In a recent study that identified highly evolutionary conserved sequences in 
three genomes of Diptera species we described an ultraconserved element found at 
an internal exon-intron junction of the Drosophila melanogaster homothorax (hth) 
gene that appeared to be involved in the control of hth pre-mRNA splicing. We 
also discussed a possible role of RNA secondary structure at this site in the 
regulation of hth pre-mRNA splicing. In this report we identify a shorter 
evolutionary conserved intronic element within the hth gene that is located 
downstream of the first element and has sequence complementarity to it. We 
demonstrate that intramolecular interactions between these two elements would 
give rise to alternative RNA secondary structures, which in turn may result in 
differential control of homothorax pre-mRNA splicing. We also provide additional 
comparative genomic data from several newly available insect genomes supporting 
our original conclusion that these conserved elements are important in the 
post-transcriptional regulation of homothorax gene expression in Diptera.