TABLE 2.
Potential putative cis-elements identified in the promoters of upregulated genes in highly tolerant genotypes (F291, F274-2a, 8391, and 8753).
| Cis-elements | Motifs | Associated TFs | %(TIC), E-value* |
| AT-hook/PE1-like | TTAAAAAC TTAAAAAATA TATTAAAAAA TTAATTTTT | MYB (PF1) MYB (PF1) MYB (PF1) MYB (PF1) | 63 (13.49), 2e-004 63 (16.52), 2e-005 63 (15.86), 5e-005 56 (15.46), 1e-004 |
| GT-element-like | CAACCACA ATTTGATTT CCAACCAA TTTGTATTTA TGCATGTA | MYB (GT-1) MYB (GT-1) MYB (GT-1) MYB (GT-3b) MYB (GT-3a) | 81 (11.63), 3e-004 81 (13.98), 5e-005 69 (11.71), 1e-004 63 (13.49), 2e-004 50 (13.95), 3e-005 |
| GARE-like | CCAACCAA | MYB (R1, R2R3) | 69 (11.71), 1e-004 |
| MYB-box-like | TAAAACAAA TAAAACAGA AAACCACA CAACCACA GCTAGCTAGA CAAGCTGC CCAAACAA CCAACCAA | MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) | 94 (12.79), 1e-004 94 (12.79), 1e-004 81 (11.63), 3e-004 81 (11.63), 3e-004 81 (12.81), 3e-004 69 (12.41), 1e-004 69 (11.71), 1e-004 69 (11.71), 1e-004 |
| MYB-box related-like | AAGCTGAG TTAATTTTT | MYB-like (CDC5) MYB-like (CCA1, CDA-1) | 69 (11.15), 9e-005 56 (15.46), 1e-004 |
| As-1/ocs-like | ATTTGATTT TGAAGCTT GATCGTGA | bZIP (Gr. D, I, S) bZIP (Gr. D, I, S) bZIP (Gr. D, I, S) | 81 (13.98), 5e-005 69 (12.23), 6e-005 56 (13.61), 5e-005 |
| ABRE-like | CAAGCTGC GATCGTGA TGCATGTA | bZIP (Gr. A) bZIP (Gr. A) bZIP (Gr. A) | 69 (12.41), 1e-004 56 (13.61), 5e-005 50 (13.95), 3e-005 |
| GCN4 motif-like | TAAAACAAA CCAAACAA AGAAAGTG | bZIP (RISBZ1, Gr. G) bZIP (RISBZ1, Gr. G) bZIP (RISBZ1, Gr. G) | 94 (12.79), 1e-004 69 (11.71), 1e-004 50 (12.42), 5e-004 |
| HY-5 binding site-like | ATTTGATTT | bZIP (Gr. H)(HY5) | 81 (13.98), 5e-005 |
| G-box-like | GATCGTGA TGCATGTA | bZIP (Gr. G) (GBF3, 5, 6) bZIP (Gr. G) (GBF3, 5) | 56 (13.61), 5e-005 50 (13.95), 3e-005 |
| CAMTA5 binding site-like | GATCGTGA | bZIP (CAMTA5) | 56 (13.61), 5e-005 |
| ABRE-like (DPBF binding site-like) | GATCGTGA TGCATGTA | bZIP (DPBF-3) bZIP (DPBF-3) (Opaque-2) | 56 (13.61), 5e-005 50 (13.95), 3e-005 |
| ABRE-like | GATCGTGA | ABI5 (bZIP) | 56 (13.61), 5e-005 |
| ABRE-like | GATCGTGA | ABF2 (bZIP) | 56 (13.61), 5e-005 |
| ERE-like | GCTCCATC | ERF/RAP 2.4 (Gr. III) | 69 (13.21), 8e-005 |
| JA response element-like | ATTTGATTT AAGTCAAA | ERF (Gr. VI, VIII, IX) ERF (Gr. VI, VIII, IX) | 81 (13.98), 5e-005 69 (13.75), 4e-004 |
| ABRE-like | CAAGCTGC GCATGGGC TGCATGTA | ABI3/V1P1 (B3 domain of AP2/ERF) FUS3, (Similar to VP1/ABI3-like proteins) FUS3, (Similar to VP1/ABI3-like proteins) | 69 (12.41), 1e-004 69 (11.61), 5e-005 50 (13.95), 3e-005 |
| B3-binding site-like | AGAAAGTG | AP2/B3-like | 50 (12.42), 5e-004 |
| Ethylene-insensitive 3 binding site-like | TCTTCCAT | EIL3 (EIN3) | 50 (13.56), 6e-005 |
| Aux-RE-like | TAAAACAAA CCAAACAA TTTGTATTTA | ARF1 ARF1 ARF1 | 94 (12.79), 1e-004 69 (11.71), 1e-004 63 (13.49), 2e-004 |
| W-box-like | ATTTGATTT AAGTCAAA | WRKY (Gr. I, IIa, IIc, III) WRKY (Gr. I, IIa, IIc, III) | 81 (13.98), 5e-005 69 (13.75), 4e-004 |
| Zinc-finger-binding site-like | ATTTGATTT GATCGTGA | ZnF (ZCT1, ZCT2, ZCT3) ZnF (GAL3) | 81 (13.98), 5e-005 56 (13.61), 5e-005 |
| Zing finger binding site-like | TAAAACAAA CCAAACAA | ZnF (C2H2-type) ZnF (C2H2-type) | 94 (12.79), 1e-004 69 (11.71), 1e-004 |
| IDD binding site-like | TAAAACAAA CCAAACAA | IDD2, 4, 5, 7 (ZnF) IDD2, 4, 5, 7 (ZnF) | 94 (12.79), 1e-004 69 (11.71), 1e-004 |
| DRE-like | CAAGCTGC TGAAGCTT TCATGGGC AAGCTGAG GATCGTGA AGAAAGTG TGCATGTA | NAC (5, 45, 62, 71, 96) VND (2, 3, 4, 6) SND3 NAC (45, 58)VND 6 NAC (57, 58, 87, 92) CUC3 NAC (45) NAC (46, 47, 55, 58, 92) NAP(NAC-like, activated by AP3/P1) NST1 (NAC) ATAF1NAC (5, 45, 62, 7, 96) VND (2, 3, 4, 6) NAC (46, 57, 78) CUC1, CUC2 | 69 (12.41), 1e-004 69 (12.23), 6e-005 69 (11.61), 5e-005 69 (11.15), 9e-005 56 (13.51), 5e-005 50 (12.42), 5e-004 50 (13.95), 3e-005 |
| AAAAG/CTTTT-element-like | TATTAAAAGA AGAAAGTG | DOF (DOF1/4/11/22) OBP3 DOF-type zinc finger | 63 (15.86), 5e-005 50 (12.42), 5e-004 |
| Heat shock binding factor element-like | AGAAAGTG | HSF (HSFB2A) | 50 (12.42), 5e-004 |
| S2-binding site-like | AAACCACA GCTCCATC GATCGTGA | AS2 (LBD16, 19) AS2 (LBD13) AS2 (LBD2, 19) | 81 (11.63), 3e-004 69 (13.21), 8e-005 56 (13.61), 5e-005 |
| TCP binding site-like | CAACCACA GCTCCATC | TCP (TCP 15, 16) TCP (TCP3) | 81 (11.63), 3e-004 69 (13.21), 8e-005 |
| HD-ZIP binding site-like | CAACCACA ATTTGATTT TGCATGTA | HD-ZIP (ATHB7) HD-ZIP (ATHB6, 7, 12 and 13) HD-ZIP (ATHB4) | 81 (11.63), 3e-004 81 (13.98), 5e-005 50 (13.95), 3e-005 |
| ARR10-binding element-like | ATTTGATTT | ARR-B (ARR10) | 81 (13.98), 5e-005 |
| CArG box-binding site-like | TAAAACAAA ATTTAGCG TCTTCCAT AGAAAGTG | MADS (AGL 6, 15) MADS (AGL 6, 15) MADS (AGL 16) MADS box (AGL 6, 15, and 16) | 94 (12.79), 1e-004 65 (12.58), 6e-004 50(13.56), 6e-005 50 (12.42), 5e-004 |
| GATA binding site-like | CAACCACA CCAACCAA | GATA1 GATA1 | 81 (11.63), 3e-004 69 (11.71), 1e-004 |
| E-box-like | GATCGTGA TGCATGTA | BES/BZR (BES1/BZR1) BES/BZR (BES/BZR1 homologue 2 and 3) | 56 (13.61), 5e-005 50 (13.95), 3e-005 |
| E-box-like/G-box-like | GATCGTGA TGCATGTA | bHLH (Gr. III, VII) bHLH (Gr. III, VII) | 56 (13.61), 5e-005 50 (13.95), 3e-005 |
| MBF1 binding element | TCCTCCTC | MBF1 (MBF1c) | 56 (13.42), 2e-004 |
| BPC-binding site-like | TTTCTCTC GTTCTCTC AGAAAGTG | BPC (BPC1, 6) BPC (BPC1) BPC (BPC1) | 81 (12.26), 3e-004 81 (12.26), 3e-004 50 (12.42), 5e-004 |
| DBP-binding site-like | TATTAAAAAA TTAATTTTT | DBP DBP | 63 (15.86), 5e-005 56 (15.46), 1e-004 |
| TATA-box-like | GTAATTATA | TBP | 56 (15.47), 2e-005 |
% = percent occurrence among all upregulated genes, TIC = total information content of homology, E-value* = E-value of homology with promoter database entry.