Catalyzes the desaturation of long-chain acyl-CoAs to 2-trans-enoyl-CoAs. Active on substrates longer than C14 and mostly with C18-CoA. Activity on long-chain mono-unsaturated substrates is double than with the corresponding saturated substrates. a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2 Binds 1 FAD per subunit. Homodimer. A number of isoforms are produced. According to EST sequences. Expressed mainly in flowers and young seedlings. Lower expression in roots, leaves and bracts. Induced by seed imbibition with a peak at day 2 and then declines steadily until day 8. Induced by dehydration and abscisic acid (ABA). Belongs to the acyl-CoA oxidase family.