[ensembl-dev] Start/Stop Codons Coordinates

[mag]

Hi Jose,

Thank you for reporting this.

We do not dump out stop or start codons that are incomplete.
Unfortunately, as your example has just highlighted, having either 
incomplete results in both not being dumped.

Apologies for the inconvenience, this will be fixed for release 80 at 
the latest.
Thanks again for raising this issue.


Regards,
Magali

On 24/03/2015 15:25, José Manuel Rodríguez wrote:
> Hi everyone,
>
> I have seen something strange in the GTF for human:
> Homo_sapiens.GRCh38.79.gtf
>
> The transcripts where the start codon (or stop codon) has not been found
> (labeled as “cds_start_NF” or “cds_end_NF”),
> I don't see the coordinates of the codons which they have found.
>
> One example gene, “ENSG00000176571”, and the transcripts:
> ENST00000521593 and ENST00000523299  are tagged with tag “cds_start_NF"
> but I don’t see the coordinates of stop_codon. Something like this:
> chr8HAVANA*stop_codon*8761206187612063.+0gene_id "ENSG00000176571.10"; 
> transcript_id "ENST00000521593.4"; gene_type "protein_coding"; 
> gene_status "KNOWN"; gene_name "CNBD1"; transcript_type 
> "protein_coding"; transcript_status "PUTATIVE"; transcript_name 
> "CNBD1-005"; exon_number 7; exon_id "ENSE00002136680.1"; level 2; 
> protein_id "ENSP00000427742.1"; tag "mRNA_start_NF"; tag 
> "cds_start_NF"; transcript_support_level "3"; havana_gene 
> "OTTHUMG00000163743.5"; havana_transcript "OTTHUMT00000375187.4";
> chr8HAVANA*stop_codon*8748770287487704.+0gene_id "ENSG00000176571.10"; 
> transcript_id "ENST00000523299.4"; gene_type "protein_coding"; 
> gene_status "KNOWN"; gene_name "CNBD1"; transcript_type 
> "protein_coding"; transcript_status "PUTATIVE"; transcript_name 
> "CNBD1-004"; exon_number 6; exon_id "ENSE00002099049.1"; level 2; 
> protein_id "ENSP00000430986.1"; tag "mRNA_start_NF"; tag 
> "cds_start_NF"; transcript_support_level "3"; tag 
> "appris_alternative_2"; havana_gene "OTTHUMG00000163743.5"; 
> havana_transcript "OTTHUMT00000375186.1";
>
>
> Is this performance correct?
>
> Thanks in advance.
> J
>
>
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