ABSTRACT The fragile X mental retardation protein FMRP contains an arginine-glycine-rich region near its C-terminal end. In other RNA binding proteins, such regions have been called glycine-arginine-rich (GAR) domains, glycine-rich domains, arginine-glycine-rich regions and RGG-boxes, and ascribed non-specific RNA binding properties or, “auxiliary ” RNA binding functions. The current literature suggests that the definition of what constitutes an RGG box is quite varied. Nevertheless, a consensus sequence, built on a limited dataset, which supposedly defines the main elements of this motif, has existed since 1993. We aligned the arginine-glycine-rich regions of members of the fragile X family of proteins (FXFP) individually to the RGG box consensus to test its generality. In all cases, we found the consensus did not fully represent the structure of the FXFP`s GAR domain. We then used these sequences and others derived from searching the SwissProt database with the consensus sequence to devise a more general RGG box consensus motif. We then used this new consensus to pull out other RGG box proteins from the NCBI database. The new data demonstrate that RGG boxes motifs are often found in multiple repeats and can be interspersed within other domains. Such diverse settings will undoubtedly lead to differences in the way specific RGG box-containing proteins interact with cellular RNAs.
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