Transcription and RNA Processing

ID #1153

Can you quickly tell me how we would compare a sequence of 7 bp to a consensus site such as the -10 site? In other words, if we are given the sequence GATAATT and told that it is 10 bases from the start, then we know that we have to compare it to the -10 site. But, here is where I am confused, do we read this sequence as ATAATT or GATAAT?

Since the spacing (-10, -35) is only approximate, you line up the sequences for a best fit with the consensus. So using the specific example you gave, what you observe is that 5 of the 6 bases in the consensus sequence match, which would make this a component of a strong promoter. The fact that the *ATAAT sequence begins with a G means it's not a perfect consensus promoter site, but 5 out of 6 is pretty darn close.

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