Hi Hao, The "TRD@" name is actually not assigned to a UCSC Gene, just to an associated mRNA. One way to see this is to enter "TRD@" in the position/search box on the main Genome Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks?hgTracks). Entering a name in the box searches many tables at once for matching identifiers. In the case of "TRD@", there are only search results for the mRNA tracks. Doing a search of the whole Genome Browser website (from this page: http://genome.ucsc.edu/FAQ/), will eventually lead you to a UCSC Gene for which "TRD@" shows up in the "Descriptions from all associated GenBank mRNAs", but it is not actually assigned as a name for a UCSC Gene.
A better method for finding the UCSC identifiers associated with names is to use the Table Browser (the link in the blue bar at the top of the page: http://genome.ucsc.edu/cgi-bin/hgTables). If you select the UCSC Genes track and the knownGene table, you can hit the "identifiers (names/accessions): paste list" button and enter your names. This searches another table, kgAlias, which relates (usually several) names to each UCSC Gene identifier. If your goal is to go from a list of names to their corresponding canonical UCSC Gene, I would suggest the following progression of tables: - start with kgAlias to relate a name to a UCSC identifier (there may be more than one) - once you have an identifier, look in the knownIsoforms table to find a cluster number - once you have the cluster number, look in the knownCanonical table to get the canonical UCSC Gene identifier I hope this is helpful. If you have further questions, please send them to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group [email protected] wrote on 10/4/10 6:04 PM: > Dear Pauline > > How can I get the the UCSC gene identifier for genes like "TRD@"? > > And I cannot find the UCSC ID uc010aju.1 in the knownCanonical table here > either: > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz. > > Thanks, > Hao > > > ----- Original Message ----- > From: "Pauline Fujita" <[email protected]> > To: [email protected] > Cc: [email protected] > Sent: Monday, October 4, 2010 8:47:59 PM GMT -05:00 US/Canada Eastern > Subject: Re: [Genome] Gene positions from the hg18 Canonical table > > Hello Hao Zheng, > > All the genes in the knownCanonical.txt.gz file are referred to by their > UCSC genes identifier ("ucNNNabc.N"): > > i.e. > chr1 1115 4272 1 uc009vip.1 uc009vip.1 > chr1 4269 19221 2 uc009viw.1 uc009viw.1 > chr1 19417 20957 3 uc009vjg.1 uc009vjg.1 > > So you would have to find the corresponding UCSC genes identifier for > these genes: > > Alternate Gene Symbols: BCL5, BCL6_HUMAN, LAZ3, NM_001706, NP_001697, > P41182, S67779, uc003frp.1, ZBTB27, ZNF51 > UCSC ID: uc003frp.2 > > Alternate Gene Symbols: MDS1_HUMAN, NM_004991, NP_004982, Q13465, Q13466 > UCSC ID: uc003ffp.1 > > (TRD@) > Alternate Gene Symbols: AK310682, uc001wea.1 > UCSC ID: uc010aju.1 > > The other gene you inquired about, "C12orf9" was not included in the > UCSC genes track. For more information about the criteria for > including/excluding genes from UCSC genes please see the track description: > > http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1 > > Hopefully this information was helpful and answers your question. If you > have further questions or require clarification feel free to contact the > mailing list at [email protected]. > > > Best regards, > > Pauline Fujita > > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > > On 9/30/10 12:07 PM, [email protected] wrote: >> Dear Colleague, >> >> There are three genes called "BCL5", "MDS1" and "TRD@". However, I am not >> able to get the coordinates of these three genes from the >> knownCanonical table here: >> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz. >> >> Do you have any suggestions? >> >> Thanks, >> >> Hao Zheng >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
