---------- 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
