RARA_1

 

 

 

 

A

C

G

T

 

Name

RARA

1

469

69

142

90

 

TF group

nuclearreceptor

2

460

15

173

23

 

Polypeptide used

DBD

3

543

5

107

1

 

Ligand sequence

TAAAAT20NTA

4

0

2

635

0

 

Batch of SELEX experiment

Q

5

0

3

628

44

 

Seed sequence

ARRGGTCANNNRRGGTCA

6

4

5

18

496

 

Hamming distance of sequences to seed

2

7

8

962

4

16

 

SELEX cycle

3

8

656

1

17

2

 

Number of repeats

dimeric

9

138

62

24

334

 

Comment

 

10

64

102

153

280

 

Representative matrix

yes

11

153

78

27

310

 

 

 

12

301

92

302

17

 

 

 

13

384

14

270

1

 

 

 

14

1

1

612

0

 

 

 

15

0

2

557

91

 

 

 

16

9

2

9

497

 

Source:

 

17

7

934

14

8

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

18

719

5

24

2

 

 

 

 

 

 

 

 

 

 

 

 

RARA_2

 

 

 

 

A

C

G

T

 

Name

RARA

1

250

1

513

4

 

TF group

nuclearreceptor

2

507

1

35

0

 

Polypeptide used

DBD

3

0

0

745

0

 

Ligand sequence

TAAAAT20NTA

4

1

0

746

19

 

Batch of SELEX experiment

Q

5

0

5

1

559

 

Seed sequence

RAGGTCAAAAGGTCAAKN

6

2

707

26

0

 

Hamming distance of sequences to seed

2

7

528

0

4

0

 

SELEX cycle

3

8

526

0

28

162

 

Number of repeats

dimeric

9

526

0

3

37

 

Comment

 

10

522

5

4

0

 

Representative matrix

yes

11

0

0

759

1

 

 

 

12

0

0

754

101

 

 

 

13

3

0

0

546

 

 

 

14

0

705

0

2

 

 

 

15

540

0

1

0

 

 

 

16

539

36

30

181

 

Source:

 

17

2

0

228

328

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

18

0

115

226

212

 

 

 

 

 

 

 

 

 

 

 

 

RARA_3

 

 

 

 

A

C

G

T

 

Name

RARA

1

1089

24

313

0

 

TF group

nuclearreceptor

2

0

0

1488

2

 

Polypeptide used

DBD

3

0

2

1451

71

 

Ligand sequence

TAAAAT20NTA

4

6

11

17

1143

 

Batch of SELEX experiment

Q

5

10

1980

9

21

 

Seed sequence

RGGTCANNNARRGGTCA

6

1391

16

11

2

 

Hamming distance of sequences to seed

2

7

301

397

84

581

 

SELEX cycle

3

8

213

432

584

223

 

Number of repeats

dimeric

9

147

677

157

502

 

Comment

 

10

972

118

198

228

 

Representative matrix

yes

11

1015

17

348

7

 

 

 

12

1126

16

269

1

 

 

 

13

2

0

1455

4

 

 

 

14

1

7

1440

35

 

 

 

15

8

11

13

1131

 

Source:

 

16

4

1923

26

22

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

17

1486

3

25

10

 

 

 

 

 

 

 

 

 

 

 

 

RARA_4

 

 

 

 

A

C

G

T

 

Name

RARA

1

3009

249

574

204

 

TF group

nuclearreceptor

2

1216

24

1401

0

 

Polypeptide used

full

3

2

1

2998

1

 

Ligand sequence

TATAGA20NCG

4

5

0

2729

430

 

Batch of SELEX experiment

AD

5

147

27

49

2924

 

Seed sequence

ARGGTCAAAAGGTCA

6

9

4075

20

48

 

Hamming distance of sequences to seed

2

7

3548

0

92

1

 

SELEX cycle

3

8

3382

20

70

316

 

Number of repeats

dimeric

9

3525

25

19

574

 

Comment

 

10

3297

5

522

0

 

Representative matrix

no

11

2

0

2940

1

 

 

 

12

0

2

2812

893

 

 

 

13

21

13

16

3106

 

Source:

 

14

2

4029

5

111

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

15

3495

3

1

1

 

 

 

 

 

 

 

 

 

 

 

 

RARA_5

 

 

 

 

A

C

G

T

 

Name

RARA

1

2187

495

321

691

 

TF group

nuclearreceptor

2

1769

471

1038

38

 

Polypeptide used

full

3

1703

23

1073

1

 

Ligand sequence

TATAGA20NCG

4

0

1

2128

3

 

Batch of SELEX experiment

AD

5

1

0

2092

31

 

Seed sequence

ARRGGTCANNNRRGGTCA

6

0

25

13

2448

 

Hamming distance of sequences to seed

2

7

7

3823

6

12

 

SELEX cycle

3

8

3120

5

18

0

 

Number of repeats

dimeric

9

876

632

115

1154

 

Comment

 

10

233

749

1429

172

 

Representative matrix

no

11

402

693

327

1197

 

 

 

12

691

52

1408

64

 

 

 

13

2036

49

709

0

 

 

 

14

1

1

2084

2

 

 

 

15

1

2

2084

55

 

 

 

16

13

10

47

2412

 

Source:

 

17

2

3826

2

16

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

18

2990

7

72

0

 

 

 

 

 

 

 

 

 

 

 

 

RARA_6

 

 

 

 

A

C

G

T

 

Name

RARA

1

4701

39

800

5

 

TF group

nuclearreceptor

2

1

4

4339

4

 

Polypeptide used

full

3

0

2

4008

461

 

Ligand sequence

TATAGA20NCG

4

18

20

55

4881

 

Batch of SELEX experiment

AD

5

8

7169

71

23

 

Seed sequence

RGGTCANNNARRGGTCA

6

5979

7

52

0

 

Hamming distance of sequences to seed

2

7

3316

605

480

1102

 

SELEX cycle

3

8

806

1707

1685

662

 

Number of repeats

dimeric

9

658

1247

1086

1736

 

Comment

 

10

4267

343

379

924

 

Representative matrix

no

11

2890

110

2448

52

 

 

 

12

4784

27

834

0

 

 

 

13

2

1

4252

0

 

 

 

14

2

7

4259

69

 

 

 

15

21

62

29

4849

 

Source:

 

16

63

7209

18

31

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

17

5808

8

29

2

 

 

 

 

 

 

 

 

 

 

 

 

Rara_7

 

 

 

 

A

C

G

T

 

Name

Rara

1

145

28

9

17

 

TF group

nuclearreceptor

2

134

3

40

3

 

Polypeptide used

DBD

3

161

2

23

0

 

Ligand sequence

TCGGTT20NCG

4

1

0

236

0

 

Batch of SELEX experiment

P

5

0

0

230

9

 

Seed sequence

ARRGGTCANNNRRGGTCA

6

0

0

3

203

 

Hamming distance of sequences to seed

2

7

0

193

0

3

 

SELEX cycle

4

8

195

1

3

1

 

Number of repeats

dimeric

9

68

52

12

60

 

Comment

 

10

23

58

82

43

 

Representative matrix

no

11

83

38

74

17

 

 

 

12

71

3

129

5

 

 

 

13

141

1

38

0

 

 

 

14

1

0

219

0

 

 

 

15

1

0

202

12

 

 

 

16

1

0

4

189

 

Source:

 

17

0

207

4

1

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

18

177

1

0

0

 

 

 

 

 

 

 

 

 

 

 

 

Rara_8

 

 

 

 

A

C

G

T

 

Name

Rara

1

237

0

30

1

 

TF group

nuclearreceptor

2

2

2

236

2

 

Polypeptide used

DBD

3

1

3

206

47

 

Ligand sequence

TCGGTT20NCG

4

1

1

7

252

 

Batch of SELEX experiment

P

5

0

354

2

3

 

Seed sequence

RGGTCANNNARRGGTCA

6

314

0

0

1

 

Hamming distance of sequences to seed

2

7

81

138

17

49

 

SELEX cycle

4

8

37

73

72

83

 

Number of repeats

dimeric

9

60

107

18

93

 

Comment

 

10

222

15

18

46

 

Representative matrix

no

11

213

3

57

4

 

 

 

12

252

3

25

0

 

 

 

13

0

1

221

0

 

 

 

14

0

1

193

30

 

 

 

15

0

1

0

234

 

Source:

 

16

1

387

0

3

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

17

281

0

5

0

 

 

 

 

 

 

 

 

 

 

 

 

Rara_9

 

 

 

 

A

C

G

T

 

Name

Rara

1

602

43

394

24

 

TF group

nuclearreceptor

2

830

7

152

0

 

Polypeptide used

DBD

3

0

0

1231

2

 

Ligand sequence

TCGGTT20NCG

4

1

0

1131

97

 

Batch of SELEX experiment

P

5

4

4

7

1070

 

Seed sequence

RRGGTCAAAAGGTCA

6

0

1071

6

3

 

Hamming distance of sequences to seed

2

7

1047

0

3

1

 

SELEX cycle

4

8

1041

3

5

20

 

Number of repeats

dimeric

9

998

1

51

35

 

Comment

 

10

996

2

65

1

 

Representative matrix

no

11

1

0

1156

0

 

 

 

12

0

1

1016

176

 

 

 

13

1

3

15

1007

 

Source:

 

14

1

1103

7

7

 

Jolma et al., Cell 152:327-339 (2013); PubMed 23332764

15

1010

0

0

2