Hello,<br><br>I was using the ENSEMBL API to get protein lengths for all genes, and I have noticed that occasionally, the canonical transcript that is returned using <span style="font-family:courier new,monospace">$gene->canonical_transcript()</span> is not the most widely "accepted" transcript from the literature, and neither is it the longest one. For example, DMD is a well-studied gene, and encodes a very large protein, yet the canonical transcript is 238 AAs in length and is obviously too short. The longest transcript is 1115 AAs. This happens in other genes as well, e.g. COL3A1. (Altogether, 200+ genes have canonical transcripts whose length is < 1/4 of the longest transcript.)<br>
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<table cellspacing="0" cols="6" border="0">
        <colgroup width="129"></colgroup>
        <colgroup width="127"></colgroup>
        <colgroup width="128"></colgroup>
        <colgroup width="62"></colgroup>
        <colgroup width="48"></colgroup>
        <colgroup width="89"></colgroup>
        <tbody><tr>
                <td align="LEFT" height="16"><b>ENSG</b></td>
                <td align="LEFT"><b>ENST</b></td>
                <td align="LEFT"><b>ENSP</b></td>
                <td align="LEFT"><b>HGNC</b></td>
                <td align="LEFT"><b>ProteinLength(AA)</b></td>
                <td align="LEFT"><b>CANONICAL?</b></td>
        </tr>
        <tr>
                <td align="LEFT" height="16">ENSG00000168542</td>
                <td align="LEFT">ENST00000450867</td>
                <td align="LEFT">ENSP00000415346</td>
                <td align="LEFT">COL3A1</td>
                <td align="RIGHT">90</td>
                <td align="RIGHT">1</td>
        </tr>
        <tr>
                <td align="LEFT" height="16">ENSG00000168542</td>
                <td align="LEFT">ENST00000317840</td>
                <td align="LEFT">ENSP00000315243</td>
                <td align="LEFT">COL3A1</td>
                <td align="RIGHT">1163</td>
                <td align="RIGHT">0</td>
        </tr>
        <tr>
                <td align="LEFT" height="16">ENSG00000198947</td>
                <td align="LEFT">ENST00000378705</td>
                <td align="LEFT">ENSP00000367977</td>
                <td align="LEFT">DMD</td>
                <td align="RIGHT">238</td>
                <td align="RIGHT">1</td>
        </tr>
        <tr>
                <td align="LEFT" height="16">ENSG00000198947</td>
                <td align="LEFT">ENST00000541735</td>
                <td align="LEFT">ENSP00000444119</td>
                <td align="LEFT">DMD</td>
                <td align="RIGHT">1115</td>
                <td align="RIGHT">0</td>
        </tr>
</tbody></table>



<br>My question is: how is canonical defined? I thought it was either curated information, or if this wasn't available, it's the longest transcript. The API version used is 68. Thanks ahead for your reply.<br><br>
Best,<br>Aliz<br><br><span><span style="border-collapse:separate"><span style="border-collapse:separate"><div style="margin:0px;font-family:'Lucida Grande';font-size:10px">
<span><span style="border-collapse:separate"><span style="border-collapse:separate"><span style="letter-spacing:0px">Aliz R. Rao</span></span></span></span><br><span style="letter-spacing:0px">UCLA Geffen School of Medicine</span></div>
<div style="margin:0px;font-family:'Lucida Grande';font-size:10px"><span style="letter-spacing:0px">Department of Human Genetics, Nelson Lab</span></div>
<div style="margin:0px;font-family:'Lucida Grande';font-size:10px"><span style="letter-spacing:0px">695 Charles E Young Drive S</span></div><div style="margin:0px;font-family:'Lucida Grande';font-size:10px">

<span style="letter-spacing:0px"><span style="background-color:rgb(255,255,204)"><span>Gonda</span></span> <span>5554A</span></span></div><p style="margin:0px 0px 3px;font-family:'Lucida Grande';font-size:10px"><span style="letter-spacing:0px">Los Angeles CA <span>90095</span>-8348 USA</span></p>

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