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. 2010 Jan 22;6(1):e1000819. doi: 10.1371/journal.pgen.1000819

Figure 3. PTC as a backup for weak splice sites in novel introns.

Figure 3

(A) The percentage of introns that use the most common 5′ and 3′ splice site motifs. Significantly fewer novel introns use the canonical GT(A/G)AGT motif at position +1 to +6 of the 5′ splice site. Likewise, fewer novel introns use CAG at −3 to −1 of the 3′ site. Error bars represent the 95% confidence intervals generated by resampling 307 introns with replacement 10,000 times (Figure S5). (B) A logistic regression identified a significant deficiency of 3n PTC-free introns within conserved introns (conserved 3n versus conserved 3n+1and2 - bottom contrast) confirming the finding of Jaillon et al. (2008) that selection acts against introns that would remain invisible to the NMD pathway upon intron retention. This effect is significantly stronger amongst novel introns (novel 3n versus novel 3n+1and2 - top contrast) and significantly stronger in a direct comparison between novel and conserved introns (second contrast) (95% CI that do not include one indicate a significant deficiency of 3n PTC-free introns).