Region of the BTNL gene cluster containing the BTNL8_BTNL3-del allele and sequence structure of deletion. (A) The figure shows 200-kb of the genomic region on human chromosome 5. The expected transcripts of the three genes in this region are shown with their transcript orientation. The CNV region, which is indicated by the dashed line, removes 56-kb, from intron four of BTNL8 to intron four of BTNL3. The black-yellow dashed box represents the SD shared between BTNL8 and BTNL3. PCR assays were designed to distinguish between non-deleted and deleted alleles (short arrows show position of PCR oligonucleotides). The PCR assay amplifies a ~420-bp product for the non-deleted allele, and a ~340-bp fragment for the deleted allele (bottom). Results from the PCR assay are shown for seven LCLs. (B) The deleted allele shows long homologous stretches at its breakpoints (~1.6-kb sequence blocks of 98% identity, of which 300-bp are shown aligned here) and thus probably results from non-allelic homologous recombination (NAHR). The “cross-over” occurred somewhere within 112-bp of identical sequence indicated as “NAHR-region”.