<commit_before><h3>Assembly</h3>

<p>Ensembl Mouse is based on the <a href="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=10090">
NCBI m37 mouse assembly</a> (April 2007, strain C57BL/6J).
</p>

<p><img src="/img/species/pic_Mus_musculus.png" style="height:80px;width:130px" class="float-right" alt="Mouse Genome Sequencing Consortium" title="squeak squeak!" />The Mouse Genome Sequencing Consortium is a joint project between 
<a href="http://www-genome.wi.mit.edu/">The Whitehead Institute/MIT Center for Genome Research</a>, 
<a href="http://genome.wustl.edu/">The Washington University Genome Sequencing Center</a>, 
<a href="http://www.sanger.ac.uk/">The Wellcome Trust Sanger Institute</a> 
and <a href="http://www.ebi.ac.uk/">EMBL - EBI</a> to provide the Mouse genome sequence to the world. 
We work closely with other Mouse groups to provide an integrated resource (see below for credits).</p>
      
<p>There are some major changes in the assembly from version m36; for more details see 
the <a 
href="http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=10090&build=37&ver=1" 
rel="external">NCBI build statistics </a>. </p>

<div class="tinted-box embedded-box" style="width:50%">To convert your old data from Mouse assembly m36 to m37, click on 'Manage your data' on any mouse page and select 'Assembly converter' from the left-hand menu.</div>

<h3>Annotation</h3>

<p>As of release 47 the gene annotation presented has been a combined 
Ensembl-Havana geneset, which incorporates more than 15,000 full-length 
protein-coding transcripts annotated by the Havana team in addition to the Ensembl 
automatic gene build. The mouse genome sequence is now considered 
sufficiently stable that since September 2006 the major genome browsers 
have come together to produce a common set of identifiers where CDS 
annotations of transcripts can be agreed and these identifiers are also 
shown.</p>
<ul>
    <li>More information about the <a
    href="/info/docs/genebuild/ccds.html">CCDS project</a>.</li>
</ul>

<p>Modifications to the systems have further improved the gene set. 95% of 
the known genes and 47% of the novel genes from build m36 retain the 
same Ensembl gene ids in this release.</p>

<p><a href="http://vega.sanger.ac.uk/Mus_musculus/"> <img src="/img/vega_small.gif" alt="Vega logo" style="width:83px;height:30px" title="Vega - Vertebrate Genome Annotation database" /></a>
Additional manual annotation of this genome can be found in
<a href="http://vega.sanger.ac.uk/Mus_musculus/">Vega</a></p>
<commit_msg>RT180119:update annotation text for release 59<commit_after><h3>Assembly</h3>

<p>Ensembl Mouse is based on the <a href="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=10090">
NCBI m37 mouse assembly</a> (April 2007, strain C57BL/6J).
</p>

<p><img src="/img/species/pic_Mus_musculus.png" style="height:80px;width:130px" class="float-right" alt="Mouse Genome Sequencing Consortium" title="squeak squeak!" />The Mouse Genome Sequencing Consortium is a joint project between 
<a href="http://www-genome.wi.mit.edu/">The Whitehead Institute/MIT Center for Genome Research</a>, 
<a href="http://genome.wustl.edu/">The Washington University Genome Sequencing Center</a>, 
<a href="http://www.sanger.ac.uk/">The Wellcome Trust Sanger Institute</a> 
and <a href="http://www.ebi.ac.uk/">EMBL - EBI</a> to provide the Mouse genome sequence to the world. 
We work closely with other Mouse groups to provide an integrated resource (see below for credits).</p>
      
<p>There are some major changes in the assembly from version m36; for more details see 
the <a 
href="http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=10090&build=37&ver=1" 
rel="external">NCBI build statistics </a>. </p>

<div class="tinted-box embedded-box" style="width:50%">To convert your old data from Mouse assembly m36 to m37, click on 'Manage your data' on any mouse page and select 'Assembly converter' from the left-hand menu.</div>

<h3>Annotation</h3>


<p>As in previous releases since October 2007, we provide a combined Ensembl-HAVANA gene set, where Ensembl annotations and HAVANA annotations from the <a href="http://vega.sanger.ac.uk/Mus_musculus/Info/Index">Vega database</a> are merged at the transcript level. Improvement to the Ensembl-HAVANA merging code means that in release 59,<br />we incorporated not only 28851 full-length protein-coding transcripts from HAVANA annotation into the Ensembl annotation, but also over 30000 HAVANA non-coding transcripts. Protein-coding transcripts from the two annotation sources were merged if they shared the same coding region,<br />while non-coding transcripts were merged if they shared identical exon-intron structures.</p><br />

<p>There are 36536 genes and 88186 transcripts in the combined gene set. Of the 88186 transcripts, 17.82% (15711) are the result of merging Ensembl and HAVANA annotations, 22.55% (19890) are found only in Ensembl, 52.62% (46401) are found only in HAVANA, and a remaining 7% were incorporated from other sources (e.g. immunoglobulin gene segments/transcripts imported from <a href="http://imgt.cines.fr/">IMGT</a> data).</p><br />

<p>Since September 2006, the mouse genome sequence has been considered sufficiently stable to start identifying those gene placements that are identical in the three major genome browsers. The <a href="http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi">CCDS project</a> was established and Ensembl is collaborating with <a href="http://vega.sanger.ac.uk/Mus_musculus/Info/Index">HAVANA,</a> <a href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI</a> and <a href="http://genome.ucsc.edu/">UCSC</a> to identify a core set of protein coding regions that are consistently annotated and of high quality. All CCDS annotations (as of October 2009) are included in the Ensembl-HAVANA gene set, and the CCDS identifiers are shown where applicable.</p><br />

<p><a href="http://vega.sanger.ac.uk/Mus_musculus/"> <img src="/img/vega_small.gif" alt="Vega logo" style="width:83px;height:30px" title="Vega - Vertebrate Genome Annotation database" /></a>
Additional manual annotation of this genome can be found in
<a href="http://vega.sanger.ac.uk/Mus_musculus/">Vega</a></p>
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