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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you very much Will.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam P. Levine<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt">From:</span></b><span lang="EN-US" style="font-size:11.0pt"> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 18 April 2016 14:47<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] 'Canonical' splice site change with VEP<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Adam,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">The SO term splice_donor_variant [1] as reported by the VEP covers this. Variants in the receiving 2bp region are defined as splice_acceptor_variant [2].<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">There's also a number of splicing predictors available as VEP plugins (e.g. [3]) which you may find useful.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Regards<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Will McLaren<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Ensembl Variation<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[1] : <a href="http://www.sequenceontology.org/miso/current_svn/term/SO:0001575">http://www.sequenceontology.org/miso/current_svn/term/SO:0001575</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[2] : <a href="http://www.sequenceontology.org/miso/current_svn/term/SO:0001574">http://www.sequenceontology.org/miso/current_svn/term/SO:0001574</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[3] : <a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/GeneSplicer.pm">https://github.com/Ensembl/VEP_plugins/blob/release/84/GeneSplicer.pm</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On 18 April 2016 at 11:14, Levine, Adam <<a href="mailto:a.levine@ucl.ac.uk" target="_blank">a.levine@ucl.ac.uk</a>> wrote:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Is there a way of getting VEP to identify whether a variant causes a 'canonical' splice site change (i.e. affects the first two nucleotides flanking an exon)?<br>
<br>
Thank you,<br>
<br>
Adam<br>
<br>
Adam P. Levine<br>
<br>
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