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Table 6 Amount of binding motifs (for 25 TFs with Tmax > T1) in the 500 bp and 5000 bp regions of 13686 genes. For each BM we show statistics with respect to sequences that passed Tmax and T5 (see text for further details). We also checked whether the BS resides on Alu or not (see methods). and give the number of BSs that reside on Alu and their percentage out of the total number of BS.

From: Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes

 

5000 upstream

500 upstream

BM name

No. of BS on Alu – Tmax

%BS on Alu- Tmax

No. of BS on Alu T5

%BS on Alu T5

No. of BS on Alu Tmax

%BS on Alu Tmax

No. of BS on Alu T5

%BS on Alu T5

V$PITX2_Q2

34188

99.4%

45546

94.9%

777

99.0%

1022

86.0%

V$LXRE.01

8193

99.2%

21686

74.9%

185

96.9%

473

42.2%

V$GSC.01

33565

96.0%

36033

90.7%

761

89.2%

812

75.5%

V$GFI1.01

32311

95.2%

33557

88.3%

713

84.0%

742

68.5%

V$SREBP.03

7695

93.0%

18264

65.9%

181

44.7%

399

18.8%

V$LYF1.01

26778

91.8%

27476

84.0%

616

73.5%

624

56.1%

V$OTX2.01

35993

84.8%

35993

84.8%

813

64.0%

813

64.0%

V$PAX4.01

9760

84.0%

23265

74.7%

207

63.9%

508

53.4%

V$AARE.01

13854

77.3%

17047

62.0%

282

51.1%

328

30.5%

V$MEF2.04

17253

76.7%

19766

65.2%

355

58.7%

414

43.6%

V$CHREBP_MLX_01

1537

70.3%

9810

68.6%

49

23.6%

261

20.5%

V$ER.02

3166

68.2%

12256

50.7%

60

27.6%

260

15.9%

V$NKX25.01

14144

67.7%

14754

48.9%

238

32.9%

249

18.7%

V$LUN1_01

15768

99.9%

50303

99.6%

340

100.0%

1143

98.1%

V$HNF4.02

2224

61.5%

11368

61.0%

39

18.9%

259

21.6%

V$MEF2.02

18807

56.9%

18807

56.9%

389

30.7%

389

30.7%

V$RSRFC4.01

18153

49.5%

18153

49.5%

381

26.3%

381

26.3%

V$RSRFC4.02

18424

49.0%

18424

49.0%

385

26.7%

385

26.7%

V$IRF1.01

2116

48.8%

5343

19.6%

57

20.0%

144

7.1%

V$MEF2.03

18027

48.2%

18027

48.2%

383

26.3%

383

26.3%

V$HNF1.03

8819

26.9%

8819

26.9%

216

12.9%

216

12.9%

V$OC2.01

4430

25.5%

8643

27.1%

98

15.2%

204

16.6%

V$RORA1.01

968

12.8%

6891

26.7%

25

5.8%

152

10.6%

V$HNF1.01

2939

10.3%

2939

10.3%

74

4.5%

74

4.5%

V$BRN2.03

2127

6.8%

2127

6.8%

60

4.0%

60

4.0%