Fig. 6

The five most frequently occurring 1×1 nucleotide internal loops in human miRNA precursors have different preferences for 5’ and 3’ closing base pairs. Please note that “5’AU” indicates a 5’AU or 5’UA closing base pair. Likewise, “5’GC” indicates a 5’GC or 5’CG closing base pair, and “5’GU” indicates a 5’GU or 5’UG closing base pair. Interestingly, changing the orientation of the loop nucleotides changes closing base pair preferences. For example, in miRNAs, C/A prefers 5’ GC > AU > GU and 3’ AU > GC > GU while A/C prefers 5’ AU > GC > GU and 3’ AU ≈ GC > GU. The distribution of closing pairs is different for highly expressed human RNAs and RNAs from other organisms. Statistically significant differences were observed for RNAs from other organisms as indicated by *, p <0.05; **, p <0.01; ***, p < 0.001