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