Blog: Exons coordinate also reports the UTR region
2
gravatar for tralynca
5.6 years ago by
tralynca50
South Africa
tralynca50 wrote:

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

ADD COMMENTlink modified 5.6 years ago by PoGibas4.8k • written 5.6 years ago by tralynca50

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

ADD REPLYlink written 5.6 years ago by Devon Ryan97k
4
gravatar for PoGibas
5.6 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

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?

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by PoGibas4.8k

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

ADD REPLYlink written 5.6 years ago by tralynca50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1120 users visited in the last hour