Gencode Genes Super-track Settings
 
Gencode Gene Annotation Tracks   (All Pilot ENCODE Regions and Genes tracks)

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Gencode Genes Mar07  Gencode Gene Annotations (March 2007)  Data version: Mar 2007
Gencode RACEfrags  5' RACE-Array experiments on Gencode loci  Data version: Mar 2007
Gencode Genes Oct05  Gencode Gene Annotations (October 2005)  Data version: ENCODE Oct 2005 Freeze
Gencode Introns Oct05  Gencode Intron Validation (October 2005)  Data version: ENCODE Oct 2005 Freeze

Overview

This super-track combines related tracks from the GENCODE project. The goal of this project is to identify all protein-coding genes in the ENCODE regions using a pipeline that uses computational predictions, experimental verification, and manual annotation, based on the Sanger Havana process.

Gencode Genes Mar07

This track shows gene annotations from the GENCODE release v3.1 (March 2007). These annotations contain updates and corrections to the GENCODE October 2005 annotations, based on validation data from 5' RACE and RT-PCR experiments, which are displayed in the Gencode RACEfrags and Gencode Introns Oct05 tracks.

Gencode RACEfrags

This track shows the products of 5' RACE reactions performed on GENCODE genes in 12 tissues and 3 cell lines, as assayed on Affymetrix ENCODE 20nt tiling arays. The results were used to annotate 5' transcription start sites and internal exons of all annotated protein-coding loci in the Oct. 2005 GENCODE freeze.

Gencode Genes Oct05

This track shows gene annotations from the GENCODE release v2.2 (Oct 2005), which was released as part of the ENCODE October 2005 data freeze.

Gencode Introns Oct05

This track shows validation status of the introns in selected gene models from the Gencode Oct 05 gene annotations, as identified by RT-PCR and RACE experiments in 24 human tissues.

Credits

This GENCODE release is the result of a collaborative effort among the following laboratories:

Lab/Institution
 Contributors
HAVANA annotation group, Wellcome Trust Sanger Insitute, Hinxton, UK Adam Frankish, Jonathan Mudge, James Gilbert, Tim Hubbard, Jennifer Harrow
Genome Bioinformatics Lab CRG, Barcelona, Spain France Denoeud, Julien Lagarde, Sylvain Foissac, Robert Castelo, Roderic Guigó (GENCODE Principal Investigator)
Department of Genetic Medicine and Development, University of Geneva, Switzerland Catherine Ucla, Carine Wyss, Caroline Manzano, Colette Rossier, Stylianos E. Antonorakis
Center for Integrative Genomics, University of Lausanne, Switzerland Jacqueline Chrast, Charlotte N. Henrichsen, Alexandre Reymond
Affymetrix, Inc., Santa Clara, CA, USA Philipp Kapranov, Thomas R. Gingeras

The RACEfrags result from a collaborative effort among the following laboratories:

Lab/Institution
 Contributors
Genome Bioinformatics Lab CRG, Barcelona, Spain France Denoeud, Julien Lagarde, Tyler Alioto, Sylvain Foissac, Robert Castelo, Roderic Guigó
Department of Genetic Medicine and Development, University of Geneva, Switzerland Catherine Ucla, Carine Wyss, Caroline Manzano, Colette Rossier, Stylianos E. Antonorakis
Center for Integrative Genomics, University of Lausanne, Switzerland Jacqueline Chrast, Charlotte N. Henrichsen, Alexandre Reymond
Affymetrix, Inc., Santa Clara, CA, USA Philipp Kapranov, Jorg Drenkow, Sujit Dike, Jill Cheng, Thomas R. Gingeras
HAVANA annotation group, Wellcome Trust Sanger Insitute, Hinxton, UK Adam Frankish, James Gilbert, Tim Hubbard, Jennifer Harrow

References

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto TS, Manzano C, Chrast J et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007 Jun;17(6):746-59.

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.