A1BG response element gene transcriptions
Associate Editor(s)-in-Chief: Henry A. Hoff
Def. nucleotide "sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents", [that] "may be found in both promoter and enhancer regions"[1] are called response elements.
Hypotheses
- A1BG has no response elements in either promoter.
- A1BG is not transcribed by a response element.
- Each response element does not participate in the transcription of A1BG.
Response element testing
Name of elements, Abbreviations, Authors | Consensus sequences, Variations | Testing | Order | Resource | nucleotides for one occurrence or likelihood found |
---|---|---|---|---|---|
1. ABA-response element-like, (ABRE-like) | ACGTGTCC | Absent | 21 | ABA-response elements 13:07, 8 October 2020 | 48 |
2. ABA-response elements, novel, (ABREN, novel ABRE) | GATCGATC, CGATCGAT, GATCGAT | Absent | 22 | ABA-response elements 13:07, 8 October 2020 | 47-48 |
3. ABA responsive elements (ABREs) | ACGTG(G/T)C | Present | 23 | ABA-response elements 05:53, 9 October 2020 | likely active or activable |
4. Abf1 regulatory factors | CGTCCTCTACGAT | Absent | 25 | Abf1 regulatory factors 18:32, 10 October 2020 | 413 |
5. A-boxes | TACGTA | Present | 16 | A-boxes 21:24, 7 October 2020 | likely active or activable |
6. Abscisic acid-responsive elements (Pho4s), G boxes | CACGTG | Present | 56 | Abscisic acid-responsive elements (Pho4s), G boxes 06:38, 10 May 2022 | likely active or activable |
7. ACGT-containing elements | ACGT | Present | 59 | ACGT-containing elements 03:02, 25 September 2022 | cores, proximals likely active or activable, few UTRs, distals may be random |
8. Activated B-cell Factor-1s (ABFs, Abfms) | CGTNNNNN(A/G)(C/T)GA(C/T) | Present | 24 | Abf1 regulatory factors 17:47, 10 October 2020 | likely active or activable |
9. Activating proteins (Murata) | GCCCACGGG | Absent | 117 | Activating proteins 05:32, 15 December 2022 | 49 |
10. Activating protein 2 alpha (AP2a) | GCCNNNGGC | Present | 61 | Activating protein 2 alpha 00:57, 29 September 2022 | likely active or activable, positive strand, positive direction within randoms |
11. Activating protein 2 (AP2), (Cohen1) | GCCTGGCC | Present | 63 | Activating protein 2 06:54, 30 September 2022 | likely active or activable |
12. Activating protein 2, (Cohen2) | TCCCCCGCCC | Present | 64 | Activating protein 2 07:41, 30 September 2022 | likely active or activable |
13. Activating protein 2, (Murata) | (C/G)CCN(3)GG(C/G) | Present | 60 | Activating protein 2 23:47, 28 September 2022 | likely active or activable |
14. Activating protein 2, (Murata) | (C/G)CCN(4)GG(C/G) | Present | 62 | Activating protein 2 19:10, 29 September 2022 | likely active or activable |
15. Activating protein 2, (Yao1) | TCTTCCC | Present | 65 | Activating protein 2 08:11, 30 September 2022 | likely active or activable |
16. Activating protein 2, (Yao2) | CTCCCA | Present | 66 | Activating protein 2 19:00, 30 September 2022 | likely active or activable |
17. Activating protein 2, (AP-2), (Yao3) | GGCCAA | Present | 67 | Activating proteins 22:23, 30 September 2022 | likely active or activable |
18. Activating protein 2, (AP-2), (Roesler) | CCCCACC(A/C) | Present | 200 | AP-2 (Roesler) samplings 19:31, 21 April 2023 | likely active or activable |
19. Activating transcription factors, (ATF), (Burton) | (A/C/G)TT(A/G/T)C(A/G)TCA | Present | 68 | Activating transcription factors 01:48, 1 October 2022 | likely active or activable |
20. Activating transcription factors, (ATF), (Kilberg) | (A/G/T)TT(A/G/T)CATCA | Present | 69 | Activating transcription factors 02:21, 1 October 2022 | likely active or activable |
21. Adenylate–uridylate rich elements, (AUREs), (Bakheet) | (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) | Present | 49 | Adenylate–uridylate rich elements 02:16, 3 October 2021 | likely active or activable |
22. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class I) | ATTTA | Present | 115 | Adenylate–uridylate rich elements 04:44, 15 December 2022 | likely active or activable, UTRs at the lower end of the randoms |
23. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class II) | TTATTTA(A/T)(A/T) | Present | 114 | Adenylate–uridylate rich elements 04:31, 15 December 2022 | likely active or activable |
24. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class III) | ATTT | Present | 113 | Adenylate–uridylate rich elements 04:06, 15 December 2022 | likely active or activable, low negative direction proximals overlap randoms |
25. Adr1ps, (ADR), (Tang 2020) | TTGG(A/G)G | Present | 110 | Adr1ps 01:36, 15 December 2022 | likely active or activable |
26. Aft1s, (AFT) | (C/T)(A/G)CACCC(A/G) | Present | 70 | Aft1s 15:48, 3 October 2022 | likely active or activable |
27. AGC boxes | AGCCGCC (Leubner-Metzger 1998) | Present | 8 | AGC boxes 14:40, 2 May 2014 | likely active or activable |
28. AhR DNA-binding consensus sequence, (AhRY), (Yao) | GCGTGNN(A/T)NNN(C/G) | Present | 97 | AhR DNA-binding consensus sequence 05:37, 5 November 2022 | likely active or activable for ZNF497 |
29. AhR-responsive elements (AHRE) (Yao 1992) | (G/T)NGCGTG(A/C)(C/G)A | Absent | 41 | AhR/ARNT complex 20:45, 17 February 2021 | 23*46 |
30. Alpha-amylase conserved elements (Sharma 2020) | TATCCATCCATCC | Absent | 30 | Alpha-amylase conserved elements 22:18, 31 October 2020 | 413 |
31. Alpha-amylase conserved elements portion | TATCCA | Present | 119 | Alpha-amylase conserved elements portion 05:39, 11 April 2023 | likely active or activable |
32. Amino acid response elements, (AARE1), (Maruyama) | ATTGCATCA | Absent | 47 | Amino acid response elements 01:32, 22 May 2021 | 49 |
33. Amino acid response elements, (AARE), (Broer) | TTTGCATCA[2][3] | Absent | 31 | Amino acid response elements 01:59, 1 November 2020 | 49 |
34. Amino acid response element-like, (AARE-like), (AARE3), (Maruyama) | TGGTGAAAG | Absent | 32 | Amino acid response element-like 02:27, 2 November 2020 | 49 |
35. Androgen response elements, (AREs), (Kouhpayeh) | GGTACANNNTGTTCT | Absent | 33 | Androgen response elements 17:01, 2 November 2020 | 412 |
36. Androgen response element1s, (Kouhpayeh) | GGTACA of GGTACAnnnTGTTCT | Present | 71 | Androgen response element1s 17:22, 4 October 2022 | likely active or activable |
37. Androgen response element2s, (Kouhpayeh) | TGTTCT of GGTACAnnnTGTTCT | Present | 72 | Androgen response element2s 17:01, 5 October 2022 | likely active or activable |
38. Androgen response elements, (AREs), (Wilson) | AGAACANNNTGTTCT | Absent | 50 | Androgen response elements 16:21, 11 November 2021 | 412 |
39. Androgen response elements, (Wilson) | AGAACANNNTGTTCT | Present | 73 | Androgen response elements 18:53, 5 October 2022 | the two portions AGAACA and TGTTCT occurring separately are likely active or activable |
40. Angiotensinogen core promoter elements (AGCE) | (A/C)T(C/T)GTG | Present | 104 | Angiotensinogen core promoter elements 20:01, 5 December 2022 | likely active or activable, positive direction distal low occurrences overlap randoms |
41. Antioxidant-electrophile responsive elements, (ARE), (Otsuki) | GTGAGGTCGC[4] or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A[5] | Absent | 34 | Antioxidant-electrophile responsive elements 06:06, 4 November 2020 | (4/3)*2*45-410 |
42. Antioxidant-electrophile responsive elements, (Lacher) | GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A | Present | 74 | Antioxidant-electrophile responsive elements 23:22, 5 October 2022 | likely active or activable |
43. Aryl hydrocarbon responsive element II, (AHRE-II) | CATGN6C(A/T)TG | Present | 105 | AhR responsive element or Aryl hydrocarbon responsive element II 18:04, 6 December 2022 | likely active or activable |
44. ATA boxes | AATAAA | Present | 109 | ATA boxes 19:59, 14 December 2022 | likely active or activable |
45. ATTTA elements, (Siegel) | (A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T) | Present | 112 | ATTTA elements 04:04, 15 December 2022 | likely active or activable |
46. Auxin response factors, (ARF), (Stigliani) | (C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T) | Present | 98 | Auxin response factors 05:55, 5 November 2022 | likely active or activable, positive direction proximals overlap high randoms, positive direction cores within randoms |
47. Auxin response factors, (ARF), (Ulmasov) | TGTCTC | Present | 99 | Auxin response factors 06:02, 5 November 2022 | likely active or activable |
48. Auxin response factors, (ARF), (Boer) | TGTCGG | Present | 75 | Auxin response factors 17:03, 7 October 2022 | likely active or activable |
49. Auxin response factors, (ARF5) | (C/G/T)N(G/T)GTC(G/T) | Present | 76 | Auxin response factors 04:15, 10 October 2022 | likely active or activable, negative direction proximals ≥ randoms |
50. B-boxes, (Johnson) | TGGGCA | Present | 78 | B-boxes 18:05, 10 October 2022 | likely active or activable, positive direction distals ≥ randoms |
51. boxes A | TGACTCT | Present | 55 | Box A 06:50, 9 May 2022 | likely active or activable |
52. boxes B, (Sanchez) | TGTCTCA | Present | 77 | boxes B 15:26, 10 October 2022 | likely active or activable |
53. B recognition elements, (BREu) | (G/C)(G/C)(G/A)CGCC | Present | 103 | B recognition elements 20:39, 4 December 2022 | likely active or activable |
54. CAACTC regulatory elements, (CAREs), (Fan) | CAACTC | Present | 53 | CARE (Fan) 17:45, 7 May 2022 | likely active or activable |
55. CAAT boxes | (C/T)(A/G)(A/G)CCAATC(A/G) | Absent | 12 | CAAT boxes 02:41, 22 March 2019 | 48, consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT. |
56. CACA elements (Orlando 2019) | CACA | Present | 45 | CACA elements 05:04, 7 May 2021 | likely active or activable |
57. CadC binding domains | TTANNNNT | Present | 79 | CadC binding domains 22:14, 12 October 2022 | likely active or activable, negative direction proximals within randoms |
58. Calcineurin-responsive transcription factors | TG(A/C)GCCNC | Present | 108 | Calcineurin-responsive transcription factors 19:14, 12 December 2022 | likely active or activable |
59. Calcium-response elements, (CaRE1s), (Tao 2002) | CTATTTCGAG | Absent | 35 | Calcium-response elements 19:43, 7 November 2020 | 410 |
60. Carbohydrate response elements, (ChREs), (ChoRE1, ChoRE2), (Long 2020) | CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG | Absent | 36 | Carbohydrate response elements 20:50, 10 November 2020 | 417 |
61. Carbohydrate response elements, (ChoRE1), (Carb) | ACCGG | Present | 57 | Carbohydrate response elements 18:56, 18 June 2022 | likely active or activable |
62. Carbohydrate response elements, (ChoRE2), (Carb1) | CCCAT | Present | 80 | Carbohydrate response elements 06:01, 13 October 2022 | likely active or activable |
63. Carbohydrate response elements, (Carb E1) | ATCTTG | Present | 81 | Carbohydrate response elements 18:45, 13 October 2022 | proximals likely active or activable |
64. Carbohydrate response elements, (Carb E2) | CACGTG | Present | 81 | Carbohydrate response elements 21:30, 13 October 2022 | likely active or activable |
65. Carbohydrate response elements, (Carb E3) | TCCGCC | Present | 82 | Carbohydrate response elements 01:21, 14 October 2022 | likely active or activable, low positive direction distals overlap high randoms |
66. Carbon source-responsive elements, (CSREs) | CATTCATCCG | Absent | 42 | Carbon source-responsive elements 17:08, 19 March 2021 | 410, confers carbon source-dependent regulation |
67. Carbon source-responsive elements, (TCCGs) | TCCG | Present | 83 | TCCG elements 02:41, 16 October 2022 | likely active or activable |
68. Carbon source-responsive elements, (CATTs) | CATTCA | Present | 84 | CATTCA elements 17:05, 18 October 2022 | likely active or activable |
69. CArG boxes, (Kamada 1992), (McDonald 2006) | CC(A/T)6GG | Absent | 85 | CArG boxes 19:08, 18 October 2022 | 26*44 |
70. CArG boxes, (Deng 2011) | CCAAAAAT(G/A)G | Absent | 86 | CArG boxes 19:08, 18 October 2022 | 2*49 |
71. CArG boxes, (suggested more general motif), (Deng 2011) | C(C/A/T)(A/T)6(A/G)G from two different CArG-box motifs at 502 bp (CTAAATATGG) and 287 bp (CAATAATTGG) upstream | Present | 87 | CArG boxes 19:08, 18 October 2022 | likely active or activable, positive strand, negative direction: CATTAAAAGG at 3441 and CAAAAAAAAG at 1399 |
72. Cat8ps, (Tang 2020) | CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA | Present | 88 | Cat8ps 22:21, 18 October 2022 | likely active or activable |
73. CAT boxes, (Saitoh 1993) | CATTCCT | Present | 89 | CAT boxes 23:56, 18 October 2022 | likely active or activable |
74. CAT-box-like elements, (Berberich 1993) | GCCATT | Present | 89 | CAT-box-like elements 19:38, 20 October 2022 | likely active or activable |
75. Cbf1 regulatory factors | TCACGTGA | Absent | 48 | Cbf1 regulatory factors 15:57, 11 June 2021 | 48 |
76. C-boxes, (Johnson) | GAGGCCATCT | Absent | 27 | C-boxes 02:51, 22 October 2020 | 410 |
77. C boxes, (Samarsky) | AGTAGT | Present | 90 | C boxes 02:22, 21 October 2022 | likely active or activable |
78. C-boxes, (Song) | GACGTC | Present | 91 | C-boxes 06:22, 21 October 2022 | likely active or activable |
79. C/A hybrid boxes, (Song) | TGACGTAT | Absent | 26 | C/A hybrid boxes 16:18, 20 October 2020 | 48 |
80. C/G hybrid boxes, (Song) | TGACGTGT | Present | 102 | CG hybrid boxes 18:35, 15 November 2022 | likely active or activable |
81. C/T hybrid boxes, (Song) | TGACGTTA | Absent | 28 | C/T hybrid boxes 01:51, 24 October 2020 | 48 |
82. C boxes, (Voronina) | GGTGATG | Present | 101 | C boxes 18:28, 15 November 2022 | likely active or activable |
83. CCAAT-enhancer-binding site (C/EBP) activating transcription factor (ATF), or C/EBP-ATF responsive elements, (CAREs), (Garaeva) | (A/G/T)TT(A/G/T)CATCA | Present | 54 | CARE (Garaeva) 01:10, 8 May 2022 | likely active or activable |
84. CCAAT-enhancer-binding site (C/EBP), C/EBP boxes | TTAGGACAT,[6] or TAGCATT.[7] | Absent | 37 | C/EBP boxes 23:21, 18 November 2020 | 47-49 |
85. CCCTC-binding factors, (CTCF) | NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) | Absent | 29 | CCCTC-binding factors 23:02, 24 October 2020 | 49 |
86. Cell-cycle boxes, (CCBs) | CACGAAAA | Absent | 43 | Cell-cycle boxes 22:13, 19 April 2021 | 48, "cell cycle box" is functional in either orientation, acting as an enhancer |
87. Cell-cycle box variants, (CCBs) | CACGAAA, ACGAAA and C-CGAAA | Present | 92 | Cell-cycle box variants 05:54, 23 October 2022 | likely active or activable |
88. Cell cycle regulation, (Sharma 2020) | CCCAACGGT | Absent | 38 | Cell cycle regulation 20:53, 25 November 2020 | 49 |
89. CENP-B boxes | TTTCGTTGGAAGCGGGA | Absent | 13 | CENP-B boxes 13:25, 11 May 2019 | 417, specifically localized at the centromere |
90. CGCG boxes, (Yang 2002) | (A/C/G)CGCG(C/G/T) | Present | 107 | CGCG boxes 07:14, 12 December 2022 | likely active or activable, probably for zinc fingers |
91. Circadian control elements | CAANNNNATC | Present | 106 | Circadian control elements 00:33, 12 December 2022 | likely active or activable but overlaps highest randoms |
92. Class C DNA binding sites, (Leal) | CACGNG | Present | 58 | Class C DNA binding sites 06:16, 5 August 2022 | likely active or activable, distals may be random |
93. Cold-responsive elements | CCGAC | Present | 93 | Cold-responsive elements 05:34, 24 October 2022 | likely active or activable |
94. Constitutive decay elements, (CDEs), (Siegel) | TTC(C/T)(A/G)(C/T)GAA | Present | 111 | Constitutive decay elements 03:50, 15 December 2022 | likely active or activable possibly for ZNF497 |
95. Copper response elements, (CuREs), (Quinn) | TTTGC(T/G)C(A/G) | Present | 94 | Copper response elements 07:57, 24 October 2022 | likely active or activable |
96. Copper response elements, (CuREs), (Park) | TGTGCTCA | Present | 95 | Copper response elements 05:45, 25 October 2022 | likely active or activable |
97. Coupling elements, (CE1), (Watanabe) | TGCCACCGG | Absent | 39 | Coupling elements 01:51, 1 December 2020 | 49 |
98. Coupling elements, (CE3s), (Watanabe) | GCGTGTC | Present | 51 | Coupling elements 15:47, 12 February 2022 | likely active or activable |
99. Coupling elements, (CE3s), (Ding) | CACGCG | Present | 52 | Coupling elements 02:59, 15 February 2022 | likely active or activable |
100. cyclic-AMP-responsive elements, (CREs), Aca1ps, Sko1ps, (Montminy 1986) | TGACGTCA | Present | 116 | cAMP-responsive elements 05:05, 15 December 2022 | likely active or activable, same as Root specific elements |
101. Cytokinin response regulators, (ARR1s) | AGATT(C/T) | Present | 120 | Cytokinin response regulators 16:21, 31 October 2022 | likely active or activable |
102. Cytokinin response regulators, (ARR10s) | (A/G)GATA(A/C)G | Present | 200 | Cytokinin response regulators 17:47, 27 October 2022 | likely active or activable or may be random |
103. Cytokinin response regulators, (ARR12s) | (A/G)AGATA | Present | 200 | Cytokinin response regulators 06:09, 28 October 2022 | likely active or activable |
104. Cytokinin response regulators, (ARRs), (Ferreira) | (G/A)GGAT(T/C) | Present | 200 | Cytokinin response regulators 03:25, 31 October 2022 | likely active or activable |
105. Cytokinin response regulators, (ARRs), (Rashotte1) | GATCTT | Present | 200 | Cytokinin response regulators 16:21, 31 October 2022 | likely active or activable |
106. Cytokinin response regulators, (ARRs), (Rashotte2) | (G/A)GAT(T/C) | Present | 200 | Cytokinin response regulators 20:24, 1 November 2022 | likely active or activable |
107. Cytoplasmic polyadenylation elements, (CPEs) | TTTTTAT | Present | 200 | Cytoplasmic polyadenylation elements 06:10, 25 July 2022 | likely active or activable |
108. DAF-16-associated elements, (DAE), (Li) | TGATAAG | Absent | 200 | DAF-16-associated elements 22:51, 3 December 2020 | 47 |
109. DAF-16 binding elements | (A/G)(C/T)AAA(C/T)A | Present | 200 | DAF-16 binding elements 19:54, 2 November 2022 | likely active or activable |
110. D-boxes, (Mracek1) | GTTGTATAAC | Absent | 200 | D-boxes 02:46, 10 December 2020 | 410 |
111. D-boxes, (Mracek2) | CTTATGTAAA | Absent | 200 | D-boxes 02:20, 12 December 2020 | 410 |
112. D-boxes, (Johnson) | TCTCACATT(A/C)AATAAGTCA | Absent | 200 | D-boxes 04:12, 8 December 2020 | 2*418 |
113. D boxes, (Samarsky) | AGTCTG | Present | 200 | D boxes 00:16, 12 December 2022 | likely active or activable |
114. D boxes, (Voronina) | TCCTG | Present | 200 | D boxes 02:28, 4 November 2022 | likely active or activable |
115. D-boxes, (Motojima) | TGAGTGG | Present | 200 | D-boxes 00:11, 12 December 2022 | likely active or activable |
116. Defense and stress-responsive elements, (Sharma) | ATTTTCTTCA | Absent | 200 | Defense and stress-responsive elements 21:02, 13 December 2020 | 410 |
117. Dioxin-responsive elements, (DREs) | TNGCGTG | Present | 96 | Dioxin-responsive elements 20:43, 4 November 2022 | likely active or activable |
118. DNA damage response elements, (DREs), (Smith) | TTTCAAT | Absent | 200 | DNA damage response elements 12:25, 17 December 2020 | 47 |
119. DNA damage response elements, (DREs), (Sumrada) | TAGCCGCCG of TAGCCGCCGRRRR | Absent | 200 | DNA damage response elements 06:31, 17 December 2022 | 49-24*49 |
120. DNA replication-related elements, (DREs), (Hirose) | TATCGATA | Absent | 200 | DNA replication-related elements 02:56, 20 December 2020 | 48 |
121. Downstream B recognition elements | (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) | Present | 200 | Downstream B recognition elements 22:45, 20 December 2022 | likely active or activable, negatives > randoms, positives overlap or outside randoms |
122. Downstream core elements, (DCESIs) | CTTC of CTTC...CTGT...AGC | Present | 200 | Downstream core elements 21:36, 22 December 2022 | likely active or activable, depending on overlaps |
123. Downstream core elements, (DCESIIs) | CTGT of CTTC...CTGT...AGC | Present | 200 | Downstream core elements 06:59, 26 December 2022 | likely active or activable, depending on overlaps |
124. Downstream core elements, (DCESIIIs) | AGC of CTTC...CTGT...AGC | Present | 200 | Downstream core elements 02:54, 28 December 2022 | likely active or activable, depending on overlaps |
125. Downstream promoter elements, (DPEs), (Juven-Gershon) | (A/G)G(A/T)(C/T)(A/C/G)T | Present | 200 | Downstream promoter elements 05:18, 17 July 2022 | most or all of the real DPE (Juven-Gershon)s are likely active or activable |
126. Downstream promoter elements (DPE) | RGWCGTG (Burke 1996), RGWYV(T) (Kadonaga 2002) | Present | 3 | Initiator elements 21:32, 20 May 2012 | likely active or activable |
127. Downstream promoter elements, (DPEs), (Kadonaga) | (A/G)G(A/T)CGTG | Present | 200 | Downstream promoter elements 20:16, 16 July 2022 | likely active or activable |
128. Downstream promoter elements, (DPEs), (Matsumoto) | AGTCTC | Present | 200 | Downstream promoter elements 21:32, 16 July 2022 | likely active or activable |
129. Downstream TFIIB recognition elements (BREd, dBRE) (Deng 2005) | (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) | Present | 6 | Downstream TFIIB recognition elements 21:32, 11 February 2013 | likely active or activable |
130. DREB boxes (CRT/DREB box) | TACCGACAT | Absent | 200 | DREB boxes 17:03, 28 December 2019 | 49 |
131. E2 boxes | (G/A)CAGNTGN | Present | 200 | E2 boxes 17:04, 3 October 2022 | likely active or activable |
132. EIF4E basal elements (poly(C) motif) | TTACCCCCCCTT | Absent | 200 | EIF4E basal elements 20:24, 30 March 2019 | 412 |
133. EIN3 binding sites | A(C/T)G(A/T)A(C/T)CT | Present | 200 | EIN3 binding sites 01:44, 29 December 2022 | likely active or activable |
134. Endoplasmic reticulum stress response elements, (ERSE) | CCAAT-N9-CCACG | Absent | 200 | Endoplasmic reticulum stress response elements 01:58, 31 December 2022 | 410 |
135. Endoplasmic reticulum stress response elements, (ESRE2) | CCACG, for part 1 (CCAAT) see Hap motif | Present | 200 | Endoplasmic reticulum stress response elements 01:57, 31 December 2022 | likely active or activable |
136. Endosperm expressions | TGTGTCA | Present | 200 | Endosperm expressions 31 December 2022 Marshallsumter | likely active or activable |
137. Enhancer boxes (E-box), (Massari 2000) | CANNTG | Present | 7 | Enhancer boxes 22:01, 17 April 2013 | likely active or activable |
138. Estrogen response elements, (EREs), (Matsumoto) | AGGTTA or GGTCAGGAT of AGGTTATTGCCTCCT or GGTCAGGATGAC | Absent | 200 | Estrogen response elements 05:34, 9 March 2023 | 46-412 |
139. Estrogen response elements, (EREs), (Yasar) | GGTCAGGATGAC | Absent | 200 | Estrogen response elements 05:37, 9 March 2023 | 412 |
140. Estrogen response elements, (ERE1s), (Driscoll) | GGTCA | Present | 200 | Estrogen response elements 03:27, 14 March 2023 | likely active or activable |
141. Estrogen response elements, (ERE2s), (Driscoll) | TGACC | Present | 200 | Estrogen response elements 03:37, 14 March 2023 | likely active or activable |
142. Ethylene responsive elements | ATTTCAAA | Present | 200 | Ethylene responsive elements 18:06, 5 November 2022 | likely active or activable |
143. F boxes, (Rose) | TGATAAG | Absent | 200 | F boxes 05:52, 28 January 2021 | 47, F-box overlaps the I-box |
144. Forkhead boxes, (FOXO1), (Yoshihara) | GTAAACAA | Absent | 200 | Forkhead boxes 04:33, 20 April 2023 | 48 |
145. Forkhead boxes, (FOXA2), (Li 2017) | (A/G)(C/T)AAA(C/T)A | Present | 200 | Forkhead boxes 03:54, 1 January 2023 | likely active or activable |
146. GAAC elements | GAACT | Present | 200 | GAAC elements 22:49, 1 January 2023 | likely active or activable |
147. Galactose-inducible transcription activator 4s, (Gal4s), (Tang) | CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG | Absent | 200 | Gal4ps 22:28, 31 December 2020 | 410 |
148. γ-interferon activated sequences, (GAS) | TTCCTAGAA | Absent | 200 | Samplings 04:43, 22 March 2018 | 49 |
149. Γ-interferon activated sequences, (GAS) | TTNCNNNAA | Present | 200 | Γ-interferon activated sequences 01:56, 3 January 2023, see STAT5 | likely active or activable |
150. GATA boxes | GATA | Present | 200 | GATA boxes 06:29, 8 December 2022 | likely active or activable, may be random in proximals |
151. GATA (GATAAG, GATAAH, GATTA) motifs, (Staschke) | GAT(A/T)A | Present | 200 | GATA (GATAAG, GATAAH, GATTA) motifs 20:11, 9 December 2022 | likely active or activable |
152. G boxes, (Song) | (G/T)CCACGTG(G/T)C | Absent | 200 | G boxes 03:20, 25 July 2021 | 49 |
153. G-box motif, (Oeda) | GCCACGTGGC | Absent | 200 | G boxes 04:25, 20 July 2021 | 410, no "perfect palindrome" G boxes in either promoter |
154. GC boxes, (Briggs 1986), (Rroji 2021) | (G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T) | Present | 200 | GC boxes 16:57, 3 January 2023 | likely active or activable |
155. GC boxes, (Ye 2019) | GGGCGG | Present | 200 | GC boxes 08:28, 4 January 2023 | likely active or activable |
156. GCC boxes, (Sato 1996) | GCCGCC | Present | 200 | GCC boxes 06:52, 5 January 2023 | likely active or activable |
157. GCN4 motifs, (Zhang 2014) | TGA(C/G)TCA | Absent | 200 | GCN4 motifs 05:52, 30 September 2022 | 47 |
158. General control nonderepressible 4 protein binding sites, (Staschke 2010), (GCRE, GCN4) | TGA(C/G/T)T(A/C/G)(A/T) | Present | 200 | General control nonderepressible 4 protein binding site 07:05, 5 January 2023 | likely active or activable |
159. Gcn4ps, (Tang) | ATGACTCTT | Absent | 200 | Gcn4ps 22:17, 15 November 2022 | 49 |
160. GGCGGC triplet | GGCGGC | Present | 200 | GGCGGC triplet 00:32, 7 January 2023 | likely active or activable |
161. GGC triplets | GGC | Present | 200 | GGC triplets 19:40, 7 January 2023 | likely active or activable |
162. Gibberellic acid responsive elements-like 1, (GAREL1s) | TAACA(A/G)A | Present | 200 | Gibberellic acid responsive elements-like 1 19:12, 5 November 2022 | likely active or activable |
163. Gibberellin responsive element-like 2, (GARE-like 2), (Fan) | TAACGTA | Absent | 200 | Gibberellin responsive element-like 2 06:39, 2 January 2021 | 47 |
164. Gibberellin responsive elements, (GREs), (Sharma) | AAACAGA | Present | 200 | Gibberellin responsive elements 01:19, 8 January 2023 | likely active or activable |
165. GLM boxes, (GCN4-like motif) | (G/A)TGA(G/C)TCA(T/C) | Absent | 200 | GLM boxes 04:17, 13 October 2019 | 23*46 |
166. Glucocorticoid response elements, (GRE), (Parsonnet 2019) | AGAACA | Present | 200 | Glucocorticoid response elements 05:34, 10 December 2022 | likely active or activable |
167. Glucose transporter gene repressor, (Rgt1), (Kim 2019) | CGG(A/G)(A/T)N(A/T)(A/T) | Present | 200 | Glucose transporter gene repressor 20:06, 21 January 2023 | likely active or activable |
168. G-protein-coupled receptors,(GCR1s), CT boxes | CTTCC | Present | 200 | G-protein-coupled receptors 03:36, 8 January 2023 | likely active or activable |
169. Grainy head transcription factor binding sites | AACCGGTT | Absent | 200 | Grainy head transcription factor binding sites 23:33, 6 January 2021 | 48 |
170. Grainy head transcription factor binding sites | GACTGGTT | Absent | 200 | Grainy head transcription factor binding sites 07:13, 22 April 2023 | 48 |
171. GT boxes, (Motojima) | TGGGTGGGGCT | Absent | 200 | GT boxes 00:39, 11 January 2021 | (-78 to -69) 411 |
172. GT boxes, (Sato) | GGGG(T/A)GGGG | Present | 200 | GT boxes 04:33, 8 January 2023 | likely active or activable |
173. Hac1, KAR2 | CAGCGTG | Present | 200 | Hac1 05:27, 8 January 2023 | likely active or activable |
174. H and ACA boxes | AGAGGA | Present | 200 | H and ACA boxes 04:33, 9 January 2023 | likely active or activable, negative distals likely random |
175. Hapless motifs (Ozsarac 1997) | CCAATCA | Absent | 200 | Hapless motifs 02:33, 30 June 2022 | heterotrimeric transcription factor, HAP2/3/4 47 |
176. Hap motif (Hap4p) | CCAAT | Present | 200 | Hap motif 20:38, 9 January 2023 and ESRE CCAAT | likely active or activable |
177. H-boxes, (Grandbastien) | CC(A/T)ACCNNNNNNN(A/C)T | Present | 200 | H-boxes 16:34, 7 May 2022 | likely active or activable |
178. H-boxes, (Lindsay) | CCTACC | Present | 200 | H-boxes 14:39, 8 May 2022 | likely active or activable, equal to or greater than the randoms for the negative direction distals |
179. H box, (Mitchell) | ANANNA | Present | 200 | H box 20:03, 12 December 2022 | likely active or activable |
180. H box, (Rozhdestvensky) | ACACCA | Present | 200 | H box 05:46, 5 May 2022 | likely active or activable |
181. Heat-responsive elements | AAAAAATTTC | Absent | 200 | Heat-responsive elements 02:10, 14 January 2021 | four nGAAn motifs 410 |
182. Heat shock elements, (HSE1), (Eastmond) | nGAAnnTTCnnGAAn | Absent | 200 | Heat shock elements 04:13, 20 January 2021 | HSE1 49 |
183. Heat shock elements, (HSE2), (Eastmond) | nTTCnnGAAnnTTCn | Absent | 200 | Heat shock elements 16:30, 10 May 2022 | HSE2 is the inverse complement of HSE1 49 |
184. Heat shock elements, (HSE3s), (Eastmond) | nGAAn-(5-bp)-nGAAnnTTCn | Present | 200 | Heat shock elements 17:47, 13 May 2022 | likely active or activable |
185. Heat shock elements, (HSEs), (Eastmond) | nGA(A/G)n-(5-bp)-nGAAnnTTCn (GAP1) | Present | 200 | Heat shock elements 16:28, 16 May 2022 | same result as HSE3, likely active or activable |
186. Heat shock elements, (HSEs), (Eastmond) | nGAAn-(5-bp)-nGA(A/G)nnTTCn (GAP2) | Present | 200 | Heat shock elements 06:36, 17 May 2022 | same result as HSE3, likely active or activable |
187. Heat shock elements, (HSE4s), (Eastmond) | nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn | Present | 200 | Heat shock elements 05:14, 14 May 2022 | likely active or activable |
188. Heat shock elements, (HSE5), (Eastmond) | nTTCn-(5-bp)-nTTCnnGAAn | Absent | 200 | Heat shock elements 02:49, 23 January 2021 | HSE5 49 |
189. Heat shock elements, (HSE6), (Eastmond) | nTTCn-nnGAAn-(5-bp)-nGAAn | Absent | 200 | Heat shock elements 18:05, 23 January 2021 | HSE6 49 |
190. Heat shock elements, (HSE7), (Eastmond) | nGA(A/G)nnTTCnnGAAn | Absent | 200 | Heat shock elements 22:36, 23 January 2021 | HSE7 PFT1 2*48 |
191. Heat shock elements, (HSE), (Eastmond) | nGAAnnTTCnnGA(A/G)n | Absent | 200 | Heat shock elements 05:45, 24 January 2021 | HSE7 PFT2 2*48 |
192. Heat shock elements, (HSE10), (Eastmond) | nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn | Absent | 200 | Heat shock elements | HSE10 49 |
193. Heat shock factors, (Hsfs), (Tang) | NGAAN | Present | 200 | Heat shock factors 06:01, 11 May 2022 | likely active or activable |
194. Hepatic nuclear factors (HNFs) | (A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T) | Present | 200 | HNF6s 17:53, 20 May 2022 | likely active or activable, although the negative direction distals are at or less than randoms |
195. Hex sequences | TGACGTGGC | Present | 200 | Hex sequences 19:57, 17 May 2022 | likely active or activable |
196. High Mobility Group boxes, (HMG boxes) | (A/T)(A/T)CAAAG | Present | 200 | High Mobility Group boxes 22:01, 30 April 2023 | likely active or activable |
197. Homeoboxes | CAAG | Present | 200 | Homeoboxes 04:28, 4 December 2022 | likely active or activable |
198. Homeodomains | TAAT | Present | 200 | Homeodomains | likely active or activable, low occurrence UTRs and negative direction distals overlap high randoms |
199. HY boxes | TG(A/T)GGG | Present | 200 | HY boxes 12:43, 25 May 2022 | likely active or activable |
200. Hypoxia-inducible factors, (HIF-1), (Li 2020) | GCCCTACGTGCTGTCTCA | Absent | Hypoxia-inducible factors | composed of HIF-1α and HIF-1β 418 | |
201. Hypoxia-inducible factors (HIF) (Orlando 2019), ABA-response element (ABRE) (Asad 2019)) | ACGTG | Present | 46 | Hypoxia-inducible factors 06:03, 7 May 2021, ABA-response element (ABRE) 03:06, 8 October 2020 | likely active of activable |
202. Hypoxia response elements (HRE) (Orlando 2019) | CACGC | Present | 44 | Hypoxia response elements 05:04, 7 May 2021 | likely active or activable |
203. I boxes | GATAAG | ? | Absent | GGATGAGATAAGA 413 | |
204. Initiator element (Inr) (Liston 1999) | YYA+1NWYY | Present | 2 | Initiator elements 17:02, 17 April 2012 | likely active or activable |
205. Initiator element (Inr) (Juven-Gershon 2008) | YYR+1NWYY | Present | 19 | Initiator elements 17:44, 27 September 2020 | likely active or activable |
206. Initiator element (Inr) (Ngoc 2017) | BBCA+1BW | Present | 11 | Initiator elements 13:24, 22 December 2018 | likely active or activable |
207. Initiator element-like (Inr-like) (Matsumoto 2020) | TTCTCT | Present | 20 | Initiator elements 01:25, 29 September 2020 | likely active or activable |
208. Initiator element-like (TCT) (Parry 2010) | (C/T)CT(C/T)T(C/T)(C/T) | Present | 118 | Initiator elements 22:06, 10 April 2023 | likely active or activable |
209. Inositol/choline-responsive elements
(ICRE) (Case) |
CANNTGAAAT | ? | Absent | version of Lopes, see below 48 | |
210. Inositol/choline-responsive elements
(ICRE) (Case, Lopes) |
CATGTGAAAT includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991) | bHLH | Present
T |
likely active or activable | |
211. Inositol/choline-responsive elements
(ICRE) (Lopes) |
ATGTGAAAT | ? | Absent | using ANNTGAAAT 47-49 | |
212. Inositol/choline-responsive elements
(ICREs) (Schwank) |
TYTTCACATGY contains the core sequence CANNTG | bHLH | Present
T |
likely active or activable | |
213. Interferon regulatory factor
(IRF3) |
GCTTTCC | HTH | Present
T |
random | |
214. Interferon-stimulated response elements
(ISREs) |
AGTTTCN2TTTCN | ? | Absent | consensus sequence AGTTTCN2TTTCN.[8] 410 | |
215. IFN-stimulated response elements
(ISREs) (Lu) |
GAAANNGAAA | HTH | Present
T |
likely active or activable | |
216. IRS consensus
(Fujii) |
AANNGAAA | HTH | Present
T |
likely active or activable | |
217. Tryptophan residues
(Lu) |
GAAA | HTH | Present
T |
likely active or activable, the tryptophan residues occur in the IRS, IFN, ICRE, Cell-cycle box variants, V-box, Pollen1, and β-Scaffold response elements | |
218. Jasmonic acid-responsive elements
(JAREs) |
TGACG | ? | Present
T |
likely active or activable | |
219. Kozak sequences | GCCGCC(A/G)CCATGG | ? | Absent | GCCGCC(A/G)CCATGG[9] 2*412 | |
220. Kozak sequences
(Matsumoto) |
GAAAATGG | ? | Absent | GAAAATGG[10] 48 | |
221. Krüppel-like factors | GGGNN(G/T)(G/T)(G/T) | ? | Present
T |
likely active or activable | |
222. L boxes | AAATTAACCAA | ? | Absent | AAATTAACCAA[11] 411 | |
223. Leu3 transcription factors, (Leu3), (Reddy 2020) | (C/G)C(G/T)NNNN(A/C)G(C/G) | Present | 200 | Leu3 transcription factors 04:52, 7 January 2023 | likely active or activable |
224. M35 or -35 sequence | TTGACA | Present | 200 | -35 sequence | likely active or activable, the UTR does overlap the randoms at the random's upper end |
225. Maf recognition element, (MAREs), (Kyo) | TGCTGA(G/C)TCAGCA | Absent | 200 | Maf recognition element | 2*412 |
226. M boxes, (Bertolotto) | GTCATGTGCT or AGTCATGTGCT | Absent | 200 | M boxes 16:05, 3 February 2021 | 410-411 |
227. M-CAT boxes, (Berberich 1993) | GCGGCCTC | Absent | 200 | M-CAT boxes 18:06, 18 April 2023 | 48 |
228. Mcm1 regulatory factors, (Rossi) | TT(A/T)CCNN(A/T)TNGG(A/T)AA | Absent | 200 | Mcm1 regulatory factors | 23*49 |
229. Mcm1 regulatory factors, (Rossi) | TTNCCNNNTNNGGNAA | Absent | 200 | Mcm1 regulatory factors | 49 |
230. Met3s, (Blaiseau) | TCACGTG | Absent | 200 | Met3s | 47 |
231. Met31ps, (Blaiseau) | AAACTGTG | Present | 200 | Met31ps | likely active or activable |
232. Metal responsive elements, (MRE) | TGC(A/G)C(A/C/G/T)C | Present | 200 | Metal responsive elements | likely active or activable |
233. Middle sporulation element, (MSE), (Branco) | ACACAAA | Present | 200 | Middle sporulation element | likely active or activable |
234. Midsporulation element
(MSE) (Ozsarac) |
C(A/G)CAAA(A/T) | ? | Present
T |
likely active or activable | |
235. MITF E-box (CAYRTG)
(MITF) |
CA(C/T)(A/G)TG | ? | Present
T |
likely active or activable, negative distals overlap randoms at low end | |
236. Motif ten elements (MTE) (Lim 2004) | CSARCSSAACGS | Absent | 5 | Motif ten elements 15:28, 10 February 2013 | 25*47 |
237. Motif ten elements | C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G) | ? | Absent | Gene ID: 6309 25*47 | |
238. Multicopy inhibitor of the GAL1 promoter
(MIG1) |
(C/G)(C/T)GGGG | bZIP | Present
T |
likely active or activable, UTRs may be random | |
239. Musashi binding elements
(MBE1s) |
(G/A)U1AGU | ? | Present
T |
likely active or activable | |
240. Musashi binding elements
(MBE2s) |
(G/A)U2AGU | ? | Present
T |
likely active or activable, negative direction distals may be random | |
241. Musashi binding elements
(MBE3s) |
(G/A)U3AGU | ? | Present
T |
likely active or activable | |
242. MYB ACGT-containing elements
(ACEs) |
CACGT | ? | Present
T |
likely active or activable, positive strand UTR is likely random, negative strand, positive direction distals are likely random | |
243. Myeloblastosis recognition element
(MRE) |
A(A/C)C(A/T)A(A/C)C | ? | Present
T |
likely active or activable | |
244. Myocyte enhancer factors, (MEFs) | (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G) | Present | 200 | Myocyte enhancer factors | likely active or activable |
245. Nanos/Pumilio response elements, (PREs) | TGTAAAT | Present | 200 | Nanos/Pumilio response elements | likely active or activable |
246. N-boxes, (Lee) | CCGGAA | Present | 200 | N-boxes | likely active or activable |
247. N-boxes
(Bai) |
CACGAG | bHLH | Present
T |
likely active or activable | |
248. N-boxes
(Gao) |
CACGGC or CACGAC, CACG(A/G)C | bHLH | Present
T |
likely active or activable | |
249. N-boxes, (Leal) | CACNAG | Present | 200 | N-boxes 06:16, 5 August 2022 | likely active or activable |
250. Non-DiTyrosine 80 transcription factor DNA binding domain, (Ndt80) | (A/G/T)NC(A/G)CAAA(A/T) | Present | 200 | Non-DiTyrosine 80 transcription factor DNA binding domain 20:36, 17 August 2022 | likely active or activable |
251. Nuclear factor of activated T cells
(NFATs) complement and inverse of the Pyrimidine boxes |
GGAAAA | β-Scaffold factors with minor groove contacts | Present
T |
likely active or activable, negative direction distals likely random | |
252. NF‐κB/Rel family of eukaryotic transcription factors | CCCCTAAGGGG | β-Scaffold factors with minor groove contacts | Absent | NF-κB 411 | |
253. NF𝜿B (Sato)
(NF𝜿BSs) |
GAATTC | ? | Present
T |
likely active or activable | |
254. Nuclear factor 1
(NF-1) |
TTGGCNNNNNGCCAA | NF I | Absent | palindromic sequence 410 | |
255. Nuclear factor Ys | CCAATGG(A/C)(A/G) | ? | Absent | NF-Y is a trimeric complex 48 | |
256. Nutrient-sensing response element 1
(NSRE) |
GTTTCATCA | ? | Present
T |
likely active or activable | |
257. Oaf1 transcription factor | CGGN3TNAN9-12CCG | ? | Present
T |
likely active or activable | |
258. ORESARA1
(ORE1) (Matallana) |
(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) | ? | Present
T |
likely active or activable | |
259. ORESARA1
(ORE1) (Olsen) |
T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) | ? | Present
T |
likely active or activable | |
260. p53 response elements | (A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T) | β-Scaffold factors with minor groove contacts | Present
T |
likely active or activable | |
261. p53 response elements
(Long1) |
CAGGCCC | β-Scaffold factors with minor groove contacts | Present
T |
likely active or activable | |
262. p53 response elements
(Long2) |
GGGCGTG | β-Scaffold factors with minor groove contacts | Present
T |
likely active or activable | |
263. p63 DNA binding sites | (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) | β-Scaffold factors with minor groove contacts | Absent | RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY 412 | |
264. P-box (Mena) | (A/T)AAAG | ? | Present
T |
likely active or activable, the positive direction proximals overlap the randoms | |
265. P-box, (Motojima) | TGAGTTCA | Present | P-box | likely active or activable | |
266. P-box
(Yu) |
GTAA(T/C) | ? | Present
T |
likely active or activable with some overlapping the randoms | |
267. Pleiotropic Drug Resistance 1p (Pdr1p), (Tang 2020) | TCCGCGGA | Absent | 200 | Pdr1p/Pdr3ps | Pdr1p/Pdr3p response elements (PDREs) 48 |
267. Pleiotropic Drug Resistance 1p (Pdr1p), (Salin 2008) | TCCG(C/T)GG(A/G) | Present | 200 | Pdr1p/Pdr3ps | likely? |
268. Peroxisome proliferator-activated receptor alpha | CGACCCC | Present | 200 | Peroxisome proliferator-activated receptor alpha 18:37, 15 February 2021 | likely active or activable, positive direction distal overlaps upper end of randoms |
269. Peroxisome proliferator hormone response elements, (PPREs) | AGGTCANAGGTCA | Absent | 200 | Peroxisome proliferator hormone response elements 18:37, 15 February 2021 | PPARs/RXRs heterodimers bind to PPRE 412 |
270. Phosphate starvation-response transcription factor (Pho4) | CAC(A/G)T(T/G) | Present | 200 | Pho4ps 16:20, 12 May 2022 | likely active or activable, positive strands of the UTRs and negative direction distals are in the random range |
271. Pollen1 element with TCCACCATA | AGAAANNNNTCCACCATA | Absent | 200 | Pollen1 with TCCACCATA 23:24, 9 January 2023 | adjacent co-dependent regulatory element TCCACCATA 49-414 |
272. Pollen1 elements | AGAAA | Present | 200 | Pollen1 elements 21:40, 10 January 2023 | likely active or activable |
273. Pollen1 element | TCCACCATA | Absent | 200 | TCCACCATA 08:30, 11 January 2023 | no regulatory element TCCACCATA was found, nor its ci. 49 |
274. Polycomb response elements | CGCCAT(A/T)TT | Absent | 200 | Polycomb response elements 06:52, 16 February 2021 | 2*48-49 |
275. Polycomb response elements, (PRE) | GCCAT | Present | 200 | Polycomb response elements 22:28, 13 January 2023 | likely active or activable |
276. Pribnow boxes | TATAAT | Present | 200 | Pribnow boxes 03:43, 15 January 2023 | likely active or activable |
277. Prolamin boxes | TG(A/T)AAAG | Present | 200 | Prolamin boxes 06:14, 18 January 2023 | likely active or activable |
278. Q elements | AGGTCA | Present | 200 | Q elements 20:23, 18 January 2023 See Retinoic acid response element | likely active or activable |
279. Quinone reductase response element, (QRDRE), (Yao) | TCCCCT of TCCCCTTGCGTG | Present | 200 | Quinone reductase response element 05:08, 5 November 2022 | likely active or activable |
280. Rap1 regulatory factors | ACCC(A/G)N(A/G)CA | Absent | 200 | Rap1 regulatory factors 05:04, 20 February 2021 | "(ACCCRnRCA), less than half of the sites were detectably bound"[12] 47 |
281. Rap1 reduced consensus | (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C) | Present | 200 | Rap1 reduced consensus 03:47, 15 November 2022 | likely active or activable |
282. Reb1 extended, (Rossi) | ATTACCCGAA | Absent | 200 | Extended Reb1 00:07, 20 June 2021 | 410 |
283. Reb1 bound and exact occurrences | TTACCC(G/T) | Present | 200 | Reb1 bound and exact occurrences16:38, 15 November 2022 | likely active or activable |
284. Retinoic acid response element | AG(A/G)TCA | Present | 200 | Retinoic acid response element 19:56, 19 January 2023 | likely active or activable, positive direction distals appear random |
285. Ribophorin (RPN) (Rpn4), PACE (proteasome associated control element) | GGTGGCAAA | Absent | 200 | Rpn4ps 03:15, 23 February 2021 | 49 |
286. Rlm1ps | CTATATATAG | Absent | 200 | Rlm1ps 05:55, 22 February 2021 | 4TAG 24*46 |
287. RORE motif, (RORE) | A(A/T)NTAGGTCA | Present | 200 | classic RORE motif 05:51, 22 January 2023 | likely active or activable |
288. RORE motif, variant | C(T/A)(G/A)GGNCA | Present | 200 | variant RORE motif 03:04, 24 January 2023 | likely active or activable |
289. Rox1ps (Tang 2020) | RRRTAACAAGAG | Absent | 200 | Rox1ps Heme-dependent repressor of hypoxic genes 21:50, 22 February 2021 | 23*49 |
290. R response elements (RRE) | CATCTG | Present | 200 | R response elements 16:04, 19 July 2022 | likely active or activable |
291. Seed-specific elements (SRE) | CATGCATG | Absent | 200 | Seed-specific elements 20:18, 23 February 2021 | 48-412 |
292. Serum response elements, (SRE) | ACAGGATGT | Present | 200 | Serum response elements 16:38, 25 January 2023 | likely active or activable |
293. Servenius sequences | GGACCCT | Present | 200 | Servenius sequences 03:07, 28 January 2023 | likely active or activable |
294. Shoot specific elements, (SREs) | CAGCAGATTGCG | Absent | 200 | Shoot specific elements 15:13, 24 February 2021 | 412 |
295. Shue box element, (Crowder 1988) | CCCTG(C/G) | Present | 200 | Shue box elements 05:24, 18 April 2023 | likely active or activable |
296. Sip4ps (Tang) | CC(C/G)T(C/T)C(C/G)TCCG | Absent | 200 | Sip4ps 02:55, 25 February 2021 | 23*48 |
297. Smp1ps (Tang) | ACTACTA(T/A)4TAG | Absent | 200 | Smp1ps 23:43, 25 February 2021 | 2*410 |
298. SP1, (Long) | GGGGCGGGCC | Absent | 200 | SP1 19:43, 25 April 2023 | 410 |
299. Sp1 element, (Berberich 1993) | GGGGCGGGT | Absent | 200 | Sp1 elements 21:03, 18 April 2023 | 49 |
300. SP1, (Zhang) | (G/T)GGGCGG(G/A)(G/A)(C/T) | Present | 200 | SP1 05:57, 2 February 2023 | likely active or activable |
301. SP-1, (Sato) | CCGCCCC | Present | 200 | SP-1 05:54, 2 February 2023 | likely active or activable |
302. SP1, (Yao) | GCGGC | Present | 200 | SP1 05:57, 4 February 2023 | likely active or activable |
303. SP1-box 1, (Motojima) | GGGGCT | Present | 200 | SP1-box 1 05:46, 29 January 2023 | likely active or activable |
304. SP1-box 2, (Motojima) | CTGCCC | Present | 200 | SP1-box 2 19:30, 30 January 2023 | likely active or activable |
305. STAT5 | TTCNNNGAA | Present | 200 | STAT5 03:41, 5 February 2023 | likely active or activable, positive distal likely random |
306. Sterile12, (STE12), (Tang 2020) | TGAAAC | Present | 200 | Sterile12 encodes a transcription factor (Ste12) 05:53, 27 April 2023 | likely active or activable |
307. Sterol response elements, (Branco) | TCGTATA | Absent | 200 | Sterol response elements 19:00, 28 February 2021 | perhaps plant specific 47 |
308. Sterol response elements, (Yao) | AGCAGATTGCG | Absent | 200 | Sterol response elements 03:22, 1 March 2021 | liver specific 411 |
309. Stress-response elements, (STREs) | CCCCT | Present | 200 | Stress-response elements 07:49, 7 February 2023 | likely active or activable, positive cores overlap randoms |
310. Sucrose boxes | NNAATCA | Present | 200 | Sucrose boxes 08:03, 10 February 2023 | likely active or activable |
311. TACTAAC boxes | TACTAA(C/T) | Present | 200 | TACTAAC boxes 06:05, 12 February 2023 | likely active or activable |
312. TAGteams | CAGGTAG | Present | 200 | TAGteams 04:15, 14 February 2023 | likely active or activable |
313. Tapetum boxes | TCGTGT | Present | 200 | Tapetum boxes 08:10, 16 February 2023 | likely active or activable |
314. TATA boxes | TATAAAA (Carninci 2006) TAT box (Yang 2006) | Present | 1 | Wikipedia:TATA box 02:36, 10 January 2011 | likely active or activable |
315. TATA boxes | TATAAA (Butler 2002) | Present | 4 | Downstream promoter elements 21:32, 20 May 2012 | likely active or activable |
314. TATA boxes (RGWYV(T)) (Burke 1996) | TATA(A/T)A(A/T) (Watson 2014) | Present | 10 | Wikipedia:TATA box 04:32, 4 December 2017 | likely active or activable |
315. TATA boxes (Yang 2007) | TATA(A/T)AA(A/G) (Juven-Gershon 2010) | Present | 14 | metazoan TATA box 01:05, 13 October 2019 | likely active or activable |
316. TATA boxes (Yang 2007) | TATA(A/T)A(A/T)(A/G) (Basehoar 2004) | Present | 9 | Wikipedia:TATA box 18:28, 21 November 2017 | likely active or activable |
317. TAT boxes (Fan 2007) | TATCCAT | Present | 100 | TAT box (Fan) samplings 06:17, 13 November 2022 | likely active or activable |
318. TATCCAC boxes | TATCCAC | Absent | 200 | TATCCAC boxes 03:59, 13 October 2019 | GA responsive complex component 47 |
319. TATCCAC boxes (Yang 2007) | TATCCAC | Absent | 15 | TATC box gene transcriptions 03:59, 13 October 2019 | 47 |
320. Tbf1 regulatory factors | A(A/G)CCCTAA | Present | 200 | Tbf1 regulatory factors 17:38, 15 November 2022 | Saccharomyces cerevisiae, likely active or activable |
321. T boxes, (Conlon) | TCACACCT | Present | 200 | T boxes 23:28, 18 November 2022 | likely active or activable |
322. T boxes, (Zhang) | AACGTT | Present | 200 | T boxes 17:21, 20 November 2022 | likely active or activable |
323. TCCACCATA elements | TCCACCATA | Absent | 200 | TCCACCATA elements 05:10, 13 February 2021 | adjacent co-dependent regulatory element of POLLEN1 49 |
324. TEA consensus sequences | CATTCY | Present | 200 | TEA consensus sequences 06:35, 24 February 2023 | likely active or activable |
325. Telomeric repeat DNA-binding factors, (TRFs) | TTAGGG | Present | 200 | Telomeric repeat DNA-binding factors 06:35, 2 March 2023 | likely active or activable |
326. Tetradecanoylphorbol-13-acetate response elements, (TREs) | TGA(G/C)TCA | Absent | 200 | Tetradecanoylphorbol-13-acetate response elements 15:07, 24 August 2020 | cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 2*46 |
327. TGF-β control elements, (TCEs) | GCGTGGGGGA | Absent | 200 | TGF-β control elements 17:38, 5 March 2021 | GCGTGGGGGA in humans 410 |
328. TGF-β inhibitory elements, (TIEs) | GAGTGGTGA | Absent | 200 | TGF-β inhibitory elements 01:57, 23 August 2020 | in the rat transin/stromelysin promoter 49 |
329. Thyroid hormone response elements, (TREs)(THRs) | AGGTCA | Present | 200 | Thyroid hormone response elements 23:06, 3 March 2023 | likely active or activable |
330. Transcription factor 3, (TCF3) | GTCTGGT | Present | 200 | Transcription factor 3 19:21, 5 March 2023 | likely active or activable |
331. Translational control sequences, (TCSs) | (A/T)TT(A/G)TCT | Present | 200 | Translational control sequences 20:33, 7 March 2023 | likely active or activable |
332. Transposon enhancement control (TEC) or Tec1 | GAATGT | Present | 200 | Tec1ps 22:49, 26 February 2023 | likely random, Ste12p cofactor |
333. Unfolded protein response element, (URE), (UPRE-1) | CANCNTG | Present | 200 | Unfolded protein response element 18:24, 8 January 2023 | likely active or activable |
334. Unfolded protein response elements, (UPREs) | TGACGTG(G/A) | Present | 200 | Unfolded protein response elements 21:02, 7 March 2023 | likely active or activable |
335. Upstream repressor site 1, (URS1, core), (Sumrada) | CCGCC | Present | 200 | Upstream repressor site 1 06:31, 17 December 2022 | likely active or activable, negative direction proximals are within randoms |
336. Upstream stimulating factors, (USFs) | GCC(A/T)NN(C/G/T)(A/G) | Present | 200 | Upstream stimulating factors 05:51, 11 March 2023 | likely active or activable, cores overlap lower randoms |
337. V boxes | (A/G)TT(A/T)(C/T) | Present | 200 | V boxes 20:50, 16 March 2023 | likely active or activable |
338. Vhr1ps, (VHR1), (Weider 2016), (Tang 2020) | AATCA-N8-TGA(C/T)T | Absent | 200 | Vhr1ps 01:26, 9 March 2021 | Response to low biotin concentrations 2*49 |
339. Vitamin D response elements, (VDRE2s) | A/GGG/TTCAnnnA/GGG/TTCA | Absent | 200 | Vitamin D response elements 03:48, 10 March 2021 | 410 |
340. Vitamin D response elements (VDRE) (Kakhki 2018) | (A/G)G(G/T)TCA | Present | 18 | Vitamin D response elements 04:37, 19 March 2023 | likely active or activable |
341. W boxes (W-boxes) (WRKY) | (C/T)TGAC(C/T) | Present | 200 | W boxes 20:46, 20 March 2023 | likely active or activable |
342. X1a boxes (Ferstl 2004) | TCTGCC | Present | 200 | X-boxes 06:43, 27 April 2023 | likely? |
342. X1b boxes (Ferstl 2004) | AGAGACAGAT | Absent | 200 | X-boxes 17:57, 30 April 2023 | 410 |
342. X2 boxes (Ferstl 2004) | AGGTCCA | Present | 200 | X-boxes 06:43, 27 April 2023 | likely? |
343. X boxes (Zhang 1993) | GTTGGCATGGCAAC | Absent | 200 | X boxes 02:35, 20 November 2018 | X2 box is AGGTCCA 414 |
344. X-boxes (Moreno) | GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC | Absent | 200 | X-boxes 16:43, 10 March 2021 | includes GTTNCCATGGNAAC (4/3)*24*47-412 |
345. X core promoter elements (XCPE1) | (A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C) | Present | 200 | X core promoter elements 19:37, 22 March 2023 | likely active or activable |
346. Xenobiotic response elements, (XREs) | (T/G)NGCGTG(A/C)(G/C)A | Absent | 200 | Xenobiotic response elements 20:45, 17 February 2021 | contains the core sequence GCGTG, see AHRE above 2*47 |
347. Xenobiotic response elements (XREs) (Shen 1992) | GCGTG | Present | 96 | Xenobiotic response elements 05:22, 5 November 2022 | likely active or activable |
348. XhoI site-binding protein 1 protein (Xbp1p), (Mai 1997), (Tang 2020) | GcCTCGA(G/A)G(C/A)g(a/g) | Absent | 200 | Xbp1ps 14:40, 11 March 2021 | Transcriptional repressor 2*410 |
349. Yap response elements (Salin 2008) | T(G/T)ACT(A/C)A | Present | 200 | Yap response elements 19:57, 24 March 2023 | likely? |
349. Yap recognition sequences (Tang 2020) | TTACTAA | Present | 200 | Yap recognition sequences 19:57, 24 March 2023 | likely active or activable |
350. Y boxes, (Koike 1997) | (A/G)CTAACC(A/G)(A/G)(C/T) | Absent | 200 | Y boxes 01:31, 20 November 2018 | inverted CAAT box, 48 |
351. YY1 binding sites | CCATTTA | Absent | 200 | YY1 binding sites 06:23, 12 March 2021 | 47 |
352. YY1 binding sites | CCATCTT | Present | 200 | YY1 binding sites 22:07, 25 March 2023 | likely active or activable |
353. Z-box (ZboxN) samplings, (ZboxNs) | ATACGGT | Absent | 200 | Z-box (ZboxN) samplings 19:47, 2 December 2022 | 47 |
354. Z-box (ZboxSo) samplings, (ZboxNs) | ATACGTGT | Absent | 200 | Z-box (ZboxSo) samplings 20:21, 3 December 2022 | 48 |
355. Z boxes, NSoSp form | A(C/T)A(C/G)G(G/T)(A/G/T)T | Present | 200 | Z boxes 17:23, 28 November 2022 | likely active or activable, negative direction distals within randoms |
356. Z boxes, ZboxG | A(C/T)A(C/G)GT(A/G)T | Present | 200 | Z boxes 03:00, 1 December 2022 | likely active or activable |
357. Z boxes, ZboxSp | CAGGT(A/G) | Present | 200 | Z boxes 05:10, 24 November 2022 | likely active or activable |
358. Zinc-responsive elements, (Zhao 1998), (Tang 2020) (ZREs) | ACCYYNAAGGT or ACC(C/T)(C/T)NAAGGT | Absent | 200 | Zap1ps 15:52, 15 March 2021 | 49 |
359. Zinc responsive elements, (ZREs), (Nicola 2007) | MHHAACCBYNMRGGT or (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT | Absent | 200 | Zinc responsive elements 19:02, 15 March 2021 | (4/3)3*49 |
Response element testing (Absent)
Name of elements | Consensus sequences | Response element class | Testing | Activity |
---|---|---|---|---|
Abbreviations | Variations | Absent (N) | Notes | |
Authors | ||||
1. novel ABA-response elements
(ABREN, novel ABRE) |
GATCGATC, CGATCGAT, GATCGAT | WD40 repeat family | N | ABREN, CGATCGAT motif, and core of ABREN and CGATCGAT motif.[13] |
2. ABA-response element-like
(ABRE-like) |
ACGTGTCC | WD40 repeat family | N | third highest scoring motif.[13] |
3. Abf1 regulatory factors | CGTCCTCTACGAT | General Regulatory Factors | N | CGTNNNNNACGAT.[12] |
4. Activating proteins
(Murata) |
GCCCACGGG | bHSH | N | Activating protein 2.[14] |
5. AhR-responsive elements
(AHRE) (Yao) |
(G/T)NGCGTG(A/C)(C/G)A | bHLH | N | in the promoter region of AhR responsive genes |
6. Alpha-amylase conserved elements | TATCCA | ? | N | TATCCATCCATCC.[15] |
7. Amino acid response elements
(AARE) (Maruyama) |
ATTGCATCA | ? | N | AARE1 (ATTGCATCA)[16] |
8. Amino acid response elements
(AARE) (Broer) |
TTTGCATCA | ? | N | TTTGCATCA.[2][3] |
9. Amino acid response element-like
(AARE-like) |
TGGTGAAAG | ? | N | AARE-like sequence (TGGTGAAAG, named AARE3).[16] |
10. Androgen response elements
(AREs) (Kouhpayeh) |
GGTACANNNTGTTCT | Zinc finger DNA-binding domain | N | GGTACACGGTGTTCT.[17] |
11. Androgen response elements
(AREs) (Wilson) |
TGATTCGTGAG | Zinc finger DNA-binding domain | N | AGAACANNNTGTTCT.[18] |
12. Antioxidant-electrophile responsive elements
(Otsuki) |
GTGAGGTCGC | bHLH | N | GTGAGGTCGC.[4] or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A[5], an antioxidant response element (ARE) |
13. CAAT boxes | (C/T)(A/G)(A/G)CCAATC(A/G) | bZIP | N | consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT. |
14. Calcium-response elements | CTATTTCGAG | ? | N | CaRE1 CTATTTCGAG.[19] |
15. Carbohydrate response elements
(ChREs) |
CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG | ? | N | ChoRE1, ChoRE2.[20] |
16. Carbon source-responsive elements
(CSREs) |
CATTCATCCG | ? | N | confers carbon source-dependent regulation |
17. Cbf1 regulatory factors | TCACGTGA | ? | N | strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end. |
18. C-boxes
(Johnson) |
GAGGCCATCT | bZIP | N | GAGGCCATCT.[21] |
19. C/A hybrid boxes | TGACGTAT | bZIP | N | TGACGTAT.[22] A at the 12 position |
20. C/T hybrid boxes | TGACGTTA | bZIP | N | TGACGTTA.[22] T at the 12 position |
21. CCCTC-binding factors
(CTCF) |
NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) | ? | N | NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C).[23] |
22. C/EBP boxes | TTAGGACAT,[6] or TAGCATT.[7] | bZIP | N | CCAAT-enhancer-binding site (C/EBP) is TAGCATT |
23. Cell-cycle boxes
(CCBs) |
CACGAAAA | ? | N | "cell cycle box" is functional in either orientation, acting as an enhancer |
24. Cell cycle regulation | CCCAACGGT[15] | ? | N | tomato genome-wide analysis |
25. CENP-B boxes | TTTCGTTGGAAGCGGGA | ? | N | specifically localized at the centromere |
26. Coupling elements
(CE1) |
TGCCACCGG[13] | ? | N | CE1 (Watanabe) |
27. DAF-16-associated elements
(DAE) |
TGATAAG | ? | N | DAF-16-associated element (DAE).[24] |
28. D-boxes
(Mracek1) |
GTTGTATAAC | ? | N | GTTGTATAAC.[25] |
29. D-boxes
(Mracek) |
CTTATGTAAA (Mracek2) | ? | N | CTTATGTAAA.[25] |
30. D-boxes
(Johnson) |
TCTCACA | ? | N | TCTCACATT(A/C)AATAAGTCA is a D-box.[21] |
31. Defense and stress-responsive elements | ATTTTCTTCA | ? | N | ATTTTCTTCA.[15] |
32. DNA damage response elements
(DREs) (Smith) |
TTTCAAT[26] | ? | N | in the upstream repression sequence (URS) |
33. DNA damage response elements
(DREs) (Sumrada) |
TAGCCGCCG of TAGCCGCCGRRRR.[27] | ? | N | in the upstream repression sequence (URS) |
34. DNA replication-related elements
(DREs) |
TATCGATA | ? | N | DNA replication-related element (DRE).[28] |
35. DREB boxes | TACCGACAT | ? | N | CRT/DREB box |
36. EIF4E basal elements | TTACCCCCCCTT | ? | N | poly(C) motif |
37. Endoplasmic reticulum stress response elements
(ERSE) |
CCAAT-N9-CCACG | bZIP | N | compare CCAAT-box and ERSE below in the (present) |
38. Estrogen response elements
(EREs) |
AGGTTA or GGTCAGGAT | Cys 4 |
N | AGGTTATTGCCTCCT or GGTCAGGATGAC |
39. F boxes | TGATAAG[29] | ? | N | F-box overlaps the I-box |
40. Forkhead boxes | GTAAACAA[30] | HTH, Forkhead | N | GTAAACAA FOXO1 |
41. Gal4ps | CGGACCGC | ? | N | CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG[31] |
42. γ-interferon activated sequences
(GAS) |
TTCCTAGAA | ? | N | ALS-GAS1 between nt −633 and nt −625 |
43. G boxes | (G/T)CCACGTG(G/T)C | ? | N | no "perfect palindrome" G boxes in either promoter |
44. GCN4 motifs | TGACTCA, TGAGTCA | bZIP | N | ACGT motif |
45. Gcn4ps | ATGACTCTT[31] | bZIP | N | GCN4 motifs |
46. Gibberellin responsive element-like 2
(GARE-like 2) (Fan) |
TAACGTA[32] | ? | N | "in the promoters of hydrolase genes".[32] |
47. GLM boxes | (G/A)TGA(G/C)TCA(T/C) | ? | N | GCN4-like motif |
48. Grainy head transcription factor binding sites | AACCGGTT | β-Scaffold factors with minor groove contacts | N | also GACTGGTT |
49. GT boxes
(Motojima) |
TGGGTGGGGCT | ? | N | (-78 to -69) |
50. Hapless motifs | CCAATCA | ? | N | heterotrimeric transcription factor, HAP2/3/4.[33] |
51. Heat-responsive elements | AAAAAATTTC | Helix-turn-helix (HTH), Heat shock factors (HSFs) | N | four nGAAn motifs |
52. Heat shock elements
(HSE1) (Eastmond) |
nGAAnnTTCnnGAAn | HTH, HSFs | N | HSE1 |
53. Heat shock elements
(HSE2) (Eastmond) |
nTTCnnGAAnnTTCn | HTH, HSFs | N | HSE2 is the inverse complement of HSE1 |
54. Heat shock elements
(HSE5) (Eastmond) |
nTTCn-(5-bp)-nTTCnnGAAn | HTH, HSFs | N | HSE5 |
55. Heat shock elements
(HSE6) (Eastmond) |
nTTCn-nnGAAn-(5-bp)-nGAAn | HTH, HSFs | N | HSE6 |
56. Heat shock elements
(HSE7) (Eastmond) |
nGA(A/G)nnTTCnnGAAn | HTH, HSFs | N | HSE7 PFT1 |
57. Heat shock elements
(HSE) (Eastmond) |
nGAAnnTTCnnGA(A/G)n | HTH, HSFs | N | HSE7 PFT2 |
58. Heat shock elements
(HSE10) (Eastmond) |
nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn | HTH, HSFs | N | HSE10 |
59. Hypoxia-inducible factors
(HIF-1) |
GCCCTACGTGCTGTCTCA[34] | bHLH | N | composed of HIF-1α and HIF-1β |
60. I boxes | GATAAG | ? | N | GGATGAGATAAGA |
61. Inositol/choline-responsive elements
(ICRE) (Case) |
CANNTGAAAT | ? | N | version of Lopes, see below |
62. Inositol/choline-responsive elements
(ICRE) (Lopes) |
ATGTGAAAT | ? | N | using ANNTGAAAT |
63. Interferon-stimulated response elements
(ISREs) |
AGTTTCN2TTTCN | ? | N | consensus sequence AGTTTCN2TTTCN.[8] |
64. Kozak sequences | GCCGCC(A/G)CCATGG | ? | N | GCCGCC(A/G)CCATGG[9] |
65. Kozak sequences
(Matsumoto) |
GAAAATGG | ? | N | GAAAATGG[10] |
66. L boxes | AAATTAACCAA | ? | N | AAATTAACCAA[11] |
67. Maf recognition element
(MAREs) |
TGCTGA(G/C)TCAGCA | ? | N | and TGCTGA(GC/CG)TCAGCA[35] |
68. Met3s | TCACGTG | bZIP | N | TCACGTG[36] |
68. M boxes | GTCATGTGCT | ? | N | or AGTCATGTGCT[37] |
69. Mcm1 regulatory factors | TT(A/T)CCNN(A/T)TNGG(A/T)AA | ? | N | Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[12] |
70. Mcm1 regulatory factors
|
TTNCCNNNTNNGGNAA | ? | N | Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[12] |
71. Motif ten elements | C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G) | ? | N | Gene ID: 6309 |
72. NF‐κB/Rel family of eukaryotic transcription factors | CCCCTAAGGGG | β-Scaffold factors with minor groove contacts | N | NF-κB |
73. Nuclear factor 1
(NF-1) |
TTGGCNNNNNGCCAA | NF I | N | palindromic sequence |
74. Nuclear factor Ys | CCAATGG(A/C)(A/G) | ? | N | NF-Y is a trimeric complex |
75. p63 DNA binding sites | (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) | β-Scaffold factors with minor groove contacts | N | RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY |
76. Pdr1p/Pdr3ps | TCCGCGGA | ? | N | Pdr1p/Pdr3p response elements (PDREs) |
77. Peroxisome proliferator hormone response elements
(PPREs) |
AGGTCANAGGTCA | ? | N | PPARs/RXRs heterodimers bind to PPRE |
78. Pollen1 with TCCACCATA | AGAAANNNNTCCACCATA | ? | N | adjacent co-dependent regulatory element TCCACCATA |
79. TCCACCATA | TCCACCATA | ? | N | no regulatory element TCCACCATA was found, nor its ci. |
80. Polycomb response elements | CGCCAT(A/T)TT | ? | N | CGCCATTT |
81. Rap1 regulatory factors | ACCC(A/G)N(A/G)CA | ? | N | "(ACCCRnRCA), less than half of the sites were detectably bound"[12] |
82. Extended Reb1 | ATTACCCGAA | ? | N | "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."[12] |
83. Rlm1ps | CTATATATAG | ? | N | CTA(T/A)4TAG |
84. Rox1ps | RRRTAACAAGAG | ? | N | Heme-dependent repressor of hypoxic genes.[31] |
85. Rpn4ps | GGTGGCAAA | ? | N | proteasome genes |
86. Seed-specific elements | CATGCATG | ? | N | SRE consensus: CAGCAGATTGCG is none |
87. Shoot specific elements | GATAATGATG | ? | N | SRE consensus: CAGCAGATTGCG is none |
88. Sip4ps | CC(C/G)T(C/T)C(C/G)TCCG | ? | N | CC(C/G)T(C/T)C(C/G)TCCG[31] |
89. Smp1ps | ACTACTA(A/T)(A/T)(A/T)(A/T)TAG | ? | N | ACTACTA(T/A)4TAG[31] |
90. SP1
(Long) |
GGGGCGGGCC | ? | N | GGGGCGGGCC[20] |
91. Sterol response elements
(Branco) |
TCGTATA | ? | N | perhaps plant specific |
92. Sterol response elements
(Yao) |
AGCAGATTGCG | ? | N | liver specific |
93. TATCCAC boxes | TATCCAC | ? | N | GA responsive complex component |
94. TCCACCATA elements | TCCACCATA | ? | N | adjacent co-dependent regulatory element of POLLEN1 |
95. Tetradecanoylphorbol-13-acetate response elements
(TREs) |
TGA(G/C)TCA | ? | N | cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 |
96. TGF-β control elements
(TCEs) |
GAGTGGGGCG | ? | N | in mouse and rat, GCGTGGGGGA in humans |
97. TGF-β inhibitory elements
(TIEs) |
GAGTGGTGA | ? | N | in the rat transin/stromelysin promoter |
98. Vhr1ps
(VHR1) |
AATCA-N8-TGA(C/T)T | ? | N | Response to low biotin concentrations |
99. Vitamin D response elements
(VDREs) |
A/GGG/TTCAnnnA/GGG/TTCA | ? | N | (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA |
100. X boxes | GTTGGCATGGCAAC[38] | ? | N | X2 box is AGGTCCA not ⌘F |
101. X-boxes | GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC[39] | ? | N | includes GTTNCCATGGNAAC |
102. Xbp1ps | GcCTCGA(G/A)G(C/A)g(a/g) | ? | N | Transcriptional repressor |
103. Xenobiotic response elements
(XREs) |
(T/G)NGCGTG(A/C)(G/C)A | ? | N | contains the core sequence GCGTG, see AHRE above |
104. Y boxes | (A/G)CTAACC(A/G)(A/G)(C/T) | ? | N | inverted CAAT box |
105. Zap1ps | ACCCTCA | ? | N | ACC(C/T)(C/T)(A/C/G/T)AAGGT |
106. Z-box (ZboxN) samplings
(ZboxNs) |
ATACGGT | ? | N | No ZboxN occur on either side of A1BG |
107. Z-box (ZboxSo) samplings
(ZboxNs) |
ATACGTGT | ? | N | No ZboxSo occur on either side of A1BG |
108. Zinc responsive elements
(ZREs) |
MHHAACCBYNMRGGT | ? | N | (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT |
Response element testing (Present)
Name of elements | Consensus sequences | Response element class | Testing | Activity/Notes |
---|---|---|---|---|
Abbreviations | Variations | Present (Y) | Random or likely active or activable | |
Authors | Table (T) | |||
1. ABA responsive elements
(ABREs) |
ACGTG(G/T)C | WD40 repeat family | Y
T |
likely active or activable |
2. Activated B-cell Factor-1s
(ABFs, Abfms) |
CGTNNNNN(A/G)(C/T)GA(C/T) | General Regulatory Factors | Y
T |
likely active or activable |
3. A-boxes | TACGTA | Basic leucine zipper (bZIP) | Y
T |
likely active or activable |
4. boxes A | TGACTCT | bZIP | Y
T |
likely active or activable |
5. Abscisic acid-responsive elements (Pho4s), G boxes | CACGTG | bZIP, bHLH | Y
T |
likely active or activable |
6. ACGT-containing elements | ACGT | bZIP | Y
T |
cores and proximals are likely active or activable, but a few of the UTRs and distal promoters may be random |
7. Activating protein 2 alpha
(AP2a) |
GCCNNNGGC | bHSH | Y
T |
likely active or activable, positive strand, positive direction AP2a within randoms |
8. Activating protein 2
(AP2) (Cohen) |
GCCTGGCC | bHSH | Y
T |
likely active or activable |
9. Activating protein 2
(Cohen) |
TCCCCCGCCC | bHSH | Y
T |
likely active or activable |
10. Activating protein 2
(Murata) |
(C/G)CCN(3)GG(C/G) | bHSH | Y
T |
likely active or activable |
11. Activating protein 2
(Murata) |
(C/G)CCN(4)GG(C/G) | bHSH | Y
T |
likely active or activable |
12. Activating protein 2
(Yao) |
TCTTCCC | bHSH | Y
T |
likely active or activable |
13. Activating protein 2
(Yao) |
CTCCCA | bHSH | Y
T |
likely active or activable |
14. Activating proteins
(AP-2) (Yao) |
GGCCAA | bHSH | Y
T |
likely active or activable |
15. Activating transcription factors
(Burton) |
(A/C/G)TT(A/G/T)C(A/G)TCA | bZIP | Y
T |
likely active or activable |
16. Activating transcription factors
(Kilberg) |
(A/G/T)TT(A/G/T)CATCA | bZIP | Y
T |
likely active or activable |
17. Adenylate–uridylate rich elements
(AUREs) (Bakheet) |
(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) | stem-loop | Y
T |
likely active or activable |
18. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class I) |
ATTTA | stem-loop | Y
T |
likely active or activable, UTRs at the lower end of the randoms |
19. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class II) |
TTATTTA(A/T)(A/T) | stem-loop | Y
T |
likely active or activable |
20. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class III) |
ATTT | stem-loop | Y
T |
likely active or activable, low negative direction proximals overlap randoms |
21. Adr1ps | TTGG(A/G)G | Cys 2His 2 zinc finger binding domain |
Y
T |
likely active or activable |
22. Aft1s | (C/T)(A/G)CACCC(A/G) | bZIP? | Y
T |
likely active or activable |
23. AGC boxes | AGCCGCC | AP-2/EREBP-related factors | Y
T |
likely active or activable |
24. AhR responsive element or Aryl hydrocarbon responsive element II
(AHRE-II) |
CATGN6C(A/T)TG | bHLH | Y
T |
likely active or activable |
25. AhR DNA-binding consensus sequence
(AhRY) (Yao) |
GCGTGNN(A/T)NNN(C/G) | bHLH | Y
T |
likely active or activable for ZNF497 |
26. Androgen response element1s
(Kouhpayeh) |
GGTACA of GGTACAnnnTGTTCT | Zinc finger DNA-binding domain | Y
T |
likely active or activable |
27. Androgen response element2s
(Kouhpayeh) |
TGTTCT of GGTACAnnnTGTTCT | Zinc finger DNA-binding domain | Y
T |
likely active or activable |
28. Androgen response elements
(Wilson) |
AGAACANNNTGTTCT | Zinc finger DNA-binding domain | Y
T |
the two portions AGAACA and TGTTCT occurring separately are likely active or activable |
29. Angiotensinogen core promoter elements | (A/C)T(C/T)GTG | bZIP? | Y
T |
likely active or activable, positive direction distal low occurrences overlap randoms |
30. Antioxidant-electrophile responsive elements
(Lacher) |
GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A | bHLH | Y
T |
likely active or activable |
31. ATA boxes | AATAAA | β-Scaffold factor? | Y
T |
likely active or activable |
32. ATTTA elements
(Siegel) |
(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T) | β-Scaffold factor? | Y
T |
likely active or activable |
33. Auxin response factors
(Stigliani) |
(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T) | WD40 repeat family | Y
T |
likely active or activable, positive direction proximals overlap high randoms, positive direction cores within randoms |
34. Auxin response factors
(Ulmasov) |
TGTCTC | WD40 repeat family | Y
T |
likely active or activable |
35. Auxin response factors
(Boer) |
TGTCGG | WD40 repeat family | Y
T |
likely active or activable |
36. Auxin response factors
(ARF5) |
(C/G/T)N(G/T)GTC(G/T) | WD40 repeat family | Y
T |
likely active or activable, negative direction proximals ≥ randoms |
37. B-boxes
(Johnson) |
TGGGCA | Zinc finger DNA-binding domains | Y
T |
likely active or activable, positive direction distals ≥ randoms |
38. boxes B
(Sanchez) |
TGTCTCA | Zinc finger DNA-binding domains | Y
T |
likely active or activable |
39. B recognition elements
(BREu) |
(G/C)(G/C)(G/A)CGCC | HTH | Y
T |
likely active or activable |
40. CACA elements (Orlando 2019) | CACA | ? | Y
T |
likely active or activable |
40. CadC binding domains | TTANNNNT | HTH | Y
T |
likely active or activable, negative direction proximals within randoms |
41. Calcineurin-responsive transcription factors | TG(A/C)GCCNC | ? | Y
T |
likely active or activable |
42. Carbohydrate response elements | ChoRE1 ACCGG | ? | Y
T |
likely active or activable |
43. Carbohydrate response elements | ChoRE2 CCCAT | ? | Y
T |
likely active or activable |
44. Carbohydrate response elements | Carb E1 ATCTTG | bHLH? | Y
T |
proximals likely active or activable |
45. Carbohydrate response elements | Carb E2 CACGTG | bHLH | Y
T |
likely active or activable |
46. Carbohydrate response elements | Carb E3 TCCGCC | bHLH? | Y
T |
likely active or activable, low positive direction distals overlap high randoms |
47. Carbon source-responsive elements TCCG elements
(TCCGs) |
TCCG | bHLH? | Y
T |
likely active or activable |
48. CATTCA elements
(CATTs) |
CATTCA | bHLH? | Y
T |
likely random |
49. CARE (Fan)
(CAREs) (Fan) |
CAACTC | WD-40 repeat family | Y
T |
likely active or activable |
50. CARE (Garaeva)
(CAREs) (Garaeva) |
(A/G/T)TT(A/G/T)CATCA | WD-40 repeat family | Y
T |
likely active or activable |
51. cAMP-responsive elements
(CREs), Aca1ps, Sko1ps |
TGACGTCA | bZIP | Y
T |
likely active or activable, same as Root specific elements |
52. CArG boxes | CCAAAAAT(G/A)G | bHLH | Y
T |
likely active or activable |
53. Cat8ps | CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA | ? | Y
T |
likely active or activable |
54. CAT boxes | CATTCCT | bHLH | Y
T |
likely active or activable |
55. CAT-box-like elements | GCCATT | bHLH | Y
T |
likely active or activable |
56. C boxes
(Samarsky) |
AGTAGT | bZIP | Y
T |
likely active or activable |
57. C-boxes
(Song) |
GACGTC | bZIP | Y
T |
likely active or activable |
58. hybrid CG-boxes
(Song) |
TGACGTGT | bZIP | Y
T |
likely active or activable |
59. C boxes
(Voronina) |
GGTGATG | bZIP | Y
T |
likely active or activable |
60. Cell-cycle box variants
(CCBs) |
CACGAAA, ACGAAA and C-CGAAA | ? | Y
T |
likely active or activable |
61. CGCG boxes | (A/C/G)CGCG(C/G/T) | ? | Y
T |
likely active or activable probably for the respective zinc fingers |
62. Circadian control elements | CAANNNNATC | ? | Y
T |
likely active or activable but overlaps highest randoms |
63. Class C DNA binding sites | CACGNG | bHLH | Y
T |
likely active or activable, although the distals may be random |
64. Cold-responsive elements | CCGAC | ? | Y
T |
likely active or activable |
65. Constitutive decay elements
(CDEs) (Siegel) |
TTC(C/T)(A/G)(C/T)GAA | stem-loop | Y
T |
likely active or activable possibly for ZNF497 |
66. Copper response elements
(CuREs) (Quinn) |
TTTGC(T/G)C(A/G) | ? | Y
T |
likely active or activable |
67. Copper response elements
(CuREs) (Park) |
TGTGCTCA | ? | Y
T |
likely active or activable |
68. Coupling elements
(CE3s) (Watanabe) |
GCGTGTC | WD-40 repeat family | Y
T |
likely active or activable |
69. Coupling elements
(CE3s) (Ding) |
CACGCG | WD-40 repeat family | Y
T |
likely active or activable |
70. Cytokinin response regulators
(ARR1s) |
AGATT(C/T) | WD40 repeat family | Y
T |
likely active or activable |
71. Cytokinin response regulators
(ARR10s) |
(A/G)GATA(A/C)G | WD40 repeat family | Y
T |
likely active or activable or may be random |
72. Cytokinin response regulators
(ARR12s) |
(A/G)AGATA | WD40 repeat family | Y
T |
likely active or activable |
73. Cytokinin response regulators
(ARRs) (Ferreira) |
(G/A)GGAT(T/C) | WD40 repeat family | Y
T |
likely active or activable |
74. Cytokinin response regulators
(ARRs) (Rashotte1) |
GATCTT | WD40 repeat family | Y
T |
likely active or activable |
75. Cytokinin response regulators
(ARRs) (Rashotte2) |
(G/A)GAT(T/C) | WD40 repeat family | Y
T |
likely active or activable |
76. Cytoplasmic polyadenylation elements
(CPEs) |
TTTTTAT | ? | Y
T |
likely active or activable |
77. DAF-16 binding elements | (A/G)(C/T)AAA(C/T)A | ? | Y
T |
likely active or activable |
78. D boxes
(Samarsky) |
AGTCTG | ? | Y
T |
likely active or activable |
79. D boxes
(Voronina) |
TCCTG | ? | Y
T |
likely active or activable |
80. D-boxes
(Motojima) |
TGAGTGG | ? | Y
T |
likely active or activable |
81. Dioxin-responsive elements
(DREs) |
TNGCGTG | bHLH? | Y
T |
likely active or activable |
82. Downstream B recognition elements | (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) | ? | Y
T |
likely active or activable, negatives > randoms, positives overlap or outside randoms |
83. Downstream core elements
(DCESIs) |
CTTC of CTTC...CTGT...AGC | ? | Y
T |
likely active or activable, depending on overlaps |
84. Downstream core elements
(DCESIIs) |
CTGT of CTTC...CTGT...AGC | ? | Y
T |
likely active or activable, depending on overlaps |
85. Downstream core elements
(DCESIIIs) |
AGC of CTTC...CTGT...AGC | ? | Y
T |
likely active or activable, depending on overlaps |
86. Downstream promoter elements
(DPEs) (Juven-Gershon) |
(A/G)G(A/T)(C/T)(A/C/G)T | ? | Y
T |
most or all of the real DPE (Juven-Gershon)s are likely active or activable |
87. Downstream promoter elements
(DPEs) (Kadonaga) |
(A/G)G(A/T)CGTG | ? | Y
T |
likely active or activable |
88. Downstream promoter elements
(DPEs) (Matsumoto) |
AGTCTC | ? | Y
T |
likely active or activable |
89. E2 boxes | (G/A)CAG(A/C/G/T)TG(A/C/G/T) | bHLH | Y
T |
likely active or activable |
90. EIN3 binding sites | A(C/T)G(A/T)A(C/T)CT | ? | Y
T |
likely active or activable |
91. Endoplasmic reticulum stress response elements | CCAAT-N9-CCACG, part 1 see Hap motif no.114 below, ESRE2, CCACG | bZIP | Y
T |
likely active or activable |
92. Endosperm expressions | TGTGTCA | ? | Y
T |
likely active or activable |
93. Enhancer boxes | CA(A/C/G/T)(A/C/G/T)TG | bHLH | Y
T |
likely active or activable |
94. Estrogen response elements
(ERE1s) (Driscoll) |
GGTCA | Cys 4 |
Y
T |
likely active or activable |
95. Estrogen response elements
(ERE2s) (Driscoll) |
TGACC | Cys 4 |
Y
T |
likely active or activable |
96. Ethylene responsive elements | ATTTCAAA | WD40 repeat family | Y
T |
likely active or activable |
97. Forkhead boxes | (A/G)(C/T)AAA(C/T)A | HTH, Forkhead | Y
T |
likely active or activable |
98. GAAC elements | GAACT | ? | Y
T |
likely active or activable |
99. Γ-interferon activated sequences
(GAS), see STAT5 |
TTNCNNNAA | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
100. GATA boxes | GATA | Zinc finger DNA-binding domains, bHLH | Y
T |
likely active or activable when occurring in the UTR or distals but may be random when occurring in the proximals |
101. GATA (GATAAG, GATAAH, GATTA) motifs
(Staschke) |
GAT(A/T)A | Zinc finger DNA-binding domains, bHLH | Y
T |
likely active or activable |
102. GC boxes
(Briggs) |
(G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T) | ? | Y
T |
likely active or activable |
103. GC boxes
(Ye) |
GGGCGG | ? | Y
T |
likely active or activable |
104. GCC boxes | GCCGCC | ? | Y
T |
likely active or activable |
105. General control nonderepressible 4 protein binding site
(GCRE, GCN4) |
TGA(C/G/T)T(A/C/G)(A/T) | bZIP | Y
T |
likely active or activable |
106. GGCGGC triplet | GGCGGC | Zn(II)2Cys6 | Y
T |
likely active or activable |
107. GGC triplets | GGC | Zn(II)2Cys6 | Y
T |
likely active or activable |
108. Gibberellic acid responsive elements
(GAREs) |
TAACAAA | WD40 repeat family | Y
T |
likely active or activable |
109. Gibberellic acid responsive elements-like 1
(GAREL1s) |
TAACA(A/G)A | WD40 repeat family | Y
T |
likely active or activable |
110. Gibberellin responsive elements
(GREs) (Sharma) |
AAACAGA[15] | WD40 repeat family | Y
T |
likely active or activable |
111. G-protein-coupled receptors
(GCR1s), CT boxes |
CTTCC | ? | Y
T |
likely active or activable. |
112. Glucocorticoid response elements | AGAACA | bHLH | Y
T |
likely active or activable |
113. GT boxes
(Sato) |
GGGG(T/A)GGGG | ? | Y
T |
likely active or activable |
114. Hac1 KAR2 | CAGCGTG | ? | Y
T |
likely active or activable |
115. H and ACA boxes | AGAGGA | Hairpin-hinge-hairpin-tail | Y
T |
likely active or activable, negative distals likely random |
116. Hap motif and ESRE CCAAT
(Hap4p) |
CCAAT | bZIP | Y
T |
likely active or activable |
117. H-boxes
(Grandbastien) |
CC(A/T)ACCNNNNNNN(A/C)T | hairpin-hinge-hairpin-tail | Y
T |
likely active or activable |
118. H-boxes
(Lindsay) |
CCTACC | hairpin-hinge-hairpin-tail | Y
T |
likely active or activable, equal to or greater than the randoms for the negative direction distals |
119. H box
(Mitchell) |
ANANNA | hairpin-hinge-hairpin-tail | Y
T |
likely active or activable |
120. H box
(Rozhdestvensky) |
ACACCA | hairpin-hinge-hairpin-tail | Y
T |
likely active or activable |
121. Heat shock elements
(HSE3s) (Eastmond) |
nGAAn-(5-bp)-nGAAnnTTCn | HTH, HSFs | Y
T |
likely active or activable |
122. Heat shock elements
(HSEs) (Eastmond) |
nGA(A/G)n-(5-bp)-nGAAnnTTCn (GAP1) | HTH, HSFs | Y
T |
same result as HSE3, likely active or activable |
123. Heat shock elements
(HSEs) (Eastmond) |
nGAAn-(5-bp)-nGA(A/G)nnTTCn (GAP2) | HTH, HSFs | Y
T |
same result as HSE3, likely active or activable |
124. Heat shock elements
(HSE4s) (Eastmond) |
nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn | HTH, HSFs | Y
T |
likely active or activable |
125. Heat shock factors
(Hsfs) (Tang) |
NGAAN | HTH, HSFs | Y
T |
likely active or activable |
126. Hex sequences | TGACGTGGC | ? | Y
T |
likely active or activable |
127. High Mobility Group boxes
(HMG boxes) |
(A/T)(A/T)CAAAG | β-Scaffold factors with minor groove contacts | Y
T |
random |
128. HNF6s | (A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T) | Cys 4 |
Y
T |
likely active or activable, although the negative direction distals are at or less than randoms |
129. Homeoboxes | CAAG | HTH | Y
T |
likely active or activable |
130. Homeodomains | TAAT | HTH | Y
T |
likely active or activable, low occurrence UTRs and negative direction distals overlap high randoms |
131. HY boxes | TG(A/T)GGG | ? | Y
T |
likely active or activable |
132. Hypoxia-inducible factors | ACGTG | bHLH | Y
T |
likely active or activable |
133. Hypoxia response elements | CACGC | WD40 repeat family | Y
T |
likely active or activable |
134. CACA elements | CACA | WD40 repeat family | Y
T |
likely active or activable |
135. Initiator elements
(Inrs) |
YYRNWYY | ? | Y
T |
likely active or activable |
136. Initiator elements
(Inrs) |
BBCABW | ? | Y
T |
likely active or activable |
137. Initiator-like elements
(Ins-Like) |
TTCTCT | ? | Y
T |
likely active or activable, where real Inr-like negative direction distals are within the range of the randoms |
138. Initiator-like elements
(TCT) |
(C/T)CT(C/T)T(C/T)(C/T) | ? | Y
T |
likely active or activable |
139. Inositol/choline-responsive elements
(ICRE) (Case, Lopes) |
CATGTGAAAT includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991) | bHLH | Y
T |
likely active or activable |
140. Inositol/choline-responsive elements
(ICREs) (Schwank) |
TYTTCACATGY contains the core sequence CANNTG | bHLH | Y
T |
likely active or activable |
141. Interferon regulatory factor
(IRF3) |
GCTTTCC | HTH | Y
T |
random |
142. IFN-stimulated response elements
(ISREs) (Lu) |
GAAANNGAAA | HTH | Y
T |
likely active or activable |
143. IRS consensus
(Fujii) |
AANNGAAA | HTH | Y
T |
likely active or activable |
144. Tryptophan residues
(Lu) |
GAAA | HTH | Y
T |
likely active or activable, the tryptophan residues occur in the IRS, IFN, ICRE, Cell-cycle box variants, V-box, Pollen1, and β-Scaffold response elements |
145. Jasmonic acid-responsive elements
(JAREs) |
TGACG | ? | Y
T |
likely active or activable |
146. Krüppel-like factors | GGGNN(G/T)(G/T)(G/T) | ? | Y
T |
likely active or activable |
147. Leu3 transcription factors | (C/G)C(G/T)NNNN(A/C)G(C/G) | Zn(II)2Cys6 | Y
T |
likely active or activable |
148. -35 sequence | TTGACA | ? | Y
T |
likely active or activable, the UTR does overlap the randoms at the random's upper end |
149. Met31ps | AAACTGTG[36] | bZIP | Y
T |
likely active or activable |
150. Metal responsive elements
(MRE) |
TGC(A/G)C(A/C/G/T)C | ? | Y
T |
likely active or activable |
151. Middle sporulation element
(MSE) (Branco) |
ACACAAA | ? | Y
T |
likely active or activable |
152. Midsporulation element
(MSE) (Ozsarac) |
C(A/G)CAAA(A/T) | ? | Y
T |
likely active or activable |
153. Multicopy inhibitor of the GAL1 promoter
(MIG1) |
(C/G)(C/T)GGGG | bZIP | Y
T |
likely active or activable, UTRs may be random |
154. MITF E-box (CAYRTG)
(MITF) |
CA(C/T)(A/G)TG | ? | Y
T |
likely active or activable, negative distals overlap randoms at low end |
155. Musashi binding elements
(MBE1s) |
(G/A)U1AGU | ? | Y
T |
likely active or activable |
156. Musashi binding elements
(MBE2s) |
(G/A)U2AGU | ? | Y
T |
likely active or activable, negative direction distals may be random |
157. Musashi binding elements
(MBE3s) |
(G/A)U3AGU | ? | Y
T |
likely active or activable |
158. MYB ACGT-containing elements
(ACEs) |
CACGT | ? | Y
T |
likely active or activable, positive strand UTR is likely random, negative strand, positive direction distals are likely random |
159. Myeloblastosis recognition element
(MRE) |
A(A/C)C(A/T)A(A/C)C | ? | Y
T |
likely active or activable |
160. Myocyte enhancer factors
(MEFs) |
(C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G) | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
161. Nanos/Pumilio response elements
(PREs) |
TGTAAAT | ? | Y
T |
likely active or activable |
162. N-boxes
(Lee) |
CCGGAA | bHLH | Y
T |
likely active or activable |
163. N-boxes
(Bai) |
CACGAG | bHLH | Y
T |
likely active or activable |
164. N-boxes
(Gao) |
CACGGC or CACGAC, CACG(A/G)C | bHLH | Y
T |
likely active or activable |
165. N-boxes
(Leal) |
CACNAG | bHLH | Y
T |
likely active or activable |
166. Non-DiTyrosine 80 transcription factor DNA binding domain
(Ndt80) |
(A/G/T)NC(A/G)CAAA(A/T) | ? | Y
T |
likely active or activable |
167. Nuclear factor of activated T cells
(NFATs) complement and inverse of the Pyrimidine boxes |
GGAAAA | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable, negative direction distals likely random |
168. NF𝜿B (Sato)
(NF𝜿BSs) |
GAATTC | ? | Y
T |
likely active or activable |
169. Nutrient-sensing response element 1
(NSRE) |
GTTTCATCA | ? | Y
T |
likely active or activable |
170. Oaf1 transcription factor | CGGN3TNAN9-12CCG | ? | Y
T |
likely active or activable |
171. ORESARA1
(ORE1) (Matallana) |
(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) | ? | Y
T |
likely active or activable |
172. ORESARA1
(ORE1) (Olsen) |
T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) | ? | Y
T |
likely active or activable |
173. p53 response elements | (A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T) | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
174. p53 response elements
(Long1) |
CAGGCCC | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
175. p53 response elements
(Long2) |
GGGCGTG | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
176. P-box (Mena) | (A/T)AAAG | ? | Y
T |
likely active or activable, the positive direction proximals overlap the randoms |
177. P-box
(Motojima) |
TGAGTTCA | ? | Y
T |
likely active or activable |
178. P-box
(Yu) |
GTAA(T/C) | ? | Y
T |
likely active or activable with some overlapping the randoms |
179. Peroxisome proliferator-activated receptor alpha | CGACCCC | ? | Y
T |
likely active or activable, positive direction distal overlaps upper end of randoms |
180. Pho4ps | CAC(A/G)T(T/G) | bHLH | Y
T |
likely active or activable, positive strands of the UTRs and negative direction distals are in the random range |
181. Pollen1 elements | AGAAA | ? | Y
T |
likely active or activable |
182. Polycomb response elements
(PRE) |
GCCAT | ? | Y
T |
likely active or activable |
183. Pribnow boxes | TATAAT | ? | Y
T |
likely active or activable |
184. Prolamin boxes | TG(A/T)AAAG | ? | Y
T |
likely active or activable |
185. Q elements | AGGTCA | ? | Y
T |
likely active or activable |
186. Quinone reductase response element
(QRDRE) (Yao) |
TCCCCT of TCCCCTTGCGTG | ? | Y
T |
likely active or activable |
187. Rap1 reduced consensus | (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C) | WD40 repeat family | Y
T |
likely active or activable |
188. Reb1 bound and exact occurrences | TTACCC(G/T) | WD40 repeat family | Y
T |
likely active or activable |
189. Retinoic acid response element | AG(A/G)TCA | ? | Y
T |
likely active or activable, positive direction distals appear random |
190. Glucose transporter gene repressor
(Rgt1) |
CGG(A/G)(A/T)N(A/T)(A/T) | ? | Y
T |
likely active or activable |
191. classic RORE motif
(RORE) |
A(A/T)NTAGGTCA | ? | Y
T |
likely active or activable |
192. variant RORE motif | C(T/A)(G/A)GGNCA | ? | Y
T |
likely active or activable |
193. R response elements
(RRE) |
CATCTG | ? | Y
T |
likely active or activable |
194. Serum response elements
(SRE) see CArG boxes |
ACAGGATGT | bHLH-ZIP | Y
T |
likely active or activable |
195. Servenius sequences | GGACCCT | ? | Y
T |
likely active or activable |
196. SP1
(Zhang) |
(G/T)GGGCGG(G/A)(G/A)(C/T) | ? | Y
T |
likely active or activable |
197. SP1-box 1
(Motojima) |
GGGGCT | ? | Y
T |
likely active or activable |
198. SP1-box 2
(Motojima) |
CTGCCC | ? | Y
T |
likely active or activable |
199. SP-1
(Sato) |
CCGCCCC | ? | Y
T |
likely active or activable |
200. SP1
(Yao) |
GCGGC | ? | Y
T |
likely active or activable |
201. STAT5 | TTCNNNGAA | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable, positive distal likely random |
202. Stress-response elements
(STREs) |
CCCCT | ? | Y
T |
likely active or activable, positive cores overlap randoms
Positive strand, negative direction: CCCCT at 3059 |
203. Sucrose boxes | NNAATCA | ? | Y
T |
likely active or activable |
204. TACTAAC boxes | TACTAA(C/T) | ? | Y
T |
likely active or activable |
205. TAGteams | CAGGTAG | ? | Y
T |
likely active or activable |
206. Tapetum boxes | TCGTGT | ? | Y
T |
likely active or activable |
207. metazoan TATA boxes | TATA(A/T)AA(A/G) | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
208. TATA boxes | TATA(A/T)A(A/T)(A/G) | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
209. TAT Boxes
(Yang) |
TATAAAA | WD40 repeat family | Y
T |
likely active or activable |
210. TAT Boxes
(Fan) |
TATCCAT | WD40 repeat family | Y
T |
likely active or activable |
211. Tbf1 regulatory factors | A(A/G)CCCTAA | General Regulatory Factors | Y
T |
Saccharomyces cerevisiae, likely active or activable |
212. T boxes
(Conlon) |
TCACACCT | bZIP | Y
T |
likely active or activable |
213. T boxes
(Zhang) |
AACGTT | bZIP | Y
T |
likely active or activable |
214. TEA consensus sequences | CATTCY | ? | Y
T |
likely active or activable |
215. Tec1ps | GAATGT | ? | Y
T |
likely random, Ste12p cofactor |
216. Telomeric repeat DNA-binding factors
(TRFs) |
TTAGGG | ? | Y
T |
likely active or activable |
217. Thyroid hormone response elements
(TREs)(THRs) |
AGGTCA | ? | Y
T |
likely active or activable |
218. Transcription factor 3
(TCF3) |
GTCTGGT | ? | Y
T |
likely active or activable |
219. Translational control sequences
(TCSs) |
(A/T)TT(A/G)TCT | ? | Y
T |
likely active or activable |
220. Unfolded protein response element
(URE) (UPRE-1) |
CANCNTG | ? | Y
T |
likely active or activable |
221. Unfolded protein response elements
(UPREs) |
TGACGTG(G/A) | bZIP | Y
T |
likely active or activable |
222. Upstream repressor site 1
(URS1, core) (Sumrada) |
CCGCC | ? | Y
T |
likely active or activable, negative direction proximals are within randoms |
223. Upstream stimulating factors
(USFs) |
GCC(A/T)NN(C/G/T)(A/G) | bHLH-ZIP | Y
T |
likely active or activable, cores overlap lower randoms |
224. UUA rich elements
(Chen) |
TTATTTA(A/T)(A/T) | ? | Y
T |
likely active or activable |
225. V boxes | (A/G)TT(A/T)(C/T) | ? | Y
T |
likely active or activable |
226. Vitamin D response elements
(VDREs) |
(A/G)G(G/T)(G/T)CA | ? | Y
T |
likely active or activable |
227. W boxes | (C/T)TGAC(C/T) | WRKY | Y
T |
likely active or activable |
228. X core promoter elements | (A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C) | ? | Y
T |
likely active or activable |
229. Xenobiotic response elements
(XREs) |
GCGTG | bHLH | Y
T |
likely active or activable |
230. Yap recognition sequences | TTACTAA | ? | Y
T |
likely active or activable |
231. YY1 binding sites | CCATCTT | Cys 2His 2 |
Y
T |
likely active or activable |
232. Z boxes
NSoSp form |
A(C/T)A(C/G)G(G/T)(A/G/T)T | ? | Y
T |
likely active or activable, negative direction distals within randoms |
233. Z boxes
ZboxG |
A(C/T)A(C/G)GT(A/G)T | ? | Y
T |
likely active or activable |
234. Z boxes
ZboxSp |
CAGGT(A/G) | ? | Y
T |
likely active or activable |
Totals
Of 358 response elements, there are 117 Ns for not present (absent) in either A1BG promoter and 241 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are four apparent random elements (CATTs, HMG boxes, IRF3s and TECs), and 236 likely active or activable (97.93 %). With 4560 nts considered between ZSCAN22 and A1BG, halfway would be at 2280. Less than 2280 suggests the nearest other gene. In the positive direction, 4445 nts considered between ZNF497 and A1BG, halfway would be 2222 for another nearest gene. Less than 2222 suggests the nearest other gene.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
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- ↑ Hideharu Hashimoto; Dongxue Wang; John R. Horton; Xing Zhang; Victor G. Corces; Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.
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- ↑ Fumiko Hirose; Masamitsu Yamaguchi; Akio Matsukage (September 1999). "Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc". Molecular and Cellular Biology. 19 (9): 6020–6028. doi:10.1128/MCB.19.9.6020. PMID 10454549. Retrieved 4 September 2020.
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value (help). Retrieved 5 September 2020. - ↑ 31.0 31.1 31.2 31.3 31.4 Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check
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value (help). Retrieved 29 August 2020. - ↑ Motoki Kyo, Tae Yamamoto, Hozumi Motohashi, Terue Kamiya, Toshihiro Kuroita, Toshiyuki Tanaka, James Douglas Engel, Bunsei Kawakami, Masayuki Yamamoto (13 February 2004). "Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique". Genes to Cells. 9 (2). doi:10.1111/j.1356-9597.2004.00711.x. Retrieved 8 September 2020.
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- ↑ XIAN-YANG ZHANG, NABILA JABRANE-FERRAT, CLEMENT K. ASIEDU, SANJA SAMAC, B. MATIJA PETERLIN, AND MELANIE EHRLICH (November 1993). "The Major Histocompatibility Complex Class II Promoter-Binding Protein RFX (NF-X) Is a Methylated DNA-Binding Protein" (PDF). MOLECULAR AND CELLULAR BIOLOGY. 13 (11): 6810–8. Retrieved 2017-04-05.
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