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Figure 2 | BMC Evolutionary Biology

Figure 2

From: Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals

Figure 2

Base composition pattern around polyadenylation [poly(A)] sites in Arabidopsis ( Arabidopsis thaliana ), tomato ( Solanum lycopersicum ), sorghum ( Sorghum bicolor ), and maize ( Zea mays ). Sequence logo (seqlogo) graphs were drawn based on the average base composition among mapped poly(A) sites. Position 31 in these seqlogo graphs is the poly(A) tail starting position, corresponding to position 1 in Figure 5. Position 30 in these seqlogo graphs is the poly(A) tail attachment position, corresponding to position −1 in Figure 5. Positions 10 and 24 in these seqlogo graphs correspond to positions −21 and −7 in Figure 5. Note that the upstream A-rich region had its peak at seqlogo position 10 (i.e., position −21 in Figure 5) and that the upstream U-rich region had its peak at seqlogo position 24 (i.e., position −7 in Figure 5). Note that i) the poly(A) tail attachment position was usually a U, although in some species, such as maize, C and U were approximately equal, and ii) the base abundance regions from left to right showed a U-A-U-A-U pattern, where the second A in this pattern is the poly(A) site.

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