Predicted introns in novel protein-coding genes. (A) A predicted intron is consistent with a two-exon coding gene predicted by CONTRAST (Gross et al. 2007). (B) Several predicted introns overlap a coding gene model predicted by NSCAN (Gross and Brent 2006). While the two downstream introns are in agreement with the NSCAN predictions, the two upstream introns are not. However, a BLASTX run of the entire region excluding the four introns (represents the spliced transcript) gives a perfect hit with a D. melanogaster protein (SwissProt Q6IL55) as well as hits in eight other Drosophila species. The positions of the four introns and the NSCAN predicted start codon in the Q6IL55 protein sequence are indicated as dashed lines.