PPOX MLPA probe set and deletion characterizations. (A). Representation from the UCSC genome browser (Mar2006. NCBI36, hg18) of the protoporphyrinogen (PPOX) gene locus on 1q22-23. Probes included in the 'PPOX MLPA probe set' are represented as vertical red lines. Deletions are represented by horizontal green lines. Repeats identified by Repeat Masker are represented by black boxes, arrows underneath indicate the respective genomic orientation. The colour of the arrow is used to highlight the sequence of the corresponding Alu in the sequence analysis showed below. (B). Sequence analysis of the exon 5–6 deletion junction. Partial alignment of the AluSg within intron 4, the deletion junction sequence and the AluSx within intron 6. Single nucleotide differences between the two Alu repeats are denoted by an asterisk (*). Nucleotides in the region of complete homology are bolded. (C). Sequence analysis of the exon 5–9 deletion junction. Partial alignment of the deletion junction with the AluSg within intron 4 and within intron 9, respectively. The two nucleotides at the junction site are bolded. (D). Partial alignment between the AluSg within intron 4 and the AluSg within intron 9, showing the homology between the two AluSg and their inverted orientation. Vertical lines denote identical nucleotides; (+) and (−) indicate the positive and negative filament, respectively. The junction sequence and the positive filament of intron 9 AluSg are shown together with arrows to facilitate the understanding of the rearrangement.