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 > -- ################################################################ Hao Zheng PhD Candidate----Bioinformatics and Digital Signal Processing Georgia Institute of Technology 210 Technology Circle Savannah, GA 31407 Phone: 404-543-2836 Web: http://users.ece.gatech.edu/~hzheng7/ ################################################################# _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
