3960 Nucleic Acids Research, 2006, Vol. 34, No. 14 Figure 3. PWMs for 50 and 30 ss for the U2-type GT–AG and GC–AG intron subtypes, for the five species. We used color-coded vertical bars stacked one over the other to represent the percentage of each nucleotide, Green (A), Blue (C), Black (G) and Red (T); similar logos have been used elsewhere (66). The bars are ordered by their percentages. extended region of conservation than previously identiﬁed (6,22,25). Speciﬁcally, the 1 position on 50ss has a strong preference for T in U12-type GT–AG, and the three exonic positions immediately downstream of the 30ss favor the sequence ATA. We have identiﬁed 671 human U12-type introns, 0.36% of all introns, which includes 314 introns that were hitherto unrecognized as U12-type introns. The GT–AG subtype accounts for 469 introns while 169 introns belong to the AT–AC subtype, and the remaining 33 lack the canonical U12-type intron borders (Table 1). We have identiﬁed 357 of the 404 U12-type introns predicted in the most recent pre- vious survey of U12-type introns (6) while the remainder are from genes not present in the RefSeq collection. Mouse frequencies for U12-type introns are very similar to those for human, consistent with a previous study (24).