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Hello,


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<div class="">I’m looking at the exons for the human gene CEBPA ENST00000498907.2.</div>


<div class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000245848;r=19:33790840-33793470;t=ENST00000498907" class="">http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000245848;r=19:33790840-33793470;t=ENST00000498907</a></div>


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<div class="">It turns out that it has one exon (with UTR sequences on either side of it) and it is protein-coding.</div>


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<div class="">However, when I use the API like this:</div>


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<div class=""><font face="Menlo" class="">my $transcript = $transcript_adaptor->fetch_by_stable_id(‘ENST00000498907’);</font></div>


<div class=""><font face="Menlo" class="">my $exon = $transcript->get_all_Exons()->[0];</font></div>


<div class=""><font face="Menlo" class="">$exon->is_coding($transcript);</font></div>


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<div class="">returns 0.</div>


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<div class="">This is because neither of the conditions in the $exon->is_coding() method evaluate to true.</div>


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<div class=""><font face="Menlo" class="">if ($transcript->coding_region_start < $self->start && $self->start < $transcript->coding_region_end) { return 1; }<br class="">


if ($transcript->coding_region_end > $self->end && $self->end > $transcript->coding_region_start) { return 1; }</font></div>


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<div class="">I realise this happens for transcripts which have only one exon (e.g. FOXL2).</div>


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<div class="">Do you think that the <font face="Menlo" class="">exon->start</font> and


<font face="Menlo" class="">exon->end</font> should be changed to <font face="Menlo" class="">


exon->coding_region_start</font> and <font face="Menlo" class="">exon->coding_region_end</font> respectively?</div>


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<div class="">I’m using API version 89.<br class="">


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<div class="">Regards,</div>


<div class="">Bhavana</div>


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---------------------------------------------<br class="">


Bhavana Harsha<br class="">


Bioinformatician<br class="">


COSMIC<br class="">


Wellcome Trust Sanger Institute<br class="">


Hinxton, UK<br class="">


CB10 1SA<br class="">


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