Hi Hao, I see what you are talking about, except I don't see NM_001126114 when I click on uc002gim.2, I see NM_000546 (which is still incorrect).
This inconsistency is due to a bug in the pipeline used to build UCSC Genes. The correct accession for uc002gim.2 is the one you see in the kgXref table, NM_001126112. The problem is that the display page uses another table, knownToRefSeq, to determine which RefSeq Summary to display. In the current gene set, there are some cases where the accession in knownToRefSeq does not match the accession in kgXref. This bug has been corrected in the latest UCSC Genes build, which you can see now on our test server: http://genome-test.cse.ucsc.edu. Be aware that there is a lot of experimental and untested data on the test server. The new UCSC Genes build will be released to the public website soon. You can watch for an announcement of the release on our home page, or you can subscribe to our low-volume announcement mailing list, [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 1/19/12 3:13 PM, Zhao, Hao wrote: > Hello UCSC staff, > > I have a question on the gene annotation of the transcript uc002gim.2, > which has 11 exons and its corresponding refSeq id is NM_001126112 (based > on kgXref.txt). However, > if we go to the genome browser and paste NM_001126112, click 'submit' and > click the link for UCSC annotation and if we click the transcript whose > name was highlighted in blue (name TP53), we will see its RefSeq Summary > (NM_001126114), instead of* *NM_001126112. I am confused about this. Could > you help for that? > > Thank you very much. > > Best, > Hao > > MD Anderson Cancer Center > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
