Extended Data Fig. 9: Effects of structure variants on retained intron levels for RPS9A variants.
From: Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo
For a given stem set or loop, violin plots depict data for the wildtype sequence and all variant sequences, with points for each unique barcode. Data for rescue sequences are shown when included in the intron library. p-values (computed by two-sided permutation tests) are indicated for comparisons between wildtype and variant sequences, and between variant and rescue sequences. There are 67 wildtype sequences compared to variant sequences in each plot. The numbers of variant sequences are as follows: 12 for stem 51-58, 75 for stem 73-79, 11 for stems 73-84, 39 for stems 73-96, 10 for stems 102-114, 81 for stem 191-195, 44 for stems 184-195, 60 for stems 182-195, 74 for stems 171-195, and 51 for loop 196-205. The numbers of rescue sequences are as follows: 18 for stem 191-195, 46 for stems 184-195, 25 for stems 182-195, and 24 for stems 171-195. Embedded box plots mark the median as the center white point and include a box from the 25th (Q1) to 75th (Q3) percentile, extending whiskers to the smallest and largest value that fall within 1.5 times the interquartile range below Q1 and above Q3. Secondary structures are colored by reactivity data, and bars alongside the secondary structure indicate stem and loop disruption sets, with each bar representing variant sequences mutating nucleotides across the full extent of the bar. These bars are colored by the retained intron (RI) score for the interval. The RI score is the negative log(p-value) comparing RI values between wildtype and variant sequences, and the sign indicates the effect direction, with positive values (shown as blue) for lower variant RI compared to wildtype, and negative values (shown as red) for higher variant RI.
