Hello, Rory. Please see the previously-answered mailing list question at https://lists.soe.ucsc.edu/pipermail/genome/2010-May/022301.html. This question addresses hg19, but it holds true for mm9 as well.
You can use our Table Browser to extract the information you need. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. You'll need to create a filter to isolate the IDs you're interested in. Perform the following steps: 1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables 2. Select the following options: Clade: Mammal Genome: Mouse Assembly: July 2007 (NCBI37/mm9) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: genome Output format: Select "all fields from selected table" if you want every field from the table in your output. If you only want a list of IDs, select "selected fields from primary and related tables". 3. On the "filter" line, click the "create" button 4. In the "Filter on Fields from mm9.knownGene" section, enter the following in the "Free-form query" box: cdsStart=cdsEnd 5. Click the "submit" button 6. Click the "get output" button 7. If you selected "selected fields from primary and related tables" in step 2, in the "Select Fields from mm9.knownGene" section, check the "name" checkbox (and any other field you would like to include in your output) 8. Click the "get output" button Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Rory Johnson Sent: Tuesday, July 31, 2012 3:20 AM To: [email protected] Subject: [Genome] Question: noncoding RNAs in UCSC genes annotation Hi (I dont think this question has been answered before) I am working with a list of expression values for mouse UCSC Gene IDs. I would like to extract from this list the set of NONCODING RNAs only. Can anybody tell me where I might find the list of ncRNAs within the UCSC Gene mm9 annotation? (My gene list looks like this: uc009gmc.1, uc007rnm.1, uc007npc.1 etc) Thanks! Rory -- ========================================= Rory Johnson Bioinformatics and Genomics Group (Professor Roderic Guigó) Centre for Genomic Regulation Dr. Aiguader, 88 08003 Barcelona Catalunya Spain Office: 439 Laboratory: 426.01 Office Phone: (+34) 93316 0245 (or extension 1245, from inside CRG) http://big.crg.cat/bioinformatics_and_genomics www.crg.eu www.roryjohnson.org <http://big.crg.cat/bioinformatics_and_genomics> <http://www.crg.eu> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
