The GENCODE track is composed of all the gene models in the GENCODE v24 release. It includes both protein-coding genes and non-coding RNA genes.
This track in general follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. The following color key is used:
This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions.
All the GENCODE genes in the comprehensive set are downloaded from the GENCODE website. Data from other sources are correlated with the GENCODE data to build the knownTo tables.
The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file. These include tables that link GENCODE Genes transcripts to external datasets (such as knownToLocusLink, which maps GENCODE Genes transcripts to Entrez identifiers, previously known as Locus Link identifiers), and tables that detail some property of GENCODE Genes transcript sequences (such as knownToPfam, which identifies any Pfam domains found in the GENCODE Genes protein-coding transcripts). One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list is then available on the table menu. Note that some of these tables refer to GENCODE Genes by its former name of Known Genes, sometimes abbreviated as known or kg. While the complete set of annotation tables is too long to describe, some of the more important tables are described below.
The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a computational pipeline developed by Jim Kent and Brian Raney.
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.
GENCODE data are available for use without restrictions.