Table 1. Summary of RNABPs for which CIMS analysis has been performed following this protocol.

The frequency of deletions are reported as the percent of unique CLIP tags with one or more deletions. Since deletions introduced by mapping errors occur in general a much lower rate, these numbers represent a reasonable estimate of deletions introduced by crosslinking. For substitutions, whether they can be introduced by crosslinking is based on several criteria, including if they can provide appreciative improvement to pinpoint the motif. Because of the complication of substitutions caused by sequencing and other types of errors, it is difficult to give a quantitative estimate of the mutation rate caused by crosslinking. The base composition of the inferred crosslinked nucleotide is shown in the last column.

RNABP	Motif	Data source	Deletions (% tags)	Substitutions	Crosslinked nucleotide (left to right) A,C,G,U)
Nova	YCAY	50	Y (21)	N		Deletion
Ago	miRNA seed matches	4	Y (>8)	N		Deletion
Ptbp2	UCUY	23	Y (>7)	N		Deletion
Hu	U stretch	19	Y (21)	N		Deletion
Mbnl2	YGCY	31	Y (>9)	Y		Deletion
						Substitution
Lin28	AAGNNGAAGNG	45	Y (16)	Y		Deletion
						Substitution