Hello Vikram, Yes, there are several tracks/tables/files with cds information. This will vary by genome and by assembly. To see what is available for your target, look in the track group Gene and Gene Predictions in the Assembly browser.
For the most recent human RefSeq sequences, use the track "RefSeq Genes". The track/table can be brought up in Table browser or you can ftp the file directly. Assembly = Human Feb. 2009 (GRCh37/hg19) Primary table = refGene Download file name = goldenPath/hg19/database/refGene.txt File format help (see genePred3): http://genome.ucsc.edu/FAQ/FAQformat.html#format9 Data access help: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 Another good option is the UCSC Genes track - RefSeq is a subset of this dataset. Review the track description in the assembly browser and the table schema in the Table browser for full details, but to obtain both the alignment coordinates and the gene information, two tables are required: knownGene and kgXref. Very sorry for not replying sooner. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support On 6/24/10 12:31 AM, Vikram wrote: > This is with respect to the coding exons file and the all exons file which i > downloaded from UCSC. This is what the first two lines/rows in the coding > exons file for the reference human genome looks like: > > chr1 67000041 67000051 NM_032291_cds_0_0_chr1_67000042_f 0 + > chr1 67091529 67091593 NM_032291_cds_1_0_chr1_67091530_f 0 + > > ------ > I wish to know if there is some file at UCSC which would contain the exon > information (start and stop coordinates, etc.) along with both the NM entry > and also the Gene ID. (Basically, i wish to identify all possible NM entries > having the same gene ID.) > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
