Human Assembly and Annotation Information

Summary

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:

• The MHC region on chromosome 6 in seven haplotypes: COX, QBL, APD, DBB, MANN, MCF, SSTO. These are shown as distinct chromosomes, for example (6-COX and 6-QBL) and are included in the Vega comparative analysis.
• The LRC region on chromosome 19 in nine haplotypes. As for the MHC regions, these are shown as distinct chromosomes, for example 19-COX_1 and are also included in the Vega comparative analysis.

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, Pubmed and RefSeq.
• Uniprot records, Gene Ontology (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.

Publications

• 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].