RT Journal
A1 Harrow, Jennifer
A1 Frankish, Adam
A1 Gonzalez, Jose M.
A1 Tapanari, Electra
A1 Diekhans, Mark
A1 Kokocinski, Felix
A1 Aken, Bronwen L.
A1 Barrell, Daniel
A1 Zadissa, Amonida
A1 Searle, Stephen
A1 Barnes, If
A1 Bignell, Alexandra
A1 Boychenko, Veronika
A1 Hunt, Toby
A1 Kay, Mike
A1 Mukherjee, Gaurab
A1 Rajan, Jeena
A1 Despacio-Reyes, Gloria
A1 Saunders, Gary
A1 Steward, Charles
A1 Harte, Rachel
A1 Lin, Michael
A1 Howald, Cédric
A1 Tanzer, Andrea
A1 Derrien, Thomas
A1 Chrast, Jacqueline
A1 Walters, Nathalie
A1 Balasubramanian, Suganthi
A1 Pei, Baikang
A1 Tress, Michael
A1 Rodriguez, Jose Manuel
A1 Ezkurdia, Iakes
A1 van Baren, Jeltje
A1 Brent, Michael
A1 Haussler, David
A1 Kellis, Manolis
A1 Valencia, Alfonso
A1 Reymond, Alexandre
A1 Gerstein, Mark
A1 Guigó, Roderic
A1 Hubbard, Tim J.
T1 GENCODE: The reference human genome annotation for The ENCODE Project
JF Genome Research 
JO Genome Research 
YR 2012 
FD September 01 
VO 22 
IS 9 
SP 1760 
OP 1774 
DO 10.1101/gr.135350.111 
UL http://genome.cshlp.org/content/22/9/1760.abstract 
AB 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.