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. 2009 Jul;15(7):1292–1304. doi: 10.1261/rna.1347409

FIGURE 7.

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.

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