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Table 1 Potential regulatory elements mapped as HFRs at the murine Hox clusters

From: Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters

HFR number Name Size Context HFR number Name Size Context
HoxA     HoxC continued    
1 A_DOWN-1.1 5210 3′ end 8 C_12-11.1 510 Intergenic
2 A_1-2.1 510 NCT 9 C_12-11.2 1460 3′ end
3 A_1-2.2 860 NCT 10 C_12-11.3 1610 NCT
4 A_1-2.3 510 3′ end 11 C_12-11.4 510 Intergenic
5 A_2-3.1 810 Intergenic 12 C_11-10.1 510 NCT
6 A_3-4.1 1410 3′ end 13 C_11-10.2 1510 NCT
7 A_3-4.2 660 Intergenic 14 C_11-10.3 760 NCT
8 A_3-4.3 510 Intergenic 15 C_11-10.4 1260 NCT
9 A_4-5.1 2460 Intergenic 16 C_11-10.5 560 TSS
10 A_4-5.2 2920 Intergenic 17 C_10.1 2230 Genic
11 A_5.1 650 Genic 18 C_9.1 1010 Genic
12 A_6-7.1 610 Intergenic 19 C_9-8.1 760 Intergenic
13 A_6-7.2 510 Intergenic 20 C_9-8.2 850 Intergenic
14 A_7-9.1 510 Intergenic 21 C_8-6.1 710 3′ end
15 A_7-9.2 680 Intergenic 22 C_8-6.2 1370 Intergenic
16 A_7-9.3 1080 Intergenic 23 C_8-6.3 1810 Intergenic
17 A_9-10.1 960 3′ end 24 C_8-6.4 1510 Intergenic
18 A_10-11.1 1060 Intergenic 25 C_6-5.1 600 TSS
19 A_10-11.2 560 NCT 26 C_5-4.1 810 Intergenic
20 A_11.1 560 Genic 27 C_5-4.2 1660 Intergenic
21 A_11-13.1 1110 NCT 28 C_5-4.3 560 Intergenic
22 A_11-13.2 3810 Intergenic 29 C_5-4.4 2660 Intergenic
23 A.UP.1 510 Intergenic 30 C_4-DOWN.1 710 3′ end
24 A.UP.2 660 Intergenic 31 C_DOWN.1 660 Intergenic
25 A.UP.3 560 Intergenic 32 C_DOWN.2 1580 Intergenic
HoxB     HoxD    
1 B_13-9.1 1160 Intergenic 1 D_UP.13 860 Intergenic
2 B_13-9.2 760 Intergenic 2 D_UP.14 1660 Intergenic
3 B_13-9.3 720 Intergenic 3 D_13.1 2030 Genic
4 B_13-9.4 810 Intergenic 4 D_12-11.1 560 3′ end
5 B_9-8.1 800 Intergenic 5 D_11-10.1 1410 Intergenic
6 B_7-6.1 510 NCT 6 D_11-10.2 510 Intergenic
7 B_5-4.1 510 TSS 7 D_10-9.1 910 3′ end
8 B_4-3.1 710 TSS 8 D_9-8.1 2080 3′ end
9 B_3.1 510 Genic 9 D_8-4.1 710 NCT
10 B_3.2 820 Genic 10 D_8-4.2 510 NCT
11 B_2-1.1 560 3′ end 11 D_8-4.3 810 TSS
12 B_2-1.2 760 Intergenic 12 D_8-4.4 760 TSS
13 B_2-1.3 1880 Intergenic 13 D_4-3.1 1510 Intergenic
14 B_2-1.4 690 Intergenic 14 D_4-3.2 1160 TSS
HoxC     15 D_3-1.1 760 Intergenic
1 C_UP.26 1020 Intergenic 16 D_3-1.2 510 3′ end
2 C_UP.27 2260 Intergenic 17 D_3-1.3 840 NCT
3 C_UP.28 510 Intergenic 18 D_3-1.4 590 NCT
4 C_UP.29 530 TSS 19 D_3-1.5 2470 NCT
5 C_13.1 1010 Genic 20 D_1-DOWN.1 1360 3′ end
6 C_13.2 1710 Genic 21 D_DOWN.1 3680 Intergenic
7 C_13-12.1 1110 Intergenic 22 D_DOWN.2 1080 Intergenic
  1. 93 HFRs at the Hox clusters showing low histone occupancy, as identified from the histone H3 ChIP-on-chip array, are listed along with their contextual location. Nomenclature of the HFR indicates the flanking Hox genes. TSS = HFRs within 1 kb of TSS; 3′end = HFRs at 3′ end of genes; NCT = HFRs within noncoding transcribed regions; Genic = HFRs within Hox genes. Regions located outside the clusters (within 10 kb upstream and downstream) have been associated with the closest Hox gene.