Hello. Please see the following previously-answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2007-September/014705.html
The answer refers to tracks for the mm8 assembly, but both tracks exist in hg19: SIB Alt-Splicing: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=sibTxGraph UCSC Genes: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene The answer also refers to the use of our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. The following is an example to identify genes in the UCSC Genes track that belong to the same cluster (i.e., are alternate transcripts of the same gene): 1. Go to http://genome.ucsc.edu 2. In the blue navigation bar at the top of the screen, click "Tables" 3. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: Select "genome" for the entire genome or "position" to specify a specific position. You can also specify multiple positions by clicking the "define regions" button Output format: selected fields from primary and related tables 4. Click the "get output" button 5. In the "Linked Tables" section, check the checkbox next to hg19.knownIsoforms 6. Scroll down and click the "allow selection from checked tables" button 7. Check the following checkboxes: hg19.knownGene.name hg19.knownIsoforms.clusterId 8. Click the "get output" button In your output, any results sharing the same clusterId are alternate transcripts of the same gene. 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 shamsher jagat Sent: Tuesday, May 29, 2012 4:24 PM To: [email protected] Subject: [Genome] Alternate splicing data base I am intrested to have a list of alternate spiliced genes so far reported in hg19, How can I get such a file, If possible I may like to have differernt classes of AS- exon skiping alterante 5' splice site or 3' site Thanks _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
