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Hi Uma,<br>
<br>
An initiator_codon_variant is a sequence ontology term used in the
variation annotation.<br>
We map variations to the reference genome and calculate consequences
for this variation.<br>
In this case, it is a missense variation that affects the first
codon of the transcript.<br>
More information can be found here:
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<a
href="http://www.ensembl.org/info/genome/variation/predicted_data.html">http://www.ensembl.org/info/genome/variation/predicted_data.html</a><br>
<br>
The transcripts you are looking at come from the Havana manual
annotation.<br>
They are protein-coding transcripts but we lack evidence to annotate
the full length CDS, hence the incomplete sequence.<br>
This can happen for example if the biological evidence (proteins,
mRNAs) are not publicly available or if there is an error in the
genome sequence, preventing us from correctly aligning said
evidence.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 12/09/13 20:37, Paila, Uma Devi
(udp3f) wrote:<br>
</div>
<blockquote cite="mid:CE579043.E654%25udp3f@eservices.virginia.edu"
type="cite">
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<div>Hi,</div>
<div> I would greatly appreciated if anybody could tell me what it
means by an initiator codon in ENSEMBL? If it refers to the
translational start site, why some of the HUMAN transcripts in
ENSEMBL show an initiator codon other than 'AUG' ? Considering
this example, <a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?g=ENSG00005917;r=2:20449625-20512017;t=ENST00000440577;transcript=ENST0000044057">http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?g=ENSG00005917;r=2:20449625-20512017;t=ENST00000440577;transcript=ENST0000044057</a>,
this transcript shows a translation with 'R' as the first amino
acid whereas you would expect to see a 'M' as in this example <a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000055917;r=2:20449625-20512017;t=ENST00000442400">http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000055917;r=2:20449625-20512017;t=ENST00000442400</a> </div>
<div><br>
</div>
<div>I see the first example shows its CDS as incomplete. Does
that mean it is actually missing some transcript info? My other
question is, how is the initiator_codon_variant defined? Does
this mean a variation in the translational start or the
transcription start site?</div>
<div><br>
</div>
<div>regards,</div>
<div>uma </div>
<br>
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