A1BG response element negative results: Difference between revisions

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|+ Response elements not occurring in promoters near A1BG
|+ Response elements not occurring in promoters near A1BG
|-
|-
! Name of elements !! Consensus sequences !! Testing !! Notes
! Name of elements !! Consensus sequences !! Testing !! Notes  
|-
|-
| [[ABA-response element gene transcriptions|ABA-response elements]] || GATCGATC, CGATCGAT, ACGTGTCC, GATCGAT || 16 || ABREN, CGATCGAT motif, ABRE, and core of ABREN and CGATCGAT motif.<ref name=Watanabe>{{ cite journal
! Abbreviations !! variations !! number of runs per symmetry !!
|-
! Authors !! !! !!
|-
| [[ABA-response element gene transcriptions|novel ABA-response elements]]  
 
(ABREN, novel ABRE)
|| GATCGATC, CGATCGAT, GATCGAT || 16 || ABREN, CGATCGAT motif, and core of ABREN and CGATCGAT motif.<ref name=Watanabe>{{ cite journal
|author=Kenneth A. Watanabe
|author=Kenneth A. Watanabe
|author2=Arielle Homayouni
|author2=Arielle Homayouni
Line 42: Line 49:
|pmid=
|pmid=
|accessdate=5 October 2020 }}</ref>  
|accessdate=5 October 2020 }}</ref>  
|-
| [[ABA-response element gene transcriptions|ABA-response element-like]]
(ABRE-like)
|| ACGTGTCC || 16 || third highest scoring motif<ref name=Watanabe/>
|-
|-
| [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] || CGTCCTCTACG || 16 || CGTNNNNNACGAT<ref name=Rossi>{{ cite journal
| [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] || CGTCCTCTACG || 16 || CGTNNNNNACGAT<ref name=Rossi>{{ cite journal
Line 60: Line 72:
|accessdate=31 August 2020 }}</ref>  
|accessdate=31 August 2020 }}</ref>  
|-
|-
| [[Activating protein gene transcriptions|Activating proteins]] || GCCCACGGG || 16 || Activating protein 2 (AP-2)<ref name=Murata>{{ cite journal
| [[Activating protein gene transcriptions|Activating proteins]]  
 
(AP-2)
|| GCCCACGGG || 16 || Activating protein 2<ref name=Murata>{{ cite journal
|author=Takayuki Murata
|author=Takayuki Murata
|author2=Chieko Noda
|author2=Chieko Noda
Line 86: Line 101:
|accessdate=4 October 2020 }}</ref>  
|accessdate=4 October 2020 }}</ref>  
|-
|-
| [[Activating protein gene transcriptions|Activating proteins]] || GGCCAA || 16 || Activating protein 2 (AP-2)<ref name=Yao/>  
| [[Activating protein gene transcriptions|Activating proteins]]  
 
(AP-2)
|| GGCCAA || 16 || Activating protein 2 (AP-2)<ref name=Yao/>  
|-
| [[Xenobiotic response element gene transcriptions|AhR-responsive elements]]
 
(AHRE)
 
(Yao)
|| (G/T)NGCGTG(A/C)(C/G)A || 16 || in the promoter region of AhR responsive genes
|-
|-
| [[Alpha-amylase conserved element gene transcriptions|Alpha-amylase conserved elements]] || TATCCA || 16 || TATCCATCCATCC<ref name=Sharma>{{ cite journal
| [[Alpha-amylase conserved element gene transcriptions|Alpha-amylase conserved elements]] || TATCCA || 16 || TATCCATCCATCC<ref name=Sharma>{{ cite journal
Line 104: Line 129:
|accessdate=27 August 2020 }}</ref>  
|accessdate=27 August 2020 }}</ref>  
|-
|-
| [[Amino acid response element gene transcriptions|Amino acid response elements]] || ATTGCATCA || 16 || AARE1 (ATTGCATCA)<ref name=Maruyama/>  
| [[Amino acid response element gene transcriptions|Amino acid response elements]]  
 
(AARE)
 
(Maruyama)
|| ATTGCATCA || 16 || AARE1 (ATTGCATCA)<ref name=Maruyama/>  
|-
|-
| [[Amino acid response element gene transcriptions|Amino acid response elements]] || TTTGCATCA || 16 || TTTGCATCA.<ref name=Broer>{{ cite journal
| [[Amino acid response element gene transcriptions|Amino acid response elements]]  
 
(AARE)
 
(Broer)
|| TTTGCATCA || 16 || TTTGCATCA.<ref name=Broer>{{ cite journal
|author=Angelika Bröer
|author=Angelika Bröer
|author2=Gregory Gauthier-Coles
|author2=Gregory Gauthier-Coles
Line 144: Line 179:
|accessdate=5 September 2020 }}</ref>  
|accessdate=5 September 2020 }}</ref>  
|-
|-
| [[Amino acid response element gene transcriptions|AARE-like]] || TGGTGAAAG || 16 || AARE-like sequence (TGGTGAAAG, named AARE3)<ref name=Maruyama>{{ cite journal
| [[Amino acid response element gene transcriptions|Amino acid response element-like]]  
 
(AARE-like)
|| TGGTGAAAG || 16 || AARE-like sequence (TGGTGAAAG, named AARE3)<ref name=Maruyama>{{ cite journal
|author=Ryuto Maruyama
|author=Ryuto Maruyama
|author2=Makoto Shimizu
|author2=Makoto Shimizu
Line 162: Line 200:
|accessdate=4 October 2020 }}</ref>  
|accessdate=4 October 2020 }}</ref>  
|-
|-
| [[Androgen response element gene transcriptions|Androgen response elements]] || GGTACANNNTGTTCT<ref name=Kouhpayeh/> || 16 || GGTACACGGTGTTCT<ref name=Kouhpayeh>{{ cite journal
| [[Androgen response element gene transcriptions|Androgen response elements]]  
 
(AREs)
 
(Kouhpayeh)
|| GGTACANNNTGTTCT<ref name=Kouhpayeh/> || 16 || GGTACACGGTGTTCT<ref name=Kouhpayeh>{{ cite journal
|author=S Kouhpayeh
|author=S Kouhpayeh
|author2=AR Einizadeh
|author2=AR Einizadeh
Line 186: Line 229:
|accessdate=3 October 2020 }}</ref>  
|accessdate=3 October 2020 }}</ref>  
|-
|-
| [[Androgen response element gene transcriptions|Androgen response elements]] || TGATTCGTGAG || 16 || AGAACANNNTGTTCT<ref name=Wilson>{{ cite journal
| [[Androgen response element gene transcriptions|Androgen response elements]]  
 
(AREs)
 
(Wilson)
|| TGATTCGTGAG || 16 || AGAACANNNTGTTCT<ref name=Wilson>{{ cite journal
|author=Stephen Wilson
|author=Stephen Wilson
|author2=Jianfei Qi
|author2=Jianfei Qi
Line 262: Line 310:
|accessdate=2 September 2020 }}</ref>  
|accessdate=2 September 2020 }}</ref>  
|-
|-
| [[Carbohydrate response element gene transcriptions|Carbohydrate response elements]] || CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG || 16 || ChoRE1, ChoRE2<ref name=Long>{{ cite journal
| [[Carbohydrate response element gene transcriptions|Carbohydrate response elements]]  
 
(ChREs)
|| CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG || 16 || ChoRE1, ChoRE2<ref name=Long>{{ cite journal
|author=Jianyin Long
|author=Jianyin Long
|author2=Daniel L. Galvan
|author2=Daniel L. Galvan
Line 284: Line 335:
|pmid=
|pmid=
|accessdate=6 October 2020 }}</ref>  
|accessdate=6 October 2020 }}</ref>  
|-
| [[Carbon source-responsive element gene transcriptions|Carbon source-responsive elements]]
(CSREs)
|| CATTCATCCG || 16 || confers carbon source-dependent regulation<ref name=Scholer>{{ cite journal
|author=A Schöler and H J Schüller
|title=A carbon source-responsive promoter element necessary for activation of the isocitrate lyase gene ICL1 is common to genes of the gluconeogenic pathway in the yeast ''Saccharomyces cerevisiae''.
|journal=Molecular and Cellular Biology
|date=June 1994
|volume=14
|issue=6
|pages=3613-3622
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC358729/pdf/molcellb00006-0095.pdf
|arxiv=
|bibcode=
|doi=
|pmid=
|accessdate=9 February 2021 }}</ref>
|-
|-
| [[Cbf1 regulatory factor gene transcriptions|Cbf1 regulatory factors]] || TCACGTGA || 8 || strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end  
| [[Cbf1 regulatory factor gene transcriptions|Cbf1 regulatory factors]] || TCACGTGA || 8 || strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end  
Line 334: Line 403:
| [[C box gene transcriptions|C/T hybrid boxes]] || TGACGTTA || 16 || TGACGTTA<ref name=Song/> T at the 12 position  
| [[C box gene transcriptions|C/T hybrid boxes]] || TGACGTTA || 16 || TGACGTTA<ref name=Song/> T at the 12 position  
|-
|-
| [[CCCTC-binding factor gene transcriptions|CCCTC-binding factors (CTCF)]] || NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) || 16 || NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)<ref name=Hashimoto>{{ cite journal
| [[CCCTC-binding factor gene transcriptions|CCCTC-binding factors]]
 
(CTCF)  
|| NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) || 16 || NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)<ref name=Hashimoto>{{ cite journal
|author=Hideharu Hashimoto
|author=Hideharu Hashimoto
|author2=Dongxue Wang
|author2=Dongxue Wang
Line 383: Line 455:
| pmid = 1318077
| pmid = 1318077
| doi = 10.1021/bi00136a019 }}</ref> || 16 || CCAAT-enhancer-binding site (C/EBP) is TAGCATT  
| doi = 10.1021/bi00136a019 }}</ref> || 16 || CCAAT-enhancer-binding site (C/EBP) is TAGCATT  
|-
| [[Cell-cycle box gene transcriptions|Cell-cycle boxes]]
(CCBs)
|| CACGAAAA || 16 || more relaxed variants are present
|-
|-
| [[Cell cycle regulation gene transcriptions|Cell cycle regulation]] || CCCAACGGT<ref name=Sharma/> || 16 || tomato genome-wide analysis  
| [[Cell cycle regulation gene transcriptions|Cell cycle regulation]] || CCCAACGGT<ref name=Sharma/> || 16 || tomato genome-wide analysis  
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| [[CENP-B box gene transcriptions|CENP-B boxes]] || TTTCGTTGGAAGCGGGA || 16 || specifically localized at the centromere  
| [[CENP-B box gene transcriptions|CENP-B boxes]] || TTTCGTTGGAAGCGGGA || 16 || specifically localized at the centromere  
|-
|-
| [[Coupling element gene transcriptions|Coupling elements]] || TGCCACCGG<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
| [[Coupling element gene transcriptions|Coupling elements]]  
 
(CEs)
|| TGCCACCGG<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
|-
|-
| [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] || TGATAAG || 16 || DAF-16-associated element (DAE)<ref name=Li>{{ cite journal
| [[Adenylate–uridylate rich element gene transcriptions|Constitutive decay elements]]
 
(Siegel)
 
(CDEs)
|| CCUUCYRYGAAGG, CCTTC(C/T)(A/G)(C/T)GAAGG || 16 || TTCCATGAA at 128 but no CC or GG at the ends
|-
| [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]]  
 
(DAE)
|| TGATAAG || 16 || DAF-16-associated element (DAE)<ref name=Li>{{ cite journal
|author=Yan-Hui Li
|author=Yan-Hui Li
|author2=Gai-Gai Zhang
|author2=Gai-Gai Zhang
Line 406: Line 496:
|accessdate=27 August 2020 }}</ref>  
|accessdate=27 August 2020 }}</ref>  
|-
|-
| [[D box gene transcriptions|D-boxes]] || GTTGTATAAC (Mracek1) || 16 || GTTGTATAAC<ref name=Mracek>{{ cite journal
| [[D box gene transcriptions|D-boxes]]  
 
(Mracek1)
|| GTTGTATAAC || 16 || GTTGTATAAC<ref name=Mracek>{{ cite journal
|author=Philipp Mracek
|author=Philipp Mracek
|author2=Cristina Santoriello
|author2=Cristina Santoriello
Line 428: Line 521:
|accessdate=10 February 2019 }}</ref>  
|accessdate=10 February 2019 }}</ref>  
|-
|-
| [[D box gene transcriptions|D-boxes]] || CTTATGTAAA (Mracek2) || 16 || CTTATGTAAA<ref name=Mracek/>  
| [[D box gene transcriptions|D-boxes]]  
 
(Mracek)
|| CTTATGTAAA (Mracek2) || 16 || CTTATGTAAA<ref name=Mracek/>  
|-
|-
| [[D box gene transcriptions|D-boxes]] || TCTCACA || 16 || TCTCACATT(A/C)AATAAGTCA is a D-box.<ref name=Johnson/>  
| [[D box gene transcriptions|D-boxes]]  
(Johnson)
|| TCTCACA || 16 || TCTCACATT(A/C)AATAAGTCA is a D-box.<ref name=Johnson/>  
|-
|-
| [[Defense and stress-responsive element gene transcriptions|Defense and stress-responsive elements]] || ATTTTCTTCA || 16 || (ATTTTCTTCA)<ref name=Sharma/>  
| [[Defense and stress-responsive element gene transcriptions|Defense and stress-responsive elements]] || ATTTTCTTCA || 16 || (ATTTTCTTCA)<ref name=Sharma/>  
|-
|-
| [[DNA damage response element gene transcriptions|DNA damage response elements (DREs)]] || TTTCAAT<ref name=Smith>{{ cite journal
| [[DNA damage response element gene transcriptions|DNA damage response elements]]
 
(DREs)  
 
(Smith)
|| TTTCAAT<ref name=Smith>{{ cite journal
|author=Joshua J. Smith, Eric S. Cole, Daniel P. Romero
|author=Joshua J. Smith, Eric S. Cole, Daniel P. Romero
|title=Transcriptional control of RAD51 expression in the ciliate ''Tetrahymena thermophila''
|title=Transcriptional control of RAD51 expression in the ciliate ''Tetrahymena thermophila''
Line 449: Line 552:
|accessdate=4 September 2020 }}</ref> || 16 || in the upstream repression sequence (URS)  
|accessdate=4 September 2020 }}</ref> || 16 || in the upstream repression sequence (URS)  
|-
|-
| [[DNA damage response element gene transcriptions|DNA damage response elements (DREs)]] || TAGCCGCCG of TAGCCGCCGRRRR<ref name=Sumrada>{{ cite journal
| [[DNA damage response element gene transcriptions|DNA damage response elements]]
 
(DREs)  
 
(Sumrada)
|| TAGCCGCCG of TAGCCGCCGRRRR<ref name=Sumrada>{{ cite journal
|author=Roberta A. Sumrada and Terrance G. Cooper
|author=Roberta A. Sumrada and Terrance G. Cooper
|title=Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast
|title=Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast
Line 464: Line 572:
|accessdate=6 September 2020 }}</ref> || 16 || in the upstream repression sequence (URS)  
|accessdate=6 September 2020 }}</ref> || 16 || in the upstream repression sequence (URS)  
|-
|-
| [[DNA replication-related element gene transcriptions|DNA replication-related elements]] || TATCGATA || 16 || DNA replication-related element (DRE)<ref name=Hirose>{{ cite journal
| [[DNA replication-related element gene transcriptions|DNA replication-related elements]]  
 
(DREs)
|| TATCGATA || 16 || DNA replication-related element (DRE)<ref name=Hirose>{{ cite journal
|author=Fumiko Hirose
|author=Fumiko Hirose
|author2=Masamitsu Yamaguchi
|author2=Masamitsu Yamaguchi
Line 485: Line 596:
| [[EIF4E basal element gene transcriptions|EIF4E basal elements]] || TTACCCCCCCTT || 16 || poly(C) motif  
| [[EIF4E basal element gene transcriptions|EIF4E basal elements]] || TTACCCCCCCTT || 16 || poly(C) motif  
|-
|-
| [[Endoplasmic reticulum stress response element gene transcriptions|Endoplasmic reticulum stress response elements]] || CCAAT || 16 || CCAATGGGCTGAAAC between ZNF497 and A1BG, compare [[A1BG response element positive results|CCAAT-box and ERSE]]  
| [[Endoplasmic reticulum stress response element gene transcriptions|Endoplasmic reticulum stress response elements]]  
 
(ERSE)
|| CCAAT || 16 || CCAATGGGCTGAAAC between ZNF497 and A1BG, compare [[A1BG response element positive results|CCAAT-box and ERSE]]  
|-
|-
| [[Estrogen response element gene transcriptions|Estrogen response elements]] || AGGTTA or GGTCAGGAT || 16 || AGGTTATTGCCTCCT or GGTCAGGATGAC  
| [[Estrogen response element gene transcriptions|Estrogen response elements]]  
 
(EREs)
|| AGGTTA or GGTCAGGAT || 16 || AGGTTATTGCCTCCT or GGTCAGGATGAC  
|-
|-
| [[I box gene transcriptions|F boxes]] || TGATAAG<ref name=Rose>{{ cite journal
| [[I box gene transcriptions|F boxes]] || TGATAAG<ref name=Rose>{{ cite journal
Line 534: Line 651:
|accessdate=18 September 2020 }}</ref>  
|accessdate=18 September 2020 }}</ref>  
|-
|-
| [[GARE gene transcriptions|Gibberellin responsive element-like 2]] (GARE-like 2) || TAACGTA<ref name=Fan>{{ cite journal
| [[GARE gene transcriptions|Gibberellin responsive element-like 2]]  
 
(GARE-like 2)  
|| TAACGTA<ref name=Fan>{{ cite journal
|author=Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng
|author=Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng
|title=Gibberellin Signal Transduction in Rice
|title=Gibberellin Signal Transduction in Rice
Line 557: Line 677:
| [[GLM box gene transcriptions|GLM boxes]] || (G/A)TGA(G/C)TCA(T/C) || 16 || GCN4-like motif  
| [[GLM box gene transcriptions|GLM boxes]] || (G/A)TGA(G/C)TCA(T/C) || 16 || GCN4-like motif  
|-
|-
| [[Γ-interferon activated sequence gene transcriptions|γ-interferon activated sequences (GAS)]] || TTCCTAGAA || 16 || ALS-GAS1 between nt −633 and nt −625  
| [[Γ-interferon activated sequence gene transcriptions|γ-interferon activated sequences]]
 
(GAS)  
|| TTCCTAGAA || 16 || ALS-GAS1 between nt −633 and nt −625  
|-
|-
| [[Grainy head transcription factor gene transcriptions|Grainy head transcription factor binding sites]] || AACCGGTT || 8 || also GACTGGTT  
| [[Grainy head transcription factor gene transcriptions|Grainy head transcription factor binding sites]] || AACCGGTT || 8 || also GACTGGTT  
|-
|-
| [[TC element gene transcriptions|GT boxes (Motojima)]] || TGGGTGGGGCT || 16 || (-78 to -69)  
| [[TC element gene transcriptions|GT boxes]]
 
(Motojima)  
|| TGGGTGGGGCT || 16 || (-78 to -69)  
|-
| [[Middle sporulation element gene transcriptions|Hapless motifs]] || CCAATCA || 16 || heterotrimeric transcription factor, HAP2/3/4.<ref name=Ozsarac>{{ cite journal
| author = Nesrin Ozsarac, Melissa J. Straffon, Hazel E. Dalton, and Ian W. Dawes
| title = Regulation of Gene Expression during Meiosis in ''Saccharomyces cerevisiae'': ''SPR3'' Is Controlled by both ABFI and a New Sporulation Control Element
| journal = Molecular and Cellular Biology
| volume = 17
| issue = 3
| pages = 1152–9
| date = March 1997
| pmid = 9032242
| pmc = 231840
| doi = 10.1128/MCB.17.3.1152 }}</ref>
|-
|-
| [[Heat-responsive element gene transcriptions|Heat-responsive elements]] || AAAAAATTTC || 16 || four nGAAn motifs  
| [[Heat-responsive element gene transcriptions|Heat-responsive elements]] || AAAAAATTTC || 16 || four nGAAn motifs  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nGAAnnTTCnnGAAn || 16 || HSE1  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE1)
 
(Eastmond)  
|| nGAAnnTTCnnGAAn || 16 || HSE1  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nTTCnnGAAnnTTCn || 16 || HSE2 is the inverse complement of HSE1  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE2)
 
(Eastmond)  
|| nTTCnnGAAnnTTCn || 16 || HSE2 is the inverse complement of HSE1  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nTTCn-(5-bp)-nTTCnnGAAn || 16 || HSE5  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE5)
 
(Eastmond)  
|| nTTCn-(5-bp)-nTTCnnGAAn || 16 || HSE5  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nTTCn-nnGAAn-(5-bp)-nGAAn || 16 || HSE6  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE6)
 
(Eastmond)  
|| nTTCn-nnGAAn-(5-bp)-nGAAn || 16 || HSE6  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nGA(A/G)nnTTCnnGAAn || 16 || HSE7 PFT1  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE7)
 
(Eastmond)  
|| nGA(A/G)nnTTCnnGAAn || 16 || HSE7 PFT1  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] || nGAAnnTTCnnGA(A/G)n || 16 || HSE7 PFT2  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE)
 
(Eastmond)  
|| nGAAnnTTCnnGA(A/G)n || 16 || HSE7 PFT2  
|-
|-
| [[Hsf1p gene transcriptions|Heat shock elements (HSE, Eastmond)]] ||  nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn || 16 || HSE10  
| [[Hsf1p gene transcriptions|Heat shock elements]]
 
(HSE10)
 
(Eastmond)  
||  nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn || 16 || HSE10  
|-
|-
| [[Hypoxia-inducible factor gene transcriptions|Hypoxia-inducible factors]] || GCCCTACGTGCTGTCTCA<ref name=Li2020>{{ cite journal
| [[Hypoxia-inducible factor gene transcriptions|Hypoxia-inducible factors]] || GCCCTACGTGCTGTCTCA<ref name=Li2020>{{ cite journal
Line 596: Line 769:
| [[I box gene transcriptions|I boxes]] || GATAAG || 16 || GGATGAGATAAGA  
| [[I box gene transcriptions|I boxes]] || GATAAG || 16 || GGATGAGATAAGA  
|-
|-
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive elements (ICRE)]] (Case) || CANNTGAAAT || 16 || version of Lopes, see below  
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive elements]]
 
(ICRE)  
 
(Case)  
|| CANNTGAAAT || 16 || version of Lopes, see below  
|-
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive elements]]
 
(ICRE)
 
(Lopes)
|| ATGTGAAAT || 16 || using ANNTGAAAT
|-
| [[Interferon regulatory factor gene transcriptions|Interferon-stimulated response elements]]
 
(ISRE)
 
(Michalska)
|| AGTTTCNNTTTCN || 16 || similar to GAAANNGAAA.<ref name=Lu>{{ cite journal
|author=Mengmeng Lu, Chuanyan Yang, Meijia Li, Qilin Yi, Guangxia Lu, Yichen Wu, Chen Qu, Lingling Wang, and Linsheng Song
|title=A conserved interferon regulation factor 1 (IRF-1) from Pacific oyster ''Crassostrea gigas'' functioned as an activator of IFN pathway
|journal=Fish & Shellfish Immunology
|date=May 2018
|volume=76
|issue=May
|pages=68-77
|url=https://www.sciencedirect.com/science/article/abs/pii/S105046481830086X
|arxiv=
|bibcode=
|doi=10.1016/j.fsi.2018.02.024
|pmid=
|accessdate=27 March 2021 }}</ref>
|-
|-
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive elements (ICRE)]] (Lopes) || ATGTGAAAT || 16 || using ANNTGAAAT
| [[K-box gene transcriptions|K-boxes]] || GTTCGGNNANCCNNAC || 16 || GTTCGG-NNAN-CCNNAC<ref name=Saito>{{ cite journal
|author=Masakazu Saito, Satoru Watanabe, Kaori Nimura-Matsune, Hirofumi Yoshikawa1, Hitoshi Nakamoto
|title=Regulation of the ''groESL1'' transcription by the HrcA repressor and a novel transcription factor Orf7.5 in the cyanobacterium ''Synechococcus elongatus'' PCC7942
|journal=The Journal of General and Applied Microbiology
|date=10 April 2020
|volume=66
|issue=2
|pages=85-92
|url=https://www.jstage.jst.go.jp/article/jgam/advpub/0/advpub_2020.02.001/_pdf
|arxiv=
|bibcode=
|doi=10.2323/jgam.2020.02.001
|pmid=
|accessdate=17 March 2021 }}</ref>
|-
|-
| [[Kozak sequence gene transcriptions|Kozak sequences]] || GCCGCC(A/G)CCATGG || 16 || GCCGCC(A/G)CCATGG<ref name=Kozak1987>{{ cite journal
| [[Kozak sequence gene transcriptions|Kozak sequences]] || GCCGCC(A/G)CCATGG || 16 || GCCGCC(A/G)CCATGG<ref name=Kozak1987>{{ cite journal
Line 612: Line 830:
|pmid=3313277 }}</ref>  
|pmid=3313277 }}</ref>  
|-
|-
| [[Kozak sequence gene transcriptions|Kozak sequences]] || GAAAATGG || 16 || GAAAATGG<ref name=Matsumoto>{{ cite journal
| [[Kozak sequence gene transcriptions|Kozak sequences]]  
 
(Matsumoto)
|| GAAAATGG || 16 || GAAAATGG<ref name=Matsumoto>{{ cite journal
|author=Takuya Matsumoto
|author=Takuya Matsumoto
|author2=Saemi Kitajima
|author2=Saemi Kitajima
Line 648: Line 869:
|accessdate=8 November 2018 }}</ref>  
|accessdate=8 November 2018 }}</ref>  
|-
|-
| [[Maf recognition element gene transcriptions|MAREs]] || TGCTGA(G/C)TCAGCA || 16 || and TGCTGA(GC/CG)TCAGCA<ref name=Kyo>{{ cite journal
| [[Maf recognition element gene transcriptions|Maf recognition element]]  
 
(MAREs)
|| TGCTGA(G/C)TCAGCA || 16 || and TGCTGA(GC/CG)TCAGCA<ref name=Kyo>{{ cite journal
|author=Motoki Kyo, Tae Yamamoto, Hozumi Motohashi, Terue Kamiya, Toshihiro Kuroita, Toshiyuki Tanaka, James Douglas Engel, Bunsei Kawakami, Masayuki Yamamoto
|author=Motoki Kyo, Tae Yamamoto, Hozumi Motohashi, Terue Kamiya, Toshihiro Kuroita, Toshiyuki Tanaka, James Douglas Engel, Bunsei Kawakami, Masayuki Yamamoto
|title=Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique
|title=Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique
Line 680: Line 904:
| [[Mcm1 regulatory factor gene transcriptions|Mcm1 regulatory factors]] || TT(A/T)CCNN(A/T)TNGG(A/T)AA || 16 || Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.<ref name=Rossi/>  
| [[Mcm1 regulatory factor gene transcriptions|Mcm1 regulatory factors]] || TT(A/T)CCNN(A/T)TNGG(A/T)AA || 16 || Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.<ref name=Rossi/>  
|-
|-
| [[Met31p box gene transcriptions|Met31ps]] || AAACTGTG<ref name=Blaiseau/> || ⌘F || Sulfur amino acid metabolism
| [[Mcm1 regulatory factor gene transcriptions|Mcm1 regulatory factors]]  
 
(Rossi)
|| TTNCCNNNTNNGGNAA || 16 || Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.<ref name=Rossi/>  
|-
|-
| [[Middle sporulation element gene transcriptions|Middle sporulation elements]] || C(A/G)CAAA(A/T) || ⌘F || ACACAAA (2017)
| [[Motif ten element gene transcriptions|Motif ten elements]] || C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G) || 16 || Gene ID: 6309
|-
|-
| [[Motif ten element gene transcriptions|Motif ten elements]] || C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G || 16 || Gene ID: 6309
| [[Nuclear factor gene transcriptions|NF‐κB/Rel family of eukaryotic transcription factors]] || CCCCTAAGGGG || 16 || [[NF-κB]]
|-
|-
| [[Ndt80p gene transcriptions|Ndt80ps]] || TCCGCA || ⌘F || DNCRCAAAW
| [[Nuclear factor gene transcriptions|Nuclear factor 1]]  
 
(NF-1)
|| TTGGCNNNNNGCCAA || 8 || palindromic sequence
|-
|-
| [[Nuclear factor Y gene transcriptions|Nuclear factor Ys]] || TACCGACAT || ⌘F || NF-Y is a trimeric complex  
| [[Nuclear factor Y gene transcriptions|Nuclear factor Ys]] || CCAATGG(A/C)(A/G) || 16 || NF-Y is a trimeric complex  
|-
|-
| [[Nutrient-sensing response element gene transcriptions|Nutrient-sensing response element 1s]] || GTTTCATCA || ⌘F || only one nucleotide difference between the ''SESN2'' CARE and the ''ASNS''
| [[P63 DNA-binding site gene transcriptions|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) || 16 || RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY
|-
|-
| [[Oaf1p gene transcriptions|Oaf1ps]] || (A/C/G/T)(A/C/G/T)(A/C/G/T)T(A/C/G/T)A(A/C/G/T) || ⌘F || CGG(A/C/G/T)<sub>3</sub>T(A/C/G/T)A(A/C/G/T)<sub>9-12</sub>CCG
| [[Pdr1,3p gene transcriptions|Pdr1p/Pdr3ps]] || TCCGCGGA || 4 || Pdr1p/Pdr3p response elements (PDREs)  
|-
|-
| [[Pdr1,3p gene transcriptions|Pdr1p/Pdr3ps]] || TCCGCGGA || ⌘F || Pdr1p/Pdr3p response elements (PDREs)
| [[Peroxisome proliferator hormone response element gene transcriptions|Peroxisome proliferator-activated receptor alpha]] || CGACCCCT || 16 || Or, CGACCGCT.<ref name=Long/>
|-
|-
| [[Polycomb response element gene transcriptions|Polycomb response elements]] || CGCCATTT || ⌘F || closely resembles the extended Pho-Phol consensus sequence
| [[Peroxisome proliferator hormone response element gene transcriptions|Peroxisome proliferator hormone response elements]]  
 
(PPREs)
|| AGGTCANAGGTCA || 16 || PPARs/RXRs heterodimers bind to PPRE
|-
|-
| [[Rap1 regulatory factor gene transcriptions|Rap1 regulatory factors]] || C(A/C/G)(A/C/G)(A/G)(C/G/T)C(A/C/T)(A/G/T)(C/G/T)(A/G/T)(A/C/G)(A/C)(A/C/T)(A/C/T) || ⌘F || Rap1 (CCCACCAACAAAA) none
| [[Pollen1 element gene transcriptions|Pollen1 with TCCACCATA]] || AGAAANNNNTCCACCATA || 16 || adjacent co-dependent regulatory element TCCACCATA
|-
|-
| [[Rgt1p gene transcriptions|Rgt1ps]] || CGGACCA || ⌘F || Glucose-responsive transcription factors
| [[Polycomb response element gene transcriptions|Polycomb response elements]] || CGCCAT(A/T)TT || 16 || CGCCATTT
|-
|-
| [[Rlm1p gene transcriptions|Rlm1ps]] || CTATATATAG || ⌘F || CTA(T/A)<sub>4</sub>TAG
| [[Rap1 regulatory factor gene transcriptions|Rap1 regulatory factors]] || ACCC(A/G)N(A/G)CA || 16 || "(ACCCRnRCA), less than half of the sites were detectably bound"<ref name=Rossi/>  
|-
|-
| [[Rox1p gene transcriptions|Rox1ps]] || GGGTAA || ⌘F || Heme-dependent repressor of hypoxic genes [78]
| [[Reb1 general regulatory factor gene transcriptions|Extended Reb1]] || ATTACCCGAA || 16 || "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."<ref name=Rossi/>
|-
|-
| [[Rpn4p gene transcriptions|Rpn4ps]] || GGTGGCAAA || ⌘F || proteasome genes
| [[Rlm1p gene transcriptions|Rlm1ps]] || CTATATATAG || 8 || CTA(T/A)<sub>4</sub>TAG
|-
|-
| [[Seed-specific element gene transcriptions|Seed-specific elements]] || CATGCATG || ⌘F || SRE consensus: CAGCAGATTGCG is none
| [[Rox1p gene transcriptions|Rox1ps]] || RRRTAACAAGAG || 16 || Heme-dependent repressor of hypoxic genes.<ref name=Tang/>
|-
|-
| [[Shoot specific element gene transcriptions|Shoot specific elements]] || GATAATGATG || ⌘F || SRE consensus: CAGCAGATTGCG is none
| [[Rpn4p gene transcriptions|Rpn4ps]] || GGTGGCAAA || 16 || proteasome genes
|-
|-
| [[Sip4p gene transcriptions|Sip4ps]] || CCGTCCGT || ⌘F || CC(C/G)T(C/T)C(C/G)TCCG
| [[Seed-specific element gene transcriptions|Seed-specific elements]] || CATGCATG || 8 || SRE consensus: CAGCAGATTGCG is none
|-
|-
| [[Smp1p gene transcriptions|Smp1ps]] || ACTACTA || ⌘F || 5-ACTACTA(T/A)4TAG
| [[Shoot specific element gene transcriptions|Shoot specific elements]] || GATAATGATG || 16 || SRE consensus: CAGCAGATTGCG is none
|-
|-
| [[Sterol response element gene transcriptions|Sterol response elements]] || TCGTATA || ⌘F || perhaps plant specific
| [[Sip4p gene transcriptions|Sip4ps]] || CCGTCCGT || 16 || CC(C/G)T(C/T)C(C/G)TCCG
|-
|-
| [[TATC box gene transcriptions|TATCCAC boxes]] || TATCCAC || 16 || GA responsive complex component
| [[Smp1p gene transcriptions|Smp1ps]] || ACTACTA || 16 || 5-ACTACTA(T/A)4TAG
|-
|-
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || TCCACCATA || ⌘F || adjacent co-dependent regulatory element of POLLEN1
| [[Specificity protein gene transcriptions|SP1]]  
 
(Long)
|| GGGGCGGGCC || 16 || GGGGCGGGCC<ref name=Long/>
|-
|-
| [[Tec1p gene transcriptions|Tec1ps]] || GAATGT || ⌘F || Ste12p cofactor
| [[Sterol response element gene transcriptions|Sterol response elements]]  
 
(Branco)
|| TCGTATA || 16 || perhaps plant specific
|-
|-
| [[Tetradecanoylphorbol-13-acetate response element gene transcriptions|Tetradecanoylphorbol-13-acetate response elements (TREs)]] || TGA(G/C)TCA || 16 || ''cis''-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40
| [[Sterol response element gene transcriptions|Sterol response elements]]
 
(Yao)  
|| NAGCAGATTGCG || 16 || liver specific
|-
|-
| [[TC element gene transcriptions|TGF-β control elements (TCEs)]] || GAGTGGGGCG || ⌘F || in mouse and rat, GCGTGGGGGA in humans
| [[TATC box gene transcriptions|TATCCAC boxes]] || TATCCAC || 16 || GA responsive complex component
|-
|-
| [[TC element gene transcriptions|TGF-β inhibitory elements (TIEs)]] || GAGTGGTGA || 16 || in the rat transin/stromelysin promoter  
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || TCCACCATA || 16 || adjacent co-dependent regulatory element of POLLEN1
|-
| [[Tetradecanoylphorbol-13-acetate response element gene transcriptions|Tetradecanoylphorbol-13-acetate response elements]]
 
(TREs)  
|| TGA(G/C)TCA || 16 || ''cis''-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40
|-
|-
| [[Thyroid hormone response element gene transcriptions|Thyroid hormone response elements (TREs)]] || AGGTCA || ⌘F || See VDREs, X boxes
| [[TC element gene transcriptions|TGF-β control elements]]
 
(TCEs)  
|| GAGTGGGGCG || 16 || in mouse and rat, GCGTGGGGGA in humans
|-
|-
| [[Unfolded protein response element gene transcriptions|Unfolded protein response elements (UPREs)]] || TGACGTG(G/A) || ⌘F || XBP1 binds to UPRE
| [[TC element gene transcriptions|TGF-β inhibitory elements]]
 
(TIEs)  
|| GAGTGGTGA || 16 || in the rat transin/stromelysin promoter
|-
|-
| [[Vhr1p gene transcriptions|Vhr1ps]] || AATCA-N<sub>8</sub>-TGA(C/T)T || ⌘F || Response to low biotin [71] concentrations
| [[Vhr1p gene transcriptions|Vhr1ps]] || AATCA-N<sub>8</sub>-TGA(C/T)T || 16 || "enhanced by low extracellular biotin."<ref name=Weider>{{ cite journal
|author=Matthias Weider, Agnes Machnik, Franz Klebl and Norbert Sauer
|title=Vhr1p, a New Transcription Factor from Budding Yeast, Regulates Biotin-dependent Expression of ''VHT1'' and ''BIO5''
|journal=Journal of Biological Chemistry
|date=12 May 2006
|volume=281
|issue=19
|pages=P13513-P13524
|url=https://www.jbc.org/article/S0021-9258(19)74889-3/fulltext
|arxiv=
|bibcode=
|doi=10.1074/jbc.M512158200
|pmid=
|accessdate=8 March 2021 }}</ref>
|-
|-
| [[Vitamin D response element gene transcriptions|Vitamin D response elements (VDREs)]] || (A/G)G(G/T)(G/T)CA || ⌘F || AGGTCA not ⌘F
| [[Vitamin D response element gene transcriptions|Vitamin D response elements]]
 
(VDREs)  
|| A/GGG/TTCAnnnA/GGG/TTCA || 16 || (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA
|-
|-
| [[X box gene transcriptions|X boxes]] || GTTGGCATGGCAAC || 16 || X2 box is AGGTCCA not ⌘F  
| [[X box gene transcriptions|X boxes]] || GTTGGCATGGCAAC || 16 || X2 box is AGGTCCA not ⌘F  
|-
|-
| [[Xbp1p gene transcriptions|Xbp1ps]] || GcCTCGA(G/A)G(C/A)g(a/g) || ⌘F || Transcriptional repressor
| [[X box gene transcriptions|X-boxes]] || GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC || 16 || includes GTTNCCATGGNAAC
|-
|-
| [[Xenobiotic response element gene transcriptions|Xenobiotic response elements (XREs)]] || (T/G)NGCGTG(A/C)(G/C)A || ⌘F || contains the core sequence GCGTG
| [[Xbp1p gene transcriptions|Xbp1ps]] || GcCTCGA(G/A)G(C/A)g(a/g) || 16 || Transcriptional repressor
|-
|-
| [[Yap1p,2p gene transcriptions|Yap1p,2ps]] || TTACTAA || ⌘F || Yap1p binding sites
| [[Xenobiotic response element gene transcriptions|Xenobiotic response elements]]  
 
(XREs)
|| (T/G)NGCGTG(A/C)(G/C)A || 16 || contains the core sequence GCGTG, see [[Xenobiotic response element gene transcriptions|AhR-responsive elements]]
|-
|-
| [[Y box gene transcriptions|Y boxes]] || (A/G)CTAACC(A/G)(A/G)(C/T) || 16 || inverted CAAT box  
| [[Y box gene transcriptions|Y boxes]] || (A/G)CTAACC(A/G)(A/G)(C/T) || 16 || inverted CAAT box  
|-
|-
| [[Zap1p gene transcriptions|Zap1ps]] || ACCCTCA || ⌘F || ACC(C/T)(C/T)(A/C/G/T)AAGGT  
| [[YY1 gene transcriptions|YY1 binding sites]] || CCATTTA || 16 || YY1 represses Tug1 transcription<ref name=Long/>
|-
| [[Zap1p gene transcriptions|Zap1ps]] || ACCCTCA || 16 || ACC(C/T)(C/T)(A/C/G/T)AAGGT  
|-
|-
|}
|}
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<!-- footer categories -->
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[[Category:Resources last modified in February 2021]]
[[Category:Resources last modified in March 2021]]

Latest revision as of 04:25, 10 June 2021

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

Main article: 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 negative results

Main article: A1BG regulatory elements and regions
Response elements not occurring in promoters near A1BG
Name of elements Consensus sequences Testing Notes
Abbreviations variations number of runs per symmetry
Authors
novel ABA-response elements

(ABREN, novel ABRE)

GATCGATC, CGATCGAT, GATCGAT 16 ABREN, CGATCGAT motif, and core of ABREN and CGATCGAT motif.[2]
ABA-response element-like

(ABRE-like)

ACGTGTCC 16 third highest scoring motif[2]
Abf1 regulatory factors CGTCCTCTACG 16 CGTNNNNNACGAT[3]
Activating proteins

(AP-2)

GCCCACGGG 16 Activating protein 2[4]
Activating proteins

(AP-2)

GGCCAA 16 Activating protein 2 (AP-2)[5]
AhR-responsive elements

(AHRE)

(Yao)

(G/T)NGCGTG(A/C)(C/G)A 16 in the promoter region of AhR responsive genes
Alpha-amylase conserved elements TATCCA 16 TATCCATCCATCC[6]
Amino acid response elements

(AARE)

(Maruyama)

ATTGCATCA 16 AARE1 (ATTGCATCA)[7]
Amino acid response elements

(AARE)

(Broer)

TTTGCATCA 16 TTTGCATCA.[8][9]
Amino acid response element-like

(AARE-like)

TGGTGAAAG 16 AARE-like sequence (TGGTGAAAG, named AARE3)[7]
Androgen response elements

(AREs)

(Kouhpayeh)

GGTACANNNTGTTCT[10] 16 GGTACACGGTGTTCT[10]
Androgen response elements

(AREs)

(Wilson)

TGATTCGTGAG 16 AGAACANNNTGTTCT[11]
Antioxidant-electrophile responsive elements GTGAGGTCGC 16 GTGAGGTCGC[12] or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A[13], an antioxidant response element (ARE)
CAAT boxes (C/T)(A/G)(A/G)CCAATC(A/G) 16 consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT
Calcium-response elements CTATTTCGAG 16 CaRE1 CTATTTCGAG[14]
Carbohydrate response elements

(ChREs)

CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG 16 ChoRE1, ChoRE2[15]
Carbon source-responsive elements

(CSREs)

CATTCATCCG 16 confers carbon source-dependent regulation[16]
Cbf1 regulatory factors TCACGTGA 8 strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end
C-boxes GAGGCCATCT 16 GAGGCCATCT[17]
C/A hybrid boxes TGACGTAT 16 TGACGTAT[18] A at the 12 position
C/T hybrid boxes TGACGTTA 16 TGACGTTA[18] T at the 12 position
CCCTC-binding factors

(CTCF)

NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T) 16 NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)[19]
C/EBP boxes TTAGGACAT,[20] or TAGCATT[5] 16 CCAAT-enhancer-binding site (C/EBP) is TAGCATT
Cell-cycle boxes

(CCBs)

CACGAAAA 16 more relaxed variants are present
Cell cycle regulation CCCAACGGT[6] 16 tomato genome-wide analysis
CENP-B boxes TTTCGTTGGAAGCGGGA 16 specifically localized at the centromere
Coupling elements

(CEs)

TGCCACCGG[2] 16 CE1 (Watanabe)
Constitutive decay elements

(Siegel)

(CDEs)

CCUUCYRYGAAGG, CCTTC(C/T)(A/G)(C/T)GAAGG 16 TTCCATGAA at 128 but no CC or GG at the ends
DAF-16-associated elements

(DAE)

TGATAAG 16 DAF-16-associated element (DAE)[21]
D-boxes

(Mracek1)

GTTGTATAAC 16 GTTGTATAAC[22]
D-boxes

(Mracek)

CTTATGTAAA (Mracek2) 16 CTTATGTAAA[22]
D-boxes

(Johnson)

TCTCACA 16 TCTCACATT(A/C)AATAAGTCA is a D-box.[17]
Defense and stress-responsive elements ATTTTCTTCA 16 (ATTTTCTTCA)[6]
DNA damage response elements

(DREs)

(Smith)

TTTCAAT[23] 16 in the upstream repression sequence (URS)
DNA damage response elements

(DREs)

(Sumrada)

TAGCCGCCG of TAGCCGCCGRRRR[24] 16 in the upstream repression sequence (URS)
DNA replication-related elements

(DREs)

TATCGATA 16 DNA replication-related element (DRE)[25]
DREB boxes TACCGACAT 16 CRT/DREB box
EIF4E basal elements TTACCCCCCCTT 16 poly(C) motif
Endoplasmic reticulum stress response elements

(ERSE)

CCAAT 16 CCAATGGGCTGAAAC between ZNF497 and A1BG, compare CCAAT-box and ERSE
Estrogen response elements

(EREs)

AGGTTA or GGTCAGGAT 16 AGGTTATTGCCTCCT or GGTCAGGATGAC
F boxes TGATAAG[26] 16 F-box overlaps the I-box
Forkhead boxes GTAAACAA[27] 16 GTAAACAA FOXO1
Gal4ps CGGACCGC 16 CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG[28]
Gibberellin responsive element-like 2

(GARE-like 2)

TAACGTA[29] 16 "in the promoters of hydrolase genes".[29]
G boxes (G/T)CCACGTG(G/T)C 16 no "perfect palindrome" G boxes in either promoter
GCN4 motifs TGACTCA, TGAGTCA 16 ACGT motif
Gcn4ps ATGACTCTT[28] 16 GCN4 motifs
GLM boxes (G/A)TGA(G/C)TCA(T/C) 16 GCN4-like motif
γ-interferon activated sequences

(GAS)

TTCCTAGAA 16 ALS-GAS1 between nt −633 and nt −625
Grainy head transcription factor binding sites AACCGGTT 8 also GACTGGTT
GT boxes

(Motojima)

TGGGTGGGGCT 16 (-78 to -69)
Hapless motifs CCAATCA 16 heterotrimeric transcription factor, HAP2/3/4.[30]
Heat-responsive elements AAAAAATTTC 16 four nGAAn motifs
Heat shock elements

(HSE1)

(Eastmond)

nGAAnnTTCnnGAAn 16 HSE1
Heat shock elements

(HSE2)

(Eastmond)

nTTCnnGAAnnTTCn 16 HSE2 is the inverse complement of HSE1
Heat shock elements

(HSE5)

(Eastmond)

nTTCn-(5-bp)-nTTCnnGAAn 16 HSE5
Heat shock elements

(HSE6)

(Eastmond)

nTTCn-nnGAAn-(5-bp)-nGAAn 16 HSE6
Heat shock elements

(HSE7)

(Eastmond)

nGA(A/G)nnTTCnnGAAn 16 HSE7 PFT1
Heat shock elements

(HSE)

(Eastmond)

nGAAnnTTCnnGA(A/G)n 16 HSE7 PFT2
Heat shock elements

(HSE10)

(Eastmond)

nTTCn-(11-bp)-nGAAn-(5 bp)-nGAAn 16 HSE10
Hypoxia-inducible factors GCCCTACGTGCTGTCTCA[31] 16 composed of HIF-1α and HIF-1β
I boxes GATAAG 16 GGATGAGATAAGA
Inositol, choline-responsive elements

(ICRE)

(Case)

CANNTGAAAT 16 version of Lopes, see below
Inositol, choline-responsive elements

(ICRE)

(Lopes)

ATGTGAAAT 16 using ANNTGAAAT
Interferon-stimulated response elements

(ISRE)

(Michalska)

AGTTTCNNTTTCN 16 similar to GAAANNGAAA.[32]
K-boxes GTTCGGNNANCCNNAC 16 GTTCGG-NNAN-CCNNAC[33]
Kozak sequences GCCGCC(A/G)CCATGG 16 GCCGCC(A/G)CCATGG[34]
Kozak sequences

(Matsumoto)

GAAAATGG 16 GAAAATGG[35]
L boxes AAATTAACCAA 16 AAATTAACCAA[36]
Maf recognition element

(MAREs)

TGCTGA(G/C)TCAGCA 16 and TGCTGA(GC/CG)TCAGCA[37]
M boxes GTCATGTGCT 16 or AGTCATGTGCT[38]
Mcm1 regulatory factors TT(A/T)CCNN(A/T)TNGG(A/T)AA 16 Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[3]
Mcm1 regulatory factors

(Rossi)

TTNCCNNNTNNGGNAA 16 Primary consensus sequence apparently: TT(A/T)CCNN(A/T)TNGG(A/T)AA.[3]
Motif ten elements C(C/G)A(A/G)C(C/G)(C/G)AACG(C/G) 16 Gene ID: 6309
NF‐κB/Rel family of eukaryotic transcription factors CCCCTAAGGGG 16 NF-κB
Nuclear factor 1

(NF-1)

TTGGCNNNNNGCCAA 8 palindromic sequence
Nuclear factor Ys CCAATGG(A/C)(A/G) 16 NF-Y is a trimeric complex
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) 16 RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY
Pdr1p/Pdr3ps TCCGCGGA 4 Pdr1p/Pdr3p response elements (PDREs)
Peroxisome proliferator-activated receptor alpha CGACCCCT 16 Or, CGACCGCT.[15]
Peroxisome proliferator hormone response elements

(PPREs)

AGGTCANAGGTCA 16 PPARs/RXRs heterodimers bind to PPRE
Pollen1 with TCCACCATA AGAAANNNNTCCACCATA 16 adjacent co-dependent regulatory element TCCACCATA
Polycomb response elements CGCCAT(A/T)TT 16 CGCCATTT
Rap1 regulatory factors ACCC(A/G)N(A/G)CA 16 "(ACCCRnRCA), less than half of the sites were detectably bound"[3]
Extended Reb1 ATTACCCGAA 16 "extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."[3]
Rlm1ps CTATATATAG 8 CTA(T/A)4TAG
Rox1ps RRRTAACAAGAG 16 Heme-dependent repressor of hypoxic genes.[28]
Rpn4ps GGTGGCAAA 16 proteasome genes
Seed-specific elements CATGCATG 8 SRE consensus: CAGCAGATTGCG is none
Shoot specific elements GATAATGATG 16 SRE consensus: CAGCAGATTGCG is none
Sip4ps CCGTCCGT 16 CC(C/G)T(C/T)C(C/G)TCCG
Smp1ps ACTACTA 16 5-ACTACTA(T/A)4TAG
SP1

(Long)

GGGGCGGGCC 16 GGGGCGGGCC[15]
Sterol response elements

(Branco)

TCGTATA 16 perhaps plant specific
Sterol response elements

(Yao)

NAGCAGATTGCG 16 liver specific
TATCCAC boxes TATCCAC 16 GA responsive complex component
TCCACCATA elements TCCACCATA 16 adjacent co-dependent regulatory element of POLLEN1
Tetradecanoylphorbol-13-acetate response elements

(TREs)

TGA(G/C)TCA 16 cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40
TGF-β control elements

(TCEs)

GAGTGGGGCG 16 in mouse and rat, GCGTGGGGGA in humans
TGF-β inhibitory elements

(TIEs)

GAGTGGTGA 16 in the rat transin/stromelysin promoter
Vhr1ps AATCA-N8-TGA(C/T)T 16 "enhanced by low extracellular biotin."[39]
Vitamin D response elements

(VDREs)

A/GGG/TTCAnnnA/GGG/TTCA 16 (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA
X boxes GTTGGCATGGCAAC 16 X2 box is AGGTCCA not ⌘F
X-boxes GT(A/C/T)N(C/T)(C/T)AT(A/G)(A/G)NAAC 16 includes GTTNCCATGGNAAC
Xbp1ps GcCTCGA(G/A)G(C/A)g(a/g) 16 Transcriptional repressor
Xenobiotic response elements

(XREs)

(T/G)NGCGTG(A/C)(G/C)A 16 contains the core sequence GCGTG, see AhR-responsive elements
Y boxes (A/G)CTAACC(A/G)(A/G)(C/T) 16 inverted CAAT box
YY1 binding sites CCATTTA 16 YY1 represses Tug1 transcription[15]
Zap1ps ACCCTCA 16 ACC(C/T)(C/T)(A/C/G/T)AAGGT

Acknowledgements

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

See also

References

  1. ↑ MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.
  2. ↑ 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. ↑ 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.
  4. ↑ 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. ↑ 5.0 5.1 Yao EF; Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
  6. ↑ 6.0 6.1 6.2 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.
  7. ↑ 7.0 7.1 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.
  8. ↑ 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.
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  10. ↑ 10.0 10.1 S Kouhpayeh; AR Einizadeh; Z Hejazi; M Boshtam; L Shariati; M Mirian; L Darzi; M Sojoudi; H Khanahmad; A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.
  11. ↑ Stephen Wilson; Jianfei Qi; Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.
  12. ↑ Akihito Otsuki; Mikiko Suzuki; Fumiki Katsuoka; Kouhei Tsuchida; Hiromi Suda; Masanobu Morita; Ritsuko Shimizu; Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.
  13. ↑ Sarah E. Lacher; Daniel C. Levings; Samuel Freeman; Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.
  14. ↑ Xu Tao; Anne E. West; Wen G. Chen; Gabriel Corfas; Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.
  15. ↑ 15.0 15.1 15.2 15.3 Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.
  16. ↑ A Schöler and H J Schüller (June 1994). "A carbon source-responsive promoter element necessary for activation of the isocitrate lyase gene ICL1 is common to genes of the gluconeogenic pathway in the yeast Saccharomyces cerevisiae" (PDF). Molecular and Cellular Biology. 14 (6): 3613–3622. Retrieved 9 February 2021.
  17. ↑ 17.0 17.1 PA Johnson; D Bunick; NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. doi:10.1095/biolreprod44.1.127. PMID 2015343. Retrieved 6 April 2019.
  18. ↑ 18.0 18.1 Young Hun Song; Cheol Min Yoo; An Pio Hong; Seong Hee Kim; Hee Jeong Jeong; Su Young Shin; Hye Jin Kim; Dae-Jin Yun; Chae Oh Lim; Jeong Dong Bahk; Sang Yeol Lee; Ron T. Nagao; Joe L. Key; Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.
  19. ↑ Hideharu Hashimoto; Dongxue Wang; John R. Horton; Xing Zhang; Victor G. Corces; Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.
  20. ↑ Ravi P. Misra; Azad Bonni; Cindy K. Miranti; Victor M. Rivera; Morgan Sheng; Michael E.Greenberg (14 October 1994). "L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway" (PDF). The Journal of Biological Chemistry. 269 (41): 25483–25493. PMID 7929249. Retrieved 7 December 2019.
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  25. ↑ Fumiko Hirose; Masamitsu Yamaguchi; Akio Matsukage (September 1999). "Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc". Molecular and Cellular Biology. 19 (9): 6020–6028. doi:10.1128/MCB.19.9.6020. PMID 10454549. Retrieved 4 September 2020.
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  30. ↑ Nesrin Ozsarac, Melissa J. Straffon, Hazel E. Dalton, and Ian W. Dawes (March 1997). "Regulation of Gene Expression during Meiosis in Saccharomyces cerevisiae: SPR3 Is Controlled by both ABFI and a New Sporulation Control Element". Molecular and Cellular Biology. 17 (3): 1152–9. doi:10.1128/MCB.17.3.1152. PMC 231840. PMID 9032242.
  31. ↑ Qingliang Li, Rezaul M. Karim, Mo Cheng, Mousumi Das, Lihong Chen, Chen Zhang, Harshani R. Lawrence, Gary W. Daughdrill, Ernst Schonbrunn, Haitao Ji and Jiandong Chen (July 2020). "Inhibition of p53 DNA binding by a small molecule protects mice from radiation toxicity". Oncogene. 39 (29): 5187–5200. doi:10.1038/s41388-020-1344-y. PMID 32555331 Check |pmid= value (help). Retrieved 29 August 2020.
  32. ↑ Mengmeng Lu, Chuanyan Yang, Meijia Li, Qilin Yi, Guangxia Lu, Yichen Wu, Chen Qu, Lingling Wang, and Linsheng Song (May 2018). "A conserved interferon regulation factor 1 (IRF-1) from Pacific oyster Crassostrea gigas functioned as an activator of IFN pathway". Fish & Shellfish Immunology. 76 (May): 68–77. doi:10.1016/j.fsi.2018.02.024. Retrieved 27 March 2021.
  33. ↑ Masakazu Saito, Satoru Watanabe, Kaori Nimura-Matsune, Hirofumi Yoshikawa1, Hitoshi Nakamoto (10 April 2020). "Regulation of the groESL1 transcription by the HrcA repressor and a novel transcription factor Orf7.5 in the cyanobacterium Synechococcus elongatus PCC7942". The Journal of General and Applied Microbiology. 66 (2): 85–92. doi:10.2323/jgam.2020.02.001. Retrieved 17 March 2021.
  34. ↑ Marilyn Kozak (October 1987). "An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Research. 15 (20): 8125–8148. doi:10.1093/nar/15.20.8125. PMID 3313277.
  35. ↑ Takuya Matsumoto; Saemi Kitajima; Chisato Yamamoto; Mitsuru Aoyagi; Yoshiharu Mitoma; Hiroyuki Harada; Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  36. ↑ Robert G. K. Donald and Anthony R. Cashmore (1990). "Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS‐1A promoter". The EMBO Journal. 9 (6): 1717–1726. doi:10.1002/j.1460-2075.1990.tb08295.x. Retrieved 8 November 2018.
  37. ↑ Motoki Kyo, Tae Yamamoto, Hozumi Motohashi, Terue Kamiya, Toshihiro Kuroita, Toshiyuki Tanaka, James Douglas Engel, Bunsei Kawakami, Masayuki Yamamoto (13 February 2004). "Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique". Genes to Cells. 9 (2). doi:10.1111/j.1356-9597.2004.00711.x. Retrieved 8 September 2020.
  38. ↑ Corine Bertolotto, Roser Buscà, Patricia Abbe, Karine Bille, Edith Aberdam, Jean-Paul Ortonne, and Robert Ballotti (February 1998). "Different cis-Acting Elements Are Involved in the Regulation of TRP1 and TRP2 Promoter Activities by Cyclic AMP: Pivotal Role of M Boxes (GTCATGTGCT) and of Microphthalmia". Molecular and Cellular Biology. 18 (2): 694–702. PMID 9447965. Retrieved 8 December 2018.
  39. ↑ Matthias Weider, Agnes Machnik, Franz Klebl and Norbert Sauer (12 May 2006). "Vhr1p, a New Transcription Factor from Budding Yeast, Regulates Biotin-dependent Expression of VHT1 and BIO5". Journal of Biological Chemistry. 281 (19): P13513–P13524. doi:10.1074/jbc.M512158200. Retrieved 8 March 2021.

External links

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