Hi Valeria, We currently don't have a feature such as the one you are describing, however, using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), you can upload a list of coordinates and retrieve UTRs and/or coding regions within these coordinates. Select a clade, genome, and assembly of your choice, and make the following selections (I'll use hg19) in this example:
group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: click 'define regions' and paste a list of coordinates output format: sequence Click 'get output' and on the following page, select 'genomic' and click 'submit'. Select the appropriate options (5'UTR, etc) and click 'get sequence'. Please contact the mail list again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 11/18/2011 4:01 PM, Vasta, Valeria wrote: > Following up on the same issue.... is it possible to also annotate if it is a > coding region or a UTR region starting from coordinates? > > Thanks > > Valeria > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Monday, January 24, 2011 10:03 AM > To: Vasta, Valeria > Cc: [email protected] > Subject: Re: [Genome] POISTION TO GENE NAME > > Please note, you can perform this function directly with the MySQL tables: > > http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes > > You can change the parameters in those SQL commands to extract > gene names in a region instead of gene names near a region. > > --Hiram > > ----- Original Message ----- > From: "Valeria Vasta"<[email protected]> > To: "Mary Goldman"<[email protected]> > Cc: [email protected] > Sent: Saturday, January 22, 2011 11:42:53 AM > Subject: Re: [Genome] POISTION TO GENE NAME > > Hello > > I was wondering if this feature has become available > > Thanks > > Valeria > > Hi Valeria, > > We appreciate your suggestion and will pass this request on to our > developers. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 11/16/10 1:10 PM, Vasta, Valeria wrote: >> Hello >> >> I wonder if you could consider adding a coordinate to gene name >> feature.This is highly desirable for instance in the context of exon >> capture and sequencing where you may have to figure out what gene it > is >> a certain region with poor coverage without bioinfo support >> >> Thanks >> >> Valeria > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information protected by law. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply e-mail and destroy all copies > of the original message. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
