Hi Rahil, Thank you so much for giving the assembly, track and table you were using when you encountered your question - it is much appreciated!
UCSC Genes does not have cdsStartStat, cdsEndStat or exonFrames fields like most of our gene prediction tracks (more information about why can be found in this previous mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2010-September/023585.html). This means that you can use the CDS start and CDS end as start and stop codons. Please keep in mind that we have made the CDS start equal the CDS end for non-coding genes. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 10/11/10 7:29 AM, [email protected] wrote: > Hello, > > I am trying to extract the codon start and codon stop for a set of genes > in a given position, from Tables in UCSC Genome Browser. Whenever I click > output for Genes and Gene Predictions in a chromosome posiition range, it > gives me all the feature of genes like exon start, exon stop, CDS start, > CDS stop, but does not give me the codon start (start position of the > first codon i.e. translation start) and codon stop (position of stop codon > i.e. translation stop). > > Please let me know how can I get this information? > > I am using: > Genome: Hg19 > Group: Genes and Gene Prediction Tracks > Track: UCSC Genes > Table: KnownGene > region: defined regions > > Thank you, > Rahil Sethi > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
