Table 1 Identified Consensus Promoter Motifs in Original LEA Genes and the Plant TFs That Were Predicted to Bind to Them in the PATCH Program
From: The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network
| Â | Consensus motif pattern | Species/gene identifier | Position | Score | Predicted plant TF | Site binding sequence |
|---|---|---|---|---|---|---|
1 | GAGAAGAAG | AT$PHYA_01 | 2 (−) | 100 | CAMTA3 | TCTTCT |
2 | GGCGCGYGG | AT$AVP1_01 | 2 (−) | 91.7 | (VOZ1&2)2, CAMTA1 | ACGCGC |
RICE$ZB8_02 | 3 (+)(−) | 91.7 | CBT | CGCGCG | ||
AS$CBT_01 | 3 (+) | 91.7 | CBT | CGCGCG CACGCG | ||
MAIZE$ADH1P_01&03 | 5 (+) | 90.0 | No match | CGTGG | ||
DAUCE$DC3_04 | 3 (−) | 91.7 | DPBF-1, DPBF-2 | CACGCG | ||
3 | CCGTCGWCC | AT$H4_05 | 1 (+) | 100 | Â | CCGTCG |
AT$COR15A_01 | 3 (−) | 90 | ANT, CBF1, CBF2, DREB1A, ERFLP1, TSI1 | CCGAC | ||
AT$RD29B_01 | 3 (−) | 90 | CBF1 | CCGAC | ||
AT$COR78_01 | 3 (−) | 90 | ANT, CBF1, CBF2, DREB1A | CCGAC | ||
AT$COR15B_01 | 3 (−) | 90 | CBF1, CBF2, DREB1A | CCGAC | ||
RAPE$BN115_01 | 3 (−) | 90 | CBF17, CBF5 | CCGAC | ||
AT$FL0521F13_01 | 3 (−) | 91.7 | DREB1A | GCCGAC | ||
BAR$HVA1_03 | 3 (−) | 90 | CBF1, CBF2 | CCGAC | ||
GOSHI$LEAD113_01 | 3 (−) | 90 | DBP1 | CCGAC | ||
AT$COR78_01 | 3 (−) | 90 | ANT, CBF1, CBF2, DREB1A | CCGAC | ||
AT$COR15A_03 | 3 (−) | 91.7 | DREB1A | GCCGAC | ||
AS$CEF1_02 | 3 (−) | 90 | CEF1 | CCGAC | ||
GOSHI$LEAD113_01 | 3 (−) | 90 | DBP1 | CCGAC | ||
4 | GCGGAGAAG | No match | Â | Â | Â | Â |
5 | GCVGGGCAG | MAIZE$ADH11S_06 | 3 (−) | 90 | GCBP-1, Sp1 | GCCCC |
6 | AACADCAAA | WHEAT$CATHB_08 | 1 (−), 2 (−) | 90 | GAMYB | TTGTT |
7 | AGCAGCAGC | No match | Â | Â | Â | Â |
8 | MCCGACGGC | AT$COR15A_03&04 | 1 (+) | 91.7 | DREB1A | GCCCAG |
MAIZE$DHN1_01 | 1 (+) | 91.7 | DBF1, DBF2 | ACCGAC | ||
AS$TINY2_01 | 1 (+) | 91.7 | TINY2 | ACCGAC | ||
HELAN$HSP176_02 | 1 (−) | 91.7 | No match | GTCGGT | ||
AT$COR15A_01 | 2 (+) | 100 | ANT, CBF1, CBF2, DREB1A, ERFLP1, TSI1 | CCGAC | ||
RAPE$BN115_02 | 2 (+) | 100 | CBF17, CBF5 | CCGAC | ||
AS$DREBLP1_01 | 2 (+) | 100 | DREBLP1 | CCGAC | ||
GOSHI$LEAD113_01 | 2 (+) | 100 | DBP1 | CCGAC | ||
AT$H4_05 | 3 (−) | 100 | No match | CCGTCG | ||
9 | ACACATACG | No match | Â | Â | Â | Â |
10 | TTCMTTTCA | DAUCE$EXT_02 | 1 (−) | 92.86 | No match | AAATGAA |
POT$KST1_01 | 1 (−) | 90 | DOF1 | AAAAG | ||
BAR$CPI_01 | 3 (−) | 90 | PBF, SED | AAAGG | ||
AT$WUSCHEL_01 | 4 (−) | 91.7 | No match | TGAAAA | ||
11 | AWATTATAT | No match | Â | Â | Â | Â |
12 | CGGCGSCGG | AT$HLS1_01 | 2 (−) | 91.7 | ATERF7, ERF-1,2,3,4,5, ERFLP1 | GCCGCC |
|  |  | TO$NP24PP_0 | 2 (−) | 91.7 | ERF-1,2,3,4 | GCCGCC |
|  |  | AS$GCCBOX_02 | 2 (−) | 91.7 | Pti4 | GCCGCC |
|  |  | AS$CEF1_01 | 2 (−) | 91.7 | CEF1 | GCCGCC |
| Â | Â | BAR$HVA1_04 | 3 (+) | 90 | CBF1 | GCCGCC |
|  |  | AT$H4_05 | 4 (−) | 91.7 | No match | CCGTCG |
|  |  | AT$COR15A_0 | 5 (−) | 90 | ANT; CBF1,2; DREB1A, ERFLP1, TSI | CCGAC |
|  |  | RAPE$BN115_01 | 5 (−) | 90 | CBF17, CBF5 | CCGAC |
13 | CTTCTTCCT | No match | Â | Â | Â | Â |
14 | AAAATAATA | SOYBN$VSPB_03 | 1 (−) |  |  | TATTTT |
15 | AAATYGARA | AS$ARR10_17 | 2 (−) | 90 | ARR10 | CGATT |
16 | AGAAGATCA | AT$PHYA_01 | 1 (−) | 100 | CAMTA3 | TCTTCT |
17 | RCAGCAGCA | No match | Â | Â | Â | Â |
18 | CGCGCGGCG | RICE$ZB8_02 | 1 (+) | 100 | CBT | CGCGCG |
19 | GTTAMATAT | AT$CAB2_03 | 1 (+) | 90 | GT-3a | GTTAC |
PV$PHS_03 | 2 (+) | 90 | No match | TTAAA | ||
RICE$ZB8_01 | 2 (−) | 92.86 | TBP2 | TATTTAA | ||
MAIZE$PMS1_ | 3 (+) | 92.86 | No match | TAAATAT | ||
20 | TTGYTTAAT | WHEAT$CATHB | 1 (+) | 90 | GAMYB | TTGTT |
AS$ARR10_18 | 2 (+) | 90 | ARR10 | TGATT | ||
PEA$RS3A_03 | 3 (+) | 91.67 | GT-1, GT-1a, SBF-1 | GGTTAA | ||
OAT$PHYA3_0 | 3 (+) | 92.86 | No match | GGTTAAT | ||
RICE$PHYA_0 | 3 (+) | 92.86 | GT-1, GT-2 | GGTTAAT | ||
PV$PHS_03 | 4 (+) | 91.67 | No match | TTTAAT | ||
PV$PHS_03 | 4 (−) | 90 | No match | TTAAA | ||
21 | TGTACTCSC | TO$LAP171A_ | 3 (−) | 100 | JAMYC2 | GAGTA |
22 | MSGATGRTG | BARL$CAB11_12 | 2 (−) | 90 | MCB1, MCB2 | CATCC |
23 | AGCACACAT | No match | Â | Â | Â | Â |
24 | CMAAAAGCT | AS$PF1_01&02 | 2 (−) | 90 | PF1 | TTTTT |
POT$KST1_01 | 3 (+) | 100 | DOF1 | AAAAG | ||
25 | CGGCTCGCC | No match | Â | Â | Â | Â |
26 | GAATGGATG | WHEAT$CAB1_ | 4 (−) | 100 | MCB1, MCB2 | ATCCA |
|  | BARL$CAB11&12 | 5 (−) | 100 | MCB1, MCB2 | CATCC | |
27 | ATCAAGGAA | AT$ATBZIP60 | 2 (+) | 100 | No match | TCAAG |
28 | TGGCGCCGC | No match | Â | Â | Â | Â |
29 | GCCGSGGCC | MAIZE$ADH1P&11 | 2 (−) | 91.67 | No match | CCCCGG |
MAIZE$ADH1P | 3 (+) | 90 | No match | CGTGG | ||
AS$mEMBP_17 | 3 (−) | 91.67 | EmBP-1a | GCCACG | ||
MAIZE$ADH11 | 4 (−) | 90 | GCBP-1, Sp1 | GCCCC | ||
30 | AATTTTRGT | AS$PF1_01 | 3 (+) | 90 | PF1 | TTTTT |