Figure 4.

Intragenic CNSs with Conserved RNA Secondary Structure.

(A) RNAz-predicted consensus RNA structure of the 3′ UTR of the EBF2 family based on the multiple alignment of sequences from rice (LOC_Os06g40360 and LOC_Os02g10700) and sorghum (Sb04g006870).

(B) RNAz-predicted consensus RNA structure of the 3′ UTR from a multiple alignment of sequences from a bHLH gene family (Supplemental Table 2). The region corresponding to dsRNA reads in AT4G29100 is indicated by arrows.

(C) RNAz-predicted consensus RNA structure from a multiple alignment of sequences from a DEAD-box RNA helicase family (Supplemental Table 2). Multiple isoforms for AT3G01540 and LOC_Os01g36860 are shown with the position of the CNS indicated by the green bar. dsRNA reads are depicted as screenshots from the IGB browser (http://bioviz.org/igb/). RNAz-predicted base-paired regions conserved throughout the multiple alignment are colored blue, with lighter shades of blue depicting the presence of incompatible pairs within the alignment; positions in which consistent or compensatory mutations have taken place are colored green, with lighter shades depicting the presence of incompatible pairs within the alignment.