Figure 3

TE3 and TE8b are inserted within a structural context in simians. Coloured bars indicate MEME-identified motifs; black lines indicate featureless sequences. The mouse and rat sequences used for motif identification were obtained using BLAT to search human exon 3 and exon 8 against the mouse and rat genomes. (A) Four motifs can be identified in mammalian and prosimian exon 3. The sequences covering the first two motifs are highly conserved. TE3 corresponds to bp 80–265 of CM3. The UCSC Genome Browser indicates that in simians, the MEA1A transposon crosses the boundary between exon 3 and intron 3; and a BLAT genome search indicates that the 300 bp at the 5′ end of intron 3 exist only in simians. The insertion of the MEA1A transposon apparently provides the GU splicing signal for exon 3. (B) MEME identifies multiple motifs at the TE8b insertion site. TE8a is absent in some mammals, but the gap corresponding to TE8a in these mammals is smaller than TE8a, and these mammalian exon 8 sequences contain several motifs found in TE8a.