Question: the location of TFBS in genome / binding affinities caused by SNP
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gravatar for tonja.r
5.8 years ago by
tonja.r490
UK
tonja.r490 wrote:

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?

snp • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Alex Reynolds31k • written 5.8 years ago by tonja.r490
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gravatar for Alex Reynolds
5.8 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

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.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Alex Reynolds31k
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