Table 3

Enrichment of putative ERF/RAV-target cis-elements in promoters of chilling upregulated genes.

Cluster

Motif

Putative elementa

Associated class of ERF (putative)b

% (TIC)c

e-value


C100A

TTTCTTTG

JA response element-like

Groups VI, VIII, IX

81 (12.14)

7e-004


ACCTGATAT

rav1b element-like

Groups II, III and RAV1

61 (11.98)

4e-004


ATTTAGAG

JA response element-like

Groups VI, VIII, IX

60 (11.82)

5e-004


TATATGAA

JA response element-like

Groups VI, VIII, IX

51 (12.46)

3e-004


C99

CAAACCGA

DRE/CRT-like

Groups II, III and RAV1

62 (11.76)

1e-004


C99A

CCTTCCAT

CArg-box-like

ERF

61 (12.17)

2e-004


GGCGGCGGC

GCC-box-like

Groups I, IV, VII, X

60 (15.85

1e-004


C97

CGCCGCCG

GCC-box-like

Groups I, IV, VII, X

73 (14.86)

3e-004


C97A

TGAAACAA

rav1b element-like

Groups II, III and RAV1

81 (11.29)

2e-004


C94

TCAAAATT

Ethylene RE-like

ERF

58 (12.32)

1e-004


GCTCCGCC

GCC-box-like

Groups I, IV, VII, X

53 (12.92)

4e-004


TATATGAA

JA response element-like

Groups VI, VIII, IX

51 (12.59)

3e-004


CGCCGCCGC

GCC-box-like

Groups I, IV, VII, X

51 (16.05)

2e-004


C91

GGGCGGCT

GCC-box-like

Groups I, IV, VII, X

54 (12.33)

3e-004


CCGCCGCCG

GCC-box-like

Groups I, IV, VII, X

50 (16.20)

1e-004


C90A

CGGCGACG

DRE/CRT-like

Groups II, III and RAV1

66 (13.32)

1e-004


GCCGCCGC

GCC-box-like

Groups I, IV, VII, X

57 (14.28)

2e-004


C88A

CGGCGGCGG

GCC-box-like

Groups I, IV, VII, X

58 (17.37)

3e-005


CGGCGGCGG

GCC-box-like

Groups I, IV, VII, X

53 (17.37)

3e-005


CGCCGCCAC

GCC-box-like

Groups I, IV, VII, X

50 (14.54)

3e-004


C87A

CAAGGCCA

GCC-box-like

Groups I, IV, VII, X

57 (11.12)

4e-004


C86

CACCTTTC

rav1b element-like

Groups II, III and RAV1

72 (11.24)

1e-003


CGCCGCCGC

GCC-box-like

Groups I, IV, VII, X

63 (15.89)

9e-004


C86A

CGTCGGAA

DRE/CRT-like

Groups II, III and RAV1

55 (12.08)

5e-004


C83

GCCGCCGCC

GCC-box-like

Groups I, IV, VII, X

69 (16.31)

3e-004


C83A

GCGT(c/t) GGC

DRE/CRT-like

Groups II, III and RAV1

53 (12.14)

2e-004


C81

GAG(c/g)AGCG

JA response element-like

Groups VI, VIII, IX

69 (12.19)

4e-004


TCT(a/c)AACA

rav1b element-like

Groups II, III and RAV1

67 (11.43)

6e-004


GTGG(a/c)GAC

DRE/CRT-like

Groups II, III and RAV1

61 (11.73)

4e-004


AATTTA(g/t)AG

JA response element-like

Groups VI, VIII, IX

59 (12.45)

3e-004


C80

GGCGGCGGC

GCC-box-like

Groups I, IV, VII, X

60 (16.53)

3e-005


GAAGCCGA

DRE/CRT-like

Groups II, III and RAV1

53 (12.66)

4e-004


C79

CGCCGCCGC

GCC-box-like

Groups I, IV, VII, X

59 (15.76)

3e-004


CGGCGACG

DRE/CRT-like

Groups II, III and RAV1

52 (13.85)

4e-004


C78

CAAACCGA

DRE/CRT-like

Groups II, III and RAV1

62 (11.76)

1e-004


aHomology with motifs identified in other plant species (TRANSFAC, PLACE and AGRIS databases).

bPossible classes of associated ERF/RAV1 proteins based on recent phylogenetic classifications [37] and co-expression.

cPercent occurrence in critical promoters relative to background sequences (Total Information Content).

Yun et al. BMC Plant Biology 2010 10:16   doi:10.1186/1471-2229-10-16

Open Data