The P element is a class II transposon, and moves by a DNA-based "cut and paste" mechanism. The recognition sequence comprises four exons separated by three introns. Complete splicing of the introns produces the transposase enzyme, while alternative partial splicing of introns 1 and 2, leaving only intron 3 in the mRNA transcript, encodes the P element repressor. The complete, autonomous P element encodes a transposase enzyme, which recognizes the 31-bp terminal inverted repeats at either end of the P element and catalyzes P element excision and re-insertion. The complete element is 2,907 bp in length; non-autonomous P elements contain an internal deletion of varying length which abolishes transposase production, but such elements can still be mobilized if a functional transposase is encoded elsewhere in the genome. P element insertion and subsequent excision necessarily leaves behind 8-bp direct repeats at the excision site; thus the presence of such repeats is indicative of previous P element activity.
All P elements have a canonical structure containing 31-bp terminal inverted repeats and 11-bp internal inverted repeats located at the THAP domain of the transposase. The shortest and longest P elements are non-autonomous elements. The longest P elements encode transposase needed for transposition. The same sequence that encodes the transposase also encodes a suppressor of transposition, which accumulates in the cytoplasm during the development of cells. Thus, in a cross of a P or M male with a P female, the female cytoplasm contains the suppressor, which binds to any P elements and prevents their transposition.