Table 1.
Potential PRT systems for DEFB4 and 20 further copy variable genes
| Gene/locus | Citation | Closely linked reference paralogue? | Unlinked reference amplicon | |
|---|---|---|---|---|
| Element | Coordinates (March 2006 assembly) | |||
| DEFB4 | (9) | — | HSPDP3 | chr5:21918479–21918925 |
| AMY1A | (26) | AMY2A | ERV1 LTR | chr12:49600721–49601110 |
| C4A | (27) | (C4B) | HERVKC4 | chr19:7769331–7769661 |
| CCL3L1 | (7) | CCL3 | LTR61 | chr10:82018627–82019006 |
| CFHR1 | (28) | CFH | AluSp | chr2:116372603–116372838 |
| CNTNAP3 | (29) | — | LTR8A | chr1:32677895–32678213 |
| CYP2D6 | (25) | CYP2D7P/8P | — | — |
| DEFA1 | (30) | DEFA3 | MLT1A0 LTR | chr7:152825444–152825655 |
| DNMT1 | (31) | — | MLT1E2 | chr7:76691729–76691822 |
| FCGR3 | (32) | — | MRE11 | chr1:47139266–47139433 |
| GSTM1 | (33) | GSTM5 | — | — |
| GSTT1 | (34) | — | FLAM-C | chr1:211834045–211834128 |
| IGL | (35) | — | (DUP) | chr22:30937538–30938261 |
| NPHP1 | (36) | — | (DUP) | chr2:88842054–88842506 |
| OPN1MW | (37) | OPN1LW | MER73 | chr15:91444669–91444891 |
| PGA5 | (38) | PGA3 | (DUP) | chr1:173259630–173259694 |
| PRAMEF8/F9 | (39) | — | L1MA4 | chr11:84670650–84670997 |
| RHD | (40) | RHCE | THE1D | chr11:96087596–96087729 |
| SMN2 | (41) | (SMN1) | LTR19C | chr17:64241628–64241737 |
| PRB1 | (42) | PRB2 | L1PB4 | chr1:96304675–96305394 |
| UGT2B17 | (43) | UGT2B15 | THE1D | chr16:13662429–13662603 |
The final ‘coordinates’ column specifies the reference locus and the placement of primers that should discriminate against other copies in the genome. In column 4, ‘(DUP)’ indicates a duplicon not associated with an identifiable dispersed repeat element. Where there is a potentially useful reference locus closely linked to the test locus, this is shown in the third column; in the specific cases of C4B and SMN2, the paralogues are not distinguished by substitutional divergence.