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Figure 2 | BMC Evolutionary Biology

Figure 2

From: Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopodacave crickets (Orthoptera, Rhaphidophoridae)

Figure 2

The dHH structure and the consensus alignment of the sHH (49 bp) and dHH (68 bp) regions from the pDo500 satDNA in Dolichopoda. The sHH and dHH regions of the pDo500 consensus sequences as derived for each population by Martinsen et al., in press [33]. The colors represent: pink = stem 0 green = stem I, yellow (light) = stem II, blue = stem III, yellow (deep) = cleavage site, magenta = invariable core residues, turquoise = compensatory mutations. A dHH structure - as suggested by Rojas et al. (2000) - is made up of two extended sHH sequences (49 bp + 19 bp) that hybridize. Stem I-III are found in both the sHH (see Figure 1) and the dHH structure. For the dHH stem III is folded exactly the same way as in the sHH - i.e. two areas (blue) from the same sequence pair with each other - while pairing of stem I and II requires two different sequences. The figure of the dHH is adopted from Rojas et al. (2000) and edited further to illustrate the alignment of the pDo500 consensus sequences. In cpr the D denotes A, T, or G, and in crq the ? denotes C, T, or gap.

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