Table 3

Comparison of sequence similarity and TFBS/miRNA target site divergence for putative cis-regulatory regions surrounding the opsin arrays of O. niloticus and M. zebra

Region

Identity

Dxy1

Length

Length

TFBS

TFBS

Est.

p-value3

(%)

(%)

On (bp)

Mz (bp)

Divt.

Shrd

Pdiv2 (%)


CNE4

1

96.84

3.23

158

158

0

2

0.0

1.000

2

96.22

3.88

240

239

2

6

25.0

0.130

3

94.74

4.53

349

359

7

1

87.5

< 0.001*

4

98.31

1.70

240

241

2

0

100.0

0.006

5

96.14

3.97

207

207

1

0

100.0

0.080

6

-

-

300

-

-

-

-

-

7

97.16

2.89

882

885

1

8

11.1

0.528

8

88.46

4.86

779

799

3

9

25.0

0.065

9

93.93

6.33

313

313

1

3

25.0

0.283

10

97.64

2.40

127

127

0

0

-

-

11

95.97

4.14

124

124

1

1

50.0

0.154

12

95.53

4.61

246

249

1

3

25.0

0.284

13

97.66

2.37

214

214

1

9

10.0

0.566

14

88.97

4.71

999

1404

1

9

10.0

0.566

15

95.32

4.84

428

428

3

6

33.3

0.030

16

91.21

9.35

182

191

0

2

0.0

1.000

17

96.14

3.96

311

313

2

3

40.0

0.054

18

93.25

7.07

1087

976

5

13

27.8

0.012

19

-

-

69

-

-

-

-

-

20

98.88

1.13

358

38

1

13

7.1

1.000


Proximal

Promoter5

LWS

97.56

2.48

1000

1000

1

16

5.9

1.000

RH2Aα

94.80

5.38

1000

1000

10

11

47.6

< 0.001*

RH2Aβ

91.77

8.60

1000

1000

14

19

42.4

< 0.001*

RH2B

61.35

9.40

1000

1000

15

7

68.1

< 0.001*

SWS1

71.49

26.37

1000

1000

18

10

64.3

< 0.001*

SWS2A

97.19

2.87

1000

1000

11

12

47.8

< 0.001*

SWS2B

81.96

16.31

1000

1000

4

10

28.6

0.021


3'-UTR6

LWS

93.39

6.92

189

189

1

4

20.0

0.341

RH2Aα

94.04

6.21

438

442

4

9

30.8

0.016

RH2Aβ

93.26

7.06

465

460

4

11

26.7

0.027

RH2B

93.15

7.18

310

319

4

4

50.0

0.002*

SWS1

96.74

3.33

217

242

1

3

25.0

0.284

SWS2A

98.37

1.64

123

123

0

1

0.0

1.000

SWS2B

95.90

4.21

124

137

4

1

80.0

< 0.001*


1 Pairwise sequence divergence between O. niloticus and M. zebra, corrected for multiple hits.

2 Actual proportion of divergent TFBSs observed for O. niloticus and M. zebra.

3 P-values for the Exact binomial test at a null proportion divergence = 8%. Tests marked with an asterisk (*) are significant after Bonferroni correction for multiple comparisons.

4 See Additional file 6 for individual counts of each TFBS identified for the CNEs.

5 See Figure 3 for individual counts of each TFBS identified for the proximal promoters.

6 See Additional file 7 for individual counts of each microRNA target site identified for the 3'-UTRs.

O'Quin et al. BMC Evolutionary Biology 2011 11:120   doi:10.1186/1471-2148-11-120

Open Data