[ensembl-dev] CDS and stop codons in Ensembl GTF releases

[mag]

Dear Wibowo,

This is a off-by-one error affecting features on the Y chromosome.
This has been fixed in our dumping code and corrected files will be 
available in release 90.


Kind regards,
Magali

On 06/06/2017 08:40, Wibowo Arindrarto wrote:
> Dear Ensembl developers,
>
> I was wondering what the rules are for stop codon and CDS features in 
> GTF files released by Ensembl. Should stop codons be part of a CDS 
> feature?
>
> As far as I understand, they should not be (also referring to this 
> Biostar post to which Ensembl replied: 
> https://www.biostars.org/p/206362/). However, I stumbled on a 
> transcript in the release 89 GTF (Homo sapiens) that has a stop codon 
> included as part of a CDS. This is transcript ENST00000383070 and I am 
> pasting the relevant columns below ($ grep ENST00000341290 {gtf} | cut 
> -f1,3,4,5,7) :
>
> Y ensembl_havana transcript 2786855 2787699 . -
> Y ensembl_havana transcript 2786855 2787699 -
> Y ensembl_havana exon 2786855 2787699 -
> Y ensembl_havana CDS 2786989 2787603 -
> Y ensembl_havana start_codon 2787601 2787603 -
> Y ensembl_havana stop_codon 2786989 2786991 -
> Y ensembl_havana five_prime_utr 2787604 2787699 -
> Y ensembl_havana three_prime_utr 2786855 2786988 -
> Y ensembl_havana three_prime_utr 2786855 2786988 . -
>
> As you can see, the stop codon spans position 2786989 and 2786991, but 
> position 2786989 onwards is already part of the (only) CDS of the 
> transcript.
>
> Would somebody clarify whether this is intentional or not?
>
> With kind regards,
> Wibowo Arindrarto
>
>
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