Regulatory cis element in light-regulated IR regions. (A) Illustration of sequence extraction for motif search. (B) The repetitive GAA motif enriched in red (top) and blue (bottom) light-regulated IR regions. The E-value indicating the statistical significance of the motif is shown on the right of the motif. Frequency distribution of the repetitive GAA motif in red (C) and blue (D) light-regulated IR regions are plotted. Frequencies of the motif were generated by counting the numbers of motif hits in windows of 20 nt near the donor and acceptor sites of light-regulated IR regions. Only input sequences extracted from donor and acceptor sites of the retained introns (longer than 200 nt) were used for motif counting. The green bar represents the exon and the solid line indicates the retained intron.