Figure 3

Gene deletions within the cB01 motif may have involved MER repeat elements. (A) The cB01-del9 structure derived from DNA source HIP09410M, (B) The cB01-del10 structure derived from DNA source HIP05435M, and (C) The cB01-del3 structure derived from DNA source IHW30048M. For all, sequences were compared with a reference cB01 motif consensus sequence compiled from 6 previously sequenced haplotypes[9]. Red lines represent the extent and portions of the mutant haplotypes that were sequenced relative to the cB01 motif, with the sequences absent represented with thin lines inserted for alignment. Immediately beneath each cartoon, each mutant haplotype sequence was aligned against two groups of wild-type sequences (outlined in blue and pink) encompassing the ends of the predicted deletion point in each mutant. The genes or intergene regions being aligned are listed vertically at the left and the derivative cell lines and corresponding haplotype names are listed within the blue or pink shading. The patterns of mismatches (black hatches) indicate the positions of minor allele SNPs among the aligned sequences. Immediately beneath, the mutant haplotype is aligned with corresponding SNP markings and blue and pink shading indicating the sequence origin, above a similarly color-coded cartoon depicting the gene structure where appropriate. The positions of repeat elements within each pair of regions flanking the deletion are indicated with the aligned sequences highlighted in orange shading above the name of the repeat element. In the two scales, the upper for the genomic region and the lower for the gene sequences, the lighter shading in the green bar indicates the extent of sequence divergence among the aligned sequences. Supporting phylogenetic and breakpoint analyses are presented in supplementary Additional file2: Figure S2.