TABLE 1.
Potential putative cis-elements identified in the promoters of upregulated genes in tolerant genotypes (Nipponbare, F291, F274-2a, 8391, and 8753).
| Cis-elements | Motifs | Associated TFs | % (TIC), E-value* |
| AT-hook/PE1-like | TTTTTTTTA | MYB (PF1) | 61 (16.56), 1e-004 |
| GT-element-like | CTGAAAAAG | MYB (GT-1/GT-3b) | 65 (12.79), 3e-004 |
| GARE-like | CAACAACA | MYB (R1, R2R3) | 74 (11.70), 0e+000 |
| MYB-box-like | GGTGGGCG | MYB (R2R3) | 78 (10.89), 3e-004 |
| CAACAACA | MYB (R2R3) | 74 (11.70), 0e+000 | |
| GACAAATT | MYB (R2R3) | 65 (12.58), 7e-004 | |
| CAAAACCA | MYB (R2R3) | 61 (13.34), 4e-004 | |
| As-1/ocs-like | CGTTGATC | bZIP (Gr. D, I, S) | 70 (11.38), 1e-004 |
| CTGAAAAAA | bZIP (Gr. D, S) | 65 (12.79), 3e-004 | |
| GCN4 motif | CAACAACA | bZIP (RISBZ1, Gr. G) | 74 (11.70), 0e+000 |
| GACAAATT | bZIP (RISBZ1, Gr. G) | 65 (12.58), 6e-004 | |
| CAMTA5 binding site-like | CCACACAA | bZIP (CAMTA5) | 65 (12.57), 6e-004 |
| GCC-box-like | AGTGGGCG | ERF (I, IV, VII, X) | 78 (10.89), 3e-004 |
| CGCCGCCG | ERF (I, IV, VII, X) | 70 (14.42), 9e-005 | |
| CGCCGCCTC | ERF (I, IV, VII, X) | 57 (14.27), 2e-004 | |
| ERE-like | GCCGAGAG GCGGCCATT TGCTCGCCG | ERF/RAP2.3, RAP2.10 (Gr. III) ERF/RAP2.2, RAP2.3 (Gr. III) ERF/RAP2.6, RAP2.10 (Gr. VII) ERF/RAP2.6 (Gr. VII) | 65 (11.42), 3e-004 52 (12.47), 4e-004 52 (13.56), 2e-004 |
| RAV1a-like | CAACAACA | ERF/RAV1 (Gr. II, III and RAV1) | 74 (11.70), 0e+000 |
| CRT/DRE-like | CGCCGCCTC | ERF (Gr., III, IV) | 57 (14.27), 2e-004 |
| JA response element-like | CTTTGATC | ERF (ERF Gr. VI, VIII, IX) | 70 (11.38), 1e-004 |
| ABRE-like | ATTTAGCG TGCTTGCCG | ABI3 (B3 domain of AP2/) ABI3 (B3 domain) | 61 (12.23), 2e-004 52 (13.66), 2e-004 |
| ABR-binding site-like | GCCGAGAG TGCTCGCCG | AP2-like ABA repressor 1 (ABR1) AP2-like ABA repressor 1 (ABR1) | 65 (11.42), 3e-004 52 (13.66), 2e-004 |
| Ethylene-insensitive 3 binding site-like | AAATGCAAA GAATGCAAA | EIL3 (EIN3) EIL3 (EIN3) | 61 (13.85), 9e-005 61 (13.85), 9e-005 |
| Aux-RE-like | CAACAACA ACGAGACC | ARF1 ARF1, ARF5, ARF7 | 74 (11.70), 0e+000 52 (11.65), 3e-004 |
| W-box-like | GTCAAATT | WRKY (Gr. I, IIa, IIc, III) | 56 (15.03), 9e-005 |
| Zing finger binding site-like | CAACAACA GCCGAGAG | ZnF (C2H2-type) ZnF (C2H2-type) | 74 (11.70), 0e+000 65 (11.42), 3e-004 |
| IDD binding site-like | CAACAACA CCACACAA | IDD 2, 4, 5, 7 (ZnF) IDD (ZnF) | 74 (11.70), 0e+000 65 (12.57), 6e-004 |
| Zinc-finger-binding site-like | AGTGGGCG | STZ (Salt tolerant zinc finger) | 78 (10.89), 3e-004 |
| DRE-like | CAACAACA GCCGAGAG AAATGCAAA TGCTTGCCG TGCTCGCCG ACGAGACC ACGAGACC | NAC (38) NAC (65) NAC (11, 45) NAC (58) NAC (62) NAC (NAM) NAP,(NAC-like, activated by AP3/P1) | 74 (11.70), 0e+000 65 (11.42), 3e-004 61 (13.85), 9e-005 52 (13.66), 2e-004 52 (13.66), 2e-004 52 (11.65), 3e-004 52 (11.65), 3e-004 |
| AAAAG/CTTTT-element-like | CTGAAAAAA CTGAAAAAG | DOF (DOF1/4/11/22) DOF (DOF1/4/11/22) | 65(12.79), 3e-004 65(12.79), 3e-004 |
| Heat shock binding factor element-like | GCCGAGAG ATTTAGCG TTCTTCCTG | HSF(HSF3) HSF(HSFA4A, HSF7) HSF (HSFA6B HSFB4, HSF7) | 65 (11.42), 3e-004 61 (12.23), 2e-004 52 (13.96), 3e-004 |
| S2-binding site-like | CCACACAA GACAAATT CTGAAAAAG ATTTAGCG GCGGCCATT TTCTTCCTG | AS2 (LBD16, 19) AS2 (LBD16) AS2 (LBD16, 18) AS2 (LBD2) AS2 (LBD23) AS2 (LBD30) | 65 (12.57), 6e-004 65 (12.58), 7e-004 65 (12.79), 3e-004 61 (12.23), 2e-004 52 (12.47), 4e-004 52 (13.96), 2e-004 |
| E2F binding site-like | ATTTAGCG ATGGGACT GCGGCCATT | E2F-like protein, E2Fa, E2Fc (DEL1) E2F (DEL1) E2F (DEL2) | 61 (12.23), 2e-004 52 (12.87), 3e-004 52 (12.47), 4e-004 |
| TCP binding site-like | ACGAGACC | TCP (TCP 3, 24) | 52 (11.65), 3e-004 |
| HD-ZIP binding site-like | AAATGCAAA | HD-ZIP (ATHB4) | 61 (13.85), 9e-005 |
| ARR-14 binding element-like | ACGAGACC | ARR-B (ARR14) | 52 (11.65), 3e-004 |
| CArG box-binding site-like | GACAAATT GCCGAGAG AAATGCAAA ATTTAGCG | MADS-box (AGL 6, 15) MADS-box (AGL 95) MADS-box (AGL16) MADS-box (AGL16) | 65 (12.58), 6e-004 65 (11.42), 3e-004 61 (13.85), 9e-005 61 (12.23), 2e-004 |
| GATA binding site-like | ACGAGACC GCGGCCATT | GATA1 GATA1 | 52 (11.65), 3e-004 52 (12.47), 4e-004 |
| DBP-binding site-like | TAAATATA | DBP1 | 56 (13.75), 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.