A1BG response element gene transcriptions: Difference between revisions

Revision as of 19:08, 17 April 2023

Associate Editor(s)-in-Chief: Henry A. Hoff

Def. nucleotide "sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents", [that] "may be found in both promoter and enhancer regions"^[1] are called response elements.

Hypotheses

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	Random or likely
1. ABA-response element-like, (ABRE-like)	ACGTGTCC	Absent	21	ABA-response elements 13:07, 8 October 2020	unlikely
2. ABA-response elements, novel, (ABREN, novel ABRE)	GATCGATC, CGATCGAT, GATCGAT	Absent	22	ABA-response elements 13:07, 8 October 2020	unlikely
3. ABA responsive elements (ABREs)	ACGTG(G/T)C	Present	23	ABA-response elements 05:53, 9 October 2020	likely active or activable
4. Abf1 regulatory factors	CGTCCTCTACGAT	Absent	25	Abf1 regulatory factors 18:32, 10 October 2020	unlikely
5. A-boxes	TACGTA	Present	16	A-boxes 21:24, 7 October 2020	likely active or activable
6. Abscisic acid-responsive elements (Pho4s), G boxes	CACGTG	Present	56	Abscisic acid-responsive elements (Pho4s), G boxes 06:38, 10 May 2022	likely active or activable
7. ACGT-containing elements	ACGT	Present	59	ACGT-containing elements 03:02, 25 September 2022	cores, proximals likely active or activable, few UTRs, distals may be random
8. Activated B-cell Factor-1s (ABFs, Abfms)	CGTNNNNN(A/G)(C/T)GA(C/T)	Present	24	Abf1 regulatory factors 17:47, 10 October 2020	likely active or activable
9. Activating proteins (Murata)	GCCCACGGG	Absent	117	Activating proteins 05:32, 15 December 2022‎	unlikely
10. Activating protein 2 alpha (AP2a)	GCCNNNGGC	Present	61	Activating protein 2 alpha 00:57, 29 September 2022‎‎	likely active or activable, positive strand, positive direction within randoms
11. Activating protein 2 (AP2), (Cohen1)	GCCTGGCC	Present	63	Activating protein 2 06:54, 30 September 2022	likely active or activable
12. Activating protein 2, (Cohen2)	TCCCCCGCCC	Present	64	Activating protein 2 07:41, 30 September 2022‎‎	likely active or activable
13. Activating protein 2, (Murata)	(C/G)CCN(3)GG(C/G)	Present	60	Activating protein 2 23:47, 28 September 2022‎	likely active or activable
14. Activating protein 2, (Murata)	(C/G)CCN(4)GG(C/G)	Present	62	Activating protein 2 19:10, 29 September 2022‎	likely active or activable
15. Activating protein 2, (Yao1)	TCTTCCC	Present	65	Activating protein 2 08:11, 30 September 2022	likely active or activable
16. Activating protein 2, (Yao2)	CTCCCA	Present	66	Activating protein 2 19:00, 30 September 2022‎	likely active or activable
17. Activating protein 2, (AP-2), (Yao3)	GGCCAA	Present	67	Activating proteins 22:23, 30 September 2022‎‎	likely active or activable
18. Activating transcription factors, (ATF), (Burton)	(A/C/G)TT(A/G/T)C(A/G)TCA	Present	68	Activating transcription factors 01:48, 1 October 2022‎	likely active or activable
19. Activating transcription factors, (ATF), (Kilberg)	(A/G/T)TT(A/G/T)CATCA	Present	69	Activating transcription factors 02:21, 1 October 2022	likely active or activable
20. Adenylate–uridylate rich elements, (AUREs), (Bakheet)	(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T)	Present	49	Adenylate–uridylate rich elements 02:16, 3 October 2021	likely active or activable
21. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class I)	ATTTA	Present	115	Adenylate–uridylate rich elements 04:44, 15 December 2022	likely active or activable, UTRs at the lower end of the randoms
22. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class II)	TTATTTA(A/T)(A/T)	Present	114	Adenylate–uridylate rich elements 04:31, 15 December 2022‎	likely active or activable
23. Adenylate–uridylate rich elements, (AREs), (Chen and Shyu, Class III)	ATTT	Present	113	Adenylate–uridylate rich elements 04:06, 15 December 2022‎	likely active or activable, low negative direction proximals overlap randoms
24. Adr1ps, (ADR), (Tang 2020)	TTGG(A/G)G	Present	110	Adr1ps 01:36, 15 December 2022‎	likely active or activable
25. Aft1s, (AFT)	(C/T)(A/G)CACCC(A/G)	Present	70	Aft1s 15:48, 3 October 2022‎	likely active or activable
26. AGC boxes	AGCCGCC (Leubner-Metzger 1998)	Present	8	AGC boxes 14:40, 2 May 2014	likely active or activable
27. AhR DNA-binding consensus sequence, (AhRY), (Yao)	GCGTGNN(A/T)NNN(C/G)	Present	97	AhR DNA-binding consensus sequence 05:37, 5 November 2022‎	likely active or activable for ZNF497
28. AhR-responsive elements (AHRE) (Yao 1992)	(G/T)NGCGTG(A/C)(C/G)A	Absent	41	AhR/ARNT complex 20:45, 17 February 2021	unlikely
29. Alpha-amylase conserved elements (Sharma 2020)	TATCCATCCATCC	Absent	30	Alpha-amylase conserved elements 22:18, 31 October 2020	unlikely
30. Alpha-amylase conserved elements portion	TATCCA	Present	119	Alpha-amylase conserved elements portion 05:39, 11 April 2023	likely active or activable
31. Amino acid response elements, (AARE1), (Maruyama)	ATTGCATCA	Absent	47	Amino acid response elements 01:32, 22 May 2021	unlikely
32. Amino acid response elements, (AARE), (Broer)	TTTGCATCA^[2]^[3]	Absent	31	Amino acid response elements 01:59, 1 November 2020	unlikely
33. Amino acid response element-like, (AARE-like), (AARE3), (Maruyama)	TGGTGAAAG	Absent	32	Amino acid response element-like 02:27, 2 November 2020‎	unlikely
34. Androgen response elements, (AREs), (Kouhpayeh)	GGTACANNNTGTTCT	Absent	33	Androgen response elements 17:01, 2 November 2020	unlikely
35. Androgen response element1s, (Kouhpayeh)	GGTACA of GGTACAnnnTGTTCT	Present	71	Androgen response element1s 17:22, 4 October 2022	likely active or activable
36. Androgen response element2s, (Kouhpayeh)	TGTTCT of GGTACAnnnTGTTCT	Present	72	Androgen response element2s 17:01, 5 October 2022‎	likely active or activable
37. Androgen response elements, (AREs), (Wilson)	AGAACANNNTGTTCT	Absent	50	Androgen response elements 16:21, 11 November 2021	unlikely
38. Androgen response elements, (Wilson)	AGAACANNNTGTTCT	Present	73	Androgen response elements 18:53, 5 October 2022	the two portions AGAACA and TGTTCT occurring separately are likely active or activable
39. Angiotensinogen core promoter elements (AGCE)	(A/C)T(C/T)GTG	Present	104	Angiotensinogen core promoter elements 20:01, 5 December 2022	likely active or activable, positive direction distal low occurrences overlap randoms
40. Antioxidant-electrophile responsive elements, (ARE), (Otsuki)	GTGAGGTCGC^[4] or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A^[5]	Absent	34	Antioxidant-electrophile responsive elements 06:06, 4 November 2020	unlikely
41. Antioxidant-electrophile responsive elements, (Lacher)	GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A	Present	74	Antioxidant-electrophile responsive elements 23:22, 5 October 2022‎	likely active or activable
42. Aryl hydrocarbon responsive element II, (AHRE-II)	CATGN₆C(A/T)TG	Present	105	AhR responsive element or Aryl hydrocarbon responsive element II 18:04, 6 December 2022‎	likely active or activable
43. ATA boxes	AATAAA	Present	109	ATA boxes 19:59, 14 December 2022‎	likely active or activable
44. ATTTA elements, (Siegel)	(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)	Present	112	ATTTA elements 04:04, 15 December 2022‎	likely active or activable
45. Auxin response factors, (ARF), (Stigliani)	(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)	Present	98	Auxin response factors 05:55, 5 November 2022‎	likely active or activable, positive direction proximals overlap high randoms, positive direction cores within randoms
46. Auxin response factors, (ARF), (Ulmasov)	TGTCTC	Present	99	Auxin response factors 06:02, 5 November 2022‎	likely active or activable
47. Auxin response factors, (ARF), (Boer)	TGTCGG	Present	75	Auxin response factors 17:03, 7 October 2022‎	likely active or activable
48. Auxin response factors, (ARF5)	(C/G/T)N(G/T)GTC(G/T)	Present	76	Auxin response factors 04:15, 10 October 2022	likely active or activable, negative direction proximals ≥ randoms
49. B-boxes, (Johnson)	TGGGCA	Present	78	B-boxes 18:05, 10 October 2022	likely active or activable, positive direction distals ≥ randoms
50. boxes A	TGACTCT	Present	55	Box A 06:50, 9 May 2022‎	likely active or activable
51. boxes B, (Sanchez)	TGTCTCA	Present	77	boxes B 15:26, 10 October 2022	likely active or activable
52. B recognition elements, (BRE^u)	(G/C)(G/C)(G/A)CGCC	Present	103	B recognition elements 20:39, 4 December 2022	likely active or activable
53. CAACTC regulatory elements, (CAREs), (Fan)	CAACTC	Present	53	CARE (Fan) 17:45, 7 May 2022	likely active or activable
54. CAAT boxes	(C/T)(A/G)(A/G)CCAATC(A/G)	Absent	12	CAAT boxes 02:41, 22 March 2019	unlikely, consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT.
55. CACA elements (Orlando 2019)	CACA	Present	45	CACA elements 05:04, 7 May 2021	likely active or activable
56. CadC binding domains	TTANNNNT	Present	79	CadC binding domains 22:14, 12 October 2022	likely active or activable, negative direction proximals within randoms
57. Calcineurin-responsive transcription factors	TG(A/C)GCCNC	Present	108	Calcineurin-responsive transcription factors 19:14, 12 December 2022‎	likely active or activable
58. Calcium-response elements, (CaRE1s), (Tao 2002)	CTATTTCGAG	Absent	35	Calcium-response elements 19:43, 7 November 2020‎	unlikely
59. Carbohydrate response elements, (ChREs), (ChoRE1, ChoRE2), (Long 2020)	CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG	Absent	36	Carbohydrate response elements 20:50, 10 November 2020	unlikely
60. Carbohydrate response elements, (ChoRE1), (Carb)	ACCGG	Present	57	Carbohydrate response elements 18:56, 18 June 2022	likely active or activable
61. Carbohydrate response elements, (ChoRE2), (Carb1)	CCCAT	Present	80	Carbohydrate response elements 06:01, 13 October 2022	likely active or activable
62. Carbohydrate response elements, (Carb E1)	ATCTTG	Present	81	Carbohydrate response elements 18:45, 13 October 2022‎	proximals likely active or activable
63. Carbohydrate response elements, (Carb E2)	CACGTG	Present	81	Carbohydrate response elements 21:30, 13 October 2022	likely active or activable
64. Carbohydrate response elements, (Carb E3)	TCCGCC	Present	82	Carbohydrate response elements 01:21, 14 October 2022‎	likely active or activable, low positive direction distals overlap high randoms
65. Carbon source-responsive elements, (CSREs)	CATTCATCCG	Absent	42	Carbon source-responsive elements 17:08, 19 March 2021	unlikely, confers carbon source-dependent regulation
66. Carbon source-responsive elements, (TCCGs)	TCCG	Present	83	TCCG elements 02:41, 16 October 2022	likely active or activable
67. Carbon source-responsive elements, (CATTs)	CATTCA	Present	84	CATTCA elements 17:05, 18 October 2022	likely random
68. CArG boxes, (Kamada 1992), (McDonald 2006)	CC(A/T)₆GG	Absent	85	CArG boxes 19:08, 18 October 2022	unlikely
69. CArG boxes, (Deng 2011)	CCAAAAAT(G/A)G	Absent	86	CArG boxes 19:08, 18 October 2022	unlikely
70. CArG boxes, (suggested more general motif), (Deng 2011)	C(C/A/T)(A/T)₆(A/G)G from two different CArG-box motifs at 502 bp (CTAAATATGG) and 287 bp (CAATAATTGG) upstream	Present	87	CArG boxes 19:08, 18 October 2022	likely active or activable, positive strand, negative direction: CATTAAAAGG at 3441 and CAAAAAAAAG at 1399
71. Cat8ps, (Tang 2020)	CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA	Present	88	Cat8ps 22:21, 18 October 2022	likely active or activable
72. CAT boxes, (Saitoh 1993)	CATTCCT	Present	89	CAT boxes 23:56, 18 October 2022‎	likely active or activable
73. CAT-box-like elements, (Berberich 1993)	GCCATT	Present	89	CAT-box-like elements 19:38, 20 October 2022‎	likely active or activable
74. Cbf1 regulatory factors	TCACGTGA	Absent	48	Cbf1 regulatory factors 15:57, 11 June 2021	unlikely
75. C-boxes, (Johnson)	GAGGCCATCT	Absent	27	C-boxes 02:51, 22 October 2020	unlikely
76. C boxes, (Samarsky)	AGTAGT	Present	90	C boxes 02:22, 21 October 2022	likely active or activable
77. C-boxes, (Song)	GACGTC	Present	91	C-boxes 06:22, 21 October 2022	likely active or activable
78. C/A hybrid boxes, (Song)	TGACGTAT	Absent	26	C/A hybrid boxes 16:18, 20 October 2020	unlikely
79. C/G hybrid boxes, (Song)	TGACGTGT	Present	102	CG hybrid boxes 18:35, 15 November 2022	likely active or activable
80. C/T hybrid boxes, (Song)	TGACGTTA	Absent	28	C/T hybrid boxes 01:51, 24 October 2020	unlikely
81. C boxes, (Voronina)	GGTGATG	Present	101	C boxes 18:28, 15 November 2022‎	likely active or activable
82. CCAAT-enhancer-binding site (C/EBP) activating transcription factor (ATF), or C/EBP-ATF responsive elements, (CAREs), (Garaeva)	(A/G/T)TT(A/G/T)CATCA	Present	54	CARE (Garaeva) 01:10, 8 May 2022	likely active or activable
83. CCAAT-enhancer-binding site (C/EBP), C/EBP boxes	TTAGGACAT,^[6] or TAGCATT.^[7]	Absent	37	C/EBP boxes 23:21, 18 November 2020	unlikely
84. CCCTC-binding factors, (CTCF)	NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)	Absent	29	CCCTC-binding factors 23:02, 24 October 2020‎	unlikely
85. Cell-cycle boxes, (CCBs)	CACGAAAA	Absent	43	Cell-cycle boxes 22:13, 19 April 2021	unlikely, "cell cycle box" is functional in either orientation, acting as an enhancer
86. Cell-cycle box variants, (CCBs)	CACGAAA, ACGAAA and C-CGAAA	Present	92	Cell-cycle box variants 05:54, 23 October 2022	likely active or activable
87. Cell cycle regulation, (Sharma 2020)	CCCAACGGT	Absent	38	Cell cycle regulation 20:53, 25 November 2020‎	unlikely
88. CENP-B boxes	TTTCGTTGGAAGCGGGA	Absent	13	CENP-B boxes 13:25, 11 May 2019	unlikely, specifically localized at the centromere
89. CGCG boxes, (Yang 2002)	(A/C/G)CGCG(C/G/T)	Present	107	CGCG boxes 07:14, 12 December 2022‎	likely active or activable, probably for zinc fingers
90. Circadian control elements	CAANNNNATC	Present	106	Circadian control elements 00:33, 12 December 2022	likely active or activable but overlaps highest randoms
91. Class C DNA binding sites, (Leal)	CACGNG	Present	58	Class C DNA binding sites 06:16, 5 August 2022	likely active or activable, distals may be random
92. Cold-responsive elements	CCGAC	Present	93	Cold-responsive elements 05:34, 24 October 2022	likely active or activable
93. Constitutive decay elements, (CDEs), (Siegel)	TTC(C/T)(A/G)(C/T)GAA	Present	111	Constitutive decay elements 03:50, 15 December 2022‎	likely active or activable possibly for ZNF497
94. Copper response elements, (CuREs), (Quinn)	TTTGC(T/G)C(A/G)	Present	94	Copper response elements 07:57, 24 October 2022	likely active or activable
95. Copper response elements, (CuREs), (Park)	TGTGCTCA	Present	95	Copper response elements 05:45, 25 October 2022	likely active or activable
96. Coupling elements, (CE1), (Watanabe)	TGCCACCGG	Absent	39	Coupling elements 01:51, 1 December 2020	unlikely
97. Coupling elements, (CE3s), (Watanabe)	GCGTGTC	Present	51	Coupling elements 15:47, 12 February 2022‎	likely active or activable
98. Coupling elements, (CE3s), (Ding)	CACGCG	Present	52	Coupling elements 02:59, 15 February 2022	likely active or activable
99. cyclic-AMP-responsive elements, (CREs), Aca1ps, Sko1ps, (Montminy 1986)	TGACGTCA	Present	116	cAMP-responsive elements 05:05, 15 December 2022	likely active or activable, same as Root specific elements
100. Cytokinin response regulators, (ARR1s)	AGATT(C/T)	Present	120	Cytokinin response regulators 16:21, 31 October 2022	likely active or activable
101. Cytokinin response regulators, (ARR10s)	(A/G)GATA(A/C)G	Present	200	Cytokinin response regulators 17:47, 27 October 2022	likely active or activable or may be random
102. Cytokinin response regulators, (ARR12s)	(A/G)AGATA	Present	200	Cytokinin response regulators 06:09, 28 October 2022	likely active or activable
103. Cytokinin response regulators, (ARRs), (Ferreira)	(G/A)GGAT(T/C)	Present	200	Cytokinin response regulators 03:25, 31 October 2022	likely active or activable
104. Cytokinin response regulators, (ARRs), (Rashotte1)	GATCTT	Present	200	Cytokinin response regulators 16:21, 31 October 2022‎	likely active or activable
105. Cytokinin response regulators, (ARRs), (Rashotte2)	(G/A)GAT(T/C)	Present	200	Cytokinin response regulators 20:24, 1 November 2022	likely active or activable
106. Cytoplasmic polyadenylation elements, (CPEs)	TTTTTAT	Cytoplasmic polyadenylation elements	likely active or activable
107. DAF-16-associated elements, (DAE), (Li)	TGATAAG	Absent	200	DAF-16-associated elements 22:51, 3 December 2020	unlikely
108. DAF-16 binding elements	(A/G)(C/T)AAA(C/T)A	Present	200	DAF-16 binding elements 19:54, 2 November 2022	likely active or activable
109. D-boxes, (Mracek1)	GTTGTATAAC	Absent	200	D-boxes 02:46, 10 December 2020	unlikely
110. D-boxes, (Mracek2)	CTTATGTAAA	Absent	200	D-boxes 02:20, 12 December 2020	unlikely
30. D-boxes (Johnson)	TCTCACA	?	N	TCTCACATT(A/C)AATAAGTCA is a D-box.^[8]
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
31. Defense and stress-responsive elements	ATTTTCTTCA	?	N	ATTTTCTTCA.^[9]
81. Dioxin-responsive elements, (DREs)	TNGCGTG	Present	96	Dioxin-responsive elements 20:43, 4 November 2022	likely active or activable
32. DNA damage response elements (DREs) (Smith)	TTTCAAT^[10]	?	N	in the upstream repression sequence (URS)
33. DNA damage response elements (DREs) (Sumrada)	TAGCCGCCG of TAGCCGCCGRRRR.^[11]	?	N	in the upstream repression sequence (URS)
34. DNA replication-related elements (DREs)	TATCGATA	?	N	DNA replication-related element (DRE).^[12]
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
24. Downstream promoter elements (DPE)	RGWCGTG (Burke 1996), RGWYV(T) (Kadonaga 2002)	Present	3	Initiator elements 21:32, 20 May 2012	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
25. 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
35. DREB boxes	TACCGACAT	?	N	CRT/DREB box
89. E2 boxes	(G/A)CAG(A/C/G/T)TG(A/C/G/T)	bHLH	Y T	likely active or activable
36. EIF4E basal elements	TTACCCCCCCTT	?	N	poly(C) motif
90. EIN3 binding sites	A(C/T)G(A/T)A(C/T)CT	?	Y T	likely active or activable
37. Endoplasmic reticulum stress response elements (ERSE)	CCAAT-N9-CCACG	bZIP	N	compare CCAAT-box and ERSE below in the (present)
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 (E-box)	CANNTG (Massari 2000)	Present	7	Enhancer boxes 22:01, 17 April 2013	likely active or activable
38. Estrogen response elements (EREs)	AGGTTA or GGTCAGGAT	Cys ₄	N	AGGTTATTGCCTCCT or GGTCAGGATGAC
94. Estrogen response elements (ERE1s) (Driscoll)	GGTCA	Cys ₄	Y T	likely active or activable
95. Estrogen response elements (ERE2s) (Driscoll)	TGACC	Cys ₄	Y T	likely active or activable
96. Ethylene responsive elements	ATTTCAAA	WD40 repeat family	Y T	likely active or activable
39. F boxes	TGATAAG^[13]	?	N	F-box overlaps the I-box
40. Forkhead boxes	GTAAACAA^[14]	HTH, Forkhead	N	GTAAACAA FOXO1
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
41. Gal4ps	CGGACCGC	?	N	CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG^[15]
42. γ-interferon activated sequences (GAS)	TTCCTAGAA	?	N	ALS-GAS1 between nt −633 and nt −625
99. Γ-interferon activated sequences (GAS), see STAT5	TTNCNNNAA	β-Scaffold factors with minor groove contacts	Y T	likely active or activable
100. GATA boxes	GATA	Zinc finger DNA-binding domains, bHLH	Y T	likely active or activable when occurring in the UTR or distals but may be random when occurring in the proximals
101. GATA (GATAAG, GATAAH, GATTA) motifs (Staschke)	GAT(A/T)A	Zinc finger DNA-binding domains, bHLH	Y T	likely active or activable
43. G boxes	(G/T)CCACGTG(G/T)C	?	N	no "perfect palindrome" G boxes in either promoter
102. GC boxes (Briggs)	(G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T)	?	Y T	likely active or activable
103. GC boxes (Ye)	GGGCGG	?	Y T	likely active or activable
104. GCC boxes	GCCGCC	?	Y T	likely active or activable
44. GCN4 motifs	TGACTCA, TGAGTCA	bZIP	N	ACGT motif
105. General control nonderepressible 4 protein binding site (GCRE, GCN4)	TGA(C/G/T)T(A/C/G)(A/T)	bZIP	Y T	likely active or activable
45. Gcn4ps	ATGACTCTT^[15]	bZIP	N	GCN4 motifs
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
109. Gibberellic acid responsive elements-like 1 (GAREL1s)	TAACA(A/G)A	WD40 repeat family	Y T	likely active or activable
46. Gibberellin responsive element-like 2 (GARE-like 2) (Fan)	TAACGTA^[16]	?	N	"in the promoters of hydrolase genes".^[16]
110. Gibberellin responsive elements (GREs) (Sharma)	AAACAGA^[9]	WD40 repeat family	Y T	likely active or activable
47. GLM boxes	(G/A)TGA(G/C)TCA(T/C)	?	N	GCN4-like motif
112. Glucocorticoid response elements	AGAACA	bHLH	Y T	likely active or activable
190. Glucose transporter gene repressor (Rgt1)	CGG(A/G)(A/T)N(A/T)(A/T)	?	Y T	likely active or activable
111. G-protein-coupled receptors (GCR1s), CT boxes	CTTCC	?	Y T	likely active or activable.
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)
113. GT boxes (Sato)	GGGG(T/A)GGGG	?	Y T	likely active or activable
114. Hac1 KAR2	CAGCGTG	?	Y T	likely active or activable
115. H and ACA boxes	AGAGGA	Hairpin-hinge-hairpin-tail	Y T	likely active or activable, negative distals likely random
50. Hapless motifs	CCAATCA	?	N	heterotrimeric transcription factor, HAP2/3/4.^[17]
116. Hap motif and ESRE CCAAT (Hap4p)	CCAAT	bZIP	Y T	likely active or activable
117. H-boxes (Grandbastien)	CC(A/T)ACCNNNNNNN(A/C)T	hairpin-hinge-hairpin-tail	Y T	likely active or activable
118. H-boxes (Lindsay)	CCTACC	hairpin-hinge-hairpin-tail	Y T	likely active or activable, equal to or greater than the randoms for the negative direction distals
119. H box (Mitchell)	ANANNA	hairpin-hinge-hairpin-tail	Y T	likely active or activable
120. H box (Rozhdestvensky)	ACACCA	hairpin-hinge-hairpin-tail	Y T	likely active or activable
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
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
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
125. Heat shock factors (Hsfs) (Tang)	NGAAN	HTH, HSFs	Y T	likely active or activable
126. Hex sequences	TGACGTGGC	?	Y T	likely active or activable
127. High Mobility Group boxes (HMG boxes)	(A/T)(A/T)CAAAG	β-Scaffold factors with minor groove contacts	Y T	random
128. HNF6s	(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)	Cys ₄	Y T	likely active or activable, although the negative direction distals are at or less than randoms
129. Homeoboxes	CAAG	HTH	Y T	likely active or activable
130. Homeodomains	TAAT	HTH	Y T	likely active or activable, low occurrence UTRs and negative direction distals overlap high randoms
131. HY boxes	TG(A/T)GGG	?	Y T	likely active or activable
59. Hypoxia-inducible factors (HIF-1)	GCCCTACGTGCTGTCTCA^[18]	bHLH	N	composed of HIF-1α and HIF-1β
27. Hypoxia-inducible factors (HIF) (Orlando 2019), ABA-response element (ABRE) (Asad 2019))	ACGTG	Present	46	Hypoxia-inducible factors 06:03, 7 May 2021, ABA-response element (ABRE) 03:06, 8 October 2020	likely active of activable
28. Hypoxia response elements (HRE) (Orlando 2019)	CACGC	Present	44	Hypoxia response elements 05:04, 7 May 2021	likely active or activable
60. I boxes	GATAAG	?	N	GGATGAGATAAGA
29. Initiator element (Inr) (Liston 1999)	YYA₊₁NWYY	Present	2	Initiator elements 17:02, 17 April 2012	likely active or activable
30. Initiator element (Inr) (Juven-Gershon 2008)	YYR₊₁NWYY	Present	19	Initiator elements 17:44, 27 September 2020	likely active or activable
31. Initiator element (Inr) (Ngoc 2017)	BBCA₊₁BW	Present	11	Initiator elements 13:24, 22 December 2018	likely active or activable
32. Initiator element-like (Inr-like) (Matsumoto 2020)	TTCTCT	Present	20	Initiator elements 01:25, 29 September 2020	likely active or activable
33. Initiator element-like (TCT) (Parry 2010)	(C/T)CT(C/T)T(C/T)(C/T)	Present	118	Initiator elements 22:06, 10 April 2023	likely active or activable
61. Inositol/choline-responsive elements (ICRE) (Case)	CANNTGAAAT	?	N	version of Lopes, see below
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
62. Inositol/choline-responsive elements (ICRE) (Lopes)	ATGTGAAAT	?	N	using ANNTGAAAT
140. Inositol/choline-responsive elements (ICREs) (Schwank)	TYTTCACATGY contains the core sequence CANNTG	bHLH	Y T	likely active or activable
141. Interferon regulatory factor (IRF3)	GCTTTCC	HTH	Y T	random
63. Interferon-stimulated response elements (ISREs)	AGTTTCN₂TTTCN	?	N	consensus sequence AGTTTCN₂TTTCN.^[19]
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
64. Kozak sequences	GCCGCC(A/G)CCATGG	?	N	GCCGCC(A/G)CCATGG^[20]
65. Kozak sequences (Matsumoto)	GAAAATGG	?	N	GAAAATGG^[21]
146. Krüppel-like factors	GGGNN(G/T)(G/T)(G/T)	?	Y T	likely active or activable
66. L boxes	AAATTAACCAA	?	N	AAATTAACCAA^[22]
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
67. Maf recognition element (MAREs)	TGCTGA(G/C)TCAGCA	?	N	and TGCTGA(GC/CG)TCAGCA^[23]
68. M boxes	GTCATGTGCT	?	N	or AGTCATGTGCT^[24]
68. M-CAT boxes, (Berberich 1993)	GCGGCCTC	Absent?	200	M-CAT boxes	unlikely
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.^[25]
70. Mcm1 regulatory factors (Rossi)	TTNCCNNNTNNGGNAA	?	N	Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.^[25]
68. Met3s	TCACGTG	bZIP	N	TCACGTG^[26]
149. Met31ps	AAACTGTG^[26]	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
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
34. Motif ten elements (MTE) (Lim 2004)	CSARCSSAACGS	Absent	5	Motif ten elements 15:28, 10 February 2013	unlikely
71. Motif ten elements	C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G)	?	N	Gene ID: 6309
153. Multicopy inhibitor of the GAL1 promoter (MIG1)	(C/G)(C/T)GGGG	bZIP	Y T	likely active or activable, UTRs may be random
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	Present	200	N-boxes 06:16, 5 August 2022	likely active or activable
166. Non-DiTyrosine 80 transcription factor DNA binding domain, (Ndt80)	(A/G/T)NC(A/G)CAAA(A/T)	Present	200	Non-DiTyrosine 80 transcription factor DNA binding domain 20:36, 17 August 2022	likely active or activable
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
72. NF‐κB/Rel family of eukaryotic transcription factors	CCCCTAAGGGG	β-Scaffold factors with minor groove contacts	N	NF-κB
168. NF𝜿B (Sato) (NF𝜿BSs)	GAATTC	?	Y T	likely active or activable
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
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
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
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
76. Pdr1p/Pdr3ps	TCCGCGGA	?	N	Pdr1p/Pdr3p response elements (PDREs)
179. Peroxisome proliferator-activated receptor alpha	CGACCCC	?	Y T	likely active or activable, positive direction distal overlaps upper end of randoms
77. Peroxisome proliferator hormone response elements (PPREs)	AGGTCANAGGTCA	?	N	PPARs/RXRs heterodimers bind to PPRE
180. Pho4ps	CAC(A/G)T(T/G)	bHLH	Y T	likely active or activable, positive strands of the UTRs and negative direction distals are in the random range
78. Pollen1 with TCCACCATA	AGAAANNNNTCCACCATA	?	N	adjacent co-dependent regulatory element TCCACCATA
181. Pollen1 elements	AGAAA	?	Y T	likely active or activable
79. TCCACCATA	TCCACCATA	?	N	no regulatory element TCCACCATA was found, nor its ci.
80. Polycomb response elements	CGCCAT(A/T)TT	?	N	CGCCATTT
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
81. Rap1 regulatory factors	ACCC(A/G)N(A/G)CA	?	N	"(ACCCRnRCA), less than half of the sites were detectably bound"^[25]
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
82. Extended Reb1	ATTACCCGAA	?	N	"extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."^[25]
188. Reb1 bound and exact occurrences	TTACCC(G/T)	WD40 repeat family	Y T	likely active or activable
189. Retinoic acid response element	AG(A/G)TCA	?	Y T	likely active or activable, positive direction distals appear random
83. Rlm1ps	CTATATATAG	?	N	CTA(T/A)₄TAG
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
84. Rox1ps	RRRTAACAAGAG	?	N	Heme-dependent repressor of hypoxic genes.^[15]
85. Rpn4ps	GGTGGCAAA	?	N	proteasome genes
193. R response elements (RRE)	CATCTG	?	Y T	likely active or activable
86. Seed-specific elements	CATGCATG	?	N	SRE consensus: CAGCAGATTGCG is none
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
87. Shoot specific elements	GATAATGATG	?	N	SRE consensus: CAGCAGATTGCG is none
87. Shue box element, (Crowder 1988)	CCCTG(C/G)	Present	200	Shue box elements	likely active or activable
88. Sip4ps	CC(C/G)T(C/T)C(C/G)TCCG	?	N	CC(C/G)T(C/T)C(C/G)TCCG^[15]
89. Smp1ps	ACTACTA(A/T)(A/T)(A/T)(A/T)TAG	?	N	ACTACTA(T/A)₄TAG^[15]
90. SP1 (Long)	GGGGCGGGCC	?	N	GGGGCGGGCC^[27]
90. Sp1 element, (Berberich 1993)	GGGGCGGGT	Absent?	200	Sp1 elements	unlikely?
196. SP1 (Zhang)	(G/T)GGGCGG(G/A)(G/A)(C/T)	?	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
197. SP1-box 1 (Motojima)	GGGGCT	?	Y T	likely active or activable
198. SP1-box 2 (Motojima)	CTGCCC	?	Y T	likely active or activable
201. STAT5	TTCNNNGAA	β-Scaffold factors with minor groove contacts	Y T	likely active or activable, positive distal likely random
91. Sterol response elements (Branco)	TCGTATA	?	N	perhaps plant specific
92. Sterol response elements (Yao)	AGCAGATTGCG	?	N	liver specific
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
35. TATA boxes	TATAAAA (Carninci 2006) TAT box (Yang 2006)	Present	1	Wikipedia:TATA box 02:36, 10 January 2011	likely active or activable
36. TATA boxes	TATAAA (Butler 2002)	Present	4	Downstream promoter elements 21:32, 20 May 2012	likely active or activable
37. 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
38. TATA boxes (Yang 2007)	TATA(A/T)AA(A/G) (Juven-Gershon 2010)	Present	14	metazoan TATA box 01:05, 13 October 2019	likely active or activable
39. 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
40. TAT boxes (Fan 2007)	TATCCAT	Present	100	TAT box (Fan) samplings 06:17, 13 November 2022	likely active or activable
93. TATCCAC boxes	TATCCAC	?	N	GA responsive complex component
41. TATCCAC boxes (Yang 2007)	TATCCAC	Absent	15	TATC box gene transcriptions 03:59, 13 October 2019	unlikely
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
94. TCCACCATA elements	TCCACCATA	?	N	adjacent co-dependent regulatory element of POLLEN1
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
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
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
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
42. Vitamin D response elements (VDRE) (Kakhki 2018)	(A/G)G(G/T)TCA	Present	18	Fibroblast growth factor 23 01:21, 10 September 2020	likely active or activable
226. Vitamin D response elements (VDREs)	(A/G)G(G/T)(G/T)CA	?	Y T	likely active or activable
100. X boxes	GTTGGCATGGCAAC^[28]	?	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^[29]	?	N	includes GTTNCCATGGNAAC
102. Xbp1ps	GcCTCGA(G/A)G(C/A)g(a/g)	?	N	Transcriptional repressor
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
103. Xenobiotic response elements (XREs)	(T/G)NGCGTG(A/C)(G/C)A	?	N	contains the core sequence GCGTG, see AHRE above
43. Xenobiotic response elements (XREs) (Shen 1992)	GCGTG	Present	96	Xenobiotic response elements 05:22, 5 November 2022	likely active or activable
230. Yap recognition sequences	TTACTAA	?	Y T	likely active or activable
104. Y boxes	(A/G)CTAACC(A/G)(A/G)(C/T)	?	N	inverted CAAT box
231. YY1 binding sites	CCATCTT	Cys ₂His ₂	Y T	likely active or activable
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
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
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 (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.^[30]
2. ABA-response element-like (ABRE-like)	ACGTGTCC	WD40 repeat family	N	third highest scoring motif.^[30]
3. Abf1 regulatory factors	CGTCCTCTACGAT	General Regulatory Factors	N	CGTNNNNNACGAT.^[25]
4. Activating proteins (Murata)	GCCCACGGG	bHSH	N	Activating protein 2.^[31]
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.^[9]
7. Amino acid response elements (AARE) (Maruyama)	ATTGCATCA	?	N	AARE1 (ATTGCATCA)^[32]
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).^[32]
10. Androgen response elements (AREs) (Kouhpayeh)	GGTACANNNTGTTCT	Zinc finger DNA-binding domain	N	GGTACACGGTGTTCT.^[33]
11. Androgen response elements (AREs) (Wilson)	TGATTCGTGAG	Zinc finger DNA-binding domain	N	AGAACANNNTGTTCT.^[34]
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.^[35]
15. Carbohydrate response elements (ChREs)	CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG	?	N	ChoRE1, ChoRE2.^[27]
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.^[8]
19. C/A hybrid boxes	TGACGTAT	bZIP	N	TGACGTAT.^[36] A at the 12 position
20. C/T hybrid boxes	TGACGTTA	bZIP	N	TGACGTTA.^[36] 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).^[37]
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^[9]	?	N	tomato genome-wide analysis
25. CENP-B boxes	TTTCGTTGGAAGCGGGA	?	N	specifically localized at the centromere
26. Coupling elements (CE1)	TGCCACCGG^[30]	?	N	CE1 (Watanabe)
27. DAF-16-associated elements (DAE)	TGATAAG	?	N	DAF-16-associated element (DAE).^[38]
28. D-boxes (Mracek1)	GTTGTATAAC	?	N	GTTGTATAAC.^[39]
29. D-boxes (Mracek)	CTTATGTAAA (Mracek2)	?	N	CTTATGTAAA.^[39]
30. D-boxes (Johnson)	TCTCACA	?	N	TCTCACATT(A/C)AATAAGTCA is a D-box.^[8]
31. Defense and stress-responsive elements	ATTTTCTTCA	?	N	ATTTTCTTCA.^[9]
32. DNA damage response elements (DREs) (Smith)	TTTCAAT^[10]	?	N	in the upstream repression sequence (URS)
33. DNA damage response elements (DREs) (Sumrada)	TAGCCGCCG of TAGCCGCCGRRRR.^[11]	?	N	in the upstream repression sequence (URS)
34. DNA replication-related elements (DREs)	TATCGATA	?	N	DNA replication-related element (DRE).^[12]
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^[13]	?	N	F-box overlaps the I-box
40. Forkhead boxes	GTAAACAA^[14]	HTH, Forkhead	N	GTAAACAA FOXO1
41. Gal4ps	CGGACCGC	?	N	CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG^[15]
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^[15]	bZIP	N	GCN4 motifs
46. Gibberellin responsive element-like 2 (GARE-like 2) (Fan)	TAACGTA^[16]	?	N	"in the promoters of hydrolase genes".^[16]
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.^[17]
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^[18]	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.^[19]
64. Kozak sequences	GCCGCC(A/G)CCATGG	?	N	GCCGCC(A/G)CCATGG^[20]
65. Kozak sequences (Matsumoto)	GAAAATGG	?	N	GAAAATGG^[21]
66. L boxes	AAATTAACCAA	?	N	AAATTAACCAA^[22]
67. Maf recognition element (MAREs)	TGCTGA(G/C)TCAGCA	?	N	and TGCTGA(GC/CG)TCAGCA^[23]
68. Met3s	TCACGTG	bZIP	N	TCACGTG^[26]
68. M boxes	GTCATGTGCT	?	N	or AGTCATGTGCT^[24]
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.^[25]
70. Mcm1 regulatory factors (Rossi)	TTNCCNNNTNNGGNAA	?	N	Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.^[25]
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"^[25]
82. Extended Reb1	ATTACCCGAA	?	N	"extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."^[25]
83. Rlm1ps	CTATATATAG	?	N	CTA(T/A)₄TAG
84. Rox1ps	RRRTAACAAGAG	?	N	Heme-dependent repressor of hypoxic genes.^[15]
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^[15]
89. Smp1ps	ACTACTA(A/T)(A/T)(A/T)(A/T)TAG	?	N	ACTACTA(T/A)₄TAG^[15]
90. SP1 (Long)	GGGGCGGGCC	?	N	GGGGCGGGCC^[27]
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^[28]	?	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^[29]	?	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		Present (Y)	Random or likely active or activable
Authors			Table (T)
1. ABA responsive elements (ABREs)	ACGTG(G/T)C	WD40 repeat family	Y T	likely active or activable
2. Activated B-cell Factor-1s (ABFs, Abfms)	CGTNNNNN(A/G)(C/T)GA(C/T)	General Regulatory Factors	Y T	likely active or activable
3. A-boxes	TACGTA	Basic leucine zipper (bZIP)	Y T	likely active or activable
4. boxes A	TGACTCT	bZIP	Y T	likely active or activable
5. Abscisic acid-responsive elements (Pho4s), G boxes	CACGTG	bZIP, bHLH	Y T	likely active or activable
6. ACGT-containing elements	ACGT	bZIP	Y T	cores and proximals are likely active or activable, but a few of the UTRs and distal promoters may be random
7. Activating protein 2 alpha (AP2a)	GCCNNNGGC	bHSH	Y T	likely active or activable, positive strand, positive direction AP2a within randoms
8. Activating protein 2 (AP2) (Cohen)	GCCTGGCC	bHSH	Y T	likely active or activable
9. Activating protein 2 (Cohen)	TCCCCCGCCC	bHSH	Y T	likely active or activable
10. Activating protein 2 (Murata)	(C/G)CCN(3)GG(C/G)	bHSH	Y T	likely active or activable
11. Activating protein 2 (Murata)	(C/G)CCN(4)GG(C/G)	bHSH	Y T	likely active or activable
12. Activating protein 2 (Yao)	TCTTCCC	bHSH	Y T	likely active or activable
13. Activating protein 2 (Yao)	CTCCCA	bHSH	Y T	likely active or activable
14. Activating proteins (AP-2) (Yao)	GGCCAA	bHSH	Y T	likely active or activable
15. Activating transcription factors (Burton)	(A/C/G)TT(A/G/T)C(A/G)TCA	bZIP	Y T	likely active or activable
16. Activating transcription factors (Kilberg)	(A/G/T)TT(A/G/T)CATCA	bZIP	Y T	likely active or activable
17. Adenylate–uridylate rich elements (AUREs) (Bakheet)	(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T)	stem-loop	Y T	likely active or activable
18. Adenylate–uridylate rich elements (AREs) (Chen and Shyu, Class I)	ATTTA	stem-loop	Y T	likely active or activable, UTRs at the lower end of the randoms
19. Adenylate–uridylate rich elements (AREs) (Chen and Shyu, Class II)	TTATTTA(A/T)(A/T)	stem-loop	Y T	likely active or activable
20. Adenylate–uridylate rich elements (AREs) (Chen and Shyu, Class III)	ATTT	stem-loop	Y T	likely active or activable, low negative direction proximals overlap randoms
21. Adr1ps	TTGG(A/G)G	Cys ₂His ₂ zinc finger binding domain	Y T	likely active or activable
22. Aft1s	(C/T)(A/G)CACCC(A/G)	bZIP?	Y T	likely active or activable
23. AGC boxes	AGCCGCC	AP-2/EREBP-related factors	Y T	likely active or activable
24. AhR responsive element or Aryl hydrocarbon responsive element II (AHRE-II)	CATGN₆C(A/T)TG	bHLH	Y T	likely active or activable
25. AhR DNA-binding consensus sequence (AhRY) (Yao)	GCGTGNN(A/T)NNN(C/G)	bHLH	Y T	likely active or activable for ZNF497
26. Androgen response element1s (Kouhpayeh)	GGTACA of GGTACAnnnTGTTCT	Zinc finger DNA-binding domain	Y T	likely active or activable
27. Androgen response element2s (Kouhpayeh)	TGTTCT of GGTACAnnnTGTTCT	Zinc finger DNA-binding domain	Y T	likely active or activable
28. Androgen response elements (Wilson)	AGAACANNNTGTTCT	Zinc finger DNA-binding domain	Y T	the two portions AGAACA and TGTTCT occurring separately are likely active or activable
29. Angiotensinogen core promoter elements	(A/C)T(C/T)GTG	bZIP?	Y T	likely active or activable, positive direction distal low occurrences overlap randoms
30. Antioxidant-electrophile responsive elements (Lacher)	GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A	bHLH	Y T	likely active or activable
31. ATA boxes	AATAAA	β-Scaffold factor?	Y T	likely active or activable
32. ATTTA elements (Siegel)	(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)	β-Scaffold factor?	Y T	likely active or activable
33. Auxin response factors (Stigliani)	(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)	WD40 repeat family	Y T	likely active or activable, positive direction proximals overlap high randoms, positive direction cores within randoms
34. Auxin response factors (Ulmasov)	TGTCTC	WD40 repeat family	Y T	likely active or activable
35. Auxin response factors (Boer)	TGTCGG	WD40 repeat family	Y T	likely active or activable
36. Auxin response factors (ARF5)	(C/G/T)N(G/T)GTC(G/T)	WD40 repeat family	Y T	likely active or activable, negative direction proximals ≥ randoms
37. B-boxes (Johnson)	TGGGCA	Zinc finger DNA-binding domains	Y T	likely active or activable, positive direction distals ≥ randoms
38. boxes B (Sanchez)	TGTCTCA	Zinc finger DNA-binding domains	Y T	likely active or activable
39. B recognition elements (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	?	Y T	likely active or activable
42. Carbohydrate response elements	ChoRE1 ACCGG	?	Y T	likely active or activable
43. Carbohydrate response elements	ChoRE2 CCCAT	?	Y T	likely active or activable
44. Carbohydrate response elements	Carb E1 ATCTTG	bHLH?	Y T	proximals likely active or activable
45. Carbohydrate response elements	Carb E2 CACGTG	bHLH	Y T	likely active or activable
46. Carbohydrate response elements	Carb E3 TCCGCC	bHLH?	Y T	likely active or activable, low positive direction distals overlap high randoms
47. Carbon source-responsive elements TCCG elements (TCCGs)	TCCG	bHLH?	Y T	likely active or activable
48. CATTCA elements (CATTs)	CATTCA	bHLH?	Y T	likely random
49. CARE (Fan) (CAREs) (Fan)	CAACTC	WD-40 repeat family	Y T	likely active or activable
50. CARE (Garaeva) (CAREs) (Garaeva)	(A/G/T)TT(A/G/T)CATCA	WD-40 repeat family	Y T	likely active or activable
51. cAMP-responsive elements (CREs), Aca1ps, Sko1ps	TGACGTCA	bZIP	Y T	likely active or activable, same as Root specific elements
52. CArG boxes	CCAAAAAT(G/A)G	bHLH	Y T	likely active or activable
53. Cat8ps	CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA	?	Y T	likely active or activable
54. CAT boxes	CATTCCT	bHLH	Y T	likely active or activable
55. CAT-box-like elements	GCCATT	bHLH	Y T	likely active or activable
56. C boxes (Samarsky)	AGTAGT	bZIP	Y T	likely active or activable
57. C-boxes (Song)	GACGTC	bZIP	Y T	likely active or activable
58. hybrid CG-boxes (Song)	TGACGTGT	bZIP	Y T	likely active or activable
59. C boxes (Voronina)	GGTGATG	bZIP	Y T	likely active or activable
60. Cell-cycle box variants (CCBs)	CACGAAA, ACGAAA and C-CGAAA	?	Y T	likely active or activable
61. CGCG boxes	(A/C/G)CGCG(C/G/T)	?	Y T	likely active or activable probably for the respective zinc fingers
62. Circadian control elements	CAANNNNATC	?	Y T	likely active or activable but overlaps highest randoms
63. Class C DNA binding sites	CACGNG	bHLH	Y T	likely active or activable, although the distals may be random
64. Cold-responsive elements	CCGAC	?	Y T	likely active or activable
65. Constitutive decay elements (CDEs) (Siegel)	TTC(C/T)(A/G)(C/T)GAA	stem-loop	Y T	likely active or activable possibly for ZNF497
66. Copper response elements (CuREs) (Quinn)	TTTGC(T/G)C(A/G)	?	Y T	likely active or activable
67. Copper response elements (CuREs) (Park)	TGTGCTCA	?	Y T	likely active or activable
68. Coupling elements (CE3s) (Watanabe)	GCGTGTC	WD-40 repeat family	Y T	likely active or activable
69. Coupling elements (CE3s) (Ding)	CACGCG	WD-40 repeat family	Y T	likely active or activable
70. Cytokinin response regulators (ARR1s)	AGATT(C/T)	WD40 repeat family	Y T	likely active or activable
71. Cytokinin response regulators (ARR10s)	(A/G)GATA(A/C)G	WD40 repeat family	Y T	likely active or activable or may be random
72. Cytokinin response regulators (ARR12s)	(A/G)AGATA	WD40 repeat family	Y T	likely active or activable
73. Cytokinin response regulators (ARRs) (Ferreira)	(G/A)GGAT(T/C)	WD40 repeat family	Y T	likely active or activable
74. Cytokinin response regulators (ARRs) (Rashotte1)	GATCTT	WD40 repeat family	Y T	likely active or activable
75. Cytokinin response regulators (ARRs) (Rashotte2)	(G/A)GAT(T/C)	WD40 repeat family	Y T	likely active or activable
76. Cytoplasmic polyadenylation elements (CPEs)	TTTTTAT	?	Y T	likely active or activable
77. DAF-16 binding elements	(A/G)(C/T)AAA(C/T)A	?	Y T	likely active or activable
78. D boxes (Samarsky)	AGTCTG	?	Y T	likely active or activable
79. D boxes (Voronina)	TCCTG	?	Y T	likely active or activable
80. D-boxes (Motojima)	TGAGTGG	?	Y T	likely active or activable
81. Dioxin-responsive elements (DREs)	TNGCGTG	bHLH?	Y T	likely active or activable
82. Downstream B recognition elements	(A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T)	?	Y T	likely active or activable, negatives > randoms, positives overlap or outside randoms
83. Downstream core elements (DCESIs)	CTTC of CTTC...CTGT...AGC	?	Y T	likely active or activable, depending on overlaps
84. Downstream core elements (DCESIIs)	CTGT of CTTC...CTGT...AGC	?	Y T	likely active or activable, depending on overlaps
85. Downstream core elements (DCESIIIs)	AGC of CTTC...CTGT...AGC	?	Y T	likely active or activable, depending on overlaps
86. Downstream promoter elements (DPEs) (Juven-Gershon)	(A/G)G(A/T)(C/T)(A/C/G)T	?	Y T	most or all of the real DPE (Juven-Gershon)s are likely active or activable
87. Downstream promoter elements (DPEs) (Kadonaga)	(A/G)G(A/T)CGTG	?	Y T	likely active or activable
88. Downstream promoter elements (DPEs) (Matsumoto)	AGTCTC	?	Y T	likely active or activable
89. E2 boxes	(G/A)CAG(A/C/G/T)TG(A/C/G/T)	bHLH	Y T	likely active or activable
90. EIN3 binding sites	A(C/T)G(A/T)A(C/T)CT	?	Y T	likely active or activable
91. Endoplasmic reticulum stress response elements	CCAAT-N9-CCACG, part 1 see Hap motif no.114 below, ESRE2, CCACG	bZIP	Y T	likely active or activable
92. Endosperm expressions	TGTGTCA	?	Y T	likely active or activable
93. Enhancer boxes	CA(A/C/G/T)(A/C/G/T)TG	bHLH	Y T	likely active or activable
94. Estrogen response elements (ERE1s) (Driscoll)	GGTCA	Cys ₄	Y T	likely active or activable
95. Estrogen response elements (ERE2s) (Driscoll)	TGACC	Cys ₄	Y T	likely active or activable
96. Ethylene responsive elements	ATTTCAAA	WD40 repeat family	Y T	likely active or activable
97. Forkhead boxes	(A/G)(C/T)AAA(C/T)A	HTH, Forkhead	Y T	likely active or activable
98. GAAC elements	GAACT	?	Y T	likely active or activable
99. Γ-interferon activated sequences (GAS), see STAT5	TTNCNNNAA	β-Scaffold factors with minor groove contacts	Y T	likely active or activable
100. GATA boxes	GATA	Zinc finger DNA-binding domains, bHLH	Y T	likely active or activable when occurring in the UTR or distals but may be random when occurring in the proximals
101. GATA (GATAAG, GATAAH, GATTA) motifs (Staschke)	GAT(A/T)A	Zinc finger DNA-binding domains, bHLH	Y T	likely active or activable
102. GC boxes (Briggs)	(G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T)	?	Y T	likely active or activable
103. GC boxes (Ye)	GGGCGG	?	Y T	likely active or activable
104. GCC boxes	GCCGCC	?	Y T	likely active or activable
105. General control nonderepressible 4 protein binding site (GCRE, GCN4)	TGA(C/G/T)T(A/C/G)(A/T)	bZIP	Y T	likely active or activable
106. GGCGGC triplet	GGCGGC	Zn(II)₂Cys₆	Y T	likely active or activable
107. GGC triplets	GGC	Zn(II)₂Cys₆	Y T	likely active or activable
108. Gibberellic acid responsive elements (GAREs)	TAACAAA	WD40 repeat family	Y T	likely active or activable
109. Gibberellic acid responsive elements-like 1 (GAREL1s)	TAACA(A/G)A	WD40 repeat family	Y T	likely active or activable
110. Gibberellin responsive elements (GREs) (Sharma)	AAACAGA^[9]	WD40 repeat family	Y T	likely active or activable
111. G-protein-coupled receptors (GCR1s), CT boxes	CTTCC	?	Y T	likely active or activable.
112. Glucocorticoid response elements	AGAACA	bHLH	Y T	likely active or activable
113. GT boxes (Sato)	GGGG(T/A)GGGG	?	Y T	likely active or activable
114. Hac1 KAR2	CAGCGTG	?	Y T	likely active or activable
115. H and ACA boxes	AGAGGA	Hairpin-hinge-hairpin-tail	Y T	likely active or activable, negative distals likely random
116. Hap motif and ESRE CCAAT (Hap4p)	CCAAT	bZIP	Y T	likely active or activable
117. H-boxes (Grandbastien)	CC(A/T)ACCNNNNNNN(A/C)T	hairpin-hinge-hairpin-tail	Y T	likely active or activable
118. H-boxes (Lindsay)	CCTACC	hairpin-hinge-hairpin-tail	Y T	likely active or activable, equal to or greater than the randoms for the negative direction distals
119. H box (Mitchell)	ANANNA	hairpin-hinge-hairpin-tail	Y T	likely active or activable
120. H box (Rozhdestvensky)	ACACCA	hairpin-hinge-hairpin-tail	Y T	likely active or activable
121. Heat shock elements (HSE3s) (Eastmond)	nGAAn-(5-bp)-nGAAnnTTCn	HTH, HSFs	Y T	likely active or activable
122. Heat shock elements (HSEs) (Eastmond)	nGA(A/G)n-(5-bp)-nGAAnnTTCn (GAP1)	HTH, HSFs	Y T	same result as HSE3, likely active or activable
123. Heat shock elements (HSEs) (Eastmond)	nGAAn-(5-bp)-nGA(A/G)nnTTCn (GAP2)	HTH, HSFs	Y T	same result as HSE3, likely active or activable
124. Heat shock elements (HSE4s) (Eastmond)	nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn	HTH, HSFs	Y T	likely active or activable
125. Heat shock factors (Hsfs) (Tang)	NGAAN	HTH, HSFs	Y T	likely active or activable
126. Hex sequences	TGACGTGGC	?	Y T	likely active or activable
127. High Mobility Group boxes (HMG boxes)	(A/T)(A/T)CAAAG	β-Scaffold factors with minor groove contacts	Y T	random
128. HNF6s	(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)	Cys ₄	Y T	likely active or activable, although the negative direction distals are at or less than randoms
129. Homeoboxes	CAAG	HTH	Y T	likely active or activable
130. Homeodomains	TAAT	HTH	Y T	likely active or activable, low occurrence UTRs and negative direction distals overlap high randoms
131. HY boxes	TG(A/T)GGG	?	Y T	likely active or activable
132. Hypoxia-inducible factors	ACGTG	bHLH	Y T	likely active or activable
133. Hypoxia response elements	CACGC	WD40 repeat family	Y T	likely active or activable
134. CACA elements	CACA	WD40 repeat family	Y T	likely active or activable
135. Initiator elements (Inrs)	YYRNWYY	?	Y T	likely active or activable
136. Initiator elements (Inrs)	BBCABW	?	Y T	likely active or activable
137. Initiator-like elements (Ins-Like)	TTCTCT	?	Y T	likely active or activable, where real Inr-like negative direction distals are within the range of the randoms
138. Initiator-like elements (TCT)	(C/T)CT(C/T)T(C/T)(C/T)	?	Y T	likely active or activable
139. Inositol/choline-responsive elements (ICRE) (Case, Lopes)	CATGTGAAAT includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991)	bHLH	Y T	likely active or activable
140. Inositol/choline-responsive elements (ICREs) (Schwank)	TYTTCACATGY contains the core sequence CANNTG	bHLH	Y T	likely active or activable
141. Interferon regulatory factor (IRF3)	GCTTTCC	HTH	Y T	random
142. IFN-stimulated response elements (ISREs) (Lu)	GAAANNGAAA	HTH	Y T	likely active or activable
143. IRS consensus (Fujii)	AANNGAAA	HTH	Y T	likely active or activable
144. Tryptophan residues (Lu)	GAAA	HTH	Y T	likely active or activable, the tryptophan residues occur in the IRS, IFN, ICRE, Cell-cycle box variants, V-box, Pollen1, and β-Scaffold response elements
145. Jasmonic acid-responsive elements (JAREs)	TGACG	?	Y T	likely active or activable
146. Krüppel-like factors	GGGNN(G/T)(G/T)(G/T)	?	Y T	likely active or activable
147. Leu3 transcription factors	(C/G)C(G/T)NNNN(A/C)G(C/G)	Zn(II)₂Cys₆	Y T	likely active or activable
148. -35 sequence	TTGACA	?	Y T	likely active or activable, the UTR does overlap the randoms at the random's upper end
149. Met31ps	AAACTGTG^[26]	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. Pho4ps	CAC(A/G)T(T/G)	bHLH	Y T	likely active or activable, positive strands of the UTRs and negative direction distals are in the random range
181. Pollen1 elements	AGAAA	?	Y T	likely active or activable
182. Polycomb response elements (PRE)	GCCAT	?	Y T	likely active or activable
183. Pribnow boxes	TATAAT	?	Y T	likely active or activable
184. Prolamin boxes	TG(A/T)AAAG	?	Y T	likely active or activable
185. Q elements 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	AG(A/G)TCA	?	Y T	likely active or activable, positive direction distals appear random
190. Glucose transporter gene repressor (Rgt1)	CGG(A/G)(A/T)N(A/T)(A/T)	?	Y T	likely active or activable
191. classic RORE motif (RORE)	A(A/T)NTAGGTCA	?	Y T	likely active or activable
192. variant RORE motif	C(T/A)(G/A)GGNCA	?	Y T	likely active or activable
193. R response elements (RRE)	CATCTG	?	Y T	likely active or activable
194. Serum response elements (SRE) see CArG boxes	ACAGGATGT	bHLH-ZIP	Y T	likely active or activable
195. Servenius sequences	GGACCCT	?	Y T	likely active or activable
196. SP1 (Zhang)	(G/T)GGGCGG(G/A)(G/A)(C/T)	?	Y T	likely active or activable
197. SP1-box 1 (Motojima)	GGGGCT	?	Y T	likely active or activable
198. SP1-box 2 (Motojima)	CTGCCC	?	Y T	likely active or activable
199. SP-1 (Sato)	CCGCCCC	?	Y T	likely active or activable
200. SP1 (Yao)	GCGGC	?	Y T	likely active or activable
201. STAT5	TTCNNNGAA	β-Scaffold factors with minor groove contacts	Y T	likely active or activable, positive distal likely random
202. Stress-response elements (STREs)	CCCCT	?	Y T	likely active or activable, positive cores overlap randoms Positive strand, negative direction: CCCCT at 3059
203. Sucrose boxes	NNAATCA	?	Y T	likely active or activable
204. TACTAAC boxes	TACTAA(C/T)	?	Y T	likely active or activable
205. TAGteams	CAGGTAG	?	Y T	likely active or activable
206. Tapetum boxes	TCGTGT	?	Y T	likely active or activable
207. metazoan TATA boxes	TATA(A/T)AA(A/G)	β-Scaffold factors with minor groove contacts	Y T	likely active or activable
208. TATA boxes	TATA(A/T)A(A/T)(A/G)	β-Scaffold factors with minor groove contacts	Y T	likely active or activable
209. TAT Boxes (Yang)	TATAAAA	WD40 repeat family	Y T	likely active or activable
210. TAT Boxes (Fan)	TATCCAT	WD40 repeat family	Y T	likely active or activable
211. Tbf1 regulatory factors	A(A/G)CCCTAA	General Regulatory Factors	Y T	Saccharomyces cerevisiae, likely active or activable
212. T boxes (Conlon)	TCACACCT	bZIP	Y T	likely active or activable
213. T boxes (Zhang)	AACGTT	bZIP	Y T	likely active or activable
214. TEA consensus sequences	CATTCY	?	Y T	likely active or activable
215. Tec1ps	GAATGT	?	Y T	likely random, Ste12p cofactor
216. Telomeric repeat DNA-binding factors (TRFs)	TTAGGG	?	Y T	likely active or activable
217. Thyroid hormone response elements (TREs)(THRs)	AGGTCA	?	Y T	likely active or activable
218. Transcription factor 3 (TCF3)	GTCTGGT	?	Y T	likely active or activable
219. Translational control sequences (TCSs)	(A/T)TT(A/G)TCT	?	Y T	likely active or activable
220. Unfolded protein response element (URE) (UPRE-1)	CANCNTG	?	Y T	likely active or activable
221. Unfolded protein response elements (UPREs)	TGACGTG(G/A)	bZIP	Y T	likely active or activable
222. Upstream repressor site 1 (URS1, core) (Sumrada)	CCGCC	?	Y T	likely active or activable, negative direction proximals are within randoms
223. Upstream stimulating factors (USFs)	GCC(A/T)NN(C/G/T)(A/G)	bHLH-ZIP	Y T	likely active or activable, cores overlap lower randoms
224. UUA rich elements (Chen)	TTATTTA(A/T)(A/T)	?	Y T	likely active or activable
225. V boxes	(A/G)TT(A/T)(C/T)	?	Y T	likely active or activable
226. Vitamin D response elements (VDREs)	(A/G)G(G/T)(G/T)CA	?	Y T	likely active or activable
227. W boxes	(C/T)TGAC(C/T)	WRKY	Y T	likely active or activable
228. X core promoter elements	(A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C)	?	Y T	likely active or activable
229. Xenobiotic response elements (XREs)	GCGTG	bHLH	Y T	likely active or activable
230. Yap recognition sequences	TTACTAA	?	Y T	likely active or activable
231. YY1 binding sites	CCATCTT	Cys ₂His ₂	Y T	likely active or activable
232. Z boxes NSoSp form	A(C/T)A(C/G)G(G/T)(A/G/T)T	?	Y T	likely active or activable, negative direction distals within randoms
233. Z boxes ZboxG	A(C/T)A(C/G)GT(A/G)T	?	Y T	likely active or activable
234. Z boxes ZboxSp	CAGGT(A/G)	?	Y T	likely active or activable

Totals

Of 342 response elements, there are 108 Ns for not present (absent) in either A1BG promoter and 232 Ys for (present) or transcription factors that occur in the promoters on either side A1BG. There are four apparent random elements (CATTs, HMG boxes, IRF3s and TECs), and 228 likely active or activable (98.28 %). 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

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↑ ^25.0 ^25.1 ^25.2 ^25.3 ^25.4 ^25.5 ^25.6 ^25.7 ^25.8 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.
↑ ^26.0 ^26.1 ^26.2 ^26.3 Pierre‐Louis Blaiseau and Dominique Thomas (2 November 1998). "Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA". The EMBO Journal. 17: 6327–6336. doi:10.1093/emboj/17.21.6327. Retrieved 4 February 2021.
↑ ^27.0 ^27.1 ^27.2 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.
↑ ^28.0 ^28.1 XIAN-YANG ZHANG, NABILA JABRANE-FERRAT, CLEMENT K. ASIEDU, SANJA SAMAC, B. MATIJA PETERLIN, AND MELANIE EHRLICH (November 1993). "The Major Histocompatibility Complex Class II Promoter-Binding Protein RFX (NF-X) Is a Methylated DNA-Binding Protein" (PDF). MOLECULAR AND CELLULAR BIOLOGY. 13 (11): 6810–8. Retrieved 2017-04-05.
↑ ^29.0 ^29.1 Eduardo Moreno, Maša Lenuzzi, Christian Rödelsperger, Neel Prabh, Hanh Witte, Waltraud Roeseler, Metta Riebesell, Ralf J. Sommer (November 2018). "DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in Pristionchus pacificus". Evolution & Development. 20 (6): 233–243. doi:10.1111/ede.12271. Retrieved 9 March 2021.
↑ ^30.0 ^30.1 ^30.2 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.
↑ ^32.0 ^32.1 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.
↑ ^36.0 ^36.1 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.
↑ ^39.0 ^39.1 Philipp Mracek; Cristina Santoriello; M. Laura Idda; Cristina Pagano; Zohar Ben-Moshe; Yoav Gothilf; Daniela Vallone; Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.

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.

[Johnson-8] 8.0 ^8.1 ^8.2 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.

[Sharma-9] 9.0 ^9.1 ^9.2 ^9.3 ^9.4 ^9.5 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.

[Smith-10] 10.0 ^10.1 Joshua J. Smith, Eric S. Cole, Daniel P. Romero (15 July 2004). "Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila". Nucleic Acids Research. 32 (14): 4313–4321. doi:10.1093/nar/gkh771. PMID 15304567. Retrieved 4 September 2020.

[Sumrada-11] 11.0 ^11.1 Roberta A. Sumrada and Terrance G. Cooper (June 1987). "Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast" (PDF). Proceedings of the National Academy of Sciences USA. 84: 3997–4001. doi:10.1073/pnas.84.12.3997. PMID 3295874. Retrieved 6 September 2020.

[Hirose-12] 12.0 ^12.1 Fumiko Hirose; Masamitsu Yamaguchi; Akio Matsukage (September 1999). "Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc". Molecular and Cellular Biology. 19 (9): 6020–6028. doi:10.1128/MCB.19.9.6020. PMID 10454549. Retrieved 4 September 2020.

[Rose-13] 13.0 ^13.1 Annkatrin Rose, Iris Meier and Udo Wienand (28 October 1999). "The tomato I-box binding factor LeMYBI is a member of a novel class of Myb-like proteins". The Plant Journal. 20 (6): 641–652. doi:10.1046/j.1365-313X.1999.00638.x. Retrieved 8 November 2018.

[Yoshihara-14] 14.0 ^14.1 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-15] 15.0 ^15.1 ^15.2 ^15.3 ^15.4 ^15.5 ^15.6 ^15.7 ^15.8 ^15.9 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.

[Fan-16] 16.0 ^16.1 ^16.2 ^16.3 Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology. 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018.

[Ozsarac-17] 17.0 ^17.1 Nesrin Ozsarac, Melissa J. Straffon, Hazel E. Dalton, and Ian W. Dawes (March 1997). "Regulation of Gene Expression during Meiosis in Saccharomyces cerevisiae: SPR3 Is Controlled by both ABFI and a New Sporulation Control Element". Molecular and Cellular Biology. 17 (3): 1152–9. doi:10.1128/MCB.17.3.1152. PMC 231840. PMID 9032242.

[Li2020-18] 18.0 ^18.1 Qingliang Li, Rezaul M. Karim, Mo Cheng, Mousumi Das, Lihong Chen, Chen Zhang, Harshani R. Lawrence, Gary W. Daughdrill, Ernst Schonbrunn, Haitao Ji and Jiandong Chen (July 2020). "Inhibition of p53 DNA binding by a small molecule protects mice from radiation toxicity". Oncogene. 39 (29): 5187–5200. doi:10.1038/s41388-020-1344-y. PMID 32555331 Check |pmid= value (help). Retrieved 29 August 2020.

[Michalska-19] 19.0 ^19.1 Agata Michalska, Katarzyna Blaszczyk, Joanna Wesoly and Hans A. R. Bluyssen (28 May 2018). "A Positive Feedback Amplifier Circuit That Regulates Interferon (IFN)-Stimulated Gene Expression and Controls Type I and Type II IFN Responses". Frontiers in Immunology. 9: 1135. doi:10.3389/fimmu.2018.01135. Retrieved 18 March 2021.

[Kozak1987-20] 20.0 ^20.1 Marilyn Kozak (October 1987). "An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Research. 15 (20): 8125–8148. doi:10.1093/nar/15.20.8125. PMID 3313277.

[Matsumoto-21] 21.0 ^21.1 Takuya Matsumoto; Saemi Kitajima; Chisato Yamamoto; Mitsuru Aoyagi; Yoshiharu Mitoma; Hiroyuki Harada; Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.

[Donald-22] 22.0 ^22.1 Robert G. K. Donald and Anthony R. Cashmore (1990). "Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS‐1A promoter". The EMBO Journal. 9 (6): 1717–1726. doi:10.1002/j.1460-2075.1990.tb08295.x. Retrieved 8 November 2018.

[Kyo-23] 23.0 ^23.1 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.

[Bertolotto-24] 24.0 ^24.1 Corine Bertolotto, Roser Buscà, Patricia Abbe, Karine Bille, Edith Aberdam, Jean-Paul Ortonne, and Robert Ballotti (February 1998). "Different cis-Acting Elements Are Involved in the Regulation of TRP1 and TRP2 Promoter Activities by Cyclic AMP: Pivotal Role of M Boxes (GTCATGTGCT) and of Microphthalmia". Molecular and Cellular Biology. 18 (2): 694–702. PMID 9447965. Retrieved 8 December 2018.

[Rossi-25] 25.0 ^25.1 ^25.2 ^25.3 ^25.4 ^25.5 ^25.6 ^25.7 ^25.8 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.

[Blaiseau-26] 26.0 ^26.1 ^26.2 ^26.3 Pierre‐Louis Blaiseau and Dominique Thomas (2 November 1998). "Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA". The EMBO Journal. 17: 6327–6336. doi:10.1093/emboj/17.21.6327. Retrieved 4 February 2021.

[Long-27] 27.0 ^27.1 ^27.2 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.

[Zhang-28] 28.0 ^28.1 XIAN-YANG ZHANG, NABILA JABRANE-FERRAT, CLEMENT K. ASIEDU, SANJA SAMAC, B. MATIJA PETERLIN, AND MELANIE EHRLICH (November 1993). "The Major Histocompatibility Complex Class II Promoter-Binding Protein RFX (NF-X) Is a Methylated DNA-Binding Protein" (PDF). MOLECULAR AND CELLULAR BIOLOGY. 13 (11): 6810–8. Retrieved 2017-04-05.

[Moreno-29] 29.0 ^29.1 Eduardo Moreno, Maša Lenuzzi, Christian Rödelsperger, Neel Prabh, Hanh Witte, Waltraud Roeseler, Metta Riebesell, Ralf J. Sommer (November 2018). "DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in Pristionchus pacificus". Evolution & Development. 20 (6): 233–243. doi:10.1111/ede.12271. Retrieved 9 March 2021.

[Watanabe-30] 30.0 ^30.1 ^30.2 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-31] 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.

[Maruyama-32] 32.0 ^32.1 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-33] 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-34] 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-35] 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.

[Song-36] 36.0 ^36.1 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-37] 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-38] 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.

[Mracek-39] 39.0 ^39.1 Philipp Mracek; Cristina Santoriello; M. Laura Idda; Cristina Pagano; Zohar Ben-Moshe; Yoav Gothilf; Daniela Vallone; Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.

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@@ Line 229: / Line 229: @@
 |103. Cytokinin response regulators, (ARRs), (Ferreira) || (G/A)GGAT(T/C) || Present || 200 || [[Cytokinin response regulator gene transcriptions|Cytokinin response regulators]] 03:25, 31 October 2022 || likely active or activable
 |-
-|74. [[Cytokinin response regulator gene transcriptions|Cytokinin response regulators]]
+|104. Cytokinin response regulators, (ARRs), (Rashotte1) || GATCTT || Present || 200 || [[Cytokinin response regulator gene transcriptions|Cytokinin response regulators]] 16:21, 31 October 2022‎ || likely active or activable
-(ARRs)
-(Rashotte1)
-|| GATCTT || WD40 repeat family || Y
-T
-|| likely active or activable
 |-
-|75. [[Cytokinin response regulator gene transcriptions|Cytokinin response regulators]]
+|105. Cytokinin response regulators, (ARRs), (Rashotte2) || (G/A)GAT(T/C) || Present || 200 || [[Cytokinin response regulator gene transcriptions|Cytokinin response regulators]] 20:24, 1 November 2022 || likely active or activable
-(ARRs)
-(Rashotte2)
-|| (G/A)GAT(T/C) || WD40 repeat family || Y
-T
-|| likely active or activable
 |-
-|76. [[Cytoplasmic polyadenylation element gene transcriptions|Cytoplasmic polyadenylation elements]]
+|106. Cytoplasmic polyadenylation elements, (CPEs) || TTTTTAT || [[Cytoplasmic polyadenylation element gene transcriptions|Cytoplasmic polyadenylation elements]] || likely active or activable
-(CPEs)
-|| TTTTTAT || ? || Y
-T
-|| likely active or activable
 |-
-|27. DAF-16-associated elements, (DAE), (Li) || TGATAAG || Absent || 40 || [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] 22:51, 3 December 2020 || unlikely
+|107. DAF-16-associated elements, (DAE), (Li) || TGATAAG || Absent || 200 || [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] 22:51, 3 December 2020 || unlikely
 |-
-|77. [[DAF-16 binding element gene transcriptions|DAF-16 binding elements]] || (A/G)(C/T)AAA(C/T)A || ? || Y
+|108. DAF-16 binding elements || (A/G)(C/T)AAA(C/T)A || Present || 200 || [[DAF-16 binding element gene transcriptions|DAF-16 binding elements]] 19:54, 2 November 2022 || likely active or activable
-T
-|| likely active or activable
 |-
-|28. [[D box gene transcriptions|D-boxes]]
+|109. D-boxes, (Mracek1) || GTTGTATAAC || Absent || 200 || [[D box gene transcriptions|D-boxes]] 02:46, 10 December 2020 || unlikely
-(Mracek1)
-|| GTTGTATAAC || ? || N || GTTGTATAAC.<ref name=Mracek/>
 |-
-|29. [[D box gene transcriptions|D-boxes]]
+|110. D-boxes, (Mracek2) || CTTATGTAAA || Absent || 200 || [[D box gene transcriptions|D-boxes]] 02:20, 12 December 2020 || unlikely
-(Mracek)
-|| CTTATGTAAA (Mracek2) || ? || N || CTTATGTAAA.<ref name=Mracek/>
 |-
 |30. [[D box gene transcriptions|D-boxes]]

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Resources	5' cap Acid-base homeostasis Actins Adenines Allergies Alpha-1-B glycoprotein Ammonoids Original research/Amino acids Amphiphiles Anabolism Animal physiology Anomeric carbons Autocatalytic reactions Autonomously replicating sequences Base pairs Biology Biodegradation Biosynthesis Biosynthesis of a human protein Biosynthesis of amino acids Blood Bodily fluids Botany Brain box Calcium signaling Capping enzymes Carbohydrates Carcinoembryonic antigen gene family Catabolism Catalysis Cells Cell signaling Centrosomes Chromatins Chromoboxes Coactivators Corepressors Cofactors Consensus sequences Cytogenetics Cytokinesis Cytosines Deoxyribonucleic acids Digestion Disaccharides Dispersed promoters Dominant group metagenomes Downregulations Endochondral ossification Enzyme inhibitors Enzymology Epigenetics Epigenomes Esters Esterification Eukaryotes Eukaryotic initiation factors Evolution Exaptation Excision repair cross-complementing Factors Fatty acids Ferredoxin Foldings Foods Forkhead boxes Functional groups Genome surveillance complexes Genealogy Genes Genetics Gene transcriptions Genomes Genomics Glycoproteins Glycosides Glycosidic bond Guanines Hair color gene expressions Helicases Heredity History of agriculture Greek and Roman histories of biology Homeostasis Human amino acid synthesis Human DNAs Human genes Human RNA Human teeth Human temperatures Immunoglobulin domain cl11960 Immunoglobulin domain genes Immunoglobulin like domain cd05751 Immunoglobulin like domain pfam13895 Immunoglobulin like domain smart00410 Immunoglobulin receptor superfamily genes Immunoglobulin supergene family Inhibitory peptides Insulators Intranuclear localizations Introduction to Cell Biology Introduction to polymer chemistry Lamarckism Leucine zipper Localization Major histocompatibility complex class I gene family Major histocompatibility complex class II gene family Major histocompatibility complex class III gene family Mammalogy Mathematical molecular biology Mediator complexes Medicine Melanocytes Membranes Metagenomes Molecular biology Molecular genetics Nitrogen metabolism Nucleotide Synthesis Origin of life Orthomolecular medicine Osteoarthritis Paleanthropology Paleontology Phosphate biochemistry Phosphate budgets Phosphate reactions Post translational modifications Principles of biosynthesis Protein isoform Proteins Proteomics Regulations Ribonucleotides Ribosomes RNA polymerases RNA polymerase II holoenzymes RNA polymerase II holoenzyme complexes RNA translations Salinity Stroke management Teeth TFIIA Transports Vascular endothelial growth factor A What is a human? Upregulations Upstream and downstream ZSCAN22 Zoology
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 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 Bridge gene transcriptions CAAT box gene transcriptions 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 Factor II B recognition element gene transcriptions 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 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 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 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 gene transcriptions 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 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