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Table 3 New pCRMs from genome-wide eCIS-ANALYST (75 highest scoring predictions)

From: Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

 

CRM

Known element overlap

Arm

pCRM start

pCRM end

pCRM length

5' gene

pCRM relative position

3' gene

pCRM relative position

Conserved sites

Conserved site density

z score

Additional gap/pair-rule gene within 20 kb

pCRM relative position

           

A

A+P

A

A+P

   

1

PCE8050

h stripes 3/4,6,7 [73]

3L

8,622,879

8,626,839

3,961

CG6486

+14646

h

-7829

36

62

9

16

20.1

  

2

PCE8051

kni upstream [74]

3L

20,614,714

20,617,020

2,307

kni

-813

CG13253

+20716

25

31

11

13

13.2

  

3

PCE8052

nub blastoderm

2L

12,604,311

12,606,913

2,603

CG15488

+1653

nub

-304

20

33

8

13

11.6

  

4

PCE8053

eve stripes 3/7 [75]

2R

5,035,493

5,037,290

1,798

CG12134

+3712

eve

-2433

21

24

12

13

11.5

Adam

+5901

5

PCE8054

hairy stripes 1,5 [73]

3L

8,628,846

8,631,011

2,166

CG6486

+20613

h

-3657

17

29

8

13

10.5

  

6

PCE8055

runt stripe 3 [76]

X

20,356,848

20,360,054

3,207

CG1338

-9192

run

-6801

17

34

5

11

10.3

  

7

PCE8056

 

X

20,323,964

20,326,397

2,434

CG11692

-12536

Cyp6v1

-4186

16

28

7

12

9.6

  

8

PCE8057

hb HZ1.4 [77]

3R

4,526,225

4,527,991

1,767

hb

-2670

CG8112

+1273

17

21

10

12

9.5

  

9

PCE8059

eve stripes 4/6 [78]

2R

5,044,597

5,046,030

1,434

eve

+4874

TER94

-3763

15

18

10

13

9.0

Adam

+15005

10

PCE8060

gt posterior [11]

X

2,186,709

2,189,069

2,361

gt

-974

tko

+11679

18

21

8

9

8.9

  

11

PCE8061

 

X

3,169,806

3,172,348

2,543

CG12535

-17954

CG14269

+21857

13

29

5

11

8.8

  

12

PCE8063

CE8021

3L

18,339,914

18,341,941

2,028

grim

-86621

rpr

+5341

16

20

8

10

8.5

  

13

PCE8064

 

3R

6,255,663

6,256,945

1,283

CG6345

-13879

Cyp12e1

-3594

13

17

10

13

8.4

  

14

PCE8065

 

3R

4,026,032

4,027,816

1,785

grn

-18853

CG7800

-15898

15

19

8

11

8.4

  

15

PCE8066

 

X

20,348,460

20,352,624

4,165

CG1338

-804

run

-14231

16

28

4

7

8.3

  

16

PCE8067

ftz upstream [23]

3R

2,682,314

2,684,591

2,278

Scr

-7972

ftz

-5455

15

22

7

10

8.3

  

17

PCE8068

 

X

18,701,007

18,702,700

1,694

CG32541

+39691

CG32541

+39691

12

22

7

13

8.2

  

18

PCE8069

 

2R

17,274,311

17,276,017

1,707

CG3380

-2521

dve

-11496

14

19

8

11

8.2

  

19

PCE8070

 

2L

7,616,050

7,618,366

2,317

CG6739

+15430

CG13792

+19862

14

23

6

10

8.1

  

20

PCE8071

sqz neurogenic

3R

14,999,463

15,001,552

2,090

sqz

+9504

CG14282

-1186

12

24

6

11

8.0

nos

+16485

21

PCE8072

 

X

5,674,422

5,676,386

1,965

CG3726

+16870

CG12728

-6597

11

24

6

12

7.8

  

22

PCE8073

 

2R

14,903,099

14,903,925

827

Toll-7

+12482

Obp56i

-27903

11

11

13

13

7.8

  

23

PCE8074

 

3R

23,192,304

23,192,750

447

CG13980

+8073

side

+40862

7

8

16

18

7.7

  

24

PCE8075

 

3R

10,762,920

10,764,750

1,831

CG3837

+18501

CG14861

-75759

13

19

7

10

7.6

  

25

PCE8076

eve stripe 2 [75]

2R

5,038,454

5,039,041

588

CG12134

+6673

eve

-682

8

10

14

17

7.6

Adam

+8862

26

PCE8077

 

2L

13,541,662

13,542,651

990

kuz

+9371

kuz

+9371

11

13

11

13

7.6

  

27

PCE8078

 

2L

14,424,056

14,425,158

1,103

BG:DS06238.4

-16773

BG:DS08340.1

+7810

12

13

11

12

7.6

  

28

PCE8080

odd stripes 3/6

2L

3,601,045

3,602,748

1,704

odd

-1728

Dot

-9112

12

19

7

11

7.5

  

29

PCE8081

 

3L

17,412,324

17,413,414

1,091

CG18265

+24035

CG7603

-1413

11

14

10

13

7.5

  

30

PCE8083

 

3L

14,121,556

14,123,127

1,572

Sox21b

-41352

D

+4373

12

17

8

11

7.3

  

31

PCE8084

 

2L

4,098,489

4,099,006

518

ed

+74542

ed

+74542

7

9

14

17

7.3

  

32

PCE8085

 

2R

12,253,766

12,255,302

1,537

CG10953

-23540

CG10950

-3625

13

15

8

10

7.2

  

33

PCE8086

 

3L

20,612,647

20,614,073

1,427

kni

+1254

CG13253

+23663

11

17

8

12

7.2

  

34

PCE8087

 

2R

3,391,037

3,391,561

525

CG30358

+10444

CG14755

-16724

7

9

13

17

7.2

  

35

PCE8088

 

3L

16,418,107

16,418,469

363

CG33158

+49435

argos

+14111

6

6

17

17

7.2

  

36

PCE8089

 

3R

12,368,159

12,368,687

529

CG11769

+28970

CG31448

-670

7

9

13

17

7.2

CG14889

-13735

37

PCE8091

 

3L

11,213,064

11,213,664

601

scylla

+3224

CG32083

+24695

8

9

13

15

7.1

  

38

PCE8092

 

2L

1,233,357

1,235,228

1,872

CG5156

+3715

CG5397

-6475

9

23

5

12

7.1

  

39

PCE8093

 

3L

15,688,222

15,691,204

2,983

comm

-10920

CG13445

-67172

13

22

4

7

7.0

  

40

PCE8094

 

2R

10,492,861

10,493,546

686

CG30472

-5321

CG12959

-26488

9

9

13

13

7.0

  

41

PCE8095

 

3R

23,894,562

23,895,459

898

CG12870

+31901

CG12870

+31901

10

11

11

12

7.0

  

42

PCE8096

 

3L

6,762,543

6,765,157

2,615

vvl

+12855

Prat2

+108336

13

20

5

8

6.9

  

43

PCE8097

 

3R

10,238,130

10,238,652

523

CG14846

-1983

CG14847

+4557

7

8

13

15

6.8

  

44

PCE8099

 

2L

18,305,051

18,306,251

1,201

Fas3

+6868

Fas3

+6868

10

14

8

12

6.7

  

45

PCE8100

eve early APR [79]

2R

5,042,174

5,042,884

711

eve

+2451

TER94

-6909

8

10

11

14

6.7

Adam

+12582

46

PCE8102

tll posterior [80]

3R

26,663,942

26,665,204

1,263

CG15544

+21005

tll

-2251

11

13

9

10

6.6

  

47

PCE8104

ems neurogenic [81]

3R

9,723,602

9,724,936

1,335

E5

-23682

ems

-2663

12

12

9

9

6.6

  

48

PCE8105

 

3R

17,817,909

17,818,791

883

Eip93F

+25598

Eip93F

+25598

9

11

10

12

6.6

  

49

PCE8106

 

3L

10,499,018

10,501,551

2,534

CG32062

+25485

CG32062

+25485

11

21

4

8

6.6

  

50

PCE8107

 

3L

4,612,891

4,614,005

1,115

CG13716

-161

CG13715

+1681

11

11

10

10

6.6

  

51

PCE8108

 

2L

14,403,771

14,404,937

1,167

CG15284

-4301

BG:DS06238.4

+2346

10

13

9

11

6.5

  

52

PCE8109

 

3R

7,941,601

7,942,426

826

CG31361

+17775

CG4702

+11512

9

10

11

12

6.5

  

53

PCE8110

 

2L

8,804,166

8,805,336

1,171

CG9468

-30684

SoxN

-12519

10

13

9

11

6.5

  

54

PCE8111

 

3L

8,612,337

8,613,016

680

CG6486

+4104

h

-21652

8

9

12

13

6.5

  

55

PCE8112

 

3L

4,377,989

4,379,208

1,220

CG7447

+13842

Syx17

-3984

11

12

9

10

6.5

  

56

PCE8113

 

2L

14,113,291

14,113,893

603

CG15292

-3974

CG31768

-6693

7

9

12

15

6.5

  

57

PCE8114

 

3L

3,997,600

3,998,923

1,324

CG14985

+13500

fd64A

-799

11

13

8

10

6.5

  

58

PCE8115

eve stripe 1 [79]

2R

5,046,559

5,047,297

739

eve

+6836

TER94

-2496

8

10

11

14

6.5

Adam

+16967

59

PCE8116

 

2R

16,921,501

16,922,240

740

CG13493

-11091

PpN58A

+4194

8

10

11

14

6.5

  

60

PCE8118

 

3R

14,822,848

14,823,484

637

gukh

+13085

gukh

+13085

8

8

13

13

6.4

  

61

PCE8119

 

3R

12,671,525

12,672,987

1,463

abd-A

-15737

CG10349

-32477

11

14

8

10

6.4

  

62

PCE8120

 

3L

10,492,688

10,495,539

2,852

CG32062

+19155

CG32062

+19155

10

23

4

8

6.4

  

63

PCE8121

 

2L

16,841,696

16,842,392

697

CG6012

-2193

CG31781

-5178

8

9

11

13

6.4

  

64

PCE8122

 

3L

6,885,832

6,887,436

1,605

Prat2

-11445

CG14820

-5022

11

15

7

9

6.4

  

65

PCE8123

 

2L

15,162,778

15,164,524

1,747

BG:DS03192.2

-6373

BG:DS07295.1

+59479

11

16

6

9

6.4

  

66

PCE8124

 

2R

6,888,483

6,889,700

1,218

CG12443

+13963

CG13192

-428

10

13

8

11

6.4

  

67

PCE8125

 

2L

20,466,022

20,467,708

1,687

CG2493

-32831

CG15476

+4184

10

17

6

10

6.4

  

68

PCE8126

 

3L

2,779,198

2,779,658

461

CG2083

+1101

CG2083

+1101

6

7

13

15

6.3

  

69

PCE8127

 

X

4,630,473

4,632,106

1,634

CG12681

+14179

CG15470

-3196

9

18

6

11

6.3

  

70

PCE8128

 

3R

27,713,381

27,715,087

1,707

heph

+35171

heph

+35171

10

17

6

10

6.3

  

71

PCE8130

 

3R

12,383,752

12,385,269

1,518

CG14889

+1858

CG14889

+1858

11

14

7

9

6.3

  

72

PCE8131

 

3R

21,329,716

21,331,058

1,343

CG5111

+8355

msi

-2351

8

17

6

13

6.3

  

73

PCE8132

 

3R

16,242,660

16,243,128

469

CG10881

+8657

CG17208

+20535

6

7

13

15

6.3

  

74

PCE8133

 

3R

24,120,296

24,122,240

1,945

CG12516

-668

larp

+19112

12

15

6

8

6.2

  

75

PCE8134

 

3L

8,733,754

8,734,394

641

CG32030

+8601

CG32030

+8601

7

9

11

14

6.2

  
  1. Seventy-five top pCRMs, ranked by a z-score based on the number and density of conserved binding sites (see text for details). Site density columns list the number of conserved sites per kilobase (relative to the D. melanogaster sequence). The number and density of conserved sites are shown under two conditions - aligned sites only (A), or aligned + preserved sites (A+P) (see Materials and methods). The 5' and 3' gene columns correspond to the closest transcription (or annotation) start 5' and 3' of the pCRM. If a pCRM is within an intron, only the intron-containing gene is reported and its name is italicized. The names of genes with early anterior-posterior patterns are in bold. Early anterior-posterior genes that start within 20 kb of the pCRM (but are not the immediate annotation in the 5' or 3' direction) are also listed. Named enhancers without a reference are from this study.