Long identical repeats in the mouse gamma 2b switch region and their implications for the mechanism of class switching.

A computer sorting method was used to construct a dictionary by which long identical repeats of nucleotides could be identified and all available sequences of immunoglobulin switch regions were examined. The genomic mouse gamma 2b switch region contains two sets of four long identical repeats comprising 102, 72, 98 and 109 nucleotides respectively. The first is separated from the second by 347 nucleotides which contain the first 46 nucleotides of the 98 nucleotide set as a third partial repeat. These sets overlap the 49-bp separation between identical five nucleotide repeats GAGCT, GGGGT, ACCAG and CGAGC. Switches from S mu to S gamma 2b in and between these sets involve deletions of all or part of a set. Frequencies and locations of short repeats show differences between S mu, S epsilon, and S alpha and the other switch regions; these could determine specificity and locations of switches.