text: user931: 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?
  Cross-posted on biostars
  
  user77: To my knowledge there's no defined way to deal with that in GTF. GFF3 handles trans-splicing (you'll have to scroll down to "trans-spliced transcript") by giving an individual transcript multiple parents (e.g., ID=some_transspliced_gene;Parent=gene1,gene2). You could use the same methodology with GTF files, but just note that it'll break most downstream programs.
  
original_text: 931: <p>For example, see this gene (nad1) in ENA:
  <a href="http://www.ebi.ac.uk/ena/data/view/ABI60879" rel="nofollow noreferrer">http://www.ebi.ac.uk/ena/data/view/ABI60879</a></p>
  
  <p>If you look at the XML for that gene you see the following:</p>
  
  <pre><code>join(
               DQ984518.1: 324706 .. 325091 ,
    complement(DQ984518.1:  24417 ..  24498),
    complement(DQ984518.1:  22828 ..  23019),
               DQ984518.1:   3484 ..   3542 ,
    complement(DQ984518.1: 153702 .. 153960)
  )
  </code></pre>
  
  <p>Which shows 5 exons joined out of phase and out of order. Is there a valid GTF representation of this?</p>
  
  <p>How to dump a 'non-canonically spliced' gene into GTF? i.e. what's the recommendation?</p>
  
  <p>Cross-posted on <a href="https://bioinformatics.stackexchange.com/questions/849/how-to-represent-trans-spliced-genes-in-gtf/855#855">biostars</a></p>
   77: <p>To my knowledge there's no defined way to deal with that in GTF. <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" rel="nofollow noreferrer">GFF3 handles trans-splicing</a> (you'll have to scroll down to "trans-spliced transcript") by giving an individual transcript multiple parents (e.g., <code>ID=some_transspliced_gene;Parent=gene1,gene2</code>). You could use the same methodology with GTF files, but just note that it'll break most downstream programs.</p>
  