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. 2016 Dec 14;18(1):28–38. doi: 10.15252/embr.201643391

Figure EV5. Primary and secondary structures of the pseudouridine sequence motif.

Figure EV5

  • A
    Sequence motifs surrounding the mitochondrial ψ sites generated by WebLogo software at http://weblogo.berkeley.edu. Three motifs are suggested for the top four ψ sites, because the COXIII (ψ 9904–9906) position is uncertain due to the ambiguity of the sequence alignments.
  • B–D
    Positions of identified ψ sites (red rectangle) within the secondary structures of individual RNAs. (B) Known secondary structure of the 3′‐terminus of 16S rRNA 37 and predicted structures for COXI (C) and COXIII mRNAs (D). Predictions were based either on sequence fragments of 100 nt and 200 nt surrounding each ψ site, or using the whole mRNA molecule as the input. Pseudouridine is predicted to be accessible in all cases, located at a loop or in the boundary between a stem and a loop/bulge structure.