TABLE 3.
Potential putative cis-elements identified in the promoters of upregulated genes in extremely tolerant genotypes (8391 and 8753).
| Cis-elements | Motifs | Associated TFs | % (TIC), E-value* |
| AT-hook/PE1-like | AAAAATAT ACAAAAAAAA | MYB (PF1) MYB (PF1) | 67 (13.84), 3e-004 52 (16,17), 0e+000 |
| GT-element-like | CATTTGTT AGACGTGG | MYB (GT-3) MYB (GT-3a) | 63 (11.57), 6e-005 63 (10.82), 9e-005 |
| GARE-like | CATTTGTT | MYB (R1, R2R3) | 63 (11.57), 6e-005 |
| MYB-box-like | TGCTACTG AGAACATAG CATTTGTT ACAAAAAAAA | MYB (R2R3) MYB (R2R3) MYB (R2R3) MYB (R2R3) | 81 (11.45), 2e-005 70 (12.40), 2e-004 63 (11.57), 6e-005 52 (16.17), 0e+000 |
| As-1/ocs-like | AAATTTGA CATTGTGA TTGAAAAAT AGACGTGG | bZIP (Gr. D, I, S) bZIP (Gr. D, S) bZIP (Gr. D, S) bZIP (Gr. D, I, S) | 67 (13.30), 4e-004 67 (12.12), 9e-005 63 (14.06), 2e-004 63 (10.82), 9e-005 |
| C-box-like/G-box-like | AGACGTGG AGACGTGG AGTCGTGG | bZIP (Gr. A, B, H) bZIP (Gr. G) (GBF 1, 3, 5, 6) bZIP (Gr. G) (GBF 6) bZIP (Gr. G), (CPRF5, CPRF6,, CPRF7) | 63 (10.82), 9e-005 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| HY-5 binding site-like | AGACGTGG | bZIP (Gr. H) (HY5) | 63 (10.82), 9e-005 |
| GCN4 motif | CATTTGTT ACAAAAAAAA | bZIP (RISBZ1, Gr. G) bZIP (RISBZ1, Gr. G) | 63 (11.57), 6e-005 52 (16.17), 0e+000 |
| CAMTA5 binding site-like | AGTCGTGG | bZIP (CAMTA5) | 63 (10.82), 9e-005 |
| ABRE-like (DPBF binding site-like) | AGACGTGG | bZIP (DPBF-3) | 63 (10.82), 9e-005 |
| ABRE-like | AGACGTGG AGTCGTGG | ABI5 (bZIP) ABI5 (bZIP) | 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| ABRE-like | AGACGTGG AGTCGTGG | ABF1, ABF2 (bZIP) ABF2 (bZIP) | 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| ERE-like | AGACGTGG AGTCGTGG | ERF/RAP2.3, (Gr. III) ERF/RAP2.3, RAP2.6 RAP2.10 (Gr. III), ERF (Gr. VII) | 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| DRE/CRT-like | AGTCGTGG | ERF/DDF1, CBF3, CBF4, (Gr. III, IV) | 63 (10.82), 9e-005 |
| ABRE-like | AGAAAGTA | AP2/B3 (Gr. II) Related to RAV2 | 63 (12.66), 8e-005 |
| JA response element-like | AAATTTGA | ERF (Gr. VI, VIII, IX) | 67 (13.30), 4e-004 |
| Ethylene-insensitive 3 binding site-like | AGAACATAG | EIL3 (EIN3) | 70 (12.40), 2e-004 |
| Aux-RE-like | CATTTGTT TTGAAAAAT | ARF1 ARF16 | 63 (11.57), 6e-005 63 (14.06), 2e-004 |
| W-box-like | TTGAAAAAT | WRKY (Gr. I, IIa, IIc, III) | 63 (14.06), 2e-004 |
| Zinc finger binding element-like | TCAAATTAA | ZnF (ZCT1, ZCT2, ZCT3) | 59 (13.81), 1e-005 |
| Zing finger binding site-like | TTGAAAAAT AGAAAGTA GAAATCCT TAGTAGTA | ZnF (C2H2-type) ZnF (C2H2-type) ZnF (C2H2-type) ZnF (C2H2-type) | 63 (14.06), 2e-004 63 (12.66), 8e-005 63 (11.69), 2e-004 52 (13.63), 2e-005 |
| IDD binding site-like | TTGAAAAAT | IDD 2, 5 (ZnF) | 63 (14.06), 2e-004 |
| DRE-like | TGCTACTG CATTGTGA AGACGTGG AGTCGTGG AGACGTGG AGTCGTGG | NAC (62, 96) NAC (46) NAC (34, 42, 46, 47, 55, 70, 94) NAC (45, 46, 47) NAC (34, 42, 45, 55, 58) NAC (NAM) NAP (NAC-like, activated by AP3/P1) NAP (NAC-like, activated by AP3/P1) | 81 (11.45), 2e-005 67 (12.12), 9e-005 63 (10.82), 9e-005 63 (10.82), 9e-005 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| ATAF1-binding site-like | AGTCGTGG | ATAF1(NAC) | 63 (10.82), 9e-005 |
| AAAAG/CTTTT-element-like | AGAAAGTA | DOF (DOF 4.5) | 63 (12.66), 8e-005 |
| Heat shock binding factor element-like | AGAACATAG CATTGTGA GAAATCCT | HSF (HSFB2A HSF) HSF (HSFB2A) (HSFA8) | 70 (12.40), 2e-004 67 (12.12), 9e-005 63 (11.69), 2e-004 |
| S2-binding site-like | CATTGTGA AGACGTGG AGTCGTGG ACAAAAAAAA | AS2 (LBD16, 18, 19) AS2 (LBD2) AS2 (LBD23) AS2 (LBD16) | 67 (12.12), 9e-005 63 (10.82), 9e-005 63 (10.82), 9e-005 52 (16.17), 0e+000 |
| HD-ZIP binding site-like | AAAATTAG | ATHB3 | 55 (12.95), 5e-005 |
| ARR14-binding element-like | AGAACATAG | ARR-B (ARR14) | 70 (12.40), 2e-004 |
| CArG box-binding site-like | ACAAAAAAAA AGAAAGTA AAGATTGCA | MADS (AGL 15, 16) MADS (AGL 6) MADS (AGL 6) | 52 (16.17), 0e+000 63 (12.66), 8e-005 74 (12.50), 2e-004 |
| E-box-like | AGACGTGG | BES/BZR (BES1/BZR1) | 63 (10.82), 9e-005 |
| E-box-like/G-box-like | AGACGTGG AGTCGTGG | bHLH (Gr. III, VII) bHLH (Gr. III, VII) | 63 (10.82), 9e-005 63 (10.82), 9e-005 |
| E-box-like | AGACGTGG | BEE2 (bHLH) BIM1, BIM3 (bHLH) | 63 (10.82), 9e-005 |
| BBRE-element-like/G-box-like | AGACGTGG | BAM8 (bHLH): BAMs | 63 (10.82), 9e-005 |
| BRRE-element/G-box-like | AGACGTGG | BEH4 (bHLH) | 63 (10.82), 9e-005 |
| DBP-binding site-like | TCAAATTAA | DBP | 59 (13.81), 1e-005 |
| TATA-box-like | TAAATATA | TBP | 56 (13.75), 1e-005 |
% = percent occurrence among all upregulated genes, TIC = total information content of homology, E-value* = E-value of homology with promoter database entry.