A1BG response element gene transcriptions: Difference between revisions

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==Totals==
==Totals==


Of 323 response elements, there are 105 Ns for not present (absent) in either A1BG promoter and 219 Ys for (present) or transcription factors that occur in the promoters of A1BG. There are four apparent random (ACGT-containing, HMG boxes, IRF3s and Quinone reductase) elements, 63 random or likely? to be evaluated and 153 likely active or activable (69.86 %). With 4560 nts considered between ZSCAN22 and A1BG, halfway would be at 2280. Less than 2280 suggests the nearest other gene. In the positive direction, 4445 nts considered between ZNF497 and A1BG, halfway would be 2222 for another nearest gene. Less than 2222 suggests the nearest other gene.
Of 323 response elements, there are 105 Ns for not present (absent) in either A1BG promoter and 219 Ys for (present) or transcription factors that occur in the promoters of A1BG. There are four apparent random (ACGT-containing, HMG boxes, IRF3s and Quinone reductase) elements, 62 random or likely? to be evaluated and 154 likely active or activable (70.32 %). With 4560 nts considered between ZSCAN22 and A1BG, halfway would be at 2280. Less than 2280 suggests the nearest other gene. In the positive direction, 4445 nts considered between ZNF497 and A1BG, halfway would be 2222 for another nearest gene. Less than 2222 suggests the nearest other gene.


==Acknowledgements==
==Acknowledgements==

Revision as of 06:26, 5 August 2022

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

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

Hypotheses

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

Response element testing (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.[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


(Rossi)

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. Polycomb response elements CGCCAT(A/T)TT ? N CGCCATTT
80. Rap1 regulatory factors ACCC(A/G)N(A/G)CA ? N "(ACCCRnRCA), less than half of the sites were detectably bound"[3]
81. Extended Reb1 ATTACCCGAA ? N "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."[3]
82. Rlm1ps CTATATATAG ? N CTA(T/A)4TAG
83. Rox1ps RRRTAACAAGAG ? N Heme-dependent repressor of hypoxic genes.[27]
84. Rpn4ps GGTGGCAAA ? N proteasome genes
85. Seed-specific elements CATGCATG ? N SRE consensus: CAGCAGATTGCG is none
86. Shoot specific elements GATAATGATG ? N SRE consensus: CAGCAGATTGCG is none
87. Sip4ps CC(C/G)T(C/T)C(C/G)TCCG ? N CC(C/G)T(C/T)C(C/G)TCCG[27]
88. Smp1ps ACTACTA(A/T)(A/T)(A/T)(A/T)TAG ? N ACTACTA(T/A)4TAG[27]
89. SP1

(Long)

GGGGCGGGCC ? N GGGGCGGGCC[14]
90. Sterol response elements

(Branco)

TCGTATA ? N perhaps plant specific
91. Sterol response elements

(Yao)

AGCAGATTGCG ? N liver specific
92. TATCCAC boxes TATCCAC ? N GA responsive complex component
93. TCCACCATA elements TCCACCATA ? N adjacent co-dependent regulatory element of POLLEN1
94. Tetradecanoylphorbol-13-acetate response elements

(TREs)

TGA(G/C)TCA ? N cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40
95. TGF-β control elements

(TCEs)

GAGTGGGGCG ? N in mouse and rat, GCGTGGGGGA in humans
96. TGF-β inhibitory elements

(TIEs)

GAGTGGTGA ? N in the rat transin/stromelysin promoter
97. Vhr1ps

(VHR1)

AATCA-N8-TGA(C/T)T ? N Response to low biotin concentrations
98. Vitamin D response elements

(VDREs)

A/GGG/TTCAnnnA/GGG/TTCA ? N (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA
99. X boxes GTTGGCATGGCAAC[38] ? N X2 box is AGGTCCA not ⌘F
100. X-boxes GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC[39] ? N includes GTTNCCATGGNAAC
101. Xbp1ps GcCTCGA(G/A)G(C/A)g(a/g) ? N Transcriptional repressor
102. Xenobiotic response elements

(XREs)

(T/G)NGCGTG(A/C)(G/C)A ? N contains the core sequence GCGTG, see AHRE above
103. Y boxes (A/G)CTAACC(A/G)(A/G)(C/T) ? N inverted CAAT box
104. Zap1ps ACCCTCA ? N ACC(C/T)(C/T)(A/C/G/T)AAGGT
105. 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
1. ABA responsive elements

(ABREs)

ACGTG(G/T)C WD40 repeat family Y likely active or activable
2. Activated B-cell Factor-1s

(ABFs)

CGTNNNNN(A/G)(C/T)GA(C/T) General Regulatory Factors Y all three regulatory factors are in the distal promoters

likely active or activable

3. A boxes TACGTA Basic leucine zipper (bZIP) Y likely active or activable
4. boxes A TGACTCT bZIP Y likely active or activable
5. Abscisic acid-responsive elements (Pho4s), G boxes CACGTG[38] bZIP, bHLH Y likely active or activable
6. ACGT-containing elements ACGT bZIP Y likely active or activable, but UTR sequences could be random
7. Activating protein 2

(AP2)

(Cohen)

GCCTGGCC bHSH Y likely active or activable
8. Activating protein 2

(Cohen)

TCCCCCGCCC bHSH Y likely active or activable
9. Activating protein 2

(Murata)

(C/G)CCN(3,4)GG(C/G) bHSH Y likely active or activable
10. Activating protein 2

(Yao)

TCTTCCC bHSH Y likely active or activable
11. Activating protein 2

(Yao)

CTCCCA bHSH Y likely active or activable
12. Activating proteins

(AP-2)

(Yao)

GGCCAA bHSH Y likely active or activable
13. Activating transcription factors

(Burton)

(A/C/G)TT(A/G/T)C(A/G)TCA bZIP Y likely active or activable
14. Activating transcription factors

(Kilberg)

(A/G/T)TT(A/G/T)CATCA bZIP Y likely active or activable
15. Adenylate–uridylate rich elements

(AUREs)

(Bakheet)

(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) stem-loop Y likely active or activable

Negative strand, negative direction: TTTTATTTATTA at 4076

16. Adenylate–uridylate rich elements

(AREs)

(Chen and Shyu, Class I)

ATTTA stem-loop Y likely active or activable
17. Adenylate–uridylate rich elements

(AREs)

(Chen and Shyu, Class II)

TTATTTA(A/T)(A/T) stem-loop Y likely active or activable
18. Adenylate–uridylate rich elements

(AREs)

(Chen and Shyu, Class III)

ATTT stem-loop Y likely active or activable

Positive strand, negative direction: AAATAAAT at 4073

19. Adr1ps TTGG(A/G)G Cys
2
His
2
zinc finger binding domain
Y likely active or activable
20. Aft1s (C/T)(A/G)CACCC(A/G) bZIP[40] Y likely active or activable
21. AGC boxes AGCCGCC AP-2/EREBP-related factors Y likely active or activable
22. Angiotensinogen core promoter elements (A/C)T(C/T)GTG bZIP? Y likely active or activable
23. AhR responsive element or Aryl hydrocarbon responsive element II

(AHRE-II)

CATGN6C(A/T)TG bHLH Y likely active or activable
24. AhR DNA-binding consensus sequence

(AhRY)

(Yao)

GCGTGNN(A/T)NNN(C/G) bHLH Y likely active or activable for ZNF497
25. Androgen response elements

(Kouhpayeh)

GGTACAnnnTGTTCT Zinc finger DNA-binding domain Y the two portions GGTACA and TGTTCT occurring independently are likely active or activable
26. Androgen response elements

(Wilson)

AGAACANNNTGTTCT.[10] Zinc finger DNA-binding domain Y the two portions AGAACA and TGTTCT occurring independently are likely active or activable
27. Antioxidant-electrophile responsive elements

(Lacher)

GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A bHLH Y likely active or activable
28. ATA boxes AATAAA β-Scaffold factor? Y likely active or activable
29. ATTTA elements

(Siegel)

ATTTA β-Scaffold factor? Y likely active or activable
30. 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 likely active or activable
31. Auxin response factors

(Ulmasov)

TGTCTC WD40 repeat family Y likely active or activable
32. Auxin response factors

(Boer)

TGTCGG WD40 repeat family Y likely active or activable
33. Auxin response factors

(ARF5)

(C/G/T)N(G/T)GTC(G/T) WD40 repeat family Y likely active or activable
34. B-boxes

(Johnson)

TGGGCA Zinc finger DNA-binding domains Y likely active or activable
35. boxes B

(Sanchez)

TGTCTCA Zinc finger DNA-binding domains Y likely active or activable
36. B recognition elements

(BREu)

(G/C)(G/C)(G/A)CGCC HTH Y likely active or activable
37. CadC binding domains TTANNNNT HTH Y likely active or activable
38. Calcineurin-responsive transcription factors TG(A/C)GCCNC ? Y likely active or activable
39. Carbohydrate response elements ChoRE1 ACCGG ? Y likely active or activable
40. Carbohydrate response elements ChoRE2 CCCAT ? Y may be likely active or activable
41. Carbohydrate response elements Carb E1 ATCTTG bHLH? Y likely active or activable
42. Carbohydrate response elements Carb E2 CACGTG bHLH Y likely active or activable
43. Carbohydrate response elements Carb E3 TCCGCC bHLH? Y likely active or activable
44. TCCG elements

(TCCGs)

TCCG bHLH? Y likely active or activable
45. CARE (Fan)

(CAREs)

(Fan)

CAACTC WD-40 repeat family Y likely active or activable
46. CARE (Garaeva)

(CAREs)

(Garaeva)

(A/G/T)TT(A/G/T)CATCA WD-40 repeat family Y likely active or activable
47. cAMP-responsive elements

(CREs), Aca1ps, Sko1ps

TGACGTCA bZIP Y likely active or activable, same as Root specific elements
48. CArG boxes CCAAAAAT(G/A)G bHLH Y likely active or activable
49. Cat8ps CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA ? Y likely active or activable
50. CAT boxes CATTCCT bHLH Y likely active or activable
51. CAT-box-like elements GCCATT bHLH Y likely active or activable
52. C boxes

(Samarsky)

AGTAGT bZIP Y likely active or activable
53. C-boxes

(Song)

GACGTC bZIP Y likely active or activable
54. hybrid C/G-boxes

(Song)

TGACGTGT bZIP Y likely active or activable
55. C boxes

(Voronina)

GGTGATG bZIP Y likely active or activable
56. Cell-cycle box variants

(CCBs)

CACGAAA, ACGAAA and C-CGAAA ? Y likely active or activable
57. CGCG boxes (A/C/G)CGCG(C/G/T) ? Y likely active or activable probably for the respective zinc fingers
58. Circadian control elements CAANNNNATC ? Y likely active or activable
59. Class C DNA binding sites CACGNG bHLH Y likely active or activable, although the distals may be random
60. Cold-responsive elements CCGAC ? Y likely active or activable
61. Constitutive decay elements

(CDEs)

(Siegel)

TTC(C/T)(A/G)(C/T)GAA stem-loop Y likely active or activable possibly for ZNF497
62. Copper response elements

(CuREs)

(Quinn)

TTTGC(T/G)C(A/G) ? Y likely active or activable
63. Copper response elements

(CuREs)

(Park)

TGTGCTCA ? Y likely active or activable
64. Coupling elements

(CE3s)

(Watanabe)

GCGTGTC WD-40 repeat family Y likely active or activable
65. Coupling elements

(CE3s)

(Ding)

CACGCG WD-40 repeat family Y likely active or activable
66. Cytokinin response regulators

(ARR1s)

AGATT(C/T) WD40 repeat family Y likely active or activable
67. Cytokinin response regulators

(ARR10s)

(A/G)GATA(A/C)G WD40 repeat family Y likely active or activable, Negative strand, negative direction: CGTATCC at 3447
68. Cytokinin response regulators

(ARR12s)

(A/G)AGATA WD40 repeat family Y likely active or activable, Negative strand, negative direction: TATCTT at 4080
69. Cytokinin response regulators

(ARRs)

(Ferreira)

(G/A)GGAT(T/C) WD40 repeat family Y likely active or activable, Positive strand, negative direction: GATCCC at 4477, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, AATCCC at 3976, AATCCC at 3067
70. Cytokinin response regulators

(ARRs)

(Rashotte1)

GATCTT WD40 repeat family Y likely active or activable, Positive strand, negative direction: AAGATC at 3276
71. Cytokinin response regulators

(ARRs)

(Rashotte2)

(G/A)GAT(T/C) WD40 repeat family Y likely active or activable, Positive strand, negative direction: GATCC at 4476, AGATC at 4475
72. Cytoplasmic polyadenylation elements

(CPEs)

TTTTTAT ? Y likely active or activable
73. DAF-16 binding elements (A/G)(C/T)AAA(C/T)A ? Y likely active or activable
74. D boxes

(Samarsky)

AGTCTG ? Y likely active or activable
75. D boxes

(Voronina)

TCCTG ? Y likely active or activable
76. D-boxes

(Motojima)

TGAGTGG ? Y likely active or activable
77. Dioxin-responsive elements

(DREs)

TNGCGTG bHLH? Y likely active or activable
78. DNA damage response elements

(DRE, core)

(Sumrada)

CCGCC ? Y likely active or activable
79. Downstream B recognition elements (A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T) ? Y likely active or activable, but the distal promoter sequences appear random in the positive direction
80. Downstream core elements

(DCEs)

CTTC...CTGT...AGC ? Y likely active or activable
80. Downstream promoter elements

(DPEs)

(Juven-Gershon)

(A/G)G(A/T)(C/T)(A/C/G)T ? Y most or all of the real DPE (Juven-Gershon)s are likely active or activable
82. Downstream promoter elements

(DPEs)

(Kadonaga)

(A/G)G(A/T)CGTG ? Y likely active or activable
83. Downstream promoter elements

(DPEs)

(Matsumoto)

AGTCTC ? Y likely active or activable
84. E2 boxes (G/A)CAG(A/C/G/T)TG(A/C/G/T) bHLH Y likely active or activable
85. EIN3 binding sites A(C/T)G(A/T)A(C/T)CT ? Y likely active or activable
86. Endoplasmic reticulum stress response elements CCAAT-N9-CCACG, part 2, CCACG bZIP Y likely active or activable
87. Endosperm expressions TGTGTCA ? Y likely active or activable
88. Enhancer boxes CA(A/C/G/T)(A/C/G/T)TG bHLH Y likely active or activable
89. Ethylene responsive elements ATTTCAAA WD40 repeat family Y likely active or activable
90. Forkhead boxes (A/G)(C/T)AAA(C/T)A HTH, Forkhead Y likely active or activable
91. GAAC elements GAACT ? Y likely active or activable
92. Γ-interferon activated sequences

(GAS), see STAT5

TTNCNNNAA β-Scaffold factors with minor groove contacts Y likely active or activable
93. GATA boxes GATA Zinc finger DNA-binding domains, bHLH Y likely active or activable when occurring in the UTR or distals but may be random when occurring in the proximals
94. GC boxes

(Briggs)

(G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T) ? Y likely active or activable
95. GC boxes

(Ye)

GGGCGG ? Y likely active or activable, but real UTRs match the upper end of the randoms
96. GCC boxes GCCGCC ? Y likely active or activable
97. General control nonderepressible 4 protein binding site

(GCRE, GCN4)

TGA(C/G/T)T(A/C/G)(A/T) bZIP Y likely active or activable
98. GGC triplets GGC Zn(II)2Cys6 Y likely active or activable
99. Gibberellic acid responsive elements

(GAREs)

TAACAAA WD40 repeat family Y likely active or activable
100. Gibberellin responsive elements

(GAREs)

(Sharma)

AAACAGA[5] WD40 repeat family Y likely active or activable
101. GARE-like 1

(Fan)

TAACA(A/G)A[28] WD40 repeat family Y likely active or activable
102. G-protein-coupled receptors

(GCR1s), CT boxes

CTTCC ? Y UTRs are just smaller than the randoms, but may be within the error so they could be random. Proximal and distal promoters are likely active or activable.
103. Glucocorticoid response elements AGAACA bHLH Y likely active or activable
104. GT boxes

(Sato)

GGGG(T/A)GGGG ? Y likely active or activable
105. Hac1 KAR2 CAGCGTG ? Y likely active or activable
106. H and ACA boxes AGAGGA Hairpin-hinge-hairpin-tail Y likely active or activable
107. Hap motif

(Hap4p)

CCAAT bZIP Y likely active or activable
108. H-boxes

(Grandbastien)

CC(A/T)ACCNNNNNNN(A/C)T hairpin-hinge-hairpin-tail Y likely active or activable
109. H-boxes

(Lindsay)

CCTACC hairpin-hinge-hairpin-tail Y likely active or activable, equal to or greater than the randoms for the negative direction distals
110. H box

(Mitchell)

ANANNA hairpin-hinge-hairpin-tail Y likely active or activable
111. H box

(Rozhdestvensky)

ACACCA hairpin-hinge-hairpin-tail Y likely active or activable
112. Heat shock elements

(HSE3s)

(Eastmond)

nGAAn-(5-bp)-nGAAnnTTCn HTH, HSFs Y likely active or activable
113. Heat shock elements

(HSEs)

(Eastmond)

nGA(A/G)n-(5-bp)-nGAAnnTTCn (GAP1) HTH, HSFs Y same result as HSE3, likely active or activable
114. Heat shock elements

(HSEs)

(Eastmond)

nGAAn-(5-bp)-nGA(A/G)nnTTCn (GAP2) HTH, HSFs Y same result as HSE3, likely active or activable
115. Heat shock elements

(HSE4s)

(Eastmond)

nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn HTH, HSFs Y likely active or activable
116. Heat shock factors

(Hsfs)

(Tang)

NGAAN HTH, HSFs Y likely active or activable
117. Hex sequences TGACGTGGC ? Y likely active or activable
118. High Mobility Group boxes

(HMG boxes)

(A/T)(A/T)CAAAG β-Scaffold factors with minor groove contacts Y random
119. 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 likely active or activable, although the negative direction distals are at or less than randoms
120. Homeoboxes CAAG HTH Y likely active or activable
121. Homeodomains TAAT HTH Y likely active or activable
122. HY boxes TG(A/T)GGG ? Y likely active or activable
123. Hypoxia-inducible factors ACGTG bHLH Y likely active or activable
124. Hypoxia response elements CACGC WD40 repeat family Y likely active or activable
125. CACA elements CACA WD40 repeat family Y likely active or activable
126. Initiator elements

(Inrs)

YYANWYY ? Y likely active or activable
127. Initiator elements

(Inrs)

BBCABW ? Y likely active or activable
128. Initiator-like elements TTCTCT ? Y likely active or activable, where real Inr-like negative direction distals are within the range of the randoms
129. 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 likely active or activable
130. Inositol/choline-responsive elements

(ICREs)

(Schwank)

TYTTCACATGY contains the core sequence CANNTG bHLH Y likely active or activable
131. Interferon regulatory factor

(IRF3)

GCTTTCC HTH Y random
132. IFN-stimulated response elements

(ISREs)

(Lu)

GAAANNGAAA HTH Y likely active or activable
133. IRS consensus

(Fujii)

AANNGAAA HTH Y likely active or activable
134. Tryptophan residues

(Lu)

GAAA HTH Y 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
135. Jasmonic acid-responsive elements

(JAREs)

TGACG ? Y likely active or activable
136. Krüppel-like factors GGGNN(G/T)(G/T)(G/T) ? Y likely active or activable
137. Leu3 transcription factors (C/G)C(G/T)NNNN(A/C)G(C/G) Zn(II)2Cys6 Y likely active or activable
138. -35 sequence TTGACA ? Y likely active or activable, the UTR does overlap the randoms at the random's upper end
139. Met31ps AAACTGTG[36] bZIP Y likely active or activable
140. Metal responsive elements

(MRE)

TGC(A/G)C(A/C/G/T)C ? Y likely active or activable
141. Middle sporulation element

(MSE)

(Branco)

ACACAAA ? Y likely active or activable
142. Midsporulation element

(MSE)

(Ozsarac)

C(A/G)CAAA(A/T) ? Y likely active or activable
143. Multicopy inhibitor of the GAL1 promoter

(MIG1)

(C/G)(C/T)GGGG bZIP Y likely active or activable, UTRs may be random
144. Musashi binding elements

(MBE1s)

(G/A)U1AGU ? Y likely active or activable
145. Musashi binding elements

(MBE2s)

(G/A)U2AGU ? Y likely active or activable, negative direction distals may be random
146. Musashi binding elements

(MBE3s)

(G/A)U3AGU ? Y likely active or activable
147. MYB ACGT-containing elements

(ACEs)

CACGT ? Y likely active or activable, positive strand UTR is likely random, negative strand, positive direction distals are likely random
148. Myeloblastosis recognition element

(MRE)

A(A/C)C(A/T)A(A/C)C ? Y likely active or activable
149. 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 likely active or activable
150. Nanos/Pumilio response elements

(PREs)

TGTAAAT ? Y likely active or activable
213. N-boxes

(Lee)

CCGGAA bHLH Y random or likely?, Negative strand, positive direction: TTCCGG at 4244
214. N-boxes

(Bai)

CACGAG bHLH Y random or likely?, Positive strand, negative direction: CACGAG at 4472, CACGAG at 3232
215. N-boxes

(Gao)

CACGGC or CACGAC, CACG(A/G)C bHLH Y random or likely?, Negative strand, negative direction: CACGAC at 3956, GTCGTG at 3733, GTCGTG at 3072
154. N-boxes

(Leal)

CACNAG bHLH Y likely active or activable
217. Non-DiTyrosine 80 transcription factor DNA binding domain

(Ndt80)

(A/G/T)NC(A/G)CAAA(A/T) ? Y random or likely?, Negative strand, negative direction: TTTTGTGTT at 3514

Positive strand: ACCACAAAA at 3767

220. Nuclear factor of activated T cells

(NFATs)

GGAAAA β-Scaffold factors with minor groove contacts Y random or likely?, Negative strand, negative direction: TTTTCC at 3441, TTTTCC at 3345

Positive strand, negative direction: GGAAAA at 2968, GGAAAA at 2927

222. Nutrient-sensing response element 1 GTTTCATCA ? Y random or likely?
223. Oaf1 transcription factor CGGN3TNAN9-12CCG ? Y random or likely?
224. ORESARA1

(ORE1)

(Matallana)

(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) ? Y random or likely?, Negative strand, negative direction: GCGTAGAAGACACA at 3558, AAGTAGTTTCTACG at 2895
225. ORESARA1

(ORE1)

(Olsen)

T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) ? Y random or likely?, Negative strand, negative direction: TGACGTGAG at 4341, TAACGTGAG at 3290

Positive strand, negative direction: ATCACGCCA at 3282

226. 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 random or likely?, Positive strand, negative direction: AGACAAGCTT at 4186
227. p53 response elements

(Long1)

CAGGCCC β-Scaffold factors with minor groove contacts Y random or likely?, Positive strand, positive direction: GGGCCTG at 745
228. p53 response elements

(Long2)

GGGCGTG β-Scaffold factors with minor groove contacts Y random or likely?, Positive strand, negative direction: GGGCGTG at 3046
230. P-box (Mena) (A/T)AAAG ? Y random or likely?, Negative strand, negative direction: CTTTT at 4395, CTTTT at 4390, CTTTT at 4383, TAAAG at 3688, TAAAG at 2884

Positive strand, negative direction: AAAAG at 4391, AAAAG at 4386, AAAAG at 4379, AAAAG at 3440, AAAAG at 3344, CTTTT at 3019, TAAAG at 2857

231. P-box

(Motojima)

TGAGTTCA ? Y random or likely?
232. P-box

(Yu)

GTAA(T/C) ? Y random or likely?, Negative strand, negative direction: ATTAC at 3658, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951

Positive strand, negative direction: GTAAT at 3973, ATTAC at 3469, GTAAT at 3064

234. Peroxisome proliferator-activated receptor alpha CGACCCC ? Y random or likely?, Negative strand, negative direction: CGACCCC at 3037
175. Pho4ps CAC(A/G)T(T/G) bHLH Y likely active or activable, positive strands of the UTRs and negative direction distals are in the random range
237. Pollen1 elements AGAAA ? Y random or likely?, Negative strand, negative direction: TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892

Positive strand, negative direction: AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342

240. Polycomb response elements

(PRE)

GCCAT ? Y random or likely?, Positive strand, negative direction: GCCAT at 3685, ATGGC at 3629, GCCAT at 3283, ATGGC at 3005, ATGGC at 2907
241. Pribnow boxes TATAAT ? Y random or likely?, Negative strand, negative direction: TATAAT at 3468, TATAAT at 3454
242. Prolamin boxes TG(A/T)AAAG ? Y random or likely?, Negative strand, negative direction: TGTAAAG at 2884
243. Pyrimidine boxes CCTTTT WD40 repeat family Y random or likely?, Negative strand, negative direction: CCTTTT at 2968, CCTTTT at 2927

Positive strand, negative direction: AAAAGG at 3441, AAAAGG at 3345

244. Q elements

See Retinoic acid response element

AGGTCA ? Y random or likely?, Positive strand, negative direction: AGGTCA at 4307
166. Quinone reductase response element

(QRDRE)

(Yao)

TCCCCT of TCCCCTTGCGTG ? Y random
247. Rap1 reduced consensus (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C) WD40 repeat family Y random or likely?, Positive strand, positive direction: GAACCCACACCTC at 1807
248. Reb1 bound and exact occurrences TTACCC(G/T) WD40 repeat family Y random or likely?, Negative strand, negative direction: TTACCCT at 3661
250. Retinoic acid response element AG(A/G)TCA ? Y random or likely?, Negative strand, negative direction: TGATCT at 3463
251. Glucose transporter gene repressor

(Rgt1)

CGG(A/G)(A/T)N(A/T)(A/T) ? Y random or likely?, Negative strand, negative direction: ATTTTCCG at 3442
253. classic RORE motif

(RORE)

A(A/T)NTAGGTCA ? Y random or likely?
254. variant RORE motif C(T/A)(G/A)GGNCA ? Y random or likely?, Negative strand, negative direction: CTGGGACA at 4369, CTGGGACA at 4208
177. R response elements

(RRE)

CATCTG ? Y likely active or activable
259. Serum response elements

(SRE)

see CArG boxes

ACAGGATGT bHLH-ZIP Y random or likely?, Negative strand, positive direction: ACAGGATGT at 3575
260. Servenius sequences GGACCCT ? Y random or likely?, Negative strand, negative direction: GGACCCT at 4548, GGACCCT at 4496, GGACCCT at 4302
264. SP1

(Zhang)

(G/T)GGGCGG(G/A)(G/A)(C/T) ? Y see GC boxes above, random or likely?
265. SP1-box 1

(Motojima)

GGGGCT ? Y random or likely?, Positive strand, negative direction: GGGGCT at 3039
266. SP1-box 2

(Motojima)

CTGCCC ? Y random or likely?, Positive strand, negative direction: CTGCCC at 3853
267. SP-1

(Sato)

CCGCCCC ? Y random or likely?, Negative strand, positive direction: GGGGCGG at 4439, GGGGCGG at 4429
269. SP1

(Yao)

GCGGC ? Y random or likely?, Negative strand, negative direction: GCCGC at 2726

Positive strand, negative direction: GCGGC at 2725

270. STAT5 TTCNNNGAA β-Scaffold factors with minor groove contacts Y random or likely?, Positive strand, negative direction: TTCCCTGAA at 3782, TTCGTTGAA at 3506
273. Stress-response elements

(STREs)

CCCCT ? Y random or likely?, Negative strand, negative direction: CCCCT at 2924

Positive strand, negative direction: CCCCT at 3059

274. Sucrose boxes NNAATCA ? Y random or likely?, Negative strand, negative direction: TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915
275. TACTAAC boxes TACTAA(C/T) ? Y random or likely?, Positive strand, positive direction: TACTAAT at 4157, ATTAGTA at 4148
276. TAGteams CAGGTAG ? Y random or likely?, Negative strand, positive direction: CAGGTAG at 4035, CTACCTG at 1198
277. Tapetum boxes TCGTGT ? Y random or likely?, Negative strand, negative direction: ACACGA at 4402, TCGTGT at 3915
278. TATA boxes TATA(A/T)A(A/T)(A/G) β-Scaffold factors with minor groove contacts Y random or likely?, Negative strand, negative direction: TTTATATA at 2871

Positive strand, negative direction: TATATAAA at 2874

279. TAT Boxes

(Yang)

TATAAAA WD40 repeat family Y random or likely?, Negative strand, negative direction: TATAAAA at 2853
280. TAT Boxes

{Fan)

TATCCAT WD40 repeat family Y random or likely?, Negative strand, negative direction: ATGGATA at 2996
282. Tbf1 regulatory factors A(A/G)CCCTAA General Regulatory Factors Y Saccharomyces cerevisiae, random or likely?
283. T boxes

(Conlon)

TCACACCT bZIP Y random or likely?, positive strand: TCACACCT at 3968, TCACACCT at 1129
284. T boxes

(Zhang)

AACGTT bZIP Y random or likely?, positive strand: AACGTT at 2691, AACGTT at 1614
286. TEA consensus sequences CATTCY ? Y random or likely?, Positive strand, negative direction: GGAATG at 4554, AGAATG at 3003
287. Tec1ps GAATGT ? Y random or likely?, Ste12p cofactor
288. Telomeric repeat DNA-binding factors

(TRFs)

TTAGGG ? Y random or likely?, Negative strand, negative direction: TTAGGG at 3976, TTAGGG at 3067
292. Thyroid hormone response elements

(TREs)(THRs)

AGGTCA ? Y random or likely?, See VDREs, X boxes, Positive strand, negative direction: AGGTCA at 4307
293. Transcription factor 3

(TCF3)

GTCTGGT ? Y random or likely?, Negative strand, negative direction: GTCTGGT at 2122
294. Translational control sequences

(TCSs)

AUUAUCU (Wee1 TCS1), AUUGUCU (Wee1 TCS2) and UUUGUCU (Mos and PCM-1 TCS) ? Y random or likely?, Negative strand, negative direction: TTTGTCT at 4518, ATTATCT at 4079, TTTGTCT at 2878.
245. Unfolded protein response element

(URE) (UPRE-1)

CANCNTG ? Y likely active or activable
246. Unfolded protein response elements

(UPREs)

TGACGTG(G/A) bZIP Y likely active or activable
297. Upstream stimulating factors

(USFs)

GCC(A/T)NN(C/G/T)(A/G) bHLH-ZIP Y random or likely?, Negative strand, negative direction: CGGTCCAC at 3953

Positive strand, negative direction: CAGATGGC at 3629

298. UUA rich elements

(Siegel)

TTATTTA(A/T)(A/T) ? Y random or likely?, Negative strand, negative direction: TTATTTATT at 4075
299. V boxes (A/G)TT(A/T)(C/T) ? Y random or likely?, Negative strand, negative direction: ATAAT at 4538, AAAAT at 4512, GTTTC at 4504, GAAAC at 4462, GTTTT at 4376, GTTTT at 4310, ATTAT at 4223, GTTTT at 4216

Positive strand, negative direction: ATTTT at 4511, AAAAC at 4396, AAAAC at 4311, ATAAT at 4225, ATAAT at 4222, AAAAT at 4219

301. Vitamin D response elements

(VDREs)

(A/G)G(G/T)(G/T)CA ? Y random or likely?, Negative strand, negative direction: TGAACC at 4268, TGAACT at 4012, TGACCC at 3750, TGAACT at 3242, TGAACT at 3103, TGAACC at 2921
303. W boxes (C/T)TGAC(C/T) WRKY Y random or likely?, Negative strand, negative direction: GGTCAA at 4416, GGTCAA at 4308, CTGACC at 3749
307. X core promoter elements (A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C) ? Y random or likely?, Negative strand, negative direction: TGGTGGGACC at 3744
207. Xenobiotic response elements

(XREs)

GCGTG bHLH Y likely active or activable, Positive strand, negative direction: CACGC at 3280, GCGTG at 3046
310. Yap recognition sequences TTACTAA ? Y random or likely?, Yap1, Yap2, Yap3, and Yap5
312. YY1 binding sites CCATCTT Cys
2
His
2
Y random or likely?, Negative strand, negative direction: CCATCTT at 1654
314. Z boxes A(C/T)A(C/G)GT(A/G)T ? Y random or likely?, Positive strand, negative direction: ACACCTGT at 3970, ATACCTAT at 2996

Totals

Of 323 response elements, there are 105 Ns for not present (absent) in either A1BG promoter and 219 Ys for (present) or transcription factors that occur in the promoters of A1BG. There are four apparent random (ACGT-containing, HMG boxes, IRF3s and Quinone reductase) elements, 62 random or likely? to be evaluated and 154 likely active or activable (70.32 %). With 4560 nts considered between ZSCAN22 and A1BG, halfway would be at 2280. Less than 2280 suggests the nearest other gene. In the positive direction, 4445 nts considered between ZNF497 and A1BG, halfway would be 2222 for another nearest gene. Less than 2222 suggests the nearest other gene.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

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External links

{{Phosphate biochemistry}}