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External References in Vega

Links from Vega features to External resources are generated in a variety of ways depending on the data type and the species. Tables of all of the external references attached to gene, its transcripts and its translations are available on the Gene 'External References' page

Links from Vega translations

CCDS

  • Links between Vega translations and CCDS project identifiers are added by comparing the coordinates of each exon with those of the CCDS exons (human and mouse). Note that with the release of human Vega on the GRCh38 assembly that the CCDS links have been generated by projecting the GRCh37 coordinates onto the GRCh38 assembly rather than by remapping.

Uniprot/SwissProt

  • Links between Vega translations and Uniprot records are generated by the Uniprot team at the EBI and imported into Vega (human, mouse and zebrafish).

GO and GOA

Links from Vega transcripts

Human

  • lncRNA transcripts for human have links to ENA
  • LoF transcripts have links to dbSNP for the variant on which the annotation is based.

Links from Vega genes

Human

  • Records are downloaded from HGNC and associations between the Vega Gene names and identifiers in the downloaded file are made. External sources added are HGNC, EntrezGene, OMIM, Pubmed and RefSeq.
  • Links to IMGT-GeneDB are added using the Vega gene names.
  • Links to IMGT/HLA are added using associations downloaded from IMGT/HLA.

Mouse

  • Records are downloaded from MGI and associations between the Vega Gene names and identifiers in the downloaded file are made. External sources added are MGI, EntrezGene and RefSeq.

Zebrafish

  • Records are downloaded from Zfin and associations between the Vega Gene names and identifiers in the downloaded file are made. External sources added are Zfin and Zfin Expression Patterns.

Rat

  • Records are downloaded from RGD and associations between the Vega Gene names and identifiers in the downloaded file are made. External sources added are RGD, EntrezGene, Uniprot/TrEMBL, RefSeq and PubMed.

Links to Ensembl identifiers

  • Links between Vega and Ensembl transcript and gene stable identifiers are created during the Ensembl genemerge and imported into Vega (human, mouse and zebrafish).