Table 3.
Repeat elements as a percentage of genomic sequence within the intervening sub-regions and the entire MHC region from HLA-F to HLA-DPA3.
| Block length bp | Alpha | FW1 | Kappa | FW2 | Beta | Class III | Class II | MHC all |
|---|---|---|---|---|---|---|---|---|
| 305,935 | 331,401 | 147,926 | 736,590 | 281,217 | 911,080 | 714,616 | 3,428,765 | |
| Repeat element (%) | ||||||||
| SINEs | 6.61 | 12.54 | 9.01 | 26.24 | 7.56 | 21.75 | 9.88 | 16.26 |
| ALUs | 6.01 | 10.24 | 7.96 | 24.09 | 6.89 | 19.83 | 8.22 | 14.59 |
| MIRs | 0.60 | 2.30 | 1.05 | 2.11 | 0.63 | 1.92 | 1.65 | 1.66 |
| LINEs | 19.70 | 26.25 | 30.81 | 11.43 | 26.32 | 12.45 | 26.12 | 18.92 |
| LINE1 (L1) | 15.91 | 21.34 | 29.77 | 6.83 | 24.00 | 8.60 | 23.00 | 15.23 |
| LINE2 (L2) | 3.70 | 4.52 | 1.04 | 3.91 | 2.27 | 3.64 | 2.84 | 3.37 |
| L3/CR1 | 0.09 | 0.21 | 0.00 | 0.32 | 0.05 | 0.21 | 0.24 | 0.20 |
| LTR | 24.77 | 9.36 | 12.48 | 11.88 | 23.05 | 4.02 | 14.05 | 12.16 |
| ERVL | 13.21 | 1.86 | 2.86 | 3.35 | 11.63 | 0.33 | 1.50 | 3.57 |
| ERVL-MaLRs | 7.03 | 4.93 | 4.83 | 2.09 | 2.66 | 0.63 | 3.25 | 2.84 |
| ERV-classI | 1.98 | 2.39 | 3.71 | 5.70 | 6.41 | 1.59 | 5.50 | 3.89 |
| ERV-classII | 2.57 | 0.00 | 1.08 | 0.41 | 2.36 | 1.39 | 3.62 | 1.68 |
| DNA elements | 5.50 | 4.60 | 3.23 | 2.18 | 1.89 | 1.84 | 4.01 | 3.00 |
| hAT-Charlie | 5.04 | 2.14 | 1.37 | 1.07 | 1.07 | 0.90 | 1.64 | 1.60 |
| TcMar-Tigger | 0.38 | 1.51 | 1.86 | 0.71 | 0.82 | 0.56 | 1.62 | 0.96 |
| Unclassified | 1.75 | 0.62 | 1.27 | 0.88 | 1.70 | 1.22 | 0.92 | 1.10 |
| Total IR | 58.33 | 53.36 | 56.80 | 52.61 | 60.52 | 41.28 | 54.97 | 51.44 |
| Simple repeats (%) | 1.28 | 0.67 | 0.99 | 0.81 | 1.06 | 0.98 | 0.80 | 0.92 |
| GC level (%) | 45.79 | 43.21 | 42.92 | 48.07 | 44.16 | 49.18 | 41.44 | 45.77 |
FW1 and FW2 indicate framework gene (non-HLA genes) segment 1 and segment 2, respectively, within the MHC class I region located between the alpha and beta blocks (Fig. 1A).