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Table 3 Enrichment of putative ERF/RAV-target cis-elements in promoters of chilling upregulated genes.

From: Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

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
  1. aHomology with motifs identified in other plant species (TRANSFAC, PLACE and AGRIS databases).
  2. bPossible classes of associated ERF/RAV1 proteins based on recent phylogenetic classifications [37] and co-expression.
  3. cPercent occurrence in critical promoters relative to background sequences (Total Information Content).
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BMC Plant Biology

ISSN: 1471-2229

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