Bulk Download all CDS and UTRs of known genes from ENSEMBL
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24 months ago

I want to download all the CDS and UTR coordinates (based on gene id ) from ensembl, is there a way to do that through biomart or biomaRt package?

UTR CDS ensembl • 563 views
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Can't you parse that info from the gtf?

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Yes I just realized that after posting and perusing through the gtf, just want to confirm.Thanks

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What if there is no information on a published genome about UTR annotation? For example, i was sure to have extracted also the UTR regions when downloading [Unspliced (Gene) option in Biomart/Ensembl] for a list of genes the gene sequences in bulk. It turned out that those sequences were not annotated. Can somebody tell me how this annotation is performed and why for some genomes have it is released and for others is not ? Is there a way to perform this annotation ex-novo for example for a list of genes of interest? thanks in advance

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