Hello Qu, The "RefSeq Genes" track on the chimpanzee assembly contains both human and chimp records, because there are relatively few chimp RefSeq genes (currently < 750). The chimp assembly has the only RefSeq Genes track that is treated as a special case in this way (at the time of this email, anyway!).
This difference is documented on the track description page, which you can get to by clicking on blue title "RefSeq" above the track pulldown, or by clicking on the blue/gray bar to the left of the track in the main display. To get only the chimp RefSeq genes from the Table Browser, select the refGene table just as you describe, and then hit "filter: create". On the next page, choose the panTro2.gbCdnaInfo table and hit the "allow filtering using fields in selected tables" button. Scroll down -- there should now be even more tables to choose from. Select the "panTro2.organism" table and hit the "allow filtering" button again. Now, under "panTro2.organism based filters", enter "Pan troglodytes" in quotes so that the filter consists of: name does match "Pan troglodytes" and hit submit. Now you should be back on the main Table Browser page, where you can hit "get output" to get your results. I hope this helps you get the information you need. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 09/22/09 11:24, Qu Zhang wrote: > Hi there, > > Sorry to bother you, but I've encountered a question when using table > browser. The table information is as follows: > > clade: mammal genome: chimp assembly: may 2006 group: gene and > gene prediction track track: refseq table: refgene. > > The problem is that many refgene IDs given in the final result refer > to a human sequence when double-checking on NCBI (NM_017891, > NM_001014980, e.g.). But it's not the case for orangutan genome. Could > you tell me what's going on here or how I can find the real chimpanzee > refgene? Your help will be appreciated! > > Best, > Qu > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
