promoter cloning - mRNBA cap site (Oct/11/2005 )
I am cloning a promoter upstream of a reporter gene.
I have cloned several different fragments of the promoter upstream of the reporter gene.
Is there a consencus sequence for the 5' cap site ? is this located near the TATA box ? and do I need to include it for transcription of the reporter gene?
Do you already know the transcription start site of the gene. Usually it can be found out by primer extension or Ribonulease protection assays. If the start site is accurately known it will be much easier to work with the promoter then. Yes , you want to include the start site in your deletional analysis of the promoter. Because TATAless promoters are known to use Inr elements for transcription.
I dont know about the consensus for the CAP site..but thats a good question. Never thougth about that.Will share with you if i find one.
Nevertheless, I hope this helps .