Hello, Hani. Based on what you've described, it sounds like the UCSC Genes knownCanonical and knownIsoforms tables contain the information you're looking for. To get the canonical gene list, perform the following steps:
1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownCanonical Region: Select "genome" for the entire genome or specify a position in the "position" box. You can also specify multiple loci by clicking the "define regions" button. Output format: Select "all fields from selected table" to list every field from the table in your output. Select "selected fields from primary and related tables" to specify which fields should be included in your output. 3. Click the "get output" button The knownIsoforms table combines all isoforms of a single gene into "clusters" and lists each cluster along with the isoforms that belong to that cluster. Note that when you select this table in the Table Browser, it displays the contents of the entire genome by default. You do not have the option of specifying individual genomic regions. To display the contents of this table, simply change the table to knownIsoforms in step 2 above. 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 [email protected] Sent: Tuesday, July 31, 2012 2:01 AM To: [email protected] Subject: [Genome] Protein coding genes list without isoforms Dear UCSC Genome Browser, I would like to get a list of all RefSeq protein coding genes (name, strand, chromosomal location, and sequences). I have tried to get them from Table option but it gave me with different isoforms. Is there any option to remove all isoforms and have one canonical gene?! Also, I am wondering if you list meta gene list (combined all isoforms to have a single meta gene) of protein coding genes? Thanks for your attention and help. Look forward to your reply soon. Regards, Hani Choudhry _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
