Editing Consensus sequence (section)

==Biological significance==
A protein binding site, represented by a consensus sequence, may be a short sequence of [[nucleotide]]s which is found several times in the [[genome]] and is thought to play the same role in its different locations. For example, many [[transcription factors]] recognize particular patterns in the [[Promoter (genetics)|promoters]] of the [[gene]]s they regulate. In the same way, [[restriction enzymes]] usually have [[palindromic]] consensus sequences, usually corresponding to the site where they cut the DNA. [[Transposons]] act in much the same manner in their identification of target sequences for transposition. Finally, [[splice site]]s (sequences immediately surrounding the [[exon]]-[[intron]] boundaries) can also be considered as consensus sequences.

Thus a consensus sequence is a model for a putative [[DNA binding site]]: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. All the actual examples shouldn't differ from the consensus by more than a few substitutions, but counting mismatches in this way can lead to inconsistencies.<ref name="Schneider2002" />

Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an '''up mutation'''. This kind of mutation will generally make the promoter stronger, and thus the RNA polymerase forms a tighter bind to the DNA it wishes to transcribe and transcription is up-regulated. On the contrary, mutations that destroy conserved nucleotides in the consensus sequence are known as '''down mutations'''. These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence.