Table 1.
Inverted Repeats in the Human Genome, >8000 bp, >99% Homology
| IR name (chromosome-pos)a | Chromo band | Arm (kb) | Spacer (kb) | % identity | Gene | Tissue | RT PCR/Northernb | Secondary structurec |
|---|---|---|---|---|---|---|---|---|
| X chromosome | ||||||||
| IRX-47.303 | Xp11.23 | 28.3 | 2.796 | 99.55 | SSX4 | Testes, CTA gene | + (Gure et al. 2002) | + (4) |
| IRX-50.36 | Xp11.22 | 25.1 | 7.392 | 99.53 | None | — | ||
| IRX-50.79 | Xp11.22 | 36.4 | 99.854 | 99.89 | MAGE-D4 | Testes, ubiquitous | + (Chomez et al. 2001) | — |
| IRX-51.17g | Xp11.22 | 142.2 | 8.34 | 99.97 | GAGE-D2,3 | Testes, CTA gene | + (Zendman et al. 2003a) | — |
| IRX-51.4958 | Xp11.22 | 28.7 | 21.642 | 99.87 | GAGE-D2 | Testes, CTA gene | + (Zendman et al. 2003a) | + (2) |
| IRX-51.73 | Xp11.22 | 59.8 | 0.239 | 99.67 | SSX2 | Testes, CTA gene | + (Gure et al. 2002) | + (1) |
| IRX-54.4798 | Xp11.21 | 26.7 | 12.909 | 99.89 | BC035907 | Breast mRNA | — | |
| IRX-61.28 | Xq11.2 | 56.6 | 8.145 | 99.95 | AK056835 | Prostate mRNA | — | |
| IRX-69.83 | Xq13.1 | 57.7 | 0.002 | 99.70 | AK093553 | Thymus, mRNAs | + (1) | |
| IRX-70.95 | Xq13.1 | 119.3 | 0.417 | 99.80 | DMRTC1 | Testes, kidney, pancreas | + (Ottolenghi et al. 2002) | — |
| IRX-71.13 | Xq13.2 | 9.5 | 71.919 | 99.55 | BC041956 | Brain mRNA | + (2) | |
| IRX-100.37 | Xq22.1 | 140.6 | 10.764 | 99.84 | NXF2 | Testes | + (Wang et al. 2001) | — |
| IRX-102.05 | Xq22.3 | 20.3 | 59.982 | 99.27 | AK091321 | Brain mRNA | + (2) | |
| IRX-104.30 | Xq22.3 | 12.6 | 8.677 | 99.13 | None | - | ||
| IRX-118.01 | Xq24 | 48.9 | 62.046 | 99.65 | PEPP-2(OTEX) | Testes | + (Wayne et al. 2002) | — |
| IRX-133.62 | Xq26.1 | 52.0 | 13.852 | 99.25 | MGC27005 | Testes mRNA | +(4) | |
| IRX-139.37 | Xq27 | 12.7 | 3.938 | 99.13 | SPANXA1,2 | Testes, CTA gene | + (Zendman et al. 2003b) | + (4) |
| IRX-144.56 | Xq27.3 | 10.5 | 0.004 | 99.84 | AW235137 | ESTs only | — | |
| IRX-147.49 | Xq28 | 28.3 | 41.009 | 99.23 | MAGE-A9f | Testes, CTA gene | + (Chomez et al. 2001) | — |
| IRX-150.52 | Xq28 | 51.2 | 8.994 | 98.96e | MAGA-A2,3,6 | Testes, CTA gene | + (Chomez et al. 2001) | + (2) |
| IRX-152.06 | Xq28 | 11.4 | 37.625 | 99.11 | None | — | ||
| IRX-152.30 | Xq28 | 35.8 | 21.759 | 99.69 | LAGE2A | Testes, ovary, CTA gene | + (Chen et al. 1997) | — |
| Y chromosome | ||||||||
| IRY-15.142 | P8 | 35.8 | 3.408 | 99.64 | VCY | Testes | — | |
| IRY-16.95 | P7 | 8.7 | 12.638 | 99.86 | None | |||
| IRY-17.35 | P6 | 110.0 | 46.229 | 99.92 | None | |||
| IRY-19.01 | P5 | 495.5 | 3.457 | 99.97 | CDY | Testes | ||
| IRY-19.72 | P4 | 190.2 | 39.642 | 99.97 | HSFY | Testes | ||
| IRY-23.2 | P3d | 283 | 169 | 99.94 | PRY | Testes | + (2) | |
| IRY-24.201 | P2d | 122.0 | 2.1 | 99.97 | DAZ | Testes | ||
| IRY-25.12 | P1.1 | 9.9 | 3.945 | 99.84 | None | |||
| IRY-25.81 | P1d | 1450 | 2.1 | 99.97 | DAZ | Testes | + (1) | |
| IRY-26.55 | P1.2 | 9.9 | 3.945 | 99.89 | None | |||
| Autosomes | ||||||||
| IR1-16.41 | 1p36.13 | 28.8 | 58.601 | 99.45 | None | — | ||
| IR1-103.57 | 1p21.1 | 29.4 | 16.216 | 99.96 | AMY1,2 | Salivary gland | + (6) | |
| IR1-147.04 | 1q21.12 | 26.1 | 6.739 | 99.71 | Histones | Ubiquitous | — | |
| IR2-95.69 | 2q11.1 | 82.7 | 82.801 | 99.14 | TRIM-43 | Placenta mRNA | + (2) | |
| IR6-26.8590 | 6p22.1 | 29.2 | 23.853 | 99.37 | No genes | + (2) | ||
| IR7-62.25 | 7q11.21 | 75.5 | 16.941 | 99.65 | BC036215 | Testes mRNA | — | |
| IR7-64.48 | 7q11.21 | 51.7 | 57.283 | 99.72 | None | + (6) | ||
| IR7-142.79 | 7q34 | 65.4 | 75.992 | 99.67 | BC043153 | Testes mRNA | + (3) | |
| IR7-142.86 | 7q34 | 28.3 | 99.969 | 99.70 | None | — | ||
| IR7-143.36 | 7q35 | 67.9 | 41.373 | 99.56 | AF327904 | Kidney, liver mRNAs | + (3) | |
| IR7-143.41 | 7q35 | 23.8 | 57.199 | 99.46 | None | + (3) | ||
| IR11-89.34 | 11q14.3 | 103.9 | 3.225 | 99.57 | RNF18 | Testes, kidney, spleen | + (Yoshikawa et al. 2000) | + (1) |
| IR13-62.12 | 13q21.31 | 10.6 | 31.553 | 99.88 | No genes | + (3) | ||
| IR15-28.49 | 15q13.2 | 58.6 | 93.355 | 99.57 | AK09040 | Spleen mRNA | + (5) | |
| IR17-19.19 | 17p11.2 | 38.0 | 48.103 | 99.74 | GRAP | Various | + (3) | |
| IR17-58.63 | 17q23.2 | 16.5 | 75.248 | 99.35 | No genes | — | ||
| IR22-20.15 | 22q11.21 | 64.5 | 48.672 | 99.16 | HIC2, AL133030 | Brain, Testes mRNA | — |
IR name-IR chromosome-genome position (in megabase pairs); for example, IRX-47.303 is the IR from the X-chromosome, center of spacer, at genomic position 47.303 Mb.
RT-PCR or Northern blot confirming testes expression. Reference in parentheses. Y-chromosome genes not included.
Secondary structure. (+) Secondary structure detected by dot-plot.—No secondary structure detected. (1) IR in IR (e.g., Fig. 3A). (2) Spacer homologous to arm (e.g., Fig. 3B). (3) IR intertwined with another IR (e.g., Fig. 3C). (4) Multigene family structure. (5) IR15-28.49 and IR15-30.53 (Supplemental data S2), separated by ∼2 Mb, are homologous to each other. (6) Secondary structure not one of the patterns (1) to (5).
As reported in Skaletsky et al. (2003). IRY-23.2 included in Table 1 replaces an internal IR (IRY-23.3047) (Supplemental data S1 and S2).
IRX-150.52 included for complete description of confirmed testes genes, although slightly less than 99% sequence identity (98.96%).
The MAGE-A9 genes were actually found in the arms of a large IR (IRX-147.36) which contains IRX-147.49 in its spacer. IRX-147.36 (arm length: 29.1 kb, spacer 164.9 kb, % identity 99.74) was detected by IRF when a spacer ≤500 kb was used (Supplemental data S2).