Alternative splicing of two leading exons partitions promoter activity between the coding regions of the maize homeobox gene Zmhox1a and Trap (transposon-associated protein)

Elucidation of the exon/intron structure of the maize Zmhox1a homeobox gene revealed two small introns in the homeodomain. Both intron positions are c onserved in animal counterparts encoded in the metazoan homeobox gene clust ers and thus may indicate a common ancestor. The transcription start of the Zmhox1a gene has been localized far from the protein-coding region. Two di stal untranslated leading exons are alternatively spliced to either the Zmh ox1a coding exons or an unrelated open reading frame comprising two exons l ocated internally of the large second Zmhox1a intron. Due to significant ho mology to the C-terminus of the Mutator transposase this alternative gene p roduct was named Trap (transposon-associated protein). Splice site selectio n may involve two sequence elements conserved at the splice acceptor sites in front of the Zmhox1a and Trap protein-coding regions. The translation of a mRNA species devoid of exon 3 which encodes the Zmhox1a transcription st art codon may give rise to an N-terminal deletion polypeptide, Delta Zmhox1 a. Ectopic expression experiments in transgenic tobacco indicate a putative function distinct from the full-length Zmhox1a protein.