How to download Gene annotations (by Ensembl) track on NCBI Sequence Viewer 3.49.0
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9 days ago
rahu • 0

I'm interested in an newer assembly of an organism available by NCBI but not by Ensembl. However, I still want to use the gene definitions by Ensembl. The annotation file on Ensembl has the coordiates based on the previous assembly. I see on NCBI Sequence Viewer 3.49.0 that it shows Ensembl gene annoations track suitable with the newer assembly I'm interested in. I assume that the coordinates of the gene annotation are corrected to match the newer assembly. However, NCBI Sequence Viewer 3.49.0 allows downloading a some range of a single chromosome. I wonder if there is a way of downloading the entire annoatation file matching the coordinates of the newer assembly by Ensembl, which is not available on the website of Ensembl.

Sequence-Viewer Ensembl NCBI • 258 views
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Can you post a screenshot (and provide some information about what organism this is)? Point out the track you are referring to. If it is precomputed then it may be available.

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Thank you for your response!

The organism is bovine (Bos taurus). A contamination was discovered for the latest two assemblies ARS-UCD1.2 (bosTau9), ARS-UCD1.3 (bosTau9), both referred to as bosTau9.

Now, there is a newer assembly, ARS-UCD2.0 (bosTau9), whose screenshot I have attached. The second track named Genes, Ensembl release 112, is the one I would like to retrieve. screenhot of the NCBI genome viewer for ARS-UCD2.0

The annotation files on Ensembl website for bovine is based on the assembly ARS-UCD1.3. I would like to download Ensembl gene annotation file compatible with ARS-UCD2.0.

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9 days ago
GenoMax 143k

Looks like ARS-UCD2.0 genome build is available via Ensembl rapid release: http://ftp.ensembl.org/pub/rapid-release/species/Bos_taurus/GCA_002263795.3/ensembl/geneset/2023_06/

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