Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice

Table 2 Enumerative selection of overrepresented motifs harbouring known cis-elements in the promoters of OsWRKY13-regulated genes

Overrepresented motif sequence^a	Strand^b	P-value^c	Known homologous cis-element
			Element^d	Transcription factor type	Potential signalling pathway	Reference
Upregulated
GTTGACC	bs	1.20e-06	W-box	WRKY	biotic/abiotic response, development	18, 19, 21
GTTGACT	bs	9.05e-06	W-box	WRKY	biotic/abiotic response, development	18, 19, 21
GTTGAC	bs	1.21e-06	W-box (core)	WRKY	biotic/abiotic response, development	18, 19, 21
TTGACCTC	bs	3.80e-06	W-box	WRKY	biotic/abiotic response, development	18, 19, 21
TGCTGCCGC	ss	7.52e-06	PRE2	Rad51-like	biotic response	22
ATGGTGAA	ss/bs	4.99e-06	GTGA motif	unknown	pollen development	45
GTGCAGAAAT	ss	3.92e-06	POLLEN1LELAT52	unknown	pollen development	46
ATTCTGTCAG	bs	6.82e-06	BIHD1OS	homeodomain	defence response	47
Downregulated
CGTACG	bs/ss	2.13e-06	CURECORECR	SBP domain family	copper response	48
GTACGTAC	bs/ss	3.05e-06	ACGTATERD1, ACGTABOX	AP2/EREBP, bZIP	dehydration response, seed development	49, 50
A(C/G)AGTGAC	bs/ss	3.81e-06	GTGA motif	unknown	pollen development	45
GAAAGTCCGG	bs/ss	6.06e-06	DOFCOREZM/EECCRCAH1 (-)	ZF-DOF	carbon metabolism	51
GGTTAGTTA	bs	7.19e-07	Myb1	MYB	defence response	40
TATTGGTTGT	ss	2.91e-06	REALPHALGLHCB21 (-), AREOSREP1	unknown	Phytochrome regulation gibberellin response	52, 53
CTACTGGC	bs	4.27e-06	CACTFTPPCA1	unknown	carbon metabolism	54
GTGCAATTAT	ss	6.69e-06	CAATBOX1	unknown	tissue-specific response	55

^a The known cis-elements in the overrepresented sequences are in bold.
^b The letters "bs" or "ss" designate whether the element was detected as overrepresented on both strands (bs) or just on the sense strand (ss); "bs/ss" refers to consensus sequence from bs and ss with priority on both strands and "ss/bs" with priority on the sense strand.
^c The P-value of motif with bs/ss or ss/bs annotation was calculated by average of the P-values for bb and ss.
^d Dash indicates that the complementary sequence of the known cis-element is harboured by the conserved motif.

ISSN: 1471-2229