Figure 4. Degenerate loxP sites are abundant in the mouse genome.

Flow chart of genome-wide search for degenerate loxP sites in mouse. Degenerate loxP site sequence was based on published Cre binding and recombination data [6,34]. This sequence is a conservative estimate for maximum-tolerated mismatches by Cre. Note that a search for loxP sites harboring just two mismatches identified 12 endogenous sites while a search for loxP sites harboring five mismatches identified more than 7500 endogenous sites. Transcriptionally relevant genes for the heart were identified by intersecting the list of loxP-like containing genes with both the publically available University of Washington (UW) ENCODE dataset and transcriptome data from [35].