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.
For more information on the different gene tracks, see our Genes FAQ.
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 30lift37 (mapped from GRCh38 to GRCh37)
corresponds to Ensembl 96.
GENCODE version 29lift37 (mapped from GRCh38 to GRCh37)
corresponds to Ensembl 94.
GENCODE version 28lift37 (mapped from GRCh38 to GRCh37)
corresponds to Ensembl 92.
GENCODE version 27lift37 (mapped from GRCh38 to GRCh37)
corresponds to Ensembl 90.
GENCODE version 24lift37 (mapped from GRCh38 to GRCh37)
corresponds to Ensembl 83.
GENCODE version 19 corresponds to Ensembl 74 and Vega 54.
GENCODE version 17
corresponds to Ensembl 72 and Vega 52.
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, EMBL European Bioinformatics Institute, Cambridge, UK |
Paul Flicek |
| GENCODE Co-Principal Investigator, EMBL European Bioinformatics Institute, Cambridge, UK |
Adam Frankish |
| GENCODE Co-Principal Investigator, Wellcome Trust Sanger Institute (WTSI), Cambridge, UK |
Bronwen Aken |
| Kings College, London, UK |
Tim Hubbard |
| HAVANA manual annotation group, EMBL European Bioinformatics Institute, Cambridge, UK |
Timothy Cutts, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel
Gonzalez, Stephen Fitzgerald, Andrew Berry, Alexandra Bignell, Claire
Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab
Mukherjee, Gemma Barson, Matt Hardy, Angela Macharia |
| Ensembl, EMBL European Bioinformatics Institute, Cambridge, UK |
Carlos Garcia, Fergal Martin, Osagie Izuogu |
| Centre de Regulació Genòmica (CRG), Barcelona, Spain |
Roderic Guigó, Julien Lagarde, Barbara Uszczyńska |
| UC Santa Cruz Genomics Institute, University of California Santa Cruz (UCSC), USA |
David Haussler, Mark Diekhans, Benedict Paten, Joel Armstrong, Ian Fiddes |
| 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, 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 |
Jennifer Harrow, James Gilbert, Electra Tapanari, Stephen Searle,
Rachel Harte, Daniel Barrell, Felix Kokocinski, Veronika Boychenko,
Toby Hunt, Catherine Snow, Gary Saunders, Sarah Grubb, Thomas Derrien,
Andrea Tanzer, Gang Fang, Mihali Felipe, Joanne Howes, Reena Halai,
Pablo Roman-Garcia, Michael Brent, Randall Brown, Jeltje van Baren
|
References
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa
A, Searle S et al.
GENCODE: the reference human genome annotation for The ENCODE Project.
Genome Res. 2012 Sep;22(9):1760-74.
PMID: 22955987; PMC: PMC3431492
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.
PMID: 16925838; PMC: PMC1810553
A full list of GENCODE publications are available
at The GENCODE
Project web site.
Data Release Policy
GENCODE data are available for use without restrictions.
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