Figure 2

Unique consensus sequences at aTIS compared to non-aTIS (AUG) in the 5'-UTR region of mRNAs. Figures 2A and 2B where generated with an adaptation of the WebLogo application [32]. The overall height of the nucleotide stack indicates the sequence conservation at that position, while the height of nucleotide symbols within the stack indicates the relative frequency of each base at that position. The start site is indicated at positions 1, 2, and 3. (A) Distinct consensus nucleotide sequences near confirmed alternative translation initiation sites in mammalian mRNAs. The relative abundance of nucleotides (A, T, C, G) at aTISs is shown for a window of -10 to +10 bases at the initiation codon, with the aTIS start codon in positions 1, 2, and 3. Conservation around all of the alternative start sites aTISs is illustrated. Note the strong conservation of (G/C) at the -6 position and C at the -7 position. (B) Consensus nucleotides near AUG translation initiation sites in mammalian mRNAs. Graphical representation of relative nucleotide abundances at AUG sites is shown for bases in the region of -10 to +10 bases relative to the initiation codon, with the AUG codon in positions 1, 2, and 3. Conservation at the -3 and +4 locations are consistent with traditional Kozak consensus sequence. These features are distinguished from that of thte aTIS sequences which show conservation at positions -6 and -7 (Figure 2A).