S. No. | Name of cis-element | Putative binding site | Function of the cis-element | TFs | Ref |
1 | ARR1AT | NGATT; N = A/T/G/C (Motif 5 & 6 of dicot) | ARR1 is a response regulator; found in Arabidopsis; N = G/A/C/T; AGATT is also present in the promoter of rice non-symbiotic haemoglobin-2 (NSHB) gene. | None | [41] [42] |
2 | BOX-4 | ATTAAT (Motif 9 of dicot) | Part of a conserved DNA molecule involved in light responsiveness | None | [43] |
3 | CAAT-BOX | CAAT (Motif 7 of dicot) | “CAAT promoter consensus sequence” found in legA gene of pea | None | [44] |
4 | DOFCOREZM | AAAG (Motif 7 of monocot) | Core dof protein binding site was found in maize; zinc finger, and is unique to plants; Four cDNAs encoding Dof proteins, Dof1, Dof2, Dof3 and PBF, have been isolated maize; PBF is an endosperm specific Dof protein that binds to form prolamin box; and enhances transcription from the promoters of both cytosolic orthophosphate promoter and non-photosynthetic PEPC gene | DOF | [45] |
5 | E-BOXNNAPA/ MYCCONSENSUAT | CANNTG; N = A/T/G/C (Motif 7 of dicot) (Motif 5 of monocot) | The site is present in the promoter of rd22 (dehydration-responsive gene) and in many other genes in Arabidopsis; Binding site of ATMYC2 (previously known as rd22BP1); N = A/T/G/C; MYC recognition sequence in CBF3 promoter; Binding site of ICE1 (inducer of CBF expression 1) that regulates the transcription of CBF/DREB1 genes in the cold in Arabidopsis. E-box of napA storage-protein gene of Brassica napus. This sequence is also known as RRE (R response element). | ICE1 | [46] [47] [48] [49] [50] |
6 | GTGANTG10 | GTGA (Motif 5 of dicot) | “GTGA motif” found in the promoter of the tobacco late pollen gene g10 which shows homology to pectate lyase and is the putative homologue of the tomato gene lat56; Located between −96 and −93 | None | [51] |
7 | POLLENLELAT52 | AGAAA (Motif 1 of monocot) | Regulatory element responsible for pollen specific activation of tomato lat52 gene; Found at −72 to −68 region. Also found in the promoter of tomato endo-beta-mannanase gene. | None | [52] [53] |
8 | RAV1AAT | CAACA (Motif 7 of dicot) | RAV1 binding consensus sequence, binds to DNA with bipartite sequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1 protein contains AP2-like and B3-like domains which recognize the CAACA and CACCTG motifs, respectively; The expression level of RAV1 is relatively high in rosette leaves and roots in Arabidopsis | RAV1 | [54] |
9 | WRKY710S | TGAC (Motif 3, 4 & 5 of dicot) | A core of TGAC-containing W-box is present in Amy32b promoter; is binding site of rice WRKY71, which acts a transcriptional repressor in the gibberellin signaling pathway; Parsley WRKY proteins bind specifically to TGAC-containing W box elements within the Pathogenesis-Related Class10 (PR-10) genes | WRKY71 | [55] |
10 | 10PEHVPSBD | TATTC (Motif 4 of dicot) | “−10 promoter element” present in psbD gene promoter of barley; is required for expression of the psbD (plastid gene) encoding chlorophyll-binding protein of photosystem II reaction center, activated by blue/UV-A light/white light. | None | [56] |