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It can happen that the cassette inserts into over 100 sites in the mouse genome, and each insertion has the potential to mutate/alter/knockout the normal regulation or transcription of genes at the insertion locus, so you want a mouse with few integration sites (ideally, only one insertion).
(a) Site-specific primers (solid triangle) were designed according the flanking sequences of each COKC insertion locus.
Finally, the recombineered fosmids are sequenced with primers flanking the insertion locus.
A small deletion of 33 bp was found at the insertion locus.
T2 plants segregated for the constricted fruit characteristic in a 1∶2∶1 ratio, suggesting a single insertion locus.
Likewise, we have identified genetic variations in the putative insertion locus of GimA (between yjiD-yjiE) of ExPEC and fecal E. coli strains.
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PacBio long-read sequencing of the corresponding transcriptome revealed that 155 isoforms are expressed from 54 novel insertion loci, indicating the existence of functional elements in human genomes that were probably undetectable using short reads (Supplementary Table 13).
Sequence data from 22 ISWpi1 insertion loci amplified and sequenced from multiple Wolbachia strains with known phylogenetic relationships were obtained from a previous study [20].
Surprisingly, among the 85 successfully sequenced sites (including 72 SNV loci, 10 insertion loci and 3 deletion loci, while the unsuccessfully sequenced sites were mainly in the PE/PPE/PE-PGRS regions), only 3 SNV loci, 2 insertion loci and 1 deletion loci are the same as the published H37Rv genomic sequence, while the remaining 79 sites are identical to those of H37Ra and CDC1551 (Table S4).
We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria.
Nearly all previously known AluYb8/9 insertion loci were also detected.
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