TABLE 5.
Potential putative cis-elements identified in the promoters of upregulated genes in two intermediately tolerant genotypes (F291 and F274-2a).
| Cis-elements | Motifs | Associated TFs | % (TIC), E-value* |
| AT-hook/PE1-like | AGAAAAATG | MYB (PF1) | 58 (14.34), 2e-004 |
| GT-element-like | TTTGTTCA CATGTGTG TTTACTCT CTCTTAAA | MYB (GT-3) MYB (GT-3a) MYB (GT1/GT2) MYB (GT1/GT2) | 71 (13.29), 2e-004 58 (12.27), 2e-004 50 (12.92), 1e-004 50 (12.19), 0e+000 |
| GARE-like | TTTGTTCA | MYB (R1, R2R3) | 71 (13.29), 2e-004 |
| MYB-box-like | CCACCATG TTTGTTCA GCAAGGTG GGTTCGTC GATGGTATT | MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) | 79 (11.60), 3e-005 71 (13.29), 2e-004 67 (12.65), 3e-005 58 (11.20), 6e-005 54 (13.12), 2e-004 |
| MYB-box related-like | GCCACCAT | MYB-like | 63 (12.88), 3e-004 |
| As-1/ocs-like | GCAAGGTG AAGTTTGA CATGTGTG | bZIP (Gr. D, I, S) bZIP (Gr. D, I, S) bZIP (Gr. D, I, S) | 67 (12.65), 3e-005 63 (12.83), 1e-004 58 (12.27), 2e-004 |
| GCN4 motif | TTTGTTCA AGAAAGTG | bZIP (RISBZ1, Gr. G) bZIP (RISBZ1, Gr. G) | 71 (13.29), 2e-004 54 (13.04), 6e-005 |
| G-box-like | GCAAGGTG CATGTGTG | bZIP (Gr. G) (GBF 3, 5) bZIP (Gr. G) (GBF 3, 5, 6) | 67 (12.65), 3e-005 58 (12.27), 2e-004 |
| ABRE-like (DPBF binding site-like) | GCAAGGTG CATGTGTG | bZIP (DPBF-3) bZIP (DPBF-3) (Opaque-2) | 67 (12.65), 3e-005 58 (12.27), 2e-004 |
| ABRE-like | GCAAGGTG CATGTGTG | ABI5 (bZIP) ABI5 (bZIP) | 67 (12.65), 3e-005 58 (12.27), 2e-004 |
| ABRE-like | CATGTGTG | ABF2 (bZIP) | 58 (12.27), 2e-004 |
| GCC-box-like | GCCACCAT GCCGGAAA | ERF (I, IV, VII, X) ERF (I, IV, VII, X) | 63 (12.88), 3e-004 50 (12.53), 3e-004 |
| ERE-like | GCAAGGTG GCCACCAT GGTTCGTC GCCGGAAA | ERF/RAP2.1, RAP2.4, RAP2.9, RAP2.10 ERF/RAP2.3, RAP2.6 (Gr. III) ERF/RAP2.3, RAP2.6 (Gr. III) RAP2.11(Gr. III) | 67 (12.65), 3e-005 63 (12.88), 3e-004 58 (11.20), 6e-005 50 (12.53), 3e-004 |
| CRT/DRE-like | GCCACCAT GCCGGAAA | ERF (Gr., III, IV) ERF (Gr., III, IV) | 63 (12.88), 3e-004 50 (12.53), 3e-004 |
| JA response element-like | AAGTTTGA | ERF (Gr. VI, VIII, IX) ERF (Gr. VI, VIII, IX) | 63 (12.83), 1e-004 69 (13.75), 4e-004 |
| ABRE-like | CATGTGTG | FUS3, (Similar to VP1/ABI3-like proteins) FUS3, (Similar to VP1/ABI3-like proteins) | 58 (12.27), 2e-004 69 (11.61), 5e-005 50 (13.95), 3e-005 |
| ABRE-like | AGAAAGTG AGAAAAATG | AP2/B3 (Gr. II) Related to RAV2 AP2/B3 (Gr. II) Related to RAV2 | 54 (13.04), 6e-005 58 (14.34), 2e-004 |
| ABR-binding site-like | GCGGGAGA | AP2-like ABA repressor 1 (ABR1) | 54 (11.84), 9e-005 |
| Ethylene-insensitive 3 binding site-like | TTTGTTCA GCCGGAAA | EIL3 (EIN3) EIN2 | 71 (13.29), 2e-004 50 (12.53), 3e-004 |
| Aux-RE-like | TTTGTTCA AGAAAAATG | ARF1 ARF16 | 71 (13.29), 2e-004 58 (14.34), 2e-004 |
| W-box-like | TTTGTTCA | WRKY (Gr. I, IIa, IIc, III) | 71 (13.29), 2e-004 |
| Zinc-finger-binding site-like | GCAAGGTG GGTTCGTC AGAAAGTG GATGCGATT GCCGGAAA | ZnF (C2H2-type) ZnF (C2H2) ZnF (C2H2) ZnF (CCCH-type) ZnF (PhD) ZnF (PhD) | 71 (13.29), 2e-004 58 (11.20), 6e-005 54 (13.04), 6e-005 54 (13.12), 2e-004 50 (12.53), 3e-004 |
| IDD binding site-like | TTTGTTCA AGAAAAATG | IDD 2, 4, 5, 7 (ZnF) IDD 4, 5 (ZnF) | 71 (13.29), 2e-004 58 (14.34), 2e-004 |
| DRE-like | CCACCATG GGTTCGTC CATGTGTG AGAAAAATG AGAAAGTG CTCTTAAA AGCCGTAG | NAC (16, 92) NAC (46, 55, 58) NAP (NAC-like, activated by AP3/P1) NAM NAC (57, 71, 83, 103) CUC1, CUC2, CUC3 NAC (5, 11) NAC (5, 11, 20, 28, 45, 50, 58, 62, 71, 75, 96) VND (2, 3, 4, 6) CUC1, CUC2, CUC3 NAC (5, 62) NAC (58, 80, 87, 92) VND1, CUC1, CUC2, CUC3 | 79 (11.60), 3e-005 58 (11.20), 6e-005 58 (12.27), 2e-004 58 (14.34), 2e-004 54 (13.04), 6e-005 50 (12.19), 0e+000 50 (12.65), 8e-005 |
| AAAAG/CTTTT-element-like | ATCCCTTT AGAAAAATG AGAAAGTG | DOF (PBF) DOF-type zinc finger DOF (DOF 4) DOF (DOF 5.7) | 67 (11.52), 1e-004 58 (14.34), 2e-004 54 (13.04), 6e-005 |
| Heat shock binding factor element-like | CTCCCCCT AGAAAAATG AGAAAGTG | HSF (HSFB2A) HSF (HSFB2A) HSF (HSFB2A) | 67 (12.51), 2e-004 58 (14.34), 2e-004 54 (13.04), 6e-005 |
| S2-binding site-like | CTCCCCCT GCCACCAT GCCGGAAA | AS2 (LBD13) AS2 (LBD23) AS2 (LBD2, 13, 16) | 67 (12.51), 2e-004 63 (12.88), 3e-004 50 (12.53), 3e-004 |
| TCP binding site-like | GGTTCTTC | TCP (3, 20) | 58 (11.20), 6e-005 |
| ARR14-binding element-like | GATGCGATT | ARR-B (ARR14) | 54 (13.12), 2e-004 |
| CArG box-binding site-like | CCACCATG GCCACCAT AGAAAAATG AGAAAGTG TTTACTCT | MADS (AGL 42, 55) MADS (AGL 55) MADS box (AGL 6, 15, 16) MADS box (AGL 6, 15, 16) MADS (AGL 16) | 79 (11.60), 3e-005 63 (12.88), 3e-004 58 (14.34), 2e-004 54 (13.04), 6e-005 50 (12.92), 1e-004 |
| GATA binding site-like | TCTTCCAT GCAAGGTG | GATA1 GATA1 | 67 (12.72), 3e-005 67 (12.65), 3e-005 |
| E-box-like | CATGTGTG | BES/BZR (BES1/BZR1 homologue 2, 3, 4) | 58 (12.27), 2e-004 |
| E-box-like/G-box-like | GAAGTAAC CATGTGTG AGCCGTAG | bHLH (Gr. III, VII) bHLH (Gr. III, VII) bHLH (Gr. III, VII) | 63 (11.53), 1e-004 58 (12.27), 2e-004 50 (12.65), 8e-005 |
| BPC-binding site-like | AGAAAAATG AGAAAGTG | BPC (BPC1) BPC (BPC1) | 58 (14.34), 2e-004 54 (13.04), 6e-005 |
% = percent occurrence among all upregulated genes, TIC = total information content of homology, E-value* = E-value of homology with promoter database entry.