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Table 6 Motifs identified by CisModule and BioProspector

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

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)
  1. 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.