Question: Gff3 Format Has "Intron" Between Cds And 3' Utr, Is This Possible?
gravatar for Arun
7.9 years ago by
Arun2.3k wrote:


One of the entries in the gff3 file I am using looks like this. This entry contains an overlapping gene. If you look at the highlighted part, for the 1st gene entry, there's a CDS followed by a 3' UTR, however there is a gap between CDS and 3' UTR (if you look at the end of highlighted CDS and start of highlighted 3'UTR). Is this in general possible? If so is this to be interpreted as an intron? or is this an error? (seems to basic an error to have occurred).

Thank you,

gff • 1.9k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Arun2.3k
gravatar for Scott Cain
7.9 years ago by
Scott Cain750
Scott Cain750 wrote:

Hi Arun,

I would be suspicious. If you look at the line just above your highlighted lines, you see an exon that has the same start as the CDS and the UTR shares the end of the exon, but there is some "no man's land" which is neither CDS nor UTR. Since there is a declared exon there, I would assume that means there is no intron there, but you'll have to go back to the originator and ask them to clarify.


ADD COMMENTlink written 7.9 years ago by Scott Cain750

Dear Scott, That's what I thought as well. I'll do that (this is still a pre-release).

ADD REPLYlink written 7.9 years ago by Arun2.3k
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