Hello Irina, Thank you for reporting this problem. We were aware of a similar problem, but not the entire scope. We have plans to update the UCSC Gene's track and make as many corrections as possible soon. Thanks, Jennifer
------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Irina Khrebtukova" <[email protected]> wrote: > From: "Irina Khrebtukova" <[email protected]> > To: [email protected] > Sent: Tuesday, September 1, 2009 4:58:38 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] discrepancy between knownGenePep and Table-cds > > Hi, > > I noticed some discrepancies between Table-tool generated coding > sequences for known genes and posted on May 10 knownGenePep > sequences. > > For example, for the human gene SIPA1 there are 5 knowngenes in the > hg18: > SIPA1 (uc009yqq.1) at chr11:65164878-65174965 > SIPA1 (uc009yqp.1) at chr11:65164168-65174965 > SIPA1 (uc009yqo.1) at chr11:65162171-65174965 > SIPA1 (uc001ofd.1) at chr11:65164168-65174965 > SIPA1 (uc001ofb.1) at chr11:65162171-65174965 > > #name chrom strand cdsStart cdsEnd proteinID > uc009yqo.1 chr11 + 65164968 65169167 > NP_006738 > uc001ofb.1 chr11 + 65164968 65174762 Q96FS4 > uc009yqp.1 chr11 + 65164968 65169167 > NP_694985 > uc001ofd.1 chr11 + 65164968 65174762 Q96FS4 > uc009yqq.1 chr11 + 65164968 65174762 Q96FS4 > > getting cds sequences using Table-tool returns sequences of following > lengths: > > uc009yqo.1 1149 > uc001ofb.1 3129 > uc009yqp.1 1149 > uc001ofd.1 3129 > uc009yqq.1 3129 > > which corresponds to shown in browser: two short and 3 longer > proteins, > 382 and 1042 aa. > > However in the knownGenePep.txt all 5 proteins are reported as longer > version: > > uc009yqo.1 1042 > uc001ofb.1 1042 > uc009yqp.1 1042 > uc001ofd.1 1042 > uc009yqq.1 1042 > > could you please clarify it? > Thanks a lot! > Irina Khrebtukova > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
