Hi Nikita, The sequence you get when you select 300 in ‘Downstream’ from the gene page is 300 bases past the end of the gene, not 300 bases past the TSS. To get what you are looking for, you can use the "DNA" button on the main genome browser page (http://genome.ucsc.edu/cgi-bin/hgTracks) instead.
To do this for a single gene, zoom in to a single base that is the transcription start site for your gene. Then hit the "DNA" button in the blue bar at the top of the page. Choose to "Add 700 extra bases upstream (5') and 300 extra downstream (3')" and hit "get sequence." If your gene is on the negative strand, you will want to also check the "Reverse complement (get '-' strand sequence)" box. If you want to do this for many genes, you can create a custom track with your transcription start sites, then use the Table Browser to output sequence. Please reply to [email protected] if you have further questions. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/18/11 11:16 AM, Luvina Guruvadoo wrote: > Hi Nikita, > > Please see this Frequently Asked Question (FAQ) for more information on > how to retrieve promoter regions: > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download18 > > Also feel free to search the Genome mailing list archives by visiting > our home page and clicking on "Contact Us" > (http://genome.ucsc.edu/contacts.html), or email us again at > [email protected] if you have any further questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > On 11/17/2011 8:51 PM, Nikita Pednekar wrote: >> Sir, >> >> Below are the step I am using… >> >> ******************************* >> >> Clicking on genomes >> >> Selecting Human >> >> Entering gene symbol in ‘gene’ textfield. Click submit >> >> Clicking on first cartoon of gene (UCSC gene based on RefSeq, UniProt, >> GenBank, CCDS and comparative genomics) >> >> In ‘sequence and links to tools& database’ , click on ‘Genomic sequence >> (chr…………) >> >> Entered 700 in ‘Promoter/upstream’ and 300 in ‘Downstream’. Rest deselect. >> Click submit. >> >> Got seq in FASTA format. >> >> ******************************* >> >> However, the downstream 300bp seem to be incorrect in all the cases. >> I would like to know how to extract 300 bases downstream of TSS using UCSC >> genome. >> >> Regards, >> Nikita Pednekar. >> _______________________________________________ >> 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
