How to represent trans-spliced genes in GTF?

Question

[Dan]

For example, see this gene (nad1) in ENA: http://www.ebi.ac.uk/ena/data/view/ABI60879

If you look at the XML for that gene you see the following:

join(
             DQ984518.1: 324706 .. 325091 ,
  complement(DQ984518.1:  24417 ..  24498),
  complement(DQ984518.1:  22828 ..  23019),
             DQ984518.1:   3484 ..   3542 ,
  complement(DQ984518.1: 153702 .. 153960)
)

Which shows 5 exons joined out of phase and out of order. Is there a valid GTF representation of this?

How to dump a 'non-canonically spliced' gene into GTF? i.e. what's the recommendation?

[Dan]

Also, how to verify that the resulting GTF is valid? Compare the translation?

[Devon Ryan]

Hello Dan!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/849/how-to-represent-trans-spliced-genes-in-gtf/855#855

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Istvan Albert]

GTF is a very simplistic and ill-defined format - it is a variant of GFF 2 that only has two required fields

gene_id "ABC"; transcript_id "EFG";

beyond that, there is no requirement. So I don't think it could be turned into a "standard" GTF form since that, in turn, does not exist.

Perhaps as Devon Ryan points out you may use GFF3 with multiple parents.

[Dan]

The issue is with tools that require GTF but not GFF3.