(a) Is it uncommon to find splicing modifier binding site in coding region?
(b) Is it possible to have splicing modifier binding site only in coding region and not in UTR region of a given gene?
we all know SNPs have the strength to form or destroy ESS or ESE sequence. The computational webserver FASTSNP is the only (as far as I know) one whcih evalustes the SNPs present/influencing splicing regulation or do we have more webservers which can do the same job?
Note: I wish to see answers backed with references
Could you indicate what this experience is based on? You probably mean to say that relatively many SNPs in coding regions are in splicing modifier binding sites. How do you know?
sSNPs are involved in splicing rgeulation and sometimes nsSNPs as well. I have perfomred in silico analysisof SNPs in more than 100 protein transcript and this is my experience.
Here are some answers that I received from a colleague (Bahar Taneri) when I mentioned your question, rephrased as: "Do you indeed think SNPs in coding sequences occur relatively often is splice regulation sites?" The answer was:
Yes, indeed Krawczak et al. have put some numbers on this. At least 10% of all mutations causing human inherited disease are due to SNPs in splice junctions. Based on their analysis on various disease causing splicing mutations and various genes described [?]here[?]; they conclude with an estimation that “1.6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype.”
[?]Here[?] is a much earlier work from the same group covering single-base pair substitutions at splice junctions, providing some numbers. Their latest article is titled [?]“Systematic evaluation of the effect of common SNPs on pre-mRNA splicing”[?], I have not read this in detail, I cannot summarize it, but I think it could be of use to your colleague.
Also your colleague could refer to a 2008 article by Kim et al. on [?]"Alternative Splicing and disease"[?] where they argue that a large proportion of SNPs are regarded as silent mutations, not affecting coding, but they could indeed affect splicing.
Could you indicate what this experience is based on? You probably mean to say that relatively many SNPs in coding regions are in splicing modifier binding sites. How do you know?
sSNPs are involved in splicing rgeulation and sometimes nsSNPs as well. I have perfomred in silico analysisof SNPs in more than 100 protein transcript and this is my experience.