Nucleic Acids Research, 2006, Vol. 34, No. 14 3961 Figure 4. PWMs for 50 and 30 ss for the GT–AG and AT–AC U12-type intron subtypes, in the five species. For C.elegans what is shown is the vestigial U12-type GT–AG splice sites. We identiﬁed 189 U12-type introns in A.thaliana (Table 1), as compared to the 165 U12-type introns derived earlier from a mapping of cDNA/ESTs to the genomic sequence (25). Overall, the fraction (0.24%) of U12-type introns in A.thaliana is smaller than the fraction in mammals. We found 18 U12-type introns in D.melanogaster (Table 1), of which 6 are of AT–AC subtype, 11 are of GT–AG subtype and 1 has GC–AG terminal dinucleotide (see below). A previ- ous study identiﬁed 19 U12-type introns in D.melanogaster (56). We are missing one of their AT–AC introns and three of their GT–AG introns, either due to the genes not being in RefSeq or due to the sequences not having a good BPS. Even though U12-type introns in D.melanogaster correspond to a very small fraction (0.04%) of all introns, in at least some cases they are essential for the development of this organism (57). Strikingly, the relative abundance of each U12 subtype in the ﬂy is very different from that of mammals and plants, in that D.melanogaster has a greater percentage of AT–AC U12-type introns compared to GT–AG U12-type introns than the other three species (33 versus 14–25%). U12-type introns have not been found in C.elegans (8) and recent systematic searches for U12-type splicing factors