Dear colleagues,
When we have a given mRNA sequence, how can I find the exact sequences of its promoter, 3'UTR and 5'UTR regions which lie inside it? Are there any specific analyzing tools? If any, please; can you explain, how to perform that process?
The first nucleotide of the mRNA is the position where transcription starts. Hence, the promoter will be upstream of this nucleotide and will be found in the DNA, not RNA.
If the mRNA is eukaryotic, the first ATG indicates the translational start of the gene. The sequence upstream is the 5' UTR. If the mRNA is bacterial, you look for ATG preceded by the Shine-Dalgarno sequence (consensus AGGAGG), which is ~ 9-11 nts upstream of the ATG, and which base-pairs with the 3' end of 16S rRNA of the ribosome, and is crucial for bacterial translation initiation.
You then find the stop codon that is in frame with the ATG and you get the open reading frame. What follows is the 3' UTR.
Dear Lahiru,
Libor Krásný provided an exact description. Please be aware that multiple transcription start sites (TSS) may exist and determination of "the promoter" using in silico or molecular methods is a science of its own. Based on 15 years of experience I can say that you can spend infinite hours on the topic sometimes without noteworthy progress.
Best
Boris
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