# $Id$ ######################################################################## # SOURCES # # # # Keys: # # name - name of this source (required) # # download - must be downloaded (Y or N, required) # # order - parsing order for this source # # priority - priority of these data files when more files belong # # to the same source 'name' # # prio_descr - label for the 'priority' # # parser - the parser to be used (required) # # release_uri - URI pointing to release information (optional) # # data_uri - URI pointing to the data files (multiple, required) # # # ######################################################################## [source MEROPS::drosophila_melanogaster] # Used by the 12 drosophila genomes name = MEROPS download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source MEROPS::drosophila_grimshawi] # Used by the 12 drosophila genomes name = MEROPS download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/current/gff/dgri-all-*.gff.gz [source MEROPS::drosophila_erecta] # Used by the 12 drosophila genomes name = MEROPS download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dere_1.3/seqdata/dere-all-r1.3.gff.gz [source MEROPS::drosophila_virilis] # Used by the 12 drosophila genomes name = MEROPS download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/dvir-all-r1.2.gff.gz [source miRBase::drosophila_melanogaster] # Used by the 12 drosophila genomes name = miRBase download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source miRBase::drosophila_pseudoobscura] # Used by the 12 drosophila genomes name = miRBase download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz [source TransFac::drosophila_melanogaster] # Used by the 12 drosophila genomes name = TransFac download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source TransFac::drosophila_pseudoobscura] # Used by the 12 drosophila genomes name = TransFac download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz [source EPD::drosophila_melanogaster] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source EPD::drosophila_pseudoobscura] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz [source EPD::drosophila_simulans] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dsim_1.3/seqdata/dsim-all-r1.3.gff.gz [source EPD::drosophila_sechellia] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dsec_1.3/seqdata/dsec-all-r1.3.gff.gz [source EPD::drosophila_mojavensis] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dmoj_1.3/seqdata/dmoj-all-r1.3.gff.gz [source EPD::drosophila_virilis] # Used by the 12 drosophila genomes name = EPD download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/dvir-all-r1.2.gff.gz [source AFFY_DrosGenome1::drosophila_melanogaster] # Used by drosophila_melanogaster name = AFFY_DrosGenome1 download = N order = 50 priority = 1 prio_descr = parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [species anas_platyrhynchos] taxonomy_id = 8839 aliases = duck, mallard, mallard duck, mallard ducks, anas platyrhynchos, anas boschas, anas domesticus source = EntrezGene::MULTI source = GO::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species anolis_carolinensis] taxonomy_id = 28377 aliases = anole, green anole lizard, green anole, american anole, redthroated anole, anoliscarolinensis, anolis_carolinensis source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI #source = Uniprot/Varsplic::MULTI [source VB_Community_Annotation::aedes_aegypti] # Used by aedes_aegypti name = VB_Community_Annotation download = Y order = 40 priority = 1 prio_descr = parser = AedesCAPParser release_uri = data_uri = file:VB_Community_Annotation/Aedes_VB_Community_Annotation.fa [source AedesGenBank::aedes_aegypti] # Used by aedes_aegypti name = AedesGenBank download = Y order = 30 priority = 1 prio_descr = parser = AedesGenBankParser release_uri = data_uri = file:AedesGenBank/Aedes_proteinID.fa [source Ixodes_ManualAnnotation::ixodes_scapularis] # Used by ixodes_scapularis name = Ixodes_ManualAnnotation download = Y order = 40 priority = 1 prio_descr = parser = IxodesCAPParser release_uri = data_uri = file:Ixodes_scapularis/ixodes_CAP.fa #[source Anopheles_symbol::anopheles_gambiae] # Used by anopheles_gambiae #name = Anopheles_symbol #download = Y #order = 40 #priority = 1 #prio_descr = #parser = AnophelesSymbolParser #release_uri = #data_uri = file:Anopheles_symbol/GeneName_translation_UniqID.txt [source VB_Community_Annotation::anopheles_gambiae] # Used by anopheles_gambiae name = VB_Community_Annotation download = Y order = 40 priority = 1 prio_descr = parser = VBCommunitySymbolParser release_uri = data_uri = file:VB_Community_Annotation/xref_Anopheles_symbol_lookup [source ImmunoDB::anopheles_gambiae] # Used by anopheles_gambiae name = ImmunoDB download = Y order = 40 priority = 1 prio_descr = parser = ImmunoDBParser release_uri = data_uri = file:ImmunoDB/Anopheles_ImmunoDB.txt [source ImmunoDB::aedes_aegypti] # Used by aedes_aegypti name = ImmunoDB download = Y order = 40 priority = 1 prio_descr = parser = ImmunoDBParser release_uri = data_uri = file:ImmunoDB/Aedes_ImmunoDB.txt [source ImmunoDB::culex_quinquefasciatus] # Used by culex_quinquefasciatus name = ImmunoDB download = Y order = 40 priority = 1 prio_descr = parser = ImmunoDBParser release_uri = data_uri = file:ImmunoDB/Culex_ImmunoDB.txt [source AnoXcel::anopheles_gambiae] # Used by anopheles_gambiae name = AnoXcel download = Y order = 40 priority = 1 prio_descr = parser = AnoXcelParser release_uri = data_uri = file:AnoXcel/anoXcel3.6-Xrefs.txt [source VB_RNA_Description::anopheles_gambiae] # Used by anopheles_gambiae name = VB_RNA_Description download = Y order = 40 priority = 1 prio_descr = parser = VBRNADescriptionParser release_uri = data_uri = file:VB_RNA_Description/An_AgamP3-5_ncRNA_description_lookup.txt [source VB_RNA_Description::aedes_aegypti] # Used by aedes_aegypti name = VB_RNA_Description download = Y order = 40 priority = 1 prio_descr = parser = VBRNADescriptionParser release_uri = data_uri = file:VB_RNA_Description/AaegL1-2_RNA_description.txt [source VB_RNA_Description::culex_quinquefasciatus] # Used by culex_quinquefasciatus name = VB_RNA_Description download = Y order = 40 priority = 1 prio_descr = parser = VBRNADescriptionParser release_uri = data_uri = file:VB_RNA_Description/CpipJ1-2_RNA_description.txt [source VB_External_Description::aedes_aegypti] # Used by aedes_aegypti name = VB_External_Description download = Y order = 40 priority = 1 prio_descr = parser = VBExternalDescriptionParser release_uri = data_uri = file:VB_External_Description/AaegL1-2_gene_description.txt [source VB_External_Description::culex_quinquefasciatus] # Used by culex_quinquefasciatus name = VB_External_Description download = Y order = 40 priority = 1 prio_descr = parser = VBExternalDescriptionParser release_uri = data_uri = file:VB_External_Description/CpipJ1-2_gene_description.txt [source BDGP_insitu_expr::drosophila_melanogaster] # Used by drosophila_melanogaster name = BDGP_insitu_expr download = N order = 50 priority = 1 prio_descr = BDGP in situ gene expression parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz #[source CCDS::MULTI] ## Used by homo_sapiens, mus_musculus #name = CCDS #download = Y #order = 10 #priority = 1 #prio_descr = #parser = CCDSParser #release_uri = #data_uri = file:CCDS/CCDS.txt [source CCDS::homo_sapiens] # Used by homo_sapiens name = CCDS download = Y order = 10 priority = 1 prio_descr = parser = CCDSParser release_uri = data_uri = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,tran_name=>ENST, [source CCDS::mus_musculus] # Used by mus_musculus name = CCDS download = Y order = 10 priority = 1 prio_descr = parser = CCDSParser release_uri = data_uri = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,tran_name=>ENSMUST, [source Celera_Pep::anopheles_gambiae] # Used by anopheles_gambiae name = Celera_Pep download = Y order = 40 priority = 1 prio_descr = parser = CeleraProteinParser release_uri = data_uri = file:Celera/Anopheles_Celera_consensus-proteins_xref.fasta [source Celera_Gene::anopheles_gambiae] name = Celera_Gene download = N order = 40 priority = 1 prio_descr = parser = CeleraProteinParser [source Celera_Trans::anopheles_gambiae] # Used by anopheles_gambiae name = Celera_Trans download = Y order = 40 priority = 1 prio_descr = parser = CeleraTranscriptParser release_uri = data_uri = file:Celera/Anopheles_Celera_consensus-transcripts_xref.fasta [source Codelink::homo_sapiens] # Used by homo_sapiens name = Codelink download = Y order = 50 priority = 1 prio_descr = parser = CodelinkParser release_uri = data_uri = file:Codelink/GEHC_Amersham_CodeLink_HWG_300026.fna [source Codelink::mus_musculus] # Used by mus_musculus name = Codelink download = Y order = 50 priority = 1 prio_descr = parser = CodelinkParser release_uri = data_uri = file:Codelink/GEHC_Amersham_CodeLink_MWG_300033.fna [source Codelink::rattus_norvegicus] # Used by rattus_norvegicus name = Codelink download = Y order = 50 priority = 1 prio_descr = parser = CodelinkParser release_uri = data_uri = file:Codelink/GEHC_Amersham_CodeLink_RWG_300031.fna [source DBASS5::homo_sapiens] # Used by homo_sapiens name = DBASS5 download = Y order = 50 priority = 1 prio_descr = Database of aberrant 5\' splice sites. parser = DBASSParser release_uri = data_uri = http://www.som.soton.ac.uk/research/geneticsdiv/dbass5/download.aspx?item=gene [source DBASS3::homo_sapiens] # Used by homo_sapiens name = DBASS3 download = Y order = 50 priority = 1 prio_descr = Database of aberrant 3\' splice sites. parser = DBASSParser release_uri = data_uri = http://www.som.soton.ac.uk/research/geneticsdiv/dbass3/download.asp?item=gene [source DEDb::drosophila_melanogaster] # Used by drosophila_melanogaster name = DEDb download = N order = 50 priority = 1 prio_descr = Drosophila melanogaster Exon DataBase parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz #[source DGRC-1::drosophila_melanogaster] # Used by drosophila_melanogaster #name = DGRC-1 #download = N #order = 50 #priority = 1 #prio_descr = #parser = FlybaseParser #release_uri = #data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz #[source DGRC-2::drosophila_melanogaster] # Used by drosophila_melanogaster #name = DGRC-2 #download = N #order = 50 #priority = 1 #prio_descr = #parser = FlybaseParser #release_uri = #data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz #[source DRSC::drosophila_melanogaster] # Used by drosophila_melanogaster #name = DRSC #download = N #order = 50 #priority = 1 #prio_descr = #parser = FlybaseParser #release_uri = #data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz #[source DrosDel::drosophila_melanogaster] # Used by drosophila_melanogaster #name = DrosDel #download = N #order = 50 #priority = 1 #prio_descr = #parser = FlybaseParser #release_uri = #data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source EntrezGene::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana name = EntrezGene download = Y order = 10 priority = 1 prio_descr = parser = EntrezGeneParser release_uri = data_uri = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz [source WikiGene::MULTI] name = WikiGene download = N order = 100 priority = 1 prio_descr = parser = EntrezGeneParser release_uri = data_uri = comes via EntrezGene [source Fantom::mus_musculus] # Used by mus_muscullus name = Fantom download = Y order = 100 priority = 1 prio_descr = parser = FantomParser release_uri = data_uri = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz [source flybase_annotation_id::drosophila_melanogaster] # Used by drosophila_melanogaster name = flybase_annotation_id download = N order = 50 priority = 1 prio_descr = Annotation ID assigned by FlyBase parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source flybase_gene_id::drosophila_melanogaster] # Used by drosophila_melanogaster name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dmel_5.25/seqdata/gff/dmel-all-r5.25.gff.gz [source flybase_gene_id::drosophila_pseudoobscura] # Used by drosophila_pseudoobscura name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dpse_2.8/seqdata/dpse-all-r2.8.gff.gz [source flybase_gene_id::drosophila_grimshawi] # Used by drosophila_grimshawi name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dgri_1.3/seqdata/dgri-all-r1.3.gff.gz [source flybase_gene_id::drosophila_willistoni] # Used by drosophila_willistoni name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dwil_1.3/seqdata/dwil-all-r1.3.gff.gz [source flybase_gene_id::drosophila_ananassae] # Used by drosophila_ananassae name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dana_1.3/seqdata/dana-all-r1.3.gff.gz [source flybase_gene_id::drosophila_yakuba] # Used by drosophila_yakuba name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dyak_1.3/seqdata/dyak-all-r1.3.gff.gz [source flybase_gene_id::drosophila_simulans] # Used by drosophila_simulans name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dsim_1.3/seqdata/dsim-all-r1.3.gff.gz [source flybase_gene_id::drosophila_sechellia] # Used by drosophila_sechellia name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dsec_1.3/seqdata/dsec-all-r1.3.gff.gz [source flybase_gene_id::drosophila_erecta] # Used by drosophila_erecta name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dere_1.3/seqdata/dere-all-r1.3.gff.gz [source flybase_gene_id::drosophila_persimilis] # Used by drosophila_persimilis name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dper_1.3/seqdata/dper-all-r1.3.gff.gz [source flybase_gene_id::drosophila_mojavensis] # Used by drosophila_mojavensis name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dmoj_1.3/seqdata/dmoj-all-r1.3.gff.gz [source flybase_gene_id::drosophila_virilis] # Used by drosophila_virilis name = flybase_gene_id download = Y order = 100 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser release_uri = data_uri = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/dvir-all-r1.2.gff.gz [source flybase_transcript_id::drosophila_melanogaster] # Used by drosophila_melanogaster name = flybase_transcript_id download = N order = 50 priority = 1 prio_descr = ID assigned by FlyBase parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source flybase_translation_id::drosophila_melanogaster] # Used by drosophila_melanogaster name = flybase_translation_id download = N order = 50 priority = 1 prio_descr = ID assigned by FlyBase parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseCGID_gene::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseCGID_gene download = N order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseCGID_transcript::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseCGID_transcript download = N order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseCGID_translation::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseCGID_translation download = N order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseName_gene::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseName_gene download = N order = 50 priority = 1 prio_descr = Name assigned to gene in FlyBase gff parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseName_transcript::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseName_transcript download = N order = 50 priority = 1 prio_descr = Name assigned to transcript in FlyBase gff parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyBaseName_translations::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyBaseName_translation download = N order = 50 priority = 1 prio_descr = Name assigned to translation in FlyBase gff parser = Flybase_dmel_GFFv3_Parser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyGrid::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyGrid download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyReactome::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyReactome download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source BioGRID::drosophila_melanogaster] # Used by drosophila_melanogaster name = BioGRID download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyExpress::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyExpress download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source GenomeRNAi::drosophila_melanogaster] # Used by drosophila_melanogaster name = GenomeRNAi download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyAtlas::drosophila_melanogaster] # Used by drosophila_melanogaster name = FlyAtlas download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source FlyAtlas::drosophila_pseudoobscura] # Used by drosophila_pseudoobscura name = FlyAtlas download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz [source InteractiveFly::drosophila_melanogaster] # Used by drosophila_melanogaster name = InteractiveFly download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source MitoDrome::drosophila_melanogaster] # Used by drosophila_melanogaster name = MitoDrome download = N order = 50 priority = 1 prio_descr = parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz [source GO::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana name = GO download = Y order = 80 priority = 1 prio_descr = main parser = GOParser release_uri = http://www.ebi.ac.uk/GOA/uniprot_release.html data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source InterproGO::MULTI] # Used by all name = GO download = Y order = 85 priority = 2 prio_descr = interpro parser = InterproGoParser release_uri = data_uri = http://www.geneontology.org/external2go/interpro2go [source GO::caenorhabditis_elegans] # Used by caenorhabditis_elegans name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.wb.gz [source GO::danio_rerio] # Used by danio_rerio name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source goslim_goa::MULTI] # Used by all name = goslim_goa download = Y order = 120 priority = 1 prio_descr = main parser = GOSlimParser release_uri = data_uri = script: #data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_61, [source goslim_goa::EG] # Used by Ensembl Genomes name = goslim_goa download = Y order = 120 priority = 1 prio_descr = main parser = GOSlimParser release_uri = data_uri = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensembl_ontology_62, [source GO::homo_sapiens] # Used by homo_sapiens name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = http://www.ebi.ac.uk/GOA/HUMAN_release.html data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source GO::mus_musculus] # Used by mus_musculus name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = http://www.ebi.ac.uk/GOA/MOUSE_release.html data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_association.goa_mouse.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source GO::mus_musculus#01] # Used by mus_musculus name = GO download = Y order = 85 priority = 1 prio_descr = goga parser = GOParser release_uri = data_uri = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source GO::rattus_norvegicus] # Used by rattus_norvegicus name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = http://www.ebi.ac.uk/GOA/rat_release.html data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source GO::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae name = GO download = Y order = 85 priority = 1 prio_descr = main parser = GOParser release_uri = data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.sgd.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source HPA::homo_sapiens] # Used by homo_sapiens name = HPA download = Y order = 50 priority = 1 prio_descr = Human Protein Atlas (HPA) database parser = HPAParser release_uri = data_uri = http://www.proteinatlas.org/download/xref.php #[source IMGT_HLA::homo_sapiens] # Used by homo_sapiens #name = IMGT_HLA #download = Y #order = 100 #priority = 1 #prio_descr = HLA Nomenclature database #parser = HLAParser #release_uri = #data_uri = http://hla.alleles.org/xrefs/embl.txt [source LRG_HGNC_notransfer] name = LRG_HGNC_notransfer download = N order = 30 priority = 5 prio_descr = parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens#01] # Used by homo_sapiens name = HGNC download = Y order = 30 #order 51 priority = 2 prio_descr = ccds parser = HGNC_CCDSParser release_uri = data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010, [source HGNC::homo_sapiens#07] # used by #02 name = HGNC download = N order = 30 priority = 1 prio_descr = ensembl_manual parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens] # Used by homo_sapiens name = HGNC download = Y order = 30 priority = 3 prio_descr = vega parser = HGNC_ENSTParser release_uri = data_uri = script: #data_uri = script:vuser=>ensro,vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vport=>3306,cuser=>ensro,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_61_37f, [source HGNC::homo_sapiens#02] # Used by homo_sapiens name = HGNC download = Y order = 29 priority = 4 prio_descr = entrezgene_manual parser = HGNCParser release_uri = data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr [source HGNC::homo_sapiens#03] # Used by #02 name = HGNC download = N order = 30 priority = 5 prio_descr = refseq_manual parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens#09] # used by #02 name = HGNC download = N order = 30 priority = 5 prio_descr = swissprot_manual parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens#04] # used by #02 which produces HGNC refseq and entrezgene types name = HGNC download = N order = 30 priority = 6 prio_descr = entrezgene_mapped parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens#05] # used by #02 which produces HGNC refseq and entrezgene types name = HGNC download = N order = 30 priority = 7 prio_descr = refseq_mapped parser = HGNCParser release_uri = data_uri = [source HGNC::homo_sapiens#06] # used by uniprotParser name = HGNC download = N order = 30 priority = 8 prio_descr = uniprot parser = uniprotparser release_uri = data_uri = see_uniprot [source HGNC::homo_sapiens#08] # used by #02 name = HGNC download = N order = 30 priority = 100 prio_descr = desc_only parser = HGNCParser release_uri = data_uri = [source IKMCs_KOs::mus_musculus] name = IKMCs_KOs download = Y order = 40 priority = 1 prio_descr = parser = IKMCParser release_uri = data_uri = script: [source IKMCs_No_products_available_yet::mus_musculus] name = IKMCs_No_products_available_yet download = N order = 40 priority = 1 prio_descr = parser = IKMCParser release_uri = data_uri = [source IKMCs_Vector_available::mus_musculus] name = IKMCs_Vector_available download = N order = 40 priority = 1 prio_descr = parser = IKMCParser release_uri = data_uri = [source IKMCs_ES_cells_available::mus_musculus] name = IKMCs_ES_cells_available download = N order = 40 priority = 1 prio_descr = parser = IKMCParser release_uri = data_uri = [source IKMCs_Mice_available::mus_musculus] name = IKMCs_Mice_available download = N order = 40 priority = 1 prio_descr = parser = IKMCParser release_uri = data_uri = [source IMGT/GENE_DB::homo_sapiens] # Used by homo_sapiens name = IMGT/GENE_DB download = Y order = 40 priority = 1 prio_descr = parser = SegmentParser release_uri = data_uri = file:Homo_sapiens/Segments/Seg_xrefs.txt [source IMGT/GENE_DB::mus_musculus] # Used by mus_musculus name = IMGT/GENE_DB download = Y order = 40 priority = 1 prio_descr = parser = SegmentParser release_uri = data_uri = file:Mus_musculus/Segments/Seg_xrefs.txt [source IMGT/LIGM_DB::homo_sapiens] # Special source used by SegmentParser. This source is not # used directly by any species. Data is created by the source # 'IMGT/GENE_DB::homo_sapiens'. name = IMGT/LIGM_DB download = N order = 40 priority = 1 prio_descr = parser = SegmentParser release_uri = data_uri = file:Homo_sapiens/Segments/Seg_xrefs.txt [source IMGT/LIGM_DB::mus_musculus] # Special source used by SegmentParser. This source is not # used directly by any species. Data is created by the source # 'IMGT/GENE_DB::mus_musculus'. name = IMGT/LIGM_DB download = N order = 40 priority = 1 prio_descr = parser = SegmentParser release_uri = data_uri = file:Mus_musculus/Segments/Seg_xrefs.txt [source IPI::bos_taurus] # Used by bos_taurus name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.BOVIN.fasta.gz [source IPI::gallus_gallus] # Used by gallus_gallus name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.CHICK.fasta.gz [source IPI::danio_rerio] # Used by danio_rerio name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.DANRE.fasta.gz [source IPI::homo_sapiens] # Used by homo_sapiens name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.fasta.gz [source IPI::mus_musculus] # Used by mus_musculus name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.MOUSE.fasta.gz [source IPI::rattus_norvegicus] # Used by rattus_norvegicus name = IPI download = Y order = 30 priority = 1 prio_descr = parser = IPIParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.RAT.fasta.gz [source Interpro::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes__scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum name = Interpro download = Y order = 70 priority = 1 prio_descr = parser = InterproParser release_uri = ftp://ftp.ebi.ac.uk/pub/databases/interpro/release_notes.txt data_uri = ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz [source MIM_GENE::homo_sapiens] # MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM name = MIM_GENE download = N order = 40 priority = 1 prio_descr = parser = MIMParser release_uri = data_uri = [source MIM_MORBID::homo_sapiens] # MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM name = MIM_MORBID download = N order = 40 priority = 1 prio_descr = parser = MIMParser release_uri = data_uri = [source MIM::homo_sapiens] # Used by homo_sapiens name = MIM download = Y order = 10 priority = 1 prio_descr = parser = MIMParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z [source MIM2GENE::homo_sapiens] # Used by homo_sapiens name = MIM2GENE download = Y order = 60 priority = 1 prio_descr = parser = Mim2GeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene [source MGI::mus_musculus#04] # Used by mus_musculus name = MGI download = N order = 30 priority = 4 prio_descr = uniprot parser = release_uri = data_uri = taken from uniprot files [source MGI::mus_musculus#01] # Used by mus_musculus name = MGI download = Y order = 30 priority = 1 prio_descr = official parser = MGIParser release_uri = data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_ENSEMBL.rpt [source MGI::mus_musculus#02] # Used by mus_musculus name = MGI download = Y order = 45 priority = 2 prio_descr = vega parser = MGI_Vega_Parser release_uri = data_uri = script: #data_uri = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n, [source MGI::mus_musculus#05] # Used by mus_musculus name = MGI download = Y order = 1 priority = 10 prio_descr = descriptions parser = MGI_Desc_Parser release_uri = data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.sql.rpt data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt [source MGI::mus_musculus#03] # Used by mus_musculus name = MGI download = Y order = 35 priority = 3 prio_descr = ccds parser = MGI_CCDS_Parser release_uri = data_uri = script:wget=>ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse/CCDS.20071128.txt, [source OTTT::homo_sapiens] # # NOW taken when merging done with havana # # Used by homo_sapiens name = OTTT download = N order = 50 priority = 1 prio_descr = parser = OTTTParser release_uri = data_uri = #data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_55_37, [source OTTT::mus_musculus] # # NOW taken when merging done with havana # # Used by mus_musculus name = OTTT download = N order = 50 priority = 1 prio_descr = parser = OTTTParser release_uri = data_uri = [source RGD::rattus_norvegicus] # Used by rattus_norvegicus name = RGD download = Y order = 30 priority = 1 prio_descr = parser = RGDParser release_uri = data_uri = ftp://rgd.mcw.edu/pub/data_release/GENES_RAT [source RefSeq_dna::MULTI-fungi] # Used by saccharomyces_cerevisiae name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/fungi/fungi*.rna.fna.gz [source RefSeq_dna::MULTI-complete] # Used by phaeodactylum_tricornutum name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/complete/complete*.rna.fna.gz [source RefSeq_dna::MULTI-protozoa] # Used by dictyostelium_discoideum name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/protozoa/protozoa*.rna.fna.gz [source RefSeq_dna::MULTI-invertebrate] # Used by drosophila_melanogaster name = RefSeq_dna download = Y order = 20 priority = 1 prio_descr = parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate*.rna.fna.gz [source RefSeq_dna::MULTI-predicted] # Special source used in RefSeqParser. No species uses this source. name = RefSeq_dna_predicted download = N order = 20 priority = 1 prio_descr = parser = RefSeqParser release_uri = [source RefSeq_dna::MULTI-vertebrate_mammalian] # Used by erinaceus_europaeus, gorilla_gorilla, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, spermophilus_tridecemlineatus, tupaia_belangeri, loxodonta_africana, callithrix_jacchus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian*.rna.fna.gz [source RefSeq_dna::MULTI-vertebrate_other] # Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other*.rna.fna.gz [source RefSeq_dna::apis_mellifera] # Used by apis_mellifera name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera/RNA/rna.gbk.gz [source RefSeq_dna::bos_taurus] # Used by bos_taurus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Bos_taurus/RNA/rna.gbk.gz [source RefSeq_dna::canis_familiaris] # Used by canis_familiaris name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Canis_familiaris/RNA/rna.gbk.gz [source RefSeq_dna::danio_rerio] # Used by danio_rerio name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.rna.fna.gz [source RefSeq_dna::equus_caballus] # Used by equus_caballus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Equus_caballus/RNA/rna.gbk.gz [source RefSeq_dna::gallus_gallus] # Used by gallus_gallus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Gallus_gallus/RNA/rna.gbk.gz [source RefSeq_dna::gasterosteus_aculeatus] # Used by gasterosteus_aculeatus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/sequences.fasta.gz [source RefSeq_dna::homo_sapiens] # Used by homo_sapiens name = RefSeq_dna download = Y order = 25 priority = 1 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = data_uri = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010, [source RefSeq_dna::homo_sapiens#01] # Used by homo_sapiens name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz [source RefSeq_dna::mus_musculus#01] # Used by mus_musculus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz [source RefSeq_dna::mus_musculus] # Used by mus_musculus name = RefSeq_dna download = Y order = 25 priority = 1 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = data_uri = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010, [source RefSeq_dna::pan_troglodytes] # Used by pan_troglodytes name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Pan_troglodytes/RNA/rna.gbk.gz [source RefSeq_dna::pongo_pygmaeus] # Used by pongo_pygmaeus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/pongo_pygmaeus/RNA/rna.gbk.gz [source RefSeq_dna::rattus_norvegicus] # Used by rattus_norvegicus name = RefSeq_dna download = Y order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.rna.fna.gz [source RefSeq_peptide::MULTI-fungi] # Used by saccharomyces_cerevisiae name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/fungi/fungi*.protein.gpff.gz [source RefSeq_peptide::MULTI-complete] # Used by phaeodactylum_tricornutum name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/complete/complete*.protein.gpff.gz [source RefSeq_peptide::MULTI-protozoa] # Used by dictyostelium_discoideum name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/protozoa/protozoa*.protein.gpff.gz [source RefSeq_peptide::MULTI-invertebrate] # Used by caenorhabditis_elegans, ciona_savignyi, drosophila_melanogaster name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate*.protein.gpff.gz [source RefSeq_peptide::MULTI-predicted] # Special source used in RefSeqGPFFParser. No species uses this source. name = RefSeq_peptide_predicted download = N order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = [source RefSeq_peptide::MULTI-vertebrate_mammalian] # Used by erinaceus_europaeus, gorilla_gorilla, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, spermophilus_tridecemlineatus, tupaia_belangeri, loxodonta_africana, callithrix_jacchus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian*.protein.gpff.gz [source RefSeq_peptide::MULTI-vertebrate_other] # Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other*.protein.gpff.gz [source RefSeq_peptide::apis_mellifera] # Used by apis_mellifera name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera/protein/protein.gbk.gz [source RefSeq_peptide::bos_taurus] # Used by bos_taurus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Bos_taurus/protein/protein.gbk.gz [source RefSeq_peptide::canis_familiaris] # Used by canis_familiaris name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Canis_familiaris/protein/protein.gbk.gz [source RefSeq_peptide::danio_rerio] # Used by danio_rerio name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.protein.gpff.gz [source RefSeq_peptide::equus_caballus] # Used by equus_caballus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Equus_caballus/protein/protein.gbk.gz [source RefSeq_peptide::gallus_gallus] # Used by gallus_gallus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Gallus_gallus/protein/protein.gbk.gz [source RefSeq_peptide::homo_sapiens] # Used by homo_sapiens name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.gpff.gz [source RefSeq_peptide::mus_musculus] # Used by mus_musculus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.protein.gpff.gz [source RefSeq_peptide::pan_troglodytes] # Used by pan_troglodytes name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/Pan_troglodytes/protein/protein.gbk.gz [source RefSeq_peptide::pongo_pygmaeus] # Used by pongo_pygmaeus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/genomes/pongo_pygmaeus/protein/protein.gbk.gz [source RefSeq_peptide::rattus_norvegicus] # Used by rattus_norvegicus name = RefSeq_peptide download = Y order = 20 priority = 1 prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.protein.gpff.gz [source SGD_GENE::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae name = SGD_GENE download = N order = 10 priority = 1 prio_descr = parser = SGDParser release_uri = [source SGD_TRANSCRIPT::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae name = SGD_TRANSCRIPT download = N order = 10 priority = 1 prio_descr = parser = SGDParser release_uri = [source SGD::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae name = SGD download = Y order = 10 priority = 1 prio_descr = parser = SGDParser release_uri = #data_uri = ftp://genome-ftp.stanford.edu/pub/yeast/gene_registry/registry.genenames.tab data_uri = http://downloads.yeastgenome.org/chromosomal_feature/SGD_features.tab [source UCSC::MULTI] # Special source used in UCSCParser. No species uses this source. name = UCSC download = Y order = 70 priority = 1 prio_descr = parser = UCSCParser [source UCSC::homo_sapiens] # Used by homo_sapiens name = UCSC_hg19 download = Y order = 70 priority = 1 prio_descr = parser = UCSCParser release_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/README.txt data_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz [source UCSC::mus_musculus] # Used by mus_musculus name = UCSC_mm9 download = Y order = 70 priority = 1 prio_descr = parser = UCSCParser release_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/README.txt data_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/knownGene.txt.gz [source UniGene::MULTI] # Used by erinaceus_europaeus, oryzias_latipes, spermophilus_tridecemlineatus, tupaia_belangeri name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Oryzias_latipes/Ola.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Oryzias_latipes/Ola.data.gz [source UniGene::aedes_aegypti] # Used by aedes_aegypti name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Aedes_aegypti/Aae.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Aedes_aegypti/Aae.data.gz [source UniGene::acyrthosiphon_pisum] # Used by acyrthosiphon_pisum name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Acyrthosiphon_pisum/Aps.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Acyrthosiphon_pisum/Aps.data.gz [source UniGene::anopheles_gambiae] # Used by anopheles_gambiae name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Anopheles_gambiae/Aga.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Anopheles_gambiae/Aga.data.gz [source UniGene::apis_mellifera] # Used by apis_mellifera name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Apis_mellifera/Ame.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Apis_mellifera/Ame.data.gz [source UniGene::bos_taurus] # Used by bos_taurus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Bos_taurus/Bt.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Bos_taurus/Bt.data.gz [source UniGene::caenorhabditis_elegans] # Used by caenorhabditis_elegans name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Caenorhabditis_elegans/Cel.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Caenorhabditis_elegans/Cel.data.gz [source UniGene::canis_familiaris] # Used by canis_familiaris name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Canis_familiaris/Cfa.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Canis_familiaris/Cfa.data.gz [source UniGene::ciona_intestinalis] # Used by ciona_intestinalis name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_intestinalis/Cin.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_intestinalis/Cin.data.gz [source UniGene::ciona_savignyi] # Used by ciona_savignyi name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_savignyi/Csa.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_savignyi/Csa.data.gz [source UniGene::culex_quinquefasciatus] # Used by culex_quinquefasciatus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Culex_quinquefasciatus/Cpi.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Culex_quinquefasciatus/Cpi.data.gz [source UniGene::danio_rerio] # Used by danio_rerio name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Danio_rerio/Dr.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Danio_rerio/Dr.data.gz [source UniGene::equus_caballus] # Used by equus_caballus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Equus_caballus/Eca.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Equus_caballus/Eca.data.gz [source UniGene::gallus_gallus] # Used by gallus_gallus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Gallus_gallus/Gga.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Gallus_gallus/Gga.data.gz [source UniGene::homo_sapiens] # Used by homo_sapiens name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz [source UniGene::macaca_mulatta] # Used by myotis_lucifugus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Macaca_mulatta/Mmu.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Macaca_mulatta/Mmu.data.gz [source UniGene::monodelphis_domestica] # Used by monodelphis_domestica name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.data.gz [source UniGene::ixodes_scapularis] # Used by ixodes_scapularis name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.data.gz [source UniGene::mus_musculus] # Used by mus_musculus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz [source UniGene::myotis_lucifugus] # Used by myotis_lucifugus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Myotis_lucifugus/Mlu.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Myotis_lucifugus/Mlu.data.gz [source UniGene::rattus_norvegicus] # Used by rattus_norvegicus name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz [source UniGene::taeniopygia_guttata] # Used by taeniopygia_guttata name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Taeniopygia_guttata/Tgu.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Taeniopygia_guttata/Tgu.data.gz [source UniGene::takifugu_rubripes] # Used by takifugu_rubripes name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Takifugu_rubripes/Tru.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Takifugu_rubripes/Tru.data.gz [source UniGene::xenopus_tropicalis] # Used by xenopus_tropicalis name = UniGene download = Y order = 30 priority = 1 prio_descr = parser = UniGeneParser release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Xenopus_tropicalis/Str.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Xenopus_tropicalis/Str.data.gz [source UniProt::protein_id-predicted] # Special source used in UniProtParser. No species uses this source. name = protein_id_predicted download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source UniProt::protein_id] # Special source used in UniProtParser. No species uses this source. name = protein_id download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source UniProt::PDB] # Special source used in UniProtParser. No species uses this source. name = PDB download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source Uniprot/SPTREMBL::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana name = Uniprot/SPTREMBL download = Y order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz [source Uniprot/SPTREMBL::MULTI-predicted] # Special source used in UniProtParser. No species uses this source. name = Uniprot/SPTREMBL_predicted download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source Uniprot/SWISSPROT::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana name = Uniprot/SWISSPROT download = Y order = 20 priority = 2 prio_descr = sequence_mapped parser = UniProtParser release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz # # Direct Uniprot mapping for mouse, human and rat. # Note these have to be done LAST so that we get all # the dependent xrefs that are available from the original. # swissprot entry [source Uniprot/SWISSPROT::DIRECT] # Used by homo_sapiens name = Uniprot/SWISSPROT download = Y order = 300 priority = 1 prio_descr = uniprot_mapped parser = UniProtDirectParser release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/contrib/xrefs/ens-sp.map [source Uniprot/SWISSPROT::MULTI-predicted] # Special source used in UniProtParser. No species uses this source. name = Uniprot/SWISSPROT_predicted download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source Uniprot_genename] # Special source used in UniProtParser foir gene names.. name = Uniprot_genename download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = data_uri = [source Uniprot/SWISSPROT::drosophila_melanogaster] # Used by drosophila_melanogaster name = Uniprot/SWISSPROT download = Y order = 20 priority = 1 prio_descr = parser = UniProtParser_descriptions_only release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/integr8/uniprot/proteomes/17.D_melanogaster.dat.gz [source Uniprot/SWISSPROT::drosophila_pseudoobscura] # Used by drosophila_pseudoobscura name = Uniprot/SWISSPROT download = Y order = 20 priority = 1 prio_descr = parser = UniProtParser_descriptions_only release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/integr8/uniprot/proteomes/25396.D_pseudoobscura.dat.gz [source Uniprot/SPTREMBL::drosophila_melanogaster] # Used by drosophila_melanogaster name = Uniprot/SPTREMBL download = Y order = 20 priority = 1 prio_descr = parser = UniProtParser_descriptions_only release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz [source Uniprot::EMBL-predicted] # Special source used in UniProtParser. No species uses this source. name = EMBL_predicted download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source Uniprot::EMBL] # Special source used in UniProtParser. No species uses this source. name = EMBL download = N order = 20 priority = 1 prio_descr = parser = UniProtParser release_uri = [source HGNC_curated_transcript::homo_sapiens] name = HGNC_curated_transcript_notransfer download = Y order = 49 priority = 1 prio_descr = curated with transcript number postfix parser = curated_transcriptParser release_uri = data_uri = script: #data_uri = script:vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vuser=>ensro,vport=>3306,chost=>ens-staging,cport=>3306,cdbname=>homo_sapiens_core_61_37f, [source HGNC_transcript_name] name = HGNC_transcript_name download = N order = 49 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source HGNC_gene_name] name = HGNC_gene_name download = N order = 49 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source MGI_curated_transcript::mus_musculus] name = MGI_curated_transcript_notransfer download = Y order = 49 priority = 1 prio_descr = parser = curated_transcriptParser release_uri = data_uri = script: #data_uri = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n, [source MGI_automatic_transcript::mus_musculus] name = MGI_automatic_transcript_notransfer download = N order = 49 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source MGI_gene_name] # Used homo_sapiens,mus_musculus name = MGI_gene_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source MGI_transcript_name] # Used homo_sapiens,mus_musculus name = MGI_transcript_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source Clone_based_vega_transcript::homo_sapiens] name = Clone_based_vega_transcript download = N order = 50 priority = 1 prio_descr = parser = HGNC_curated_transcriptParser release_uri = data_uri = loaded as part of HGNC_curated_transcript [source Clone_based_ensembl_transcript::homo_sapiens] name = Clone_based_ensembl_transcript download = N order = 50 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source Clone_based_vega_gene::homo_sapiens] name = Clone_based_vega_gene download = N order = 50 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source Clone_based_ensembl_gene::homo_sapiens] name = Clone_based_ensembl_gene download = N order = 50 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source Xenopus_Jamboree::xenopus_tropicalis] # Used by xenopus_tropicalis name = Xenopus_Jamboree download = Y order = 20 priority = 1 prio_descr = parser = XenopusJamboreeParser release_uri = data_uri = ftp://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt [source ZFIN_ID::danio_rerio#01] # Used by danio_rerio name = ZFIN_ID download = Y order = 30 priority = 2 prio_descr = uniprot/refseq parser = ZFINParser release_uri = data_uri = http://zfin.org/data_transfer/Downloads/refseq.txt data_uri = http://zfin.org/data_transfer/Downloads/uniprot.txt data_uri = http://zfin.org/data_transfer/Downloads/aliases.txt data_uri = http://zfin.org/data_transfer/Downloads/gene_seq.txt [source ZFIN_ID::danio_rerio#02] # Used by danio_rerio name = ZFIN_ID download = Y order = 30 priority = 1 prio_descr = vega parser = ZFIN_DARTParser release_uri = data_uri = script:vuser=>ensro,vhost=>ens-staging,vdbname=>danio_rerio_vega_61_9a,vport=>3306, [source ZFIN_ID::danio_rerio#03] # Used by danio_rerio name = ZFIN_ID download = Y order = 1 priority = 10 prio_descr = description_only parser = ZFINDescParser release_uri = data_uri = http://zfin.org/data_transfer/Downloads/genetic_markers.txt [source ZFIN_ID_curated_transcript::danio_rerio] name = ZFIN_ID_curated_transcript_notransfer download = Y order = 49 priority = 1 prio_descr = curated with transcript number postfix parser = curated_transcriptParser release_uri = data_uri = script: [source ZFIN_ID_transcript_name] name = ZFIN_ID_transcript_name download = N order = 49 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source ZFIN_ID_gene_name] name = ZFIN_ID_gene_name download = N order = 49 priority = 1 prio_descr = parser = done_in_official_naming release_uri = [source cint_aniseed_jgi_v1::ciona_intestinalis] # Used by ciona_intestinalis name = cint_aniseed_jgi_v1 download = Y order = 50 priority = 1 prio_descr = parser = JGI_ProteinParser release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v1.0/ciona.prot.fasta.gz [source cint_aniseed_jgi_v2::ciona_intestinalis] # Used by ciona_intestinalis name = cint_aniseed_jgi_v2 download = Y order = 50 priority = 1 prio_descr = parser = JGI_ProteinParser release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v2.0/FM1.aa.fasta.gz [source cint_jgi_v1::ciona_intestinalis] # Used by ciona_intestinalis name = cint_jgi_v1 download = Y order = 50 priority = 1 prio_descr = parser = JGI_ProteinParser release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v1.0/ciona.prot.fasta.gz [source cint_jgi_v2::ciona_intestinalis] # Used by ciona_intestinalis name = cint_jgi_v2 download = Y order = 50 priority = 1 prio_descr = parser = JGI_ProteinParser release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v2.0/FM1.aa.fasta.gz [source RFAM::MULTI] # Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_pseudoobscura, erinaceus_europaeus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_pygmaeus, rattus_norvegicus, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus name = RFAM download = N order = 70 priority = 1 prio_descr = parser = comes via ncRNAParser release_uri = data_uri = [source miRBase::MULTI] # Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, erinaceus_europaeus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_pygmaeus, rattus_norvegicus, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus name = miRBase download = N order = 70 priority = 1 prio_descr = parser = comes via ncRNAParser release_uri = data_uri = [source miRBase_gene_name] # Used homo_sapiens,mus_musculus name = miRBase_gene_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source miRBase_transcript_name] # Used homo_sapiens,mus_musculus name = miRBase_transcript_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source ncRNA::MULTI] name = ncRNA download = Y order = 70 priority = 1 prio_descr = parser = ncRNA_DBParser release_uri = data_uri = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs, [source RFAM_gene_name] # Used homo_sapiens,mus_musculus name = RFAM_gene_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source RFAM_transcript_name] # Used homo_sapiens,mus_musculus name = RFAM_transcript_name download = N order = 70 priority = 1 prio_descr = parser = comes via official naming release_uri = data_uri = [source RNAMMER::MULTI-asp] # Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri name = RNAMMER download = N order = 70 priority = 1 prio_descr = parser = release_uri = data_uri = [source TRNASCAN-SE::MULTI-asp] # Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri name = TRNASCAN-SE download = N order = 70 priority = 1 prio_descr = parser = release_uri = data_uri = [source wormpep_id::caenorhabditis_elegans] # Used by caenorhabditis_elegans name = wormpep_id download = Y order = 50 priority = 1 prio_descr = parser = WormPepParser release_uri = data_uri = ftp://ftp.sanger.ac.uk/pub/databases/wormpep/wormpep180/wormpep.table180 [source wormpep_id::caenorhabditis_elegans#01] # Used by caenorhabditis_elegans name = wormpep_id download = Y order = 50 priority = 1 prio_descr = parser = WormbaseDatabaseStableIDParser release_uri = data_uri = mysql:ensembldb.ensembl.org::caenorhabditis_elegans_core_46_170b:anonymous [source wormbase_gene::caenorhabditis_elegans] # Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser name = wormbase_gene download = N order = 50 priority = 1 prio_descr = parser = comes from WormbaseDatabaseStableIDParser release_uri = data_uri = [source wormbase_locus::caenorhabditis_elegans] # Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser name = wormbase_locus download = N order = 50 priority = 1 prio_descr = parser = comes from WormbaseDatabaseStableIDParser release_uri = data_uri = [source wormbase_transcript::caenorhabditis_elegans] # Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser name = wormbase_transcript download = N order = 50 priority = 1 prio_descr = parser = comes from WormbaseDatabaseStableIDParser release_uri = data_uri = [source Platypus_olfactory_receptor::ornithorhynchus_anatinus] # Used by ornithorhynchus_anatinus name = Platypus_olfactory_receptor download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:platypus/olfactory_receptor_list [source Oxford_FGU_Oa_gene::ornithorhynchus_anatinus] # Used by ornithorhynchus_anatinus name = Oxford_FGU_Oa_gene download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:platypus/oxford_gene_list [source Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus] # Used by ornithorhynchus_anatinus name = Oxford_FGU_Oa_tscript download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:platypus/oxford_transcript_list [source Genoscope_pred_gene::tetraodon_nigroviridis] # Used by name = Genoscope_pred_gene download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:tetraodon_nigroviridis/genoscope_gene_list [source Genoscope_pred_transcript::tetraodon_nigroviridis] # Used by name = Genoscope_tnig_transcript download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:tetraodon_nigroviridis/genoscope_transcript_list [source Genoscope_pred_translation::tetraodon_nigroviridis] # Used by name = Genoscope_pred_translation download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:tetraodon_nigroviridis/genoscope_translation_list [source Genoscope_annotated_gene::tetraodon_nigroviridis] # Used by name = Genoscope_annotated_gene download = Y order = 40 priority = 1 prio_descr = parser = DirectParser release_uri = data_uri = file:tetraodon_nigroviridis/genescope_annotated_gene_list [source PUBMED::anopheles_gambiae] # Used by Anopheles gambiae name = PUBMED download = Y order = 40 priority = 1 prio_descr = parser = VBPubMedParser release_uri = data_uri = file:PubMed/PubMed_citations_Anopheles_gambiae_PEST.txt [source PUBMED::aedes_aegypti] # Used by Aedes aegypti name = PUBMED download = Y order = 40 priority = 1 prio_descr = parser = VBPubMedParser release_uri = data_uri = file:PubMed/PubMed_citations_Aedes_aegypti_Liverpool.txt [source Ribosomal_Protein_Gene_DB::anopheles_gambiae] # Used by Anopheles gambiae name = Ribosomal_Protein_Gene_DB download = Y order = 40 priority = 1 prio_descr = parser = VBribosomalParser release_uri = data_uri = file:Ribosomal_Protein_Gene_Database/RPG_Anopheles_gambiae_PEST.txt ######################################################################## # SPECIES # # # # Keys: # # taxonomy_id - taxonomy ID of species/strain (multiple, required) # # aliases - comma-separated list of aliases (optional) # # source - sources use for this species/strain # # (multiple, required) # # # ######################################################################## [species aedes_aegypti] taxonomy_id = 7159 aliases = aaegypti, aedes, aedesaegypti #source = AedesGenBank::aedes_aegypti source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = UniGene::aedes_aegypti source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ImmunoDB::aedes_aegypti source = VB_External_Description::aedes_aegypti source = VB_RNA_Description::aedes_aegypti source = VB_Community_Annotation::aedes_aegypti source = PUBMED::aedes_aegypti [species acyrthosiphon_pisum] taxonomy_id = 7029 aliases = apisum, acyrthosiphon, acyrthosiphonpisum, pea aphid source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = UniGene::acyrthosiphon_pisum source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species ailuropoda_melanoleuca] taxonomy_id = 9646 aliases = Panda, panda, giant panda, ailuropodamelanoleuca source = EntrezGene::MULTI source = GO::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species anopheles_gambiae] taxonomy_id = 7165 taxonomy_id = 180454 aliases = agambiae, anopheles, anophelesgambiae, mosquito source = Celera_Pep::anopheles_gambiae source = Celera_Gene::anopheles_gambiae source = Celera_Trans::anopheles_gambiae source = VB_Community_Annotation::anopheles_gambiae source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = UniGene::anopheles_gambiae source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = VB_RNA_Description::anopheles_gambiae source = ImmunoDB::anopheles_gambiae source = PUBMED::anopheles_gambiae source = Ribosomal_Protein_Gene_DB::anopheles_gambiae source = AnoXcel::anopheles_gambiae [species apis_mellifera] taxonomy_id = 7460 aliases = amellifera, apismellifera, honeybee source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::apis_mellifera source = RefSeq_peptide::apis_mellifera source = UniGene::apis_mellifera source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species aspergillus_clavatus] taxonomy_id = 5057 taxonomy_id = 344612 aliases = aspergillusclavatus, aclavatus, Aspergillus clavatus, Aspergillus clavatus NRRL 1 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_flavus] taxonomy_id = 5059 taxonomy_id = 332952 aliases = aspergillusflavus, aflavus, Aspergillus flavus, Aspergillus flavus NRRL3357 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_fumigatus] taxonomy_id = 330879 aliases = aspergillusfumigatus, afumigatus, Aspergillus fumigatus, Aspergillus fumigatus Af293,Sartorya fumigata,sartoryafumigata,sfumigata source = EntrezGene::MULTI source = goslim_goa::EG source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species afumigatusa1163] taxonomy_id = 451804 aliases = aspergillusfumigatus, afumigatus, Aspergillus fumigatus, Aspergillus fumigatus A1163,Aspergillus fumigatus CEA10,Sartorya fumigata,sartoryafumigata,sfumigata source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_nidulans] taxonomy_id = 162425 taxonomy_id = 227321 aliases = aspergillusnidulans, anidulans, Aspergillus nidulellus, aspergillusnidulellus, anidulellus, Emericella nidulans, emericellanidulans, enidulans, Aspergillus nidulans FGSC A4 source = EntrezGene::MULTI source = goslim_goa::EG source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_niger] taxonomy_id = 425011 aliases = aspergillusniger, aniger, Aspergillus niger, Aspergillus niger CBS 513.88 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_oryzae] taxonomy_id = 5062 taxonomy_id = 510516 aliases = aspergillusoryzae, aoryzae, Aspergillus oryzae, Aspergillus oryzae RIB40 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species aspergillus_terreus] taxonomy_id = 33178 taxonomy_id = 341663 aliases = aspergillusterreus, aterreus, Aspergillus terreus, Aspergillus terreus NIH2624 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species neosartorya_fischeri] taxonomy_id = 36630 taxonomy_id = 331117 aliases = neosartoryafischeri, nfischeri, Neosartorya fischeri, Neosartorya fischeri NRRL 181 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species puccinia_graministritici] taxonomy_id = 418459 taxonomy_id = 56615 aliases = pucciniagraministritici, pgraminis, Puccinia graminis f. sp. tritici, Puccinia graminis f. sp. tritici CRL 75-36-700-3 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species trichoplax_adhaerens] taxonomy_id = 10228 aliases = trichoplaxadhaerens, tadhaerens, Trichoplax adhaerens, Trichoplax adhaerens Grell-BS-1999 source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species schistosoma_mansoni] taxonomy_id = 6183 aliases = schistosomamansoni, smansoni, Schistosoma mansoni, Schistosoma mansoni Puerto Rico source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species bos_taurus] taxonomy_id = 9913 aliases = bostaurus, btaurus, cow source = EntrezGene::MULTI source = GO::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = IPI::bos_taurus source = RefSeq_dna::bos_taurus source = RefSeq_peptide::bos_taurus source = UniGene::bos_taurus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI source = goslim_goa::MULTI [species caenorhabditis_elegans] taxonomy_id = 6239 aliases = caenorhabditiselegans, celegans, elegans source = EntrezGene::MULTI source = GO::caenorhabditis_elegans source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = UniGene::caenorhabditis_elegans source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = wormpep_id::caenorhabditis_elegans source = wormpep_id::caenorhabditis_elegans#01 [species callithrix_jacchus] taxonomy_id = 9483 aliases = Marmoset, marmoset, white-tufted-ear marmoset, callithrixjacchus, callithrix_jacchus source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species canis_familiaris] taxonomy_id = 9615 aliases = canisfamiliaris, cfamiliaris, dog, doggy source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::canis_familiaris source = RefSeq_peptide::canis_familiaris source = UniGene::canis_familiaris source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species ciona_intestinalis] taxonomy_id = 7719 aliases = cintestinalis, cionaintestinalis, seasquirt source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::ciona_intestinalis source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = cint_aniseed_jgi_v1::ciona_intestinalis source = cint_aniseed_jgi_v2::ciona_intestinalis source = cint_jgi_v1::ciona_intestinalis source = cint_jgi_v2::ciona_intestinalis source = ncRNA::MULTI [species ciona_savignyi] taxonomy_id = 51511 aliases = ciona_savi, csav, savi source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-invertebrate source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::ciona_savignyi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species culex_quinquefasciatus] taxonomy_id = 7176 aliases = cpipiens, culex, culexpipiens, culex quinquefasciatus, cquinquefasciatus, culexquinquefasciatus source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = Interpro::MULTI source = UniGene::culex_quinquefasciatus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI #source = ncRNA::culex_quinquefasciatus source = ImmunoDB::culex_quinquefasciatus source = VB_External_Description::culex_quinquefasciatus source = VB_RNA_Description::culex_quinquefasciatus [species danio_rerio] taxonomy_id = 7955 aliases = danio, daniorerio, drerio, zebrafish source = EntrezGene::MULTI source = GO::danio_rerio source = goslim_goa::MULTI source = InterproGO::MULTI source = IPI::danio_rerio source = Interpro::MULTI source = RefSeq_dna::danio_rerio source = RefSeq_peptide::danio_rerio source = UniGene::danio_rerio source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ZFIN_ID::danio_rerio#01 source = ZFIN_ID::danio_rerio#02 source = ZFIN_ID::danio_rerio#03 source = ncRNA::MULTI #source = ZFIN_ID_curated_transcript::danio_rerio [species dasypus_novemcinctus] taxonomy_id = 9361 aliases = armadillo, dasypusnovemcinctus, dnovemcinctus source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species dictyostelium_discoideum] taxonomy_id = 366501 taxonomy_id = 44689 aliases = dictyostelium, dictyostelium_discoideum,Slime_mold source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-protozoa source = RefSeq_peptide::MULTI-protozoa source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species dipodomys_ordii] taxonomy_id = 10020 aliases = kangaroorat, roorat source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species drosophila_melanogaster] taxonomy_id = 7227 aliases = dmelongaster, drosophila, drosophilamelanogaster source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::DIRECT source = flybase_gene_id::drosophila_melanogaster source = EPD::drosophila_melanogaster source = MEROPS::drosophila_melanogaster source = miRBase::drosophila_melanogaster source = TransFac::drosophila_melanogaster source = FlyReactome::drosophila_melanogaster source = BioGRID::drosophila_melanogaster source = MitoDrome::drosophila_melanogaster source = GenomeRNAi::drosophila_melanogaster source = FlyExpress::drosophila_melanogaster source = InteractiveFly::drosophila_melanogaster #source = Uniprot/SPTREMBL::drosophila_melanogaster #source = Uniprot/SWISSPROT::drosophila_melanogaster #source = Uniprot/Varsplic::MULTI??? [species drosophila_pseudoobscura] taxonomy_id = 7237 aliases = dpseudoobscura, drosophila, drosophilapseudoobscura source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_pseudoobscura source = EPD::drosophila_pseudoobscura source = TransFac::drosophila_pseudoobscura source = miRBase::drosophila_pseudoobscura source = RFAM::MULTI [species drosophila_grimshawi] taxonomy_id = 7222 aliases = dgrimshawi, drosophila, drosophilagrimshawi source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = Interpro::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_grimshawi source = MEROPS::drosophila_grimshawi [species drosophila_willistoni] taxonomy_id = 7260 aliases = dwillistoni, drosophila, drosophilawillistoni source = EntrezGene::MULTI source = Interpro::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI #source = Uniprot/SPTREMBL::drosophila_melanogaster #source = Uniprot/SWISSPROT::drosophila_willistoni #source = Uniprot/Varsplic::MULTI??? source = flybase_gene_id::drosophila_willistoni [species drosophila_ananassae] taxonomy_id = 7217 aliases = dananassae, drosophila, drosophilaananassae source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = Interpro::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_ananassae [species drosophila_yakuba] taxonomy_id = 7245 aliases = dyakuba, drosophila, drosophilayakuba source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_yakuba [species drosophila_simulans] taxonomy_id = 7240 aliases = dsimulans, drosophila, drosophilasimulans source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_simulans source = EPD::drosophila_simulans [species drosophila_sechellia] taxonomy_id = 7238 aliases = dsechellia, drosophila, drosophilasechellia source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_sechellia source = EPD::drosophila_sechellia [species drosophila_erecta] taxonomy_id = 7220 aliases = derecta, drosophila, drosophilaerecta source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_erecta source = MEROPS::drosophila_erecta [species drosophila_persimilis] taxonomy_id = 7234 aliases = dpersimilis, drosophila, drosophilapersimilis source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_persimilis [species drosophila_mojavensis] taxonomy_id = 7230 aliases = dmojavensis, drosophila, drosophilamojavensis source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_mojavensis source = EPD::drosophila_mojavensis [species drosophila_virilis] taxonomy_id = 7244 aliases = dvirilis, drosophila, drosophilavirilis source = EntrezGene::MULTI source = Interpro::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = flybase_gene_id::drosophila_virilis source = EPD::drosophila_virilis source = MEROPS::drosophila_virilis #source = TF::drosophila_virilis #source = GLEANR::drosophila_virilis #source = GPCR::drosophila_virilis [species echinops_telfairi] taxonomy_id = 9371 aliases = echinopstelfairi, etelfairi, tenrec source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species erinaceus_europaeus] taxonomy_id = 9365 aliases = hedgehog source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species equus_caballus] taxonomy_id = 9796 aliases = horse source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::equus_caballus source = RefSeq_peptide::equus_caballus source = UniGene::equus_caballus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species felis_catus] taxonomy_id = 9685 aliases = cat, fcatus, feliscatus, moggy, tiddles source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species gallus_gallus] taxonomy_id = 9031 aliases = chick, chicken, gallusgallus, ggallus source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = IPI::gallus_gallus source = RefSeq_dna::gallus_gallus source = RefSeq_peptide::gallus_gallus source = UniGene::gallus_gallus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species gasterosteus_aculeatus] taxonomy_id = 69293 aliases = gaculeatus, gasterosteusaculeatus, stickleback source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_dna::gasterosteus_aculeatus source = RefSeq_peptide::MULTI-vertebrate_other source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species gorilla_gorilla] taxonomy_id = 9593 aliases = gorilla source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species homo_sapiens] taxonomy_id = 9606 aliases = homosapiens, hsapiens, human source = CCDS::homo_sapiens source = DBASS5::homo_sapiens source = DBASS3::homo_sapiens source = EntrezGene::MULTI source = GO::homo_sapiens source = HPA::homo_sapiens source = InterproGO::MULTI source = HGNC::homo_sapiens source = HGNC::homo_sapiens#01 source = HGNC::homo_sapiens#02 source = IPI::homo_sapiens source = Interpro::MULTI source = MIM::homo_sapiens source = MIM2GENE::homo_sapiens source = RefSeq_dna::homo_sapiens source = RefSeq_dna::homo_sapiens#01 source = RefSeq_peptide::homo_sapiens source = UniGene::homo_sapiens source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::DIRECT source = ncRNA::MULTI source = UCSC::homo_sapiens source = HGNC_curated_transcript::homo_sapiens source = goslim_goa::MULTI [species ixodes_scapularis] taxonomy_id = 6945 aliases = ixodes, ixodesscapularis, ixodes scapularis source = Ixodes_ManualAnnotation::ixodes_scapularis source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = UniGene::ixodes_scapularis source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species loxodonta_africana] taxonomy_id = 9785 aliases = elephant, lafricana, loxodontaafricana source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian [species macaca_mulatta] taxonomy_id = 9544 aliases = macaque, rhesus, rhesus macaque, rmacaque source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = UniGene::macaca_mulatta source = ncRNA::MULTI [species monodelphis_domestica] taxonomy_id = 13616 aliases = mdomestica, mono, monodelphis, monodelphisdomestica, opossum, possum source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = UniGene::monodelphis_domestica source = ncRNA::MULTI [species mus_musculus] taxonomy_id = 10090 aliases = mmusculus, mouse, musmusculus source = CCDS::mus_musculus source = EntrezGene::MULTI source = GO::mus_musculus source = GO::mus_musculus#01 source = goslim_goa::MULTI source = InterproGO::MULTI source = IMGT/GENE_DB::mus_musculus source = IKMCs_KOs::mus_musculus source = IPI::mus_musculus source = MGI::mus_musculus#01 source = MGI::mus_musculus#02 source = MGI::mus_musculus#03 source = MGI::mus_musculus#05 source = MGI_curated_transcript::mus_musculus source = Interpro::MULTI source = RefSeq_dna::mus_musculus source = RefSeq_dna::mus_musculus#01 source = RefSeq_peptide::mus_musculus source = UniGene::mus_musculus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::DIRECT source = ncRNA::MULTI source = UCSC::mus_musculus source = Fantom::mus_musculus [species myotis_lucifugus] taxonomy_id = 59463 aliases = little brown bat, microbat source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = UniGene::myotis_lucifugus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species ochotona_princeps] taxonomy_id = 9978 aliases = pika, American pika source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species ornithorhynchus_anatinus] taxonomy_id = 9258 aliases = duckbilled_platypus, duckbilledplatypus, ornithorhynchusanatinus, platypus source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus source = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus source = Platypus_olfactory_receptor::ornithorhynchus_anatinus source = ncRNA::MULTI [species oryctolagus_cuniculus] taxonomy_id = 9986 aliases = ocuniculus, oryctolaguscuniculus, rabbit source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species oryzias_latipes] taxonomy_id = 8090 aliases = japanese medaka, japanese ricefish, medaka source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = UniProt::protein_id source = Uniprot::EMBL source = ncRNA::MULTI [species pan_troglodytes] taxonomy_id = 9598 aliases = pantroglodytes, ptroglodytes, chimpanzee, chimp source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::pan_troglodytes source = RefSeq_peptide::pan_troglodytes source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species pediculus_humanus] taxonomy_id = 121225 aliases = pediculushumanus, pediculus, phumanus source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = UniGene::aedes_aegypti source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species pongo_pygmaeus] taxonomy_id = 9600 aliases = pongopygmaeus, ppygmaeus, orangutan, orang source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::pongo_pygmaeus source = RefSeq_peptide::pongo_pygmaeus source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species procavia_capensis] taxonomy_id = 9813 aliases = rockhyrax, hyrax, procap source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species pteropus_vampyrus] taxonomy_id = 132908 aliases = megabat, pvampyrus, largeflyingfox source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species rattus_norvegicus] taxonomy_id = 10116 aliases = rat, rattusnorvegicus, rnovegicus source = EntrezGene::MULTI source = GO::rattus_norvegicus source = goslim_goa::MULTI source = InterproGO::MULTI source = IPI::rattus_norvegicus source = Interpro::MULTI source = RGD::rattus_norvegicus source = RefSeq_dna::rattus_norvegicus source = RefSeq_peptide::rattus_norvegicus source = UniGene::rattus_norvegicus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::DIRECT source = ncRNA::MULTI [species saccharomyces_cerevisiae] taxonomy_id = 4932 taxonomy_id = 559292 aliases = saccharomyces, saccharomycescerevisiae, scerevisiae, yeast source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = SGD::saccharomyces_cerevisiae source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species phaeodactylum_tricornutum] taxonomy_id = 2850 taxonomy_id = 556484 aliases = diatom, phaeodactlyum_tricornutum, phaeodactlyum, source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-complete source = RefSeq_peptide::MULTI-complete source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species thalassiosira_pseudonana] taxonomy_id = 35128 taxonomy_id = 296543 aliases = diatom,thalassiosira_pseudonana,thalassiosira source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-complete source = RefSeq_peptide::MULTI-complete source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species spermophilus_tridecemlineatus] taxonomy_id = 43179 aliases = squirrel, thirteen-lined ground squirrel source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species taeniopygia_guttata] taxonomy_id = 59729 aliases = zebrafinch, zebra_finch, taeniopygiaguttata, tguttata, poephila_guttata, taenopygia_guttata, poephilaguttata, taenopygiaguttata source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::taeniopygia_guttata source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species takifugu_rubripes] taxonomy_id = 31033 aliases = frubripes, fugu, fugu_rubripes, fugurubripes, pufferfish source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::takifugu_rubripes source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species tarsius_syrichta] taxonomy_id = 9478 aliases = tarsier, bonyfingers source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species tetraodon_nigroviridis] taxonomy_id = 99883 aliases = tetraodon, tnigroviridis, tnig, tetraodon_nigroviridis source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI source = Genoscope_pred_gene::tetraodon_nigroviridis source = Genoscope_pred_transcript::tetraodon_nigroviridis source = Genoscope_pred_translation::tetraodon_nigroviridis source = Genoscope_annotated_gene::tetraodon_nigroviridis [species tupaia_belangeri] taxonomy_id = 37347 aliases = treeshrew source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species tursiops_truncatus] taxonomy_id = 9739 aliases = dolphin, bottlenose_dolphi source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species vicugna_pacos] taxonomy_id = 30538 aliases = alpaca, lama_pacos source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species choloepus_hoffmanni] taxonomy_id = 9358 aliases = sloth source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ncRNA::MULTI [species xenopus_tropicalis] taxonomy_id = 8364 aliases = pipid, pipidfrog, xenopus, xenopustropicalis, xtropicalis source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = UniGene::xenopus_tropicalis source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Xenopus_Jamboree::xenopus_tropicalis source = ncRNA::MULTI [species magnaporthe_oryzae] taxonomy_id = 242507 taxonomy_id = 148305 aliases = rice blast, magnaporthe, magnaportheoryzae, moryzae source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-fungi source = RefSeq_peptide::MULTI-fungi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = RFAM::MULTI source = TRNASCAN-SE::MULTI-asp source = RNAMMER::MULTI-asp [species phytophthora_infestans] taxonomy_id = 403677 taxonomy_id = 4787 aliases = phytophthora_infestans source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-complete source = RefSeq_peptide::MULTI-complete source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species phytophthora_sojae] taxonomy_id = 67593 aliases = phytophthora_sojae source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-complete source = RefSeq_peptide::MULTI-complete source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species phytophthora_ramorum] taxonomy_id = 164328 aliases = phytophthora_ramorum source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-complete source = RefSeq_peptide::MULTI-complete source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI [species nomascus_leucogenys] taxonomy_id = 61853 aliases = nomascus_leucogenys, gibbon, Gibbon source = EntrezGene::MULTI source = GO::MULTI source = InterproGO::MULTI source = Interpro::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI