Table 7

Rate of evolution of ESE and (a) non-ESE sequence and (b) pseudoESE sequence at four-fold degenerate sites
Dataset Median ESE Median non-ESE % Difference P two-sided
A
ESR 0.3 0.39 -23.1 1.10E-13
INT2.400 0.32 0.36 -11.1 1.10E-13
INT3 0.3 0.36 -16.7 1.10E-13
INT3.400 0.3 0.35 -14.2 1.10E-13
INT3_ESR 0.3 0.35 -14.2 1.10E-13
INT3_ESR_400 0.29 0.35 -17.1 3.40E-13
Ke-ESE 0.35 0.34 2.9 8.20E-08
Ke-ESE400 0.38 0.34 11.8 1.10E-13
PESE 0.31 0.37 -16 1.10E-13
RESCUE 0.32 0.35 -8.5 5.70E-13
B
ESR 0.3 0.35 -14.3 4.50E-13
INT2.400 0.32 0.35 -8.5 4.50E-13
INT3 0.3 0.35 -14.3 4.50E-13
INT3.400 0.3 0.34 -11.8 4.50E-13
INT3_ESR 0.3 0.34 -11.8 4.50E-13
INT3_ESR_400 0.29 0.34 -14.7 2.30E-12
Ke-ESE 0.35 0.35 0 4.10E-06
Ke-ESE400 0.38 0.36 5.6 4.50E-13
PESE 0.31 0.35 -11.4 4.50E-13
RESCUE 0.32 0.35 -8.5 4.50E-13

We consider the proportion of four fold degenerate sites that are changed or unchanged when comparing mouse-human alignments. We split sites by whether in human the sequence matches an ESE or not (Table A) or ESE versus pseudoESE (Table B). We then perform a Wilcoxon paired test considering the rate of evolution of ESE and non-ESE or pseudoESE at each position away from an exon boundary. We also present the % difference between the medians, this being (median for ESE - median for non-ESE)/median for non-ESE. All tests are significant after Bonferonni correction (for consistency the P values are shown in bold).

Cáceres and Hurst

Cáceres and Hurst Genome Biology 2013 14:R143   doi:10.1186/gb-2013-14-12-r143

Open Data