I am currently reading about transcription factors. I come from a pure math background so please try to make this easy for me. Anyways, I am reading a paper that talks about the Sp1 binding site locations (and does some statistics on it). I took the locations and put it up on the genome browser to see how it affects a gene. Here is my picture:
The custom user track is the SP1 transcription factor binding site (TFBS). So my questions are
1) Does the location of the TFBS tell us something about the promoter/enhancer regions of this gene?
2) Does it tell us anything about histone modifications?
3) (aside) why are the refseq and ucsc genes not aligned? I thought the ucsc genes included refseq genes)