Fig. 5

The G-to-A SNP changes the RNA secondary structure of an RNA segment from CGR3. A Predicted secondary structures of 115-nt CGR3 reference and alternative sequences (chr5:26339678–26339792). The SNP is identified by an arrow. Structures were folded using RNAstructure and outputted using R2R (https://help.rc.ufl.edu/doc/R2R) [40]. B MutaRNA dot plot [39] displays the probability of base pairing of the reference (above the diagonal) and alternative (below the diagonal) sequences. The color scale on the right shows the strength of base pairing probability. The position of the SNP is denoted with the dashed red crosshairs. C–F DMS reactivity of a 78-nt-long portion of the 115-nt-long CGR3 sequence (nucleotides corresponding to the primer binding site for the in vitro probing and compressed data at the top of the gel could not be mapped) is plotted in C from an in vivo dataset from plants grown at 21 °C [6], as well as for two in vitro DMS experiments conducted at D 20 °C and E 37 °C. In vitro DMS reactivity was derived from two sequencing gels provided in Additional file 4: Fig. S2. F The delta DMS reactivity of alternative and reference sequences at both 20 °C and 37 °C