New qualifier was introduced in version 1.08 (December 1, 1995) of the Feature table definitions: /db_xref. This new qualifier serves as a vehicle for the linking of DNA sequence records to other external databases.
The text below outlines the format and the present list of allowed database cross references. Inquiries about the addition of other database types should be made to one of the collaborating databases, listed above.
Qualifier: /db_xref=”database:identifier“
Definition: database cross-reference: pointer to related information in another database
Scope: all feature keys
Value format: “database:identifier” where database is the name of the database containing related information, and
identifier is the internal identifier of the related information according to the naming conventions of the cross-referenced
database.
Examples:
cross reference to GDB identifier: /db_xref=”GDB:39999″
cross reference to Swiss-Prot entry: /db_xref=”Swiss-Prot:P12345″
For all databases types ‘Case’ is important. All databases member of the International Collaboration (DDBJ, EMBL/EBI and GenBank/NCBI) may make recommendations for additions or removal of databases to this list at their convenience, and need not rely on the release cycle of the Feature Table documentation.
Database: Description of database, and type with example(s).
Presently the list includes:
| AceView/WormGenes | AceView Worm Genome | /db_xref=”AceView/WormGenes:vha-6″ | ||
| AFTOL | Assembling the Fungal Tree of Life | /db_xref=”AFTOL:959″ | ||
| AntWeb | Ant Database | /db_xref=”AntWeb:CASENT0058943-D01″ | ||
| APHIDBASE | Aphid Genome Database | /db_xref=”APHIDBASE:ACYPI007424″ | ||
| ApiDB | Apicomplexan Database Resources | /db_xref=”ApiDB:cgd1_1090″ | ||
| ApiDB_CryptoDB | Cryptosporidium Genome Resources | /db_xref=”ApiDB_CryptoDB:cgd7_20″ | ||
| ApiDB_PlasmoDB | Plasmodium Genome Resources | /db_xref=”ApiDB_PlasmoDB: PF11_0344″ | ||
| ApiDB_ToxoDB | Toxoplasma Genome Resources | /db_xref=”ApiDB_ToxoDB:49.m00014″ | ||
| Araport | Arabidopsis Information Portal | /db_xref=”Araport:AT1G01010″ | ||
| ASAP | A Systematic Annotation Package for Community Analysis of Genomes | /db_xref=”ASAP:ABE-0000006″ | ||
| ATCC | American Type Culture Collection database | /db_xref=”ATCC:123456″ | ||
| ATCC(in host) | American Type Culture Collection database |
/db_xref=”ATCC(in host):123456″ |
||
| ATCC(dna) | American Type Culture Collection database | /db_xref=”ATCC(dna):123456” | ||
| Axeldb | A Xenopus laevis database | /db_xref=”Axeldb:32B3.1″ | ||
| BDGP_EST | Berkeley Drosophila Genome Project EST database | /db_xref=”BDGP_EST:123456″ | ||
| BDGP_INS | Berkeley Drosophila Genome Project database — Insertion | /db_xref=”BDGP_INS:123456″ | ||
| BEEBASE | BeeBase | db_xref= BEEBASE:GB55480 | ||
| BEETLEBASE | Tribolium Genome Database — Insertion | /db_xref=”BEETLEBASE:TC030551″ | ||
| BEI | BEI Resources | /db_xref=”BEI:NR-50065″ | ||
| BGD | Bovine Genome Database | /db_xref=”BGD:BT10004″ | ||
| BOLD | Barcode of Life database | /db_xref=”Bold:EPAF263″ | ||
| CABRI | Common Access to Biological Resources and Information project | /db_xref=”CABRI: ACC 424″ | ||
| CCAP | Culture Collection of algae and protozoa | /db_xref=”CCAP: 1460/15″ | ||
| CDD | Conserved Domain Database | /db_xref=”CDD:02194 | ||
| CGD | Candida Genome Database | /db_xref=”CGD:CAL0005934 | ||
| dbEST | EST database maintained at the NCBI. | /db_xref=”dbEST:123456″ /db_xref=”dbEST:BP535535″ |
||
| dbProbe | NCBI Probe database Public registry of nucleic acid reagents | /db_xref=”dbProbe:38″ | ||
| dbSNP | Variation database maintained at the NCBI. | /db_xref=”dbSNP:4647″ /db_xref=”dbSNP:rs133073″ |
||
| dbSTS | STS database maintained at the NCBI. | /db_xref=”dbSTS:456789″ /db_xref=”dbSTS:BV210161″ |
||
| dictyBase | Dictyostelium genome database | /db_xref=”dictyBase:DDB0191090″ | ||
| EcoGene | Database of Escherichia coli Sequence and Function | /db_xref=”EcoGene:EG11277″ | ||
| ECOCYC | EcoCyc E. coli database | /db_xref=”ECOCYC:sroC” /db_xref=”ECOCYC:C0343″ |
||
| ENSEMBL | Database of automatically annotated genomic data | /db_xref=”ENSEMBL:HUMAN-Clone-AC005612″ /db_xref=”ENSEMBL:HUMAN-Gene-ENSG00000007102″ |
||
| EnsemblGenomes | Extending Ensembl across the taxonomic space | /db_xref=”EnsemblGenomes:AAC73116″/db_xref=”EnsemblGenomes:b0005″ | ||
| EPD | Eukaryotic Promotor Database | /db_xref=”EPD:EP00576″ | ||
| ERIC | Enteropathogen Resource Integration Center | /db_xref=”ERIC:ABY-0246137″ | ||
| ESTLIB | EBI’s EST library identifier | /db_xref=”ESTLIB:1200″ | ||
| FANTOM_DB | Database of Functional Annotation of Mouse | /db_xref=”FANTOM_DB:0610005A07″ | ||
| FBOL | International Fungal Working Group Fungal Barcoding | /db_xref=”FBOL:2224″ | ||
| FLYBASE | Database of Genetic and molecular data of Drosophila. | /db_xref=”FLYBASE:FBgn0000024″ | ||
| Fungorum | Index Fungorum | /db_xref=”Fungorum:ID550186″ | ||
| GABI | Network of Different Plant Genomic Research Projects | /db_xref=”GABI:HA05J18″ | ||
| GDB | Human Genome Database accession numbers | /db_xref=”GDB:G00-128-600″ | ||
| GeneDB | Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei | /db_xref=”GeneDB:SPCC285.16c” | ||
| GeneID | Entrez Gene Database (replaces NCBI Locus Link) | /db_xref=”GeneID:3054987″ | ||
| GI | GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins | /db_xref=”GI:1234567890″ | ||
| GO | Gene Ontology Database identifier | /db_xref=”GO:123″ | ||
| GOA | Gene Ontology Annotation Database Identifier | /db_xref=” GOA :P01100″ | ||
| Greengenes | 16S rRNA gene database | /db_xref=”Greengenes:269185″ | ||
| GRIN | Germplasm Resources Information Network | /db_xref=”GRIN:1005973″ | ||
| HGNC | Human Gene Nomenclature Database | /db_xref=”HGNC:2041″ | ||
| H-InvDB | H-Invitational Database | /db_xref=”H-InvDB:HIT000000001″ /db_xref=”H-InvDB:HIX0000001″ |
||
| HMP | Human Microbiome Project | /db_xref=”HMP:0536″ | ||
| HOMD | Human Oral Microbiome Database | /db_xref=”HOMD:tax_078″
/db_xref=”HOMD:seq_1603” |
||
| HPM | Human Proteome Map | /db_xref=”HPM:8106″ | ||
| HSSP | Database of homology-derived secondary structure of proteins | /db_xref=”HSSP:12GS” | ||
| IKMC | International Knockout Mouse Consortium | /db_xref=”IKMC:66303 | ||
| IMGT/GENE-DB | Immunogenetics database, immunoglobulin and T-cell receptor genes | /db_xref=”IMGT/GENE-DB:IGKC” | ||
| IMGT/LIGM | Immunogenetics database, immunoglobulins and T-cell receptors | /db_xref=”IMGT/LIGM:U03895″ | ||
| IMGT/HLA | Immunogenetics database, human MHC | /db_xref=”IMGT/HLA:HLA00031″ | ||
| Interpro | InterPro protein sequence database | /db_xref=”InterPro:IPR002928″ | ||
| IntrepidBio | Intrepid BioInformatics | /db_xref=”IntrepidBio:5259707746″ | ||
| IRD | Influenza Research Database | /db_xref=”IRD:CEIRS-CIP045-123456.2″ | ||
| ISFinder | Insertion sequence elements database | /db_xref=”ISFinder:ISA1083-2″ | ||
| ISHAM-ITS |
ITS reference database for pathogenic fungi |
/db_xref=”ISHAM-ITS:MITS310″ | ||
| JCM | Japan Collection of Microorganisms | /db_xref=”JCM:1339″ | ||
| JGIDB | JGI Genome Portal | /db_xref=”JGIDB:Chluvu1_81011″ | ||
| JGI’s Phytozome | Comparative genomics of plants | /db_xref=”Phytozome:Glyma0021s00410″
/db_xref=”Phytozme:POPTR_1446s00200″ |
||
| LocusID | NCBI LocusLink ID **Discontinued March 2005 | /db_xref=”LocusID:51199″ | ||
| MaizeGDB | Maize Genome Database unique identifiers | /db_xref=”MaizeGDB:635633″ | ||
| MarpolBase | Genome Database for Marchantia polymorpha | /db_xref=”MarpolBase:Mp1g00010.1″ | ||
| MedGen | Human Medical Genetics | /db_xref=”MedGen:C0010674″ | ||
| MGI | Mouse Genome Informatics | /db_xref=”MGI:1894891″ | ||
| MIM | Mendelian Inheritance in Man numbers | /db_xref=”MIM:123456″ | ||
| miRBase | The microRNA database | /db_xref=”miRBase: MI0001857″ | ||
| MycoBank | Fungal Databases, Nomenclature and Species Banks | /db_xref=”MycoBank:MB519473″ | ||
| NBRC | NITE Biological Resource Center | /db_xref=”NBRC:3189″ | ||
| NextDB | Nematode Expression Pattern DataBase | /db_xref=”NextDB:CELK01662″ | ||
| niaEST | NIA Mouse cDNA Project | /db_xref=”niaEST:L0304H12-3″ | ||
| NMPDR | National Microbial Pathogen Data Resource | /db_xref=”NMPDR:fig|306254.1.peg.183″ | ||
| NRESTdb | Natural Rubber EST database | /db_xref=”NRESTdb:Y01A01″ | ||
| OrthoMCL | Ortholog Groups of Protein Sequences | /db_xref=”OrthoMCL:OG5_130679″ | ||
| Osa1 | Rice Genome Annotation Project | /db_xref=”Osa1:LOC_Os01g12345″ | ||
| Pathema | Pathema Genome Resource | /db_xref=”Pathema:BA_4405″ /db_xref=”Pathema:191218″ |
||
| PBmice | PiggyBac Mutagenesis Information Center | /db_xref=”PBmice:38″ | ||
| PDB | Biological macromolecule three dimensional structure database | /db_xref=”PDB:12GS” | ||
| PFAM | Collection of protein families | /db_xref=”PFAM:PF00003″ | ||
| PGN | Plant Genome Network | /db_xref=”PGN:aam01-1ms3-a05″ | ||
| PIR | Protein Information Resource accession numbers | /db_xref=”PIR:S12345″ | ||
| PomBase | Database of Structural and Functional Data for Schizosaccaromyces pombe | /db_xref=”PomBase:SPBC1709.20″ | ||
| PSEUDO | EMBL pseudo protein identifier | /db_xref=”PSEUDO:CAC44644.1″ | ||
| PseudoCap | Pseudomonas Genome Database | /db_xref=”PseudoCap:PA0001″ | ||
| RAP-DB | Rice Annotation Project Database | /db_xref=”RAP-DB:Os01g1234567″ | ||
| RATMAP | Rat Genome Database | /db_xref=”RATMAP:5″ | ||
| RBGE_garden | Royal Botanic Garden Edinburgh Living Collections | /db_xref=”RBGE_garden:20021433″ | ||
| RBGE_herbarium | Royal Botanic Garden Edinburgh Herbarium | /db_xref=”RBGE_herbarium:E00217291″ | ||
| RFAM | RNA families database of alignments and CMs | /db_xref=”RFAM:RF00230″ | ||
| RGD | Rat Genome Database | /db_xref=”RGD:620528″ | ||
| RiceGenes | Rice database accession numbers | /db_xref=”RiceGenes:AA231856″ | ||
| RNAcentral | The non-coding RNA sequence database | /db_xref=”RNAcentral:URS00001B9622″ | ||
| RZPD | Resource Centre Primary Database Clone Identifiers | /db_xref=”RZPD:IMAGp998I142450Q6″ | ||
| SEED | The SEED Database | /db_xref=”SEED:fig|83331.1.peg.1″ | ||
| SGD | Saccharomyces Genome Database | /db_xref=”SGD:L0000470″ | ||
| SGN | SOL Genomics Network | /db_xref=”SGN:E553090″ | ||
| SK-FST | Saskatoon Arabidopsis T-DNA mutant population – SK Collection | /db_xref=”SK-FST: FST:SK32219″ | ||
| SoyBase | Glycine max Genome Database | /db_xref=”SoyBase:Satt005″ | ||
| SRPDB | Signal Recognition Particle Database | /db_xref=”SRPDB:Arth.aure._CP000474.fasta“ | ||
| SubtiList | Bacillus subtilis genome sequencing project | /db_xref=”SubtiList:BG10001″ | ||
| taxon | NCBI’s taxonomic identifier | /db_xref=”taxon:4932″ | ||
| The Arabidopsis IR | The Arabidopsis Information Resource | /db_xref=”TAIR:AT1F51370″ | ||
| TIGRFAM | TIGR protein families | /db_xref=”TIGRFAM:TIGR00094″ | ||
| TubercuList | TubercuList knowledge base | /db_xref=”TubercuList:Rv3322c” | ||
| UNILIB | Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap | /db_xref=”UNILIB:1002″ | ||
| UniProtKB/Swiss-Prot | section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature | /db_xref=”UniProtKB/Swiss-Prot:P12345″ | ||
| UniProtKB/TrEMBL | section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation | /db_xref=” UniProtKB/TrEMBL:Q00177″ | ||
| UniSTS | Database of Sequence Tagged Sites | /db_xref=” UniSTS:486599″ | ||
| UNITE | Molecular database for the identification of fungi | /db_xref=” UNITE:UDB000157″ | ||
| VBASE2 | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse | /db_xref=”VBASE2:humIGKV165″ | ||
| VectorBase | Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens | /db_xref=”VectorBase:ENSANGG00000007825″ | ||
| VGNC | Vertebrate Gene Nomenclature Committee | /db_xref= “VGNC:VGNC:4927” | ||
| ViPR | Virus Pathogen Resource | /db_xref=”ViPR:HRV-A34_p1058_sR263_2008″ | ||
| WorfDB | C. elegans ORFeome cloning project | /db_xref=”WorfDB:pos-1″ | ||
| WormBase | Caenorhabditis elegans Genome Database | /db_xref=”WormBase:R13H7″ | ||
| Xenbase | Xenopus laevis and tropicalis biology and genomics resource | /db_xref=Xenbase:XB-GENE-1019547 | ||
| ZFIN | Zebrafish Information Network | /db_xref=”ZFIN:ZDB-GENE-011205-17″ | ||
Revised October 30, 2014