Blog:Exons coordinate also reports the UTR region

Question

[tralynca]

Hi,

I've used the UCSC Table browser to extract the 3'UTR, 5'UTR, intronic, exonic and promoter coordinates (1000 bases upstream of TSS) for a list of candidate genes. I've noticed however that my exonic coordinates also reports the part of the UTR's position as part of the exon's coordinates.

e.g.

3'UTR                                                       exon
chr 1     215793960   215795149   +                         chr 1     215793398   215795149   +

I know they are attached when you view them in the Genome browser, but I need the the specific coordinates of just the UTR portion and I need the exon's coordinates that doesn't overlap with that of the UTR. Does anyone know how I can separate the two.

In some cases, it's even exactly the same.

e.g.

3'UTR                                                       exon
chr 1     93307322  93307481   +                            chr 1     93307322   93307481   +

Is there a plausible explanation for this? I know there are many different splice variants for the same gene, but it just seems really odd. I have 175 candidate genes and I see this occurrence quite frequently for the 5'UTR and its exon as well.

e.g.

5'UTR                                                       exon
chr 1     215747128   215747182   +                         chr 1      215787128  215787182

Thank you in advance
Tracey

[Devon Ryan]

Since UTRs are expressed, they're part of exons, by definition.

Answer 1

[PoGibas]

According to this picture from wikipedia.org UTRs are parts of exons.

Probably what you want is: UTR and CDS.

Btw, here is thread from seqanswers.com: Are UTRs parts of exons?

[tralynca]

You guys are amazing. Thank you for your quick responses. Devon, I guess I was just hoping that there would be a way to separate the 'transcribed, but not translated' section and compare it separately to all exons in the pre-mRNA. Pgibas, I was going to use the CDS as my final resort. I guess I was hesitant because my script is looking for variants that lie within defined genomic regions and I was afraid that after the splicing together the coordinates might be reported differently for the CDS and so would not show a match. I think I just need to wrap my head around this a bit and do another quick comparison between the exonic and CDS coordinates.

Thanks again