Fig. 1.

Different distributions of secondary structures in the 5′ portions of mRNAs. The predicted RNA folding energy (ΔG kcal/mol) of 35 nucleotide windows (y-axis) are plotted for the 10% most highly translated mRNAs (high TR, black) and the 10% most poorly translated (low TR, red). The x-axis shows the position of the 5′ most nucleotide of each window. Windows for every one nucleotide offset were calculated. At each location, the free energies for the mean (continuous lines) and the interval between the 25th and 75th percentile (shading) are shown. mRNAs were aligned at their 5′ cap (left), at the iAUG (center), or at the 3′ of the CDS (right). In S. cerevisiae, S. pombe, and Arabidopsis, the differences between the two cohorts are greatest proximal to the iAUG. In the two mammals, the differences are greatest towards the 5′ cap