Knockdown of sema3E resulted in CHARGE‐like phenotypes. A, The head development in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA at 3 dpf. Red arrows indicate the flattened head in sema3E morphants. B, The eye development in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA at 48 hpf. Red arrows indicate the ocular tissue defect in sema3E morphants. C, The development of the otic vesicle in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA. A red asterisk indicates the absence of an otolith, and a red dashed circle denotes an abnormally positioned otolith. D, Cranial cartilage development in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA at 5 dpf. Red arrows indicate the malformations in the auditory ossicles and ceratobranchials. Eth, ethmoid plate; mk, Meckel's cartilage; pty, pterygoid process of the quadrate; aud, auditory ossicles; ch, ceratohyal; qu, quadrate; cb, ceratobranchials. E, Cranial nerve development in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA at 48 hpf. Red asterisks indicate the shortened branches of vagal (nX) motor neurons, and red arrows denote the aberrant medio‐lateral positioning and cell‐to‐cell spacing of the trigeminal (nV) and facial (nVII) branchiomotor neurons. F, Statistical analysis of the CHARGE‐like phenotypes in control, sema3E morphants and sema3E morphants co‐injected with sema3E mRNA. Numbers above the columns represent the total number of embryos in each experiment. ***P < 0.001, (n = 3)