<div dir="ltr"><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Thank you! That answers my question!</div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">I would really like to be able to access that tag (non-ATG start) programmatically. Are there plans for putting it with the other transcript flags in the GTF file?<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 10 Mar 2021 at 10:09, Emily Perry <<a href="mailto:emily@ebi.ac.uk">emily@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hi Julie<div><br></div><div>We have some information about non-ATG start codons in our blog post from release 102:</div><div><a href="https://www.ensembl.info/2020/11/30/ensembl-102-has-been-released/" target="_blank">https://www.ensembl.info/2020/11/30/ensembl-102-has-been-released/</a></div><div><br></div><div>Quite simply, there is not a rule. This is a situation of exceptional biology which we are only able to annotate correctly because of our expert manual gene annotators analysing the data in detail.</div><div><br></div><div>All the best</div><div><br></div><div>Emily<br><div><br><blockquote type="cite"><div>On 10 Mar 2021, at 09:08, Julie Sullivan <<a href="mailto:julie.sullivan@gmail.com" target="_blank">julie.sullivan@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000288649;r=20:33667144-33668235;t=ENST00000678634" target="_blank">https://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000288649;r=20:33667144-33668235;t=ENST00000678634</a><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">The first codon is GTG. I would not have expected that to be Methionine.</div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">I looked in the text files, and there are 123 of these transcripts where the start codon is NOT ATG but the aa is M, in Homo sapiens.</div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><pre style="box-sizing:inherit;margin:4px 0px;padding:8px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;font-family:Monaco,Menlo,Consolas,"Courier New",monospace;border-radius:4px;color:rgb(29,28,29);font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial">{'error': 0,<br style="box-sizing:inherit"> 'methionine': 91434,<br style="box-sizing:inherit"> 'GTG': 22,<br style="box-sizing:inherit"> 'ATA': 10,<br style="box-sizing:inherit"> 'CTG': 67,<br style="box-sizing:inherit"> 'ACG': 8,<br style="box-sizing:inherit"> 'TTG': 9,<br style="box-sizing:inherit"> 'ATT': 5,<br style="box-sizing:inherit"> 'AAC': 1,<br style="box-sizing:inherit"> 'AAG': 1}</pre><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Why is that? <br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Specifically I would like a rule I can use, as my HGVSp strings are different from VEP for this reason.</div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Thanks!<br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Julie<br></div></div>
_______________________________________________<br>Dev mailing list    <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br><div>
<div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div>—</div><div><br></div><div>Dr Emily Perry (Pritchard)<br>Ensembl Outreach Project Leader <br>(she/her)<br><br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory <br>Wellcome Genome Campus<br>Hinxton<br>Cambridge<br>CB10 1SD<br>UK </div><div><br></div></div><br><br>
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