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<div class="moz-cite-prefix">On 04/10/2012 17:04, Daniel Hughes
wrote:<br>
</div>
<blockquote
cite="mid:CAP8X9uLABHMas=x+QX9+J3f-V+5Zv+58tPzcUd1h5oEQWR8C5g@mail.gmail.com"
type="cite">if you're wanting to discuss why there are stop codons
in the translations that haven't been marked as having genomic
errors/selenocysteine etc., then probably gramene. if you want to
discuss why they aren't rendered in ensembl then EG plants.<br>
</blockquote>
<br>
but we will look into this and liase with the Gramene people if
appropriate.<br>
<br>
best wishes,<br>
<br>
Paul<br>
<br>
<br>
<blockquote
cite="mid:CAP8X9uLABHMas=x+QX9+J3f-V+5Zv+58tPzcUd1h5oEQWR8C5g@mail.gmail.com"
type="cite">
<br>
dan.<br clear="all">
<br clear="all">
Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>
-------------------------------------------------------------------------------------<br>
<a moz-do-not-send="true" href="mailto:dsth@cantab.net">dsth@cantab.net</a><br>
<a moz-do-not-send="true" href="mailto:dsth@cpan.org">dsth@cpan.org</a><br>
<br>
<br>
<br>
<div class="gmail_quote">2012/10/4 Sam Seaver <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:samseaver@gmail.com"
target="_blank">samseaver@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Arnaud,<br>
<br>
One example we have in Oryza sativa is: LOC_Os10g21210.1<br>
<br>
which translates to:<br>
MTIALGRVTKEENDLFDIMDDWLRRDRFVFVGWSGLFFFLVLISL*EVGLQGQLL*LLGI<br>
PMDWRVPIWKVAIS*PQQFPPLPIV*HTLCCYYGARKHKGILLVGVN*VVCGLLLLSMGL<br>
LH**VSCYVNLNLLGLFNCGLIMQFHSLAQSLFLFPYS*FIHWGNPVGSLRRVLA*QRYF<br>
DSSSSSKDFIIGR*THFI*WELPEY*ARLCYALFMGQPWKTLYLRTVMVQIPSALLTQLK<br>
LKKLIQWSPLIAFGPKSLVLLFPINVGYISLCYLYRSPVYG*VLLA*SAWL*TYVPMTSF<br>
PRKSVQRKILNLRLSTPKIFF*TRVFVRGWQLRISLMKILYSLRRFYHVEMLF<br>
<br>
However, I'm also trying to find the actual Ensembl release
this came<br>
from, we got the data from Gramene and the release numbers
don't<br>
match. To be perfectly honest with you, we are confused as to
whether<br>
to discuss these issues with Gramene or Ensembl Plants, does
this<br>
depend on the species?<br>
<span class="HOEnZb"><font color="#888888"><br>
S<br>
</font></span>
<div class="im HOEnZb"><br>
On Thu, Oct 4, 2012 at 10:23 AM, Arnaud Kerhornou<br>
<<a moz-do-not-send="true"
href="mailto:arnaudbioinfo@gmail.com">arnaudbioinfo@gmail.com</a>>
wrote:<br>
> On 04/10/2012 15:45, Sam Seaver wrote:<br>
>><br>
</div>
<div class="im HOEnZb">>> Dear Arnaud,<br>
>><br>
>> Apparently these embedded stop codons were found in
a few sequences in<br>
>> O. sativa and V. vinifera. There was a
miscommunication and by<br>
>> "ignored", my colleague actually meant '*'.<br>
><br>
</div>
<div class="im HOEnZb">> Re. V. vinifera, we have noticed
some genes had their translation holding<br>
> internal stop codon. This will be fixed in the next
release with is coming<br>
> at the end of this month.<br>
> Because of their number (44 cases), it would be
difficult to go through each<br>
> of them to find out how to fix them, so we have removed
their translation<br>
> and updated their biotype to 'nontranslating_cds'.<br>
><br>
> Re. O. sativa, I can not find any cases of translations
with internal stop<br>
> codons or of translation where we perform amino acid
substitution, can you<br>
> direct us to a gene or translation ?<br>
><br>
</div>
<div class="im HOEnZb">>> However, your email provokes
another question, how do you define<br>
>> whether a stop codon actually belongs to another
amino acid such as<br>
>> Selenocystein. Is this a case where, for the
species, every instance<br>
>> of TGA is known to belong to Selenocystein?<br>
><br>
</div>
<div class="im HOEnZb">> Not all TGAs are Selenocystein.
Selenocystein amonoacids are defined by the<br>
> presence of an RNA motif, called SECIS, in the 3' UTR
of the transcript.<br>
> Ideally, they are specified in the gff3 file we load to
build our core<br>
> databases, but it is not always the case.<br>
> What I usually do is to look at the gene function, as
these genes are<br>
> associated with oxydo-reduction reaction. Then in
Ensembl we have mechanisms<br>
> to substitute one or more aminoacid at a given position
in the protein<br>
> sequence.<br>
> That what we did for Chlamydomonas, e.g.:<br>
> <a moz-do-not-send="true"
href="http://plants.ensembl.org/Chlamydomonas_reinhardtii/Transcript/Sequence_Protein?db=core;g=CHLREDRAFT_206086;r=DS496117:1347779-1349885;t=EDP05676"
target="_blank">http://plants.ensembl.org/Chlamydomonas_reinhardtii/Transcript/Sequence_Protein?db=core;g=CHLREDRAFT_206086;r=DS496117:1347779-1349885;t=EDP05676</a><br>
><br>
> Arnaud<br>
><br>
>><br>
</div>
<div class="HOEnZb">
<div class="h5">>> Thanks<br>
>> Sam<br>
>><br>
>> On Thu, Oct 4, 2012 at 8:50 AM, Arnaud Kerhornou
<<a moz-do-not-send="true"
href="mailto:arnaud@ebi.ac.uk">arnaud@ebi.ac.uk</a>>
wrote:<br>
>>><br>
>>> Dear Sam,<br>
>>><br>
>>> Could you give us the list of species where
it is the case ?<br>
>>> There are some cases where the transcribed
DNA sequence has stop codons<br>
>>> but<br>
>>> they're not real, and we have a mechanism in
the Ensembl API to replace<br>
>>> the<br>
>>> stop codon by the right amino acid.<br>
>>><br>
>>> Typical case is for Selenocystein genes where
an internal stop codon<br>
>>> (TGA),<br>
>>> which is replaced by a 'U' in the amino acid
sequence.<br>
>>><br>
>>> In all cases, they should not be ignored. If
we don't specify the correct<br>
>>> amino acid behind a stop codon, it is not
discarded and the amino acid<br>
>>> sequence would hold an internal '*'
character.<br>
>>><br>
>>> Arnaud<br>
>>><br>
>>><br>
>>> On 04/10/2012 14:30, Sam Seaver wrote:<br>
>>>><br>
>>>> Dear ensembl-dev,<br>
>>>><br>
>>>> A colleague has discovered that in a few
of the plant genomes, the<br>
>>>> underlying DNA sequence of a CDS may have
some embedded stop codons.<br>
>>>> He subsequently found that the resulting
translation, as performed by<br>
>>>> Ensembl, ignores these completely.<br>
>>>><br>
>>>> We were wondering what, if any, other
problems are encountered when<br>
>>>> translating plant genes, and what the
Ensembl translation code does to<br>
>>>> address these?<br>
>>>><br>
>>>> Thanks<br>
>>>> Sam<br>
>>>><br>
>><br>
>><br>
><br>
<br>
<br>
<br>
--<br>
Postdoctoral Fellow<br>
Mathematics and Computer Science Division<br>
Argonne National Laboratory<br>
9700 S. Cass Avenue<br>
Argonne, IL 60439<br>
<br>
<a moz-do-not-send="true"
href="http://www.linkedin.com/pub/sam-seaver/0/412/168"
target="_blank">http://www.linkedin.com/pub/sam-seaver/0/412/168</a><br>
<a moz-do-not-send="true"
href="mailto:samseaver@gmail.com">samseaver@gmail.com</a><br>
<a moz-do-not-send="true" href="tel:%28773%29%20796-7144"
value="+17737967144">(773) 796-7144</a><br>
<br>
"We shall not cease from exploration<br>
And the end of all our exploring<br>
Will be to arrive where we started<br>
And know the place for the first time."<br>
--T. S. Eliot<br>
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