i want to analyse region on dna of gene of known transcrition start site ,what should be region i will take upstream and downstream of tss for to get transcription binding site.
There are in silico transcription factor binding sites prediction websites for many genes. I read this some times before. You can search:
May be these links be helpful, I havent read.
https://www.ncbi.nlm.nih.gov/pubmed/21780002
https://www.ncbi.nlm.nih.gov/pubmed/16922688
https://www.ncbi.nlm.nih.gov/pubmed/15383209
https://www.ncbi.nlm.nih.gov/pubmed/14681436
Well theoretically, a TF can act on a promoter from any distance, given that binding sites are often found in distant regulatory regions called enhancers. You won't know if a TF binding site has an effect on you gene of interest before you 1) show that the TF in question actually binds this site (tested by inserting mutations in the binding site and by EMSA), 2) show that your binding site has an effect and / or a relationship with your TSS of interest (tested by chromosome conformation capture and functional analysis of gene expression after introducing mutations in a particular binding site). In silico search for binding site will only give you an idea of where to look at. Good luck!
There are many publications on promoter analysis of genes, and choice of region to be considered varies across studies. I have been following literature on promoter analysis for last four years, and have not seen any of the published studies explain clearly the reason for choosing specific region (-500 to +500 or -1000 to +1000 or -2000 to +2000) for analysis. So it is difficult to suggest a specific region.
But based on experience I can tell you that larger the region you consider more TFBS you identify and majority of them being false positives. The tools that scan for TFBSs in promoter sequences, use position weight matrices(PWM) or consensus sequences.
What I would suggest is to perform promoter analysis considering larger region (-2000 KB to +2000 KB) and consider TFBSs that are located in CpG island region or Evolutionarily conserved across species (These information you can get from UCSC).
This strategy will facilitate removing most of false positives and choosing important region for experimental validation.
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