Description

The Old Known Genes track shows genes from the 2006 Known Genes build. RGD Genes has now replaced Known Genes as the main gene track for rat.

The Old Known Genes track shows known protein-coding genes based on protein data from UniProt (SWISS-PROT and TrEMBL) and mRNA data from the NCBI reference sequences collection (RefSeq) and GenBank. Each Known Gene is represented by an mRNA and a protein.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks.

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.

Methods

This release of UCSC Known Genes was built by a new process, KG II, as described below.

UniProt protein sequences (including alternative splicing isoforms) and mRNA sequences from RefSeq and GenBank were aligned against the base genome using BLAT. RefSeq alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. GenBank mRNA alignments having a base identity level within 0.2% of the best and at least 97% base identity with the genomic sequence were kept. Protein alignments having a base identity level within 0.2% of the best and at least 80% base identity with the genomic sequence were kept.

Then the genomic mRNA and protein alignments were compared, and protein-mRNA pairings were determined from their overlaps. mRNA CDS data were obtained from RefSeq and GenBank data and supplemented by CDS structures derived from UCSC protein-mRNA BLAT alignments. The initial set of UCSC Known Genes candidates consists of all protein-mRNA pairs with valid mRNA CDS structures. A gene-check program (similar to the one used for the Consensus CDS (CCDS) project) is used to remove questionable candidates, such as those with in-frame stop codons, missing start or stop codons, etc.

From each group of gene candidates that share the same CDS structure, the protein-mRNA pair having the best ranking and protein-mRNA alignment score is selected as a UCSC Known Gene. The ranking of a gene candidate depends on its gene-check quality measures. When all else is equal, a preference is given to RefSeq mRNAs and next to MGC mRNAs. Similarly a preference is given to gene candidates represented by Swiss-Prot proteins. The protein-mRNA alignment score is calculated based on protein to mRNA alignment using TBLASTN, plus weighted sub-scores according to the date and length of the mRNA.

Credits

The UCSC Known Genes track was produced using protein data from UniProt and mRNA data from NCBI RefSeq and GenBank.

Data Use Restrictions

The UniProt data have the following terms of use, UniProt copyright(c) 2002 - 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 each copy.

For commercial use, all databases and documents in the UniProt FTP directory except the files

• ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
• ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz

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.

References

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. 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. PMID: 16500937

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518