Need a signal for a start. AUG ? Met All proteins start with this codon.
There is a concensus sequence that is optimal of translation start called a
Kozak sequence. GCC A/G CC AUG G
The second tool and the effort made for this presentation is a pattern
finding algorithm that can score inexact matches to known concensus
sequences. Neurospora has a sequence similar to that found in vertebrate DNA
that surrounds the start codon, Met, with a variable consensus depending on
position (Jon et al.). The pattern is called the Kozak sequence. Script
numbers represent % occurrence of the particular nucleotide and (!T)
indicates the conserved absence of that particular nucleotide. Each
nucleotide must be present in at least 50% of all tested sequences to be
included. If two nucleotides, each having less than 50%, give a summed total
of at least 75% representation for a single position, then both are shown in
parentheses. N indicates any nucleotide.
C57 NNN C 77 A81 (A 44 /C 43 ) (!T) 3A99 T100 G99 G51 C53