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

Yun, Kil-Young; Park, Myoung Ryoul; Mohanty, Bijayalaxmi; Herath, Venura; Xu, Fuyu; Mauleon, Ramil; Wijaya, Edward; Bajic, Vladimir B; Bruskiewich, Richard; de los Reyes, Benildo G

doi:10.1186/1471-2229-10-16

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 element^a	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).

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