GENCODE: The reference human genome annotation for The ENCODE Project

TLDR

The GENCODE Consortium aims to identify all gene features in the human genome. This is achieved through a combination of computational analysis, manual annotation, and experimental validation. Since its first release, GENCODE 7 has added few new protein‑coding loci but many alternative splicing transcripts, now cataloguing 20,687 protein‑coding and 9,640 lncRNA loci, 33,977 coding transcripts not in UCSC or RefSeq, with 35 % of transcription start sites supported by CAGE, 62 % of protein‑coding genes having annotated polyA sites, over one‑third supported by peptide hits, and 3,689 new loci identified from Illumina Body Map 2.0, including 3,127 two‑exon models likely unannotated lncRNAs. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

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.