Hello, Your questions are good ones, but they are of a scientific nature that is can only be determined by examination and judgement. There is no standard answer about which is correct. They both could be correct (represent variation). Or some could be finished and some provisional. Or another reason(s).
It is almost certain that translation differences will result from the various transcripts available for gene bounds. And that incorporating mRNA/EST data will add in some useful and some erroneous information. The best method is to open up the gene location (include the UCSC Gene track, too) and examine the data to determine which transcripts to keep or leave out of your analysis. The canonical transcriptome for the human genome has yet to be determined, Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Hannah Cheung" <[email protected]> wrote: > From: "Hannah Cheung" <[email protected]> > To: [email protected] > Sent: Friday, August 28, 2009 8:13:06 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] exon size discrepancies > > Hello, > > I have been analyzing a particular set of genes for copy number > changes that would affect exons. In doing this work, I found some exon > size discrepancies between RefSeq sequences and the transcript > sequences provided by Ensembl. I have attached the examples that I > have found. There are probably more than this. > > I understand that this may stem from differences in algorithms used > for alignment, but I am concerned that this would affect the > translated protein sequence because there would be frameshifts > occurring. > > Which transcript is correct? Do we have to wait until more RNA > sequencing is done to really know the answer? What about all the > libraries of cDNA expression clones that have been made? Would they be > at risk of being erroneous? > > Sincerely, > > > Hannah Cheung, PhD > Postdoctoral Associate > Department of Pediatrics > 1120 Bates St. > Feigin Center, Rm 1200.18 > Texas Children's Hospital > Houston, TX 77030 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
