Fig. 3
From: RNA secondary structure profiling in zebrafish reveals unique regulatory features
Comparison of RNA structures of ubc 3’UTR as determined by PARS based pairing probability and enzymatic footprinting using RNase V1 and S1 Nuclease. a. Bar plot represents PARS scores of 3’UTR region of ubiquitin c (ubc). Out of 105 positions, 87 positions are captured by PARS. b. Enzymatic footprinting of ubc 3’UTR probed by S1 Nuclease and RNase V1. Nucleotide positions are correlated with alkaline hydrolysis (AH) ladder and RNase T1 (G) ladder. Positions with similar structural pattern with PARS scores are highlighted. Red dots indicate unpaired positions; green indicates paired positions while yellow represents ambiguous regions. c. Heatmap representing secondary structure of 68 positions of ubc 3’UTR as determined by PARS and enzymatic footprinting (FP). Top panel represents PARS pairing probability; bottom panel indicates enzymatic footprinting pairing probability; middle panel represents the consensus between the two (PARS: FP). Red represents unpaired, green represents paired and yellow represents ambiguous regions