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

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)24⁵-4¹⁰
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, (BRE^u)	(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	Present	?	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 (BRE^d, 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 20:08, 11 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)	Present	?	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	CGGN₃TNAN_9-12CCG	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)N_5,6(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)2⁴4⁷-4¹²
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 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 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 (BRE^u)	(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 estrogen response element-dependent signaling pathway	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	? ABA-signaling pathway, Ethylene signaling pathway	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 Gibberellin (GA) growth regulator pathway, GA-biosynthesis pathway	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	? unfolded protein response (UPR) pathway	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 phenylpropanoid pathway	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)	? Wnt/beta-catenin signaling pathway	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 GH/HNF-6 pathway, HNF6/HNF1β pathway, HNF6 pathway, KLF4/HNF-6 pathway	Y T	likely active or activable, although the negative direction distals are at or less than randoms
129. Homeoboxes	CAAG	HTH lignin pathway, Wnt dorsalisation pathway, lefty-signaling pathway	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	CGGN₃TNAN_9-12CCG	?	Y T	likely active or activable
171. ORESARA1 (ORE1) (Matallana)	(A/C/G)(A/C)GT(A/G)N_5,6(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 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 371 response elements, there are 121 Ns for not present (absent) in either A1BG promoter and 251 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are 251 likely active or activable (67.65 %). 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.

References

↑ MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.
↑ ^2.0 ^2.1 Angelika Bröer; Gregory Gauthier-Coles; Farid Rahimi; Michelle van Geldermalsen; Dieter Dorsch􏰀; Ansgar Wegener; Jeff Holst; Stefan Bröer (March 15, 2019). "Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells" (PDF). Journal of Biological Chemistry. 294 (11): 4012–4026. doi:10.1074/jbc.RA118.006378. Retrieved 4 October 2020.
↑ ^3.0 ^3.1 Alisa A. Garaeva; Irina E. Kovaleva; Peter M. Chumakov; Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.
↑ ^4.0 ^4.1 Akihito Otsuki; Mikiko Suzuki; Fumiki Katsuoka; Kouhei Tsuchida; Hiromi Suda; Masanobu Morita; Ritsuko Shimizu; Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.
↑ ^5.0 ^5.1 Sarah E. Lacher; Daniel C. Levings; Samuel Freeman; Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.
↑ ^6.0 ^6.1 Ravi P. Misra; Azad Bonni; Cindy K. Miranti; Victor M. Rivera; Morgan Sheng; Michael E.Greenberg (14 October 1994). "L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway" (PDF). The Journal of Biological Chemistry. 269 (41): 25483–25493. PMID 7929249. Retrieved 7 December 2019.
↑ ^7.0 ^7.1 Yao EF; Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 Matthew J. Rossi; William K.M. Lai; B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.
↑ ^9.0 ^9.1 ^9.2 Kenneth A. Watanabe; Arielle Homayouni; Lingkun Gu; Kuan‐Ying Huang; Tuan‐Hua David Ho; Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.
↑ Takayuki Murata; Chieko Noda; Yohei Narita1; Takahiro Watanabe; Masahiro Yoshida; Keiji Ashio; Yoshitaka Sato; Fumi Goshima; Teru Kanda; Hironori Yoshiyama; Tatsuya Tsurumi; Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.
↑ ^11.0 ^11.1 ^11.2 ^11.3 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.
↑ ^12.0 ^12.1 Ryuto Maruyama; Makoto Shimizu; Juan Li, Jun Inoue; Ryuichiro Sato (24 March 2016). "Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region". Bioscience, Biotechnology, and Biochemistry. 80 (5): 929–934. doi:10.1080/09168451.2015.1135045. Retrieved 4 October 2020.
↑ S Kouhpayeh; AR Einizadeh; Z Hejazi; M Boshtam; L Shariati; M Mirian; L Darzi; M Sojoudi; H Khanahmad; A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.
↑ Stephen Wilson, Jianfei Qi & Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.
↑ Xu Tao; Anne E. West; Wen G. Chen; Gabriel Corfas; Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.
↑ ^16.0 ^16.1 Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.
↑ ^17.0 ^17.1 PA Johnson; D Bunick; NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. doi:10.1095/biolreprod44.1.127. PMID 2015343. Retrieved 6 April 2019.
↑ ^18.0 ^18.1 Young Hun Song; Cheol Min Yoo; An Pio Hong; Seong Hee Kim; Hee Jeong Jeong; Su Young Shin; Hye Jin Kim; Dae-Jin Yun; Chae Oh Lim; Jeong Dong Bahk; Sang Yeol Lee; Ron T. Nagao; Joe L. Key; Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.
↑ 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.
↑ Yan-Hui Li; Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.
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↑ 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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External links

{{Phosphate biochemistry}}

[MeSHD020218-1] MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.

[Broer-2] 2.0 ^2.1 Angelika Bröer; Gregory Gauthier-Coles; Farid Rahimi; Michelle van Geldermalsen; Dieter Dorsch􏰀; Ansgar Wegener; Jeff Holst; Stefan Bröer (March 15, 2019). "Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells" (PDF). Journal of Biological Chemistry. 294 (11): 4012–4026. doi:10.1074/jbc.RA118.006378. Retrieved 4 October 2020.

[Garaeva-3] 3.0 ^3.1 Alisa A. Garaeva; Irina E. Kovaleva; Peter M. Chumakov; Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.

[Otsuki-4] 4.0 ^4.1 Akihito Otsuki; Mikiko Suzuki; Fumiki Katsuoka; Kouhei Tsuchida; Hiromi Suda; Masanobu Morita; Ritsuko Shimizu; Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.

[Lacher-5] 5.0 ^5.1 Sarah E. Lacher; Daniel C. Levings; Samuel Freeman; Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.

[Misra-6] 6.0 ^6.1 Ravi P. Misra; Azad Bonni; Cindy K. Miranti; Victor M. Rivera; Morgan Sheng; Michael E.Greenberg (14 October 1994). "L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway" (PDF). The Journal of Biological Chemistry. 269 (41): 25483–25493. PMID 7929249. Retrieved 7 December 2019.

[Yao-7] 7.0 ^7.1 Yao EF; Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.

[Rossi-8] 8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 Matthew J. Rossi; William K.M. Lai; B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.

[Watanabe-9] 9.0 ^9.1 ^9.2 Kenneth A. Watanabe; Arielle Homayouni; Lingkun Gu; Kuan‐Ying Huang; Tuan‐Hua David Ho; Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.

[Murata-10] Takayuki Murata; Chieko Noda; Yohei Narita1; Takahiro Watanabe; Masahiro Yoshida; Keiji Ashio; Yoshitaka Sato; Fumi Goshima; Teru Kanda; Hironori Yoshiyama; Tatsuya Tsurumi; Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.

[Sharma-11] 11.0 ^11.1 ^11.2 ^11.3 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

[Maruyama-12] 12.0 ^12.1 Ryuto Maruyama; Makoto Shimizu; Juan Li, Jun Inoue; Ryuichiro Sato (24 March 2016). "Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region". Bioscience, Biotechnology, and Biochemistry. 80 (5): 929–934. doi:10.1080/09168451.2015.1135045. Retrieved 4 October 2020.

[Kouhpayeh-13] S Kouhpayeh; AR Einizadeh; Z Hejazi; M Boshtam; L Shariati; M Mirian; L Darzi; M Sojoudi; H Khanahmad; A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.

[Wilson-14] Stephen Wilson, Jianfei Qi & Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.

[Tao-15] Xu Tao; Anne E. West; Wen G. Chen; Gabriel Corfas; Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.

[Long-16] 16.0 ^16.1 Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.

[Johnson-17] 17.0 ^17.1 PA Johnson; D Bunick; NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. doi:10.1095/biolreprod44.1.127. PMID 2015343. Retrieved 6 April 2019.

[Song-18] 18.0 ^18.1 Young Hun Song; Cheol Min Yoo; An Pio Hong; Seong Hee Kim; Hee Jeong Jeong; Su Young Shin; Hye Jin Kim; Dae-Jin Yun; Chae Oh Lim; Jeong Dong Bahk; Sang Yeol Lee; Ron T. Nagao; Joe L. Key; Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.

[Hashimoto-19] 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.

[Li-20] Yan-Hui Li; Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.

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[Yoshihara-26] Eiji Yoshihara (18 August 2020). "TXNIP/TBP-2: A Master Regulator for Glucose Homeostasis". Antioxidants. 9 (8): 765–84. doi:10.3390/antiox9080765. PMID 32824669 Check |pmid= value (help). Retrieved 5 September 2020.

[Tang-27] 27.0 ^27.1 ^27.2 ^27.3 ^27.4 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 |pmid= value (help). Retrieved 18 September 2020.

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v t e Gene project
Articles	Complex locus A1BG and ZNF497 Grainyhead-like Genes in Regulating Development and Genetic Defects Lysenin Lysine: biosynthesis, catabolism and roles RIG-I like receptors ShK toxin: history, structure and therapeutic applications for autoimmune diseases
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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions Abscisic acid-responsive elements ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B box gene transcriptions Bioinformatics tool gene transcriptions Box gene transcriptions B recognition element upstream Bridge gene transcriptions CAAT box gene transcriptions CACA elements CadC binding domain gene transcriptions Calcineurin-responsive transcription factor gene transcriptions Calcium-response element gene transcriptions cAMP response element gene transcriptions C and D boxes gene transcriptions Carbohydrate response element gene transcriptions Carbon source-responsive element gene transcriptions Carcinoembryonic antigen gene family CARE gene transcriptions CArG box gene transcriptions CAT box gene transcriptions Cat8p gene transcriptions Cbf1 regulatory factor gene transcriptions C box gene transcriptions CCCTC-binding factor gene transcriptions C-EBP box gene transcriptions Cell-cycle box gene transcriptions Cell cycle regulation gene transcriptions CENP-B box gene transcriptions CGCG box gene transcriptions Circadian control element gene transcriptions Cold-responsive element gene transcriptions Complement copy gene transcriptions Complement-inverse copy gene transcriptions Consensus sequence gene transcriptions Copper response element gene transcriptions Core promoter gene transcriptions Coupling element gene transcriptions CRE box gene transcriptions Cytokinin response regulator gene transcriptions Cytoplasmic polyadenylation element gene transcriptions DAF-16-associated element gene transcriptions DAF-16 binding element gene transcriptions D box gene transcriptions Defense and stress-responsive element gene transcriptions Degenerate nucleotide gene transcriptions Dispersed promoter gene transcriptions Distal promoter gene transcriptions DNA melting gene transcriptions DNA damage response element gene transcriptions DNA replication-related element gene transcriptions Downstream core element gene transcriptions Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions