GENCODE: The reference human genome annotation for The ENCODE Project
Name
Harrow-2012-GENCODE_ The referen.pdf
Size
1.8 MB
Format
Adobe PDF
Checksum (MD5)
4423ee04c322ff26af0269b1f5a5e949
Author(s)
Lin, Michael F.
Kellis, Manolis
Date Issued
September 2012
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory Press
Citation
Harrow, J. et al. “GENCODE: The Reference Human Genome Annotation for The ENCODE Project.” Genome Research 22.9 (2012): 1760–1774.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1101/gr.135350.111
