Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription

One of the widely used applications of the popular Cre-loxP method for
targeted recombination is the permanent activation of marker genes, such
as reporter genes or antibiotic resistance genes, by excision of a
preceding transcriptional stop signal. The STOP cassette consists of three
identical SV40-derived poly(A) signal repeats and is flanked by two loxP
sites. We found that in addition to complete loxP-mediated recombination,
limiting levels of the Cre recombinase also cause incomplete recombination
of the STOP cassette. Partial recombination leads to the loss of only one
or two of the three identical poly(A) repeats with recombination
breakpoints always precisely matching the end/start of each poly(A) signal
repeat without any relevant similarity to the canonical or known cryptic
loxP sequences, suggesting that this type of Cre-mediated recombination is
loxP-independent. Incomplete deletion of the STOP cassette results in
partial read-through transcription, explaining at least some of the
variability often observed in marker gene expression from an otherwise
identical locus.