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Fig. s1 A. Multiple sequence alignments of Eif4a3, Rbm8a and Magoh protein sequences from organisms on the left. Consensus sequence is at the bottom with upper case letters indicating identity and lower case letters indicating similarity. Green indicates complete identity across all species, yellow and blue indicate the identical and unique amino acids in the regions with similarity. Identity between human and zebrafish EJC proteins: Eif4a3 (97%), Rbm8a (93%) and Magoh (100%). B. Western blot detecting proteins listed on the left in RNase I-treated zebrafish embryo total extract (TE, lane 1), depleted extract (DE, lanes 2, 4 and 6) and immunoprecipitates (IP, lanes 3, 5 and 7) with the Rbm8a antibody. Detergents supplemented to increase IP stringency are indicated on top of each lane. Optimized IP condition used in S1C is indicated by the dashed red box. C. Autoradiogram of γ32P 5′-end labeled RNAs from anti-Rbm8a RIP elution (lane 4) as well as indicated size-markers which include the low-molecular weight single-stranded DNA ladder (lane 1), 0.1 pmol 28 nt synthetic RNA (lane 2) and 100 bp DNA ladder (lane 3). D. Scatter plots comparing read counts for each gene in a pair of RIP-Seq replicates. The replicates (Rep1, Rep2, and Rep3) are indicated on the x- and y-axes. A pseudocount of 0.0001 was added to all genic read counts before log2 transformation. Pearson correlation coefficient (r) and p-value for the correlation test for each comparison is on the top left of each plot. E. Genome browser screenshots showing read coverage of Rbm8a RIP-Seq (only Rep 3, the deepest replicate is shown) in green and RNA-Seq in gray of select highly-expressed genes, krt4, eef2b, eif4g1a, and hist1h4l (intron-less gene).