Deletions with a breakpoint in exons. Figure 3 shows CytoSure display of aCGH data with probes targeting the PAH gene and EMD. The top panel displays the entire gene view, and the lower panel zooms into the region showing a deletion. Below the CytoSure display are the corresponding exon tracks, and the UCSC RepeatMasker track showing repeat elements at the deletion locus. Vertical red lines mark the breakpoints. At the bottom is an illustration of the PCR design. Primers are shown as arrows. 3a) 801-bp deletion encompassing part of exon 6 of the PAH gene, with electropherogram of sequenced PAH gene across deletion. The breakpoints are shown with vertical red lines. The inserted 11 bases, shown with a green bracket, correspond to the reverse compliment of the bases labeled with a black bracket in the reference sequence across one of the breakpoints. 3b) 367-bp deletion encompassing part of exon 1 and all of exon 2 of the EMD gene, with electropherogram of sequenced EMD gene across deletion. The two-base pair microhomology at the breakpoints is shown within the two vertical red lines that demarcate the breakpoints.