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<TITLE>FW: [ensembl-dev] why is NEFL ENSG00000104725 ENST00000221169 annotated as "No protein product"?</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi All<BR>
<BR>
Human chromosome 8 is being curated at the Genome Institute at the University of Washington (TGI). In the ticket that corresponds to this region (HG-307), it is noted that the reference component in question, AC107373.4, is clone CTD-2168K21. Source DNA is not available for this library, therefore it is unclear whether the nucleotide in the reference reflects a rare allele (based on the PCR results from a panel of 24 DNAs) or an error in the clone sequence. Investigation of the 1000 genomes data also suggests either an error or a rare allele. Investigations are ongoing to fully determine the nature of this discrepancy and the subsequent action that is required to resolve it. Updates to the ticket can be viewed here:<BR>
<BR>
<a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-307">http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-307</a><BR>
<BR>
Kind regards,<BR>
<BR>
Kate<BR>
<BR>
------ Forwarded Message<BR>
<B>From: </B>Kerstin Howe <<a href="kerstin@sanger.ac.uk">kerstin@sanger.ac.uk</a>><BR>
<B>Date: </B>Tue, 8 May 2012 11:44:05 +0100<BR>
<B>To: </B>Katherine Auger <<a href="kaa@sanger.ac.uk">kaa@sanger.ac.uk</a>><BR>
<B>Subject: </B>Fwd: [ensembl-dev] why is NEFL ENSG00000104725 ENST00000221169 annotated as "No protein product"?<BR>
<BR>
Hi Kate,<BR>
<BR>
can you please have a look at this and comment if necessary?<BR>
<BR>
Thanks<BR>
<BR>
Kerstin<BR>
<BR>
Begin forwarded message:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Helvetica, Verdana, Arial"><SPAN STYLE='font-size:12pt'><B>From: </B>Matthew Astley <<a href="mca@sanger.ac.uk">mca@sanger.ac.uk</a>><BR>
<B>Date: </B>8 May 2012 10:55:05 GMT+01:00<BR>
<B>To: </B><a href="dev@ensembl.org">dev@ensembl.org</a><BR>
<B>Subject: Re: [ensembl-dev] why is NEFL ENSG00000104725 ENST00000221169 annotated as "No protein product"?<BR>
Reply-To: </B>Ensembl developers list <<a href="dev@ensembl.org">dev@ensembl.org</a>><BR>
</SPAN></FONT><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
On Sun, May 06, 2012 at 12:30:27PM -0700, Michael Yourshaw wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>This issue came up when the variant effect predictor failed<BR>
recognize a Charcot-Marie-Tooth disease variant in NEFL<BR>
(neurofilament, light polypeptide) as as a coding variant.<BR>
<BR>
Gene ENSG00000104725 transcript ENST00000221169 is annotated as "No<BR>
protein product” by Ensembl.<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
In short, it seems likely there is a genomic sequencing error<BR>
affecting the CDS.<BR>
<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>On Ensembl the prediction method is given as "Manual annotation<BR>
(determined on a case-by-case basis) from the Havana project”.<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
I asked an annotator about this (thanks Mark).<BR>
<BR>
The GRC has a ticket[1] on this clone, which you can see by switching<BR>
on the "GRC region NCBI_37" DAS track[2] in Ensembl.<BR>
<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>The gene is annotated as protein coding by UniProt, RefSeq, and<BR>
UCSC. CCDS apparently recognizes the mouse flavor of the gene but<BR>
not the human.<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
There is another transcript in our database which is marked so it will<BR>
not be published, because of this genomic sequence issue.<BR>
<BR>
I will open a helpdesk ticket in your name with Havana, in case there<BR>
is more to be said about it.<BR>
<BR>
<BR>
hth,<BR>
-- <BR>
Matthew<BR>
<BR>
[1]<BR>
<a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-307">http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-307</a><BR>
<BR>
[2] this should enable it for you,<BR>
<a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000104725;r=8:24801089-24825012;t=ENST00000221169;contigviewbottom=das_DS_775=labels">http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000104725;r=8:24801089-24825012;t=ENST00000221169;contigviewbottom=das_DS_775=labels</a><BR>
<BR>
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</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
</SPAN></FONT><FONT FACE="Helvetica, Verdana, Arial"><SPAN STYLE='font-size:12pt'>--<BR>
Dr. Kerstin Howe<BR>
Senior Scientific Manager<BR>
Genome Reference Informatics (Team 135)<BR>
<a href="kerstin@sanger.ac.uk">kerstin@sanger.ac.uk</a><BR>
<BR>
Wellcome Trust Sanger Institute<BR>
Hinxton, Cambridge CB10 1SA, UK<BR>
<BR>
<BR>
</SPAN></FONT><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
<BR>
<BR>
<BR>
------ End of Forwarded Message<BR>
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