Dear Diandra. I did a little research for this interesting question. In their article, Lambert et al 2014 have stressed about canonical motifs (RNA consensus sequences recognized by RBPs) that classical techniques allow to identify “just the strongest binding motifs and may not detect moderate and lower affinity motifs. Only about ⅓ to ½ of Rbfox2 binding sites identified in vivocontain these canonical motifs (Jangi et al., 2014; Yeo et al., 2009), but it has remained unclear whether this RBP can recognize other sequence motifs. In general, motifs recognized by RBPs with lower affinity are more challenging to characterize, but such motifs may play biological roles that are as important as those played by higher affinity motifs.”

Refs RNA binding proteins ex of splicing factors

Lambert et al 2014 https://pmc.ncbi.nlm.nih.gov/articles/PMC4142047/

Yeo et al 2009 https://pmc.ncbi.nlm.nih.gov/articles/PMC2735254/

Jangi et al 2014 https://pmc.ncbi.nlm.nih.gov/articles/PMC3967051/

Jin et al 2003 https://pmc.ncbi.nlm.nih.gov/articles/PMC145449/

Ponthier et al 2006 https://www.jbc.org/article/S0021-9258(19)46574-5/fulltext

The RNA binding site for one RNA is not necessarily the same as the binding site for a different RNA on the same protein. RNA-binding proteins (RBPs) can have specific binding sites for different RNA molecules, which are determined by the sequence and structure of the RNA. These binding sites can vary depending on the specific interactions required for the protein to perform its function with different RNAs.