Figure 4

Secondary structure prediction of RNA encoded by MSHORT1 and RSHORT1. A) The model of the secondary structure of MSHORT1 is based on minimal free energy. The colors represent the positional entropy from low (red) to high (blue). The hairpin that forms pre-miRNAs of some MSHORT1 copies is indicated. B) Positional entropy is shown for the corresponding positions of the secondary structure. The pre-miRNA corresponding region is highlighted in white. C) &D) Same representation for the secondary structure of RSHORT1 (rats). Please note the region that potentially forms a pre-miRNA in MSHORT1 is more stable as compared to the corresponding region in RSHORT1. E) Detailed view of the predicted miRNA containing hairpin structures of MSHORT1 and RSHORT1. The two arms of the RSHORT1 hairpin contain a different number of nucleotides (left arm vs. right arm), while the number of nucleotides is equal in the two arms of the MSHORT1 hairpin. Energy rich, asymmetric bulges in the hairpin-stem of RSHORT1 result from an imbalance in hairpin arm length. In MSHORT1, intramolecular base pairing occurred between nt 125 and nt 140 (pink), while in RSHORT1 nt 125 pairs to nt 150. Sequence coordinates correspond to the pairwise alignment of the two sequences. The asterisk marks sites of deletion of two nucleotides in RSHORT1 compared to MSHORT1 (adapted from [32]).