Figure 7

Co-occurring pairs are associated with weaker exons. (a) Two sets of constitutive exons were compared, one with co-occurring pairs in the indicated region and one without such pairs. The two sets were matched for GC content in the pertinent regions. ESE and ESS coverage refers to the proportion of exonic nucleotides that reside in a composite set of ESE and ESS hexamers [10]. 5' and 3' splice site scores are based on the method of Shapiro and Senapathy [50]. For each comparison the mean of the two exon sets was subtracted from all values to create a mean of zero and the maximum difference between the values of the two exon sets and this mean was set to 1; all other values were adjusted accordingly. All four UpDp, UpDd, UdDp, and UdDd combinations were treated separately. Error bars are the standard error of the mean. Asterisks below the bars indicate P-values: *P < 0.05; **P < 0.001; ***P < 0.0001; ****P < 0.00001. SS, splice site. The range of actual values across all four regional comparisons were: ESE coverage, 0.439 to 0.467; ESS coverage, 0.109 to 0.125; 3' splice site scores, 74.295 to 75.514; 5' splice site scores, 81.519 to 82.124. (b) As (a), but two sets of alternatively spliced exons were compared, one with co-occurring pairs in the indicated region and one without such pairs. The range of actual values across all four regional comparisons were: ESE coverage, 0.393 to 0.432; ESS coverage, 0.092 to 0.109; 3' splice site scores, 68.676 to 71.780; 5' splice site scores, 78.914 to 80.087.