Various sequences within Tag1, the endogenous transposon of Arabidopsis, were examined to determine how Tag1 excision and expression are regulated. The 5' intron for the major 2.3-kb Tag1 transcript was found to be critical for the accumulation of Tag1 transcripts and for high rates of somatic excision. This was true for the autonomous element in cauliflower mosaic virus 35S-Tag1-beta-glucuronidase constructs and for a two-component system using the 35S promoter to produce Tag1 transposase and a beta-glucuronidase::dTag1 marker construct to score for excision. The 3' introns of Tag1, although not needed for high transposase expression in primary transgenic plants, were important for maintaining high levels of somatic excision and accumulation of the major but not the minor Tag1 transcripts in subsequent generations. With both 5' and 3' introns present, exchanging the 5' promoter region of Tag1 with the 35S promoter did not affect the timing of Tag1 excision significantly, but it did disrupt germinal excision. Removal of the 5' intron did not abolish germinal excision activity, however. These results indicate that somatic and germinal excision of Tag1 are differentially controlled, with the 5' promoter region being critical for germinal excision activity and the 5' intron playing an important role for somatic excision, possibly via intron-mediated enhancement.