Fig. 4.

Dynamic changes of 3′UTR length. a Box plots of the RUD of the genes with APA during retinal development. Two-tailed pairwise t test was performed and revealed significant differences between all neighboring stages (***p < 0.001). b Number of the lengthened (blue)/shortened (red) genes that vary by 100 nt between E13.5 and later stages. c–f qRT-PCR validation of representative lengthened (Bcat, c, d) and shortened (Aak1, e, f) genes caused by differential usage of alternative pA sites. The height of each wiggle plot represents the number of PA-seq tags for the identified pA site (P proximal, D distal) at each developmental stage (c, e). The location of primer pairs used for PCR validation is indicated (c, e). The histograms represent the amount ratio of proximal/distal regions of the RNA transcript determined by qRT-PCR assays of retinal samples at the indicated developmental stages (d, f)