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.