Comparative sequence analysis defines the HSA 21:22 junction on mouse chromosome 10 (MMU 10). (a) Comparative Genomic Analysis Tools (CGAT) analysis (http://inertia.bs.jhmi.edu/roger/CGAT/CGAT.html) of the 275-kb mouse reference sequence relative to sequence compiled from HSA 21 and HSA 22 databases (see Table 1). Weakest sequence matches (>62% across 100 bp) are indicated by yellow blocks, stronger matches by progressively darker colors. The reverse complement of the HSA 22 sequence is shown to demonstrate the head-to-tail orientation of Slc5a4b on MMU 10. The positions of sequenced mouse P1 artificial chromosomes are indicated. An interactive web-site supplement with further detail can be viewed athttp://inertia.bs.jhmi.edu/roger. (b) Annotation of mouse sequence across the breakpoint region precisely defines two chromosomal junctions (brackets). HSA 21 sequence is expanded relative to mouse because of insertion of repetitive DNA elements; dashed lines connect mouse sequence blocks conserved with HSA 21. Boxed regions denote conserved sequence. Transcripts are indicated. Orientations of the duplicated SLC5A4 homologs in mouse (green blocks) are indicated by arrows. (c) Both junction regions are composed primarily of repetitive sequences. Entrez accession numbers are given for ESTs.