Hi Andrew, I'm sorry, but we can only show the most closely related RefSeq Gene in the refSeq column for kgXref. If we included mRNAs IDs from genbank and RefSeq Gene IDs in the refSeq column, our software, as well as our users, would not know which table/database to reference.
As is stated in this mailing list question https://lists.soe.ucsc.edu/pipermail/genome/2005-February/006788.html, "The relationship between KG (UCSC Known Genes) and RefSeq entries in kgXref table indicates that they are related, but may NOT be identical. This relationship is derived from HUGO and LocusLink." You may be pleased to know that one of the columns from the kgXref table is mRNA, which are mRNA IDs from genbank. The kgXref table does in fact list your mRNA AK294778 as being related to the UCSC Gene uc011azf.1: kgID: uc011azf.1 mRNA: AK294778 spID: B4DGU4 spDisplayID: B4DGU4_HUMAN geneSymbol: CTNNB1 refseq: NM_001904 protAcc: NP_001895 description: beta-catenin I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/23/10 3:19 PM, Andrew Yee wrote: > Take for example the output from kgXref for the kgID uc011azf.1 > > #kgID mRNA spID spDisplayID geneSymbol refseq protAcc description > uc011azf.1 AK294778 B4DGU4 B4DGU4_HUMAN CTNNB1 NM_001904 NP_001895 > beta-catenin > > In this example, it lists NM_001904 as the associated refseq. However, the > sequence for uc011azf.1 doesn't match up that well with the reference > sequence listed here for NM_001904 > http://www.ncbi.nlm.nih.gov/nuccore/148228165 > > Instead it matches up better with sequence listed for mRNA AK294778 > http://www.ncbi.nlm.nih.gov/nuccore/194378309 > > Is the output for refseq meant to be more of a guide, or is there meant to > be a correspondence between the refseq ID and the actual sequence in kgID? > > Thanks, > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
