GENCODE Super-track Settings
 
GENCODE Gene Annotation Tracks   (All Genes and Gene Predictions tracks)

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GENCODE Genes V19  Gene Annotations from ENCODE/GENCODE Version 19
GENCODE Genes V17  Gene Annotations from ENCODE/GENCODE Version 17
GENCODE Genes V14  Gene Annotations from ENCODE/GENCODE Version 14
GENCODE Genes V7  Gene Annotations from ENCODE/GENCODE Version 7

wgEncodeGencodeSuper

Description

The aim of the GENCODE Genes project (Harrow et al., 2006) is to produce a set of highly accurate annotations of evidence-based gene features on the human reference genome. This includes the identification of all protein-coding loci with associated alternative splice variants, non-coding with transcript evidence in the public databases (NCBI/EMBL/DDBJ) and pseudogenes. A high quality set of gene structures is necessary for many research studies such as comparative or evolutionary analyses, or for experimental design and interpretation of the results.

The GENCODE Genes tracks display the high-quality manual annotations merged with evidence-based automated annotations across the entire human genome. The GENCODE gene set presents a full merge between HAVANA manual annotation and Ensembl automatic annotation. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. With each release, there is an increase in the number of annotations that have undergone manual curation. This annotation was carried out on the GRCh37 (hg19) genome assembly.

Experimental verification details are given in each descriptions for each track. Transcript Support Levels were determined for version 10 onwards based on evidence provided by GenBank mRNA and EST sequences. Versions 7 and 10 are being used in data analysis by the ENCODE consortium.

NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial sequences are not available in the UCSC Genome Browser. These annotations are available for download in the GENCODE GTF files.

Display Conventions

These are multi-view composite tracks that contain differing data sets (views). Instructions for configuring multi-view tracks are here. Only some subtracks are shown by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the track descriptions.

Release Notes

GENCODE version 19 corresponds to Ensembl 74 and Vega 54.

GENCODE version 17 corresponds to Ensembl 72 and Vega 52 and is the most current release.

GENCODE version 14 corresponds to Ensembl 69 and Vega 49

GENCODE version 7 corresponds to Ensembl 62 and Vega 42 and is used in ENCODE analysis.

See also: The GENCODE Project Release History.

Credits

This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute)

Lab/Institution Contributors
GENCODE Principal Investigator Tim Hubbard
HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Jennifer Harrow, Stephen Searle, Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel Gonzalez, Electra Tapanari, Daniel Barrell, Adam Frankish, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Catherine Snow, Gemma Barson, Matt Hardy, Joanne Howes
Centre de Regulació Genòmica (CRG), Barcelona, Spain Roderic Guigó, Julien Lagarde, Barbara Uszczy𑀪ska
Genome Bioinformatics, University of California Santa Cruz (UCSC), USA David Haussler, Rachel Harte, Mark Diekhans, Benedict Paten, Joel Armstrong
Computer Science and Artificial Intelligence Lab,Broad Institute of MIT and Harvard, USA Manolis Kellis, Irwin Jungreis
Computational Biology and Bioinformatics, Yale University (Yale), USA Mark Gerstein, Suganthi Balasubramanian, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe
Center for Integrative Genomics,University of Lausanne, Switzerland Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast
Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Alfonso Valencia, Michael Tress, José Manuel Rodríguez, Victor de la Torre
Former members of the GENCODE project Felix Kokocinski, Toby Hunt, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Michael Brent, Randall Brown, Jeltje van Baren

Contact: GENCODE at the Sanger Institute

References

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S et al. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet. 2011 Jul;19(7):827-31.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S et al. Ensembl 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9.

Publications

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213.

Ezkurdia I, Del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function. Mol Biol Evol. 2012 Apr 17;.

Publications link for the GENCODE project

Data Release Policy

GENCODE data are available for use without restrictions.