Hello Phenix, You actually don't need the table I described to get the genomic sequence corresponding to the exons of the gene prediction. (Sorry; I think I made that confusing!) To get the sequence, on the gene details page, hit the "Genomic Sequence" link next to the mRNA link, then choose to retrieve sequence for the 5' UTR Exons, the CDS Exons, and the 3' UTR Exons, and hit "submit."
If you would like to do this for several genes at once, use the Table Browser. Hit the "Tables" link in the blue bar at the top of the page. Select the UCSC Genes track, and set the position to the region you are interested in (alternately, you can leave the region set to "genome" and paste a list of identifiers). Set "output format" to "sequence" and hit "get output." On the next page, choose only the exons, and hit "get sequence." If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/17/11 6:08 PM, Phenix Hydra wrote: > ---------- Forwarded message ---------- > From: Brooke Rhead<[email protected]> > Date: 2011/11/18 > Subject: Re: [Genome] consultation about the mRNA sequence of uc001aoe.1 > To: Phenix Hydra<[email protected]> > > > Hi Phenix, > > Would you mind re-sending your question to [email protected]? That way, > it will go into our tracking system, our whole team will be able to see it, > and the answers will go into a searchable archive for future users. > > Thanks, > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/17/11 6:02 PM, Phenix Hydra wrote: > >> Dear Brooke Rhead, >> >> Thank you for your reply. However I still can’t quite understand the >> letter. >> >> While the mRNA sequence obtained from the "mRNA (may differ from >> genome)" link is actually not the predicted full length transcript >> sequence of uc001aoe, why don’t you put the “full length transcript >> sequence” there? >> >> Is there a convenient way to get the “full length transcript sequence” now? >> >> >> >> 2011/11/18 Brooke Rhead<[email protected]<mailto:[email protected]>> >> >> >> Hi Phenix, >> >> The UCSC Genes set is created in part by considering many mRNA >> sequences. See details about the pipeline here: >> >> >> http://genome.ucsc.edu/cgi-__**bin/hgTrackUi?db=hg19&g=__**knownGene<http://genome.ucsc.edu/cgi-__bin/hgTrackUi?db=hg19&g=__knownGene> >> >> >> <http://genome.ucsc.edu/cgi-**bin/hgTrackUi?db=hg19&g=**knownGene<http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene> >>> >> >> The mRNA sequence you get by clicking the "mRNA (may differ from >> genome)" link on the details page of a UCSC Gene (or by looking in the >> table knownGeneMrna) is a representative mRNA sequence that is chosen >> because it most closely matches the gene prediction generated by the >> UCSC Genes pipeline. >> >> In the next data update of the UCSC Genes track, we are going to include >> a table, in addition to the knownGeneMrna table, that contains sequence >> generated from the reference genome using the gene model. (This table >> will be called "knownGeneTxMrna.") >> >> I hope this helps explain the UCSC Genes track. If you have further >> questions, please contact us again at [email protected] >> <mailto:[email protected]>. >> >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 11/16/11 6:55 PM, Phenix Hydra wrote: >> >> Dear Luvina Guruvadoo or someone others, >> >> >> >> I get the mRNA sequence of uc001aoe.1 from the web source. It starts >> with “gttgggggcag...”. But the genome sequence of the first exon >> starts with “gtccct...”. I have compared the two sequences. The exon >> sequence has an additional 42 bp sequence on the 5’ end. Is that a >> mistake or just some genomic phenomenon I don’t know? >> ______________________________**___________________ >> Genome maillist - [email protected]<mailto:[email protected]> >> >> https://lists.soe.ucsc.edu/__**mailman/listinfo/genome<https://lists.soe.ucsc.edu/__mailman/listinfo/genome> >> >> <https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> >> >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
