This site presents data from the manual annotation of the
human genome by the Havana group at the Welcome Trust Sanger Institute. A first pass annotation of the whole genome has been completed as part of the Gencode project. Vega also shows Loss Of Function (LoF) loci.
Additional MHC and LRC Haplotypes
Vega also shows manual annotation of loci and regions of particular interest:
Havana annotation update
The human data includes an Havana Update track
to rapidly refelect changes in annotation outside the regular release
schedule. This track is updated biweekly.
External database identifiers
- Vega human has CCDS identifiers assigned to translations where appropriate. Transcripts that have CCDS identifiers attached are highlighted in light blue on Location based views. The actual CCDS identifiers are accesible on Gene Summary, Gene External References, and Transcript Summary Pages. More information about CCDS.
- 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,
- Uniprot records,
(GO) terms and Gene Ontology Annotation (GOA)
records are imported into Vega. These are generated by the EBI Uniprot and GOA teams.
- lncRNAs are Vega are incorporated into the ENA and reciporocal links to the
ENA are added to the transcripts in Vega.
- Links to IMGT-GeneDB
are added using the Vega gene names, and links to IMGT/HLA are added using
associations downloaded from IMGT/HLA.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.
GENCODE: the reference human genome annotation for The ENCODE Project.
Genome Res. 2012 Sep;22(9):1760-74. [Pubmed] [doi:10.1101/gr.135350.111].