Question: location of mutations
0
gravatar for yoosefyud
9 months ago by
yoosefyud20
yoosefyud20 wrote:

Hello everyone I want to add a picture to my article and summarize published mutations of a gene and its protein. I tried ucsc or NCBI but i couldn't find exact location of that mutations there because It was complicated and difficult for me . for example I got no results after i searched c.599C>A in https://www.ncbi.nlm.nih.gov/gene in Genomic regions, transcripts, and products Tab. I need a database to show exact location of mutations in exon and introns. I also tried MutationMapper but it didn't work; I assume because my gene isn't related to cancer disease. I really appreciate your help to solve my problem.

gene • 383 views
ADD COMMENTlink modified 9 months ago by YaGalbi1.4k • written 9 months ago by yoosefyud20

I tried ucsc or NCBI but it didn't work

https://meta.stackexchange.com/questions/147616/

ADD REPLYlink written 9 months ago by Pierre Lindenbaum117k

I edited my question, thanks.

ADD REPLYlink written 9 months ago by yoosefyud20
1
gravatar for YaGalbi
9 months ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

Surely the published article provides the genomic coordinates of the mutation? In which case you can then insert the coordinates into the UCSC Genome Browser

ADD COMMENTlink written 9 months ago by YaGalbi1.4k

No unfortunately only mutations in genome and protein are reported not the exact chromosomal location. how can i find exact chromosome coordinates?

ADD REPLYlink written 9 months ago by yoosefyud20
2

So a published article about a mutation doesn't provide the location of the mutation? That cant be right. Have you checked the supplementary material? Please provide a link to the article.

ADD REPLYlink modified 9 months ago • written 9 months ago by YaGalbi1.4k

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668026/ This is link to one the related articles about CNNM4 gene mutation. There is no chromosomal coordinates in article.

ADD REPLYlink written 9 months ago by yoosefyud20
1

@OP: Gene it self is a location information and it has only transcript. On transcript, variation is at c.599C>A. In manuscript, authors furnished aa position as well Ser200Tyr. Now it needs little home work to reconstruct genomic coordinates.

https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=79424354
    CM000664.2:g.96761598C>A
    NC_000002.11:g.97427335C>A
    NC_000002.12:g.96761598C>A
    NG_016608.1:g.5697C>A
    NM_020184.3:c.599C>A
    NP_064569.3:p.Ser200Tyr
    XP_005263971.1:p.Ser200Tyr
    XP_005263972.1:p.Ser200Tyr
    XP_011509257.1:p.Ser200Tyr
    XP_011509258.1:p.Ser200Tyr

One should look at variation position in a gene (for eg. in this case.CNNM4)- https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=26504

ADD REPLYlink modified 9 months ago • written 9 months ago by cpad011211k

Thanks for your help. I'll try the instructions you mentioned. I think it completely solves the problem, but I really need to improve my bioinformatics.

ADD REPLYlink written 9 months ago by yoosefyud20
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