Figure 1

A. Dotplot analysis comparing repeat A to repeats B to H using the NCBI m33 mouse assembly (freeze May 27, 2004, strain C57BL/6J). Black lines represent regions of identity interspersed with LINEs (horizontal pink lines). The orientation and approximate size of each repeat unit is presented as black arrows. The relative position and orientation of Rhox1 (green lines, black arrowhead) and Rhox2, 3 and 4 (blue lines, white arrowhead) and Rhox5 (which is upstream of this region, black arrowhead) are shown. The X chromosome co-ordinates are provided below the dotplot. B. BLAST analysis comparing genomic sequence of each repeat to all others. LINE repeats and rearrangements were not added. Top row represents a comparison of repeat A to B-H, second row repeat B to C-H and so on. C. Southern Blot analysis. CGR8 ES cell genomic DNA digested with Asp718 (lane 1) and HindIII (lane2) and hybridised to Rhox4 exon 1 and intron 1 probe. Multiple bands can be seen with both digests (arrowed) of approximately 20, 13, 10 and 5 kb (HindIII) and 23, 18, 13, 10, and 8 kb (Asp718). Mus domesticus (lane 3) and Mus spretus (lane 4) genomic DNA digested with HindIII and hybridised to a Rhox4 exon 2 probe. Fragment sizes common to the Mus musculus (ES cells) and Mus domesticus are arrowed. Additional bands are predicted to be due to the differences between the probes used. Positions of size standards are provided in kilobases.