CpG-island mouse/human - (Sep/17/2008 )
i analyzed a CpG-island located in a gene coding for a human protease. Now i wanted to analyze the mouse homolog, but i cannot find a CpG-island there. Is that common that there are Cpg-islands present in the one organism, but not in the other?
Right now this confuses me very much, since i know that expression of a Methyl-binding-protein has an influence on the gene expression of this gene, not only in human, but also in mice. How can that be when there is no CpG-island in the mouse gene?
I'm very grateful for any thoughts, discussion, ideas,
It depends on what you classify a CpG Island, your conditions may be too strict. Is there generally not much CG (could mean there actually isn't a CpG island) or have you just pasted your sequence into some software which says there is no island? If this is the case, try lowering the minimum CpG island size to about 100bp. How far upstream have you looked?
could you be looking at an alturnative TSS and promoter when comparing between the mouse and human?
have you tried blatting your promoter sequence against the mouse genome?
thank you all for your ideas. You had the right idea methylnick. I looked at an alternative TSS. I have checked the other TSS and there i can find a CpG-island !