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. 2022 Nov 2;50(20):11834–11857. doi: 10.1093/nar/gkac991

Figure 3.

Figure 3.

Analysis of global 5′ss changes for prp-8(D1549N) and snrp-200(N18K) and 3′ss changes for prp-8(D1549N). (A) Histogram showing relative distances of alternative 5′ss for prp-8(D1549N) (n = 73) (Table 1 and Supplementary Table S2). (B) Histogram showing relative distances of alternative 5′ss for snrp-200(N18K) (n = 19) (Table 1 and Supplementary Table S2). The arrow at zero in (A) and (B) is the position of the 5′ss whose usage is reduced in the presence of the mutant allele. The distances of the sites whose usage is increased in the presence of the mutants are shown in the histogram. Note that there is no apparent bias for use of an upstream or downstream 5′ss with either suppressor allele. (C) The consensus of the first 7nt of 10 000 randomly chosen C. elegans intron starts is shown at the top. The second and third logos compare the 73 alternative 5′ss from the prp-8(D1549N) RNAseq library analysis identified in Table 1. The alternative 5′ss whose usage is lessened in the presence of prp-8(D1549N) is shown first, followed by the alternative 5′ss whose usage is increased in the presence of the prp-8(D1549N) allele. The fourth and fifth logos compare the 19 alternative 5′ss from the snrp-200(N18K) mutants. The alternative 5′ss whose usage is lessened in the presence of snrp-200(N18K) is shown first, followed by the logo for the alternative 5′ss in the pair whose usage is increased in the presence of the snrp-200(N18K) allele. Consensus sequence logos were generated using WebLogo (34). (D) Histogram showing the positions of the 30 alternative 3′ss promoted by prp-8(D1549N) relative to the partner alternative 3′ss whose usage is reduced. Note that all but one of the mutant-promoted sites is downstream. (E) The consensus logo of the last 7nt of 10 000 randomly chosen introns is shown at the top, matching the TTTTCAG consensus. The second and third logos compare the 30 alternative 3′ss from the prp-8(D1549N) RNAseq analysis from Table 1 and Supplementary Table S2. The sequence logo of the alternative 3′ss whose usage is lessened in the presence of prp-8(D1549N) is shown first, followed by the alternative 3′ss whose usage is increased.