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<div dir="auto">This wrong message for me.</div>
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<div class="gmail_quote">On 5 Nov 2024 08:55, Alessia Virzě <alessia.virzi@kuleuven.be> wrote:<br type="attribution">
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<p class="MsoNormal"><span style="">Dear Leanne,</span></p>
<p class="MsoNormal"><span style=""> </span></p>
<p class="MsoNormal"><span lang="EN-IN" style="">Thank you very much. Indeed I realize that the problem was the version of
</span><span lang="EN-IN">ARS-UI-Ramb-v2 we used for the mapping. We did not use the Ensembl but the NIH version which is less curated. So many thanks for your explanation!</span></p>
<p class="MsoNormal"><span lang="EN-IN"> </span></p>
<p class="MsoNormal"><span lang="EN-IN">Best wishes</span></p>
<p class="MsoNormal"><span lang="EN-IN"> </span></p>
<p class="MsoNormal"><span lang="EN-IN">Alessia</span><span lang="EN-IN" style=""></span></p>
<p class="MsoNormal"><span lang="EN-IN" style=""> </span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Leanne Haggerty<br>
<b>Sent:</b> 04 November 2024 16:44<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] question ovis aries</span></p>
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<p class="MsoNormal">Hi Alessia</p>
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<p class="MsoNormal">I hope I can help clarify the data in Ensembl. We import mitochondrial (MT) annotations from RefSeq, and this hasn’t been updated since April 2023 (<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_001941.1/" target="_new">RefSeq link</a>).</p>
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<p>The gene you mentioned appears to be correctly labeled in the Ensembl browser: <a href="https://www.ensembl.org/Ovis_aries_rambouillet/Gene/Summary?db=core;g=ENSOARG00020000007;r=MT:2745-3699;t=ENSOART00020000007" target="_new">Ensembl link</a>.</p>
<p>Here’s the information as it appears in Ensembl’s GTF file for this MT annotation:</p>
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<pre>MT RefSeq gene <span class="hljs-number">2745</span> <span class="hljs-number">3699</span> . + . gene_id <span class="hljs-string">"ENSOARG00020000007"</span>; gene_version <span class="hljs-string">"1"</span>; gene_name <span class="hljs-string">"ND1"</span>; gene_source <span class="hljs-string">"RefSeq"</span>; gene_biotype <span class="hljs-string">"protein_coding"</span>;</pre>
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<p>In this case, <code><span style="font-size:10.0pt">gene_id</span></code> refers to the Ensembl stable ID, while <code><span style="font-size:10.0pt">gene_name</span></code> holds the name “ND1.”</p>
<p>Similarly, in the GFF file:</p>
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<pre><code>MT RefSeq gene </code><span class="hljs-number">2745</span><code> </code><span class="hljs-number">3699</span><code> . + . ID=gene:ENSOARG00020000007;Name=ND1;biotype=protein_coding;description=NADH dehydrogenase subunit </code><span class="hljs-number">1</span><code> </code><span class="hljs-selector-attr">[Source:NCBI gene (formerly Entrezgene)%3BAcc:808249]</span><code>;gene_id=ENSOARG00020000007;logic_name=mt_genbank_import;version=</code><span class="hljs-number">1</span><code></code></pre>
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<p>Here, <code><span style="font-size:10.0pt">ID</span></code> represents the stable ID, and “ND1” is located in the <code><span style="font-size:10.0pt">Name</span></code> field.</p>
<p>As far as I can tell, the name “ND1” appears correctly throughout Ensembl. The label “KEF53_p13” seems to be a locus tag found in the RefSeq files.</p>
<p>Please let me know if I’ve misunderstood your query or if I can provide any further clarification.</p>
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<p class="MsoNormal">All the best</p>
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<p class="MsoNormal">Leanne</p>
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<p class="MsoNormal">On 4 Nov 2024, at 14:33, Alessia Virzě <<a href="mailto:alessia.virzi@kuleuven.be">alessia.virzi@kuleuven.be</a>> wrote:</p>
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<p class="MsoNormal">Hi Leanne,</p>
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<p class="MsoNormal"><span lang="EN-IN">Thank you so much for this info. Looking forward. Do you know if MT genes will be better annotated? In this version, we have this situation:</span></p>
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<p class="MsoNormal"><span lang="EN-IN">NC_001941.1 RefSeq gene 2745 3699 . + . <span class="apple-converted-space"> </span><b>ID=gene-KEF53_p13</b>;Dbxref=GeneID:808249;<b>Name=ND1</b>;gbkey=Gene;gene=ND1;gene_biotype=protein_coding;locus_tag=KEF53_p13</span></p>
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<p class="MsoNormal"><span lang="EN-IN"> </span></p>
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<p class="MsoNormal"><span lang="EN-IN">Where ID=gene-KEF53_p13 is present instead of the name ND1 (as well as for many other genes).</span></p>
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<p class="MsoNormal"><span lang="EN-IN"> </span></p>
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<p class="MsoNormal"><span lang="EN-IN">Thank you again</span></p>
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<p class="MsoNormal"><span lang="EN-IN"> </span></p>
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<p class="MsoNormal"><span lang="EN-IN">Alessia</span></p>
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<p class="MsoNormal"><span lang="EN-IN"> </span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Dev <<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>><span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>Leanne Haggerty<br>
<b>Sent:</b><span class="apple-converted-space"> </span>04 November 2024 12:04<br>
<b>To:</b><span class="apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<b>Cc:</b><span class="apple-converted-space"> </span><a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] question ovis aries</span></p>
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<p class="MsoNormal">Hi Alessia</p>
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<p class="MsoNormal">The Ensembl annotation of ARS-UI_Ramb_v3.0 is not available yet, and so the browser displays the older version, ARS-UI_Ramb_v2. Annotation of the latest assembly is in progress and data will be available via our new website,<a href="http://beta.ensembl.org/">beta.ensembl.org</a> before
the end of the year. In the meantime, we provide annotation data for 21 sheep assemblies, including many different breeds, in case this is useful for you:</p>
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<p class="MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black"><a href="https://beta.ensembl.org/species-selector/search?query=sheep"><span style="color:#272727; text-decoration:none">Species selector</span></a></span></p>
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<p class="MsoNormal">I hope this helps</p>
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<p class="MsoNormal">All the best</p>
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<p class="MsoNormal">Leanne</p>
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<p class="MsoNormal">On 4 Nov 2024, at 10:46, Alessia Virzě <<a href="mailto:alessia.virzi@kuleuven.be">alessia.virzi@kuleuven.be</a>> wrote:</p>
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<p class="MsoNormal">Hello,</p>
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<p class="MsoNormal"><span lang="EN-IN">I would like to know why in the ensemble website the ovis aries genome<span class="apple-converted-space"> </span></span><a href="https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index"><span lang="EN-IN" style="color:#0563C1">Ovis_aries_rambouillet
- Ensembl genome browser 113</span></a><span class="apple-converted-space"> </span><span lang="EN-IN">refer to the version:<span class="apple-converted-space"> </span>ARS-UI-Ramb-v2</span></p>
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<p class="MsoNormal"><span lang="EN-IN">While in the NIH NCBI website the reccomanded version is the ARS-UI_Ramb_v3.0<a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.2/"><span style="color:#0563C1">https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.2/</span></a></span></p>
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<p class="MsoNormal"><span lang="EN-IN"> </span></p>
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<p class="MsoNormal"><span lang="EN-IN">Any insides would be great!</span></p>
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<p class="MsoNormal"><span lang="EN-IN">Thanks</span></p>
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<p class="MsoNormal"><span lang="EN-IN">Alessia</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">_______________________________________________<br>
Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:#0563C1">Dev@ensembl.org</span></a><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif"><br>
Posting guidelines and subscribe/unsubscribe info:<span class="apple-converted-space"> </span></span><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:#0563C1">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif"><br>
Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:#0563C1">http://www.ensembl.info/</span></a></p>
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<p class="MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">_______________________________________________<br>
Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">Dev@ensembl.org</span></a><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif"><br>
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Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">http://www.ensembl.info/</span></a></p>
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