GENCODE and untranslated regions

Question

[j.lunger18]

I want to pull variants from a specific gene and for that I need chromosomal locations. I'm using the UCSC browser to get a range of positions for my gene. I want to include untranslated regions that flank the transcript. I found that the GENCODE transcripts are easy to click on to find their chromosomal locations, but I want to know if I need to add cushions to either side of the locations to include untranslated regions, or if those regions will be included in the range that they give for the transcript? It looks on the browser that they start with EXON1, and do not have any non-coding region before the transcript starts, which makes me wonder how I'm supposed to know how long the transcript actually is before translation and even before processing...

[natasha.sernova]

This post looks helpful.

Get Utr5' And Utr3' Data For Genes From Ucsc Genome Browser

Answer 1

[Emily]

The UTRs are part of the transcript, and their positions within the cDNA are annotated. In the browser you will see that some exons are thick and some are thin: the thick exons are coding, the thin exons are UTR.

[j.lunger18]

           Great, thank yoU!