For a given gene sequence, how do we find the 5' transcription start site. What is the % similarity to consensus initiator sequence responsible for transcription initiation. How do we identify and mark the binding site for TF 1 B.
The 5' transcription start site is located in the promoter region. In prokaryotes, the promoter consists of two short sequences at -10 and -35 positions upstream from the transcription start site. The sequence at -10 is called the Pribnow box, or the -10 element, and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes. The other sequence at -35 (the -35 element) usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.