Characterization of circRNA-predominant alternative cassette exons. (A) A strategic pipeline to identify high-confidence circRNA-predominant alternative cassette exons. By comparing the alternative cassette exon selection between p(A)+ and p(A)− RNA-seq data sets, circRNA-predominant alternative cassette exons were selected using stringent criteria. (B) The high-confidence circRNA-predominant cassette exons were determined with expression in at least two cell lines. (C) The strength of the 5′/3′ splice sites of high-confidence circRNA-predominant cassette exons (blue) was comparable with those of cassette exons identified in linear RNAs (light gray) and constitutive exons (dark gray). (ns) Not significant, (**) P value <0.01, Wilcoxon rank-sum test. (D) Similar densities of exonic splicing enhancers (ESE) were identified between high-confidence circRNA-predominant cassette exons (blue) and cassette exons identified in linear RNAs (light gray) and constitutive exons (dark gray). (ns) Not significant, (*) P value < 0.05, Wilcoxon rank-sum test. (E) The high-confidence circRNA-predominant cassette exons (blue) were slightly less conserved than were cassette exons identified in linear RNAs (light gray) and constitutive exons (dark gray).
