Snps In Conserved Regions??

Question

[Elena]

Hi Friends,

i ve set of SNPs which are present in conserved region and also in non-conserved region. If the SNPs are present in the conserved regions what does it implies?

Answer 1

[Michael]

Here the overly simplified non-citeable computer scientist's version of the hypotheses and the chain of logical inference underlying the study of conservation:

A) Conservation can be a result of evolutionary pressure.

B) If there is evolutionary pressure on a certain sequence to be conserved, it is important.

C) Conserved regions are more important than non-conserved regions.

D) An observation in an important region is iteself more important.

A => B => C => D => SNP in conserved regions are relevant.

Caveat1: IMHO Caveat2: If one of the hypothesis is violated the chain of inference breaks

[Larry_Parnell]

Nice way to put this and +1! "C" of course depends on one's perspective where less conserved may indicate some specific to that species.

Answer 2

[Jorge Amigo]

as far as I know, sequence conservation relates to the genome similarity among species. this has some implications on how those regions of the genome may function similarly across such species, but does not mean that they shouldn't vary at all. mutations occur through the genome, and some of them get established on the population at certain frequency depending on the "viability" or "harmfulness" of that mutation.

think about the gene metaphor as an example. since a gene is a functional piece of the genome one would expect not to vary very much, but it does in fact vary. sure the gene variation is less than the one present on non-coding DNA, but it definitely exists. something similar happens on conserved regions, since sequence conservation had to do something with functionality, but although the average SNP density on those regions is not as low as the coding one (those conserved regions use to carry genes on them, although not always necessarily), it is lower than the average non-coding non-conserved regions of the genome.

[Larry_Parnell]

Rather than add another answer and restate what Jorge writes, I can simply say this is how I feel about the topic.