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Table 4 Comparisons between M. spretus and M. musculus promoters

From: Gene expression regulation in the context of mouse interspecific mosaic genomes

Genes with modified mRNA level between SEG and B6

        

Gene name

Induction ratio IRCS/B6

Length of B6 promoter (bp)

Length of SEG promoter (bp)

Number of sequence differences

Percentage of sequence divergence

Total number of TFBSs detected with Genomatix

Number of TFBSs differing between M. spretus and M. musculus

Percentage of TFBS differing between M. spretus and M. musculus

   Pde7a

0.02

749

728

29

3.87

137

21

15.33

   Aldh1a7

0.04

598

587

11

1.84

101

30

29.70

   1810058I14rik

0.05

638

613

28

4.39

100

38

38.00

   Plcz1

0.09

1,432

1,392

42

2.93

228

51

22.37

   Itga2

0.10

769

749

21

2.73

94

14

14.89

   Nol9

0.11

1,034

1,021

15

1.45

198

32

16.16

   4833412L08Rik

0.12

601

583

18

3.00

106

20

18.87

   4921521F21Rik

0.16

603

597

7

1.16

137

8

5.84

   Plek

4.34

698

679

27

3.87

134

33

24.63

   Cast

5.28

648

629

21

3.24

101

22

21.78

   Slc6a3

5.94

657

650

7

1.07

90

16

17.78

   Hnf4g

6.64

601

589

14

2.33

105

29

27.62

   6130401L20Rik

7.22

758

743

26

3.43

138

53

38.41

   Mbl2

7.45

629

615

14

2.23

101

24

23.76

   E030010A14

10.06

622

600

33

5.31

143

63

44.06

   Hebp1

10.19

604

596

9

1.49

83

11

13.25

   Pcsk1

20.74

839

834

5

0.60

110

9

8.18

   Slc6a19

23.39

667

648

22

3.30

96

22

22.92

   Pdcd1lg2

38.40

662

647

17

2.57

88

20

22.73

   Mean

 

726.8

710.5

19.3

2.7

120.5

27.2

21.6

   Standard deviation

 

201.9

197.4

9.9

1.2

37.9

15.2

11.1

Genes with unchanged mRNA level between SEG and B6

        

   Tle4

1.19

1,289

1,284

5

0.39

250

5

2.00

   Bhlhb5

1.20

791

788

3

0.38

165

11

6.67

   Cypt12

1.07

603

593

12

1.99

161

14

8.70

   Spag16

0.81

511

506

6

1.17

87

13

14.94

   Zmat5

0.94

619

610

9

1.45

90

18

20.00

   Mean

 

762.6

756.2

7.0

1.1

150.6

12.2

10.5

   Standard deviation

 

311.2

312.3

3.5

0.7

66.9

4.8

7.1

   p -value

 

NS

NS

0.008

0.016

NS

0.019

0.023

  1. Sequence and comparative analysis of putative TFBSs between M. musculus and M. spretus. Genes with unchanged mRNA levels between SEG and B6 consist of M. spretus genes that were not dysregulated when introgressed in the B6 genome. We observed (see text) that modified genes present half as much sequence variation and difference in putative TFBSs. Statistical values (mean and standard deviations) are represented in bold, as well as the p-values showing statistically significant differences in sequence divergence and TFBSs between modified and unmodified genes (Mann-Whitney non-parametric test). NS, not significant.
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Genome Biology

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