Question: Get genomic coordinates for protein domain
0
gravatar for Mr Locuace
2.6 years ago by
Mr Locuace100
Chile
Mr Locuace100 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 • 988 views
ADD COMMENTlink modified 2.6 years ago by finswimmer14k • written 2.6 years ago by Mr Locuace100
1
gravatar for finswimmer
2.6 years ago by
finswimmer14k
Germany
finswimmer14k 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 2.6 years ago by finswimmer14k

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

ADD REPLYlink written 2.6 years ago by Mr Locuace100
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 2.6 years ago • written 2.6 years ago by finswimmer14k
1

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

ADD REPLYlink written 17 months ago by cocchi.e89110

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

ADD REPLYlink written 10 months ago by Shicheng Guo8.5k

Thank you @fin swimmer !!

ADD REPLYlink written 2.6 years ago by Mr Locuace100
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