Oncogenic mutations in apc cause widespread splice variations including mRNAs encoding regulators of cell migration: (A) The MAJIQ analysis of splicing variations, represented as changes in fractions spliced in (dPSI) for each splicing event filtered for dPSI ≥ 0.20 with a probability >0.90, identified 340 splicing variations in apcmcr larvae. (B) The frequency of local splice variants, including exon skipping (ES), alternative 3′ splice site (A3SS), alternative 5′ splice site (A5SS), and complex splice variants. (C) The GO analysis of alternative spliced genes. (D) Voila output showing alternative splicing of sema3f (“a” allele). Red line indicates splicing from exon 5 to exon 6 and blue line indicates splicing from exon 5 to exon 7. Violin plots show the frequency of each splice form in WT (left) and apcmcr mutants (right) at 48 hpf. (E). Diagram showing unspliced, nascent mRNA from exon 5–exon 8. Orange arrows indicate PCR primers for “long” splice form that includes exon 6; green arrows show the primer pair for constitutively spliced exons 7 and 8, used to measure all mRNA isoforms. Histogram shows relative abundance based on RT-qPCR for the “long” splice form containing exon 6 in WT and apcmcr mutant larvae at 48 hpf. p < 0.0001 (Student’s paired t-test, n = 3 replicates).
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