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Table 2 Sequence and binding-site conservation in pCRMs between D. melanogaster and D. pseudoobscura

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

 

pCRM

Name

CRM activity

pCRM length (D. melanogaster)

pCRM length (D. pseudoobscura)

Percent identity

D. melanogaster sites

D. pseudoobscura sites

Conserved sites

Fraction conserved

         

A

A+P

A

A+P

1

PCE7001

runt stripe 3

+

1,089

1,504

71%

27

20

11

20

41%

74%

2

PCE7002

eve stripes 3/7

+

1,278

1,114

61%

28

25

21

25

75%

89%

3

PCE7003

eve stripe 2

+

587

771

67%

14

10

9

10

64%

71%

4

PCE7004

eve stripes 4/6

+

799

1,003

70%

20

18

13

17

65%

85%

5

PCE7005

hairy stripe 7

+

895

869

66%

20

16

12

16

60%

80%

6

PCE7006

hairy stripe 6

+

868

952

62%

23

19

11

19

48%

83%

7

PCE7007

hairy stripes 1,5

+

787

723

56%

16

15

9

13

56%

81%

8

PCE7008

kni upstream

+

1,356

1,654

68%

33

31

24

30

73%

91%

9

PCE7009

hb HZ1.4

+

1,207

1,383

69%

24

23

17

21

71%

88%

10

PCE8001

gt posterior domain

+

944

1,092

64%

23

19

15

18

65%

78%

11

PCE8010

odd stripes 3/6

+

760

825

70%

17

19

12

16

71%

94%

12

PCE8011

nub blastoderm

+

695

894

70%

18

13

10

12

56%

67%

13

PCE8024

ftz stripes 1/5

+

693

744

77%

14

10

10

10

71%

71%

14

PCE8012

pdm2 neurogenic

+

723

723

72%

14

8

4

8

29%

57%

15

PCE8027

sqz neurogenic

+

810

818

69%

16

17

11

14

69%

88%

16

PCE8005

cluster_at_7A

amb.

548

819

54%

13

4

2

2

15%

15%

17

PCE8016

cluster_at_55C

amb.

703

1,617

55%

16

6

3

6

19%

38%

18

PCE8020

cluster_at_70F

amb.

710

538

47%

14

2

2

2

14%

14%

19

PCE8006

cluster_at_7B

-

639

663

69%

15

9

8

8

53%

53%

20

PCE8008

cluster_at_8F

-

745

716

58%

14

2

1

2

7%

14%

21

PCE8013

cluster_at_34E

-

850

919

61%

17

8

6

8

35%

47%

22

PCE8014

cluster_at_36F

-

701

596

53%

15

6

5

6

33%

40%

23

PCE8015

cluster_at_47A

-

655

652

66%

16

3

3

3

19%

19%

24

PCE8017

cluster_at_56B

-

633

331

33%

15

9

4

8

27%

53%

25

PCE8018

cluster_at_59B

-

716

960

59%

16

4

3

4

19%

25%

26

PCE8019

cluster_at_67B

-

667

675

62%

15

7

5

6

33%

40%

27

PCE8021

cluster_at_75C

-

752

640

59%

19

13

10

12

53%

63%

28

PCE8022

cluster_at_76C

-

704

725

67%

15

9

7

9

47%

60%

29

PCE8023

cluster_at_84A

-

765

1,001

55%

16

7

5

7

31%

44%

30

PCE8025

cluster_at_85C

-

838

827

54%

16

6

1

5

6%

31%

31

PCE8026

cluster_at_88F

-

682

1,096

62%

16

6

5

5

31%

31%

32

PCE8028

cluster_at_95C

-

624

723

60%

15

6

4

6

27%

40%

33

PCE8003

cluster_at_5C.1

-

628

None

 

15

     

34

PCE8004

cluster_at_5C.2

-

694

None

 

15

     

35

PCE8009

cluster_at_12E

-

663

None

 

15

     

36

PCE8002

cluster_at_4B

-

1,341

None

 

28

     

37

PCE8007

cluster_at_7F

Unknown

658

None

 

15

     
 

Mean (pCRMs 1-15)

 

899

1,005

67%

20

18

13

17

61%

80%

 

Mean (pCRMs 19-32)

 

712

752

58%

16

7

5

6

30%

40%

  1. Conservation properties are listed for the pCRMs described in Table 1. The number and fraction of conserved sites are shown under two conditions - aligned sites only (A), or aligned + preserved sites (A+P) (see Materials and methods). D. pseudoobscura sequences used to determine these properties are available as supplemental material at [42].