db_xrefs

The /db_xref qualifier serves as a vehicle for linking 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.

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 member databases of the International Collaboration (DDBJ, ENA/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:

db_xref List
         

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 -- 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"
         
         

ECOCYC

 

E. coli database

 

/db_xref="ECOCYC:sroC"

/db_xref="ECOCYC:C0343"

EcoGene   Database of Escherichia coli Sequence and Function   /db_xref="EcoGene:EG11277"
         

ENSEMBL

 

Database of automatically annotated genomic data

 

/db_xref="ENSEMBL:HUMAN-Clone-AC005612"

/db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"

         

EnsemblGenomes

 

Extending Ensembl across taxonomic space

 

/db_xref="EnsemblGenomes:AAC73116"

/db_xref="EnsemblGenomes:b0005"

         

EnsemblGenomes-Gn

 

EnsemblGenomes Gene

 

/db_xref="EnsemblGenomes-Gn"

         

EnsemblGenomes-Tr

 

EnsemblGenomes Transcript

 

/db_xref="EnsemblGenomes-Tr:MAPG_00606T0"

EPD

 

Eukaryotic Promoter 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 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: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

         

I5KNAL

 

i5k Workspace

 

/db_xref="I5KNAL:OFAS008986"

         

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"

         

LocusID

 

NCBI LocusLink ID **Discontinued March 2005

 

/db_xref="LocusID:51199"

         

MaizeGDB

 

Maize Genome Database unique identifiers

 

/db_xref="MaizeGDB:635633 "

         

MedGen

 

Human Medical Genetics

 

/db_xref="MedGen:C0010674"

         

MGI

 

Mouse Genome Informatics

 

/db_xref="MGI:MGI:1894891"

         

MIM

 

Mendelian Inheritance in Man numbers

 

/db_xref="MIM:123456"

         

miRBase

 

miRNA Database

 

/db_xref="miRBase:MI0000681"

         

MycoBank

 

Fungal Nomenclature and Species Bank

 

/db_xref="MycoBank:8284"

         

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

 

/dbxref="PDB:12GS"

         
PFAM   Collection of protein families   /db_xref="PFAM:PF00003
         

PGN

 

Plant Genome Network

 

/db_xref="PGN:aam01-1ms3-a05"

         

JGI Phytozome

 

Plant Genome Network

 

/db_xref="Phytozome:Glyma0021s00410"

/db_xref="Phytozome:ppb016588m_2_1.p"

         

PIR

 

Protein Information Resource accession numbers

 

/db_xref="PIR:S12345"

         

PomBase

 

Database of Structural and Functional Data for Schizosaccaromyces pombe

 

/db_xref="PomBase:SPBC11B10.09"

         

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

 

Noncoding RNA Sequence Database

 

/db_xref="RNAcentral:URS00001B9622_9606"

         

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"

         

SubtiList

 

Bacillus subtilis genome sequencing project

 

/db_xref="SubtiList:BG10001"

         

TAIR

 

Arabidopsis IR

 

/db_xref="TAIR:AT1F51370"

         

taxon

 

NCBI's taxonomic identifier

 

/db_xref="taxon:4932"

         

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"

         

ViPR

 

Virus Pathogen Resource

 

/db_xref="ViPR:HRV-A34_p1058_sR263_2008"

         

VISTA

 

Vista Enhancer Browser

 

db_xref="VISTA:hs123"

         

VectorBase

 

Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens

 

db_xref="VectorBase:ENSANGG00000007825"

         

VGNC

 

Vertebrate Gene Nomenclature Committee

 

db_xref="VGNC:VGNC:4927"

         

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"

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Last updated: 2017-11-13T23:20:57Z