We identified 240,712 and 218,281 RBM10 sequence clusters (putative binding sites) in the two replicates, respectively (Supporting Information Table S1, Fig S1C and D for the length distribution of binding clusters as well as the number of PAR-CLIP reads within each cluster).
The length of continuous binding residues is termed as a binding segment.
The intrinsic flexibility of the Nup, the repeated occurrence and short length of the binding motif seem to create a highly reactive binding surface, which renders the individual FG-motifs prone to bind at any time without compromising the Nup's inherent plasticity.
In this simple regulatory model, we assume binding site motifs match exactly one sequence of length n, but in practice most binding site motifs match several sequences; therefore, we cannot use the length of known binding site motifs to accurately parameterize n.
As Lynch showed, this mutational bias can be parameterized via two empirical sequence properties: α=4 n / L, where n is the average length of a binding site and L is the length of DNA which may harbor a binding site.
The entropic change upon the binding between microRNA and the mRNA ΔS(l eff, S) depends on the length of the binding site S and the effect loop length l eff.
This efficiency can be quantified in terms of the length of the binding motif, and the length of the promoter region, and the fitness landscape for factor binding, which is amenable to quite explicit modeling.
