Hi Again, Just to clarify -
When I stated that 5' and 3' do not matter for non-coding mRna, I should be very clear and say that "5' UTR and 3' UTR do not matter". Since there is no coding region to define the UTR transcript ends. Of course knowing which end of the mRna sequence is 5' and which is 3' is important and both are a known from the alignment direction since the sequence is contains splice sites. If a non-coding mRna is within a single exon, then the 5' and 3' end of the mRna would be an unknown, but still relevant - perhaps using additional lines of evidence could be used to determine the direction of transcription. I hope this is clear. My apologies if this was confusing, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Vinay K Mittal" <[email protected]> > Cc: "genome UCSC genome query" <[email protected]> > Sent: Wednesday, November 4, 2009 11:46:35 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Regarding gene prediciton track on browser > > 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" <[email protected]> wrote: > > > From: "Vinay K Mittal" <[email protected]> > > To: "genome UCSC genome query" <[email protected]> > > 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 - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
