Genetics as it applies to evolution, molecular biology, and medical aspects.
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I was asked to see if some of the SNP that I've identified in a portion of a gene are in conservative regions or not. I am using USCS browser to do it, but I don't know what can I conclude from it. I mean is it more or less relevant that a SNP is located in a conservative region???
Thak you ;o)
I can speculate on several reasons why knowing whether a SNP is in a conserved region could be useful.
First, conserved regions are likely to encode a useful functional motif of a protein. Evolutionary theory suggests that conserved regions vary less because their sequence is selected for by natural selection. Think of a protein as being divided into structural and functional parts (nothing it really that straightforward, but it is a useful fiction). The structural areas could undergo some random drift in amino acid residues -- some changes would be harmful, but others wouldn't matter. The functional areas, such as catalytic sites, must retain particular amino acid configurations or the protein will lose or alter a function. If the proteins is doing something that helps the organism survive and reproduce, the critical features of the amino acid sequence in the functional sites would be expected to be conserved by natural selection.
Second, if you are going to bind nucleic acids or nucleic acid analogs to a target site in the SNP you might want to know whether the target regions may vary across alleles or even across species. Part of my days is spent targeting Morpholino antisense molecules for gene knockdowns. Sometimes investigators want a single molecules that can be used to knock down a gene in several species. If the target is in a conserved region, that can be easy to do. If there is much sequence variation between species, I may not be able to design a single molecule that is perfectly complementary to a 25-base target in a targetable region of both species. A handful of SNPs scattered across the antisense target can ruin target recognition by the antisense oligo.
Likely you were asked to determine whether the SNP is in a conserved region for the first reason, that is, to determine whether the SNP is likely to interfere with a critical function of the gene product.
3 posts • Page 1 of 1
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