Figure 3.

Four H/ACA snoRNA structural candidates. Three of these are intergenic (A–C) and the other (D) is consistently found in the intron of a vacuolar sorting protein. For each structure, the H box (ANANNA) and ACA box (ACA) motifs are highlighted in yellow and labeled. Nucleotides are colored according to degree of conservation per the legend. Base pairs highlighted in green are statistically significantly covarying. Putative interactions between the guide regions of the H/ACA snoRNAs and rRNAs are illustrated in blue, with the proposed site of pseudouridylation designated as ψ. R-scape uses R2R to draw the structures (43). The sequences have been trimmed to highlight the region of covariation. Positions with more than 50% gaps are not displayed unless they are base paired.