Question: UTR size range for 5' UTR & 3' UTR variants
0
gravatar for anu014
2.6 years ago by
anu014170
India
anu014170 wrote:

Hello Biostars,

What should be the size range of UTRs at 5' & 3' end so that if a variant falls in this range I can call it 5' UTR variant or 3' UTR variant? Is there any official terminology/definition for it?

I saw this : http://utrdb.ba.itb.cnr.it/ but couldn't find anything related to UTRs size..

Please help me. Thanks in advance! :)

variant biology sequence gene • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Emily_Ensembl20k • written 2.6 years ago by anu014170
4
gravatar for Emily_Ensembl
2.6 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

It's called a UTR variant if it falls in the UTR. There is no size range. The UTR is the part of the mRNA which is transcribed but not translated.

If you're thinking of upstream/downstream variants, these are usually measured as within 5kb of the transcription start and end.

ADD COMMENTlink written 2.6 years ago by Emily_Ensembl20k

Thank you for the reply. Actually, in this this paper : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC139023/ it's written "5'UTR ranges between 100 and 200 nucleotides, whereas the average length of 3' UTRs is much more variable, ranging from about 200 nucleotides in plants and fungi to 800 nucleotides in humans" . But I'm not sure if this is the golden standard. I am trying to include these ranges in my script to test my variants for UTR variants.

ADD REPLYlink written 2.6 years ago by anu014170
2

Hello,

please read Emilys post again. There is no golden standard for the size of the UTR as it has a clear biological definition and sense.

fin swimmer

ADD REPLYlink written 2.6 years ago by finswimmer13k
1

Those are the average sizes. A UTR is a defined entity. You should look for the variants that fall in the defined entity, not within some arbitrary region.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Emily_Ensembl20k

Thanks Emily. That cleared my understanding about UTRs & scripting :)

ADD REPLYlink written 2.6 years ago by anu014170
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