8300 PIR \N XREF 5 PIR MISC \N \N \N
828 FlyBaseCGID_translation \N XREF 50 FlyBase translation CGID MISC \N \N \N
50855 wormbase_cds \N KNOWNXREF 5 WormBase CDS MISC \N \N \N
9410 TetNig_fugu_econtig \N XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
50653 WashingtonUniversity \N KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
12410 Clone_based_vega_transcript \N KNOWNXREF 5 Clone-based (Vega) transcript MISC \N \N \N
1801 RefSeq_mRNA \N KNOWN 200 RefSeq mRNA MISC \N \N \N
50873 BurtonLabUCSD \N KNOWN 100 BurtonLabUCSD MISC \N \N The Burton Lab, Scripps Institution of Oceanography, UCSD Marine Biology Research Division (https://burtonlab.weebly.com).
5720 Ens_Cf_translation \N XREF 5 Ensembl Dog Translation MISC \N \N \N
3400 SGD \N KNOWN 50 SGD PRIMARY_DB_SYNONYM \N \N \N
50867 BRC4_seq_region_name \N KNOWNXREF 1 BRC4_seq_region_name PRIMARY_DB_SYNONYM \N \N Marking default seq region synonyms for BRC4.
50625 SGSC \N KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
50741 dbSNP \N XREF 101 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
50719 ENA_TRANSCRIPT \N KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source transcript model when importing from ENA.
2800 RGD \N KNOWNXREF 50 RGD Symbol PRIMARY_DB_SYNONYM \N \N \N
805 flybase_symbol \N KNOWNXREF 50 FlyBase symbol MISC \N \N \N
50720 LGBPratt_EST_Cluster \N KNOWNXREF 1 LGBPratt_EST_Cluster MISC \N \N \N
20066 HAMAP \N KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
50796 PATO \N KNOWNXREF 1 Phenotypic Qualities Ontology MISC \N \N http://obofoundry.org/wiki/index.php/PATO:Main_Page
50629 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 23, from Vega
50824 Reactome_gene \N KNOWNXREF 0 Reactome gene PRIMARY_DB_SYNONYM \N \N Reactome entries linked to genes
50776 LNCC \N XREF 30 LNCC MISC \N \N The National Laboratory of Scientific Computation (Laboratorio Nacional de Computacao Cientifica: LNCC), Brazil
20200 EMBLBANK_GENE \N KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
20061 DisProt \N KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
1806 RefSeq_mRNA_predicted \N PRED 199 RefSeq mRNA predicted MISC \N \N \N
20365 tuber_genoscope_gene \N KNOWNXREF 0 Tuber Genome Browser PRIMARY_DB_SYNONYM \N \N \N
12710 WTSI_gorilla_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
50737 CGNC \N KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
50723 Ens_Bt_translation \N XREF 5 Ensembl Cow Translation MISC \N \N \N
50679 Ens_Ac_translation \N XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
4680 shares_CDS_and_UTR_with_OTTT \N XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
20340 BROAD_G_zeae \N KNOWNXREF 0 Broad Institute MISC \N \N \N
5810 Ens_Dr_transcript \N XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
2320 Vega_translation \N KNOWNXREF 5 Vega translation MISC \N \N \N
50666 IGDBCAS-v1.4_GENE \N KNOWN 1 IGDBCAS v1.4 Gene MISC \N \N \N
9420 TetNig_human_econtig \N XREF 40 Genoscope human exofish econtig MISC \N \N \N
2440 wormbase_locus \N KNOWN 5 WormBase Locus MISC \N \N \N
9200 TakRub_est \N XREF 40 Takifugu EST MISC \N \N \N
50757 UniPathway \N XREF 0 UniPathway MISC \N \N UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions.
50632 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 26, from Vega
50792 CL \N KNOWNXREF 0 Cell Type Ontology MISC \N \N Cell type ontology annotations (http://cellontology.org/)
50733 Chicken_Genome_Consortium \N KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
50840 RefSeq \N KNOWNXREF 0 NCBI Reference Sequences MISC \N \N NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
2000 Uniprot/SPTREMBL \N KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
50835 VectorBase_Proteome \N KNOWN 50 VectorBase Proteome MISC \N \N \N
20072 IntAct \N KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
20309 CADRE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
20088 Reactome \N KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
5100 IMGT_HLA \N KNOWN 7 IMGT/HLA MISC \N \N \N
7300 Ens_Mg_transcript \N XREF 40 Ensembl Turkey Transcript MISC \N \N \N
1810 RefSeq_peptide \N KNOWN 210 RefSeq peptide MISC \N \N \N
50877 LJMU_translation \N KNOWN 100 Liverpool John Moores University translations data MISC \N \N Data provided by the Liverpool John Moores University (https://www.ljmu.ac.uk) for translations.
20215 phatr_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
2410 wormbase_transcript \N KNOWN 5 WormBase Transcript MISC \N \N \N
211 BRC4_Community_Symbol \N KNOWN 50 BRC4 Community Symbol MISC \N \N \N
50715 TIGR_ID \N XREF 1 TIGR Internal ID MISC \N \N cross-references to TIGR internal identifiers, attached to genes.
50859 KNETMINER_ARA \N KNOWNXREF 5 KNETMINER_ARA MISC \N \N \N
12315 Clone_based_ensembl_gene \N XREF 5 Clone-based (Ensembl) gene MISC \N \N \N
50815 Ensembl_Fungi \N XREF 1 Ensembl Fungi ENSEMBL \N \N Ensembl Fungi identifiers serving GO projections from a reference species to other fungal species.
833 MitoDrome \N KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
50541 LRG \N KNOWN 10 Locus Reference Genomic MISC \N \N \N
50697 NCBI_TAXONOMY \N KNOWNXREF 1 NCBI species MISC \N \N Organism listed in NCBI
50740 PHIE \N KNOWNXREF 1 PHI-base condition ontology MISC \N \N PHI-base experimental evidence ontology for genes proven to affect the outcome of pathogen-host interactions
50200 GRO \N XREF 0 Plant Growth Stage MISC \N \N \N
812 gadfly_translation_cgid \N XREF 10 Gadfly translation CGID MISC \N \N \N
825 FlyBaseName_transcript \N XREF 50 FlyBase transcript name MISC \N \N \N
50620 Illumina_Bodymap_transcriptome \N XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
20310 CADRE_GENE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
4810 ENST_ident \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
50872 MARIMBA \N KNOWN 100 MARIMBA MISC \N \N Marine Invertebrate Models Database (https://marimba.obs-vlfr.fr)
50820 PGSB_WHEAT_GENE \N KNOWNXREF 1 Wheat survey sequence PGSB gene identifier MISC \N \N Bread wheat survey sequence gene models from PGSB Wheat Genome Database (formerly MIPS). Release 2.2
7200 IMGT/LIGM_DB \N XREF 10 IMGT/LIGM-DB MISC \N \N \N
50728 ENA_FEATURE_PROTEIN \N KNOWNXREF 1 European Nucleotide Archive feature (translation source) MISC \N \N Cross-reference to the ENA object from which the translation has been inferred, when loading a genome from ENA records.
50661 BRAD_GENE \N XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
12310 Clone_based_vega_gene \N KNOWNXREF 5 Clone-based (Vega) gene MISC \N \N \N
50744 EntrezGene_trans_name \N KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
9600 Trace_archive \N XREF 40 Trace Archive id MISC \N \N \N
4600 OTTG \N XREF 1 Havana gene ALT_GENE \N \N \N
50854 Schisto_previous_id \N KNOWNXREF 5 Related identifier from previous versions of S. mansoni annotation MISC \N \N \N
20217 phatr_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
10100 EPD \N KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
50643 PomBase_Systematic_ID \N KNOWNXREF 5 PomBase Systematic ID MISC \N \N \N
50648 BROAD_Magnaporthe_DB_GENE \N KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
2510 ZFIN_ID \N KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
50832 EpiRR \N KNOWN 0 EpiRR MISC \N \N EpiRR is a registry of reference epigenomes.
50889 CNCB_NGDC \N XREF 100 CNCB-NGDC MISC \N \N The National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn), part of the China National Center for Bioinformation (CNCB).
50628 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 22, from Vega
50701 PGSC_GENE \N XREF 1 PGSC MISC \N \N Potato Genome Sequencing Consortium database
50637 CSAC \N KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
50838 NHPRTR \N KNOWN 5 Nonhuman Primate Reference Transcriptome Resource MISC \N \N \N
20085 REBASE \N KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
20358 BROAD_P_triticina_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20043 TubercuList \N KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
50846 BARLEX \N KNOWN 1 BARLEX: The Barley Genome Explorer MISC \N \N The barley genome explorer allows a visual inspection of BAC overlaps. In addition to a graph view the user can access dotplots and fingerprints to compare two individual BACs with each other. Information to genes and markers is available as well.
50692 GRC_alignment_import \N XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
50000 BGI_EST_Cluster \N XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
20308 ASPGD_TRANSCRIPT \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
50886 submitter_sequence_name \N KNOWN 1 Submitter sequence name PRIMARY_DB_SYNONYM \N \N \N
801 flybase_translation_id \N KNOWNXREF 5 FlyBase translation MISC \N \N \N
50827 GEO \N XREF 0 Gene Expression Omnibus MISC \N \N \N
50755 BindingDB \N XREF 0 BindingDB MISC \N \N BindingDB is a public, web-accessible database of measured binding affinities
20339 BROAD_F_oxysporum_TRANSCRIPT \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
12630 BGI_duck_transcriptome \N XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
50542 ENS_LRG_gene \N KNOWN 10 LRG display in Ensembl gene MISC \N \N \N
20354 BROAD_U_maydis \N KNOWNXREF 0 Broad Institute MISC \N \N \N
50784 Ensembl_Metazoa \N XREF 1 Ensembl Metazoa ENSEMBL \N \N Ensembl Metazoa identifiers serving GO projections from a reference species to other metazoa species.
20301 RNAMMER \N KNOWNXREF 0 RNAmmer MISC \N \N \N
50730 AGP \N KNOWN 5 Anolis Genome Project MISC \N \N \N
20390 MOD \N KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
4100 UniGene \N KNOWN 5 UniGene MISC \N \N \N
50624 PFAM \N XREF 0 PFAM MISC \N \N Pfam from Vega
20360 SpBase \N KNOWNXREF 0 SpBase MISC \N \N \N
50658 ToxoDB \N KNOWNXREF 1 ToxoDB PRIMARY_DB_SYNONYM \N \N Toxoplasma Genomic Resource Database.
50916 rice_pan_genes \N XREF 5 Rice Pan Gene Identifiers MISC \N \N Pan gene identifiers from the rice Pan Oryza project.
50870 BEEBASE \N KNOWN 100 BeeBase MISC \N \N BeeBase( https://hymenoptera.elsiklab.missouri.edu/beebase ) data source for the bee research community. Now part of the Hymenoptera Genome Database(HGD).
50180 TIGR_GeneIndex \N XREF 0 Gene Index MISC \N \N \N
50823 MTGD \N KNOWNXREF 0 MTGD PRIMARY_DB_SYNONYM \N \N The Medicago truncatula Genome Database (MTGD), maintained by JCVI.
1800 RefSeq_dna \N KNOWN 200 RefSeq DNA MISC \N \N \N
6410 Ens_Gg_transcript \N XREF 40 Ensembl Chicken Transcript MISC \N \N \N
20372 BROAD_P_NODORUM_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
50641 PomBase_Interaction_PHYSICAL \N KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
12500 DBASS3 \N XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
1000 GO \N XREF 5 GO MISC \N \N \N
12510 HPA \N XREF 50 Human Protein Atlas MISC \N \N \N
50748 Ensembl_Plants \N XREF 1 Ensembl Plants ENSEMBL \N \N Ensembl Plants identifiers serving GO projections from a reference species to other plants species.
50818 Smar_Community_Annotation \N KNOWN 50 Strigamia maritima Community Annotation MISC \N \N \N
50642 PomBase_Gene_Name \N KNOWNXREF 5 PomBase Gene Name MISC \N \N \N
50878 Ensembl_Metazoa_transcript \N XREF 100 Ensembl Metazoa transcripts data ENSEMBL \N \N Data provided by Ensembl Metazoa for transcripts.
50782 Sanger \N KNOWN 5 Sanger Wellcome Trust Institute MISC \N \N \N
831 GenomeRNAi \N KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
9500 OryLat_est \N XREF 40 Medaka EST MISC \N \N \N
2310 Vega_transcript \N KNOWNXREF 160 Vega transcript MISC \N \N \N
50868 INSDC_submitted_name \N KNOWNXREF 1 INSDC_submitted_name PRIMARY_DB_SYNONYM \N \N Initial sequence name submitted by the assembly provider to GenBank (raw/source names that are replaced by INSDC ids after publication)
8200 PRF \N XREF 5 PRF MISC \N \N \N
50799 University of Texas \N KNOWN 5 University of Texas MISC \N \N \N
50826 PB_REF \N KNOWNXREF 1 PomBase Reference MISC \N \N Specific accession used by PomBase for source reference
12601 Tgut_symbol \N KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
7620 Ens_Fc_translation \N XREF 40 Ensembl Cat Translation MISC \N \N \N
50745 BROAD_M_violaceum \N KNOWNXREF 0 Broad Institute MISC \N \N Broad Institute Microbotryum violaceum Database
410 Celera_Pep \N PRED 5 Celera peptide MISC \N \N \N
50626 RIKEN \N KNOWN 5 Riken Institute MISC \N \N \N
50836 Ensembl_Protists \N XREF 1 Ensembl Protists ENSEMBL \N \N Ensembl Protists identifiers serving GO projections from a reference species to other protist species.
230 Ribosomal_Protein_Gene_Database \N XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
50609 HGNC_trans_name \N KNOWNXREF 5 Transcript name MISC \N \N transcript name from HGNC
50864 peatmoss_lookup \N KNOWNXREF 5 PEATmoss Gene Model Lookup DB MISC \N \N \N
50849 Plant_Reactome_Pathway \N KNOWNXREF 0 Plant Reactome Pathway ID MISC \N \N Plant Reactome is a database of plant metabolic and regulatory pathways maintained by Gramene. This ID links to a Pathway in Plant Reactome.
12700 goslim_goa \N XREF 5 GOSlim GOA MISC \N \N \N
50005 EC_NUMBER \N XREF 0 Enzyme EC Number MISC \N \N \N
20220 thaps_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
50749 ChEMBL \N KNOWNXREF 5 ChEMBL MISC \N \N ChEMBL external references imported via Uniprot mappings
9400 TetNig_mouse_econtig \N XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
6820 Ens_Tr_transcript \N XREF 40 Ensembl Fugu Transcript MISC \N \N \N
8400 TetNig_cdna \N XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
4620 OTTP \N XREF 1 Havana translation MISC \N \N \N
50797 UniProtKB-KW \N KNOWNXREF 0 UniProtKB Keywords MISC \N \N UniProtKB Keywords for describing UniProt annotations
7180 BRC4_Community_Annotation \N KNOWN 50 BRC4 Community Annotation MISC \N \N \N
50853 Gasser_lab \N KNOWNXREF 5 Gene names assigned by Gasser Lab MISC \N \N \N
827 FlyBaseCGID_transcript \N XREF 50 FlyBase transcript CGID MISC \N \N \N
8800 CioInt_est \N XREF 40 Ciona intestinalis EST MISC \N \N \N
50841 Archive_Plants \N XREF 0 Ensembl Plants Archive MISC \N \N Historical gene identifier linking to the Ensembl Plants Archive site.
50695 SIB_platypus_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
50610 MGI_trans_name \N KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
701 EMBL_predicted \N PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
50885 Lepidoptera_proteomes \N XREF 40 Lepbase proteins MISC \N \N Proteins from Lepbase
50672 IRGSPv1_GENE \N KNOWNXREF 1 IRGSP v1 Gene MISC \N \N \N
20380 CBS \N KNOWNXREF 0 CBS Server MISC \N \N \N
20337 BROAD_F_oxysporum \N KNOWNXREF 0 Broad Institute MISC \N \N \N
20377 PomBase_TRANSCRIPT \N KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
20334 SCHISTODB \N KNOWNXREF 0 SchistoDB MISC \N \N \N
50691 SGN \N KNOWNXREF 1 Sol Genomics Network MISC \N \N \N
10300 MEROPS \N KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
50110 PlantGDB_PUT \N XREF 1 PlantGDB Transcript MISC \N \N \N
8900 CioInt_cdna \N XREF 40 Ciona intestinalis cDNA MISC \N \N \N
6400 Ens_Gg_gene \N XREF 40 Ensembl Chicken Gene MISC \N \N \N
50654 BDGP_cDNA \N KNOWN 50 Fly cDNA MISC \N \N cDNA from the Berkeley Drosophila Genome Project
5500 Oxford_FGU_Oa_tscript \N PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
6500 IMCB_Tr_gene \N XREF 40 IMCB Fugu Gene MISC \N \N \N
4820 ENST_CDS \N XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
50631 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 25, from Vega
50888 APHIDBASE \N XREF 100 AphidBase MISC \N \N AphidBase is a reference information system providing genomic resources for the study of aphids (https://bipaa.genouest.org/is/aphidbase/). Part of the BIPAA platform (https://bipaa.genouest.org/is/)
11000 UCSC \N KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
2710 Ens_Hs_transcript \N XREF 170 Ensembl Human Transcript MISC \N \N \N
50650 BGI Shenzhen \N KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
50647 BROAD_Magnaporthe_DB \N KNOWNXREF 0 Magnaporthe comparative DB MISC \N \N Broad Institute Magnaporthe comparative Database
50819 RFAM_GENE \N KNOWN 0 Rfam Gene Name MISC \N \N Name for gene assigned from Rfam alignment
50756 STRING \N XREF 0 STRING MISC \N \N STRING - Known and Predicted Protein-Protein Interactions
20306 ASPGD \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
3800 CCDS \N KNOWN 240 CCDS MISC \N \N \N
5400 Oxford_FGU_Oa_gene \N PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
2610 cint_aniseed_v1 \N KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
50140 TIGR_LOCUS \N XREF 1 MSU/TIGR Locus MISC \N \N \N
2950 Genoscope_ann_translation \N KNOWN 40 Genoscope annotated translation MISC \N \N \N
50696 SIB_orangutan_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
824 FlyBaseName_translation \N KNOWN 5 FlyBase translation name MISC \N \N \N
8100 Platypus_olfactory_receptor \N XREF 40 Platypus olfactory receptor gene MISC \N \N \N
20071 HSSP \N KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
50856 BGD \N KNOWNXREF 0 BGD ALT_GENE \N \N http://bovinegenome.org
20311 CADRE_TRANSCRIPT \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
8600 OrnAna_454_cdna \N XREF 40 Platypus 454 cDNA MISC \N \N \N
50736 AGI_TRANSCRIPT \N XREF 1 AGI Transcript MISC \N \N annotation provided by Arizona Genome Institute
50822 ARAPORT_GENE \N KNOWNXREF 0 Araport MISC \N \N Gene identifiers from Araport, the Arabidopsis information portal (formerly TAIR).
50667 IGDBCAS-v1.4_TRANSCRIPT \N KNOWN 1 IGDBCAS v1.4 Transcript MISC \N \N \N
800 flybase_gene_id \N KNOWNXREF 5 FlyBase gene MISC \N \N \N
50772 Ant Genomes Portal \N KNOWNXREF 0 Ant Genomes Portal MISC \N \N \N
2530 ZFIN_xpat \N KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
5020 Ens_Mm_translation \N XREF 40 Ensembl Mouse Translation MISC \N \N \N
50793 ChEBI \N KNOWNXREF 0 ChEBI Chemical Database MISC \N \N ChEBI chemical database
50808 DOI \N KNOWN 5 Digital Object Identifier LIT \N \N Digital Object Identifier used to uniquely identify an object such as an electronic document.
50120 RAP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
20059 DIP \N KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
4200 RFAM \N XREF 190 RFAM PRIMARY_DB_SYNONYM \N \N \N
50863 external_wheat_gene_names \N XREF 5 External wheat gene names MISC \N \N \N
50678 BROAD_coelacanth_transcriptome \N XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
20383 ProSite \N XREF 0 ProSite ID MISC \N \N \N
4670 shares_CDS_with_OTTT \N XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
50875 BananaGenomeHub \N KNOWN 1 BananaGenomeHub PRIMARY_DB_SYNONYM \N \N \N
50837 MGP \N KNOWNXREF 0 Mouse Genomes Project MISC \N \N Mouse Genomes Project
20343 BROAD_G_moniliformis \N KNOWNXREF 0 Broad Institute MISC \N \N \N
20338 BROAD_F_oxysporum_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20357 BROAD_P_triticina \N KNOWNXREF 0 Broad Institute MISC \N \N \N
50090 NASC_GENE_ID \N XREF 1 NASC Gene ID MISC \N \N \N
2940 Genoscope_ann_transcript \N KNOWN 40 Genoscope annotated transcript MISC \N \N \N
50786 PomBase_GO_AnnotationExtensions \N KNOWN 1 PomBase GO AnnotationExtensions MISC \N \N Specific accession used by PomBase for ontology annoation extensions
2910 Genoscope_pred_transcript \N XREF 39 Genoscope pred transcript MISC \N \N \N
50732 Yutaka_Satou_Kyoto_University \N KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
2602 cint_jgi_v2 \N KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
1820 RefSeq_rna \N KNOWN 230 RefSeq RNA MISC \N \N \N
50050 Gramene_MarkersDB_EST \N XREF 0 GenBank EST (Gramene) MISC \N \N \N
50752 PRIDE \N XREF 0 PRIDE MISC \N \N \N
50718 ENA_GENE \N KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source gene model when importing from ENA.
20014 EcoGene \N KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
50843 MaizeGDB \N XREF 0 MaizeGDB MISC \N \N MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.
213 BRC4_RNA_Description \N PRED 50 BRC4 RNA Description MISC \N \N \N
10000 wormbase_id \N XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
50662 BRAD_TRANSCRIPT \N XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
20378 PomBase_TRANSLATION \N KNOWNXREF 0 PomBase (peptide) PRIMARY_DB_SYNONYM \N \N \N
50801 KEGG_Enzyme \N XREF 0 KEGG Pathway and Enzyme MISC \N \N KEGG pathway and enzyme
50777 RGD_trans_name \N KNOWNXREF 50 RGD transcript name MISC \N \N transcript name from RGD
50683 GeneIndex \N XREF 50 GeneIndex MISC \N \N \N
7201 IMGT/GENE_DB \N KNOWN 40 IMGT/GENE-DB MISC \N \N \N
50621 Uniprot_gn \N KNOWN 116 UniProtKB Gene Name MISC \N \N \N
9700 CioSav_est \N XREF 40 Ciona savignyi EST MISC \N \N \N
50788 SP_SL \N KNOWN 0 UniProtKB/SwissProt Subcellular Locatisation MISC \N \N UniProt Subcellular Location (http://www.uniprot.org/manual/subcellular_location)
1700 protein_id \N KNOWNXREF 5 INSDC protein ID MISC \N \N \N
50871 LJMU \N KNOWN 100 Liverpool John Moores University MISC \N \N Data provided by the Liverpool John Moores University (https://www.ljmu.ac.uk).
6420 Ens_Gg_translation \N XREF 40 Ensembl Chicken Translation MISC \N \N \N
50833 VGNC \N KNOWNXREF 100 VGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
2400 wormbase_gene \N KNOWN 5 WormBase Gene MISC \N \N \N
50865 peatmoss_expression \N KNOWNXREF 5 PEATmoss Expression Viewer MISC \N \N \N
50709 tamu_vibs \N KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
50646 Psinensis_sequencing_consortium \N KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
50848 Plant_Reactome_Reaction \N KNOWNXREF 0 Plant Reactome Reaction ID MISC \N \N Plant Reactome is a database of plant metabolic and regulatory pathways maintained by Gramene. This ID links to a Reaction in Plant Reactome.
20221 thaps_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
20391 AGD_GENE \N KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
50700 AnoXcel \N KNOWN 50 AnoXcel MISC \N \N VectorBase xref.
50608 RFAM_trans_name \N KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
50802 gfbgp \N KNOWN 0 Glanville Fritillary Butterfly Genome Project MISC \N \N \N
400 Celera_Gene \N PRED 5 Celera gene MISC \N \N \N
1808 RefSeq_ncRNA_predicted \N PRED 199 RefSeq ncRNA predicted MISC \N \N \N
20320 physo1_jgi_v1.1 \N KNOWNXREF 0 JGI ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
50869 Uniprot_isoform \N XREF 1 UniProtKB isoform MISC \N \N Direct mappings to UniProtKB isoforms
50682 BGI_Gene \N XREF 50 BGI Gene MISC \N \N BGI gene identifier
20389 FYPO \N KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
4700 Medaka \N XREF 1 Medaka Genome Project MISC \N \N \N
20046 ArrayExpress \N XREF 0 Expression Atlas MISC \N \N \N
50644 PomBase_Ortholog \N KNOWNXREF 5 Orthologous Gene MISC \N \N \N
1825 RefSeq_rna_predicted \N PRED 195 RefSeq RNA predicted MISC \N \N \N
20330 triad_jgi_v1.0_transcript \N KNOWNXREF 0 JGI Transcript ID (JGI Triad 1.0) PRIMARY_DB_SYNONYM \N \N \N
20082 PeroxiBase \N KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
50668 JGI_GENE \N XREF 1 JGI Gene MISC \N \N gene ID/NAME in the JGI gff3 file
4690 ENSG \N XREF 1 Ensembl gene ALT_GENE \N \N \N
700 EMBL \N KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
50627 SHSC \N KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
50651 ICGSC \N KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
50884 Ens_Rn_transcript \N XREF 40 Ensembl Rat Transcript MISC \N \N \N
50743 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 27, from Vega
50694 SIB_mondelphis_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
2611 cint_aniseed_v2 \N KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
50798 PBQ \N KNOWNXREF 0 PomBase Quiescence Ontology MISC \N \N Used in the annotation of quiescent cell phenotypes.
20101 IntEnz \N KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
50656 Ens_Tg_translation \N KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
20074 KEGG \N KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
50673 IRGSPv1_TRANSCRIPT \N KNOWNXREF 1 IRGSP v1 Transcript MISC \N \N \N
50713 TAIR_SYMBOL \N KNOWN 60 TAIR Gene Name PRIMARY_DB_SYNONYM \N \N TAIR gene names
50726 ENA_FEATURE_GENE \N KNOWNXREF 1 European Nucleotide Archive feature (gene source) MISC \N \N Cross-reference to the ENA object from which the gene has been inferred, when loading a genome from ENA records.
5820 Ens_Dr_translation \N XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
50881 GenBank_translation \N XREF 100 GenBank translations data MISC \N \N GenBank translations data
50185 TO \N XREF 0 Plant Trait Ontology MISC \N \N \N
20009 BioCyc \N KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
1803 RefSeq_ncRNA \N KNOWN 200 RefSeq ncRNA MISC \N \N \N
20307 ASPGD_GENE \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
50690 RefSeq_gene_name \N KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
12600 WikiGene \N XREF 50 WikiGene MISC \N \N \N
1400 MGI \N KNOWNXREF 270 MGI Symbol PRIMARY_DB_SYNONYM \N \N \N
1300 EntrezGene \N KNOWNXREF 250 NCBI gene (formerly Entrezgene) PRIMARY_DB_SYNONYM \N \N \N
50703 Uniprot_gn_trans_name \N KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
50634 Ens_Ga_gene \N XREF 5 Ensembl Stickleback Gene MISC \N \N \N
50857 ENCODE \N KNOWN 0 ENCODE MISC \N \N \N
50753 LegioList \N XREF 0 LegioList MISC \N \N Database dedicated to the analysis of the genomes of Legionella
50759 SWISS_MODEL \N XREF 0 SWISS-MODEL MISC \N \N The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
20013 EchoBASE \N KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
50735 AGI_GENE \N XREF 1 AGI Gene MISC \N \N annotation provided by Arizona Genome Institute
3300 miRBase \N KNOWNXREF 180 miRBase PRIMARY_DB_SYNONYM \N \N \N
50630 PFAM \N XREF 0 PFAM MISC \N \N Pfam release 24, from Vega
808 flybase_transcript_id \N KNOWNXREF 299 FlyBase transcript MISC \N \N \N
50722 Rhea \N KNOWNXREF 1 Rhea MISC \N \N Cross-references to Rhea attached to translation objects
50710 INSDC \N KNOWNXREF 5 International Nucleotide Sequence Database Collaboration MISC INSDC \N This external_db_id was initially made for use in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The INSDC accession is stored as a synonym.
8500 GasAcu_cdna \N XREF 40 Stickleback cDNA MISC \N \N \N
20097 RegulonDb_Transcript \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
50635 Ens_Ga_transcript \N XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
20312 SGD_GENE \N KNOWNXREF 0 SGD gene name PRIMARY_DB_SYNONYM \N \N \N
20344 BROAD_G_moniliformis_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
50790 PUBMED_POMBASE \N KNOWN 1 PomBase PubMed ID LIT \N \N PomBase specific publications
5010 Ens_Mm_transcript \N XREF 40 Ensembl Mouse Transcript MISC \N \N \N
50862 WHEATEXP_TRANS \N KNOWNXREF 5 Wheat Expression MISC \N \N \N
2202 Uniprot/Varsplic \N KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
9450 TetNig_rat_econtig \N XREF 40 Genoscope rat exofish econtig MISC \N \N \N
12620 Duck_consortium \N XREF 0 Duck consortium MISC \N \N \N
50739 PHIP \N KNOWNXREF 1 PHI-base phenotype ontology MISC \N \N PHI-base phenotype ontology for genes proven to affect the outcome of pathogen-host interactions
50742 PubMedCentral \N KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
20303 dictyBase \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
50817 RNAcentral \N KNOWNXREF 0 RNAcentral PRIMARY_DB_SYNONYM \N \N Sequence identity to RNAcentral ids
2601 cint_jgi_v1 \N KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
829 BioGRID \N KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
50852 RAP-DB \N KNOWNXREF 0 Rice Annotation Project Database MISC \N \N The Rice Annotation Project Database (RAP-DB) provides a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare (Itoh 2013).
50738 MetaCyc \N KNOWNXREF 1 MetaCyc MISC \N \N MetaCyc database of metabolic pathways
50611 ZFIN_ID_trans_name \N KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
50771 MINT \N XREF 0 MINT MISC \N \N MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators.
20362 necha_jgi_v2.0_gene \N KNOWNXREF 0 Nectria JGI gene PRIMARY_DB_SYNONYM \N \N \N
20364 necha_jgi_v2.0 \N KNOWNXREF 0 Nectria JGI MISC \N \N \N
50778 Xenbase_trans_name \N KNOWNXREF 1 Xenbase transcript name MISC \N \N transcript name from Xenbase
50170 TAIR_LOCUS_MODEL \N XREF 8 TAIR Locus (Model) MISC \N \N \N
50809 zngp \N KNOWNXREF 0 Zootermopsis nevadensis Genome Project MISC \N \N \N
50794 FYPO_EXT \N KNOWNXREF 1 FYPO Extensions MISC \N \N Annotation extension terms for the Fission Yeast Phenotype Ontology (FYPO)
20216 phatr_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
50842 Ensembl_Plants \N XREF 0 Ensembl Plants MISC \N \N Maping from translation to XREF
50746 BROAD_M_violaceum_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
50814 FGDB \N KNOWNXREF 0 FGDB ALT_GENE \N \N MIPS Fusarium graminearum Genome Database
50717 GOA \N KNOWNXREF 1 UniProtKB-Gene Ontology Annotation MISC \N \N GOA xrefs (to UniProt identifiers)
50040 Gramene_MarkersDB_mRNA \N XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
50663 Quick_Go \N KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
420 Celera_Trans \N PRED 5 Celera transcript MISC \N \N \N
50775 Ens_Mg_translation \N XREF 40 Ensembl Turkey Translation MISC \N \N \N
50190 PO \N XREF 0 Plant Structure Ontology MISC \N \N \N
20392 AGD_TRANSCRIPT \N KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
212 BRC4_External_Description \N PRED 50 BRC4 External Description MISC \N \N \N
50879 Ensembl_Metazoa_translation \N XREF 100 Ensembl Metazoa translations data ENSEMBL \N \N Data provided by Ensembl Metazoa for translations.
50860 KNETMINER_RICE \N KNOWNXREF 5 KNETMINER_RICE MISC \N \N \N
2900 Genoscope_pred_gene \N XREF 38 Genoscope pred gene MISC \N \N \N
20356 BROAD_U_maydis_TRANSCRIPT \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20368 Mycgr3_jgi_v2.0_gene \N KNOWNXREF 0 Mycosphaerella JGI gene PRIMARY_DB_SYNONYM \N \N \N
50687 Uppsala University \N KNOWN 5 Uppsala University MISC \N \N \N
3900 PUBMED \N KNOWN 5 Sequence Publications LIT \N \N \N
50731 Turkey Genome Consortium \N KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
50874 Phytozome \N KNOWN 1 Phytozome PRIMARY_DB_SYNONYM \N \N \N
50622 GGSC \N KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
50795 EcoCyc \N KNOWNXREF 1 EcoCyc MISC \N \N Scientific database for E. coli and a division of MetaCyc (http://ecocyc.org/)
50850 CGSNL \N KNOWNXREF 0 Committee on Gene Symbolization, Nomenclature and Linkage of the Rice Genetics Cooperative MISC \N \N The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community (McCouch 2008).
1701 protein_id_predicted \N PRED 4 Predicted INSDC Protein ID MISC \N \N \N
20331 triad_jgi_v1.0 \N KNOWNXREF 0 JGI ID (JGI Triad 1.0) MISC \N \N \N
50913 Oryzabase_trans_name \N KNOWNXREF 0 Integrated Rice Science Database transcript name MISC \N \N transcript name from Oryzabase
50677 RGSC \N KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
50655 BDGP_cDNA_Gold_Collection \N KNOWN 50 Fly gold cDNA MISC \N \N Gold Collection cDNA from the Berkeley Drosophila Genome Project
20062 DrugBank \N KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
2250 UniProtKB_all \N XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
821 FlyBaseName_gene \N KNOWN 5 FlyBase gene name PRIMARY_DB_SYNONYM \N \N \N
3500 IPI \N KNOWN 5 IPI MISC \N \N \N
20386 SPD \N KNOWNXREF 0 SPD ID MISC \N \N \N
1200 Interpro \N XREF 5 InterPro MISC \N \N \N
9460 TetNig_chick_econtig \N XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
20008 BRENDA \N KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
5300 Oxford_FGU_Md_tscript \N PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
50858 KNETMINER_WHEAT \N KNOWNXREF 5 KNETMINER_WHEAT MISC \N \N \N
1001 GO_REF \N KNOWN 5 GO Reference Collection LIT \N \N \N
20363 necha_jgi_v2.0_transcript \N KNOWNXREF 0 Nectria JGI transcript PRIMARY_DB_SYNONYM \N \N \N
50834 VGNC_trans_name \N KNOWNXREF 5 VGNC transcript name MISC \N \N transcript name from VGNC
6900 Ens_Ga_translation \N XREF 5 Ensembl Stickleback Translation MISC \N \N \N
50847 Ngyuen_et_al_2012 \N PRED 0 PMID 23153364 MISC \N \N The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome. BMC Genomics201213:584 PMID: 23153364
1830 RefSeq_genomic \N KNOWN 193 RefSeq Genomic MISC \N \N This external_db_id can be used in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The RefSeq_genomic is stored as a synonym. eg. NC_000011.10, NT_187365.1
1805 RefSeq_dna_predicted \N PRED 199 RefSeq DNA predicted MISC \N \N \N
50876 LJMU_transcript \N KNOWN 100 Liverpool John Moores University transcripts data MISC \N \N Data provided by the Liverpool John Moores University (https://www.ljmu.ac.uk) for transcripts.
10500 TransFac \N KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
2700 Ens_Hs_gene \N XREF 5 Ensembl Human Gene MISC \N \N \N
50762 CYGD \N XREF 0 CYGD MISC \N \N The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae.
20348 PGD_GENE \N KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
20382 CGD \N KNOWN 0 Candida Genome Database MISC \N \N \N
50196 GO_to_gene \N XREF 0 Gene Ontology MISC \N \N \N
50607 miRBase_trans_name \N KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
7170 Ixodes_ManualAnnotation \N PRED 30 Ixodes ManualAnnotation MISC \N \N \N
50698 PHI \N KNOWNXREF 1 PHI-base accession MISC \N \N Parasite-host interaction identifiers from PHI-base
50633 GRC_primary_assembly \N XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
1510 MIM_GENE \N KNOWNXREF 5 MIM gene MISC \N \N \N
50669 JGI_TRANSCRIPT \N XREF 1 JGI Transcript MISC \N \N transcript/mRNA ID/NAME in the JGI gff3 file
50727 ENA_FEATURE_TRANSCRIPT \N KNOWNXREF 1 European Nucleotide Archive feature (transcript source) MISC \N \N Cross-reference to the ENA object from which the transcript has been inferred, when loading a genome from ENA records.
50821 GDEC_GENE \N KNOWNXREF 1 GDEC 3B gene identifier MISC \N \N Bread wheat 3B pseudomolecule gene models from INRA GDEC group.
50645 Ens_Ss_translation \N XREF 5 Ensembl Pig Translation MISC \N \N \N
50688 GenBank \N XREF 1 GenBank MISC \N \N GenBank identifier
7400 Ens_Tg_transcript \N XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
20317 phyra_jgi_v1.1 \N KNOWNXREF 0 JGI ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
2600 GeneDB \N KNOWN 5 GeneDB MISC \N \N \N
50779 NasoniaBase \N KNOWN 0 NasoniaBase MISC \N \N \N
50825 Reactome_transcript \N KNOWNXREF 0 Reactome transcript PRIMARY_DB_SYNONYM \N \N Reactome entries linked to transcripts
20325 BROAD_P_infestans \N KNOWNXREF 0 Broad Institute MISC \N \N \N
50160 TAIR_LOCUS \N XREF 8 TAIR MISC \N \N \N
20388 PBO \N KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
50780 wormbase_gseqname \N KNOWN 6 WormBase Gene Sequence-name MISC \N \N \N
20078 PDBsum \N KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
50831 EFO \N KNOWNXREF 0 Experimental Factor Ontology MISC \N \N The Experimental Factor Ontology provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology.
50845 Botrytis_community_symbol \N KNOWN 50 Botrytis community symbol MISC \N \N \N
50660 SO \N KNOWNXREF 0 Sequence Ontology MISC \N \N Sequence Ontology
12415 Clone_based_ensembl_transcript \N XREF 5 Clone-based (Ensembl) transcript MISC \N \N \N
4400 Xenbase \N KNOWN 1 Xenbase PRIMARY_DB_SYNONYM \N \N \N
20313 SGD_TRANSCRIPT \N KNOWNXREF 0 SGD transcript name PRIMARY_DB_SYNONYM \N \N \N
2920 Genoscope_annotated_gene \N KNOWN 40 Genoscope annotated gene MISC \N \N \N
50828 GigaDB_A_tauschii \N KNOWNXREF 1 Aegilops tauschii GigaDB identifier MISC \N \N Aegilops tauschii GigaDB gene identifier
20040 SubtiList \N KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
50543 ENS_LRG_transcript \N KNOWN 10 LRG display in Ensembl transcript MISC \N \N \N
50734 TAIR_TRANSLATION \N XREF 1 TAIR Translation identifier MISC \N \N TAIR identifier to link to Ensembl Translation entities. The main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translation objects.
1815 RefSeq_peptide_predicted \N PRED 197 RefSeq peptide predicted MISC \N \N \N
20345 BROAD_G_moniliformis_TRANSCRIPT \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
50887 Atroparvus_proteomes \N XREF 40 Anopheles proteomes MISC \N \N Proteins from Uniprot [PE 1/2] and past ensembl release, PCG models based on the an old assembly of Anopheles atroparvus.
50851 Oryzabase \N KNOWNXREF 0 Integrated Rice Science Database MISC \N \N The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (Yamazaki 2006).
50747 BROAD_M_violaceum_TRANSCRIPT \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
50839 GeneID \N KNOWNXREF 0 Database of genes from NCBI RefSeq genomes MISC \N \N Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
883 FlyReactome \N KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
1520 MIM_MORBID \N KNOWNXREF 150 MIM morbid MISC \N \N \N
50783 ENSP_ident \N XREF 1 Ensembl translation having exact match with Havana ALT_TRANS \N \N \N
250 ImmunoDB \N KNOWN 50 ImmunoDB MISC \N \N \N
4610 OTTT \N XREF 1 Havana transcript ALT_TRANS \N \N \N
50708 GMGC_GENE \N KNOWNXREF 1 GMGC PRIMARY_DB_SYNONYM \N \N Global Musa Genomics Consortium gene cross-references
50770 PseudoCAP \N XREF 0 Pseudomonas Genome Database MISC \N \N The Pseudomonas Genome database has been a resource for peer-reviewed, continually-updated annotations for the Pseudomonas aeruginosa PAO1 reference strain's genome and, more recently, comparative analyses of several related Pseudomonas species.
50785 Ens_Mmu_translation \N XREF 40 Ensembl Macaque Translation MISC \N \N \N
20359 BROAD_P_triticina_TRANSCRIPT \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
50880 GenBank_transcript \N XREF 100 GenBank transcripts data MISC \N \N GenBank transcripts data
2930 Genoscope_pred_translation \N XREF 40 Genoscope pred translation MISC \N \N \N
20350 RegulonDb_Operon \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
50664 Quick_Go_Evidence \N KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
50803 ensembl_internal_synonym \N KNOWNXREF 100 Ensembl internal synonym MISC \N \N \N
50711 ISGC \N KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
50623 Broad Institute \N KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
2420 wormpep_id \N KNOWN 5 Wormpep ID MISC \N \N \N
20302 TRNASCAN_SE \N KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
20329 triad_jgi_v1.0_gene \N KNOWNXREF 0 JGI Gene ID (JGI Triad 1.0) PRIMARY_DB_SYNONYM \N \N \N
50861 WHEATEXP_GENE \N KNOWNXREF 5 Wheat Expression MISC \N \N \N
826 FlyBaseCGID_gene \N XREF 5 FlyBase gene CGID PRIMARY_DB_SYNONYM \N \N \N
50640 PomBase_Interaction_GENETIC \N KNOWNXREF 5 PomBase Interaction Genetic MISC \N \N \N
20005 UniParc \N KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
50693 BROAD_monodelphis_transcriptome \N XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
50035 Gramene_MarkersDB \N XREF 0 Gramene MISC \N \N \N
2300 Vega_gene \N KNOWNXREF 5 Vega gene MISC \N \N \N
20385 SMART \N XREF 0 SMART ID MISC \N \N \N
20355 BROAD_U_maydis_GENE \N KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
1100 HGNC \N KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
50789 PR \N KNOWNXREF 0 Protein Ontology MISC \N \N Protein Ontology term (previously PR) - http://pir.georgetown.edu/pro/pro.shtml
50721 BaylorCollege \N KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
2200 Uniprot/SWISSPROT \N KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
50674 Ens_Lc_gene \N XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
50866 ACWP \N KNOWNXREF 50 Whitefly Genome Database MISC \N \N http://www.cassavawhitefly.org/
20381 COG \N KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
2720 Ens_Hs_translation \N XREF 5 Ensembl Human Translation MISC \N \N \N
1600 PDB \N KNOWNXREF 5 PDB MISC \N \N \N
12505 DBASS5 \N XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
50010 FSTs \N XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
50750 IBSC \N KNOWNXREF 50 IBSC Gene ID MISC \N \N International Barley Sequencing Consortium gene identifier
832 InteractiveFly \N KNOWNXREF 5 The Interactive Fly MISC \N \N \N
50684 EO \N XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms. More information: http://www.gramene.org/plant_ontology/ontology_browse.html#eo
8700 TakRub_cdna \N XREF 40 Takifugu cDNA MISC \N \N \N
20228 CADRE_Afum_A1163 \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
50649 BROAD_Magnaporthe_DB_TRANSCRIPT \N KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
50893 Perniciosus_proteomes \N XREF 40 Perniciosus proteomes MISC \N \N Proteins from Uniprot [PE 1/2] and past ensembl release, PCG models based on the an GCA_000262795.1 assembly of Phlebotomus papatasi
50892 ROSLIN_INST \N KNOWNXREF 100 The Roslin Institute MISC \N \N Data provided by the Roslin Institute, The University of Edinburgh ( https://www.ed.ac.uk/roslin/about)
50891 EggNOG \N KNOWN 100 EggNOG MISC \N \N A database of orthology relationships, functional annotation, and gene evolutionary histories (http://eggnog5.embl.de/)
50890 MGnify \N KNOWN 100 MGnify metagenomics data MISC \N \N MGnify: the microbiome analysis resource from EMBL-EBI (https://www.ebi.ac.uk/metagenomics/)
50894 curated_gene_synonyms \N KNOWN 5 Gene synonyms manually curated from the literature MISC \N \N \N
50896 BRC4_Community_Annotation_transcript \N KNOWN 50 BRC4 Community Annotation (Transcripts) MISC \N \N BRC4 Community Annotation data for transcripts
50897 BRC4_Community_Annotation_translation \N KNOWN 50 BRC4 Community Annotation (Translations) MISC \N \N BRC4 Community Annotation data for translations
50895 I5KNAL \N XREF 100 i5k Workspace at NAL MISC \N \N The i5k Workspace@NAL (https://i5k.nal.usda.gov/) is a platform for communities around ‘orphaned’ arthropod genome projects. The partner of the the i5k initiative project (http://i5k.github.io/).
50900 Uniprot/GCRP \N KNOWNXREF 50 UniProtKB gene-centric reference proteome (Uniprot/GCRP) MISC \N \N UniProtKB gene-centric reference proteome (GCRP)
50903 AlphaFold_DB_gene \N KNOWNXREF 50 AlphaFold Protein Structure Database MISC \N \N AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/) -- EMBLs European Bioinformatics Institute (EMBL-EBI) provided database of protein 3D structures predicted by AI from DeepMind. (gene xref)
50899 DRscDB \N KNOWNXREF 50 DRscDB -- manually curated single-cell RNA-seq search database MISC \N \N DRscDB (https://www.flyrnai.org/tools/single_cell/web/) is a user-friendly, manually curated single-cell RNA-seq (scRNA-seq) search database based on datasets derived from published literature. DRscDB allows users to search, mine, and compare multiple genes and cell clusters across diverse species including Drosophila and Humans
50902 AlphaFold_DB \N KNOWNXREF 50 AlphaFold Protein Structure Database MISC \N \N AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/) -- EMBLs European Bioinformatics Institute (EMBL-EBI) provided database of protein 3D structures predicted by AI from DeepMind.
50898 GeneCards \N XREF 50 GeneCards MISC \N \N \N
50904 Ensembl_Bacteria \N XREF 1 Ensembl Bacteria ENSEMBL \N \N Ensembl Bacteria identifiers (including imported with missing source)
50901 Uniprot/GCRP_gene \N KNOWNXREF 50 UniProtKB gene-centric reference proteome (UniProt/GCRP) MISC \N \N UniProtKB gene-centric reference proteome (UniProt/GCRP), gene xref
50906 flybase_annot_id_transcr \N KNOWNXREF 5 FlyBase annotation for transcript MISC \N \N \N
50907 flybase_annot_id_transl \N KNOWNXREF 5 FlyBase annotation for translation MISC \N \N \N
50905 flybase_annot_id \N KNOWNXREF 5 FlyBase annotation MISC \N \N \N
50915 Phytozome_trans_name \N KNOWN 0 Phytozome transcript name MISC \N \N transcript name from Phytozome
50911 RNAMMER_trans_name \N KNOWNXREF 0 RNAmmer transcript name MISC \N \N transcript name from RNAmmer
50914 RAP-DB_trans_name \N KNOWNXREF 0 Rice Annotation Project Database transcript name MISC \N \N transcript name from RAP-DB
50912 ENA_GENE_trans_name \N KNOWNXREF 0 European Nucleotide Archive transcript name MISC \N \N transcript name from ENA
50909 external_wheat_gene_names_trans_name \N XREF 0 External wheat transcript names MISC \N \N transcript name from external wheat
50908 TRNASCAN_SE_trans_name \N KNOWNXREF 0 tRNAScan-SE transcript name MISC \N \N transcript name from tRNAScan-SE
50910 RFAM_GENE_trans_name \N KNOWN 0 RFAM transcript name MISC \N \N transcript name from RFAM