Recently, we identified a large number of ultraconserved (uc) sequences in 
noncoding regions of human, mouse, and rat genomes that appear to be essential 
for vertebrate and amniote ontogeny. Here, we used similar methods to identify 
ultraconserved genomic regions between the insect species Drosophila 
melanogaster and Drosophila pseudoobscura, as well as the more distantly related 
Anopheles gambiae. As with vertebrates, ultraconserved sequences in insects 
appear to occur primarily in intergenic and intronic sequences, and at 
intron-exon junctions. The sequences are significantly associated with genes 
encoding developmental regulators and transcription factors, but are less 
frequent and are smaller in size than in vertebrates. The longest identical, 
nongapped orthologous match between the three genomes was found within the 
homothorax (hth) gene. This sequence spans an internal exon-intron junction, 
with the majority located within the intron, and is predicted to form a highly 
stable stem-loop RNA structure. Real-time quantitative PCR analysis of different 
hth splice isoforms and Northern blotting showed that the conserved element is 
associated with a high incidence of intron retention in hth pre-mRNA, suggesting 
that the conserved intronic element is critically important in the 
post-transcriptional regulation of hth expression in Diptera.