Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis

Table 6 Motifs identified by CisModule and BioProspector

cluster	motifs	Known TF binding sequence contained (Reverse)	Binding (Reverse)
CisModule
Cluster 1 (NRT1.1)	ARARRARRAG	AAAG	Dof
	CWMGTGKSSC
	YAWAWAWMWAWAA	TAACAAA (GATA)	Myb (GATA)
	SRSCCACCAC
	ARAGRARRAG	AAAG	Dof
Cluster 2 (NiR)	MAMAAAHAWAWA
	CAYATCYMYCWC	(GATA, GGATA)	(GATA, Myb)
	GRRAGARRRRRR	AAAG	Dof
	ASAWRTATATR
	RRAGARRARRRG	AAAG	Dof
Cluster 3 (GS1-1)	AMMAAAMAAAAAAA
	RRARRARRAGA	AAAG	Dof
	YGRHSACGTSR
	WDMTATATRWW
	YGGHSACGTSR
Cluster 4 (GS1-4)	TWKGTTTKGKT
	CGTGRYYGSTVS	TGAC (CCAAT)	WRKY (CCAAT)
	KATATAKAKAT	GATA	GATA
	AGAARAMRAAR	AAAG	Dof
	GRSMCRYGWSR
BioProspector
Cluster 1 (NRT1.1)	MAAMARAMAAAAAAAA	AAAG	Dof
Cluster 2 (NiR)	MWTRGMCAWTCMTWWY	CCAAT	CCAAT
	RATAKGAATGTCYAWK	CCAAT
	RAWTTGRTMGGAWTK	GATA (CCAAT)	GATA (CCAAT)
	TKTTTYTYTTTTTTTT	(AAAG)	(Dof)
	WTRGAYATTCMTATY	GATA	GATA
		GGATA	Myb
Cluster 3 (GS1-1)	GGWSACGTGGMRA
	AARWAAAAAAAWAAAA
Cluster 4 (GS1-4)	WWWTWTTRTTTTMTT
	GARACAGASAGWKWSA	GATA (TAACTG)	GATA (Myb)

Candidate motifs from each cluster were identified by CisModule or BioProspector. They were subsequently searched against PLACE database to identify those containing previously published plant cis elements in the forward and reverse strand. Nucleotide abbreviations: R: A or G; Y: C or T; W: A or T; S: G or C; M: A or C; K: G or T; H: A, C or T; B: G, C or T; V: G, A or C; D: G, A or T; N: G, A, C or T.

ISSN: 1471-2164