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<p>Hi Bhavana</p>
<p>Thanks for pointing it out. We will get it fixed in release 91.</p>
Best Regards<br>
Prem (Ensembl Core Team)<br>
<br>
<div class="moz-cite-prefix">On 06/10/2017 09:49, Bhavana Harsha
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:0C366FD6-4C3E-4592-89B3-02336DE3E635@sanger.ac.uk">
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Hello,
<div class=""><br class="">
</div>
<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="" moz-do-not-send="true">http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000245848;r=19:33790840-33793470;t=ENST00000498907</a></div>
<div class=""><br class="">
</div>
<div class="">It turns out that it has one exon (with UTR
sequences on either side of it) and it is protein-coding.</div>
<div class=""><br class="">
</div>
<div class="">However, when I use the API like this:</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Menlo">my $transcript =
$transcript_adaptor->fetch_by_stable_id(‘ENST00000498907’);</font></div>
<div class=""><font class="" face="Menlo">my $exon =
$transcript->get_all_Exons()->[0];</font></div>
<div class=""><font class="" face="Menlo">$exon->is_coding($transcript);</font></div>
<div class=""><br class="">
</div>
<div class="">returns 0.</div>
<div class=""><br class="">
</div>
<div class="">This is because neither of the conditions in the
$exon->is_coding() method evaluate to true.</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Menlo">if ($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>
<div class=""><br class="">
</div>
<div class="">I realise this happens for transcripts which have
only one exon (e.g. FOXL2).</div>
<div class=""><br class="">
</div>
<div class="">Do you think that the <font class="" face="Menlo">exon->start</font>
and
<font class="" face="Menlo">exon->end</font> should be
changed to <font class="" face="Menlo">
exon->coding_region_start</font> and <font class=""
face="Menlo">exon->coding_region_end</font> respectively?</div>
<div class=""><br class="">
</div>
<div class="">I’m using API version 89.<br class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Bhavana</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica;
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<br class="Apple-interchange-newline">
---------------------------------------------<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="">
</div>
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