Abstract: Through regulating the post-transcriptional maturation of UsnRNAs (U-rich small nuclear RNAs), integrator complex has an effect on the intron splicing of pre-mRNA. Therefore, integrator complex plays an important role in the production of mature mRNA. However, the regulation and developmental functions of integrator complex are poorly understood in vertebrates. In this study, zebrafish (Danio rerio) was used to generate the ints12 knockout model by CRISPR/Cas9, and two homozygous lines were generated with different frame-shifts. Observation on the misprocessing of UsnRNA 3′ ends in zygotic mutant of ints12 (Zints12) was conducted through real-time quantitative PCR analysis. When compared with the control fish, the overall growth of Zints12 was largely retarded, and the Zints12 population was all-male. Further studies showed that cell proliferation was significantly interfered, and the level of introns retention of ints12 transcripts was significantly increased in Zints12, suggesting an " auto-regulation loop” in the splicing regulation by ints12. Overall, we obtained homozygous mutants of zebrafish ints12 by gene knockout technology and revealed that zebrafish ints12 regulates UsnRNA 3′-box processing to exert various effects on early embryonic development and body growth.