25 arrays, and represents one of the largest most widespread megasatellite DNA families. Conclusion This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families."/>
Skip to main content

Table 2 Tandem arrays, repeat units >2 kb

From: Analysis of the largest tandemly repeated DNA families in the human genome

Chromo Band Array (kb) Unit (kb) Copy % Identity CNV Assembly Gene/TE ref Hg18 coordinates
A) Tandem arrays with one gene per repeat unit
1q21.1 250.0 38.8 5   + Gdis, inv AMY [11] chr1:103,893,838–104,143,838
1q21.3 30.4 10.1 3 >90.3% +   LCE2   chr1:150,897,180–150,927,534
1q23.3 33.9 7.4 4.5 >99% +   tRNA   chr1:159,675,041–159,708,915
1q42.13 42.1 2.5 16 >99% -   5sRNA   chr1:226,809,390–226,851,530
4p16.1 42.7 4.7 9 >99% + Gdis, inter (1) DUB3 [32] chr4:8,935,516–8,978,292
4q35.2 23.8 3.3 7 >99% -- Inter (2) DUX4 [10] chr4:191,224,553–191,248,328
7p14.1 26.9 4.4 5.8 >91% +   TRGV   chr7:38,347,944–38,374,805
8p23.1 127.0 12.1 10 >98% +   DEFA   chr8:6,774,101–6,901,753
8q21.2 166.7 12.2 6 >99% + Gint Gor1   chr8:86,744,493–86,911,178
10q26.3 18.4 3.3 6 >99% -- Inter (2) DUX4 [10] chr10:135,328,811–135,347,195
13q21.1 31.1 6.6 5 >99% +   FLJ40296   .chr13:56,613,947–56,645,084
16p11.1 9.5 1.5 7   +   5sRNA   chr16:34,837,642–34,847,159
17q23.3 59.8 22.9 3 >95% --   CSH1,2   chr17:59,292,406–59,340,026
Xp22.31 10.1 1.9 5 >95% +   5sRNA   chrX:9,331,977–9,342,069
Xp11.23 38 2.5 15 >99% - Gint Gage4   chrX:49,059,954–49,271,622
Xq24 56.0 4.8 12 >99% +   CT47 [31] chrX:119,893,246–119,948,579
Xq26.3 108.1 19.9 4 >99% +   CT45   chrX:134,683,931–134,792,078
Yp11.2 791.7 20.3 9 >99% + Gint TSPY   chrY:9,226,249–10,017,916
Yq11.223 55.3 23.6 2.3 >98% + Intra (3) RMBY   chrY:22,069,208–22,124,461
Yq11.223 46.2 23.6 2 >98% + Intra (3) RBMY   chrY:22,431,619–22,477,826
B) Tandem arrays wholly contained within a gene
1q21.1 66.3 1.5 41 >97% + Gdis, Gprox, intra (4) NBPF [30] chr1:142,869,841–142,935,173
1q21.1 56.1 1.5 35.7 >95% + Intra (4) NBPF [30] chr1:144,022,952–144,079,081
1q21.1 10.8 1.5 6.9 >95% + Gprox, Intra(4) NBPF [12] chr1:146,472,125–146,482,922
1q21.3 7.8 1.4 5.6   +   HRNR   chr1:150,452,354–150,460,167
1q32.2 59.4 18.6 3 >97% +   CR1   chr1:205,769,057–205,828,425
2q11.2 49.5 1.9 26.5 85% - SD, intra (5) FLJ41632 [40] chr2:95,910,350–95,959,888
2q11.2 39.9 1.9 21.3 85% + SD, intra (5) UNG2430   chr2:97,208,306–97,248,230
2q11.2 25.2 1.9 13.5 82% + SD, intra (5) KIAA 1641   chr2:97,519,639–97,544,901
6q26 26.4 5.6 5 >99% + SD LPA [32] chr6:160,953,270–160,979,666
7q22.1 7.0 1.4 5.1 98% - SD BC056606   chr7:99,743,773–99,750,792
8p23.1 47.8 7.1 6.2 >99% + SD, intra (6) AK090418   chr8:7,098,335–7,146,182
8p23.1 61.7 7.1 8 >97% + SD, intra (6) AK090418   chr8:7,606,874–7,668,576
8p23.1 23.5 7.7 3 >97% + SD, intra (6) AK090418   chr8:7,905,630–7,929,101
10p11.21 47.4 11.1 4 >95% + SD ANKRD30A   chr10:37,483,216–37,530,613
10q26.13 42.0 2.9 13 >79% +   DMBT1 [33] chr10:124,329,825–124,371,833
19q13.2 48.0 15.7 3 >95% +   FCGBP   chr19:45,056,041–45,104,055
Yq11.223 17.5 2.4 7   + Intra (7) Daz1 [19] chrY:23,706,609–23,724,156
Yq11.223 29.5 2.4 12   + Intra (7) Daz2   chrY:23,783,768–23,813,249
Yq11.223 16.7 2.4 7   + Intra (7) Daz2   chrY:23,820,447–23,837,326
Yq11.23 22.3 2.4 9   + Intra (7) Daz3   chrY:25,337,948–25,360,227
Yq11.23 22.3 2.4 9   + Intra (7) Daz4   chrY:25,409,003–25,431,283
Yq11.23 14.8 2.4 6   + Intra (7) Daz4   chrY:25,438,190–25,453,002
Yq11.23 26.2 10.8 2.4   + Intra (7) Daz1   chrY:23,726,459–23,752,640
C) Tandem arrays that contain gene, EST or exon
1p36.66 14.4 3.4 4 >98% + SD AK125248   chr1:655,059–669,457
2p13.2 28.4 4.9 5.7 >95% +   FLJ43987   chr2:73,862,733–73,891,172
4q28.3 41.3 2.5 17 >95% + SD, inter (8) SST [35] chr4:132,864,491–132,905,799
5q13.2 36.9 21.3 2 >99% + SD GUSBP   chr5:69,823,338–69,860,219
16p11.2 6.4 1.9 3.4 >88% + SD, inter (5) BC012355   chr16:33,450,421–33,456,850
7p11.2 7.0 2.4 3 >87% + SD Div SST   chr7:57,712,475–57,719,436
17p11.2 11.1 2.4 4 >84% + SD Div SST   chr17:21,825,509–21,836,586
20p11.1 16.1 1.9 8.2 >87%    Div SST   chr20:25,781,895–25,797,997
D) Megasatellite arrays
2q11.2 6.4 1.9 3.4 >89% - SD, intra (5) Mer5A1   chr2:95,986,764–95,993,173
2q37.1 28.1 1.5 18.7   +   Mer20   chr2:232,396,082–232,424,219
4p16.1 16.5 5.6 3 >99% +   Mer65A   chr4:8,673,058–8,689,560
4p11 51.4 6.0 8 >96% + SD, inv, Gprox Acro   chr4:48,976,229–49,027,623
5p15.1 71.0 3.4 20 >97% + SD, Inv Charlie 2a   chr5:17,570,661–17,641,581
7q36.1 10.1 1.7 5   + SD HERVE   chr7:149,361,474–149,371,533
8p23.1 38.8 7.7 5 >98% + SD, intra (6) LTR5A   chr8:7,392,330–7,431,109
8p23.1 12.9 4.7 3 >94% + SD, intra (1) CA [39] chr8:7,175,100–7,187,953
8p23.1 12.5 4.7 3 >87% + SD, intra (1) CA   chr8:12,023,084–12,035,607
9q32 32.1 5.5 5.9 >96% +   L1MA7   chr9:114,860,525–114,892,874
18q22.1 6.3 2.3 3.2 >96% +   L1PB4   chr18:64,354,361–64,360,677
19p13.2 53.7 7.5 7.5 >97% +   Charlie 5   chr19:8,708,195–8,761,926
19q13.12 44.5 2.5 18 >95% - SD, intra (8) SST [35] chr19:41,448,243–41,492,723
19q13.31 38.5 2.5 16 >95% - SD, intra (8) SST [35] chr19:42,451,366–42,489,869
19q13.32 54.4 5.4 10 >98% + SD, intra (9) Mer33   chr19:53,098,557–53,152,942
19q13.33 56.2 5.4 10 >97% + SD, intra (9) Mer33   chr19:55,280,783–55,336,942
Xq23 51.7 3.0 17 >99% +   DXZ4 [36] chrX:114,867,433–114,919,088
  1. Assembly- Gdis- Gap at distal end of array, Gprox-Gap at proximal end of array, Gint- Gap internal to array. Inv- inversion within array. SD- array is associated with a surrounding segmental duplication (not including segmental duplications due merely to repeat unit homology within array). Intra- intrachromosomal duplication of related arrays on same chromosome Inter- Interchromosomal duplication of related arrays on different chromosomes. (1) – (9) Related arrays are grouped by number, either intra or interchromosomal, or both, as indicated.