<div dir="ltr"><div>Now I am really confused !</div><div><br></div><div><div>Even the UCSC tables link <span style="font-size:12.8px">NM_003036.3 as the canonical transcript. Does this mean there can be 2 possible canonical transcripts </span></div></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">one for curated annotations and one for predicted?</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Here is the table linkage of refseq transcripts in the knownCanonical </span><span style="font-size:12.8px">table</span></div><div><span style="font-size:12.8px"><br></span></div><div><pre style="color:rgb(0,0,0);word-wrap:break-word;white-space:pre-wrap">#filter: kgXref.geneSymbol = 'SKI'
#hg19.knownCanonical.chrom hg19.knownCanonical.chromStart hg19.knownCanonical.chromEnd hg19.knownCanonical.clusterId hg19.knownCanonical.transcript hg19.knownCanonical.protein hg19.kgXref.geneSymbol hg19.kgXref.refseq hg19.kgXref.protAcc hg19.kgXref.description
chr1 2160133 2241652 98 uc001aja.4 uc001aja.4 SKI NM_003036 NP_003027 Homo sapiens v-ski sarcoma viral oncogene homolog (avian) (SKI), mRNA.</pre></div><div><pre class="gmail-genbank" style="font-family:monospace,serif;font-size:13px;white-space:pre-wrap;margin-top:0px;margin-bottom:0px;overflow:visible;word-wrap:break-word;width:50em;zoom:1;color:rgb(0,0,0);line-height:16.9px"><pre style="line-height:normal;word-wrap:break-word;white-space:pre-wrap"><pre style="word-wrap:break-word;white-space:pre-wrap"><br></pre></pre></pre></div><div class="gmail_extra">
<br><div class="gmail_quote">On 26 July 2016 at 16:06, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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Hi Duarte,<br>
<br>
A canonical transcript is usually the transcript with the longest
translation for a given gene<br>
<a href="http://www.ensembl.org/Help/Glossary?id=346" target="_blank">http://www.ensembl.org/Help/Glossary?id=346</a><br>
<br>
In your example, XP_005244832.1 has a translation of 730 aa while
NP_003027.1 only has 728.<br>
Hence, it is chosen as the canonical transcript.<br>
<br>
As Kieron mentioned, if you want specifically curated RefSeq
annotation, it might be better to fetch all external annotations
then filter out the ones you are interested in.<br>
<br>
<br>
Regards,<br>
Magali<div><div class="gmail-h5"><br>
<br>
<div>On 25/07/2016 17:07, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I will try and produce here the relevant parts of
the script.
<div><br>
</div>
<div>But I still am at loss why <span style="font-size:12.8px"> </span><a href="http://www.ncbi.nlm.nih.gov/protein/XP_005244832.1" style="font-size:12.8px" target="_blank">XP_005244832.1</a> has
been tagged as canonical</div>
<div><br>
</div>
<div>For what you are saying is that I simply might not have
cycled trough all of the refseq transcripts... but is there
going to be more than one refseq transcript tagged as
canonical for each gene?</div>
<div><br>
</div>
<div>Not sure I follow!</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
Duarte</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
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<div class="gmail_quote">On 25 July 2016 at 11:58, Kieron Taylor
<span dir="ltr"><<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi Duarte,<br>
<br>
Can you send us a snippet of code that accesses the external
database adaptor (DBEntryAdaptor?). It sounds like you may
not be reading enough of your results to get the RefSeq ID
you expect. We have all of the RefSeq IDs you mention
associated at some level to the transcript, but some are
from "RefSeq peptide predicted" for example.<br>
<br>
Kieron<br>
<br>
<br>
<br>
Kieron Taylor PhD.<br>
Ensembl Developer<br>
<br>
EMBL, European Bioinformatics Institute<br>
<div>
<div><br>
<br>
<br>
<br>
<br>
<br>
> On 22 Jul 2016, at 10:47, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>>
wrote:<br>
><br>
> Hi Guys<br>
><br>
> I have a script that based on a gene symbol
connects to ensembl and retrieves the canonical
transcript and then does the same using the external
database adaptor to get the canonical refseq transcript.<br>
><br>
> However this does not seem to give me the correct
result<br>
><br>
> Take for example the gene SKI ( I am using GRCh37
assembly btw)<br>
><br>
> If you open this gene on the Ensembl browser:<br>
><br>
> <a href="http://grch37.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000157933;r=1:2159997-2161343" rel="noreferrer" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000157933;r=1:2159997-2161343</a><br>
><br>
><br>
> On SKI, Ensembl annotates as the canonical
transcript: ENST00000378536<br>
><br>
> However, using by script, the external database
adaptor returns the refseq XP_005244832.1 as the refseq
canonical transcript, even though the correct canonical
transcripts is NM_003036.3<br>
><br>
> <a href="http://www.ncbi.nlm.nih.gov/gene/6497" rel="noreferrer" target="_blank">http://www.ncbi.nlm.nih.gov/gene/6497</a><br>
><br>
> Unless I am understanding this incorrectly if the
coding regions is the same length in 2 transcripts the
longest should be the canonical<br>
><br>
> The longer Refseq is NM_003036.3 (has a longer
5prime UTR)<br>
><br>
> Can you help me understand this?<br>
><br>
> Many thanks<br>
><br>
> Duarte<br>
</div>
</div>
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