Table 2

X-box comparisons in promoters of dRFX regulated genes, between Drosophila melanogaster and Drosophila pseudoobscura

D. melanogaster

D. pseudoobscura

D. melanogaster

D. pseudoobscura


No. of X-box

No. of X-box


Strand

Strand

Conserved blocks around X-box


Gene ID

+

-

Gene ID

+

-

No. of conserved X-box*

X-box

Dist.

X-box

Dist.

100 bp

25 bp


Genes down regulated in dRfx mutant

CG1126-PA

2

4

GA10872-PA

2

1

1

GTTGCC T AGCAAC

66

GTTGCC T AGCAAC

91

-

+

CG3259-PA

4

4

GA17011-PA

2

2

1

GTTGCC AG GACAAC

81

GTTGTC AG GACAAC

96

-

+

CG3769-PA

2

3

GA17674-PA

4

3

1

GTTGCT AGT AGCAAC

71

GTTGCC AG GACAAC

56

-

+

CG4525-PA

2

3

GA18233-PA

1

1

1

GTTGCC A AGCGAC

134

GTTGCC A AGCGAC

239

+

+

CG8853-PA

2

4

GA21369-PA

1

5

1

GTTACC TT GGCGAC

87

GTTACC AT GGAAAC

110

-

+

CG9227-PA

5

1

GA21627-PA

3

1

1

GTTACT TT GACAAC

119

GTTGCC AG AGCAAC

146

+

+

CG9595-PA

3

2

GA21901-PA

3

2

1+ 2

GTTGCC G GGCAAC

126

GTTGTC CG GGCAAC

141

+

+

ATTTTT GTT AGCAAC

264

ACTTTT GC AAAAAC

699

-

+

GCTGTT ACA AGAGAC

2,969

GCTGCT GCA GGAAAC

2,671

NA

NA

CG12548-PA

7

2

GA11690-PA

2

4

2

ATCACC AA GGCAAC

2,335

ATCACC TT GGAAAC

868

-

-

GCCTTT C GGAGAC

2,833

GCCGCT T GATGAC

2,638

-

-

CG13178-PA

4

2

GA12098-PA

5

4

1

GCCGTT AGC AAGAAC

2,551

GCCACC AGG AAAAAC

2,106

NA

NA

CG13809-PA

1

2

GA12544-PA

2

2

1

GTTGCC AC AACAAC

123

GTTGCC AC AACAAC

103

+

+

CG15161-PA

2

1

GA13541-PA

4

2

2

GTTGTC AG GACGAC

321

GTTGTC AA GACAAC

311

-

-

GTTGTC AG GACGAC

321

GTTTTT GCA GGCAAC

391

-

-

CG30441-PA

1

3

GA15848-PA

3

1

1

GTTGTC AAT AGCAAC

60

GTTGTC TGT GACAAC

122

-

-

CG17599-PA

1

5

GA14573-PA

1

1

1

GTTACC T AGCAAC

141

GTTGCC T GGCAAC

206

-

-

CG18631-PA

2

2

GA15024-PA

6

1

1

GTTGCC CAT GGCAAC

2,731

GTTGCC GTT AGCAAC

2,633

-

+

CG15666-PA

3

3

GA13881-PA

2

3

1

GTTGCC AA GGCAAC

88

GTGGCC AT GGCAAC§

5

-

-

CG14870-PA

1

1

GA13310-PA

1

1

1

GTCTCC CG GGCAAC

-22

GTATCC TG GGCAAC§

-6

+

+

CG1399-PB

3

3

GA12678-PA

3

0

0

CG5142-PA

3

2

GA18687-PA

2

1

0

CG9333-PA

4

1

GA21709-PA

2

1

0

CG9398-PA

2

2

GA21760-PA

3

3

0

CG11048-PA

1

0

GA10726-PA

5

4

0

CG13691-PA

1

1

GA12462-PA

1

1

0

CG14367-PA

0

3

GA12937-PA

3

3

0

Invariantly expressed genes in dRfx mutant

CG5195-PA

0

4

GA18727-PA

3

4

0

CG5359-PA

4

4

GA17011-PA

2

1

1

GTTATT CGT GGTGAC

141

GTTGTT G AGGAAC

51

-

-

CG6504-PA

3

0

GA19567-PA

6

4

0

CG6560-PA

3

0

GA19685-PA

0

2

0

CG7161-PA

2

5

GA20145-PA

0

3

0

CG9710-PA

2

0

GA21982-PA

1

0

0

CG10642-PA

4

2

GA10463-PA

1

3

1

GTCGTT TAA GGAAAC

1,041

GTTGTC ATG AGTAAC

1,226

-

+

CG11755-PA

1

5

GA11176-PA

2

1

1

ACCGCC CAG AAGAAC

2,418

ACTACC GT GAAAAC

1,576

NA

NA

CG11237-PA

3

2

GA10856-PA

1

2

0

CG11759-PA

1

3

GA11178-PA

3

2

0

CG11838-PA

3

0

GA11225-PA

3

4

0

CG31249-PA

1

1

GA16123-PA

1

1

0

CG32392-PA

4

2

GA16867-PA

3

3

0


*RYYNYYN[1-3]RRNRAC. Dist., distance upstream of the ATG. The percentage of identities of either 100 bp or 25 bp sequence blocks around the X-box was estimated by Vista comparison as positive (+) if identities are above 50%, or negative (-) if below 50%. Palindrome. §The X-box fits the more degenerated consensusRYNNYYN[1-3]RRNRAC. NA, not applicable because of nearby coding sequence environment or gap in the sequences.

Laurençon et al. Genome Biology 2007 8:R195   doi:10.1186/gb-2007-8-9-r195

Open Data