Catalyzes the desaturation of short-chain acyl-CoAs to 2-trans-enoyl-CoAs (PubMed:10212254, PubMed:15743450). Active on butyryl-CoA (C4), hexanoyl-CoA (C6), and octanoyl-CoA (C8) (PubMed:10212254). Has no activity as acyl-CoA dehydrogenase or on crotonyl-CoA (an unsaturated C4:1 carbocyclic ester) or glutaryl-CoA (a dicarboxylic ester) (PubMed:10212254). Peroxisomal fatty acid beta-oxidation is essential for embryo development (PubMed:12682048). Acts as a suppressor of transcriptional silencing (PubMed:31064880). Required for nuclear histone acetylation and DNA demethylation at some endogenous genomic loci (PubMed:31064880). a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2 butanoyl-CoA + O2 = (2E)-butenoyl-CoA + H2O2 hexanoyl-CoA + O2 = (2E)-hexenoyl-CoA + H2O2 Optimum pH is 8.5-9.0. Homotetramer. Particularly abundant in etiolated cotyledons. Also present in flowers, roots and siliques, but not detected in green cotyledons, rosette leaves and stems. Induced by seed imbibition with a peak at day 5 to 7. Decreases after illumination but still detectable 5 days after illumination (PubMed:10212254). Induced by dehydration and abscisic acid (ABA). Belongs to the acyl-CoA dehydrogenase family.