Hi again, I accidentally sent a link to the UCSC Genes methods page on our test server, which is currently slightly different from the one on our production site. For the record, the link is http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 1/13/12 12:28 PM, Brooke Rhead wrote: > Hi Anna, > > I was looking at this question again as part of the update we are doing > on the UCSC Genes track. With the latest build (not yet available), we > made changes to our pipeline that fixed some naming issues. However, > this it turns out that this particular case did not have a naming > problem, after all. > > The names of UCSC Genes that you see in the kgXref table come from the > associated RefSeq gene or UniProt protein if there is one, and from the > GenBank mRNA name if not. uc011dhu.1 is based on the CU674603 mRNA and > does not have a supporting RefSeq gene or UniProt protein. If you turn > on the mRNA track, you will see the CU674603 mRNA aligned to this spot, > and if you click through to the details page you will see that it is > indeed named "TUBB2A." > > You might want to take this annotation and its name with a grain of > salt: it is based only on a non-RefSeq transcript (and hence is colored > light blue, see the UCSC Genes methods page: > http://hgwdev.cse.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1), and the > description for CU674603 says it is a "Synthetic construct." You should > also know that GenBank mRNA names can only be changed by the original > submitter of the transcript, so the names are not curated like RefSeq > and UniProt names. > > I hope this information is helpful. If you have further questions, > please contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/28/11 10:54 AM, Pauline Fujita wrote: >> Hello Anna, >> >> This is a known issue that we are working to fix in the next UCSC genes >> release. We expect the release will be out in the near future. >> >> Best regards, >> >> Pauline Fujita >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> On 11/7/11 1:42 AM, Antigoni Elefsinioti wrote: >>> Hi I am a postdoc student in MDC Berlin. I have a question regarding the >>> antisense gene with id uc011dhu.1 (+ strand, chr6:3,224,986-3,226,037). >>> in the kgXref table the Genesymbol name for this id is TUBB2A. But >>> TUBB2A corresponds to tubulin gene that is in minus strand in position >>> (chr6:3,153,904-3,157,783). Why do these two sequences have the same name? >>> best >>> Anna Elefsinioti >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
