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. 2021 Oct 28;12:730045. doi: 10.3389/fmicb.2021.730045

FIGURE 6.

FIGURE 6

The primary and higher order structures of the 3′UTRs of JEV. (A) The primary sequences of the JEV 3′UTRs. (B) The higher order structures of the JEV 3′UTRs. Differently colored nucleotide bases signify different structures, cis-acting elements or significant sequence motifs: blue, the very variable region (VVR); orange, the exoribonuclease resistant RNA (xrRNA1); purple, the 3′UTR variable region stem loop (3′vrSL); light yellow, the exoribonuclease resistant RNA (xrRNA2); dark green, dumbbell structure 1 (DB1); light green, dumbbell structure 2 (DB2); bold (black and aquamarine), the 3′UTR DB region small hairpin (3′dbsHP); aquamarine, 3′cyclization sequence (3′cCS); gray, the 3′UTR short hairpin (3′sHP); brick red, the 3′UTR stem loop (3′SL). The cis-acting elements or sequence motifs which were overlapped with other structures were labeled with different colored dashed line box: black, pseudoknot PK; blue, the 3′UTR variable region conserved sequences 1 (3′vrCS1); purple, the 3′UTR dumbbell structure repeated conserved sequences (3′dbRCS); light blue, the 3′UTR dumbbell structure conserved sequences 2 (3′dbCS2); bright pink, the 3′UTR DB region small hairpin (3′dbsHP); red, the 3′downstream AUG region (3′DAR); yellow, the 3′ upstream AUG region (3′UAR). The magenta blocks represent the differences within five JEV genotypes. The Domain I, II, and III are indicated with light gray, dark gray and black bars, respectively. The mentioned units are labeled similarly in the higher order structures. The red pentagram represents the JEV specific structure or sequence motifs.