Hello, This is just a corner case in the Table browser nomenclature used for the various tracks (UCSC Genes vs RefSeq Genes). For non-coding mRna, the idea of 5' or 3' is meaningless. How we store the data coordinates is interpreting the designation of '3 or 5'. Sometimes we make the alignment txtStart coordinate the same for cdsStart/End and sometimes the txtEnd coordinate. Best advice is to just ignore it and use the sequences as non-coding.
Thanks, Jennfer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Vinay K Mittal" <vinaykmit...@gatech.edu> wrote: > From: "Vinay K Mittal" <vinaykmit...@gatech.edu> > To: "genome UCSC genome query" <gen...@soe.ucsc.edu> > Sent: Wednesday, November 4, 2009 9:23:45 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Regarding gene prediciton track on browser > > Hi, > I was wondering how UTR regions(3' or 5') are defined for non coding > regions on browser. > For an example: Refseq gene FAM138F (NR_026820.1) and UCSC gene > uc001aak.1 are both non coding and have exactly same sequence and > located in the same region o the browser. Also both are on negative > strand. When I tried to download the genomic sequence(excluding intron > region) for both the genes separately, I get only 3'UTR sequence for > NR_026820.1 where as the same sequence is defined as 5'UTR for > uc001aak.1. > > I am wondering about the UCSC browser conventions for defining these > UTR regions. I tried to look at the help page on: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning > but couldn't find enough information from there. > > Thanks. > > > > -- > -------- > Vinay Kumar Mittal > MS,Bioinformatics > Georgia Institute of Technology > _______________________________________________ > 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
