Figure 2.

A canonical V-J rearrangement of the kappa immunoglobulin light chain locus of the LCL. The rearrangement occurred by inversion of a >1 Mb segment of 2p11.2. A schematic of the initial allele and the resulting product of the recombination are shown at the top. V and J segments are shown as gray boxes; recombination signal sequences (RSSs) are shown with arrows and marked with their corresponding genome coordinates. Arrow orientation reflects the direction of the RSS (heptamer-to-nonamer), filled arrows illustrate RSS with 23 bp (two turn) spacers, and open arrows illustrate 12 bp (one turn) spacers. The centromere side is marked with a circle, not distanced to scale. The RSS-RSS junction was detected by the sequencing strategy (right lower panel); blue reads denote pairs mapping across the junction. V and J segments are shown in red below the reads. The rearrangement was confirmed by Sanger sequencing, with the recovered sequence matching the junction spanning sequence found with a split-reads (left lower panel, middle sequence). The split-reads sequence is shown aligned to the two sequences present in the reference genome (hg19). The RSS heptamers and nonamers are shown in black. The IGKJ1 RSS is shown reverse complemented while the IGKV1D-43 is shown in proper 5' to 3' orientation, reflecting the nature of a split-reads over an inversion.