One way to do that is to use ChIP-seq data if available. You would have to look among the binding peaks for the ones near the gene/s you are interested in. This wouldn't give you exact binding sites, but it can narrow down the search space.

Depending on the species, tissue, or cell line you expect the transcription factor is important, more or fewer resources are available. I would check the ENCODE project first. Another is the Cistrome database, particularly if you will be working with cancer cell lines. Chipatlas and GEO can be helpful as well.

Hi Blerta,

If I understand your question correctly, tools used to identify DNA-binding domains of proteins have been detailed in another Researchgate forum: https://www.researchgate.net/post/How-can-I-predict-DNA-binding-site-in-my-protein. In short, there are many options, but the tools suggested were as follows:

If you know the amino acid sequence of the TF's DNA binding domain, you can reverse translate the amino acid sequence into DNA sequence, and find out its corresponding sequence in the TF's cDNA from GenBank. If you don't know the DNA binding domain, you can BLASTP (or its like) its amino acid sequence against nr data in GenBank, the BLASTP results may provide you information about its DNA binding domain sequence.

Hi @Mark Pepin, thank you for the kind suggestion.

Actually I need to know which is the seq of DNA corresponding to the list of amino acid responsible for the binding affinity of the Transcription factor.

Thank you Zhong-Min Dai

by using snap gene I can see the AA sequence but don't know if from blastp I can obtain the right sequence of the DNA binding domain...

Blerta Stringa

1) If you already know the AA sequence of the DNA binding domain, you can find out the start and stop site of this domain in its entire protein sequence. For example from 101 AA- 150 AA, which is translated by the 301 nt -450 nt in the coding region of its cDNA.

or 2) You can reverse translate the AA sequence of its DNA binding domain into degenerate nucleotide sequence, and find it out from the cDNA of your interest or BLAST it against the cDNA of your interest. For example, I have a cDNA sequence with ORF: ATGACCGTTGCCAGCAAATGCgcgtgcgatgaatttggccatattaaactgACGGATCGATACGTACAGTAA, if I need to find out what the exact cDNA sequence corresponding to the AA sequence ACDEFGHIKL, I first reverse translate the AA sequence into gcntgygaygarttyggncayathaarytn (if Snap gene can't do the reverse translation, you can use online tool https://www.bioinformatics.org/sms2/rev_trans.html ), this sequence can be used to search (if Snap gene software allows you search sequence with ambiguity), blast or align against the cDNA sequence.