Figure 2

O2 cRS are found at multiple locations within mouse Vκ gene segments. RIC₂₃ was computed for all 39-bp sequences beginning with a CA-dinucleotide in 135 mouse Vκ gene segments. RIC₂₃scores are plotted for those 39-bp sequences in O2 and with RIC₂₃>-65. RIC₂₃ is shown on the Y-axis, and nucleotide position (IMGT numbering) within the gene segment is shown on the X-axis. Complementarity determining regions (CDR) are demarcated by vertical lines. The red rectangles indicate RIC scores located at the sites of cRS cleaved in vivo. The horizontal lines in FR1 indicate the location of the LM-PCR primers. Note that, because of the primer locations, cleavage events in FR1 are unlikely to be detected in our assay.