GENCODE: The reference human genome annotation for The ENCODE Project

The GENCODEConsortium 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 annotationdata set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotatedhas steadily increased. The GENCODE7 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 annotationof long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotationand found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotatedpolyA sites. Over one-third of GENCODEprotein-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. GENCODE7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.