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.