Fig. 3
From: Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions
Genomic CLCNKA/CLCNKB locus and the common CLCNKA 3′ UTR sequence transposition haplotype on chromosome 1p36.13. The genomic environment surrounding the CLCNKA/CLCNKB gene locus contains two highly homologous genomic regions (A and A’, sequence homology approx. 80 %). A and A’ are indicated by the yellow and orange boxes, respectively. The homologous region A stretches over 20.157 bp from chr1:16,346,920-16,367,077 (GRCh37/Hg19), region A’ stretches over 20.827 bp from chr1:16,368,759-16,389,585 (GRCh37/Hg19). The exonic sequence homology of CLCNKA and CLCNKB is 94% [8]. In the alternative transposition haplotype, a 2.2–3-kb large DNA fragment of the CLCNKA 3′ UTR (small orange box, arrow head) is replaced by the homologous fragment from the 3′ UTR of CLCNKB (small orange box, arrow tail), resulting in the loss of the genomic material downstream of CLCNKA and an extra copy of the DNA fragment duplicated from the CLCNKB 3′ UTR. Gene length and orientation of CLCNKA and CLCNKB are indicated by the grey arrows. Exons are indicated as grey bars