<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Alessia<div><br></div><div><div>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 rel="noopener" target="_new" href="https://www.ncbi.nlm.nih.gov/nuccore/NC_001941.1/">RefSeq link</a>).</div><div><p>The gene you mentioned appears to be correctly labeled in the Ensembl browser: <a rel="noopener" target="_new" href="https://www.ensembl.org/Ovis_aries_rambouillet/Gene/Summary?db=core;g=ENSOARG00020000007;r=MT:2745-3699;t=ENSOART00020000007">Ensembl link</a>.</p><p>Here’s the information as it appears in Ensembl’s GTF file for this MT annotation:</p><pre class="!overflow-visible"><div class="contain-inline-size rounded-md border-[0.5px] border-token-border-medium relative bg-token-sidebar-surface-primary dark:bg-gray-950"><div class="sticky top-9 md:top-[5.75rem]"><div class="absolute bottom-0 right-2 flex h-9 items-center"><div class="flex items-center rounded bg-token-sidebar-surface-primary px-2 font-sans text-xs text-token-text-secondary dark:bg-token-main-surface-secondary">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>;</div></div></div></div></pre><p>In this case, <code>gene_id</code> refers to the Ensembl stable ID, while <code>gene_name</code> holds the name “ND1.”</p><p>Similarly, in the GFF file:</p><pre class="!overflow-visible"><div class="contain-inline-size rounded-md border-[0.5px] border-token-border-medium relative bg-token-sidebar-surface-primary dark:bg-gray-950"><div class="overflow-y-auto p-4" dir="ltr"><code class="!whitespace-pre hljs language-css">MT RefSeq gene <span class="hljs-number">2745</span> <span class="hljs-number">3699</span> . + . ID=gene:ENSOARG00020000007;Name=ND1;biotype=protein_coding;description=NADH dehydrogenase subunit <span class="hljs-number">1</span> <span class="hljs-selector-attr">[Source:NCBI gene (formerly Entrezgene)%3BAcc:808249]</span>;gene_id=ENSOARG00020000007;logic_name=mt_genbank_import;version=<span class="hljs-number">1</span>
</code></div></div></pre><p>Here, <code>ID</code> represents the stable ID, and “ND1” is located in the <code>Name</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></div><div>All the best</div><div>Leanne</div><div><br></div><div><br><blockquote type="cite"><div>On 4 Nov 2024, at 14:33, Alessia Virzì <alessia.virzi@kuleuven.be> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span>Hi Leanne,<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><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:<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><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<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Where ID=gene-KEF53_p13 is present instead of the name ND1 (as well as for many other genes).<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Thank you again<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Alessia<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"><o:p> </o:p></span></div><div><div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(225, 225, 225) currentcolor currentcolor; border-image: none; padding: 3pt 0cm 0cm;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><b><span lang="EN-US">From:</span></b><span lang="EN-US"><span class="Apple-converted-space"> </span>Dev <<a href="mailto:dev-bounces@ensembl.org" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">dev@ensembl.org</a>><br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:helpdesk@ensembl.org" style="color: blue; text-decoration: underline;">helpdesk@ensembl.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] question ovis aries<o:p></o:p></span></div></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Hi Alessia<o:p></o:p></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">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/" style="color: blue; text-decoration: underline;">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:<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div><div><table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="300" style="width: 225pt; background: rgb(229, 230, 233); border-collapse: collapse;"><tbody><tr><td style="padding: 0cm;"><table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="300" style="width: 225pt; background: rgb(229, 230, 233);"><tbody><tr><td style="padding: 6pt 0cm;"><div style="margin-left: 12pt; margin-right: 12pt; max-width: 100%; overflow: hidden;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 9pt; font-family: Helvetica, sans-serif;"><a href="https://beta.ensembl.org/species-selector/search?query=sheep" style="color: blue; text-decoration: underline;"><span style="color: rgb(39, 39, 39); text-decoration: none;">Species selector</span></a></span><span style="font-size: 9pt; font-family: Helvetica, sans-serif;"><o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 8.5pt; font-family: Helvetica, sans-serif;"><a href="https://beta.ensembl.org/species-selector/search?query=sheep" style="color: blue; text-decoration: underline;"><span style="color: gray; text-decoration: none;">beta.ensembl.org</span></a></span><span style="font-size: 8.5pt; font-family: Helvetica, sans-serif;"><o:p></o:p></span></div></div></td><td width="36" style="width: 27pt; padding: 4.5pt 9pt 4.5pt 0cm;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span style=""><a href="https://beta.ensembl.org/species-selector/search?query=sheep" style="color: blue; text-decoration: underline;"><span style="font-family: Helvetica, sans-serif; text-decoration: none;"><span id="cid:image001.png@01DB2ECE.F3217B40"><image001.png></span></span></a></span><span style="font-family: Helvetica, sans-serif;"><o:p></o:p></span></div></td></tr></tbody></table></td></tr></tbody></table></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">I hope this helps<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">All the best<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Leanne<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><br><br><o:p></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;"><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">On 4 Nov 2024, at 10:46, Alessia Virzì <<a href="mailto:alessia.virzi@kuleuven.be" style="color: blue; text-decoration: underline;">alessia.virzi@kuleuven.be</a>> wrote:<o:p></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Hello,<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><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" style="color: blue; text-decoration: underline;"><span lang="EN-IN" style="color: rgb(5, 99, 193);">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><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><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/" style="color: blue; text-decoration: underline;"><span style="color: rgb(5, 99, 193);">https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.2/</span></a></span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"> </span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Any insides would be great!</span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"> </span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Thanks</span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN"> </span><o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-IN">Alessia</span><o:p></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 9pt; font-family: Helvetica, sans-serif;">_______________________________________________<br>Dev mailing list </span><a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline;"><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: rgb(5, 99, 193);">Dev@ensembl.org</span></a><span style="font-size: 9pt; 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" style="color: blue; text-decoration: underline;"><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: rgb(5, 99, 193);">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;"><br>Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/" style="color: blue; 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