Extended Data Figure 3. RBFOX2 iCLIP demonstrates broad agreement with nsRBNS.

a. Some secondary motifs show sharp peaks near 0 in a metaplot centered at the motif in introns (black) and 3' UTRs (grey) in RBFOX2 iCLIP data²⁷. 5' ends of iCLIP reads containing the motif of interest were aligned with position one of the pentamer at 0 and normalized to the minimum read count in an 80-nt window (50-nt window shown). Y-axis range was reduced for secondary motifs. See Methods for read counts. b. AU-rich nsRBNS motifs do not show characteristic read peaks near 0 in a metaplot centered at the motif in introns (black) and 3' UTRs (grey) in RBFOX2 iCLIP data²⁷. iCLIP reads containing the motif of interest were aligned with position one of the pentamer at 0 and normalized to the minimum read count in an 80-nt window (50-nt window shown). Y-axis range was reduced for secondary motifs. See methods for read counts. c. Schematic showing the generation of a clip enrichment (CE) score from iCLIP data. After generation of a metaplot, the read count at the peak apex was divided by the read count at its lowest point to generate a CE score analogous to an enrichment. d. Correlation of iCLIP- and nsRBNS-enriched 5mers in 3' UTRs (n = 1024). CLIP enrichment (CE) scores were computed for iCLIP peaks. Secondary motifs indicated in teal, primary motifs indicated in gold.