A1BG response element gene transcriptions: Difference between revisions

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==Totals==
==Totals==


Of 358 response elements, there are 117 Ns for not present (absent) in either A1BG promoter and 238 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are 238 likely active or activable (66.48 %). 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.
Of 358 response elements, there are 109 Ns for not present (absent) in either A1BG promoter and 238 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are 238 likely active or activable (66.48 %). 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==
==Acknowledgements==

Revision as of 01:22, 13 May 2023

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

  1. A1BG has no response elements in either promoter.
  2. A1BG is not transcribed by a response element.
  3. Each response element does not participate in the transcription of A1BG.

Response element testing

Response element
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 28 ABA-response elements 13:07, 8 October 2020 48
2. ABA-response elements, novel, (ABREN, novel ABRE) GATCGATC, CGATCGAT, GATCGAT Absent 29 ABA-response elements 13:07, 8 October 2020 47-48
3. ABA responsive elements (ABREs) ACGTG(G/T)C Present 30 ABA-response elements 05:53, 9 October 2020 likely active or activable
4. Abf1 regulatory factors CGTNNNNNACGAT Absent 32 Abf1 regulatory factors 18:32, 10 October 2020 413
5. A-boxes TACGTA Present 27 A-boxes 21:24, 7 October 2020 likely active or activable
6. Abscisic acid-responsive elements (Pho4s), G boxes CACGTG Present 128 Abscisic acid-responsive elements (Pho4s), G boxes 06:38, 10 May 2022 likely active or activable
7. ACGT-containing elements ACGT Present 183 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 31 Abf1 regulatory factors 17:47, 10 October 2020 likely active or activable
9. Activating proteins (Murata) GCCCACGGG Absent 276 Activating proteins 05:32, 15 December 2022‎ 49
10. Activating protein 2 alpha (AP2a) GCCNNNGGC Present 186 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 188 Activating protein 2 06:54, 30 September 2022 likely active or activable
12. Activating protein 2, (Cohen2) TCCCCCGCCC Present 189 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 184 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 187 Activating protein 2 19:10, 29 September 2022‎ likely active or activable
15. Activating protein 2, (Yao1) TCTTCCC Present 190 Activating protein 2 08:11, 30 September 2022 likely active or activable
16. Activating protein 2, (Yao2) CTCCCA Present 191 Activating protein 2 19:00, 30 September 2022‎ likely active or activable
17. Activating protein 2, (AP-2), (Yao3) GGCCAA Present 192 Activating proteins 22:23, 30 September 2022‎‎ likely active or activable
18. Activating protein 2, (AP-2), (Roesler) CCCCACC(A/C) Present 353 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 193 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 194 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 117 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 274 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 273 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 272 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 269 Adr1ps 01:36, 15 December 2022‎ likely active or activable
26. Aft1s, (AFT) (C/T)(A/G)CACCC(A/G) Present 195 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 235 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 85 AhR/ARNT complex 20:45, 17 February 2021 23*46
30. Alpha-amylase conserved elements (Sharma 2020) TATCCATCCATCC Absent 37 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 111 Amino acid response elements 01:32, 22 May 2021 49
33. Amino acid response elements, (AARE), (Broer) TTTGCATCA[2][3] Absent 39 Amino acid response elements 01:59, 1 November 2020 49
34. Amino acid response element-like, (AARE-like), (AARE3), (Maruyama) TGGTGAAAG Absent 40 Amino acid response element-like 02:27, 2 November 2020‎ 49
35. Androgen response elements, (AREs), (Kouhpayeh) GGTACANNNTGTTCT Absent 41 Androgen response elements 17:01, 2 November 2020 412
36. Androgen response element1s, (Kouhpayeh) GGTACA of GGTACAnnnTGTTCT Present 197 Androgen response element1s 17:22, 4 October 2022 likely active or activable
37. Androgen response element2s, (Kouhpayeh) TGTTCT of GGTACAnnnTGTTCT Present 198 Androgen response element2s 17:01, 5 October 2022‎ likely active or activable
38. Androgen response elements, (AREs), (Wilson) AGAACANNNTGTTCT Absent 118 Androgen response elements 16:21, 11 November 2021 412
39. Androgen response elements, (Wilson) AGAACANNNTGTTCT Present 199 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 257 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 42 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 200 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 258 AhR responsive element or Aryl hydrocarbon responsive element II 18:04, 6 December 2022‎ likely active or activable
44. ATA boxes AATAAA Present 268 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 271 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 236 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 237 Auxin response factors 06:02, 5 November 2022‎ likely active or activable
48. Auxin response factors, (ARF), (Boer) TGTCGG Present 201 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 202 Auxin response factors 04:15, 10 October 2022 likely active or activable, negative direction proximals ≥ randoms
50. B-boxes, (Johnson) TGGGCA Present 204 B-boxes 18:05, 10 October 2022 likely active or activable, positive direction distals ≥ randoms
51. boxes A TGACTCT Present 126 Box A 06:50, 9 May 2022‎ likely active or activable
52. boxes B, (Sanchez) TGTCTCA Present 203 boxes B 15:26, 10 October 2022 likely active or activable
53. B recognition elements, (BREu) (G/C)(G/C)(G/A)CGCC Present 256 B recognition elements 20:39, 4 December 2022 likely active or activable
54. CAACTC regulatory elements, (CAREs), (Fan) CAACTC Present 123 CARE (Fan) 17:45, 7 May 2022 likely active or activable
55. CAAT boxes (C/T)(A/G)(A/G)CCAATC(A/G) Absent 15 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 109 CACA elements 05:04, 7 May 2021 likely active or activable
57. CadC binding domains TTANNNNT Present 205 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 266 Calcineurin-responsive transcription factors 19:14, 12 December 2022‎ likely active or activable
59. Calcium-response elements, (CaRE1s), (Tao 2002) CTATTTCGAG Absent 43 Calcium-response elements 19:43, 7 November 2020‎ 410
60. Carbohydrate response elements, (ChREs), (ChoRE1, ChoRE2), (Long 2020) CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG Absent 44 Carbohydrate response elements 20:50, 10 November 2020 417
61. Carbohydrate response elements, (ChoRE1), (Carb) ACCGG Present 144 Carbohydrate response elements 18:56, 18 June 2022 likely active or activable
62. Carbohydrate response elements, (ChoRE2), (Carb1) CCCAT Present 206 Carbohydrate response elements 06:01, 13 October 2022 likely active or activable
63. Carbohydrate response elements, (Carb E1) ATCTTG Present 207 Carbohydrate response elements 18:45, 13 October 2022‎ proximals likely active or activable
64. Carbohydrate response elements, (Carb E2) CACGTG Present 208 Carbohydrate response elements 21:30, 13 October 2022 likely active or activable
65. Carbohydrate response elements, (Carb E3) TCCGCC Present 209 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 19 Carbon source-responsive elements 17:08, 19 March 2021 410, confers carbon source-dependent regulation
67. Carbon source-responsive elements, (TCCGs) TCCG Present 210 TCCG elements 02:41, 16 October 2022 likely active or activable
68. Carbon source-responsive elements, (CATTs) CATTCA Present 211 CATTCA elements 17:05, 18 October 2022 likely active or activable
69. CArG boxes, (Kamada 1992), (McDonald 2006) CC(A/T)6GG Absent 21 CArG boxes 19:08, 18 October 2022 26*44
70. CArG boxes, (Deng 2011) CCAAAAAT(G/A)G Absent 213 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 214 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 215 Cat8ps 22:21, 18 October 2022 likely active or activable
73. CAT boxes, (Saitoh 1993) CATTCCT Present 216 CAT boxes 23:56, 18 October 2022‎ likely active or activable
74. CAT-box-like elements, (Berberich 1993) GCCATT Present 217 CAT-box-like elements 19:38, 20 October 2022‎ likely active or activable
75. Cbf1 regulatory factors TCACGTGA Absent 113 Cbf1 regulatory factors 15:57, 11 June 2021 48
76. C-boxes, (Johnson) GAGGCCATCT Absent 34 C-boxes 02:51, 22 October 2020 410
77. C boxes, (Samarsky) AGTAGT Present 218 C boxes 02:22, 21 October 2022 likely active or activable
78. C-boxes, (Song) GACGTC Present 219 C-boxes 06:22, 21 October 2022 likely active or activable
79. C/A hybrid boxes, (Song) TGACGTAT Absent 33 C/A hybrid boxes 16:18, 20 October 2020 48
80. C/G hybrid boxes, (Song) TGACGTGT Present 245 CG hybrid boxes 18:35, 15 November 2022 likely active or activable
81. C/T hybrid boxes, (Song) TGACGTTA Absent 35 C/T hybrid boxes 01:51, 24 October 2020 48
82. C boxes, (Voronina) GGTGATG Present 244 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 124 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 44 C/EBP boxes 23:21, 18 November 2020 47-49
85. CCCTC-binding factors, (CTCF), (Hashimoto 2017) NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) Absent 36 CCCTC-binding factors 23:02, 24 October 2020‎ 49
86. CCCTC-binding factors, (CTCF), (Lobanenkov 1990) CCCTC Present 370 CCCTC-binding factors 23:44, 12 May 2023 likely active or activable
87. C clamp, (HMG DBD), (Cadigan 2012) (C/G)CTTTGAT(C/G) Absent 367 C clamp 06:03, 10 May 2023‎ 48
86. Cell-cycle boxes, (CCBs) CACGAAAA Absent 108 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 20 Cell-cycle box variants 05:54, 23 October 2022 likely active or activable
88. Cell cycle regulation, (Sharma 2020) CCCAACGGT Absent 46 Cell cycle regulation 20:53, 25 November 2020‎ 49
89. CENP-B boxes TTTCGTTGGAAGCGGGA Absent 17 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 265 CGCG boxes 07:14, 12 December 2022‎ likely active or activable, probably for zinc fingers
91. Circadian control elements CAANNNNATC Present 264 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 165 Class C DNA binding sites 06:16, 5 August 2022 likely active or activable, distals may be random
93. Cold-responsive elements CCGAC Present 221 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 270 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 222 Copper response elements 07:57, 24 October 2022 likely active or activable
96. Copper response elements, (CuREs), (Park) TGTGCTCA Present 223 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 119 Coupling elements 15:47, 12 February 2022‎ likely active or activable
99. Coupling elements, (CE3s), (Ding) CACGCG Present 120 Coupling elements 02:59, 15 February 2022 likely active or activable
100. cyclic-AMP-responsive elements, (CREs), Aca1ps, Sko1ps, (Montminy 1986) TGACGTCA Present 275 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 228 Cytokinin response regulators 16:21, 31 October 2022 likely active or activable
102. Cytokinin response regulators, (ARR10s) (A/G)GATA(A/C)G Present 224 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 225 Cytokinin response regulators 06:09, 28 October 2022 likely active or activable
104. Cytokinin response regulators, (ARRs), (Ferreira) (G/A)GGAT(T/C) Present 226 Cytokinin response regulators 03:25, 31 October 2022 likely active or activable
105. Cytokinin response regulators, (ARRs), (Rashotte1) GATCTT Present 227 Cytokinin response regulators 16:21, 31 October 2022‎ likely active or activable
106. Cytokinin response regulators, (ARRs), (Rashotte2) (G/A)GAT(T/C) Present 229 Cytokinin response regulators 20:24, 1 November 2022 likely active or activable
107. Cytoplasmic polyadenylation elements, (CPEs) TTTTTAT Present 161 Cytoplasmic polyadenylation elements 06:10, 25 July 2022‎ likely active or activable
108. DAF-16-associated elements, (DAE), (Li) TGATAAG Absent 48 DAF-16-associated elements 22:51, 3 December 2020 47
109. DAF-16 binding elements (A/G)(C/T)AAA(C/T)A Present 230 DAF-16 binding elements 19:54, 2 November 2022 likely active or activable
110. D-boxes, (Mracek1) GTTGTATAAC Absent 50 D-boxes 02:46, 10 December 2020 410
111. D-boxes, (Mracek2) CTTATGTAAA Absent 51 D-boxes 02:20, 12 December 2020 410
112. D-boxes, (Johnson) TCTCACATT(A/C)AATAAGTCA Absent 49 D-boxes 04:12, 8 December 2020 2*418
113. D boxes, (Samarsky) AGTCTG Present 263 D boxes 00:16, 12 December 2022 likely active or activable
114. D boxes, (Voronina) TCCTG Present 231 D boxes 02:28, 4 November 2022 likely active or activable
115. D-boxes, (Motojima) TGAGTGG Present 262 D-boxes 00:11, 12 December 2022 likely active or activable
116. Defense and stress-responsive elements, (Sharma) ATTTTCTTCA Absent 52 Defense and stress-responsive elements 21:02, 13 December 2020 410
115. Destruction box, (D box), (Pfleger and Kirschner 2000) CGN(C/T)TNAAN ? ? Destruction boxes 19:34, 10 May 2023 likely active or activable?
117. Dioxin-responsive elements, (DREs) TNGCGTG Present 232 Dioxin-responsive elements 20:43, 4 November 2022 likely active or activable
118. DNA damage response elements, (DREs), (Smith) TTTCAAT Absent 53 DNA damage response elements 12:25, 17 December 2020 47
119. DNA damage response elements, (DREs), (Sumrada) TAGCCGCCG of TAGCCGCCGRRRR Absent 277 DNA damage response elements 06:31, 17 December 2022‎ 49-24*49
120. DNA replication-related elements, (DREs), (Hirose) TATCGATA Absent 54 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 279 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 280 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 281 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 282 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 158 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 156 Downstream promoter elements 20:16, 16 July 2022‎ likely active or activable
128. Downstream promoter elements, (DPEs), (Matsumoto) AGTCTC Present 157 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 22 DREB boxes 17:03, 28 December 2019 49
131. E2 boxes (G/A)CAGNTGN Present 196 E2 boxes 17:04, 3 October 2022‎ likely active or activable
132. EIF4E basal elements (poly(C) motif) TTACCCCCCCTT Absent 16 EIF4E basal elements 20:24, 30 March 2019 412
133. EIN3 binding sites A(C/T)G(A/T)A(C/T)CT Present 283 EIN3 binding sites 01:44, 29 December 2022 likely active or activable
134. Endoplasmic reticulum stress response elements, (ERSE) CCAAT-N9-CCACG Absent 285 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 284 Endoplasmic reticulum stress response elements 01:57, 31 December 2022‎ likely active or activable
136. Endosperm expressions TGTGTCA Present 286 Endosperm expressions 03:16, 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 336 Estrogen response elements 05:34, 9 March 2023 46-412
139. Estrogen response elements, (EREs), (Yasar) GGTCAGGATGAC Absent 337 Estrogen response elements 05:37, 9 March 2023 412
140. Estrogen response elements, (ERE1s), (Driscoll) GGTCA Present 339 Estrogen response elements 03:27, 14 March 2023‎ likely active or activable
141. Estrogen response elements, (ERE2s), (Driscoll) TGACC Present 340 Estrogen response elements 03:37, 14 March 2023 likely active or activable
142. Ethylene responsive elements ATTTCAAA Present 238 Ethylene responsive elements 18:06, 5 November 2022‎ likely active or activable
143. F boxes, (Rose) TGATAAG Absent 68 F boxes 05:52, 28 January 2021 47, F-box overlaps the I-box
144. Forkhead boxes, (FOXO1), (Yoshihara) GTAAACAA Absent 352 Forkhead boxes 04:33, 20 April 2023 48
145. Forkhead boxes, (FOXA2), (Li 2017) (A/G)(C/T)AAA(C/T)A Present 287 Forkhead boxes 03:54, 1 January 2023 likely active or activable
146. GAAC elements GAACT Present 288 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 55 Gal4ps 22:28, 31 December 2020‎ 410
148. γ-interferon activated sequences, (GAS) TTCCTAGAA Absent 11 Samplings 04:43, 22 March 2018 49
149. Γ-interferon activated sequences, (GAS) TTNCNNNAA Present 289 Γ-interferon activated sequences 01:56, 3 January 2023, see STAT5 likely active or activable
150. GATA boxes GATA Present 259 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 260 GATA (GATAAG, GATAAH, GATTA) motifs 20:11, 9 December 2022‎ likely active or activable
152. GATC repeats, (ABREN), (Watanabe et al. 2017) GATC Present 369 GATC samplings 13:07, 24 May 2023? GATC UTRs, proximals and positive strand, negative direction distals greater than randoms, negative strand, negative direction distals, positive direction distals likely randoms. GATCs are likely active or activable
152. G boxes, (Song) (G/T)CCACGTG(G/T)C Absent 116 G boxes 03:20, 25 July 2021‎ 49
153. G-box motif, (Oeda) GCCACGTGGC Absent 115 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 290 GC boxes 16:57, 3 January 2023 likely active or activable
155. GC boxes, (Ye 2019) GGGCGG Present 291 GC boxes 08:28, 4 January 2023‎ likely active or activable
156. GCC boxes, (Sato 1996) GCCGCC Present 292 GCC boxes 06:52, 5 January 2023 likely active or activable
157. GCN4 motifs, (Zhang 2014) TGA(C/G)TCA Absent 185 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 293 General control nonderepressible 4 protein binding site 07:05, 5 January 2023‎ likely active or activable
159. Gcn4ps, (Tang) ATGACTCTT Absent 246 Gcn4ps 22:17, 15 November 2022 49
160. GGCGGC triplet GGCGGC Present 294 GGCGGC triplet 00:32, 7 January 2023 likely active or activable
161. GGC triplets GGC Present 296 GGC triplets 19:40, 7 January 2023 likely active or activable
162. Gibberellic acid responsive elements-like 1, (GAREL1s) TAACA(A/G)A Present 239 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 56 Gibberellin responsive element-like 2 06:39, 2 January 2021 47
164. Gibberellin responsive elements, (GREs), (Sharma) AAACAGA Present 297 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 21 GLM boxes 04:17, 13 October 2019 23*46
166. Glucocorticoid response elements, (GRE), (Parsonnet 2019) AGAACA Present 261 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 311 Glucose transporter gene repressor 20:06, 21 January 2023‎ likely active or activable
168. G-protein-coupled receptors,(GCR1s), CT boxes CTTCC Present 298 G-protein-coupled receptors 03:36, 8 January 2023 likely active or activable
169. Grainy head transcription factor binding sites AACCGGTT Absent 57 Grainy head transcription factor binding sites 23:33, 6 January 2021 48
170. Grainy head transcription factor binding sites GACTGGTT Absent 354 Grainy head transcription factor binding sites 07:13, 22 April 2023 48
171. GT boxes, (Motojima) TGGGTGGGGCT Absent 58 GT boxes 00:39, 11 January 2021 (-78 to -69) 411
172. GT boxes, (Sato) GGGG(T/A)GGGG Present 299 GT boxes 04:33, 8 January 2023 likely active or activable
173. Hac1, KAR2 CAGCGTG Present 300 Hac1 05:27, 8 January 2023‎ likely active or activable
174. H and ACA boxes AGAGGA Present 302 H and ACA boxes 04:33, 9 January 2023‎ likely active or activable, negative distals likely random
175. Hapless motifs (Ozsarac 1997) CCAATCA Absent 150 Hapless motifs 02:33, 30 June 2022‎ heterotrimeric transcription factor, HAP2/3/4 47
176. Hap motif (Hap4p) CCAAT Present 303 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 122 H-boxes 16:34, 7 May 2022‎ likely active or activable
178. H-boxes, (Lindsay) CCTACC Present 125 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 267 H box 20:03, 12 December 2022‎ likely active or activable
180. H box, (Rozhdestvensky) ACACCA Present 121 H box 05:46, 5 May 2022 likely active or activable
181. Heat-responsive elements AAAAAATTTC Absent 59 Heat-responsive elements 02:10, 14 January 2021 four nGAAn motifs 410
182. Heat shock elements, (HSE1), (Eastmond) nGAAnnTTCnnGAAn Absent 60 Heat shock elements 04:13, 20 January 2021 HSE1 49
183. Heat shock elements, (HSE2), (Eastmond) nTTCnnGAAnnTTCn Absent 127 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 131 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 133 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 134 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 132 Heat shock elements 05:14, 14 May 2022‎ likely active or activable
188. Heat shock elements, (HSE5), (Eastmond) nTTCn-(5-bp)-nTTCnnGAAn Absent 61 Heat shock elements 02:49, 23 January 2021 HSE5 49
189. Heat shock elements, (HSE6), (Eastmond) nTTCn-nnGAAn-(5-bp)-nGAAn Absent 62 Heat shock elements 18:05, 23 January 2021 HSE6 49
190. Heat shock elements, (HSE7), (Eastmond) nGA(A/G)nnTTCnnGAAn Absent 63 Heat shock elements 22:36, 23 January 2021‎ HSE7 PFT1 2*48
191. Heat shock elements, (HSE), (Eastmond) nGAAnnTTCnnGA(A/G)n Absent 64 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 65 Heat shock elements 22:33, 26 January 2021 HSE10 49
193. Heat shock factors, (Hsfs), (Tang) NGAAN Present 129 Heat shock factors 06:01, 11 May 2022‎ likely active or activable
85. Helper site, (Atcha et al. 2007), (Cadigan and Waterman 2012) (C/G)C(C/G)G(C/G) Present 368 Helper site 10:54, 10 May 2023 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 136 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 135 Hex sequences 19:57, 17 May 2022‎ likely active or activable
196. High Mobility Group boxes, (HMG boxes) (A/T)(A/T)CAAAG Present 358 High Mobility Group boxes 22:01, 30 April 2023‎ likely active or activable
197. Homeoboxes CAAG Present 254 Homeoboxes 04:28, 4 December 2022 likely active or activable, occurs in Rox1ps
198. Homeodomains TAAT Present 255 Homeodomains 19:46, 4 December 2022‎ likely active or activable, low occurrence UTRs and negative direction distals overlap high randoms, occurs in CArG boxes and Pribnow boxes
199. HY boxes TG(A/T)GGG Present 137 HY boxes 12:43, 25 May 2022‎ likely active or activable
200. Hypoxia-inducible factors, (HIF-1), (Li 2020) GCCCTACGTGCTGTCTCA Absent 66 Hypoxia-inducible factors 16:43, 27 January 2021 composed of HIF-1α and HIF-1β 418
201. Hypoxia-inducible factors (HIF) (Orlando 2019), ABA-response element (ABRE) (Asad 2019)) ACGTG Present 38 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 110 Hypoxia response elements 05:04, 7 May 2021 likely active or activable
203. I boxes GATAAG of GGATGAGATAAGA Absent 67 I boxes 05:49, 28 January 2021 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 25 Initiator elements 17:44, 27 September 2020 likely active or activable
206. Initiator element (Inr) (Ngoc 2017) BBCA+1BW Present 14 Initiator elements 13:24, 22 December 2018 likely active or activable
207. Initiator element-like (Inr-like) (Matsumoto 2020) TTCTCT Present 26 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 347 Initiator elements 22:06, 10 April 2023 likely active or activable
209. Inositol/choline-responsive elements, (ICRE), (Case) CANNTGAAAT Absent 69 Inositol/choline-responsive elements 21:43, 29 January 2021 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 Present 140 Inositol/choline-responsive elements 23:14, 9 June 2022‎ likely active or activable
211. Inositol/choline-responsive elements, (ICRE), (Lopes) ATGTGAAAT Absent 138 Inositol/choline-responsive elements 23:01, 7 June 2022 using ANNTGAAAT 47-49
212. Inositol/choline-responsive elements, (ICREs), (Schwank) TYTTCACATGY contains the core sequence CANNTG Present 139 Inositol/choline-responsive elements 05:39, 9 June 2022 likely active or activable
213. Interferon regulatory factor, (IRF3) GCTTTCC Present 359 Interferon regulatory factor 03:07, 2 May 2023‎ likely active or activable
214. Interferon-stimulated response elements, (ISREs), (Michalska) AGTTTCN2TTTCN Absent 107 Interferon-stimulated response elements 15:43, 28 March 2021 410
215. Interferon-stimulated response elements, (ISREs), (Lu) GAAANNGAAA Present 141 IFN-stimulated response elements 06:41, 12 June 2022‎ likely active or activable
216. IRS consensus, (Fujii) AANNGAAA Present 142 IRS consensus 03:16, 14 June 2022‎ likely active or activable
217. Jasmonic acid-responsive elements, (JAREs) TGACG Present 145 Jasmonic acid-responsive elements 23:12, 20 June 2022‎ likely active or activable
218. K-boxes, (Saito 2020) GTTCGG-NNAN-CCNNAC Absent 105 K-boxes 22:22, 17 March 2021‎ 411
219. K-box1s, (Saito 2020) GTTCGG Present 366 K-boxes 20:59, 4 May 2023‎ likely active or activable
115. KEN box, (Pfleger and Kirschner 2000) AA(A/G)GA(A/G)AA(C/T) ? ? Destruction boxes 19:34, 10 May 2023 likely active or activable?
220. Kozak sequences, (Kozak 1987) GCCGCC(A/G)CCATGG Absent 104 Kozak sequences 18:12, 17 March 2021 2*412
221. Kozak sequences, (Matsumoto) GAAAATGG Absent 70 Kozak sequences 01:16, 2 February 2021 48
222. Krüppel-like factors GGGNN(G/T)(G/T)(G/T) Present 146 Krüppel-like factors 18:25, 23 June 2022‎ likely active or activable
223. L boxes (Donald) AAATTAACCAA Absent 71 L boxes 04:21, 2 February 2021 411
224. Leu3 transcription factors, (Leu3), (Reddy 2020) (C/G)C(G/T)NNNN(A/C)G(C/G) Present 295 Leu3 transcription factors 04:52, 7 January 2023 likely active or activable
225. M35 or -35 sequence TTGACA Present 147 -35 sequence 16:16, 25 June 2022‎ likely active or activable, the UTR does overlap the randoms at the random's upper end
226. Maf recognition element, (MAREs), (Kyo) TGCTGA(G/C)TCAGCA Absent 72 Maf recognition element 03:29, 3 February 2021 2*412
227. M boxes, (Bertolotto) GTCATGTGCT or AGTCATGTGCT Absent 73 M boxes 16:05, 3 February 2021 410-411
228. M-CAT boxes, (Berberich 1993) GCGGCCTC Absent 350 M-CAT boxes 18:06, 18 April 2023 48
229. Mcm1 regulatory factors, (Rossi) TT(A/T)CCNN(A/T)TNGG(A/T)AA Absent 74 Mcm1 regulatory factors 03:17, 4 February 2021 23*49
230. Mcm1 regulatory factors, (Rossi) TTNCCNNNTNNGGNAA Absent 112 Mcm1 regulatory factors 04:32, 9 June 2021 49
231. Met3s, (Blaiseau) TCACGTG Absent 149 Met3s 08:09, 27 June 2022‎ 47
232. Met31ps, (Blaiseau) AAACTGTG Present 148 Met31ps 07:26, 27 June 2022‎ likely active or activable
233. Metal responsive elements, (MRE) TGC(A/G)C(A/C/G/T)C Present 151 Metal responsive elements 02:25, 30 June 2022‎ likely active or activable
234. Middle sporulation element, (MSE), (Branco) ACACAAA Present 152 Middle sporulation element 05:04, 2 July 2022‎ likely active or activable
235. Midsporulation element, (MSE), (Ozsarac) C(A/G)CAAA(A/T) Present 169 Midsporulation element 15:07, 14 August 2022 likely active or activable
236. MITF E-box, (MITF) CA(C/T)(A/G)TG, (CAYRTG) Present 366 MITF E-box (CAYRTG) 16:09, 2 May 2023‎ likely active or activable, negative distals overlap randoms at low end
237. Motif ten elements (MTE) (Lim 2004) C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G), CSARCSSAACGS Absent 5 Motif ten elements 15:28, 10 February 2013 25*47
238. Multicopy inhibitor of the GAL1 promoter, (MIG1), (Gancedo 1998) (C/G)(C/T)GGGG Present 361 Multicopy inhibitor of the GAL1 promoter 16:09, 2 May 2023 likely active or activable, UTRs may be random
239. Musashi binding elements, (MBE1s) (G/A)U1AGU Present 153 Musashi binding elements 15:31, 10 July 2022‎ likely active or activable
240. Musashi binding elements, (MBE2s) (G/A)U2AGU Present 154 Musashi binding elements 06:37, 14 July 2022‎ likely active or activable, negative direction distals may be random
241. Musashi binding elements, (MBE3s) (G/A)U3AGU Present 155 Musashi binding elements 19:37, 16 July 2022‎ likely active or activable
242. Myeloblastosis (MYB) ACGT-containing elements, (ACEs) CACGT Present 160 MYB ACGT-containing elements 17:07, 22 July 2022 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 162 Myeloblastosis recognition element 15:36, 25 July 2022‎ likely active or activable
244. Myocyte enhancer factors, (MEFs) (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G) Present 163 Myocyte enhancer factors 05:44, 28 July 2022 likely active or activable
245. Nanos/Pumilio response elements, (PREs) TGTAAAT Present 164 Nanos/Pumilio response elements 15:29, 31 July 2022‎ likely active or activable
246. N-boxes, (Lee) CCGGAA Present 170 N-boxes 05:07, 14 August 2022 likely active or activable
247. N-boxes, (Bai) CACGAG Present 168 N-boxes 17:10, 10 August 2022‎ likely active or activable
248. N-boxes, (Gao) CACGGC or CACGAC, CACG(A/G)C Present 167 N-boxes 05:54, 7 August 2022‎ likely active or activable
249. N-boxes, (Leal) CACNAG Present 166 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 171 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) GGAAAA Present 172 Nuclear factor of activated T cells 22:08, 19 August 2022 likely active or activable, negative direction distals likely random, complement and inverse of the Pyrimidine boxes
252. NF‐κB/Rel family of eukaryotic transcription factors, (NF-κB) CCCCTAAGGGG Absent 75 NF‐κB/Rel family of eukaryotic transcription factors 02:53, 9 February 2021 411
253. NF𝜿B (Sato)(NF𝜿BSs) GAATTC Present 324 NF𝜿B (Sato) 07:30, 8 February 2023‎ likely active or activable
254. Nuclear factor 1, (NF-1) TTGGCNNNNNGCCAA Absent 76 Nuclear factor 1 03:51, 9 February 2021 palindromic sequence 410
255. Nuclear factor Ys CCAATGG(A/C)(A/G) Absent 77 Nuclear factor Ys 04:48, 9 February 2021 NF-Y is a trimeric complex 48
256. Nutrient-sensing response element 1, (NSRE) GTTTCATCA Present 173 Nutrient-sensing response element 1 04:29, 21 August 2022 likely active or activable
257. Oaf1 transcription factor CGGN3TNAN9-12CCG Present 174 Oaf1 transcription factor 05:57, 31 August 2022 likely active or activable
258. Oresara1, (ORE1), (Matallana) (A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) Present 175 ORESARA1 05:42, 4 September 2022 likely active or activable
259. Oresara1, (ORE1), (Olsen) T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) Present 176 ORESARA1 23:53, 7 September 2022‎ 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) Present 177 p53 response elements 18:30, 8 September 2022 likely active or activable
261. p53 response elements, (Long1) CAGGCCC Present 178 p53 response elements 03:26, 11 September 2022 likely active or activable
262. p53 response elements, (Long2) GGGCGTG Present 179 p53 response elements 20:10, 13 September 2022‎ likely active or activable
263. p63 DNA binding sites, (Perez 2007) (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), RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY Absent 79 p63 DNA binding sites 04:14, 14 February 2021 412
264. P-box (Mena) (A/T)AAAG Present 181 P-box (Mena) 22:30, 21 September 2022‎ likely active or activable, the positive direction proximals overlap the randoms
265. P-box, (Motojima) TGAGTTCA Present 182 P-box 18:27, 24 September 2022‎ likely active or activable
266. P-box, (Yu) GTAA(T/C) Present 180 P-box 02:46, 18 September 2022‎ likely active or activable with some overlapping the randoms
267. Pleiotropic drug resistance 1p (Pdr1p), (Tang 2020) TCCGCGGA Absent 80 Pdr1p/Pdr3ps 04:07, 15 February 2021 Pdr1p/Pdr3p response elements (PDREs) 48
268. Pleiotropic drug resistance 1p (Pdr1p), (Salin 2008) TCCG(C/T)GG(A/G) Present 363 Pdr1p/Pdr3ps 03:11, 4 May 2023 likely active or activable
269. Peroxisome proliferator-activated receptor alpha CGACCCC Present 81 Peroxisome proliferator-activated receptor alpha 18:37, 15 February 2021 likely active or activable, positive direction distal overlaps upper end of randoms
270. Peroxisome proliferator hormone response elements, (PPREs) AGGTCANAGGTCA Absent 82 Peroxisome proliferator hormone response elements 18:37, 15 February 2021 PPARs/RXRs heterodimers bind to PPRE 412
271. Phosphate starvation-response transcription factor (Pho4) CAC(A/G)T(T/G) Present 130 Pho4ps 16:20, 12 May 2022 likely active or activable, positive strands of the UTRs and negative direction distals are in the random range
272. Pollen1 element with TCCACCATA AGAAANNNNTCCACCATA Absent 304 Pollen1 with TCCACCATA 23:24, 9 January 2023 adjacent co-dependent regulatory element TCCACCATA 49-414
273. Pollen1 elements AGAAA Present 305 Pollen1 elements 21:40, 10 January 2023 likely active or activable
274. Pollen1 element TCCACCATA Absent 306 TCCACCATA 08:30, 11 January 2023 no regulatory element TCCACCATA was found, nor its ci. 49
275. Polycomb response elements CGCCAT(A/T)TT Absent 83 Polycomb response elements 06:52, 16 February 2021 2*48-49
276. Polycomb response elements, (PRE) GCCAT Present 307 Polycomb response elements 22:28, 13 January 2023 likely active or activable
277. Pribnow boxes TATAAT Present 308 Pribnow boxes 03:43, 15 January 2023 likely active or activable
278. Prolamin boxes TG(A/T)AAAG Present 309 Prolamin boxes 06:14, 18 January 2023 likely active or activable
279. Q elements AGGTCA Present 310 Q elements 20:23, 18 January 2023‎ See Retinoic acid response element likely active or activable
280. Quinone reductase response element, (QRDRE), (Yao) TCCCCT of TCCCCTTGCGTG Present 233 Quinone reductase response element 05:08, 5 November 2022‎ likely active or activable
281. Rap1 regulatory factors ACCC(A/G)N(A/G)CA Absent 86 Rap1 regulatory factors 05:04, 20 February 2021 "(ACCCRnRCA), less than half of the sites were detectably bound"[8] 47
282. Rap1 reduced consensus (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C) Present 241 Rap1 reduced consensus 03:47, 15 November 2022‎ likely active or activable
283. Reb1 extended, (Rossi) ATTACCCGAA Absent 114 Extended Reb1 00:07, 20 June 2021 410
284. Reb1 bound and exact occurrences TTACCC(G/T) Present 242 Reb1 bound and exact occurrences 16:38, 15 November 2022 likely active or activable
285. Retinoic acid response element AG(A/G)TCA Present 311 Retinoic acid response element 19:56, 19 January 2023 likely active or activable, positive direction distals appear random
286. Ribophorin (RPN) (Rpn4), PACE (proteasome associated control element) GGTGGCAAA Absent 89 Rpn4ps 03:15, 23 February 2021‎ 49
287. Rlm1ps CTATATATAG Absent 87 Rlm1ps 05:55, 22 February 2021‎ 4TAG 24*46
288. RORE motif, (RORE) A(A/T)NTAGGTCA Present 313 classic RORE motif 05:51, 22 January 2023 likely active or activable
289. RORE motif, variant C(T/A)(G/A)GGNCA Present 314 variant RORE motif 03:04, 24 January 2023‎ likely active or activable
290. Rox1ps (Tang 2020) RRRTAACAAGAG Absent 88 Rox1ps Heme-dependent repressor of hypoxic genes 21:50, 22 February 2021 23*49
291. R response elements (RRE) CATCTG Present 159 R response elements 16:04, 19 July 2022‎ likely active or activable
292. Seed-specific elements (SRE) CATGCATG Absent 90 Seed-specific elements 20:18, 23 February 2021 48-412
293. Serum response elements, (SRE) ACAGGATGT Present 315 Serum response elements 16:38, 25 January 2023 likely active or activable
294. Servenius sequences GGACCCT Present 316 Servenius sequences 03:07, 28 January 2023‎ likely active or activable
295. Shoot specific elements, (SREs) CAGCAGATTGCG Absent 91 Shoot specific elements 15:13, 24 February 2021‎ 412
296. Shue box element, (Crowder 1988) CCCTG(C/G) Present 349 Shue box elements 05:24, 18 April 2023‎ likely active or activable
297. Sip4ps (Tang) CC(C/G)T(C/T)C(C/G)TCCG Absent 92 Sip4ps 02:55, 25 February 2021 23*48
298. Smp1ps (Tang) ACTACTA(T/A)4TAG Absent 93 Smp1ps 23:43, 25 February 2021 2*410
299. SP1, (Long) GGGGCGGGCC Absent 355 SP1 19:43, 25 April 2023 410
300. Sp1 element, (Berberich 1993) GGGGCGGGT Absent 351 Sp1 elements 21:03, 18 April 2023 49
301. SP1, (Zhang) (G/T)GGGCGG(G/A)(G/A)(C/T) Present 320 SP1 05:57, 2 February 2023‎ likely active or activable
302. SP-1, (Sato) CCGCCCC Present 319 SP-1 05:54, 2 February 2023‎ likely active or activable
303. SP1, (Yao) GCGGC Present 321 SP1 05:57, 4 February 2023 likely active or activable
304. SP1-box 1, (Motojima) GGGGCT Present 317 SP1-box 1 05:46, 29 January 2023‎ likely active or activable
305. SP1-box 2, (Motojima) CTGCCC Present 318 SP1-box 2 19:30, 30 January 2023‎ likely active or activable
306. STAT5 TTCNNNGAA Present 322 STAT5 03:41, 5 February 2023‎ likely active or activable, positive distal likely random
307. Sterile12, (STE12), (Tang 2020) TGAAAC Present 356 Sterile12 encodes a transcription factor (Ste12) 05:53, 27 April 2023‎‎ likely active or activable
308. Sterol response elements, (Branco) TCGTATA Absent 94 Sterol response elements 19:00, 28 February 2021‎ perhaps plant specific 47
309. Sterol response elements, (Yao) AGCAGATTGCG Absent 95 Sterol response elements 03:22, 1 March 2021 liver specific 411
310. Stress-response elements, (STREs) CCCCT Present 323 Stress-response elements 07:49, 7 February 2023‎ likely active or activable, positive cores overlap randoms
311. Sucrose boxes NNAATCA Present 325 Sucrose boxes 08:03, 10 February 2023‎ likely active or activable
312. TACTAAC boxes TACTAA(C/T) Present 326 TACTAAC boxes 06:05, 12 February 2023‎ likely active or activable
313. TAGteams CAGGTAG Present 327 TAGteams 04:15, 14 February 2023‎ likely active or activable
314. Tapetum boxes TCGTGT Present 328 Tapetum boxes 08:10, 16 February 2023‎ likely active or activable
315. TATA boxes TATAAAA (Carninci 2006) TAT box (Yang 2006) Present 1 Wikipedia:TATA box 02:36, 10 January 2011 likely active or activable
316. TATA boxes TATAAA (Butler 2002) Present 4 Downstream promoter elements 21:32, 20 May 2012 likely active or activable
317. 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
318. TATA boxes (Yang 2007) TATA(A/T)AA(A/G) (Juven-Gershon 2010) Present 18 metazoan TATA box 01:05, 13 October 2019 likely active or activable
319. 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
320. TAT boxes (Fan 2007) TATCCAT Present 240 TAT box (Fan) samplings 06:17, 13 November 2022 likely active or activable
321. TATCCAC boxes TATCCAC Absent 19 TATCCAC boxes 03:59, 13 October 2019 GA responsive complex component 47
322. TATCCAC boxes (Yang 2007) TATCCAC Absent 20 TATC box gene transcriptions 03:59, 13 October 2019 47
323. Tbf1 regulatory factors A(A/G)CCCTAA Present 243 Tbf1 regulatory factors 17:38, 15 November 2022 Saccharomyces cerevisiae, likely active or activable
324. T boxes, (Conlon) TCACACCT Present 247 T boxes 23:28, 18 November 2022 likely active or activable
325. T boxes, (Zhang) AACGTT Present 248 T boxes 17:21, 20 November 2022‎ likely active or activable
326. TCCACCATA elements TCCACCATA Absent 78 TCCACCATA elements 05:10, 13 February 2021 adjacent co-dependent regulatory element of POLLEN1 49
327. TEA consensus sequences CATTCY Present 329 TEA consensus sequences 06:35, 24 February 2023‎ likely active or activable
328. Telomeric repeat DNA-binding factors, (TRFs) TTAGGG Present 331 Telomeric repeat DNA-binding factors 06:35, 2 March 2023 likely active or activable
329. Tetradecanoylphorbol-13-acetate response elements, (TREs) TGA(G/C)TCA Absent 24 Tetradecanoylphorbol-13-acetate response elements 15:07, 24 August 2020‎ cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 2*46
330. TGF-β control elements, (TCEs) GCGTGGGGGA Absent 96 TGF-β control elements 17:38, 5 March 2021 GCGTGGGGGA in humans 410
331. TGF-β inhibitory elements, (TIEs) GAGTGGTGA Absent 23 TGF-β inhibitory elements 01:57, 23 August 2020 in the rat transin/stromelysin promoter 49
332. Thyroid hormone response elements, (TREs)(THRs) AGGTCA Present 332 Thyroid hormone response elements 23:06, 3 March 2023‎ likely active or activable
333. Transcription factor 3, (TCF3) GTCTGGT Present 333 Transcription factor 3 19:21, 5 March 2023‎ likely active or activable
334. Translational control sequences, (TCSs) (A/T)TT(A/G)TCT Present 334 Translational control sequences 20:33, 7 March 2023‎ likely active or activable
335. Transposon enhancement control (TEC) or Tec1 GAATGT Present 330 Tec1ps 22:49, 26 February 2023 likely random, Ste12p cofactor
336. Tryptophan residues, (Lu) GAAA Present 143 Tryptophan residues 03:55, 18 June 2022‎ 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
337. Unfolded protein response element, (URE), (UPRE-1) CANCNTG Present 301 Unfolded protein response element 18:24, 8 January 2023 likely active or activable
338. Unfolded protein response elements, (UPREs) TGACGTG(G/A) Present 335 Unfolded protein response elements 21:02, 7 March 2023 likely active or activable
339. Upstream repressor site 1, (URS1, core), (Sumrada) CCGCC Present 278 Upstream repressor site 1 06:31, 17 December 2022 likely active or activable, negative direction proximals are within randoms
340. Upstream stimulating factors, (USFs) GCC(A/T)NN(C/G/T)(A/G) Present 338 Upstream stimulating factors 05:51, 11 March 2023‎ likely active or activable, cores overlap lower randoms
341. V boxes (A/G)TT(A/T)(C/T) Present 341 V boxes 20:50, 16 March 2023‎ likely active or activable
342. Vhr1ps, (VHR1), (Weider 2016), (Tang 2020) AATCA-N8-TGA(C/T)T Absent 97 Vhr1ps 01:26, 9 March 2021 Response to low biotin concentrations 2*49
343. Vitamin D response elements, (VDRE2s) A/GGG/TTCAnnnA/GGG/TTCA Absent 98 Vitamin D response elements 03:48, 10 March 2021 410
344. Vitamin D response elements (VDRE) (Kakhki 2018) (A/G)G(G/T)TCA, RGKTCA Present 342 Vitamin D response elements 04:37, 19 March 2023 likely active or activable
345. W boxes (W-boxes) (WRKY) (C/T)TGAC(C/T) Present 343 W boxes 20:46, 20 March 2023 likely active or activable
346. X1a boxes (Ferstl 2004) TCTGCC Present 360 X-boxes 04:29, 4 May 2023‎ likely active or activable
347. X1b boxes (Ferstl 2004) AGAGACAGAT Absent 357 X-boxes 17:57, 30 April 2023‎ 410
348. X2 boxes (Ferstl 2004) AGGTCCA Present 362 X-boxes 01:41, 4 May 2023‎‎ likely active or activable
349. X boxes (Zhang 1993) GTTGGCATGGCAAC Absent 13 X boxes 02:35, 20 November 2018 X2 box is AGGTCCA 414
350. X-boxes (Moreno) GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC Absent 99 X-boxes 16:43, 10 March 2021‎ includes GTTNCCATGGNAAC (4/3)*24*47-412
351. X core promoter elements (XCPE1) (A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C) Present 344 X core promoter elements 19:37, 22 March 2023‎ likely active or activable
352. Xenobiotic response elements, (XREs) (T/G)NGCGTG(A/C)(G/C)A Absent 84 Xenobiotic response elements 20:45, 17 February 2021 contains the core sequence GCGTG, see AHRE above 2*47
353. Xenobiotic response elements (XREs) (Shen 1992) GCGTG Present 234 Xenobiotic response elements 05:22, 5 November 2022 likely active or activable
354. XhoI site-binding protein 1 protein (Xbp1p), (Mai 1997), (Tang 2020) GcCTCGA(G/A)G(C/A)g(a/g) Absent 100 Xbp1ps 14:40, 11 March 2021 Transcriptional repressor 2*410
355. Yap response elements (Salin 2008) T(G/T)ACT(A/C)A Present 365 Yap response elements 05:18, 4 May 2023 likely active or activable
356. Yap recognition sequences (Tang 2020) TTACTAA Present 345 Yap recognition sequences 19:57, 24 March 2023 likely active or activable
357. Y boxes, (Koike 1997) (A/G)CTAACC(A/G)(A/G)(C/T) Absent 12 Y boxes 01:31, 20 November 2018 inverted CAAT box, 48
358. YY1 binding sites CCATTTA Absent 101 YY1 binding sites 06:23, 12 March 2021 47
359. YY1 binding sites CCATCTT Present 346 YY1 binding sites 22:07, 25 March 2023 likely active or activable
360. Z-box (ZboxN) samplings, (ZboxNs) ATACGGT Absent 252 Z-box (ZboxN) samplings 19:47, 2 December 2022‎ 47
361. Z-box (ZboxSo) samplings, (ZboxNs) ATACGTGT Absent 253 Z-box (ZboxSo) samplings 20:21, 3 December 2022‎ 48
362. Z boxes, NSoSp form A(C/T)A(C/G)G(G/T)(A/G/T)T Present 250 Z boxes 17:23, 28 November 2022‎ likely active or activable, negative direction distals within randoms
363. Z boxes, ZboxG A(C/T)A(C/G)GT(A/G)T Present 251 Z boxes 03:00, 1 December 2022 likely active or activable
364. Z boxes, ZboxSp CAGGT(A/G) Present 249 Z boxes 05:10, 24 November 2022‎ likely active or activable
365. Zinc-responsive elements, (Zhao 1998), (Tang 2020) (ZREs) ACCYYNAAGGT or ACC(C/T)(C/T)NAAGGT Absent 102 Zap1ps 15:52, 15 March 2021 49
366. 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 103 Zinc responsive elements 19:02, 15 March 2021 (4/3)3*49

Response element testing (Absent)

Response element
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.[9]
2. ABA-response element-like

(ABRE-like)

ACGTGTCC WD40 repeat family N third highest scoring motif.[9]
3. Abf1 regulatory factors CGTCCTCTACGAT General Regulatory Factors N CGTNNNNNACGAT.[8]
4. Activating proteins

(Murata)

GCCCACGGG bHSH N Activating protein 2.[10]
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.[11]
7. Amino acid response elements

(AARE)

(Maruyama)

ATTGCATCA ? N AARE1 (ATTGCATCA)[12]
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).[12]
10. Androgen response elements

(AREs)

(Kouhpayeh)

GGTACANNNTGTTCT Zinc finger DNA-binding domain N GGTACACGGTGTTCT.[13]
11. Androgen response elements

(AREs)

(Wilson)

TGATTCGTGAG Zinc finger DNA-binding domain N AGAACANNNTGTTCT.[14]
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.[15]
15. Carbohydrate response elements

(ChREs)

CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG ? N ChoRE1, ChoRE2.[16]
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.[17]
19. C/A hybrid boxes TGACGTAT bZIP N TGACGTAT.[18] A at the 12 position
20. C/T hybrid boxes TGACGTTA bZIP N TGACGTTA.[18] 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).[19]
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[11] ? N tomato genome-wide analysis
25. CENP-B boxes TTTCGTTGGAAGCGGGA ? N specifically localized at the centromere
26. Coupling elements

(CE1)

TGCCACCGG[9] ? N CE1 (Watanabe)
27. DAF-16-associated elements

(DAE)

TGATAAG ? N DAF-16-associated element (DAE).[20]
28. D-boxes

(Mracek1)

GTTGTATAAC ? N GTTGTATAAC.[21]
29. D-boxes

(Mracek)

CTTATGTAAA (Mracek2) ? N CTTATGTAAA.[21]
30. D-boxes

(Johnson)

TCTCACA ? N TCTCACATT(A/C)AATAAGTCA is a D-box.[17]
31. Defense and stress-responsive elements ATTTTCTTCA ? N ATTTTCTTCA.[11]
32. DNA damage response elements

(DREs)

(Smith)

TTTCAAT[22] ? N in the upstream repression sequence (URS)
33. DNA damage response elements

(DREs)

(Sumrada)

TAGCCGCCG of TAGCCGCCGRRRR.[23] ? N in the upstream repression sequence (URS)
34. DNA replication-related elements

(DREs)

TATCGATA ? N DNA replication-related element (DRE).[24]
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[25] ? N F-box overlaps the I-box
40. Forkhead boxes GTAAACAA[26] HTH, Forkhead N GTAAACAA FOXO1
41. Gal4ps CGGACCGC ? N CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG[27]
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[27] bZIP N GCN4 motifs
46. Gibberellin responsive element-like 2

(GARE-like 2)

(Fan)

TAACGTA[28] ? N "in the promoters of hydrolase genes".[28]
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.[29]
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[30] 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.[31]
64. Kozak sequences GCCGCC(A/G)CCATGG ? N GCCGCC(A/G)CCATGG[32]
65. Kozak sequences

(Matsumoto)

GAAAATGG ? N GAAAATGG[33]
66. L boxes AAATTAACCAA ? N AAATTAACCAA[34]
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.[8]
70. Mcm1 regulatory factors


(Rossi)

TTNCCNNNTNNGGNAA ? N Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[8]
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"[8]
82. Extended Reb1 ATTACCCGAA ? N "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."[8]
83. Rlm1ps CTATATATAG ? N CTA(T/A)4TAG
84. Rox1ps RRRTAACAAGAG ? N Heme-dependent repressor of hypoxic genes.[27]
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[27]
89. Smp1ps ACTACTA(A/T)(A/T)(A/T)(A/T)TAG ? N ACTACTA(T/A)4TAG[27]
90. SP1

(Long)

GGGGCGGGCC ? N GGGGCGGGCC[16]
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)

Response element
Name of elements Consensus sequences Response element class Testing Activity/Notes
Abbreviations Variations Pathways Present (Y) Random or likely active or activable
Authors Table (T)
1. A-boxes

(A-box)

(Nawkar 2017)

TACGTA Basic leucine zipper (bZIP)

Light signaling and stress response pathways

Y

T

likely active or activable
2. Abscissic acid response elements

(ABREs)

(Watanabe 2017)

ACGTG(G/T)C WD40 repeat family

ABA-signaling pathway, Ethylene signaling pathway

Y

T

likely active or activable
3. Activated B-cell Factor-1s

(ABFs, Abfms)

(Rossi 2018)

CGTNNNNN(A/G)(C/T)GA(C/T) General Regulatory Factors

B-cell receptor signal transduction pathway

Y

T

likely active or activable
4. boxes A

(AP-1 box A)

(Kokoroishi 2015)

TGACTCT bZIP

PKC-dependent pathway

Y

T

likely active or activable
5. Abscisic acid-responsive elements (Pho4s), G boxes

(G-box)

(Loake 1992)

CACGTG bZIP, bHLH

Purine and histidine biosynthesis pathways, Phenylpropanoid pathway, Light signaling and stress response pathways

Y

T

likely active or activable
6. ACGT-containing elements ACGT bZIP

Purine and histidine biosynthesis pathways, Phenylpropanoid pathway

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

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable, positive strand, positive direction AP2a within randoms
8. Activating protein 2

(AP2)

(Cohen)

GCCTGGCC bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
9. Activating protein 2

(Cohen)

TCCCCCGCCC bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
10. Activating protein 2

(Murata)

(C/G)CCN(3)GG(C/G) bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
11. Activating protein 2

(Murata)

(C/G)CCN(4)GG(C/G) bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
12. Activating protein 2

(Yao)

TCTTCCC bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
13. Activating protein 2

(Yao)

CTCCCA bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
14. Activating proteins

(AP-2)

(Yao)

GGCCAA bHSH

Rapamycin (TOR) regulatory pathways

Y

T

likely active or activable
15. Activating transcription factors

(Burton)

(A/C/G)TT(A/G/T)C(A/G)TCA bZIP

Signal transduction pathways

Y

T

likely active or activable
16. Activating transcription factors

(Kilberg)

(A/G/T)TT(A/G/T)CATCA bZIP

Signal transduction pathways

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
2
His
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

PKC-dependent pathway

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 ?

calcineurin-dependent signaling pathways

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?

gluconeogenic pathway

Y

T

likely active or activable
48. CATTCA elements

(CATTs)

CATTCA bHLH?

gluconeogenic pathway

Y

T

likely active or activable
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

cAMP-dependent pathway

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. CCCTC-binding factors

(CTCF)

(Lobanenkov 1990)

CCCTC ? 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) ?

signal transduction pathways

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
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
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 ?

Ethylene signaling pathway

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

metabolic pathways

Y

T

likely active or activable
94. Estrogen response elements

(ERE1s)

(Driscoll)

GGTCA Cys
4

estrogen response element-dependent signaling pathway

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

Ethylene signaling pathway

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

STAT5 pathway

Y

T

likely active or activable
101. GATA (GATAAG, GATAAH, GATTA) motifs

(Staschke)

GAT(A/T)A Zinc finger DNA-binding domains, bHLH

Rapamycin (TOR) Regulatory Pathways

Y

T

likely active or activable
102. GATC repeats

(ABREN)

(Watanabe et al. 2017)

GATC ?

?

Y

T

GATC UTRs, proximals and positive strand, negative direction distals greater than randoms, negative strand, negative direction distals, positive direction distals likely randoms. GATCs are likely active or activable
103. 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 ?

Ethylene signaling pathway

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

Rapamycin (TOR) Regulatory Pathways

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[11] WD40 repeat family Y

T

likely active or activable
111. G-protein-coupled receptors

(GCR1s), CT boxes

CTTCC ?

cAMP signal pathway, phosphatidylinositol signal pathway

Y

T

likely active or activable.
112. Glucocorticoid response elements AGAACA bHLH

gluconeogenesis pathway

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
85. Helper site

(Atcha et al. 2007), (Cadigan and Waterman 2012)

(C/G)C(C/G)G(C/G) ? 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

likely active or activable
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

likely active or activable
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. Phosphate starvation-response transcription factor

(Pho4)

(Tang 2020)

CAC(A/G)T(T/G) bHLH

purine and histidine biosynthesis pathways

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

See Retinoic acid response element

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

(RARE)

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
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

aryl hydrocarbon receptor pathways

Y

T

likely active or activable
230. Yap recognition sequences TTACTAA ? Y

T

likely active or activable
231. YY1 binding sites CCATCTT Cys
2
His
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 109 Ns for not present (absent) in either A1BG promoter and 238 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are 238 likely active or activable (66.48 %). 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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External links

{{Phosphate biochemistry}}