Discovery of a Gaijin -like MITE in the 4th intron of PLRRP gene. (a) Expression profile of PLRRP gene in different organs of two rice cultivars, Zhonghua 11 and Xiushui 11. RNA samples were extracted from callus (lane 1), root (lane 2), stem (lane 3), leaf (lane 4) and embryo (lane 5) and amplified by the AS primer pair. The size of the lower molecular weight RT-PCR amplicons of Zhonghua 11 (Z1) and Xiushui 11 (X1) were similar. However, the size of the higher molecular weight amplicons in Xiushui 11 (X 2) was bigger than Zhonghua 11 (Z2). (b) DNA polymorphism of PLRRP gene. gDNAs were extracted from rice cultivars and amplified by the AS primer pair. The molecular weight of PCR amplicon from Zhonghua 11 (Zg) was smaller than Xiushui 11 (Xg). (c) PLRRP gene and its spliced mRNA transcripts. PLRRP gene (Zg, thick black lines) was composed of 9 exons (white and grey boxes) and 8 introns (thin black lines). The additional fragment at the 4th intron was indicated with vertical strip lines and the two additional fragments, 8 bp ATTAATAT fragment and a 146 bp fragment (mGing) were illustrated in the pictograph. Amplicons of Zhonghua 11 (Z1, Z2 and Zg) and Xiushui 11 (X1, X 2 and Xg) from part (a) and part (b) were indicated. (d) Sequence analysis of PLRRP gene in Xiushui 11. Underlines showed the AS primer pair sequences. Double-underlines and arrows indicated the ATA duplication and the TIRs, respectively. The position of ATTAATAT sequence was boxed. Capital letters revealed the 146 bp fragment. (e) Sequence alignment of mGing against Gaijin. The Gaijin sequence was obtained from Repbase. The alignment was made using the online ClustalW program with the different residue at each position highlighted. The arrows indicated the mGing TD primers.