The alternative exon splicing model was implemented in a program called ExAlt and tested on a target genome – Drosophila melanogaster using three informant species: Drosophila simulans, Drosophila yakuba, and Drosophila erecta. This study focuses on the three most closely related species to D. melanogaster (with available genomic data) to avoid using inaccurate multiple sequence alignments, which can occur when dealing with more distantly related species. Testing is based on 1339 D. melanogaster exons from 1160 gene loci. 572 of the original 600 alternatively spliced test exons (95%) were aligned to at least one of the three informant species and 767 of 777 constitutive exons (99%) were aligned to at least one of the three informant species. As an option, ExAlt predicts exons in the absence of alignment evidence; however, the candidate exons with no cross-species sequence conservation left too small a data set (3% = 38/1377) to make meaningful comparisons between performance on exons with and without detectable cross-species conservation. Therefore, the remaining 97% of the exons showing some cross-species sequence conservation were selected to evaluate the impact of sequence conservation on prediction performance, with the understanding that additional work will be needed (as more data becomes available) to analyze prediction performance in the non-conserved exons.