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<div class="gmail_quote">On 4 Nov 2024 15:45, Leanne Haggerty <leanne@ebi.ac.uk> wrote:<br type="attribution">
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<div>Hi Alessia
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<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>
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<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>
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<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>
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<div>All the best</div>
<div>Leanne</div>
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<div>On 4 Nov 2024, at 14:33, Alessia Virzě <alessia.virzi@kuleuven.be> wrote:</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span>Hi Leanne,</span></div>
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<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:</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</span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </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).</span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN">Thank you again</span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN">Alessia</span></div>
<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
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<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</span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">Hi Alessia</div>
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<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:</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">I hope this helps</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">All the best</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">Leanne</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">On 4 Nov 2024, at 10:46, Alessia Virzě <<a href="mailto:alessia.virzi@kuleuven.be" style="color:blue; text-decoration:underline">alessia.virzi@kuleuven.be</a>> wrote:</div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">Hello,</div>
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<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></div>
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<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></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN">Any insides would be great!</span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN">Thanks</span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN"> </span></div>
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<div style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif"><span lang="EN-IN">Alessia</span></div>
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