Question: Snps Which Are Present In Upstream Region Or Downstream Region?
0
gravatar for Elena
8.1 years ago by
Elena240
Elena240 wrote:

Hi friends,

I have found out few SNP locations in a gene sequence. Now how can i find which SNPs are present in upstream region and downstream region of the genes and also the same SNPs locations present in upstream and downstream regions of the chromosome?

gene snp chromosome • 4.0k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 8.1 years ago by Elena240
1

There are already many answers on Biostar for that question.

ADD REPLYlink written 8.1 years ago by Pierre Lindenbaum119k
1

Your question is not completely clear to me. Do you want to know where the SNPs that you have identified (and which are defined relative to a gene) are located on the genome? Or do you want to identify additional SNPs to the ones you already have up- and downstream of your gene of interest?

ADD REPLYlink written 8.1 years ago by Bert Overduin3.6k

e.g: http://biostar.stackexchange.com/questions/413 ( close ? )

ADD REPLYlink written 8.1 years ago by Pierre Lindenbaum119k

It's a dup, I'm closing

ADD REPLYlink written 8.1 years ago by Daniel Swan13k

ya but the above link is for those users who are using uscs browser. But the SNP location which i have found is different, its not from any of the databases, i have found out the location using programming, and the data tells about the position of SNP on the gene( For eg: 23, 26, 28, 299)

ADD REPLYlink written 8.1 years ago by Elena240

i dont have the id, my input looks like C-103T, C4144G, T5238C, G6528A

ADD REPLYlink written 8.1 years ago by Elena240

and i have found out the information not only for human , for primates also.. kindly help!

ADD REPLYlink written 8.1 years ago by Elena240
4
gravatar for Pablo
8.1 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

A little bit of self promotion...

Take a look at SnpEff http://snpeff.sourceforge.net/

ADD COMMENTlink written 8.1 years ago by Pablo1.9k
1
gravatar for Chris Evelo
8.1 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

I may have completely misunderstood your question, but if you got the SNP positions yourself using your own gene sequences the only thing you need to know is the start and end positions of the genes in these sequences and it will immediately be clear which SNPs are upstream or downstream.

If I misunderstood this might be the dumbest answer ever. The example coordinates you gave are so low that I started to think that these are single gene sequences, that might be wrong.

ADD COMMENTlink written 8.1 years ago by Chris Evelo10.0k
1

Without the right tools it would be. But since you seem to have the whole gene sequence and know the position of the SNP in the gene I think you will only have to BLAST the gene against the chromosome to find the position of your gene sequence. The SNP position can then just be inferred.

ADD REPLYlink written 8.1 years ago by Chris Evelo10.0k

@Chris: ya u are correct by knowing the start and end positions of the genes i can easily find out the SNPs present in the upstream and downstream region. But how can i locate the same SNPs on the chromosome? i guess locating these SNPs on the chromosome is really very tough job.

ADD REPLYlink written 8.1 years ago by Elena240

oh okay Chris i have got an idea now.... thanku

ADD REPLYlink written 8.1 years ago by Elena240
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