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Table 2 X-box comparisons in promoters of dRFX regulated genes, between Drosophila melanogaster and Drosophila pseudoobscura

From: Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species

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

      
  1. *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.