A1BG response element gene transcriptions: Difference between revisions
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|| CCGGAA || bHLH || Y || random or likely?, Negative strand, positive direction: TTCCGG at 4244 | || CCGGAA || bHLH || Y || random or likely?, Negative strand, positive direction: TTCCGG at 4244 | ||
|- | |- | ||
| | |152. [[N box gene transcriptions|N-boxes]] | ||
(Bai) | (Bai) | ||
|| CACGAG || bHLH || Y || | || CACGAG || bHLH || Y || likely active or activable | ||
|- | |- | ||
|153. [[N box gene transcriptions|N-boxes]] | |153. [[N box gene transcriptions|N-boxes]] |
Revision as of 17:06, 10 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
- 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 (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. 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)
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 2His 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 |
152. N-boxes
(Bai) |
CACGAG | bHLH | Y | likely active or activable |
153. N-boxes
(Gao) |
CACGGC or CACGAC, CACG(A/G)C | bHLH | Y | likely active or activable |
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 | 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 2His 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, 60 random or likely? to be evaluated and 156 likely active or activable (71.23 %). 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
- ↑ MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.
- ↑ 2.0 2.1 2.2 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.
- ↑ 3.0 3.1 3.2 3.3 3.4 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.
- ↑ 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.
- ↑ 5.0 5.1 5.2 5.3 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check
|pmid=
value (help). Retrieved 27 August 2020. - ↑ 6.0 6.1 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.
- ↑ 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.
- ↑ 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.
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