Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-21T18:48:06.197Z
Answers.Text: To be fair, annotating this in spec-compliant GFF3 would break the vast majority of GFF3 parsers, too. :-)
Answers.UserDisplayName: Daniel Standage
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-21T10:33:07.927Z
Answers.LastActivityDate: 2017-06-21T10:33:07.927Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-21T09:36:29.243Z
Comments.Text: Maybe you could explain better what is the particularity of splicing for this gene. It is not easy to see in the link you give.
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-21T09:48:34.940Z
Comments.Text: Yes, that's much clearer. I don't have an answer, though
Comments.UserDisplayName: bli
Tags: <file-formats><gtf><rna-splicing>
Title: How to represent trans-spliced genes in GTF?
ThreadText: # How to represent trans-spliced genes in GTF?
  
  (Asked by: username_0 on 2017-06-21)
  
  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](https://bioinformatics.stackexchange.com/questions/849/how-to-represent-trans-spliced-genes-in-gtf/855#855)
  
  **Tags:** file-formats, gtf, rna-splicing
  
  > **Comments:**
  > **username_1**: Maybe you could explain better what is the particularity of splicing for this gene. It is not easy to see in the link you give.  
  > **username_1**: Yes, that's much clearer. I don't have an answer, though  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-06-21. Score: 3
  
  To my knowledge there's no defined way to deal with that in GTF. [GFF3 handles trans-splicing](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) (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.
  
  > **Comments:**
  > **username_3**: To be fair, annotating this in spec-compliant GFF3 would break the vast majority of GFF3 parsers, too. :-)  
  
  ---
  
  