I have available to be the entire set of SNPs of quite a few cows (don't know the precise number at the moment). I am investigating the consequences of these SNPs. As a first step I have looked at the SNPs in exons and found their consequences using the ensembl consequence feature. I have then looked at SNPs that were identified as non-synonymous to see their effect on protein structure using polyphen.
I would like to see if I can find out anything useful about the other SNPs of which there are hundreds of thousands.
Here are some of my ideas. I was wondering if I was missing anything else obvious
1) Use tools to investigate the consequences of SNPs in non-essential splice sites e.g. SpliceSiteFinder, MaxEntScan. I appreciate that the results of these programs can be inaccurate but I believe you can get 80-90% accurancy with splice sites close to the exon/intron boundaries
2) Use tools to scan cattle genome for potential intron splicing regulatory elements (enhancers and silencers) and look for SNPs in those regions. I believe tools to look for these types of regulatory regions are much less reliable than tools to look for splice sites as the 'consensus' sequence is so degenerate.
3) Identify SNPs in known RNA genes in ensembl cattle database. Also Look for any putative RNA elements in the cattle genome using RNA prediction tools, and identify SNPs here.
What are the best tools to look for RNA genes (though I have another question open about this) Are there any tools to predict the consequences of SNPs in miRNA?
4) Look for transcription factor binding sites in the genome and identify SNPs here. I'm not sure about this one and haven't really given it much thought. If anyone reading this question knows any opportunities/caveats off the top of their head it would certainly give me a head start but I admit this is just a cursory idea to me at the moment.
Are there any other major regulatory elements that I am missing. Molecular biology has changed so much that I don't know half of the things that exist anymore. No-one had heard of miRNA when I did my degree!!
I imagine there are lots of different DNA regulatory features. I just want to make sure I haven't missed the obvious ones. It would be impossible to cover all of the minor ones.
Many thanks in advance to anyone who answers. This forum is a really great resource. There seems to be a core of users who answer my questions and I appreciate every bit of input you give me.