Hi Duke, Here is an easier way to get the 3' UTR sequences with refSeq ID's.
In the table browser, please select the following: group: Genes and Gene Prediction track track: RefSeq Genes table: refGene region: genome output format: sequence Click "get output" Select: "genomic" Click "submit" Select: "3'UTRs" Click "get sequence" Hope this helps! Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Duke" <[email protected]> To: [email protected] Sent: Tuesday, March 8, 2011 2:33:26 PM Subject: [Genome] Extract 3' UTR sequence with refSeq Hi, Following this (https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008882.html) instruction, I was able to extract the 3' UTR sequence from Table Browser, but the fasta headers are gene ID and other infos (for example: ">mm9_refFlat_Xkr4 range=chr1:3204563-3206102 5'pad=0 3'pad=0 strand=- repeatMasking=none"). Please let me know a proper way of getting 3' UTR but with refSeq IDs instead of gene IDs. Converting from gene ID to refSeq in this case seems not to be a solution since there are lots of identical gene IDs (and range etc...). One example would be: ">mm9_refFlat_Tcea1 range=chr1:4886446-4887990 5'pad=0 3'pad=0 strand=+ repeatMasking=none" (there are three such identifications). Thank you in advance, D. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
