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<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
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-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">Hi Michael</span><br style="color: rgb(34, 34, 34);
font-family: Arial, Verdana, sans-serif; font-size: 12px;
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<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
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<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">There is information about Ensembl variation in our
documentation, which you'll find here:</span><br style="color:
rgb(34, 34, 34); font-family: Arial, Verdana, sans-serif;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/variation/index.html">http://www.ensembl.org/info/docs/variation/index.html</a></span><br
style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">For each gene or transcript, you can find external
references, showing that gene or protein in other databases, some
of which are manually curated and have links to publications. For
example here are the pages for your gene and transcript of
interest:</span><br style="color: rgb(34, 34, 34); font-family:
Arial, Verdana, sans-serif; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000105851;r=7:106505723-106547590">http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000105851;r=7:106505723-106547590</a></span><br
style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650">http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650</a></span><br
style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">You can find variants within your gene or transcript of
interest by going to the Variation table, or by highlighting
variants within the sequence (eg gene, exons, cDNA). You can then
click on your variant of interest to go to the variant tab:</span><br
style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650;v=rs199845412;vdb=variation;vf=54512601">http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650;v=rs199845412;vdb=variation;vf=54512601</a></span><br
style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">From here you can explore aspects of this variant, for
example its source, and external data (such as SNPedia) and
population genetics.</span><br style="color: rgb(34, 34, 34);
font-family: Arial, Verdana, sans-serif; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">In future please direct all such queries only to helpdesk,
not to helpdesk and dev.</span><br style="color: rgb(34, 34, 34);
font-family: Arial, Verdana, sans-serif; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">Hope this helps,</span><br style="color: rgb(34, 34, 34);
font-family: Arial, Verdana, sans-serif; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;">
<br style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">Emily</span><br style="color: rgb(34, 34, 34); font-family:
Arial, Verdana, sans-serif; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;">
<span style="color: rgb(34, 34, 34); font-family: Arial, Verdana,
sans-serif; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline !important; float:
none;">Ensembl helpdesk<br>
<br>
</span>
<div class="moz-cite-prefix">On 21/02/2013 14:00, M. Diamantidis
wrote:<br>
</div>
<blockquote
cite="mid:17AF90C338BAEA4BA257517456AC226611C10C@EXCH-RX02.erasmusmc.nl"
type="cite">
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<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Dear Ensemble
Database,
<!--?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /-->
<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">My name is Dr.
Michael D. Diamantidis, MSc, PhD. I am a haematologist and
working at Erasmus MC, at the haematology department
conducting a post doc.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">The release
number of the Ensembl version i used and i am posing the
question is release 70.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">My question
involves Ensembl data.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">I am
investigating PIK3CG mutations.<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">I would like to
ask you to provide me with the possible references regarding
the human transcript PIK3CG-001 in two positions.<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">The first
position i am interested is in exon 2, amino acid 514, which
is ATG (Methionine), which has a capital R on top of A,
meaning that A or G could occur in the same position. If G
occurs, then the aminoacid in this position is GTG (Valine).
I would like to ask if this is a known somatic mutation or a
polymorphism (SNIP), what is the relative reference and in
which organ this possible mutation occured (tissue sample) -
if known. (Was it large intestine, lung, breast, etc?)<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">The second
position is in exon 7, amino acid 849, which can be either
arginine (CGA) or glutamine (CAA), since there is also an R
on top of the base G. I would also like to ask if this is a
known somatic mutation or a polymorphism (SNIP), what is the
relative reference and in which organ this possible mutation
occured (tissue sample) - if known. (Was it large intestine,
lung, breast, etc?)<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">I can see that
there are also 69 known reported mutations for PIK3CG gene
harboring several organs. Could you provide me with the
relative references, if possible? Is this material published
or informal and unpublished, but just reported to your site?<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Thank you in
advance for your time. I am kindly waiting for your help and
answer. I am indebted.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Yours,
sincerely<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB"> <o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Dr. Michael D.
Diamantidis, MSc, PhD<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Haematologist<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">Erasmus MC -
Haematology Dept. - Faculty of Medicine<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt">Dr. Molewaterplein 50<br>
3015 GE, Rotterdam <br>
the Netherlands<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">tel: +31 (0) 10
70 38 852<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">fax: +31 (0) 10
70 44 745<o:p></o:p></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE:
10pt; mso-ansi-language: EN-GB" lang="EN-GB">emails:
</span><span style="FONT-FAMILY: Tahoma; COLOR: black;
FONT-SIZE: 10pt"><a moz-do-not-send="true"
href="mailto:m.diamantidis@erasmusmc.nl"><span
style="mso-ansi-language: EN-GB;
mso-fareast-font-family: 'Arial Unicode MS'"
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<pre wrap="">_______________________________________________
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<pre class="moz-signature" cols="72">--
Dr Emily Pritchard
Ensembl Outreach Officer
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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