<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>

CC BY-SA 3.0
2017-06-21T18:48:06.197Z
To be fair, annotating this in spec-compliant GFF3 would break the vast majority of GFF3 parsers, too. :-)
Daniel Standage
CC BY-SA 3.0
2017-06-21T10:33:07.927Z
2017-06-21T10:33:07.927Z
Devon Ryan
<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>

CC BY-SA 3.0
2017-06-21T09:36:29.243Z
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.
bli
CC BY-SA 3.0
2017-06-21T09:48:34.940Z
Yes, that's much clearer. I don't have an answer, though
bli
<file-formats><gtf><rna-splicing>
How to represent trans-spliced genes in GTF?
# 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

**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. :-)  

---

