Genomic characterization of the mouse Dxz4 locus. (a) Ideograms of the human (HSAX) and mouse (MMUX) X chromosomes. Regions relevant to the search for Dxz4 are expanded to the right of the chromosome. Genes are represented by solid arrows pointing in the direction of transcription. Length represents extent of the gene. Human DXZ4 is represented as the red box. The location of the putative Dxz4 homolog and the downstream tandem repeat are highlighted proximal to mouse Pls3 as red and blue boxes, respectively. (b) Pair-wise alignment of approximately 360 kb (scale in kilobases given on the y-axis) downstream of the mouse Agtr2 gene (20.7 to 21.1 Mb, mm9, indicated for the x-axis). Sequence similarity is shown in blue with inverted similarity in yellow. Black bars on the top and left edges indicate extensive repeats. (c) Pair-wise alignment of approximately 240 kb encompassing the Pls3 gene (72.9 to 73.1 Mb, mm9) and distal sequence. (d) Pairwise alignment of the 36-kb mouse Dxz4 array. The block arrows on the top and left edges represent Dxz4 tandem repeat monomers. (e) Pairwise alignment of the largest and smallest Dxz4 monomers (block arrows on top and left edges) highlighting the existence of an internal variable number tandem repeat (VNTR) represented by the black arrows above the blue boxes. Perpendicular black lines within the monomers indicate the locations of simple repeats. (f) Extended DNA fiber fluorescence in situ hybridization (FISH) of the Dxz4 array. At the top is a schematic of a single Dxz4 monomer. The regions of Dxz4 used to generate direct-labeled FISH probes are indicated to the left (red) and right (green) of the VNTR (blue). Immediately below are examples of hybridization results. All pairwise alignments used the DNA sequence compared with a repeat-masked version of itself with the exception of that shown in (c), which compared non-repeat-masked sequences to show the inverted satellite repeat. Alignments were all made with YASS , and the output was pseudocolored to avoid red-green.
Horakova et al. Genome Biology 2012 13:R70 doi:10.1186/gb-2012-13-8-r70