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. 2009 Dec;15(12):2385–2397. doi: 10.1261/rna.1821809

FIGURE 5.

FIGURE 5.

Comparison of secondary structure with PTB binding. Secondary structure was modeled using Sfold for each of the 2879 oligonucleotides that contained CUCUCU, the highest possible scoring match to the PTB motif (Ding et al. 2005). (A) The predicted structures are classified according to the degree of predicted base-pairing over the windows that encompass the 6-nt PTB motif, CUCUCU. The y-axis plots the average number of predicted structures in each category for the particular bin of oligonucleotides defined by the x-axis. The x-axis represents 10-nt bins of percentile ranks (100–91, 90–89, …), where oligonucleotides are ranked according to enrichment in the PTB bound fraction. (B) Compares types of base-pairing observed. Predicted base pairs were grouped into three categories: pre-mRNA/pre-mRNA, primer/pre-mRNA, and primer/primer. For each category, the number of predicted base pairs in the (pink bar) top and (blue bar) bottom 1% of oligonucleotides ranked by array enrichment was normalized to the pool-wide average and plotted as a histogram.