the location of TFBS in genome / binding affinities caused by SNP

Question

[tonja.r]

I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the TF if I have a SNP in my locus. As my SNPs are annotated ( I know wether it is in an intron variant, downstream gene variant, missions variant etc) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant, upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that TFBS might be located before gene and after it.

What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons, introns, 5' UTR etc?

Answer 1

[Alex Reynolds]

Can a TFBS be located in the exon of a gene?

Scans within footprinting data over exons suggest yes. You can use computational tools for TFBS prediction, e.g., FIMO.