Novel transcripts from the Ultrabithorax domain of the bithorax complex

We present a detailed analysis of the transcriptional products of the bithoraxoid (bxd) region of the Ultrabithorax domain in the bithorax complex of Drosophila melanogaster. This region is transcribed twice during development: between 3 and 6 hr of embryogenesis, a set of early transcripts, 1.1 to 1.3 kb in size, is synthesized; from the midthird larval instar through the adult stages, a late 0.8-kb transcript is synthesized. We have sequenced five cloned cDNAs representing early transcripts and three cDNAs representing the late transcript and have located their exons within the 40 kb of DNA comprising the bxd region. S1 nuclease protection and primer extension of both the early and late transcripts were used to further elucidate their structure. The early RNAs are produced by complex differential splicing of a series of exons derived from a 26-kb primary transcript. Curiously, these RNAs do not possess significant protein coding potential. The late bxd RNA comprises a single exon transcribed from an intronic region of the early transcription unit. This RNA, by contrast, possesses excellent coding potential and, if translated, would yield a 101-amino-acid polypeptide.