A1BG response element gene transcriptions: Difference between revisions
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! Name of elements, Abbreviations, Authors !! Consensus sequences, Variations !! Testing !! Order !! Resource !! Random or likely | ! Name of elements, Abbreviations, Authors !! Consensus sequences, Variations !! Testing !! Order !! Resource !! Random or likely | ||
|- | |- | ||
|1. ABA-response element-like, (ABRE-like) || ACGTGTCC || Absent || | |1. ABA-response element-like, (ABRE-like) || ACGTGTCC || Absent || 13 || [[ABA-response element gene transcriptions|ABA-response elements]] 13:07, 8 October 2020 || Unlikely | ||
|- | |- | ||
|2. ABA-response elements, novel, (ABREN, novel ABRE) | |2. ABA-response elements, novel, (ABREN, novel ABRE) | ||
|| GATCGATC, CGATCGAT, GATCGAT || Absent || | || GATCGATC, CGATCGAT, GATCGAT || Absent || 14 || [[ABA-response element gene transcriptions|ABA-response elements]] 13:07, 8 October 2020 || Unlikely | ||
|- | |- | ||
|3. ABA responsive elements (ABREs) || ACGTG(G/T)C || Present || | |3. ABA responsive elements (ABREs) || ACGTG(G/T)C || Present || 15 || [[ABA-response element gene transcriptions|ABA-response elements]] 05:53, 9 October 2020 || likely active or activable | ||
|- | |- | ||
|4. Abf1 regulatory factors || CGTCCTCTACGAT || Absent || | |4. Abf1 regulatory factors || CGTCCTCTACGAT || Absent || 17 || [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] 18:32, 10 October 2020 || Unlikely | ||
|- | |- | ||
|5. Activated B-cell Factor-1s (ABFs, Abfms) || CGTNNNNN(A/G)(C/T)GA(C/T) || Present || | |5. Activated B-cell Factor-1s (ABFs, Abfms) || CGTNNNNN(A/G)(C/T)GA(C/T) || Present || 16 || [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] 17:47, 10 October 2020 || likely active or activable | ||
|- | |- | ||
|6. A-boxes || TACGTA || Present || | |6. A-boxes || TACGTA || Present || 11 || [[A box gene transcriptions|A-boxes]] 21:24, 7 October 2020 || likely active or activable | ||
|- | |- | ||
|7. AGC boxes || AGCCGCC (Leubner-Metzger 1998) || Present || 9 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Boxes/AGCs AGC boxes] 14:40, 2 May 2014 || likely active or activable | |7. AGC boxes || AGCCGCC (Leubner-Metzger 1998) || Present || 9 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Boxes/AGCs AGC boxes] 14:40, 2 May 2014 || likely active or activable | ||
|- | |- | ||
| | |8. Downstream promoter elements (DPE) || RGWCGTG (Burke 1996), RGWYV(T) (Kadonaga 2002) || Present || 5 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Elements/Initiators Initiator elements] 21:32, 20 May 2012 || likely active or activable | ||
|- | |- | ||
| | |9. Downstream TFIIB recognition elements (BRE<sup>d</sup>, dBRE) (Deng 2005) || (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) || Present || 7 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Elements/Downstream_TFIIB_recognitions Downstream TFIIB recognition elements] 21:32, 11 February 2013 || likely active or activable | ||
|- | |- | ||
| | |10. Enhancer boxes (E-box) || CANNTG (Massari 2000) || Present || 8 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Boxes/Enhancers Enhancer boxes] 22:01, 17 April 2013 || likely active or activable | ||
|- | |- | ||
| | |11. Hypoxia-inducible factors (HIF) (Orlando 2019), ABA-response element (ABRE) (Asad 2019)) || ACGTG || Present || 12 || [[Hypoxia-inducible factor gene transcriptions|Hypoxia-inducible factors]] 06:03, 7 May 2021, [[ABA-response element gene transcriptions|ABA-response element (ABRE)]] 03:06, 8 October 2020 || likely active of activable? | ||
|- | |- | ||
| | |12. Initiator element (Inr) (Liston 1999) || YYA<sub>+1</sub>NWYY || Present || 4 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Elements/Initiators Initiator elements] 17:02, 17 April 2012 || likely active or activable | ||
|- | |- | ||
| | |13. Motif ten elements (MTE) (Lim 2004) || CSARCSSAACGS || Absent || 6 || [https://en.wikiversity.org/wiki/Gene_transcriptions/Elements/Motif_tens Motif ten elements] 15:28, 10 February 2013 || Unlikely | ||
|- | |- | ||
| | |14. TATA boxes || TATAAAA (Carninci 2006) || Present || 1 || [[Wikipedia:TATA box]] 02:36, 10 January 2011 || likely active or activable? | ||
|- | |- | ||
| | |15. TATA boxes (RGWYV(T)) (Burke 1996) || TATA(A/T)A(A/T) (Watson 2014) || Present || 2 || [[TFIIA]] 21:53, 28 April 2012 || likely active or activable? | ||
|- | |- | ||
| | |16. TATA boxes (RGWYV(T)) (Burke 1996) || TATA(A/T)A(A/T)(A/G) (Basehoar 2004) || Present || 3 || [[TFIIA]] 21:53, 28 April 2012 || likely active or activable | ||
|- | |- | ||
| | |17. Vitamin D response elements (VDRE) (Kakhki 2018) || (A/G)G(G/T)TCA || Present || 10 || [[Fibroblast growth factor 23]] 01:21, 10 September 2020 || likely active or activable | ||
|} | |} | ||
Revision as of 05:37, 1 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
Name of elements, Abbreviations, Authors | Consensus sequences, Variations | Testing | Order | Resource | Random or likely |
---|---|---|---|---|---|
1. ABA-response element-like, (ABRE-like) | ACGTGTCC | Absent | 13 | ABA-response elements 13:07, 8 October 2020 | Unlikely |
2. ABA-response elements, novel, (ABREN, novel ABRE) | GATCGATC, CGATCGAT, GATCGAT | Absent | 14 | ABA-response elements 13:07, 8 October 2020 | Unlikely |
3. ABA responsive elements (ABREs) | ACGTG(G/T)C | Present | 15 | ABA-response elements 05:53, 9 October 2020 | likely active or activable |
4. Abf1 regulatory factors | CGTCCTCTACGAT | Absent | 17 | Abf1 regulatory factors 18:32, 10 October 2020 | Unlikely |
5. Activated B-cell Factor-1s (ABFs, Abfms) | CGTNNNNN(A/G)(C/T)GA(C/T) | Present | 16 | Abf1 regulatory factors 17:47, 10 October 2020 | likely active or activable |
6. A-boxes | TACGTA | Present | 11 | A-boxes 21:24, 7 October 2020 | likely active or activable |
7. AGC boxes | AGCCGCC (Leubner-Metzger 1998) | Present | 9 | AGC boxes 14:40, 2 May 2014 | likely active or activable |
8. Downstream promoter elements (DPE) | RGWCGTG (Burke 1996), RGWYV(T) (Kadonaga 2002) | Present | 5 | Initiator elements 21:32, 20 May 2012 | likely active or activable |
9. Downstream TFIIB recognition elements (BREd, dBRE) (Deng 2005) | (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) | Present | 7 | Downstream TFIIB recognition elements 21:32, 11 February 2013 | likely active or activable |
10. Enhancer boxes (E-box) | CANNTG (Massari 2000) | Present | 8 | Enhancer boxes 22:01, 17 April 2013 | likely active or activable |
11. Hypoxia-inducible factors (HIF) (Orlando 2019), ABA-response element (ABRE) (Asad 2019)) | ACGTG | Present | 12 | Hypoxia-inducible factors 06:03, 7 May 2021, ABA-response element (ABRE) 03:06, 8 October 2020 | likely active of activable? |
12. Initiator element (Inr) (Liston 1999) | YYA+1NWYY | Present | 4 | Initiator elements 17:02, 17 April 2012 | likely active or activable |
13. Motif ten elements (MTE) (Lim 2004) | CSARCSSAACGS | Absent | 6 | Motif ten elements 15:28, 10 February 2013 | Unlikely |
14. TATA boxes | TATAAAA (Carninci 2006) | Present | 1 | Wikipedia:TATA box 02:36, 10 January 2011 | likely active or activable? |
15. TATA boxes (RGWYV(T)) (Burke 1996) | TATA(A/T)A(A/T) (Watson 2014) | Present | 2 | TFIIA 21:53, 28 April 2012 | likely active or activable? |
16. TATA boxes (RGWYV(T)) (Burke 1996) | TATA(A/T)A(A/T)(A/G) (Basehoar 2004) | Present | 3 | TFIIA 21:53, 28 April 2012 | likely active or activable |
17. Vitamin D response elements (VDRE) (Kakhki 2018) | (A/G)G(G/T)TCA | Present | 10 | Fibroblast growth factor 23 01:21, 10 September 2020 | likely active or activable |
Response element testing (Absent)
Name of elements | Consensus sequences | Response element class | Testing | Activity |
---|---|---|---|---|
Abbreviations | Variations | Absent (N) | Notes | |
Authors | ||||
1. novel ABA-response elements
(ABREN, novel ABRE) |
GATCGATC, CGATCGAT, GATCGAT | WD40 repeat family | N | ABREN, CGATCGAT motif, and core of ABREN and CGATCGAT motif.[2] |
2. ABA-response element-like
(ABRE-like) |
ACGTGTCC | WD40 repeat family | N | third highest scoring motif.[2] |
3. Abf1 regulatory factors | CGTCCTCTACGAT | General Regulatory Factors | N | CGTNNNNNACGAT.[3] |
4. Activating proteins
(Murata) |
GCCCACGGG | bHSH | N | Activating protein 2.[4] |
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.[5] |
7. Amino acid response elements
(AARE) (Maruyama) |
ATTGCATCA | ? | N | AARE1 (ATTGCATCA)[6] |
8. Amino acid response elements
(AARE) (Broer) |
TTTGCATCA | ? | N | TTTGCATCA.[7][8] |
9. Amino acid response element-like
(AARE-like) |
TGGTGAAAG | ? | N | AARE-like sequence (TGGTGAAAG, named AARE3).[6] |
10. Androgen response elements
(AREs) (Kouhpayeh) |
GGTACANNNTGTTCT | Zinc finger DNA-binding domain | N | GGTACACGGTGTTCT.[9] |
11. Androgen response elements
(AREs) (Wilson) |
TGATTCGTGAG | Zinc finger DNA-binding domain | N | AGAACANNNTGTTCT.[10] |
12. Antioxidant-electrophile responsive elements
(Otsuki) |
GTGAGGTCGC | bHLH | N | GTGAGGTCGC.[11] or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A[12], 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.[13] |
15. Carbohydrate response elements
(ChREs) |
CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG | ? | N | ChoRE1, ChoRE2.[14] |
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.[15] |
19. C/A hybrid boxes | TGACGTAT | bZIP | N | TGACGTAT.[16] A at the 12 position |
20. C/T hybrid boxes | TGACGTTA | bZIP | N | TGACGTTA.[16] 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).[17] |
22. C/EBP boxes | TTAGGACAT,[18] or TAGCATT.[19] | 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[5] | ? | N | tomato genome-wide analysis |
25. CENP-B boxes | TTTCGTTGGAAGCGGGA | ? | N | specifically localized at the centromere |
26. Coupling elements
(CE1) |
TGCCACCGG[2] | ? | N | CE1 (Watanabe) |
27. DAF-16-associated elements
(DAE) |
TGATAAG | ? | N | DAF-16-associated element (DAE).[20] |
28. D-boxes
(Mracek1) |
GTTGTATAAC | ? | N | GTTGTATAAC.[21] |
29. D-boxes
(Mracek) |
CTTATGTAAA (Mracek2) | ? | N | CTTATGTAAA.[21] |
30. D-boxes
(Johnson) |
TCTCACA | ? | N | TCTCACATT(A/C)AATAAGTCA is a D-box.[15] |
31. Defense and stress-responsive elements | ATTTTCTTCA | ? | N | ATTTTCTTCA.[5] |
32. DNA damage response elements
(DREs) (Smith) |
TTTCAAT[22] | ? | N | in the upstream repression sequence (URS) |
33. DNA damage response elements
(DREs) (Sumrada) |
TAGCCGCCG of TAGCCGCCGRRRR.[23] | ? | N | in the upstream repression sequence (URS) |
34. DNA replication-related elements
(DREs) |
TATCGATA | ? | N | DNA replication-related element (DRE).[24] |
35. DREB boxes | TACCGACAT | ? | N | CRT/DREB box |
36. EIF4E basal elements | TTACCCCCCCTT | ? | N | poly(C) motif |
37. Endoplasmic reticulum stress response elements
(ERSE) |
CCAAT-N9-CCACG | bZIP | N | compare CCAAT-box and ERSE below in the (present) |
38. Estrogen response elements
(EREs) |
AGGTTA or GGTCAGGAT | Cys 4 |
N | AGGTTATTGCCTCCT or GGTCAGGATGAC |
39. F boxes | TGATAAG[25] | ? | N | F-box overlaps the I-box |
40. Forkhead boxes | GTAAACAA[26] | HTH, Forkhead | N | GTAAACAA FOXO1 |
41. Gal4ps | CGGACCGC | ? | N | CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG[27] |
42. γ-interferon activated sequences
(GAS) |
TTCCTAGAA | ? | N | ALS-GAS1 between nt −633 and nt −625 |
43. G boxes | (G/T)CCACGTG(G/T)C | ? | N | no "perfect palindrome" G boxes in either promoter |
44. GCN4 motifs | TGACTCA, TGAGTCA | bZIP | N | ACGT motif |
45. Gcn4ps | ATGACTCTT[27] | bZIP | N | GCN4 motifs |
46. Gibberellin responsive element-like 2
(GARE-like 2) (Fan) |
TAACGTA[28] | ? | N | "in the promoters of hydrolase genes".[28] |
47. GLM boxes | (G/A)TGA(G/C)TCA(T/C) | ? | N | GCN4-like motif |
48. Grainy head transcription factor binding sites | AACCGGTT | β-Scaffold factors with minor groove contacts | N | also GACTGGTT |
49. GT boxes
(Motojima) |
TGGGTGGGGCT | ? | N | (-78 to -69) |
50. Hapless motifs | CCAATCA | ? | N | heterotrimeric transcription factor, HAP2/3/4.[29] |
51. Heat-responsive elements | AAAAAATTTC | Helix-turn-helix (HTH), Heat shock factors (HSFs) | N | four nGAAn motifs |
52. Heat shock elements
(HSE1) (Eastmond) |
nGAAnnTTCnnGAAn | HTH, HSFs | N | HSE1 |
53. Heat shock elements
(HSE2) (Eastmond) |
nTTCnnGAAnnTTCn | HTH, HSFs | N | HSE2 is the inverse complement of HSE1 |
54. Heat shock elements
(HSE5) (Eastmond) |
nTTCn-(5-bp)-nTTCnnGAAn | HTH, HSFs | N | HSE5 |
55. Heat shock elements
(HSE6) (Eastmond) |
nTTCn-nnGAAn-(5-bp)-nGAAn | HTH, HSFs | N | HSE6 |
56. Heat shock elements
(HSE7) (Eastmond) |
nGA(A/G)nnTTCnnGAAn | HTH, HSFs | N | HSE7 PFT1 |
57. Heat shock elements
(HSE) (Eastmond) |
nGAAnnTTCnnGA(A/G)n | HTH, HSFs | N | HSE7 PFT2 |
58. Heat shock elements
(HSE10) (Eastmond) |
nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn | HTH, HSFs | N | HSE10 |
59. Hypoxia-inducible factors
(HIF-1) |
GCCCTACGTGCTGTCTCA[30] | bHLH | N | composed of HIF-1α and HIF-1β |
60. I boxes | GATAAG | ? | N | GGATGAGATAAGA |
61. Inositol/choline-responsive elements
(ICRE) (Case) |
CANNTGAAAT | ? | N | version of Lopes, see below |
62. Inositol/choline-responsive elements
(ICRE) (Lopes) |
ATGTGAAAT | ? | N | using ANNTGAAAT |
63. Interferon-stimulated response elements
(ISREs) |
AGTTTCN2TTTCN | ? | N | consensus sequence AGTTTCN2TTTCN.[31] |
64. Kozak sequences | GCCGCC(A/G)CCATGG | ? | N | GCCGCC(A/G)CCATGG[32] |
65. Kozak sequences
(Matsumoto) |
GAAAATGG | ? | N | GAAAATGG[33] |
66. L boxes | AAATTAACCAA | ? | N | AAATTAACCAA[34] |
67. Maf recognition element
(MAREs) |
TGCTGA(G/C)TCAGCA | ? | N | and TGCTGA(GC/CG)TCAGCA[35] |
68. Met3s | TCACGTG | bZIP | N | TCACGTG[36] |
68. M boxes | GTCATGTGCT | ? | N | or AGTCATGTGCT[37] |
69. Mcm1 regulatory factors | TT(A/T)CCNN(A/T)TNGG(A/T)AA | ? | N | Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[3] |
70. Mcm1 regulatory factors
|
TTNCCNNNTNNGGNAA | ? | N | Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[3] |
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"[3] |
82. Extended Reb1 | ATTACCCGAA | ? | N | "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."[3] |
83. Rlm1ps | CTATATATAG | ? | N | CTA(T/A)4TAG |
84. Rox1ps | RRRTAACAAGAG | ? | N | Heme-dependent repressor of hypoxic genes.[27] |
85. Rpn4ps | GGTGGCAAA | ? | N | proteasome genes |
86. Seed-specific elements | CATGCATG | ? | N | SRE consensus: CAGCAGATTGCG is none |
87. Shoot specific elements | GATAATGATG | ? | N | SRE consensus: CAGCAGATTGCG is none |
88. Sip4ps | CC(C/G)T(C/T)C(C/G)TCCG | ? | N | CC(C/G)T(C/T)C(C/G)TCCG[27] |
89. Smp1ps | ACTACTA(A/T)(A/T)(A/T)(A/T)TAG | ? | N | ACTACTA(T/A)4TAG[27] |
90. SP1
(Long) |
GGGGCGGGCC | ? | N | GGGGCGGGCC[14] |
91. Sterol response elements
(Branco) |
TCGTATA | ? | N | perhaps plant specific |
92. Sterol response elements
(Yao) |
AGCAGATTGCG | ? | N | liver specific |
93. TATCCAC boxes | TATCCAC | ? | N | GA responsive complex component |
94. TCCACCATA elements | TCCACCATA | ? | N | adjacent co-dependent regulatory element of POLLEN1 |
95. Tetradecanoylphorbol-13-acetate response elements
(TREs) |
TGA(G/C)TCA | ? | N | cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 |
96. TGF-β control elements
(TCEs) |
GAGTGGGGCG | ? | N | in mouse and rat, GCGTGGGGGA in humans |
97. TGF-β inhibitory elements
(TIEs) |
GAGTGGTGA | ? | N | in the rat transin/stromelysin promoter |
98. Vhr1ps
(VHR1) |
AATCA-N8-TGA(C/T)T | ? | N | Response to low biotin concentrations |
99. Vitamin D response elements
(VDREs) |
A/GGG/TTCAnnnA/GGG/TTCA | ? | N | (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA |
100. X boxes | GTTGGCATGGCAAC[38] | ? | N | X2 box is AGGTCCA not ⌘F |
101. X-boxes | GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC[39] | ? | N | includes GTTNCCATGGNAAC |
102. Xbp1ps | GcCTCGA(G/A)G(C/A)g(a/g) | ? | N | Transcriptional repressor |
103. Xenobiotic response elements
(XREs) |
(T/G)NGCGTG(A/C)(G/C)A | ? | N | contains the core sequence GCGTG, see AHRE above |
104. Y boxes | (A/G)CTAACC(A/G)(A/G)(C/T) | ? | N | inverted CAAT box |
105. Zap1ps | ACCCTCA | ? | N | ACC(C/T)(C/T)(A/C/G/T)AAGGT |
106. Z-box (ZboxN) samplings
(ZboxNs) |
ATACGGT | ? | N | No ZboxN occur on either side of A1BG |
107. Z-box (ZboxSo) samplings
(ZboxNs) |
ATACGTGT | ? | N | No ZboxSo occur on either side of A1BG |
108. Zinc responsive elements
(ZREs) |
MHHAACCBYNMRGGT | ? | N | (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT |
Response element testing (Present)
Name of elements | Consensus sequences | Response element class | Testing | Activity/Notes |
---|---|---|---|---|
Abbreviations | Variations | Present (Y) | Random or likely active or activable | |
Authors | Table (T) | |||
1. ABA responsive elements
(ABREs) |
ACGTG(G/T)C | WD40 repeat family | Y
T |
likely active or activable |
2. Activated B-cell Factor-1s
(ABFs, Abfms) |
CGTNNNNN(A/G)(C/T)GA(C/T) | General Regulatory Factors | Y
T |
likely active or activable |
3. A-boxes | TACGTA | Basic leucine zipper (bZIP) | Y
T |
likely active or activable |
4. boxes A | TGACTCT | bZIP | Y
T |
likely active or activable |
5. Abscisic acid-responsive elements (Pho4s), G boxes | CACGTG | bZIP, bHLH | Y
T |
likely active or activable |
6. ACGT-containing elements | ACGT | bZIP | Y
T |
cores and proximals are likely active or activable, but a few of the UTRs and distal promoters may be random |
7. Activating protein 2 alpha
(AP2a) |
GCCNNNGGC | bHSH | Y
T |
likely active or activable, positive strand, positive direction AP2a within randoms |
8. Activating protein 2
(AP2) (Cohen) |
GCCTGGCC | bHSH | Y
T |
likely active or activable |
9. Activating protein 2
(Cohen) |
TCCCCCGCCC | bHSH | Y
T |
likely active or activable |
10. Activating protein 2
(Murata) |
(C/G)CCN(3)GG(C/G) | bHSH | Y
T |
likely active or activable |
11. Activating protein 2
(Murata) |
(C/G)CCN(4)GG(C/G) | bHSH | Y
T |
likely active or activable |
12. Activating protein 2
(Yao) |
TCTTCCC | bHSH | Y
T |
likely active or activable |
13. Activating protein 2
(Yao) |
CTCCCA | bHSH | Y
T |
likely active or activable |
14. Activating proteins
(AP-2) (Yao) |
GGCCAA | bHSH | Y
T |
likely active or activable |
15. Activating transcription factors
(Burton) |
(A/C/G)TT(A/G/T)C(A/G)TCA | bZIP | Y
T |
likely active or activable |
16. Activating transcription factors
(Kilberg) |
(A/G/T)TT(A/G/T)CATCA | bZIP | Y
T |
likely active or activable |
17. Adenylate–uridylate rich elements
(AUREs) (Bakheet) |
(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) | stem-loop | Y
T |
likely active or activable |
18. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class I) |
ATTTA | stem-loop | Y
T |
likely active or activable, UTRs at the lower end of the randoms |
19. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class II) |
TTATTTA(A/T)(A/T) | stem-loop | Y
T |
likely active or activable |
20. Adenylate–uridylate rich elements
(AREs) (Chen and Shyu, Class III) |
ATTT | stem-loop | Y
T |
likely active or activable, low negative direction proximals overlap randoms |
21. Adr1ps | TTGG(A/G)G | Cys 2His 2 zinc finger binding domain |
Y
T |
likely active or activable |
22. Aft1s | (C/T)(A/G)CACCC(A/G) | bZIP? | Y
T |
likely active or activable |
23. AGC boxes | AGCCGCC | AP-2/EREBP-related factors | Y
T |
likely active or activable |
24. Angiotensinogen core promoter elements | (A/C)T(C/T)GTG | bZIP? | Y
T |
likely active or activable, positive direction distal low occurrences overlap randoms |
25. AhR responsive element or Aryl hydrocarbon responsive element II
(AHRE-II) |
CATGN6C(A/T)TG | bHLH | Y
T |
likely active or activable |
26. AhR DNA-binding consensus sequence
(AhRY) (Yao) |
GCGTGNN(A/T)NNN(C/G) | bHLH | Y
T |
likely active or activable for ZNF497 |
27. Androgen response element1s
(Kouhpayeh) |
GGTACA of GGTACAnnnTGTTCT | Zinc finger DNA-binding domain | Y
T |
likely active or activable |
28. Androgen response element2s
(Kouhpayeh) |
TGTTCT of GGTACAnnnTGTTCT | Zinc finger DNA-binding domain | Y
T |
likely active or activable |
29. 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 |
30. Antioxidant-electrophile responsive elements
(Lacher) |
GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A | bHLH | Y
T |
likely active or activable |
31. ATA boxes | AATAAA | β-Scaffold factor? | Y
T |
likely active or activable |
32. ATTTA elements
(Siegel) |
(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T)(A/T) | β-Scaffold factor? | Y
T |
likely active or activable |
33. Auxin response factors
(Stigliani) |
(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T) | WD40 repeat family | Y
T |
likely active or activable, positive direction proximals overlap high randoms, positive direction cores within randoms |
34. Auxin response factors
(Ulmasov) |
TGTCTC | WD40 repeat family | Y
T |
likely active or activable |
35. Auxin response factors
(Boer) |
TGTCGG | WD40 repeat family | Y
T |
likely active or activable |
36. Auxin response factors
(ARF5) |
(C/G/T)N(G/T)GTC(G/T) | WD40 repeat family | Y
T |
likely active or activable, negative direction proximals ≥ randoms |
37. B-boxes
(Johnson) |
TGGGCA | Zinc finger DNA-binding domains | Y
T |
likely active or activable, positive direction distals ≥ randoms |
38. boxes B
(Sanchez) |
TGTCTCA | Zinc finger DNA-binding domains | Y
T |
likely active or activable |
39. B recognition elements
(BREu) |
(G/C)(G/C)(G/A)CGCC | HTH | Y
T |
likely active or activable |
40. 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. 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[5] | 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 | TTCTCT | ? | Y
T |
likely active or activable, where real Inr-like negative direction distals are within the range of the randoms |
138. 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 |
139. Inositol/choline-responsive elements
(ICREs) (Schwank) |
TYTTCACATGY contains the core sequence CANNTG | bHLH | Y
T |
likely active or activable |
140. Interferon regulatory factor
(IRF3) |
GCTTTCC | HTH | Y
T |
random |
141. IFN-stimulated response elements
(ISREs) (Lu) |
GAAANNGAAA | HTH | Y
T |
likely active or activable |
142. IRS consensus
(Fujii) |
AANNGAAA | HTH | Y
T |
likely active or activable |
143. 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 |
144. Jasmonic acid-responsive elements
(JAREs) |
TGACG | ? | Y
T |
likely active or activable |
145. Krüppel-like factors | GGGNN(G/T)(G/T)(G/T) | ? | Y
T |
likely active or activable |
146. Leu3 transcription factors | (C/G)C(G/T)NNNN(A/C)G(C/G) | Zn(II)2Cys6 | Y
T |
likely active or activable |
147. -35 sequence | TTGACA | ? | Y
T |
likely active or activable, the UTR does overlap the randoms at the random's upper end |
148. Met31ps | AAACTGTG[36] | bZIP | Y
T |
likely active or activable |
149. Metal responsive elements
(MRE) |
TGC(A/G)C(A/C/G/T)C | ? | Y
T |
likely active or activable |
150. Middle sporulation element
(MSE) (Branco) |
ACACAAA | ? | Y
T |
likely active or activable |
151. Midsporulation element
(MSE) (Ozsarac) |
C(A/G)CAAA(A/T) | ? | Y
T |
likely active or activable |
152. Multicopy inhibitor of the GAL1 promoter
(MIG1) |
(C/G)(C/T)GGGG | bZIP | Y
T |
likely active or activable, UTRs may be random |
153. MITF E-box (CAYRTG)
(MITF) |
CA(C/T)(A/G)TG | ? | Y
T |
likely active or activable, negative distals overlap randoms at low end |
154. Musashi binding elements
(MBE1s) |
(G/A)U1AGU | ? | Y
T |
likely active or activable |
155. Musashi binding elements
(MBE2s) |
(G/A)U2AGU | ? | Y
T |
likely active or activable, negative direction distals may be random |
156. Musashi binding elements
(MBE3s) |
(G/A)U3AGU | ? | Y
T |
likely active or activable |
157. 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 |
158. Myeloblastosis recognition element
(MRE) |
A(A/C)C(A/T)A(A/C)C | ? | Y
T |
likely active or activable |
159. 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 |
160. Nanos/Pumilio response elements
(PREs) |
TGTAAAT | ? | Y
T |
likely active or activable |
161. N-boxes
(Lee) |
CCGGAA | bHLH | Y
T |
likely active or activable |
162. N-boxes
(Bai) |
CACGAG | bHLH | Y
T |
likely active or activable |
163. N-boxes
(Gao) |
CACGGC or CACGAC, CACG(A/G)C | bHLH | Y
T |
likely active or activable |
164. N-boxes
(Leal) |
CACNAG | bHLH | Y
T |
likely active or activable |
165. Non-DiTyrosine 80 transcription factor DNA binding domain
(Ndt80) |
(A/G/T)NC(A/G)CAAA(A/T) | ? | Y
T |
likely active or activable |
166. 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 |
167. NF𝜿B (Sato)
(NF𝜿BSs) |
GAATTC | ? | Y
T |
likely active or activable |
168. Nutrient-sensing response element 1
(NSRE) |
GTTTCATCA | ? | Y
T |
likely active or activable |
169. Oaf1 transcription factor | CGGN3TNAN9-12CCG | ? | Y
T |
likely active or activable |
170. ORESARA1
(ORE1) (Matallana) |
(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) | ? | Y
T |
likely active or activable |
171. ORESARA1
(ORE1) (Olsen) |
T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) | ? | Y
T |
likely active or activable |
172. 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 |
173. p53 response elements
(Long1) |
CAGGCCC | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
174. p53 response elements
(Long2) |
GGGCGTG | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
175. P-box (Mena) | (A/T)AAAG | ? | Y
T |
likely active or activable, the positive direction proximals overlap the randoms |
176. P-box
(Motojima) |
TGAGTTCA | ? | Y
T |
likely active or activable |
177. P-box
(Yu) |
GTAA(T/C) | ? | Y
T |
likely active or activable with some overlapping the randoms |
178. Peroxisome proliferator-activated receptor alpha | CGACCCC | ? | Y
T |
likely active or activable, positive direction distal overlaps upper end of randoms |
179. 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 |
180. Pollen1 elements | AGAAA | ? | Y
T |
likely active or activable |
181. Polycomb response elements
(PRE) |
GCCAT | ? | Y
T |
likely active or activable |
182. Pribnow boxes | TATAAT | ? | Y
T |
likely active or activable |
183. Prolamin boxes | TG(A/T)AAAG | ? | Y
T |
likely active or activable |
184. Q elements | AGGTCA | ? | Y
T |
likely active or activable |
185. Quinone reductase response element
(QRDRE) (Yao) |
TCCCCT of TCCCCTTGCGTG | ? | Y
T |
likely active or activable |
186. 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 |
187. Reb1 bound and exact occurrences | TTACCC(G/T) | WD40 repeat family | Y
T |
likely active or activable |
188. Retinoic acid response element | AG(A/G)TCA | ? | Y
T |
likely active or activable, positive direction distals appear random |
189. Glucose transporter gene repressor
(Rgt1) |
CGG(A/G)(A/T)N(A/T)(A/T) | ? | Y
T |
likely active or activable |
190. classic RORE motif
(RORE) |
A(A/T)NTAGGTCA | ? | Y
T |
likely active or activable |
191. variant RORE motif | C(T/A)(G/A)GGNCA | ? | Y
T |
likely active or activable |
192. R response elements
(RRE) |
CATCTG | ? | Y
T |
likely active or activable |
193. Serum response elements
(SRE) see CArG boxes |
ACAGGATGT | bHLH-ZIP | Y
T |
likely active or activable |
194. Servenius sequences | GGACCCT | ? | Y
T |
likely active or activable |
195. SP1
(Zhang) |
(G/T)GGGCGG(G/A)(G/A)(C/T) | ? | Y
T |
likely active or activable |
196. SP1-box 1
(Motojima) |
GGGGCT | ? | Y
T |
likely active or activable |
197. SP1-box 2
(Motojima) |
CTGCCC | ? | Y
T |
likely active or activable |
198. SP-1
(Sato) |
CCGCCCC | ? | Y
T |
likely active or activable |
199. SP1
(Yao) |
GCGGC | ? | Y
T |
likely active or activable |
200. STAT5 | TTCNNNGAA | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable, positive distal likely random |
201. Stress-response elements
(STREs) |
CCCCT | ? | Y
T |
likely active or activable, positive cores overlap randoms
Positive strand, negative direction: CCCCT at 3059 |
202. Sucrose boxes | NNAATCA | ? | Y
T |
likely active or activable |
203. TACTAAC boxes | TACTAA(C/T) | ? | Y
T |
likely active or activable |
204. TAGteams | CAGGTAG | ? | Y
T |
likely active or activable |
205. Tapetum boxes | TCGTGT | ? | Y
T |
likely active or activable |
206. TATA boxes | TATA(A/T)A(A/T)(A/G) | β-Scaffold factors with minor groove contacts | Y
T |
likely active or activable |
207. TAT Boxes
(Yang) |
TATAAAA | WD40 repeat family | Y
T |
likely active or activable |
208. TAT Boxes
(Fan) |
TATCCAT | WD40 repeat family | Y
T |
likely active or activable |
209. Tbf1 regulatory factors | A(A/G)CCCTAA | General Regulatory Factors | Y
T |
Saccharomyces cerevisiae, likely active or activable |
210. T boxes
(Conlon) |
TCACACCT | bZIP | Y
T |
likely active or activable |
211. T boxes
(Zhang) |
AACGTT | bZIP | Y
T |
likely active or activable |
212. TEA consensus sequences | CATTCY | ? | Y
T |
likely active or activable |
213. Tec1ps | GAATGT | ? | Y
T |
likely random, Ste12p cofactor |
214. Telomeric repeat DNA-binding factors
(TRFs) |
TTAGGG | ? | Y
T |
likely active or activable |
215. Thyroid hormone response elements
(TREs)(THRs) |
AGGTCA | ? | Y
T |
likely active or activable |
216. Transcription factor 3
(TCF3) |
GTCTGGT | ? | Y
T |
likely active or activable |
217. Translational control sequences
(TCSs) |
(A/T)TT(A/G)TCT | ? | Y
T |
likely active or activable |
218. Unfolded protein response element
(URE) (UPRE-1) |
CANCNTG | ? | Y
T |
likely active or activable |
219. Unfolded protein response elements
(UPREs) |
TGACGTG(G/A) | bZIP | Y
T |
likely active or activable |
220. Upstream repressor site 1
(URS1, core) (Sumrada) |
CCGCC | ? | Y
T |
likely active or activable, negative direction proximals are within randoms |
221. 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 |
222. UUA rich elements
(Chen) |
TTATTTA(A/T)(A/T) | ? | Y
T |
likely active or activable |
223. V boxes | (A/G)TT(A/T)(C/T) | ? | Y
T |
likely active or activable |
224. Vitamin D response elements
(VDREs) |
(A/G)G(G/T)(G/T)CA | ? | Y
T |
likely active or activable |
225. W boxes | (C/T)TGAC(C/T) | WRKY | Y
T |
likely active or activable |
226. 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 |
227. Xenobiotic response elements
(XREs) |
GCGTG | bHLH | Y
T |
likely active or activable |
228. Yap recognition sequences | TTACTAA | ? | Y
T |
likely active or activable |
229. YY1 binding sites | CCATCTT | Cys 2His 2 |
Y
T |
likely active or activable |
230. 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 |
231. Z boxes
ZboxG |
A(C/T)A(C/G)GT(A/G)T | ? | Y
T |
likely active or activable |
232. 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.
See also
References
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External links