Question: Get genomic coordinates for protein domain
0
gravatar for Mr Locuace
8 months ago by
Mr Locuace80
Chile
Mr Locuace80 wrote:

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 !

coordinate protein domain • 307 views
ADD COMMENTlink modified 8 months ago by finswimmer8.2k • written 8 months ago by Mr Locuace80
1
gravatar for finswimmer
8 months ago by
finswimmer8.2k
Germany
finswimmer8.2k wrote:

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

ADD COMMENTlink written 8 months ago by finswimmer8.2k

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

ADD REPLYlink written 8 months ago by Mr Locuace80
1

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

ADD REPLYlink modified 8 months ago • written 8 months ago by finswimmer8.2k

Thank you @fin swimmer !!

ADD REPLYlink written 8 months ago by Mr Locuace80
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