[ensembl-dev] question ovis aries

[Alessia Virzì]

Dear Leanne,

Thank you very much. Indeed I realize that the problem was the version of 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!

Best wishes

Alessia

From: Dev <dev-bounces at ensembl.org> On Behalf Of Leanne Haggerty
Sent: 04 November 2024 16:44
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] question ovis aries

Hi Alessia

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 (RefSeq link<https://www.ncbi.nlm.nih.gov/nuccore/NC_001941.1/>).

The gene you mentioned appears to be correctly labeled in the Ensembl browser: Ensembl link<https://www.ensembl.org/Ovis_aries_rambouillet/Gene/Summary?db=core;g=ENSOARG00020000007;r=MT:2745-3699;t=ENSOART00020000007>.

Here’s the information as it appears in Ensembl’s GTF file for this MT annotation:

MT      RefSeq  gene    2745    3699    .       +       .       gene_id "ENSOARG00020000007"; gene_version "1"; gene_name "ND1"; gene_source "RefSeq"; gene_biotype "protein_coding";

In this case, gene_id refers to the Ensembl stable ID, while gene_name holds the name “ND1.”

Similarly, in the GFF file:

MT      RefSeq  gene    2745    3699    .       +       . ID=gene:ENSOARG00020000007;Name=ND1;biotype=protein_coding;description=NADH dehydrogenase subunit 1 [Source:NCBI gene (formerly Entrezgene)%3BAcc:808249];gene_id=ENSOARG00020000007;logic_name=mt_genbank_import;version=1

Here, ID represents the stable ID, and “ND1” is located in the Name field.

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.

Please let me know if I’ve misunderstood your query or if I can provide any further clarification.
All the best
Leanne



On 4 Nov 2024, at 14:33, Alessia Virzì <alessia.virzi at kuleuven.be<mailto:alessia.virzi at kuleuven.be>> wrote:

Hi Leanne,

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:
NC_001941.1     RefSeq  gene    2745    3699    .       +       .       ID=gene-KEF53_p13;Dbxref=GeneID:808249;Name=ND1;gbkey=Gene;gene=ND1;gene_biotype=protein_coding;locus_tag=KEF53_p13

Where ID=gene-KEF53_p13 is present instead of the name ND1 (as well as for many other genes).

Thank you again

Alessia

From: Dev <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> On Behalf Of Leanne Haggerty
Sent: 04 November 2024 12:04
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Cc: helpdesk at ensembl.org<mailto:helpdesk at ensembl.org>
Subject: Re: [ensembl-dev] question ovis aries

Hi Alessia

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,beta.ensembl.org<http://beta.ensembl.org/> 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:

Species selector<https://beta.ensembl.org/species-selector/search?query=sheep>
beta.ensembl.org<https://beta.ensembl.org/species-selector/search?query=sheep>
<image001.png><https://beta.ensembl.org/species-selector/search?query=sheep>


I hope this helps
All the best
Leanne



On 4 Nov 2024, at 10:46, Alessia Virzì <alessia.virzi at kuleuven.be<mailto:alessia.virzi at kuleuven.be>> wrote:

Hello,

I would like to know why in the ensemble website the ovis aries genome Ovis_aries_rambouillet - Ensembl genome browser 113<https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index> refer to the version: ARS-UI-Ramb-v2
While in the NIH NCBI website the reccomanded version is the ARS-UI_Ramb_v3.0https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.2/

Any insides would be great!

Thanks

Alessia
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