Hello, The RefSeq sequences at UCSC are directly from the NCBI release. Differences are likely due to the different programs used to generate the alignment. To double check that the mRna is the same, extract the mRNa from the Table browser or the track description page and compare it to the record at NCBI. Also note that the update data is included on the track description page, too. We hope this helps, Jennifer
------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Daniel Herman" <daniel.her...@gmail.com> wrote: > From: "Daniel Herman" <daniel.her...@gmail.com> > To: gen...@soe.ucsc.edu > Sent: Wednesday, September 30, 2009 4:25:45 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Refseq refGene version > > Hello -- > > I've been trying to make amino acid change predictions using UCSC > genePred > files (hg18; refseq refGene). However, it seems that for at least a > couple > transcripts (ex. NM_000256) the refGene exons are incorrect and > different > from NCBI Genbank, which I presume to be a version difference. > > I was considering rebuilding the refGene table (installing the UCSC > source > table for > gtfToGenePred<http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred>and > trying to convert transcript definitions from NCBI or ENSEMBL), but I > am > wondering whether the refGene table will be updated in the near > future. > > Thank you for any help. > > -Dan > _______________________________________________ > Genome maillist - Genome@lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
