Table 2.
Potential cis-elements identified in the promoters of downregulated genes in rad mutant
| Cis-elements | Motifs | Associated TFs | % (TIC), E-value* |
|---|---|---|---|
| AT-hook/PE1-like | ATATTTTTT | MYB (PF1) | 72 (14.31), 3e-004 |
| TCCAAAAA | MYB (PF1) | 71 (11.53), 6e-004 | |
| ATTTTTAAA | MYB (PF1) | 58 (13.45), 3e-004 | |
| TTTTTTTCTT | MYB (PF1) | 54 (14.95), 6e-004 | |
| MYB-box-like | TCCAAAAA | MYB (R2R3, MCB1/2) | 71 (11.53), 6e-004 |
| GATTAGTG | MYB (R2R3) | 68 (10.71), 6e-004 | |
| CAACCACA | MYB (R2R3) | 51 (11.98), 3e-004 | |
| CCACCCAGC | MYB (R2R3) | 51 (12.20), 3e-004 | |
| AAAATCCA | MYB (R2R3) | 50 (12.89), 2e-004 | |
| GT-element-like | GATTAGTG | MYB (GT-1/GT-3b) | 68 (10.71), 6e-004 |
| TTTTTTTCTT | MYB (GT-1) | 54 (14.95), 6e-004 | |
| GARE-like | AAAATCCA | MYB (R1, R2R3) | 50 (12.89), 2e-004 |
| Pyrimidine-box-like | TTTTTTTCTT | MYB (R1, R2R3) | 54 (14.95), 6e-004 |
| TCTTTTTT | MYB (R1, R2R3 | 54 (13.57), 3e-004 | |
| As-1/ocs/TGA-like | TCCGTCAC | bZIP (Gr. D, I, S) | 53 (11.81), 2e-004 |
| GAAGATGA | bZIP (Gr. D, I, S) | 54 (12.78), 2e-004 | |
| ABRE-like/G-box-like | CAACCACA | bZIP (Gr A) | 51 (11.98), 3e-004 |
| AuxRe-like | GATTAGTG | ARF | 68 (10.71), 6e-004 |
| Binding site of the HDZIPs-like | GATTAGTG | HDZIPs | 68 (10.71), 6e-004 |
| GCC-box-like | CGGCGGCG | ERF (I, IV, VII, X) | 60 (14.85), 6e-004 |
| AAAAG-element-like | TCTTTTT | DOF1/4/11/22 | 54 (13.57), 3e-004 |
| GAGA element-like | TCTCTCCC | GAGA-binding factor | 53(12.93), 8e-004 |
| TATA-box-like | TTTATTTT | TBP | 66 (13.19), 4e-004 |
| DBP1 binding site-like | ATTATAATA | DBP1 | 56 (12.79), 2e-004 |
* % percent occurrence among all upregulated genes, TIC total information content of homology, E-value E-value of homology with promoter database entry