Hello Biostars, I have been using iGV to visual my transcripts, genome, and reads. However, once I check a certain gene's sequence on a database (in this case Xenbase for Xenopus Laevis), it lacks a 5' UTR coding region. This is likely due to an incomplete genome and annotation on the database. However I find that when I look at my own reads and transcripts, there seems to be no possible 5' UTR region as the exons/coding regions begins immediately where the transcript is indicated. Is it possible that there is just no 5' UTR region on this particular gene or is there a different way to visualize it? I have aligned my reads against the genome that is retrieved from the database so I don't believe that there would be a 5' UTR region annotated but shouldn't I be able to visualize it through my reads/transcripts?
Ah I have exons in my annotation but not CDS specifically. But if you look at my gene of interest, abi2.S, this is the S version of a homeolog, on xenbase there is no annotated 5' UTR. I use the same annotation for my own RNA Seq purposes but what would be the best way to try to find the 5' UTR?
Here is the link of the specific sequence I'm looking at: http://gbrowse.xenbase.org/fgb2/gene_model_details/xl9_1?feature_id=851835
There is no 5' UTR annotated but when I look at my sequence output there is additional transcripts but on the opposite strand (positive instead of negative like this gene. Is it possible that this is where the potential UTR region is despite the opposing strands. They overlap completely regardless and there is an overhang on both ends for a potential 5' or more 3' UTR regions.