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

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

Overrepresented motif sequencea Strandb P-valuec Known homologous cis-element
    Elementd 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
  1. a The known cis-elements in the overrepresented sequences are in bold.
  2. 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.
  3. 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.
  4. d Dash indicates that the complementary sequence of the known cis-element is harboured by the conserved motif.