[ensembl-dev] Start/Stop Codons Coordinates

[José Manuel Rodríguez]

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:
chr8	HAVANA	stop_codon	87612061	87612063	.	+	0	gene_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";
chr8	HAVANA	stop_codon	87487702	87487704	.	+	0	gene_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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