Definition of promoter

[gene_x]

Guys,
I always wonder how people came up with the artificial definition of promoters. I know some papers use 1kb both upstream and downstream of transcription start site.. Does anyone know some good evidence supporting a particularly cutoff of how long the promoter is? What is your way of defining promoter? Is there a difference between the length of a promoter for mouse and human?

Thanks!

[swbarnes2]

In theory, a promotor is a region of DNA to which proteins bind to control the expression of that gene.

The problem is that in practice, no one can look at a sequence know all the proteins that might bind there. Sometimes we have empirical data of where certain proteins bind, and maybe we can identify motifs that might indicate the kind of site a protein would bind to, but it's far from an exact science.

So we say 1 kb upstream, because most of the proteins which control expression do so by binding within 1 kb of the start.

[gene_x]

Right, that's my understanding of how this 1kb choice came about.. biology in many ways is not an exact science

[maubp]

Also check the literature for your organism, as there is variation at this level too in the typical promoter distance. But I'd agree with 1kb upstream as a good ball park figure to start with.

[gene_x]

Also check the literature for your organism, as there is variation at this level too in the typical promoter distance. But I'd agree with 1kb upstream as a good ball park figure to start with.

Sure, there are some empirical evidences