Inconsistency in annotation of 5' UTR

[joelnitta]

For several genes, I have observed that the 5' UTR is inconsistently annotated, even when the isoforms are very similar (only varying slightly in exon length). For example:

The question marks indicate isoforms that have unusually long 5' UTRs.

I would be happy to share my data via email if that would help.

tappAS 1.0.7 on a mac.

[aarzalluz]

Hi @joelnitta,

I am not sure I understand the inconsistency -do you mean that the starting positions of the (?) isoforms should be the same, but are painted to be longer than they should? I understand that you are using your own, custom annotation, not one of the GFF3 files supplied by tappAS. If so, it would be interesting to see the annotation file for this gene's isoforms in order to verify whether the Genomic View graphics are correct, perhaps you could supply a screenshot of these few lines of the GFF3?

Thanks,

Ángeles

[joelnitta]

@aarzalluz Thanks for the prompt reply!

do you mean that the starting positions of the (?) isoforms should be the same, but are painted to be longer than they should

Yes, precisely. Also, yes I'm using a custom annotation. I will send you the files (and later post here any information that may be helpful to others).