Table 5 Verification of prediction by experimental analysis

AGI code	Position from TSS¹	RARf		Predicted *cis*-element	REG	Prediction assessment	Reference⁴	Response	Element name	MEME	Gibbs Sampler
		Drought²	SA³
AT5G52310 (RD29A)	-231	3.12		ATACCGACATCA		Positive	Yamaguchi-Shinozaki, 1994	Drought	DRE	No detect.	No detect.
	-175	3.94		ACTACCGACATGAG		Positive	Narusaka, 2003	Drought	DRE	No detect.	No detect.
	-137	4.22		AAGCCGACACA		Positive	Narusaka, 2003	Drought	DRE-core	No detect.	No detect.
	-125	3.76		ACACGCGTAGA	AtREG536	?⁵	Narusaka, 2003	Drought		No detect. ⁷	No detect.
	-82	3.44		ACAGACGC		False positive	Yamaguchi-Shinozaki, 1994	Drought		No detect	No detect
	-71	5.01		ATACGTGTCCCT	AtREG557,472	Positive	Narusaka, 2003	Drought	ABRE	No detect.	No detect.⁷
AT5G52300 (RD29B)	-163	3.16		CGTACGTGTCA	AtREG450	False positive	Uno, 2000	Drought		No detect	No detect⁷
	-137	*				Absent ⁷	Uno, 2000	Drought	ABRE	No detect.	No detect.⁷
	-112	3.21		GTACGTGTCA	AtREG557, 389	Positive	Uno, 2000	Drought	ABRE	No detect.	No detect. ⁷
AT2G14610 (PR1)	-669		3.82	ACGTCACT		Positive	Pape, 2010	INA⁶/SA	LS5	No detect.	No detect.
	-657		6.38	TACTTACGTCAT		Positive	Lebel, 1998; Pape, 2010	INA⁶/SA	LS7	No detect.	No detect.
	-607		3.65	TAGGCAAG		False positive	Lebel, 1998	INA⁶/SA		No detect	No detect

¹Position from major TSS data from ppdb. ²1 h-treatment. ³See Table 3 for experimental conditions. ⁴Source of functional analysis. *RARf for ABA response is 3.7. ⁵Lack of the corresponding functional data. ⁶INA: 2,6-dichloro isonicotinic acid, a SA analog. ⁷Detected with the promoter set of ABA response. For analysis of RD29B by MEME and Gibbs Sampler, it was included to the applied promoter set. Promoter scan for prediction was achieved for the regions where linker scan or intensive functional analyses were achieved, and peaks with RARf > 3.0 were selected as prediction. Utilized RARf tables are shown in the table.

ISSN: 1471-2229