GENCODE: The reference human genome annotation for The ENCODE Project

Author:

Harrow Jennifer,Frankish Adam,Gonzalez Jose M.,Tapanari Electra,Diekhans Mark,Kokocinski Felix,Aken Bronwen L.,Barrell Daniel,Zadissa Amonida,Searle Stephen,Barnes If,Bignell Alexandra,Boychenko Veronika,Hunt Toby,Kay Mike,Mukherjee Gaurab,Rajan Jeena,Despacio-Reyes Gloria,Saunders Gary,Steward Charles,Harte Rachel,Lin Michael,Howald Cédric,Tanzer Andrea,Derrien Thomas,Chrast Jacqueline,Walters Nathalie,Balasubramanian Suganthi,Pei Baikang,Tress Michael,Rodriguez Jose Manuel,Ezkurdia Iakes,van Baren Jeltje,Brent Michael,Haussler David,Kellis Manolis,Valencia Alfonso,Reymond Alexandre,Gerstein Mark,Guigó Roderic,Hubbard Tim J.

Abstract

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

Publisher

Cold Spring Harbor Laboratory

Subject

Genetics(clinical),Genetics

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