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Even though a single Nab3 binding site may elicit termination, Nrd1/Nab3 sites are not recognized within gene bodies more than 1000nt away from the promoter [133,173].
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A lost binding site may have been replaced with a new, species-specific binding site - i.e. binding site turnover.
Placing a fluorophore too close to the binding site may disrupt binding, and fluorophores too far away from the binding site may not result in fluorescence changes.
IP6 binding to the peripheral binding site may also enhance PIP3 affinity in the canonical binding site and sensitize Btk to PIP3 levels.
Both binding sites may serve as a template for structure-based design of novel complement therapeutics.
Similar binding sites often imply similar protein-protein interactions and similar functions; however, similar binding sites may also constitute traps for nonfunctional associations.
Therefore, true binding sites may have SNPs less frequently than the non-binding sites.
Unoccupied 'perfect' STAT1 binding sites may include cell type specific binding sites and suggest a required but not sufficient function of the nucleotide sequence for DNA-protein binding.
Pum1 binding sites may also overlap with CUGBP1 sites, as both proteins have preferences for U/purine rich sequences.
These data suggest that intronic binding sites may prove to be a nonspecific contaminant.
Such repetitive occurrence of PUF binding sites may affect RNA regulation: different sites could have different affinities for PUF binding leading to dose-dependent or allosteric regulation.
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