A large palindromic segmental duplication on mouse chromosome 12 marks an evolutionarily fragile genomic interval

Palindromic segmental duplications (SDs), in which duplicated sequence arms flank a central spacer in inverted orientation, are among the most structurally consequential configurations in mammalian genomes, yet their occurrence in the mouse genome remains poorly characterized. Here, SD12A1 is systematically characterized as a large palindromic SD locus on mouse chromosome 12 (chr12:17.95-24.51 Mb, mm10).

Analysis of 9,263 UCSC mm10 pairwise SD entries, integrated with de novo CpG island (CGI) profiling, directional sequence matching, block-level sequence identity analysis, and mouse-rat-human synteny comparison, showed that SD12A1 comprises two SD-rich arms flanking a 530 kb SD-depleted central gap. Inter-arm SD pairs were predominantly inverted, whereas intra-arm pairs were predominantly direct. Reverse-complement CGI analysis identified 18 left-arm CGIs with high-confidence right-arm matches (best-match RC cosine similarity > 0.75), and directional matching of 50 bp Block 1 queries showed forward hits enriched in the left arm and reverse-complement hits enriched in the right arm. Cross-arm sequence identity was broadly uniform (median 93.0%; median Jukes-Cantor distance = 0.0730), with nearly identical within-arm and cross-arm divergence distributions (median JC 0.0747 vs. 0.0735), providing no evidence for ongoing inter-arm gene conversion. Two block pairs showed substantially higher sequence identity than the main palindrome bulk (B03<-> B17, 98.6%; B06<-> B20, 97.1%), suggesting more recent localized duplication. Three-species synteny comparison identified a 7.1 Mb orientation-discordant interval, shared by mouse and rat relative to human, that encompasses SD12A1 and corresponds to a rearrangement-prone human orthologous region.

These findings establish SD12A1 as a mouse-specific palindromic manifestation of an evolutionarily labile genomic interval and provide a reference-based framework for recognizing large autosomal palindromic SD architecture in mammalian genomes.