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Fig. s4 A. Histogram depicting the frequency of all zebrafish 3′UI transcripts in Ensembl GRCz10 (with APPRIS annotation) as a measure of the distance of the 3′UI from the stop codon. Data are shown in 5 nts bins and bins beyond 500 nts are not shown. Bins of proximal 3′UI genes are in blue and distal 3′UI bins are in gray. Inset: Histogram of all zebrafish proximal 3′UI transcripts binned by 1 nt. B. PANTHER14.0 [87] gene ontology (GO) term enrichment analysis of proximal 3′UI-containing genes (top, shades of blue) and all 3′UI-containing genes (bottom, shades of gray). All significant terms (Benjamini-Hochberg corrected p-value < 0.05) are shown for each set. C. A scatter plot showing gene-level fold change (FC) for transcripts with proximal 3′UI (dark blue: FC > 1.5 and light blue: FC < 1.5) and distal 3′UI (black: FC > 1.5 and gray: FC < 1.5) in rbm8a mutant embryos at 21 hpf compared to wild-type siblings. Genes encircled in red also contain a uORF as determined from a previously published dataset (see Materials and Methods). D. A scatter plot as in C showing fold changes of 3′UI-containing genes for 12 hpf upf1 morphants compared to wild-type control embryos. E. Integrated genome browser (IGV) screenshots of Sashimi plots showing RNA-seq reads observed for foxo3b, phlda2 and cdkn1ba in four zebrafish 24 hpf whole embryo RNA-seq datasets (as labeled on figure in different colors) obtained from the DanioCode consortium. Range of the number of reads mapping to the genes are indicated to the left of each track in black. Number of junction reads are indicated at the spliced junction in the color corresponding to the specific track. In case of foxo3b, due to the length of the second intron the screenshots of the first two and the last two exons are shown separately. F. Empirical CDF plot showing the fold changes in magoh mutants (21 hpf) of genes upregulated that contain a proximal (green) or distal (light purple) 3′UI or intron-less genes (black). Genes that also contained an uORF were excluded from analysis. Kolmogorov-Smirnov (KS) test p-value for differences in fold changes between the two groups is indicated on the bottom right. G. CDF plot as in F showing the fold changes in rbm8a mutants (27 hpf) of genes upregulated that contain a proximal (green) or distal (light purple) 3′UI or intron-less genes (black). Kolmogorov-Smirnov (KS) test p-value for differences in fold changes between the two groups is indicated on the bottom right.