin response factor		42162
302IPR000717
Proteasome component (PCI) domain		42149
303IPR027356
NPH3 domain		42195
304IPR036758
At5g01610-like superfamily		4247
305IPR045087
Multicopper oxidase		4271
306IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4274
307IPR006073
GTP binding domain		42258
308IPR029021
Protein-tyrosine phosphatase-like		41116
309IPR039637
CCR4-NOT transcription complex subunit 7/8/Pop2		4149
310IPR034161
Pepsin-like domain, plant		4148
311IPR007658
Protein of unknown function DUF594		4154
312IPR034294
Aquaporin transporter		4174
313IPR018467
CO/COL/TOC1, conserved site		4159
314IPR004265
Dirigent protein		4161
315IPR045005
BTB/POZ and MATH domain-containing protein 1-6		4166
316IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		41105
317IPR029069
HotDog domain superfamily		41109
318IPR002939
Chaperone DnaJ, C-terminal		4176
319IPR028889
Ubiquitin specific protease domain		41105
320IPR010399
Tify domain		41131
321IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		41103
322IPR001117
Multicopper oxidase, type 1		4065
323IPR036691
Endonuclease/exonuclease/phosphatase superfamily		4093
324IPR001594
Palmitoyltransferase, DHHC domain		40110
325IPR002119
Histone H2A		40269
326IPR003653
Ulp1 protease family, C-terminal catalytic domain		40114
327IPR003008
Tubulin/FtsZ, GTPase domain		40113
328IPR040390
TIFY/JAZ family		4061
329IPR027409
GroEL-like apical domain superfamily		4076
330IPR001849
Pleckstrin homology domain		40159
331IPR011706
Multicopper oxidase, C-terminal		4065
332IPR011043
Galactose oxidase/kelch, beta-propeller		4079
333IPR011707
Multicopper oxidase, N-termianl		4062
334IPR044817
Squamosa promoter-binding-like protein		40105
335IPR002913
START domain		40186
336IPR037278
ARFGAP/RecO-like zinc finger		3974
337IPR029061
Thiamin diphosphate-binding fold		39108
338IPR005630
Terpene synthase, metal-binding domain		3965
339IPR000795
Translational (tr)-type GTP-binding domain		39653
340IPR007650
Zf-FLZ domain		3997
341IPR026961
PGG domain		39124
342IPR004252
Probable transposase, Ptta/En/Spm, plant		3955
343IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		3980
344IPR001164
Arf GTPase activating protein		39317
345IPR000727
Target SNARE coiled-coil homology domain		3892
346IPR013149
Alcohol dehydrogenase, C-terminal		3883
347IPR007657
Glycosyltransferase 61		38158
348IPR032454
Histone H2A, C-terminal domain		3849
349IPR043502
DNA/RNA polymerase superfamily		3859
350IPR008480
Protein of unknown function DUF761, plant		3849
351IPR029062
Class I glutamine amidotransferase-like		3895
352IPR001757
P-type ATPase		38222
353IPR006094
FAD linked oxidase, N-terminal		3851
354IPR015797
NUDIX hydrolase-like domain superfamily		3880
355IPR010525
Auxin response factor domain		38125
356IPR017938
Riboflavin synthase-like beta-barrel		3786
357IPR003106
Leucine zipper, homeobox-associated		3762
358IPR004140
Exocyst complex component Exo70		37106
359IPR010989
SNARE		3765
360IPR004813
Oligopeptide transporter, OPT superfamily		3766
361IPR023299
P-type ATPase, cytoplasmic domain N		3776
362IPR010658
Nodulin-like		3758
363IPR036812
NADP-dependent oxidoreductase domain superfamily		3779
364IPR000679
Zinc finger, GATA-type		37219
365IPR006153
Cation/H+ exchanger		3667
366IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3642
367IPR000315
B-box-type zinc finger		36153
368IPR017887
Transcription factor TCP subgroup		3698
369IPR005135
Endonuclease/exonuclease/phosphatase		3675
370IPR011013
Galactose mutarotase-like domain superfamily		3679
371IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		3672
372IPR001906
Terpene synthase, N-terminal domain		3663
373IPR003855
Potassium transporter		36194
374IPR002942
RNA-binding S4 domain		35112
375IPR036893
SBP domain superfamily		3584
376IPR044848
PHR1-like		3597
377IPR008280
Tubulin/FtsZ, C-terminal		3571
378IPR011074
CRAL/TRIO, N-terminal domain		35105
379IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		3592
380IPR002963
Expansin		35275
381IPR039421
Type 1 protein exporter		3570
382IPR044791
Beta-glucanase/XTH		3558
383IPR023210
NADP-dependent oxidoreductase domain		3579
384IPR005175
PPC domain		35237
385IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		35553
386IPR017927
FAD-binding domain, ferredoxin reductase-type		3474
387IPR015940
Ubiquitin-associated domain		34179
388IPR032710
NTF2-like domain superfamily		3475
389IPR036010
2Fe-2S ferredoxin-like superfamily		3447
390IPR027413
GroEL-like equatorial domain superfamily		3459
391IPR000408
Regulator of chromosome condensation, RCC1		341311
392IPR004333
SBP domain		34166
393IPR004014
Cation-transporting P-type ATPase, N-terminal		3453
394IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		3460
395IPR022796
Chlorophyll A-B binding protein		3449
396IPR002035
von Willebrand factor, type A		34123
397IPR004938
Xyloglucan fucosyltransferase		3477
398IPR016161
Aldehyde/histidinol dehydrogenase		3477
399IPR036427
Bromodomain-like superfamily		3493
400IPR000757
Glycoside hydrolase family 16		34104
401IPR027267
AH/BAR domain superfamily		3356
402IPR006689
Small GTPase superfamily, ARF/SAR type		33286
403IPR025110
AMP-binding enzyme, C-terminal domain		3357
404IPR018490
Cyclic nucleotide-binding-like		3393
405IPR000194
ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain		3348
406IPR004100
ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain		3348
407IPR001163
LSM domain, eukaryotic/archaea-type		3342
408IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3348
409IPR005467
Histidine kinase domain		3360
410IPR004046
Glutathione S-transferase, C-terminal		3358
411IPR000086
NUDIX hydrolase domain		33130
412IPR000595
Cyclic nucleotide-binding domain		33270
413IPR001487
Bromodomain		33421
414IPR036443
Zinc finger, RanBP2-type superfamily		33202
415IPR015590
Aldehyde dehydrogenase domain		3371
416IPR012438
Protein of unknown function DUF1639		3260
417IPR035952
Rhomboid-like superfamily		3270
418IPR001360
Glycoside hydrolase family 1		32434
419IPR013154
Alcohol dehydrogenase, N-terminal		3275
420IPR002498
Phosphatidylinositol-4-phosphate 5-kinase, core		32143
421IPR029057
Phosphoribosyltransferase-like		3261
422IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3245
423IPR029993
Plant galacturonosyltransferase GAUT		3272
424IPR016461
O-methyltransferase COMT-type		31103
425IPR013865
Protein FAM32A		3195
426IPR023753
FAD/NAD(P)-binding domain		3176
427IPR036121
ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily		3140
428IPR001344
Chlorophyll A-B binding protein, plant and chromista		3147
429IPR027725
Heat shock transcription factor family		3162
430IPR044675
E3 ubiquitin-protein ligase RING1-like		3132
431IPR036815
14-3-3 domain superfamily		3151
432IPR044839
Protein NDR1-like		3134
433IPR027923
Hydrophobic seed protein domain		3167
434IPR000876
Ribosomal protein S4e		3154
435IPR000232
Heat shock factor (HSF)-type, DNA-binding		31187
436IPR002937
Amine oxidase		3162
437IPR027410
TCP-1-like chaperonin intermediate domain superfamily		3154
438IPR006867
Domain of unknown function DUF632		3156
439IPR003100
PAZ domain		30152
440IPR036085
PAZ domain superfamily		3076
441IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3041
442IPR007612
LURP-one-related		3080
443IPR006068
Cation-transporting P-type ATPase, C-terminal		3043
444IPR011016
Zinc finger, RING-CH-type		30140
445IPR008422
Homeobox KN domain		3072
446IPR004161
Translation elongation factor EFTu-like, domain 2		3077
447IPR006941
Ribonuclease CAF1		3042
448IPR001199
Cytochrome b5-like heme/steroid binding domain		30223
449IPR003690
Transcription termination factor, mitochondrial/chloroplastic		30133
450IPR000742
EGF-like domain		3052
451IPR045035
Metal-nicotianamine transporter YSL-like		3056
452IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		3046
453IPR005821
Ion transport domain		3084
454IPR001876
Zinc finger, RanBP2-type		30315
455IPR036400
Cytochrome b5-like heme/steroid binding domain superfamily		3050
456IPR044759
RF2-like transcription factor, bZIP domain		3060
457IPR024788
Malectin-like domain		3062
458IPR000836
Phosphoribosyltransferase domain		3083
459IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		3096
460IPR008948
L-Aspartase-like		3048
461IPR004240
Nonaspanin (TM9SF)		29104
462IPR001433
Oxidoreductase FAD/NAD(P)-binding		2950
463IPR012678
Ribosomal protein L23/L15e core domain superfamily		2936
464IPR008984
SMAD/FHA domain superfamily		2974
465IPR022801
Ribosomal protein S4/S9		2937
466IPR018316
Tubulin/FtsZ, 2-layer sandwich domain		2956
467IPR018392
LysM domain		29108
468IPR004320
Protein of unknown function DUF241, plant		2930
469IPR025422
Transcription factor TGA like domain		29187
470IPR003337
Trehalose-phosphatase		2987
471IPR023410
14-3-3 domain		2954
472IPR001077
O-methyltransferase domain		2948
473IPR020946
Flavin monooxygenase-like		2970
474IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		2983
475IPR025486
Domain of unknown function DUF4378		2979
476IPR035966
Phosphofructokinase superfamily		2951
477IPR007145
Microtubule-associated protein, MAP65/Ase1/PRC1		2943
478IPR006594
LIS1 homology motif		28113
479IPR000308
14-3-3 protein		28256
480IPR024097
Basic helix-loop-helix leucine zipper transcription factor		2895
481IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		2839
482IPR036885
SWIB/MDM2 domain superfamily		2868
483IPR006694
Fatty acid hydroxylase		2859
484IPR002123
Phospholipid/glycerol acyltransferase		2864
485IPR007592
GLABROUS1 enhancer-binding protein family		28101
486IPR033443
Pentacotripeptide-repeat region of PRORP		2872
487IPR045055
DNA2/NAM7-like helicase		2853
488IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		2851
489IPR002641
Patatin-like phospholipase domain		2879
490IPR044788
Carbohydrate-binding X8 domain-containing protein, plant		2852
491IPR002171
Ribosomal protein L2		2829
492IPR029064
50S ribosomal protein L30e-like		2852
493IPR013601
FAE1/Type III polyketide synthase-like protein		2738
494IPR017946
PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily		2788
495IPR036378
FAS1 domain superfamily		2751
496IPR006195
Aminoacyl-tRNA synthetase, class II		2771
497IPR017066
E3 ubiquitin-protein ligase BOI-like		2745
498IPR036420
BRCT domain superfamily		2796
499IPR013845
Ribosomal protein S4e, central region		2736
500IPR004182
GRAM domain		2740
+
diff --git a/gramene/htdocs/ssi/species/stats_Zea_maysb73v4.html b/gramene/htdocs/ssi/species/stats_Zea_maysb73v4.html new file mode 100644 index 00000000..27ff5f8d --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Zea_maysb73v4.html @@ -0,0 +1,66 @@ + +

Summary

+ + + + + + + + + + + + + + + + + +
Assembly:AGPv4, Mar 2016
Database version:87.7
Base Pairs:2,104,350,183
Golden Path Length:2,135,083,061
Genebuild by: CSHL
Genebuild method: MAKER-P
Genebuild started: Dec 2016
Genebuild released: Dec 2015
Genebuild last updated/patched: Dec 2016
Genebuild version: CampbellMaker2016Dec
+

Gene counts

+ + + + + + + + + + +
Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:		39,498
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:136,473
+ + +

Coordinate Systems

+ + + + + + + + +
chromosome
+
12 sequences
+
+ +
+ + + +
SequenceLength (bp)
1307041717
2244442276
3235667834
4246994605
5223902240
6174033170
7182381542
8181122637
9159769782
10150982314
Pt140384
Mt569630
+
+
contig3132 sequences
diff --git a/gramene/htdocs/ssi/species/stats_Zea_maysb73v4_IPtop500.html b/gramene/htdocs/ssi/species/stats_Zea_maysb73v4_IPtop500.html new file mode 100644 index 00000000..29d9ee1a --- /dev/null +++ b/gramene/htdocs/ssi/species/stats_Zea_maysb73v4_IPtop500.html @@ -0,0 +1,3519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
No.InterPro nameNumber of genesNumber of Ensembl hits
1IPR011009
Protein kinase-like domain superfamily		16856403
2IPR027417
P-loop containing nucleoside triphosphate hydrolase		167510346
3IPR000719
Protein kinase domain		15139776
4IPR001841
Zinc finger, RING-type		5812206
5IPR009057
Homeobox-like domain superfamily		5541732
6IPR002885
Pentatricopeptide repeat		54511490
7IPR001245
Serine-threonine/tyrosine-protein kinase, catalytic domain		5433043
8IPR016024
Armadillo-type fold		5237462
9IPR029058
Alpha/Beta hydrolase fold		4911173
10IPR036291
NAD(P)-binding domain superfamily		4581296
11IPR035979
RNA-binding domain superfamily		4273011
12IPR038765
Papain-like cysteine peptidase superfamily		4211208
13IPR001611
Leucine-rich repeat		4042151
14IPR001005
SANT/Myb domain		4024751
15IPR000504
RNA recognition motif domain		3735651
16IPR011990
Tetratricopeptide-like helical domain superfamily		3721962
17IPR025476
Helitron helicase-like domain		349435
18IPR017930
Myb domain		349910
19IPR036322
WD40-repeat-containing domain superfamily		3462409
20IPR029063
S-adenosyl-L-methionine-dependent methyltransferase		3401311
21IPR036249
Thioredoxin-like superfamily		333858
22IPR036396
Cytochrome P450 superfamily		330465
23IPR012337
Ribonuclease H-like superfamily		318888
24IPR012340
Nucleic acid-binding, OB-fold		3181643
25IPR001128
Cytochrome P450		3181661
26IPR036259
MFS transporter superfamily		317738
27IPR036047
F-box-like domain superfamily		315520
28IPR010285
DNA helicase Pif1-like		298383
29IPR001680
WD40 repeat		2958424
30IPR017853
Glycoside hydrolase superfamily		2771056
31IPR013210
Leucine-rich repeat-containing N-terminal, plant-type		267555
32IPR002401
Cytochrome P450, E-class, group I		2592030
33IPR011992
EF-hand domain pair		2531050
34IPR016177
DNA-binding domain superfamily		245435
35IPR036638
Helix-loop-helix DNA-binding domain superfamily		232404
36IPR001471
AP2/ERF domain		2281398
37IPR002048
EF-hand domain		2262942
38IPR011598
Myc-type, basic helix-loop-helix (bHLH) domain		224714
39IPR036390
Winged helix DNA-binding domain superfamily		215833
40IPR036236
Zinc finger C2H2 superfamily		213475
41IPR036412
HAD-like superfamily		2051038
42IPR001810
F-box domain		204536
43IPR003653
Ulp1 protease family, C-terminal catalytic domain		203574
44IPR029044
Nucleotide-diphospho-sugar transferases		202894
45IPR007087
 		2021318
46IPR001932
PPM-type phosphatase domain		1931298
47IPR036457
PPM-type phosphatase domain superfamily		192493
48IPR010255
Haem peroxidase superfamily		176288
49IPR036188
FAD/NAD(P)-binding domain superfamily		175614
50IPR014001
Helicase superfamily 1/2, ATP-binding domain		1731619
51IPR043502
DNA/RNA polymerase superfamily		171419
52IPR001650
Helicase, C-terminal		1683038
53IPR002016
Haem peroxidase		1681550
54IPR003441
NAC domain		1671093
55IPR036691
Endonuclease/exonuclease/phosphatase superfamily		167373
56IPR002213
UDP-glucuronosyl/UDP-glucosyltransferase		166389
57IPR011011
Zinc finger, FYVE/PHD-type		1641598
58IPR015424
Pyridoxal phosphate-dependent transferase		163431
59IPR036869
Chaperone J-domain superfamily		157448
60IPR003959
ATPase, AAA-type, core		1531175
61IPR020846
Major facilitator superfamily domain		150343
62IPR044974
Disease resistance protein, plants		148623
63IPR003439
ABC transporter-like, ATP-binding domain		1472348
64IPR001623
DnaJ domain		1461965
65IPR036770
Ankyrin repeat-containing domain superfamily		144726
66IPR001356
Homeobox domain		1431526
67IPR000823
Plant peroxidase		1431439
68IPR013320
Concanavalin A-like lectin/glucanase domain superfamily		141297
69IPR009072
Histone-fold		140221
70IPR021109
Aspartic peptidase domain superfamily		138344
71IPR044810
WRKY transcription factor, plant		137189
72IPR033905
Secretory peroxidase		134164
73IPR033121
Peptidase family A1 domain		132397
74IPR004827
Basic-leucine zipper domain		132570
75IPR002110
Ankyrin repeat		1311361
76IPR003657
WRKY domain		130831
77IPR020472
G-protein beta WD-40 repeat		1281666
78IPR000477
Reverse transcriptase domain		128327
79IPR002182
NB-ARC		127507
80IPR011333
SKP1/BTB/POZ domain superfamily		126366
81IPR011545
DEAD/DEAH box helicase domain		126727
82IPR001461
Aspartic peptidase A1 family		124693
83IPR011050
Pectin lyase fold/virulence factor		123414
84IPR043129
ATPase, nucleotide binding domain		123788
85IPR035892
C2 domain superfamily		120539
86IPR001087
GDSL lipase/esterase		119176
87IPR036908
RlpA-like domain superfamily		118179
88IPR005123
Oxoglutarate/iron-dependent dioxygenase		117545
89IPR019734
Tetratricopeptide repeat		1141558
90IPR036312
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily		114140
91IPR000270
PB1 domain		114558
92IPR013766
Thioredoxin domain		113466
93IPR029071
Ubiquitin-like domain superfamily		110403
94IPR003480
Transferase		110127
95IPR008972
Cupredoxin		109326
96IPR005828
Major facilitator, sugar transporter-like		109319
97IPR007117
Expansin, cellulose-binding-like domain		108336
98IPR036915
Cyclin-like superfamily		108655
99IPR000008
C2 domain		1061154
100IPR008906
HAT, C-terminal dimerisation domain		106213
101IPR036749
Expansin, cellulose-binding-like domain superfamily		106169
102IPR011051
RmlC-like cupin domain superfamily		105231
103IPR035669
GDSL lipase/esterase-like, plant		103131
104IPR015300
DNA-binding pseudobarrel domain superfamily		103442
105IPR041118
Rx, N-terminal		102359
106IPR003340
B3 DNA binding domain		1011249
107IPR032799
Xylanase inhibitor, C-terminal		100146
108IPR029052
Metallo-dependent phosphatase-like		100348
109IPR007112
Expansin/pollen allergen, DPBB domain		99147
110IPR032861
Xylanase inhibitor, N-terminal		99148
111IPR000048
IQ motif, EF-hand binding site		993020
112IPR001806
Small GTPase		98673
113IPR007118
Expansin/Lol pI		96748
114IPR020683
Ankyrin repeat-containing domain		96514
115IPR009009
RlpA-like protein, double-psi beta-barrel domain		95133
116IPR019787
Zinc finger, PHD-finger		951280
117IPR000073
Alpha/beta hydrolase fold-1		93464
118IPR000571
Zinc finger, CCCH-type		931974
119IPR005202
Transcription factor GRAS		92308
120IPR002347
Short-chain dehydrogenase/reductase SDR		911289
121IPR013763
Cyclin-like		91378
122IPR023395
Mitochondrial carrier domain superfamily		91234
123IPR001752
Kinesin motor domain		914177
124IPR003676
Small auxin-up RNA		9198
125IPR016135
Ubiquitin-conjugating enzyme/RWD-like		90377
126IPR018108
Mitochondrial substrate/solute carrier		891066
127IPR036163
Heavy metal-associated domain superfamily		88216
128IPR032867
DYW domain		88142
129IPR024752
Myb/SANT-like domain		88141
130IPR000210
BTB/POZ domain		87430
131IPR004045
Glutathione S-transferase, N-terminal		87364
132IPR029055
Nucleophile aminohydrolases, N-terminal		86390
133IPR004843
Calcineurin-like phosphoesterase domain, ApaH type		85286
134IPR000109
Proton-dependent oligopeptide transporter family		85260
135IPR020568
Ribosomal protein S5 domain 2-type fold		85374
136IPR003613
U box domain		85343
137IPR026992
Non-haem dioxygenase N-terminal domain		83109
138IPR016181
Acyl-CoA N-acyltransferase		82308
139IPR006121
Heavy metal-associated domain, HMA		82540
140IPR000608
Ubiquitin-conjugating enzyme E2		82893
141IPR036426
Bulb-type lectin domain superfamily		82110
142IPR036282
Glutathione S-transferase, C-terminal domain superfamily		81161
143IPR023298
P-type ATPase, transmembrane domain superfamily		81542
144IPR016039
Thiolase-like		80290
145IPR002100
Transcription factor, MADS-box		80852
146IPR036879
Transcription factor, MADS-box superfamily		80172
147IPR004864
Late embryogenesis abundant protein, LEA_2 subgroup		7998
148IPR016140
Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain		7993
149IPR007021
Domain of unknown function DUF659		79143
150IPR001480
Bulb-type lectin domain		78285
151IPR036890
Histidine kinase/HSP90-like ATPase superfamily		77411
152IPR013057
Amino acid transporter, transmembrane domain		76176
153IPR000225
Armadillo		761094
154IPR033389
AUX/IAA domain		75298
155IPR025287
Wall-associated receptor kinase, galacturonan-binding domain		74118
156IPR003609
PAN/Apple domain		74183
157IPR000626
Ubiquitin-like domain		73454
158IPR035513
Invertase/pectin methylesterase inhibitor domain superfamily		72112
159IPR006671
Cyclin, N-terminal		72163
160IPR015915
Kelch-type beta propeller		72230
161IPR041569
AAA ATPase, AAA+ lid domain		72513
162IPR008949
Isoprenoid synthase domain superfamily		71154
163IPR026057
PC-Esterase		71123
164IPR025846
PMR5 N-terminal domain		71104
165IPR036875
Zinc finger, CCHC-type superfamily		70265
166IPR029962
Trichome birefringence-like family		69120
167IPR036612
K Homology domain, type 1 superfamily		69606
168IPR036865
CRAL-TRIO lipid binding domain superfamily		69382
169IPR010987
Glutathione S-transferase, C-terminal-like		69117
170IPR000876
Ribosomal protein S4e		69139
171IPR017884
SANT domain		68280
172IPR038005
Virus X resistance protein-like, coiled-coil domain		68193
173IPR036852
Peptidase S8/S53 domain superfamily		68153
174IPR006501
Pectinesterase inhibitor domain		68101
175IPR014756
Immunoglobulin E-set		68479
176IPR013094
Alpha/beta hydrolase fold-3		6880
177IPR007125
Histone H2A/H2B/H3		6791
178IPR041982
Ribosomal protein S4, KOW domain		67122
179IPR039361
Cyclin		67139
180IPR008978
HSP20-like chaperone		66114
181IPR015500
Peptidase S8, subtilisin-related		66611
182IPR001878
Zinc finger, CCHC-type		66592
183IPR000858
S-locus glycoprotein domain		6587
184IPR004853
Sugar phosphate transporter domain		65204
185IPR011006
CheY-like superfamily		65247
186IPR003663
Sugar/inositol transporter		65603
187IPR036855
Zinc finger, CCCH-type superfamily		65681
188IPR001789
Signal transduction response regulator, receiver domain		65393
189IPR016040
NAD(P)-binding domain		64166
190IPR011701
Major facilitator superfamily		64149
191IPR003245
Phytocyanin domain		64130
192IPR008979
Galactose-binding-like domain superfamily		64551
193IPR008889
VQ		6464
194IPR002921
Fungal lipase-like domain		63108
195IPR001563
Peptidase S10, serine carboxypeptidase		63692
196IPR039391
Phytocyanin		6365
197IPR000668
Peptidase C1A, papain C-terminal		63278
198IPR016159
Cullin repeat-like-containing domain superfamily		63170
199IPR000209
Peptidase S8/S53 domain		63147
200IPR008942
ENTH/VHS		62218
201IPR001251
CRAL-TRIO lipid binding domain		62864
202IPR009060
UBA-like superfamily		62306
203IPR036465
von Willebrand factor A-like domain superfamily		62344
204IPR002109
Glutaredoxin		6289
205IPR008930
Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid		62268
206IPR036640
ABC transporter type 1, transmembrane domain superfamily		61578
207IPR001509
NAD-dependent epimerase/dehydratase		61116
208IPR011527
ABC transporter type 1, transmembrane domain		611133
209IPR011047
Quinoprotein alcohol dehydrogenase-like superfamily		60279
210IPR008250
P-type ATPase, A domain superfamily		59359
211IPR002528
Multi antimicrobial extrusion protein		59215
212IPR004088
K Homology domain, type 1		59561
213IPR010402
CCT domain		58284
214IPR000182
GNAT domain		58265
215IPR009000
Translation protein, beta-barrel domain superfamily		58319
216IPR012946
X8 domain		58112
217IPR011012
Longin-like domain superfamily		58199
218IPR029045
ClpP/crotonase-like domain superfamily		58634
219IPR044965
Glycoside hydrolase family 17, plant		58101
220IPR000490
Glycoside hydrolase family 17		5892
221IPR039266
Autonomous transposable element EN-1 mosaic protein		5893
222IPR033896
MADS MEF2-like		57138
223IPR010259
Peptidase S8 propeptide/proteinase inhibitor I9		5797
224IPR003656
Zinc finger, BED-type		57167
225IPR006045
Cupin 1		57130
226IPR001214
SET domain		57748
227IPR002487
Transcription factor, K-box		57252
228IPR044808
Ethylene-responsive transcription factor		5767
229IPR011032
GroES-like superfamily		56161
230IPR041469
Subtilisin-like protease, fibronectin type-III domain		55104
231IPR005795
Major pollen allergen Lol pI		55600
232IPR025322
Protein of unknown function DUF4228, plant		5557
233IPR036525
Tubulin/FtsZ, GTPase domain superfamily		55126
234IPR001296
Glycosyl transferase, family 1		55254
235IPR004263
Exostosin-like		55302
236IPR001938
Thaumatin family		55324
237IPR008928
Six-hairpin glycosidase superfamily		55197
238IPR015655
Protein phosphatase 2C family		55163
239IPR019378
GDP-fucose protein O-fucosyltransferase		55262
240IPR025398
Domain of unknown function DUF4371		5558
241IPR000743
Glycoside hydrolase, family 28		55228
242IPR004159
Putative S-adenosyl-L-methionine-dependent methyltransferase		54514
243IPR044822
Myb/SANT-like DNA-binding domain 4		5497
244IPR000873
AMP-dependent synthetase/ligase		54238
245IPR014014
RNA helicase, DEAD-box type, Q motif		54222
246IPR036273
CRAL/TRIO, N-terminal domain superfamily		54219
247IPR039261
Ferredoxin-NADP reductase (FNR), nucleotide-binding domain		54149
248IPR013955
Replication factor A, C-terminal		54171
249IPR004367
Cyclin, C-terminal domain		5389
250IPR002083
MATH/TRAF domain		53600
251IPR004839
Aminotransferase, class I/classII		53162
252IPR005174
Domain unknown function DUF295		5363
253IPR005824
KOW		53108
254IPR002068
Alpha crystallin/Hsp20 domain		52140
255IPR003137
PA domain		52116
256IPR002902
Gnk2-homologous domain		52252
257IPR023299
P-type ATPase, cytoplasmic domain N		52308
258IPR013126
Heat shock protein 70 family		51374
259IPR043519
Nucleotidyltransferase superfamily		51204
260IPR002912
ACT domain		51276
261IPR000620
EamA domain		51149
262IPR004000
Actin family		50916
263IPR013525
ABC-2 type transporter		50562
264IPR034197
Cucumisin-like catalytic domain		5089
265IPR003165
Piwi domain		50567
266IPR039417
Papain-like cysteine endopeptidase		5074
267IPR002067
Mitochondrial carrier protein		50463
268IPR031657
Replication protein A, OB domain		4994
269IPR025659
Tubby-like, C-terminal		4999
270IPR029000
Cyclophilin-like domain superfamily		49156
271IPR010920
LSM domain superfamily		49102
272IPR005333
Transcription factor, TCP		49442
273IPR023271
Aquaporin-like		49120
274IPR003594
Histidine kinase/HSP90-like ATPase		49272
275IPR005150
Cellulose synthase		49325
276IPR004883
Lateral organ boundaries, LOB		49112
277IPR003851
Zinc finger, Dof-type		49108
278IPR011043
Galactose oxidase/kelch, beta-propeller		4963
279IPR013845
Ribosomal protein S4e, central region		4891
280IPR003406
Glycosyl transferase, family 14		4892
281IPR000425
Major intrinsic protein		48644
282IPR029069
HotDog domain superfamily		48186
283IPR001220
Legume lectin domain		48100
284IPR025315
Domain of unknown function DUF4220		4876
285IPR004041
NAF domain		4788
286IPR002130
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain		47849
287IPR018451
NAF/FISL domain		4788
288IPR008991
Translation protein SH3-like domain superfamily		47115
289IPR000717
Proteasome component (PCI) domain		47362
290IPR000330
SNF2, N-terminal		47746
291IPR038933
Ovate protein family		4750
292IPR013216
Methyltransferase type 11		47101
293IPR001353
Proteasome, subunit alpha/beta		47161
294IPR001394
Peptidase C19, ubiquitin carboxyl-terminal hydrolase		47431
295IPR000644
CBS domain		47508
296IPR030184
WAT1-related protein		4793
297IPR009091
Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II		47251
298IPR037176
Osmotin/thaumatin-like superfamily		4751
299IPR001929
Germin		46161
300IPR044835
Auxin response factor		46372
301IPR017887
Transcription factor TCP subgroup		4647
302IPR005135
Endonuclease/exonuclease/phosphatase		46193
303IPR022742
Serine aminopeptidase, S33		4696
304IPR006652
Kelch repeat type 1		46234
305IPR002963
Expansin		46384
306IPR027409
GroEL-like apical domain superfamily		46187
307IPR028889
Ubiquitin specific protease domain		46423
308IPR000070
Pectinesterase, catalytic		46119
309IPR008971
HSP40/DnaJ peptide-binding		45200
310IPR034161
Pepsin-like domain, plant		4576
311IPR007658
Protein of unknown function DUF594		4562
312IPR043454
NPH3/RPT2-like family		45138
313IPR002495
Glycosyl transferase, family 8		45189
314IPR006458
Ovate protein family, C-terminal		4590
315IPR003311
AUX/IAA protein		4587
316IPR015947
PUA-like superfamily		45160
317IPR029021
Protein-tyrosine phosphatase-like		44199
318IPR007650
Zf-FLZ domain		4498
319IPR034294
Aquaporin transporter		44152
320IPR004265
Dirigent protein		4467
321IPR001849
Pleckstrin homology domain		44433
322IPR006702
Casparian strip membrane protein domain		4449
323IPR043926
ABC transporter family G domain		43436
324IPR036318
FAD-binding, type PCMH-like superfamily		43128
325IPR000217
Tubulin		43695
326IPR024709
Putative O-fucosyltransferase, plant		43231
327IPR013201
Cathepsin propeptide inhibitor domain (I29)		4368
328IPR040390
TIFY/JAZ family		4373
329IPR003855
Potassium transporter		43338
330IPR006073
GTP binding domain		43318
331IPR007493
Protein of unknown function DUF538		42276
332IPR016166
FAD-binding domain, PCMH-type		42120
333IPR001757
P-type ATPase		42846
334IPR045087
Multicopper oxidase		42123
335IPR002939
Chaperone DnaJ, C-terminal		42114
336IPR010658
Nodulin-like		4256
337IPR010399
Tify domain		42143
338IPR045069
Multidrug and toxic compound extrusion family, eukaryotic		4273
339IPR044817
Squamosa promoter-binding-like protein		42163
340IPR001117
Multicopper oxidase, type 1		4183
341IPR017938
Riboflavin synthase-like beta-barrel		41143
342IPR000315
B-box-type zinc finger		41184
343IPR027934
Cellulose synthase, RING-type zinc finger		41123
344IPR005630
Terpene synthase, metal-binding domain		41100
345IPR002423
Chaperonin Cpn60/TCP-1 family		41202
346IPR003008
Tubulin/FtsZ, GTPase domain		41155
347IPR011706
Multicopper oxidase, C-terminal		4193
348IPR000679
Zinc finger, GATA-type		41231
349IPR006016
UspA		40153
350IPR002659
Glycosyl transferase, family 31		40231
351IPR007657
Glycosyltransferase 61		40128
352IPR001594
Palmitoyltransferase, DHHC domain		40149
353IPR004140
Exocyst complex component Exo70		40102
354IPR027356
NPH3 domain		40260
355IPR029062
Class I glutamine amidotransferase-like		40148
356IPR016161
Aldehyde/histidinol dehydrogenase		40175
357IPR010525
Auxin response factor domain		40267
358IPR037278
ARFGAP/RecO-like zinc finger		39159
359IPR006153
Cation/H+ exchanger		39285
360IPR000795
Translational (tr)-type GTP-binding domain		391429
361IPR026961
PGG domain		39128
362IPR018467
CO/COL/TOC1, conserved site		3956
363IPR008480
Protein of unknown function DUF761, plant		3939
364IPR004938
Xyloglucan fucosyltransferase		3988
365IPR011707
Multicopper oxidase, N-termianl		3978
366IPR005175
PPC domain		39191
367IPR002913
START domain		39416
368IPR032710
NTF2-like domain superfamily		38109
369IPR029061
Thiamin diphosphate-binding fold		38251
370IPR045005
BTB/POZ and MATH domain-containing protein 1-6		3866
371IPR001906
Terpene synthase, N-terminal domain		38103
372IPR000727
Target SNARE coiled-coil homology domain		37119
373IPR000864
Proteinase inhibitor I13, potato inhibitor I		37104
374IPR036893
SBP domain superfamily		37102
375IPR043325
Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein		3750
376IPR044848
PHR1-like		3784
377IPR002119
Histone H2A		37203
378IPR011013
Galactose mutarotase-like domain superfamily		37202
379IPR004333
SBP domain		37204
380IPR015813
Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily		37244
381IPR036410
Heat shock protein DnaJ, cysteine-rich domain superfamily		37104
382IPR022796
Chlorophyll A-B binding protein		3745
383IPR001164
Arf GTPase activating protein		37691
384IPR036427
Bromodomain-like superfamily		37255
385IPR036354
Proteinase inhibitor I13, potato inhibitor I superfamily		3741
386IPR015797
NUDIX hydrolase-like domain superfamily		3787
387IPR001433
Oxidoreductase FAD/NAD(P)-binding		3673
388IPR003106
Leucine zipper, homeobox-associated		3642
389IPR001163
LSM domain, eukaryotic/archaea-type		3657
390IPR036010
2Fe-2S ferredoxin-like superfamily		3697
391IPR011074
CRAL/TRIO, N-terminal domain		36153
392IPR010989
SNARE		3679
393IPR044839
Protein NDR1-like		3637
394IPR039421
Type 1 protein exporter		36168
395IPR044791
Beta-glucanase/XTH		3657
396IPR001487
Bromodomain		361052
397IPR036812
NADP-dependent oxidoreductase domain superfamily		3696
398IPR000757
Glycoside hydrolase family 16		3697
399IPR015590
Aldehyde dehydrogenase domain		36158
400IPR015940
Ubiquitin-associated domain		35366
401IPR018490
Cyclic nucleotide-binding-like		35163
402IPR026960
Reverse transcriptase zinc-binding domain		3587
403IPR004252
Probable transposase, Ptta/En/Spm, plant		3567
404IPR004014
Cation-transporting P-type ATPase, N-terminal		35162
405IPR036866
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like		35126
406IPR016035
Acyl transferase/acyl hydrolase/lysophospholipase		3580
407IPR004813
Oligopeptide transporter, OPT superfamily		35104
408IPR006094
FAD linked oxidase, N-terminal		3556
409IPR010713
Xyloglucan endo-transglycosylase, C-terminal		3545
410IPR000595
Cyclic nucleotide-binding domain		35432
411IPR006186
Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase		35803
412IPR006867
Domain of unknown function DUF632		35110
413IPR006689
Small GTPase superfamily, ARF/SAR type		34360
414IPR024097
Basic helix-loop-helix leucine zipper transcription factor		34117
415IPR036378
FAS1 domain superfamily		3446
416IPR013149
Alcohol dehydrogenase, C-terminal		3492
417IPR045074
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant		3445
418IPR023753
FAD/NAD(P)-binding domain		34218
419IPR044174
Glycosyltransferase BC10-like		3477
420IPR005516
Remorin, C-terminal		3497
421IPR032454
Histone H2A, C-terminal domain		3440
422IPR014977
WRC domain		34158
423IPR025422
Transcription factor TGA like domain		34240
424IPR003958
Transcription factor CBF/NF-Y/archaeal histone domain		3465
425IPR002035
von Willebrand factor, type A		34163
426IPR008927
6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily		34155
427IPR035966
Phosphofructokinase superfamily		34125
428IPR002937
Amine oxidase		34128
429IPR008948
L-Aspartase-like		3473
430IPR017927
FAD-binding domain, ferredoxin reductase-type		33123
431IPR025110
AMP-binding enzyme, C-terminal domain		3382
432IPR012392
Very-long-chain 3-ketoacyl-CoA synthase		3337
433IPR001360
Glycoside hydrolase family 1		33844
434IPR001344
Chlorophyll A-B binding protein, plant and chromista		3341
435IPR013154
Alcohol dehydrogenase, N-terminal		3380
436IPR004264
Transposase, Tnp1/En/Spm-like		3350
437IPR036815
14-3-3 domain superfamily		3375
438IPR005821
Ion transport domain		33169
439IPR004046
Glutathione S-transferase, C-terminal		3370
440IPR044759
RF2-like transcription factor, bZIP domain		3357
441IPR027410
TCP-1-like chaperonin intermediate domain superfamily		33123
442IPR000095
CRIB domain		3373
443IPR036443
Zinc finger, RanBP2-type superfamily		33357
444IPR000782
FAS1 domain		3275
445IPR013601
FAE1/Type III polyketide synthase-like protein		3236
446IPR016461
O-methyltransferase COMT-type		3294
447IPR013747
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal		3244
448IPR003347
JmjC domain		32512
449IPR005467
Histidine kinase domain		32180
450IPR036885
SWIB/MDM2 domain superfamily		32160
451IPR027725
Heat shock transcription factor family		3261
452IPR008280
Tubulin/FtsZ, C-terminal		32102
453IPR004182
GRAM domain		3269
454IPR000408
Regulator of chromosome condensation, RCC1		322999
455IPR001077
O-methyltransferase domain		3244
456IPR029047
Heat shock protein 70kD, peptide-binding domain superfamily		32148
457IPR024788
Malectin-like domain		3266
458IPR002641
Patatin-like phospholipase domain		32146
459IPR023210
NADP-dependent oxidoreductase domain		3295
460IPR001041
2Fe-2S ferredoxin-type iron-sulfur binding domain		32194
461IPR044653
C2H2-type zinc-finger protein AZF1/2/3-like		3137
462IPR011016
Zinc finger, RING-CH-type		31193
463IPR003121
SWIB/MDM2 domain		31277
464IPR002498
Phosphatidylinositol-4-phosphate 5-kinase, core		31351
465IPR000742
EGF-like domain		3160
466IPR041679
DNA2/NAM7 helicase-like, C-terminal		31546
467IPR000232
Heat shock factor (HSF)-type, DNA-binding		31179
468IPR003100
PAZ domain		30921
469IPR036085
PAZ domain superfamily		30418
470IPR006195
Aminoacyl-tRNA synthetase, class II		30121
471IPR035952
Rhomboid-like superfamily		3084
472IPR008984
SMAD/FHA domain superfamily		30198
473IPR008422
Homeobox KN domain		3089
474IPR004161
Translation elongation factor EFTu-like, domain 2		30186
475IPR018392
LysM domain		30104
476IPR027413
GroEL-like equatorial domain superfamily		30118
477IPR003337
Trehalose-phosphatase		30175
478IPR036052
Tryptophan synthase beta subunit-like PLP-dependent enzyme		3077
479IPR036910
High mobility group box domain superfamily		3081
480IPR001876
Zinc finger, RanBP2-type		30422
481IPR011004
Trimeric LpxA-like superfamily		30121
482IPR029993
Plant galacturonosyltransferase GAUT		30162
483IPR001701
Glycoside hydrolase family 9		3057
484IPR029064
50S ribosomal protein L30e-like		3058
485IPR004294
Carotenoid oxygenase		2974
486IPR006594
LIS1 homology motif		29307
487IPR000308
14-3-3 protein		29373
488IPR012678
Ribosomal protein L23/L15e core domain superfamily		2967
489IPR007612
LURP-one-related		2978
490IPR005027
Glycosyl transferase, family 43		29277
491IPR006068
Cation-transporting P-type ATPase, C-terminal		29120
492IPR002293
Amino acid/polyamine transporter I		2964
493IPR006694
Fatty acid hydroxylase		2965
494IPR002123
Phospholipid/glycerol acyltransferase		2992
495IPR044675
E3 ubiquitin-protein ligase RING1-like		2930
496IPR003690
Transcription termination factor, mitochondrial/chloroplastic		29109
497IPR023410
14-3-3 domain		2973
498IPR029057
Phosphoribosyltransferase-like		29132
499IPR045035
Metal-nicotianamine transporter YSL-like		2986
500IPR020946
Flavin monooxygenase-like		2946
+
diff --git a/gramene/htdocs/taxon_tree_data.js b/gramene/htdocs/taxon_tree_data.js index 79ddb390..e11752f8 100644 --- a/gramene/htdocs/taxon_tree_data.js +++ b/gramene/htdocs/taxon_tree_data.js @@ -2,89 +2,23 @@ taxonTreeData = [ { "isFolder" : true, "children" : [ - { - "title" : "Beta vulgaris subsp. vulgaris", - "key" : "beta_vulgaris" - }, { "isFolder" : true, "children" : [ - { - "title" : "Arabidopsis lyrata subsp. lyrata", - "key" : "arabidopsis_lyrata" - }, { "title" : "Arabidopsis thaliana", - "key" : "arabidopsis_thaliana" - }, - { - "title" : "Brassica napus", - "key" : "brassica_napus" - }, - { - "title" : "Brassica oleracea var. oleracea", - "key" : "brassica_oleracea" - }, - { - "title" : "Brassica rapa subsp. pekinensis", - "key" : "brassica_rapa" + "key" : "Arabidopsis_thaliana" } ], - "title" : "Brassicaceae (5)", + "title" : "Brassicaceae (1)", "key" : "Brassicaceae" }, - { - "isFolder" : true, - "children" : [ - { - "title" : "Glycine max", - "key" : "glycine_max" - }, - { - "title" : "Medicago truncatula", - "key" : "medicago_truncatula" - }, - { - "title" : "Trifolium pratense", - "key" : "trifolium_pratense" - } - ], - "title" : "Fabaceae (3)", - "key" : "Fabaceae" - }, - { - "title" : "Populus trichocarpa", - "key" : "populus_trichocarpa" - }, - { - "title" : "Prunus persica", - "key" : "prunus_persica" - }, - { - "isFolder" : true, - "children" : [ - { - "title" : "Solanum lycopersicum", - "key" : "solanum_lycopersicum" - }, - { - "title" : "Solanum tuberosum", - "key" : "solanum_tuberosum" - } - ], - "title" : "Solanaceae (2)", - "key" : "Solanaceae" - }, - { - "title" : "Theobroma cacao", - "key" : "theobroma_cacao" - }, { "title" : "Vitis vinifera", - "key" : "vitis_vinifera" + "key" : "Vitis_vinifera" } ], - "title" : "Dicots (15)", + "title" : "Dicots (2)", "key" : "Dicots" }, { @@ -93,157 +27,174 @@ taxonTreeData = [ { "isFolder" : true, "children" : [ - { - "title" : "Brachypodium distachyon", - "key" : "brachypodium_distachyon" - }, { "title" : "Leersia perrieri", - "key" : "leersia_perrieri" + "key" : "Leersia_perrieri" }, { "isFolder" : true, "children" : [ { "title" : "Oryza barthii", - "key" : "oryza_barthii" + "key" : "Oryza_barthii" }, { "title" : "Oryza brachyantha", - "key" : "oryza_brachyantha" + "key" : "Oryza_brachyantha" }, { "title" : "Oryza glaberrima", - "key" : "oryza_glaberrima" + "key" : "Oryza_glaberrima" }, { "title" : "Oryza glumipatula", - "key" : "oryza_glumaepatula" - }, - { - "title" : "Oryza longistaminata", - "key" : "oryza_longistaminata" + "key" : "Oryza_glumaepatula" }, { "title" : "Oryza meridionalis", - "key" : "oryza_meridionalis" + "key" : "Oryza_meridionalis" }, { "title" : "Oryza nivara", - "key" : "oryza_nivara" + "key" : "Oryza_nivara" }, { "title" : "Oryza punctata", - "key" : "oryza_punctata" + "key" : "Oryza_punctata" }, { "title" : "Oryza rufipogon", - "key" : "oryza_rufipogon" + "key" : "Oryza_rufipogon" }, { - "title" : "Oryza sativa Indica Group", - "key" : "oryza_indica" + "title" : "Oryza sativa Indica Group 93-11", + "key" : "Oryza_indica" + }, + { + "title" : "Oryza sativa Indica Group IR8", + "key" : "Oryza_indicair8" }, { "title" : "Oryza sativa Japonica Group", - "key" : "oryza_sativa" - } - ], - "title" : "Rices (11)", - "key" : "Rices" - }, - { - "isFolder" : true, - "children" : [ + "key" : "Oryza_sativa" + }, + { + "title" : "oryza carolina", + "key" : "Oryza_carolina" + }, + { + "title" : "oryza sativa117425", + "key" : "Oryza_sativa117425" + }, { - "title" : "Aegilops tauschii", - "key" : "aegilops_tauschii" + "title" : "oryza sativa125619", + "key" : "Oryza_sativa125619" }, { - "title" : "Hordeum vulgare subsp. vulgare", - "key" : "hordeum_vulgare" + "title" : "oryza sativa125827", + "key" : "Oryza_sativa125827" }, { - "title" : "Triticum aestivum", - "key" : "triticum_aestivum" + "title" : "oryza sativa127518", + "key" : "Oryza_sativa127518" }, { - "title" : "Triticum urartu", - "key" : "triticum_urartu" + "title" : "oryza sativa127564", + "key" : "Oryza_sativa127564" + }, + { + "title" : "oryza sativa127652", + "key" : "Oryza_sativa127652" + }, + { + "title" : "oryza sativa127742", + "key" : "Oryza_sativa127742" + }, + { + "title" : "oryza sativa128077", + "key" : "Oryza_sativa128077" + }, + { + "title" : "oryza sativa132278", + "key" : "Oryza_sativa132278" + }, + { + "title" : "oryza sativa132424", + "key" : "Oryza_sativa132424" + }, + { + "title" : "oryza sativaazucena", + "key" : "Oryza_sativaazucena" + }, + { + "title" : "oryza sativair64", + "key" : "Oryza_sativair64" + }, + { + "title" : "oryza sativamh63", + "key" : "Oryza_sativamh63" + }, + { + "title" : "oryza sativazs97", + "key" : "Oryza_sativazs97" + }, + { + "title" : "oryza sativakitaake", + "key" : "Oryza_sativakitaake" } ], - "title" : "Triticeae (4)", - "key" : "Triticeae" + "title" : "Rices (27)", + "key" : "Rices" }, { "isFolder" : true, "children" : [ { - "title" : "Setaria italica", - "key" : "setaria_italica" + "title" : "Sorghum bicolor", + "key" : "Sorghum_bicolor" }, { - "title" : "Sorghum bicolor", - "key" : "sorghum_bicolor" + "title" : "Zea maysB73", + "key" : "Zea_maysb73" }, { - "title" : "Zea mays", - "key" : "zea_mays" + "title" : "Zea maysB73v4", + "key" : "Zea_maysb73v4" } ], "title" : "Warm season grasses (C4) (3)", "key" : "Warm season grasses (C4)" } ], - "title" : "Grasses (20)", + "title" : "Grasses (31)", "key" : "Grasses" - }, - { - "title" : "Musa acuminata subsp. malaccensis", - "key" : "musa_acuminata" } ], - "title" : "Monocots (21)", + "title" : "Monocots (31)", "key" : "Monocots" }, { "isFolder" : true, "children" : [ { - "title" : "Cyanidioschyzon merolae strain 10D", - "key" : "cyanidioschyzon_merolae" - }, - { - "title" : "Galdieria sulphuraria", - "key" : "galdieria_sulphuraria" - }, - { - "title" : "Chondrus crispus", - "key" : "chondrus_crispus" - }, - { - "title" : "Ostreococcus lucimarinus CCE9901", - "key" : "ostreococcus_lucimarinus" + "title" : "Selaginella moellendorffii", + "key" : "Selaginella_moellendorffii" }, { "title" : "Chlamydomonas reinhardtii", - "key" : "chlamydomonas_reinhardtii" + "key" : "Chlamydomonas_reinhardtii" }, { - "title" : "Physcomitrella patens", - "key" : "physcomitrella_patens" + "title" : "Drosophila melanogaster", + "key" : "Drosophila_melanogaster" }, { - "title" : "Amborella trichopoda", - "key" : "amborella_trichopoda" - }, - { - "title" : "Selaginella moellendorffii", - "key" : "selaginella_moellendorffii" + "title" : "Oryza sativa aus subgroup", + "key" : "Oryza_aus" } ], - "title" : "Other (8)", + "title" : "Other (4)", "key" : "Other" } ] -; \ No newline at end of file +; diff --git a/gramene/modules/EnsEMBL/Web/Component/Gene/GeneSummary.pm.nouse b/gramene/modules/EnsEMBL/Web/Component/Gene/GeneSummary.pm.nouse new file mode 100755 index 00000000..68a8568e --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Component/Gene/GeneSummary.pm.nouse @@ -0,0 +1,42 @@ +=head1 LICENSE + +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute +Copyright [2016] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Component::Gene::GeneSummary; + +use strict; + +#use previous qw(content); + +sub content { + my $self = shift; + my $html = $self->PREV::content(@_); + + # remove 'Ensembl version' row table row + $html =~ s|]*>]*>Ensembl version]*>

[^<>]+

||; + +my $gene_stable_id = $self->object->gene->stable_id; +my $sbase_link = 'OryzaGramene Genes search'; + $html .= "
$sbase_link

"; + +# $html .= qq{

OryzaGramene

$sbase_link

}; + + return $html; +} + +1; diff --git a/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm b/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm index ba8cc795..2b6c848d 100755 --- a/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm +++ b/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm @@ -40,13 +40,12 @@ sub content { ## EG my $columns = [ - { key => 'go', title => 'Accession', sort => 'none', width => '10%', align => 'left' }, - { key => 'term', title => 'Term', sort => 'none', width => '20%', align => 'left' }, - { key => 'evidence', title => 'Evidence', sort => 'none', width => '3%', align => 'left' }, - { key => 'source', title => 'Annotation source', sort => 'none', width => '15%', align => 'left' }, - { key => 'mapped', title => 'Mapped using', sort => 'html', width => '15%', align => 'left', 'hidden' => 1 }, - { key => 'transcript_id', title => 'Transcript IDs', sort => 'none', width => '10%', align => 'left' }, - { key => 'extra_link', title => '', sort => 'none', width => '10%', align => 'left' }, + { key => 'go', title => 'Accession', sort => 'none', width => '10%', align => 'left' }, + { key => 'description', title => 'Term', sort => 'none', width => '25%', align => 'left' }, + { key => 'evidence', title => 'Evidence', sort => 'none', width => '3%', align => 'left' }, + { key => 'desc', title => 'Annotation Source', sort => 'none', width => '20%', align => 'left' }, + { key => 'transcript_id', title => 'Transcript IDs', sort => 'none', width => '15%', align => 'left' }, + { key => 'extra_link', title => '', sort => 'none', width => '10%', align => 'left' }, ]; ## @@ -80,9 +79,9 @@ sub biomart_link { #return '' unless $self->hub->species_defs->ENSEMBL_MART_ENABLED; return '' if $SiteDefs::EG_DIVISION eq 'bacteria'; - my $vschema = 'default'; #sprintf '%s_mart', $self->hub->species_defs->GENOMIC_UNIT; + my $vschema = sprintf '%s_mart', $self->hub->species_defs->GENOMIC_UNIT; my (@species) = split /_/, $self->object->species; - my $attr_prefix = lc(substr($species[0], 0, 1) . $species[-1] . "_eg_gene"); + my $attr_prefix = lc(substr($species[0], 0, 1) . $species[1] . "_eg_gene"); my ($ontology) = split /:/, $term; my $biomart_filter = EnsEMBL::Web::Constants::ONTOLOGY_SETTINGS->{$ontology}->{biomart_filter}; @@ -111,32 +110,57 @@ sub process_data { ## EG my @bgs = qw(bg1 bg2); my @row_styles; +## my $chromosomes = $hub->species_defs->ENSEMBL_CHROMOSOMES; -## foreach my $go (sort keys %$data) { my $hash = $data->{$go} || {}; my $go_link = $hub->get_ExtURL_link($go, $extdb, $go); - my $mart_link = $self->biomart_link($go) ? "
  • ".$self->biomart_link($go)."
    • ": ""; -## EG + my $mart_link = ''; #$self->biomart_link($go) ? "
  • ".$self->biomart_link($go)."
    • ": ""; + my $loc_link = '
  • View on karyotype
    • ' : '">View associated genes' ); -## + my $goslim = $hash->{'goslim'} || {}; my $row = {}; my $go_evidence = [ split /\s*,\s*/, $hash->{'evidence'} || '' ]; (my $trans = $hash->{transcript_id}) =~ s/^,/ /; # GO terms with multiple transcripts my %all_trans = map{$_ => $hub->url({type => 'Transcript', action => 'Summary',t => $_,})} split(/,/,$trans) if($hash->{transcript_id} =~ /,/); - my $mapped; + my ($desc); + if ($hash->{'info'}) { + my ($gene, $type, $common_name); + + # create URL + if ($hash->{'info'} =~ /from ([a-z]+[ _][a-z]+) (gene|translation) (\S+)/i) { + $gene = $3; + $type = $2; + $common_name = ucfirst $1; + } else { + warn 'regex parse failure in EnsEMBL::Web::Component::Transcript::go()'; # parse error + } + + (my $species = $common_name) =~ s/ /_/g; + + my $param_type = $type eq 'translation' ? 'p' : substr $type, 0, 1; + my $url = $hub->url({ + species => $species, + type => 'Gene', + action => $type eq 'translation' ? 'Ontologies/'.$hub->function : 'Summary', + $param_type => $gene, + __clear => 1, + }); + + $desc = qq{Propagated from $common_name $gene by orthology}; + } + if($hash->{'term'}) { $row->{'go'} = $go_link; - $row->{'term'} = $hash->{'term'}; - $row->{'evidence'} = join ', ', map helptip($_, $description_hash->{$_} // 'No description available'), @$go_evidence; - $row->{'mapped'} = $hash->{'mapped'} || ''; - $row->{'source'} = $hash->{'source'} || ''; - $row->{'transcript_id'} = %all_trans ? join("
    ", map { qq{$_} } keys %all_trans) : ''.$hash->{transcript_id}.''; + $row->{'description'} = $hash->{'term'}; + $row->{'evidence'} = join ', ', map $self->helptip($_, $description_hash->{$_} // 'No description available'), @$go_evidence; + $row->{'desc'} = join ', ', grep $_, ($desc, $hash->{'source'}); + $row->{'transcript_id'} = %all_trans ? join("
    ", map { qq{$_} } keys %all_trans) : ''.$hash->{transcript_id}.''; $row->{'extra_link'} = $mart_link || $loc_link ? qq{
      $mart_link$loc_link
    } : ""; $table->add_row($row); @@ -153,10 +177,9 @@ sub process_data { ## } } - -## EG + $table->{'options'}{'rows'} = \@row_styles; -## + return $table; } diff --git a/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm.bk b/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm.bk new file mode 100755 index 00000000..ba8cc795 --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Component/Gene/Go.pm.bk @@ -0,0 +1,163 @@ +=head1 LICENSE + +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Component::Gene::Go; +use strict; + +use EnsEMBL::Web::Constants; + +sub content { + my $self = shift; + my $object = $self->object; + + # return $self->non_coding_error unless $object->translation_object; + + # This view very much depends on existance of the ontology db, + # but it does not have to - you can still display the ontology terms with the links to the corresponding + # ontology website. + + my $hub = $self->hub; + my $function = $hub->function; + my $adaptor = $hub->get_adaptor('get_OntologyTermAdaptor', 'go'); + my %clusters = $hub->species_defs->multiX('ONTOLOGIES'); + my $terms_found = 0; + my $label = 'Ontology'; + +## EG + my $columns = [ + { key => 'go', title => 'Accession', sort => 'none', width => '10%', align => 'left' }, + { key => 'term', title => 'Term', sort => 'none', width => '20%', align => 'left' }, + { key => 'evidence', title => 'Evidence', sort => 'none', width => '3%', align => 'left' }, + { key => 'source', title => 'Annotation source', sort => 'none', width => '15%', align => 'left' }, + { key => 'mapped', title => 'Mapped using', sort => 'html', width => '15%', align => 'left', 'hidden' => 1 }, + { key => 'transcript_id', title => 'Transcript IDs', sort => 'none', width => '10%', align => 'left' }, + { key => 'extra_link', title => '', sort => 'none', width => '10%', align => 'left' }, + ]; +## + + my $html = '
      '; + my $tables = ''; + my $i = 0; + my $oid = (grep { $clusters{$_}{'description'} eq $function } keys %clusters)[0]; + my $go_hash = $object->get_go_list($clusters{$oid}{'db'}, $clusters{$oid}{'root'}); + + if (%$go_hash) { +## EG + my $table = $self->new_table($columns, []); +## + (my $desc = ucfirst $clusters{$oid}{'description'}) =~ s/_/ /g; + + $self->process_data($table, $go_hash, $clusters{$oid}{'db'}); + + $tables .= $table->render; + $terms_found = 1; + $i++; + } + + $html .= '
    '.$tables; + + return $terms_found ? $html : '

    No ontology terms have been annotated to this entity.

    '; +} + +sub biomart_link { + my ($self, $term) = @_; + + #return '' unless $self->hub->species_defs->ENSEMBL_MART_ENABLED; + return '' if $SiteDefs::EG_DIVISION eq 'bacteria'; + + my $vschema = 'default'; #sprintf '%s_mart', $self->hub->species_defs->GENOMIC_UNIT; + my (@species) = split /_/, $self->object->species; + my $attr_prefix = lc(substr($species[0], 0, 1) . $species[-1] . "_eg_gene"); + my ($ontology) = split /:/, $term; + my $biomart_filter = EnsEMBL::Web::Constants::ONTOLOGY_SETTINGS->{$ontology}->{biomart_filter}; + + my $url = sprintf( + qq{/biomart/martview?VIRTUALSCHEMANAME=%s&ATTRIBUTES=%s.default.feature_page.ensembl_gene_id|%s.default.feature_page.ensembl_transcript_id&FILTERS=%s.default.filters.%s.%s&VISIBLEPANEL=resultspanel}, + $vschema, + $attr_prefix, + $attr_prefix, + $attr_prefix, + $biomart_filter, + $term + ); + + my $link = qq{Search BioMart}; + + return $link; +} + +sub process_data { + my ($self, $table, $data, $extdb) = @_; + + my $hub = $self->hub; + # this is a dirty way of having all the go term description until core decide to have a table for them, this is how we will have to do thing + my $description_hash = {'EXP' => 'Inferred from Experiment', 'IC' => 'Inferred by Curator', 'IDA' => 'Inferred from Direct Assay', 'IEA' => 'Inferred from Electronic Annotation', 'IEP' => 'Inferred from Expression Pattern', 'IGC' => 'Inferred from Genomic Context', 'IGI' => 'Inferred from Genetic Interaction', 'IMP' => 'Inferred from Mutant Phenotype', 'IPI' => 'Inferred from Physical Interaction', 'ISA' => 'Inferred from Sequence Alignment', 'ISM' => 'Inferred from Sequence Model', 'ISO' => 'Inferred from Sequence Orthology', 'ISS' => 'Inferred from Sequence or Structural Similarity', 'NAS' => 'Non-traceable Author Statement', 'ND' => 'No biological Data available', 'RCA' => 'Inferred from Reviewed Computational Analysis', 'TAS' => 'Traceable Author Statement', 'NR' => 'Not Recorded', 'IBA' => 'Inferred from Biological aspect of Ancestor'}; + +## EG + my @bgs = qw(bg1 bg2); + my @row_styles; + + my $chromosomes = $hub->species_defs->ENSEMBL_CHROMOSOMES; +## + + foreach my $go (sort keys %$data) { + my $hash = $data->{$go} || {}; + my $go_link = $hub->get_ExtURL_link($go, $extdb, $go); + my $mart_link = $self->biomart_link($go) ? "
  • ".$self->biomart_link($go)."
    • ": ""; +## EG + my $loc_link = '
  • View on karyotype
    • ' : '">View associated genes' ); +## + my $goslim = $hash->{'goslim'} || {}; + my $row = {}; + my $go_evidence = [ split /\s*,\s*/, $hash->{'evidence'} || '' ]; + (my $trans = $hash->{transcript_id}) =~ s/^,/ /; # GO terms with multiple transcripts + my %all_trans = map{$_ => $hub->url({type => 'Transcript', action => 'Summary',t => $_,})} split(/,/,$trans) if($hash->{transcript_id} =~ /,/); + + my $mapped; + + if($hash->{'term'}) { + $row->{'go'} = $go_link; + $row->{'term'} = $hash->{'term'}; + $row->{'evidence'} = join ', ', map helptip($_, $description_hash->{$_} // 'No description available'), @$go_evidence; + $row->{'mapped'} = $hash->{'mapped'} || ''; + $row->{'source'} = $hash->{'source'} || ''; + $row->{'transcript_id'} = %all_trans ? join("
    ", map { qq{$_} } keys %all_trans) : ''.$hash->{transcript_id}.''; + $row->{'extra_link'} = $mart_link || $loc_link ? qq{
      $mart_link$loc_link
    } : ""; + + $table->add_row($row); +## EG + push @row_styles, $bgs[0]; + + foreach (@{$hash->{extensions}}) { + $_->{desc} = delete $_->{source}; # rename column source -> desc + $table->add_row($_); + push @row_styles, $bgs[0]; + } + + push @bgs, shift @bgs; +## + } + } + +## EG + $table->{'options'}{'rows'} = \@row_styles; +## + return $table; +} + +1; diff --git a/gramene/modules/EnsEMBL/Web/Component/Gene/GrameneSearch.pm b/gramene/modules/EnsEMBL/Web/Component/Gene/GrameneSearch.pm new file mode 100644 index 00000000..4ac60bb0 --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Component/Gene/GrameneSearch.pm @@ -0,0 +1,66 @@ +=head1 LICENSE + +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute +Copyright [2016] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Component::Gene::GrameneSearch; + +use strict; + +use EnsEMBL::Web::Document::Image::R2R; + +use base qw(EnsEMBL::Web::Component::Gene); + +sub _init { + my $self = shift; + $self->cacheable(0); + $self->ajaxable(1); +} + +sub content { + my $self = shift; + my $hub = $self->hub; + my $object = $self->object; + my $gene = $object->gene; + my $species_defs = $hub->species_defs; + my $table = $self->new_twocol; + my $site_type = $species_defs->ENSEMBL_SITETYPE; + my @CCDS = @{$object->Obj->get_all_DBLinks('CCDS')}; + my @Uniprot = @{$object->Obj->get_all_DBLinks('Uniprot/SWISSPROT')}; + my $db = $object->get_db; + my $alt_genes = $self->_matches('alternative_genes', 'Alternative Genes', 'ALT_GENE', 'show_version'); #gets all xrefs, sorts them and stores them on the object. Returns HTML only for ALT_GENES + my @RefSeqMatches = @{$gene->get_all_Attributes('refseq_compare')}; + my $display_xref = $gene->display_xref; + my ($link_url) = $display_xref ? $self->get_gene_display_link($gene, $display_xref) : (); + + my $gene_stable_id = $gene->stable_id; + #my $sbase_link = 'OryzaGramene Genes search'; + +# $table->add_row('Gramene Search', $sbase_link); + + #my $html = 'GrameneSearchExample'; + + my $html = 'GrameneSearchExample'; + $html .= '

    ' . $gene_stable_id . '

    '; + + + return $html; + +} + + +1; diff --git a/gramene/modules/EnsEMBL/Web/Component/Info/HomePage.pm b/gramene/modules/EnsEMBL/Web/Component/Info/HomePage.pm index 35a9bf7a..a503c94c 100755 --- a/gramene/modules/EnsEMBL/Web/Component/Info/HomePage.pm +++ b/gramene/modules/EnsEMBL/Web/Component/Info/HomePage.pm @@ -360,8 +360,14 @@ sub _genebuild_text { if ($species_defs->ENSEMBL_FTP_URL) { my $dataset = $species_defs->SPECIES_DATASET; - my $fasta_url = $hub->get_ExtURL('SPECIES_FTP_URL',{GENOMIC_UNIT=>$species_defs->GENOMIC_UNIT,VERSION=>$ensembl_version, FORMAT=>'fasta', SPECIES=> ($dataset ne $species) ? lc($dataset) . "_collection/" . lc $species : lc $species},{class=>'nodeco'}); - my $gff3_url = $hub->get_ExtURL('SPECIES_FTP_URL',{GENOMIC_UNIT=>$species_defs->GENOMIC_UNIT,VERSION=>$ensembl_version, FORMAT=>'gff3', SPECIES=> ($dataset ne $species) ? lc($dataset) . "_collection/" . lc $species : lc $species},{class=>'nodeco'}); + #my $fasta_url = $hub->get_ExtURL('SPECIES_FTP_URL',{GENOMIC_UNIT=>$species_defs->GENOMIC_UNIT,VERSION=>$ensembl_version, FORMAT=>'fasta', SPECIES=> ($dataset ne $species) ? lc($dataset) . "_collection/" . lc $species : lc $species},{class=>'nodeco'}); + #my $gff3_url = $hub->get_ExtURL('SPECIES_FTP_URL',{GENOMIC_UNIT=>$species_defs->GENOMIC_UNIT,VERSION=>$ensembl_version, FORMAT=>'gff3', SPECIES=> ($dataset ne $species) ? lc($dataset) . "_collection/" . lc $species : lc $species},{class=>'nodeco'}); + + my $fasta_url = sprintf '%s/release-%s/fasta/%s/', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, lc $species; +#$hub->get_ExtURL('SPECIES_FTP_URL',{GENOMIC_UNIT=>$species_defs->GENOMIC_UNIT,VERSION=>$eg_version, FORMAT=>'fasta', SPECIES=> $self->is_bacteria ? $species_defs->SPECIES_DATASET . "_collection/" . lc $species : lc $species},{class=>'nodeco'}); + + my $gff3_url = sprintf '%s/release-%s/gff3/%s/', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, lc $species; + $html .= qq[

    Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3

    ]; } @@ -370,7 +376,7 @@ sub _genebuild_text { my $im_url; if( $species =~ /Zea_mays/i ){ ###weix-start - $im_url = "ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/gene_id_mapping_v3_to_v4/"; + $im_url = "http://ftp.gramene.org/CURRENT_RELEASE/gff3/zea_mays/gene_id_mapping_v3_to_v4/"; }elsif( $species =~ /Sorghum_bicolor/i ){ $im_url = "http://genome.jgi.doe.gov/Phytozome/download/_JAMO/55fca1de0d8785306f968fa1/Sbicolor_255_v2.1.locus_transcript_name_map.txt"; }elsif($species =~ /Oryza_sativa/i ){ @@ -379,15 +385,15 @@ sub _genebuild_text { $im_url = undef; } ###weix-end - $html .= qq(

    Update your old Ensembl IDs

    ) if $im_url; #weix + #$html .= qq(

    Update your old Ensembl IDs

    ) if $im_url; #weix if( $species =~ /Zea_mays/i ){ ##weix-start - my $func_url = "ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/gene_function"; + my $func_url = "http://ftp.gramene.org/CURRENT_RELEASE/gff3/zea_mays/gene_function"; $html .= qq(

    Gene function summary

    ) if $func_url; } ##weix-end if( $species =~ /Zea_mays/i ){ ##weix-start - my $func_url = "ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/repeat_annotation/"; + my $func_url = "http://ftp.gramene.org/CURRENT_RELEASE/gff3/zea_mays/repeat_annotation/"; $html .= qq(

    Transposon annotation download

    ) if $func_url; } ##weix-end @@ -473,13 +479,13 @@ sub _compara_text { else { $html .= '

    What can I find? Homologues, gene trees, and whole genome alignments across multiple species.

    '; } - $html .= qq(

    More about comparative analyses

    ); + $html .= qq(

    More about comparative analyses

    ); $html .= qq(

    Phylogenetic overview of gene families

    ); if ($species_defs->ENSEMBL_FTP_URL) { - my $ftp_url = sprintf '%s/release-%s/emf/ensembl-compara/', $species_defs->ENSEMBL_FTP_URL, $ensembl_version; - $html .= qq(

    Download alignments (EMF)

    ) - unless $self->is_bacteria; + #my $ftp_url = sprintf '%s/release-%s/emf/ensembl-compara/', $species_defs->ENSEMBL_FTP_URL, $ensembl_version; + #$html .= qq(

    Download alignments (EMF)

    ) + # unless $self->is_bacteria; } $html .= $compara_table; @@ -537,16 +543,16 @@ sub _variation_text { } my $site = $species_defs->ENSEMBL_SITETYPE; - $html .= qq(

    More about variation in $site

    ); + $html .= qq(

    More about variation in $site

    ); if ($species_defs->ENSEMBL_FTP_URL) { my @links; foreach my $format (qw/gvf vcf/){ - push(@links, sprintf('%s', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, $format, lc $species, $display_name, uc $format,uc $format)); + #push(@links, sprintf('%s', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, $format, lc $species, $display_name, uc $format,uc $format)); } - push(@links, sprintf('VEP', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, lc $species, $ensembl_version, $species_defs->ASSEMBLY_NAME, $display_name)); - my $links = join(" - ", @links); - $html .= qq[

    Download all variants - $links

    ]; + #push(@links, sprintf('VEP', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, lc $species, $ensembl_version, $species_defs->ASSEMBLY_NAME, $display_name)); + #my $links = join(" - ", @links); + #$html .= qq[

    Download all variants - $links

    ]; } } else { @@ -595,7 +601,7 @@ sub _funcgen_text { if ($species_defs->ENSEMBL_FTP_URL) { my $ftp_url = sprintf '%s/release-%s/regulation/%s/', $species_defs->ENSEMBL_FTP_URL, $ensembl_version, lc $species; - $html .= qq(

    Download all regulatory features (GFF)

    ); + #$html .= qq(

    Download all regulatory features (GFF)

    ); } } else { diff --git a/gramene/modules/EnsEMBL/Web/Component/Info/SpeciesBlurb.pm b/gramene/modules/EnsEMBL/Web/Component/Info/SpeciesBlurb.pm new file mode 100755 index 00000000..086533e1 --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Component/Info/SpeciesBlurb.pm @@ -0,0 +1,144 @@ +=head1 LICENSE + +Copyright [2009-2014] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +# $Id: SpeciesBlurb.pm,v 1.14 2013-09-06 15:30:15 jh15 Exp $ + +package EnsEMBL::Web::Component::Info::SpeciesBlurb; + +use strict; + +use EnsEMBL::Web::Controller::SSI; +use Data::Dumper; + +use base qw(EnsEMBL::Web::Component); + +sub content { + my $self = shift; + my $hub = $self->hub; + my $species_defs = $hub->species_defs; + my $species = $hub->species; + +# # $self->wheatHomePage found in eg-plugins/plants +# if ($species eq 'Triticum_aestivum' && $self->can('wheatHomePage')){ +# return $self->wheatHomePage(); +# } + + my $common_name = $species_defs->SPECIES_COMMON_NAME; + my $display_name = $species_defs->SPECIES_SCIENTIFIC_NAME; + my $ensembl_version = $species_defs->ENSEMBL_VERSION; + my $current_assembly = $species_defs->ASSEMBLY_NAME; + my $accession = $species_defs->ASSEMBLY_ACCESSION; + my $source = $species_defs->ASSEMBLY_ACCESSION_SOURCE || 'NCBI'; + my $source_type = $species_defs->ASSEMBLY_ACCESSION_TYPE; + my %archive = %{$species_defs->get_config($species, 'ENSEMBL_ARCHIVES') || {}}; + my %assemblies = %{$species_defs->get_config($species, 'ASSEMBLIES') || {}}; + my $previous = $current_assembly; + + my $html = qq( +
    +
    +
    + +

    $common_name Assembly and Gene Annotation

    +
    +
    +
    + ); + + $html .= ' +
    +
    +
    '; +## EG START +# We use the old pages named about_{species}.html - maybe we should replace them later +#### ASSEMBLY +# $html .= '

    Assembly

    '; +# $html .= EnsEMBL::Web::Controller::SSI::template_INCLUDE($self, "/ssi/species/${species}_assembly.html"); + +# $html .= '

    Gene annotation

    '; +# $html .= EnsEMBL::Web::Controller::SSI::template_INCLUDE($self, "/ssi/species/${species}_annotation.html"); +## ....EG.... + $html .= EnsEMBL::Web::Controller::SSI::template_INCLUDE($self, "/ssi/species/about_${species}.html"); +# $self->cut_tagged_section(\$html,'about'); +## EG END + + ## Link to Wikipedia + $html .= $self->_wikipedia_link; + + $html .= ' +
    +
    +
    +
    '; + + ## ASSEMBLY STATS + my $file = '/ssi/species/stats_' . $self->hub->species . '.html'; + #$html .= '

    Statistics

    '; + #$html .= $self->species_stats; + +$html .= EnsEMBL::Web::Controller::SSI::template_INCLUDE($self, $file); + + $html .= ' +
    +
    +
    '; + +# process any subs + my @scripts = $html =~ /\{\{sub_([^\}]+)\}\}/; + foreach my $script (@scripts){ + if($self->can($script)){ + my $output = $self->$script; + $html =~ s/\{\{sub_$script\}\}/$output/; + } + } +# + return $html; +} + +=head2 cut_tagged_section + Arg [1]: string pointer + Arg [2]: tag name + Example: cut_by_tag(\$html, 'about') + Description: Remove sections of the page demarcated by + Meta: ENSEMBL-1881 + +=cut + +sub cut_tagged_section{ + my ($self,$ptr,$tag) = @_; + $$ptr =~ s/^(.*?)(.*)(.*)$/\1\3/msg; + return 1; +} + +sub _wikipedia_link { + my $self = shift; + my $url = $self->hub->species_defs->WIKIPEDIA_URL; + my $html = ''; + + if ($url) { + $html .= qq(

    More information

    +

    General information about this species can be found in +Wikipedia. +

    ); + } + + return $html; +} + + +1; diff --git a/gramene/modules/EnsEMBL/Web/Configuration/Gene.pm b/gramene/modules/EnsEMBL/Web/Configuration/Gene.pm new file mode 100644 index 00000000..c5e718da --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Configuration/Gene.pm @@ -0,0 +1,288 @@ +=head1 LICENSE + +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute +Copyright [2016] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Configuration::Gene; + +use strict; + +use base qw(EnsEMBL::Web::Configuration); + +sub set_default_action { + my $self = shift; + $self->{'_data'}->{'default'} = $self->object ? $self->object->default_action : 'Summary'; +} + +sub user_tree { return 1; } + +sub populate_tree { + my $self = shift; + my $hub = $self->hub; + my $species_defs = $hub->species_defs; + my $strain = $species_defs->RELATED_TAXON; # species that are in a compara strain tree + my $collapse = $species_defs->IS_STRAIN_OF ? 0 : 1; # check if species is a strain + + my $summary_menu = $self->create_node('Summary', 'Summary', + [qw( + gene_summary EnsEMBL::Web::Component::Gene::GeneSummary + navbar EnsEMBL::Web::Component::ViewNav + transcripts EnsEMBL::Web::Component::Gene::TranscriptsImage + )], + { 'availability' => 'gene' } + ); + + $summary_menu->append($self->create_node('Splice', 'Splice variants', + [qw( image EnsEMBL::Web::Component::Gene::SpliceImage )], + { 'availability' => 'gene has_transcripts', 'concise' => 'Splice variants' } + )); + + $summary_menu->append($self->create_node('TranscriptComparison', 'Transcript comparison', + [qw( + select EnsEMBL::Web::Component::Gene::TranscriptComparisonSelector + seq EnsEMBL::Web::Component::Gene::TranscriptComparison + )], + { 'availability' => 'gene multiple_transcripts not_rnaseq' } + )); + + $summary_menu->append($self->create_node('Alleles', 'Gene alleles', + [qw(alleles EnsEMBL::Web::Component::Gene::Alleles)], + { 'availability' => 'core has_alt_alleles', 'concise' => 'Gene Alleles' } + )); + + my $seq_menu = $self->create_node('Sequence', 'Sequence', + [qw( sequence EnsEMBL::Web::Component::Gene::GeneSeq )], + { 'availability' => 'gene', 'concise' => 'Marked-up sequence' } + ); + + $seq_menu->append($self->create_node('SecondaryStructure', 'Secondary Structure', + [qw( + secondary EnsEMBL::Web::Component::Gene::RnaSecondaryStructure + )], + { 'availability' => 'gene can_r2r has_2ndary'} + )); + + my $compara_menu = $self->create_node('Compara', 'Comparative Genomics', + [qw(strain_button_panel EnsEMBL::Web::Component::Gene::Compara_Portal)], + {'availability' => 'gene database:compara core not_strain'} + ); + + $compara_menu->append($self->create_node('Compara_Alignments', 'Genomic alignments', + [qw( + selector EnsEMBL::Web::Component::Compara_AlignSliceSelector + alignments EnsEMBL::Web::Component::Gene::Compara_Alignments + )], + { 'availability' => 'gene database:compara core has_alignments' } + )); + + $compara_menu->append($self->create_node('Compara_Tree', 'Gene tree', + [qw( image EnsEMBL::Web::Component::Gene::ComparaTree )], + { 'availability' => 'gene database:compara core has_gene_tree not_strain' } + )); + + $compara_menu->append($self->create_node('SpeciesTree', 'Gene gain/loss tree', + [qw( image EnsEMBL::Web::Component::Gene::SpeciesTree )], + { 'availability' => 'gene database:compara core has_species_tree not_strain' } + )); + + my $ol_node = $self->create_node('Compara_Ortholog', 'Orthologues', + [qw( orthologues EnsEMBL::Web::Component::Gene::ComparaOrthologs )], + { 'availability' => 'gene database:compara core has_orthologs not_strain', 'concise' => 'Orthologues' } + ); + + $ol_node->append($self->create_subnode('Compara_Ortholog/Alignment', 'Orthologue alignment', + [qw( alignment EnsEMBL::Web::Component::Gene::HomologAlignment )], + { 'availability' => 'gene database:compara core has_orthologs not_strain', 'no_menu_entry' => 1 } + )); + + $compara_menu->append($ol_node); + + my $pl_node = $self->create_node('Compara_Paralog', 'Paralogues', + [qw(paralogues EnsEMBL::Web::Component::Gene::ComparaParalogs)], + { 'availability' => 'gene database:compara core has_paralogs not_strain', 'concise' => 'Paralogues' } + ); + + $pl_node->append($self->create_subnode('Compara_Paralog/Alignment', 'Paralogue alignment', + [qw( alignment EnsEMBL::Web::Component::Gene::HomologAlignment )], + { 'availability' => 'gene database:compara core has_paralogs not_strain', 'no_menu_entry' => 1 } + )); + + $compara_menu->append($pl_node); + + my $fam_node = $self->create_node('Family', 'Ensembl protein families', + [qw( family EnsEMBL::Web::Component::Gene::Family )], + { 'availability' => 'family not_strain', 'concise' => 'Ensembl protein families' } + ); + + $fam_node->append($self->create_subnode('Family/Genes', uc($species_defs->get_config($hub->species, 'SPECIES_COMMON_NAME')) . ' genes in this family', + [qw( genes EnsEMBL::Web::Component::Gene::FamilyGenes )], + { 'availability' => 'family not_strain', 'no_menu_entry' => 1 } + )); + + $fam_node->append($self->create_subnode('Family/Alignments', 'Multiple alignments in this family', + [qw( jalview EnsEMBL::Web::Component::Gene::FamilyAlignments )], + { 'availability' => 'family database:compara core not_strain', 'no_menu_entry' => 1 } + )); + + $compara_menu->append($fam_node); + + # Compara menu for strain (strain menu available on main species but collapse, main menu not available/grey out/collapse on strain page) + # The node key (Strain_) is used by Component.pm to determine if it is a strain link on the main species page, so be CAREFUL when changing this + if($strain || $species_defs->IS_STRAIN_OF) { + my $strain_compara_menu = $self->create_node('Strain_Compara', 'Strains', + [qw(strain_button_panel EnsEMBL::Web::Component::Gene::Compara_Portal)], + {'availability' => 'gene database:compara core', 'closed' => $collapse } + ); + + $strain_compara_menu->append($self->create_node('Strain_Compara_Tree', 'Gene tree', + [qw( image EnsEMBL::Web::Component::Gene::ComparaTree )], + { 'availability' => 'gene database:compara core has_strain_gene_tree' } + )); + + my $strain_ol_node = $self->create_node('Strain_Compara_Ortholog', 'Orthologues', + [qw( orthologues EnsEMBL::Web::Component::Gene::ComparaOrthologs )], + { 'availability' => 'gene database:compara core has_strain_orthologs', 'concise' => 'Orthologues' } + ); + + $strain_ol_node->append($self->create_subnode('Strain_Compara_Ortholog/Alignment', 'Orthologue alignment', + [qw( alignment EnsEMBL::Web::Component::Gene::HomologAlignment )], + { 'availability' => 'gene database:compara core has_strain_orthologs', 'no_menu_entry' => 1 } + )); + + $strain_compara_menu->append($strain_ol_node); + + my $strain_pl_node = $self->create_node('Strain_Compara_Paralog', 'Paralogues', + [qw(paralogues EnsEMBL::Web::Component::Gene::ComparaParalogs)], + { 'availability' => 'gene database:compara core has_strain_paralogs', 'concise' => 'Paralogues' } + ); + + $strain_pl_node->append($self->create_subnode('Strain_Compara_Paralog/Alignment', 'Paralogue alignment', + [qw( alignment EnsEMBL::Web::Component::Gene::HomologAlignment )], + { 'availability' => 'gene database:compara core has_strain_paralogs', 'no_menu_entry' => 1 } + )); + + $strain_compara_menu->append($strain_pl_node); + $compara_menu->append($strain_compara_menu); + } + + # get all ontologies mapped to this species + my $go_menu = $self->create_submenu('Ontologies', 'Ontologies'); + my %olist = map {$_ => 1} @{$species_defs->SPECIES_ONTOLOGIES || []}; + + if (%olist) { + # get all ontologies available in the ontology db + my %clusters = $species_defs->multiX('ONTOLOGIES'); + + # get all the clusters that can generate a graph + my @clist = grep {$olist{$clusters{$_}->{db}}} sort {$clusters{$a}->{db} cmp $clusters{$b}->{db}} keys %clusters; # Find if this ontology has been loaded into ontology db + + foreach my $oid (@clist) { + my $cluster = $clusters{$oid}; + + (my $desc2 = $cluster->{db}.": ".ucfirst($cluster->{description})) =~ s/_/ /g; + + $go_menu->append($self->create_node('Ontologies/'. $cluster->{description}, $desc2, [qw( go EnsEMBL::Web::Component::Gene::Go )], {'availability' => "gene has_go_$oid", 'concise' => $desc2 })); + } + } + + $self->create_node('Phenotype', 'Phenotypes', + [qw( + phenotype EnsEMBL::Web::Component::Gene::GenePhenotype + variation EnsEMBL::Web::Component::Gene::GenePhenotypeVariation + orthologue EnsEMBL::Web::Component::Gene::GenePhenotypeOrthologue + )], + { 'availability' => 'core' } #can't be any cleverer than this since checking orthologs is too slow + ); + + my $var_menu = $self->create_submenu('Variation', 'Genetic Variation'); + + $var_menu->append($self->create_node('Variation_Gene/Table', 'Variant table', + [qw( snptable EnsEMBL::Web::Component::Gene::VariationTable )], + { 'availability' => 'gene database:variation core not_patch' } + )); + + $var_menu->append($self->create_node('Variation_Gene/Image', 'Variant image', + [qw( image EnsEMBL::Web::Component::Gene::VariationImage )], + { 'availability' => 'gene database:variation core not_patch' } + )); + + $var_menu->append($self->create_node('StructuralVariation_Gene', 'Structural variants', + [qw( + svimage EnsEMBL::Web::Component::Gene::SVImage + svtable EnsEMBL::Web::Component::Gene::SVTable + )], + { 'availability' => 'gene has_structural_variation core not_patch' } + )); + + $self->create_node('ExpressionAtlas', 'Gene expression', + [qw( atlas EnsEMBL::Web::Component::Gene::ExpressionAtlas )], + { 'availability' => 'gene has_gxa' } + ); + + $self->create_node('Regulation', 'Regulation', + [qw( + regulation EnsEMBL::Web::Component::Gene::RegulationImage + features EnsEMBL::Web::Component::Gene::RegulationTable + )], + { 'availability' => 'regulation not_patch not_rnaseq' } + ); + + $self->create_node('Matches', 'External references', + [qw( + matches EnsEMBL::Web::Component::Gene::SimilarityMatches + )], + { 'availability' => 'gene has_similarity_matches', 'concise' => 'External references' } + ); + + $self->create_node('Evidence', 'Supporting evidence', + [qw( evidence EnsEMBL::Web::Component::Gene::SupportingEvidence )], + { 'availability' => 'gene', 'concise' => 'Supporting evidence' } + ); + + $self->create_node('Evidence', 'Supporting evidence', + [qw( evidence EnsEMBL::Web::Component::Gene::SupportingEvidence )], + { 'availability' => 'gene', 'concise' => 'Supporting evidence' } + ); + + my $history_menu = $self->create_submenu('History', 'ID History'); + + $history_menu->append($self->create_node('Idhistory', 'Gene history', + [qw( + display EnsEMBL::Web::Component::Gene::HistoryReport + associated EnsEMBL::Web::Component::Gene::HistoryLinked + map EnsEMBL::Web::Component::Gene::HistoryMap + )], + { 'availability' => 'history', 'concise' => 'ID History' } + )); + + $self->create_subnode('Output', 'Export Gene Data', + [qw( export EnsEMBL::Web::Component::Export::Output )], + { 'availability' => 'gene', 'no_menu_entry' => 1 } + ); + + + my $grmsrch_menu = $self->create_node('GrameneSearch', 'Gramene Search', + [qw( + gramene_search EnsEMBL::Web::Component::Gene::GrameneSearch + )], + { 'availability' => 'gene' } + ); + + +} + +1; diff --git a/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm b/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm new file mode 100755 index 00000000..a85891a8 --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm @@ -0,0 +1,42 @@ +=head1 LICENSE + +Copyright [2009-2014] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Document::Element::Copyright; + +### Copyright notice for footer (basic version with no logos) + +use strict; + +sub content { + my $self = shift; + + my $sd = $self->species_defs; + + return sprintf( qq( +
    +

    + %s release %d - %s + © CSHL + CSHL +

    +
    ), $sd->SITE_NAME, $sd->SITE_RELEASE_VERSION, $sd->SITE_RELEASE_DATE + ); +} + +1; + diff --git a/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm.bk b/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm.bk new file mode 100644 index 00000000..8245928c --- /dev/null +++ b/gramene/modules/EnsEMBL/Web/Document/Element/Copyright.pm.bk @@ -0,0 +1,60 @@ +=head1 LICENSE + +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute +Copyright [2016] EMBL-European Bioinformatics Institute + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +=cut + +package EnsEMBL::Web::Document::Element::Copyright; + +### Copyright notice for footer (basic version with no logos) + +use strict; + +use base qw(EnsEMBL::Web::Document::Element); + +sub new { + return shift->SUPER::new({ + %{$_[0]}, + sitename => '?' + }); +} + +sub sitename :lvalue { $_[0]{'sitename'}; } + +sub content { + my $self = shift; + my @time = localtime; + my $year = @time[5] + 1900; + my $privacy_url = $self->hub->species_defs->GDPR_POLICY_URL; + + my $privacy_link = $privacy_url ? qq((Privacy policy)) : ''; + + return qq{ +
    +

    © $year + EMBL-EBI + EMBL-EBI. + $privacy_link +

    +
    + }; +} + +sub init { + $_[0]->sitename = $_[0]->species_defs->ENSEMBL_SITETYPE; +} + +1; diff --git a/gramene/modules/EnsEMBL/Web/Document/Element/FatFooter.pm b/gramene/modules/EnsEMBL/Web/Document/Element/FatFooter.pm index b910ca02..7b02f65c 100644 --- a/gramene/modules/EnsEMBL/Web/Document/Element/FatFooter.pm +++ b/gramene/modules/EnsEMBL/Web/Document/Element/FatFooter.pm @@ -26,40 +26,44 @@ use base qw(EnsEMBL::Web::Document::Element); sub content { my $species_defs = shift->species_defs; - my $sister_sites = qq(

    OGE Browser

    -

    Maize B73_RefGen_v4 PreRelease Browser

    ); + #my $sister_sites = qq(

    OGE Browser

    + #

    Maize B73_RefGen_v4 PreRelease Browser

    ); + + my $sister_sites = qq(

    Grapevine Gramene Browser

    +

    Maize Gramene Browser

    +

    Sorghumbase Browser

    ); my $html = '