longitudinals lacking (lola) is a complex Drosophila gene encoding at least 20 protein isoforms,each bearing the same N-terminal constant region linked to a different C-terminal variable region. Different isoforms specify different aspects of axon growth and guidance. We show here that lola mRNAs are generated by alternative trans-splicing of exons sequentially encoded by the same DNA strand. Chromosomal pairing facilitates interallelic trans-splicing,allowing complementation between mutations in the constant and those in the variable exons. We demonstrate that at least one variable exon is transcribed from its own promoter,and trans-spliced to the constant exons transcribed separately.