Hi Mary, Thanks for the answer but I would like to know why the transaltion result for many genes come out to be different when CDS start mentioned in USCS Genome Browser Table is considered to be the translation start? For example I downloaded a complete chromosome 1 of hg19 from UCSC Genome Browser ftp downloads whole genome and then I carefully extracted the all the exonic regions starting from base at CDS start till base at CDS end for a gene/transcript(uc010nya.1), the exon start and end positions and CDS start and end obtained from UCSC. Then I translated those regions assuming that reading frame begins from CDS start(translation start) and the string of amino acids differ from the protein sequence of uc010nya.1 obtained from UCSC Genome Browser.
The two sequences are: >Manual translation from CDS start till CDS end for uc010nya.1 MSESRQTHVTLHDIDPQALDQLVQFAYTAEIVVGEGNVQDSAPSRQSPAA EWRPRRLLQVSTESARPLQLPGYPGLCRCALLQRPAQGRPQVRAAALRGR GQDRGVYAAAPETGNSWRAQPSXXXXXXXXLCL*LPTPFCS*HSPAHNP* CLLCVPETFLDLGPPGASSVAPDSARPLPV*TLSPHLLTX >uc010nya.1 obtained from UCSC Genome Browser table MSESRQTHVTLHDIDPQALDQLVQFAYTAEIVVGEGNVQTLLPAASLLQLNGVRDACCKF LLSQLDPSNCLGIRGFADAHSCSDLLKAAHRYVLQHFVDVAKTEEFMLLPLKQVTAGGPS PRPPPHPTPVFVFDSRPRFVPDTALPTILSACCVSPRPFWIWAPQEPRLWLLTLLGPSQY EHSAPTC >From first line of the first sequence after "GNVQ" you will start seeing the deviation from the second sequence. Please let me know why does it then differ. Thank you, Rahil Sethi > 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
