Hi Meghan, Getting the sequence with the RefSeq identifiers can be done by using the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and selecting the following: * *clade: Mammal genome: Rat assembly: rn4 (or the one that interests you) group: Genes and Gene Prediction Tracks track: RefSeq Genes table: refGene region: Genome identifiers (names/accessions): Click "Paste list" and follow the instructions output format: sequence output file: FileName (if you want to save it to your computer)
click "get output" select " genomic" click "submit" select: 3' UTR Exons One FASTA record per gene click "get sequence" The RefSeq identifier will be contained in the output like this: rn4_refGene_NM_031069 If you are interested in extracting the 3'UTRs using the UCSC Genes track, please see this previously answered mailing list: https://lists.soe.ucsc.edu/pipermail/genome/2008-May/016356.html If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Flanigan, Meghan (NIH/NIAAA) [F] <[email protected]> Date: Thu, Nov 10, 2011 at 2:15 PM Subject: [Genome] 3'UTRs To: "[email protected]" <[email protected]> Hello, I am trying to figure out a way to view only the sequences of 3'UTRs for particular genes (in rat). I saw in some help archives that it was possible to download a full list of 3'UTRs using their RefSeq IDs. However, when I tried this the output document labeled the sequences by position rather than RefSeq IDs. If anyone could clarify how to obtain a list of 3'UTRs with RefSeq IDs, or by any other useful label besides position, it would be greatly appreciated. Thank you Meghan Flanigan _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
