The UCSC Genes track shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. This is a moderately conservative set of predictions, requiring the support of one GenBank RNA sequence plus at least one additional line of evidence. The RefSeq RNAs are an exception to this, requiring no additional evidence. The track includes both protein-coding and putative non-coding transcripts. Some of these non-coding transcripts may actually code for protein, but the evidence for the associated protein is weak at best. Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants.
This track in general follows the display conventions for gene prediction tracks. The exons for putative noncoding 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. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature.
The UCSC Genes are built using a multi-step pipeline:
The UCSC Genes track was produced at UCSC using a computational pipeline developed by Jim Kent, Chuck Sugnet and Mark Diekhans. It is based on data from NCBI RefSeq, UniProt (including TrEMBL and TrEMBL-NEW), CCDS, and GenBank. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them.
Copyright information from the UniProt website:
Copyright 2002-2009 UniProt Consortium. We have chosen to apply the Creative Commons Attribution-NoDerivs License to all copyrightable parts of our databases. This means that you are free to copy, distribute, display and make commercial use of these databases, provided you give us credit. However, if you intend to distribute a modified version of one of our databases, you must ask us for permission first. All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32:D23-6.
Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46.
Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.