What is the implication that a consensus sequence... - (Oct/06/2006 )

Dear all,

My first time here and greetings.

I would like to ask, what is the implication that a consensus sequence of gene A occurs at upstream of gene B?

B is a receptor and A is some regulator that regulates cell growth.

So by knowing there is a consensus sequence from gene A appears upstream of gene B, what can we draw from that?

cheers
LJ

if this is homework, there is a specific forum for that...

that being said, I would like to clarifiy what you are asking?

is there a consensus sequence for the binding of the protein product from gene A? is that what you mean?

hi aimikins,

thanks for replying. no this is not homework, but as bioinformatics is not my specialised field, i'm trying to figure things out. I don't have a very strong foundation in bioinformatics but that is what i gather from my information after Blast, seq analysis search etc.

all i know is that, after alignment, a consensus sequence of about 120bp of gene A (mRNA is about 1kb-9kb long encodes for a protein, don't know why there are the big differences in length, maybe because of variants? but anyway...) is found upstream of gene B.

I would like to know what is the implication of this result? Basically what does this mean? What can be potentially drawn from this?

Does that mean the protein A are able to bind this place (DNA) to perhaps regulate gene B?

The term "consensus sequence" means nothing. In any alignment of multiple sequences, amino acid or nucleotide, there will be a consensus sequence, even if the sequences are unrelated to one another. In the same respect, there will also always be a "best" alignment (mathematically) of multiple sequences, again even if they're unrelated to one another -- the question is whether the alignment means anything.

Now, if you're talking about a conserved segement of a consensus sequence of a multiple alignment, there might be functional implications.

If the conserved (relatively invariant) segment is in the coding domain of the mRNA, it might indicate a catalytic domain or other structural feature required for function in the enzyme produced.

If the conserved segment is outside of the coding domain of the mRNA, it might indicate a translational regulatory domain.

If you're aligning DNA, and the the conserved segment is outside of the coding domain, it might indicate a transcriptional regulatory domain.

The fact that gene A is upstream of gene B, and that one or more conserved segements exist in gene A says nothing in and of itself with regard to gene A's possible ability to interact with gene B.