Supplementary Figure 2: Temporal patterns of RNA-seq signals at RP introns.

89 RP genes from Intron1 cluster were included in the analysis. (a) The ratio of intron to exon was calculated for every gene in the cluster and the means are displayed across 16 time points in the top panel. The bottom panel is total numbers of junction reads spanning the 3’ end of RP introns at 16 time points. Note that the numbers of 3' junction reads are consistently higher than the numbers of 5′ junction reads (Figure 2c), consistent with an arrest of splicing at the “2/3 intermediate” stage of splicing. Heat maps show the temporal patterns of junction reads spanning the 5’ end (b) and the 3’ end (c) of RP introns and exon-exon junctions (d) of RP genes. Data is centered to mean zero. “T4” or “T5” mark the time point where signals reach the peak. (e) The RNA levels of CK2 subunits, catalytic subunits CKA1 and CKA2, and regulatory subunits CKB1 and CKB2, are plotted across the 16 time points. Time point 4 and 5 are labeled by “T4” and “T5”. (f) RT-qPCRs of 4 Ribi (top panel), 4 RP (middle panel) and 4 RP intron (bottom panel) transcripts across 16 ultra-dense OX time points (1.5~2 min intervals). Signals are normalized by the level at time point 1. 16 values of each transcript are plotted in a smoothed line. The vertical lines in each panel mark the mean peak time of the 4 transcripts and the estimation values are labeled at the right side of the lines.