Hi Lavi, There aren't any annotated 5' or 3' UTRs in the gene tracks on sacCer3 that are not part of genes that are entirely non-coding.
One way you can see this is by comparing the gene annotations in the yeast browser with the gene annotations in the human browser. In human, you will see most gene annotations with thinner blocks at the ends, representing UTRs. In yeast, all of the annotations are either completely thick, representing regions annotated only as coding, or completely thin, representing regions annotated entirely as non-coding. I hope this helps explain what you are seeing in the Table Browser. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/4/12 11:19 PM, Lavi Barziv wrote: > Thanks for the quick response. > > I tried the suggested table, and got output containing only 3'UTRs of tRNAs > and regulatory RNAs. > > Is there a way to get mRNA 3'UTRs? > > > > Lavi Barziv > > > > > > From: Luvina Guruvadoo [mailto:[email protected]] > Sent: Friday, February 03, 2012 7:48 PM > To: Lavi Barziv > Cc: [email protected] > Subject: Re: [Genome] Yeast 3' UTR sequence > > > > Hi Lavi, > > Thank you for bringing this to our attention. We are looking into this > issue. In the meantime, you can use the Ensembl track to retrieve 3' UTRs. > In the Table Browser, set track to "Ensembl Genes" and table to "ensGene". > > Please contact us again at [email protected] if you have any further > questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > On 2/2/2012 1:31 AM, Lavi Barziv wrote: > > Dear UCSC Genome Bioinformaitcs Group > > I'm an M.Sc. student working on translation regulation. > > I was trying to use UCSC Table Browser to retrieve S.cervisiae 3'UTRs, but > got an empty file at the end of the process. > > I'm attaching screen pics to show the parameters I used. > > I would appreciate your help retrieving those sequences. > > > > thanks > > > > Lavi Barziv > > Dr. Yoav Arava's Lab. > > department of Biology > > Technion- Israeli institute of technology. > > Haifa, 32000 > > Israel > > > > +972-48293404 > <mailto:[email protected]> <mailto:[email protected]> > [email protected] > > > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > 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
