EcR³¹/EcR⁹⁹ third instar larvae have slightly fewer Burs-immunoreactive CCAP neurons compared to wild-type controls.

EcR³¹/EcR⁹⁹ mutants, that lack EcR-B isoforms, exhibit significant differences to EcR^B2.Scer\UAS or EcR^B1.Scer\UAS rescued lines. Complete lack of programmed cell death is observed in 18% of the EcR-B mutants central nervous system, and partial cell death in the remaining 82% of specimens. Overall, approximately 75% of Crz-expressing ventral nerve cord neurons do not undergo programmed cell death in EcR-B mutants.

Late stage EcR⁹⁹/EcR³¹ larvae fail to pupariate normally, but become stationary at the end of the third larval instar and later complete apolysis of their larval cuticle. Pruning of the larval Tv-neurons is inhibited in these animals.

Most EcR⁹⁹/EcR^M554fs animals fail to survive to the second larval instar stage and few mutant animals survive to the 3rd larval instar stage. 65-80% of larvae arrested prior to the second instar stage have both 1st and 2nd instar mouth hooks, while those arrested prior to the third instar stage have both 2nd and 3rd instar mouth hooks. The changes in CNS morphology seen in wild-type animals between the time of pupariation and head eversion are seen in homozygotes arrested at late stages of development.