TY  - JOUR
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
Y1  - 2012/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1760 
EP  - 1774 
DO  - 10.1101/gr.135350.111 
VL  - 22 
IS  - 9 
UR  - http://genome.cshlp.org/content/22/9/1760.abstract 
N2  - 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. 
ER  -