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.
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.
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.
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.
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 |
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.