Soybean secondary structure

Proposed secondary structures for all four plant RNAs based on the information gained experimentally are presented in Fig. 5A. It is clearly evident that the secondary structures within this region of RNA from the four species are highly homologous. The predicted RNA structures from the two dicot species, soybean and Arabidopsis, differ only in that an adenine at position SO in soybean is a guanine in Arabidopsis, thus promoting formation of an additional base pair with the cytosine at position 63 in Arabidopsis. Other sequence differences between the two dicot species have no effect on the secondary structure of this region. The predicted... 

When sequences involved in base pairing are clearly identified, the weighting of a transversion in these regions in rRNA can be more fully evaluated. Furthermore, when the Watson and Crick strands of each base-paired region are both known, then the impact of transversion on structure and stability can be taken into account. For example, based only on numbers of sequence differences in the rather limited 3 region analyzed for the four plant rRNAs, the dicot sequence from soybean appears as closely related to the sequence from the monocot (maize) as it does to that from a distant dicot, Arabidopsis. The aquatic monocot Lemna is the most distant in sequence. An overview of secondary structure suggests that Arabidopsis and maize are more closely related (compare the terminal stems in Fig. 5A, nucleotides 46-67). However, as discussed earlier, a... 

Figure 3. Predicted secondary structure alignment for a-CT subunits of E. coli and soybean chloroplastic ACCases. Probabilities are plotted against the amino acid sequences of homologous regions.

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