The UCSC Genes track shows gene predictions based on data
from RefSeq, GenBank, and the tRNA Genes
track. 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
about twice as many splice variants.
For more information on the different gene tracks, see our Genes FAQ.
Display Conventions and Configuration
This track in general follows the display conventions for
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:
- Black -- feature has a corresponding entry in the Protein Databank (PDB)
- Dark blue -- transcript has been reviewed or validated by either the
RefSeq or SwissProt staff
- Medium blue -- other RefSeq transcripts
- Light blue -- non-RefSeq transcripts
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:
- RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping
only the best
alignments for each RNA and discarding alignments of less than 98% identity.
- Alignments are broken up at non-intronic gaps, with small isolated
fragments thrown out.
- A splicing graph is created for each set of overlapping alignments. This
has an edge for each exon or intron, and a vertex for each splice site, start,
Each RNA that contributes to an edge is kept as evidence for that edge.
- A similar splicing graph is created in the mouse, based on mouse RNA and
the mouse graph has an edge that is orthologous to an edge in the human graph,
that is added to the evidence for the human edge.
- If an edge in the splicing graph is supported by two or more human ESTs,
it is added as evidence for the edge.
- If there is an Exoniphy prediction for an exon, that is added as evidence.
- The graph is traversed to generate all unique transcripts. The traversal is
guided by the initial RNAs to avoid a combinatorical explosion in alternative
splicing. All refSeq transcripts are output. For other multi-exon transcripts
to be output, an edge supported by at least one additional line of evidence
beyond the RNA is required. Single-exon genes require either two RNAs or two
additional lines of evidence beyond the single RNA.
- Protein predictions are generated. For non-RefSeq transcripts we use the
txCdsPredict program to determine if the transcript is protein-coding and if so,
the locations of the start and stop codons.
The program weighs as positive evidence the length of the protein, the
presence of a Kozak consensus sequence at the start codon, and the length of
the orthologous predicted protein in other species.
As negative evidence it considers nonsense-mediated decay and start codons in
any frame upstream of the predicted start codon. For RefSeq transcripts
the RefSeq protein prediction is used.
- The corresponding UniProt protein is found, if any.
- The transcript is assigned a permanent "uc" accession.
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
(including TrEMBL and TrEMBL-NEW) and
GenBank. Our thanks to the people running these databases
and to the scientists worldwide who have made contributions to them.
Data Use Restrictions
2004 UniProt consortium:
For non-commercial use, 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
For commercial use, all databases and documents in the UniProt FTP
directory except the files
may be copied and redistributed freely, without advance permission,
provided that this copyright statement is reproduced with each copy.
More information for commercial users can be found
From January 1, 2005, all databases and documents in the UniProt FTP
directory may be copied and redistributed freely by all entities,
without advance permission, provided that this copyright statement is
reproduced with each copy.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
PMID: 14681350; PMC: PMC308779
Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D.
The UCSC Known Genes.
Bioinformatics. 2006 May 1;22(9):1036-46.
BLAT--the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518