Gff3 Format Has "Intron" Between Cds And 3' Utr, Is This Possible?

Question

[Arun]

Hi,

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,
Arun.

Answer 1

[Scott Cain]

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.

Scott

[Arun]

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