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Table 1 Stability of mRNA secondary structures

From: Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

  Protocol Mean ΔG P Mean Z(ΔG) Mean %pairs
Real (mouse)   -737.98 ± 55.52    60.96 ± 0.28
Modification Swap G4C4 -734.10 ± 55.08 0.0169   62.11 ± 0.33
Randomization Sh.4-fold -725.76 ± 54.71 9e-15 -1.41 ± 0.14 60.77 ± 0.23
  Sh.codon -728.49 ± 55.01 6e-10 -1.04 ± 0.14 60.61 ± 0.23
  Re-sub.K -733.28 ± 55.15 4e-05 -0.64 ± 0.15 61.06 ± 0.24
  Re-sub.N3 -734.14 ± 55.20 4e-04 -0.51 ± 0.14 61.09 ± 0.24
  1. Means ± SEM are shown, N = 70. P-values for modifications were determined by paired t-tests (μ = Real < Modification) on ΔG. P-values for randomizations were by one-sample t-tests (expected mean (μ) = 0) on Z(ΔG). %Pairs is the proportion of the coding sequence involved in base-pairing interactions. Artificial sequences generated by the first five protocols encode the same protein as the mouse sequence. A brief description of each protocol follows (see Results for details). 'Sh.4-fold': nucleotides at all 4-fold degenerate sites are shuffled. 'Sh.codon': for each amino acid, the synonymous codons are permuted. 'Re-sub.K': synonymous substitutions are reverted back to the rat-mouse common ancestor (rat-mouse common ancestor) state, followed by reallocation of the same number of synonymous point mutations. 'Re-sub.N3': like the previous protocol, except that the nucleotide replacement is also selected at random from the nucleotide distribution at third sites observed in the mouse sequence. 'Swap G4C4': all guanine bases at 4-fold sites are replaced by cytosine, and vice versa.