Get genomic coordinates for protein domain
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3.7 years ago
Mr Locuace ▴ 130

Hello, I have a protein domain, PF03256, and I would like to know what are its start and end genomic coordinates (Hg19) for the gene ZZEF1. Any suggestion would be welcome !

protein domain coordinate • 1.4k views
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3.7 years ago

Hello,

maybe I missunderstood. But for getting the position of a single gene in hg19, just visit the hg19 Version of ensembl and search for your gene.

For ZZEF1 you receive this coordinates: Chromosome 17: 3,907,739-4,046,314 reverse strand

fin swimmer

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Thank you @finswimmer. I mean the genomic coordinates for the protein domain, which is encoded by a part of that gene.

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Ah, ok. In the ensembl link to your gene you must first choose your transcript of interest. Than you have in the menu on the left side "Domains & Features".

I think the start/stop position there means the codon. So to get genomic position you must go to the cdna tab and find the sequence that encode the codons. With this information you can than go back to the exon tab and find the genomic position.

fin swimmer

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And there is an available database to have the start&stop codons of each PANTHER domain? Instead of manually searching it every time?

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I also want to obtain this file so that we can have all the genomic regions for all domains.

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Thank you @fin swimmer !!

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