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
