FIGURE 7.
Base prevalence found in accumulated mRNAs resulting from mutations in U5 loop 1. (A) Base prevalence found near the 5′ splice site for all intron containing pre-mRNAs is displayed at the top for reference. The sequences of the pre-mRNAs identified as giving rise to more spliced mRNA in U5-1 and U5-2 (cluster 1) were examined in the same way as described in Figure 5. Only one position had significant change from the consensus sequences; the third nucleotide from the end of 5′ exon (5′SS −3) shows a highly significant increase in the proportion of adenosine at that position and decrease in the proportion of cytidine. (B) U5 loop 1 interactions with the exons after the first step of splicing and the structure of the U5 loop 1 is shown (bold) along with the U5-1 and U5-2 sequences. Known interactions between U5 and the 5′ and 3′ exons are indicated (hashed lines). The third nucleotide upstream of the 5′ splice site in the 5′ exon that displayed a significant increase in the incidence of adenosine at that position in pre-mRNAs exhibiting an increase in mature RNA in U5-1 and U5-2 compared to WT U5 is emboldened.