A1BG response element negative results: Difference between revisions

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! Name of elements !! Consensus sequences !! Testing !! Notes
! Name of elements !! Consensus sequences !! Testing !! Notes
|-
|-
| [[ABA-response element gene transcriptions|ABA-response elements]] || 5'-GATCGATC-3', 5'-CGATCGAT-3', 5'-ACGTGTCC-3', 5'-GATCGAT-3' || 16 || ABREN, CGATCGAT motif, ABRE, and core of ABREN and CGATCGAT motif.<ref name=Watanabe>{{ cite journal
| [[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
|author=Kenneth A. Watanabe
|author=Kenneth A. Watanabe
|author2=Arielle Homayouni
|author2=Arielle Homayouni
Line 43: Line 43:
|accessdate=5 October 2020 }}</ref>  
|accessdate=5 October 2020 }}</ref>  
|-
|-
| [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] || 5'-CGTCCTCTACG-3' || 16 || 5'-CGTNNNNNACGAT-3'<ref name=Rossi>{{ cite journal
| [[Abf1 regulatory factor gene transcriptions|Abf1 regulatory factors]] || CGTCCTCTACG || 16 || CGTNNNNNACGAT<ref name=Rossi>{{ cite journal
|author=Matthew J. Rossi
|author=Matthew J. Rossi
|author2=William K.M. Lai
|author2=William K.M. Lai
Line 60: Line 60:
|accessdate=31 August 2020 }}</ref>  
|accessdate=31 August 2020 }}</ref>  
|-
|-
| [[Activating protein gene transcriptions|Activating proteins]] || 5'-GCCCACGGG-3' || 16 || Activating protein 2 (AP-2)<ref name=Murata>{{ cite journal
| [[Activating protein gene transcriptions|Activating proteins]] || GCCCACGGG || 16 || Activating protein 2 (AP-2)<ref name=Murata>{{ cite journal
|author=Takayuki Murata
|author=Takayuki Murata
|author2=Chieko Noda
|author2=Chieko Noda
Line 86: Line 86:
|accessdate=4 October 2020 }}</ref>  
|accessdate=4 October 2020 }}</ref>  
|-
|-
| [[Activating protein gene transcriptions|Activating proteins]] || 5'-GGCCAA-3' || 16 || Activating protein 2 (AP-2)<ref name=Yao/>  
| [[Activating protein gene transcriptions|Activating proteins]] || GGCCAA || 16 || Activating protein 2 (AP-2)<ref name=Yao/>  
|-
|-
| [[Alpha-amylase conserved element gene transcriptions|Alpha-amylase conserved elements]] || 5'-TATCCA-3' || 16 || 5'-TATCCATCCATCC-3'<ref name=Sharma>{{ cite journal
| [[Alpha-amylase conserved element gene transcriptions|Alpha-amylase conserved elements]] || TATCCA || 16 || TATCCATCCATCC<ref name=Sharma>{{ cite journal
|author=Bhaskar Sharma
|author=Bhaskar Sharma
|author2=Joemar Taganna  
|author2=Joemar Taganna  
Line 104: Line 104:
|accessdate=27 August 2020 }}</ref>  
|accessdate=27 August 2020 }}</ref>  
|-
|-
| [[Amino acid response element gene transcriptions|Amino acid response elements]] || 5'-ATTGCATCA-3' || 16 || AARE1 (5'-ATTGCATCA-3')<ref name=Maruyama/>  
| [[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]] || 5'-TTTGCATCA-3' || 16 || 5'-TTTGCATCA-3'.<ref name=Broer>{{ cite journal
| [[Amino acid response element gene transcriptions|Amino acid response elements]] || 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 144:
|accessdate=5 September 2020 }}</ref>  
|accessdate=5 September 2020 }}</ref>  
|-
|-
| [[Amino acid response element gene transcriptions|AARE-like]] || 5'-TGGTGAAAG-3' || 16 || AARE-like sequence (5′- TGGTGAAAG-3′, named AARE3)<ref name=Maruyama>{{ cite journal
| [[Amino acid response element gene transcriptions|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 162:
|accessdate=4 October 2020 }}</ref>  
|accessdate=4 October 2020 }}</ref>  
|-
|-
| [[Androgen response element gene transcriptions|Androgen response elements]] || 5'-GGTACANNNTGTTCT-3'<ref name=Kouhpayeh/> || 16 || 5′-GGTACACGGTGTTCT-3′<ref name=Kouhpayeh>{{ cite journal
| [[Androgen response element gene transcriptions|Androgen response elements]] || 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 186:
|accessdate=3 October 2020 }}</ref>  
|accessdate=3 October 2020 }}</ref>  
|-
|-
| [[Androgen response element gene transcriptions|Androgen response elements]] || 5'-TGATTCGTGAG-3' || 16 || 5'-AGAACANNNTGTTCT-3'<ref name=Wilson>{{ cite journal
| [[Androgen response element gene transcriptions|Androgen response elements]] || TGATTCGTGAG || 16 || AGAACANNNTGTTCT<ref name=Wilson>{{ cite journal
|author=Stephen Wilson
|author=Stephen Wilson
|author2=Jianfei Qi
|author2=Jianfei Qi
Line 203: Line 203:
|accessdate=3 October 2020 }}</ref>  
|accessdate=3 October 2020 }}</ref>  
|-
|-
| [[Antioxidant-electrophile responsive element gene transcriptions|Antioxidant-electrophile responsive elements]] || 5'-GTGAGGTCGC-3' || 16 || 5'-GTGAGGTCGC-3'<ref name=Otsuki>{{ cite journal
| [[Antioxidant-electrophile responsive element gene transcriptions|Antioxidant-electrophile responsive elements]] || GTGAGGTCGC || 16 || GTGAGGTCGC<ref name=Otsuki>{{ cite journal
|author=Akihito Otsuki
|author=Akihito Otsuki
|author2=Mikiko Suzuki
|author2=Mikiko Suzuki
Line 223: Line 223:
|doi=10.1016/j.freeradbiomed.2015.12.005
|doi=10.1016/j.freeradbiomed.2015.12.005
|pmid=26677805
|pmid=26677805
|accessdate=21 August 2020 }}</ref> or 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3'<ref name=Lacher>{{ cite journal
|accessdate=21 August 2020 }}</ref> or GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A<ref name=Lacher>{{ cite journal
|author=Sarah E. Lacher
|author=Sarah E. Lacher
|author2=Daniel C. Levings
|author2=Daniel C. Levings
Line 241: Line 241:
|accessdate=6 October 2020 }}</ref>, an antioxidant response element (ARE)  
|accessdate=6 October 2020 }}</ref>, an antioxidant response element (ARE)  
|-
|-
| [[CAAT box gene transcriptions|CAAT boxes]] || 5'-(C/T)(A/G)(A/G)CCAATC(A/G)-3' || 16 || consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT  
| [[CAAT box gene transcriptions|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 element gene transcriptions|Calcium-response elements]] || 5'-CTATTTCGAG-3' || 16 || CaRE1 5'-CTATTTCGAG-3'<ref name=Tao>{{ cite journal
| [[Calcium-response element gene transcriptions|Calcium-response elements]] || CTATTTCGAG || 16 || CaRE1 CTATTTCGAG<ref name=Tao>{{ cite journal
|author=Xu Tao
|author=Xu Tao
|author2=Anne E. West
|author2=Anne E. West
Line 262: Line 262:
|accessdate=2 September 2020 }}</ref>  
|accessdate=2 September 2020 }}</ref>  
|-
|-
| [[Carbohydrate response element gene transcriptions|Carbohydrate response elements]] || 5'-CACGTGACCGGATCTTG-3', 5'-TCCGCCCCCATCACGTG-3' || 16 || ChoRE1, ChoRE2<ref name=Long>{{ cite journal
| [[Carbohydrate response element gene transcriptions|Carbohydrate response elements]] || 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 285: Line 285:
|accessdate=6 October 2020 }}</ref>  
|accessdate=6 October 2020 }}</ref>  
|-
|-
| [[Cbf1 regulatory factor gene transcriptions|Cbf1 regulatory factors]] || 5'-TCACGTGA-3' || 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  
|-
|-
| [[C box gene transcriptions|C-boxes]] || 5'-GAGGCCATCT-3' || 16 || 5'-GAGGCCATCT-3'<ref name=Johnson>{{ cite journal
| [[C box gene transcriptions|C-boxes]] || GAGGCCATCT || 16 || GAGGCCATCT<ref name=Johnson>{{ cite journal
|author=PA Johnson
|author=PA Johnson
|author2=D Bunick
|author2=D Bunick
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|accessdate=6 April 2019 }}</ref>  
|accessdate=6 April 2019 }}</ref>  
|-
|-
| [[C box gene transcriptions|C/A hybrid boxes]] || 5'-TGACGTAT-3' || 16 || 5'-TGACGTAT-3'<ref name=Song>{{ cite journal
| [[C box gene transcriptions|C/A hybrid boxes]] || TGACGTAT || 16 || TGACGTAT<ref name=Song>{{ cite journal
|author=Young Hun Song
|author=Young Hun Song
|author2=Cheol Min Yoo
|author2=Cheol Min Yoo
Line 332: Line 332:
|accessdate=26 March 2019 }}</ref>  
|accessdate=26 March 2019 }}</ref>  
|-
|-
| [[C box gene transcriptions|C/T hybrid boxes]] || 5'-TGACGTTA-3' || 16 || 5'-TGACGTTA-3'<ref name=Song/>  
| [[C box gene transcriptions|C/T hybrid boxes]] || TGACGTTA || 16 || TGACGTTA<ref name=Song/>  
|-
|-
| [[CCCTC-binding factor gene transcriptions|CCCTC-binding factors (CTCF)]] || 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3' || 16 || 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′<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 354: Line 354:
|accessdate=28 August 2020 }}</ref>  
|accessdate=28 August 2020 }}</ref>  
|-
|-
| [[C-EBP box gene transcriptions|C/EBP boxes]] || 5'-TTAGGACAT-3',<ref name=Misra>{{ cite journal
| [[C-EBP box gene transcriptions|C/EBP boxes]] || TTAGGACAT,<ref name=Misra>{{ cite journal
|author=Ravi P. Misra
|author=Ravi P. Misra
|author2=Azad Bonni
|author2=Azad Bonni
Line 372: Line 372:
|doi=
|doi=
|pmid=7929249
|pmid=7929249
|accessdate=7 December 2019 }}</ref> or 5'-TAGCATT-3'<ref name=Yao>{{ cite journal
|accessdate=7 December 2019 }}</ref> or TAGCATT<ref name=Yao>{{ cite journal
| author = Yao EF
| author = Yao EF
|author2=Denison MS
|author2=Denison MS
Line 384: Line 384:
| 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 regulation gene transcriptions|Cell cycle regulation]] || 5'-CCCAACGGT-3'<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  
|-
|-
| [[CENP-B box gene transcriptions|CENP-B boxes]] || 5'-TTTCGTTGGAAGCGGGA-3' || 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]] || 5'-TGCCACCGG-3'<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
| [[Coupling element gene transcriptions|Coupling elements]] || TGCCACCGG<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
|-
|-
| [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] || 5'-TGATAAG-3' || 16 || DAF-16-associated element (DAE)<ref name=Li>{{ cite journal
| [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] || 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 406:
|accessdate=27 August 2020 }}</ref>  
|accessdate=27 August 2020 }}</ref>  
|-
|-
| [[D box gene transcriptions|D-box]] || 5'-GTTGTATAAC-3' (Mracek1) || 16 || 5′-GTTGTATAAC-3′<ref name=Mracek>{{ cite journal
| [[D box gene transcriptions|D-box]] || GTTGTATAAC (Mracek1) || 16 || GTTGTATAAC<ref name=Mracek>{{ cite journal
|author=Philipp Mracek
|author=Philipp Mracek
|author2=Cristina Santoriello
|author2=Cristina Santoriello
Line 428: Line 428:
|accessdate=10 February 2019 }}</ref>  
|accessdate=10 February 2019 }}</ref>  
|-
|-
| [[D box gene transcriptions|D-box]] || 5'-CTTATGTAAA-3' (Mracek2) || 16 || 5′-CTTATGTAAA-3′<ref name=Mracek/>  
| [[D box gene transcriptions|D-box]] || CTTATGTAAA (Mracek2) || 16 || CTTATGTAAA<ref name=Mracek/>  
|-
|-
| [[D box gene transcriptions|D-box]] || 5'-TCTCACA-3' || 16 || TCTCACATT(A/C)AATAAGTCA is a D-box.<ref name=Johnson/>  
| [[D box gene transcriptions|D-box]] || 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]] || 5'-ATTTTCTTCA-3' || 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)]] || 5'-TAGCCGCCG-3' or 5'-TTTCAAT-3' || ⌘F || in the upstream repression sequence (URS)  
| [[DNA damage response element gene transcriptions|DNA damage response elements (DREs)]] || TTTCAAT<ref name=Smith>{{ cite journal
|author=Joshua J. Smith, Eric S. Cole, Daniel P. Romero
|title=Transcriptional control of RAD51 expression in the ciliate ''Tetrahymena thermophila''
|journal=Nucleic Acids Research
|date=15 July 2004
|volume=32
|issue=14
|pages=4313-4321
|url=https://academic.oup.com/nar/article/32/14/4313/1279821
|arxiv=
|bibcode=
|doi=10.1093/nar/gkh771
|pmid=15304567
|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
|author=Roberta A. Sumrada and Terrance G. Cooper
|title=Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast
|journal=Proceedings of the National Academy of Sciences USA
|date=June 1987
|volume=84
|issue=
|pages=3997-4001
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC305008/pdf/pnas00277-0054.pdf
|arxiv=
|bibcode=
|doi=10.1073/pnas.84.12.3997
|pmid=3295874
|accessdate=6 September 2020 }}</ref> || ⌘F || in the upstream repression sequence (URS)  
|-
|-
| [[DNA replication-related element gene transcriptions|DNA replication-related elements]] || 5'-TATCGATA-3' || ⌘F || DNA replication-related element (DRE)<ref name=Hirose>{{ cite journal
| [[DNA replication-related element gene transcriptions|DNA replication-related elements]] || TATCGATA || ⌘F || DNA replication-related element (DRE)<ref name=Hirose>{{ cite journal
|author=Fumiko Hirose
|author=Fumiko Hirose
|author2=Masamitsu Yamaguchi
|author2=Masamitsu Yamaguchi
Line 453: Line 481:
|accessdate=4 September 2020 }}</ref>  
|accessdate=4 September 2020 }}</ref>  
|-
|-
| [[DREB box gene transcriptions|DREB boxes]] || 5'-TACCGACAT-3' || 16 || CRT/DREB box  
| [[DREB box gene transcriptions|DREB boxes]] || TACCGACAT || 16 || CRT/DREB box  
|-
|-
| [[EIF4E basal element gene transcriptions|EIF4E basal elements]] || 5'-TTACCCCCCCTT-3' || 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]] || 5'-CCAAT-3' || ⌘F || 5'-CCAATGGGCTGAAAC-3' between ZNF497 and A1BG  
| [[Endoplasmic reticulum stress response element gene transcriptions|Endoplasmic reticulum stress response elements]] || CCAAT || ⌘F || CCAATGGGCTGAAAC between ZNF497 and A1BG  
|-
|-
| [[Estrogen response element gene transcriptions|Estrogen response elements]] || 5'-AGGTTA-3' or 5'-GGTCAGGAT-3' || ⌘F || 5'-AGGTTATTGCCTCCT-3' or 5'-GGTCAGGATGAC-3'
| [[Estrogen response element gene transcriptions|Estrogen response elements]] || AGGTTA or GGTCAGGAT || ⌘F || AGGTTATTGCCTCCT or GGTCAGGATGAC  
|-
|-
| [[Forkhead box gene transcriptions|Forkhead boxes]] || 5'-(A/G)(C/T)AAA(C/T)A-3' || ⌘F || 5'-GTAAACAA-3' FOXO1  
| [[Forkhead box gene transcriptions|Forkhead boxes]] || (A/G)(C/T)AAA(C/T)A || ⌘F || GTAAACAA FOXO1  
|-
|-
| [[Gal4p gene transcriptions|Gal4ps]] || 5'-CGGACCGC-3' || ⌘F || 5'-CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG-3'
| [[Gal4p gene transcriptions|Gal4ps]] || CGGACCGC || ⌘F || CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG  
|-
|-
| [[G box gene transcriptions|G boxes]] || 5'-(G/T)CCACGTG(G/T)C-3' || ⌘F || no "perfect palindrome" G boxes in either promoter  
| [[G box gene transcriptions|G boxes]] || (G/T)CCACGTG(G/T)C || ⌘F || no "perfect palindrome" G boxes in either promoter  
|-
|-
| [[GLM box gene transcriptions#GCN4 motifs|GCN4 motifs]] || 5'-TGACTCA-3', 5'-TGAGTCA-3' || ⌘F || ACGT motif  
| [[GLM box gene transcriptions#GCN4 motifs|GCN4 motifs]] || TGACTCA, TGAGTCA || ⌘F || ACGT motif  
|-
|-
| [[Gcn4p gene transcriptions|Gcn4ps]] || 5'-ATGACTCTT-3' || ⌘F || [[GLM box gene transcriptions#GCN4 motifs|GCN4 motifs]]  
| [[Gcn4p gene transcriptions|Gcn4ps]] || ATGACTCTT || ⌘F || [[GLM box gene transcriptions#GCN4 motifs|GCN4 motifs]]  
|-
|-
| [[GLM box gene transcriptions|GLM boxes]] || 5′-(G/A)TGA(G/C)TCA(T/C)-3′ || 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)]] || 5'-TTCCTAGAA-3' || ⌘F || ALS-GAS1 between nt −633 and nt −625  
| [[Γ-interferon activated sequence gene transcriptions|γ-interferon activated sequences (GAS)]] || TTCCTAGAA || ⌘F || ALS-GAS1 between nt −633 and nt −625  
|-
|-
| [[Grainy head transcription factor gene transcriptions|Grainy head transcription factor binding sites]] || 5'-AACCGGTT-3' || ⌘F || also 5'-GACTGGTT-3'
| [[Grainy head transcription factor gene transcriptions|Grainy head transcription factor binding sites]] || AACCGGTT || ⌘F || also GACTGGTT  
|-
|-
| [[TC element gene transcriptions|GT boxes]] || 5'-GGGGTGGGG-3' || ⌘F || (-78 to -69)  
| [[TC element gene transcriptions|GT boxes]] || GGGGTGGGG || ⌘F || (-78 to -69)  
|-
|-
| [[Hac1p gene transcriptions|Hac1ps]] || 5'-CAGCGTG-3' || ⌘F || Regulates the unfolded protein response  
| [[Hac1p gene transcriptions|Hac1ps]] || CAGCGTG || ⌘F || Regulates the unfolded protein response  
|-
|-
| [[Heat-responsive element gene transcriptions|Heat-responsive elements]] || 5'-AAAAAATTTC-3' || ⌘F || four nGAAn motifs  
| [[Heat-responsive element gene transcriptions|Heat-responsive elements]] || AAAAAATTTC || ⌘F || four nGAAn motifs  
|-
|-
| [[Hex gene transcriptions|Hex sequences]] || 5'-TGACGTGGC-3' || ⌘F || the Hex sequence (TGACGTGGC)<ref name=Song/>  
| [[Hex gene transcriptions|Hex sequences]] || TGACGTGGC || ⌘F || the Hex sequence (TGACGTGGC)<ref name=Song/>  
|-
|-
| [[HMG box gene transcriptions|HMG boxes]] || 5'-(A/T)(A/T)CAAAG-3' || ⌘F || two or more HMG boxes  
| [[HMG box gene transcriptions|HMG boxes]] || (A/T)(A/T)CAAAG || ⌘F || two or more HMG boxes  
|-
|-
| [[C box gene transcriptions|Hybrid C, A boxes]] || 5'-TGACGTAT-3' || ⌘F || A at the 12 position  
| [[C box gene transcriptions|Hybrid C, A boxes]] || TGACGTAT || ⌘F || A at the 12 position  
|-
|-
| [[C box gene transcriptions|Hybrid C, G boxes]] || 5'-TGACGTGT-3' || ⌘F || G at the 12 position  
| [[C box gene transcriptions|Hybrid C, G boxes]] || TGACGTGT || ⌘F || G at the 12 position  
|-
|-
| [[C box gene transcriptions|Hybrid C, T boxes]] || 5'-TGACGTTA-3' || ⌘F || T at the 12 position  
| [[C box gene transcriptions|Hybrid C, T boxes]] || TGACGTTA || ⌘F || T at the 12 position  
|-
|-
| [[Hypoxia-inducible factor gene transcriptions|Hypoxia-inducible factors]] || 5'-GCCCTACGT-3' || ⌘F || composed of HIF-1α and HIF-1β  
| [[Hypoxia-inducible factor gene transcriptions|Hypoxia-inducible factors]] || GCCCTACGT || ⌘F || composed of HIF-1α and HIF-1β  
|-
|-
| [[I box gene transcriptions|I boxes]] || 5'-GATAAG-3' || ⌘F || 5'-GGATGAGATAAGA-3'
| [[I box gene transcriptions|I boxes]] || GATAAG || ⌘F || GGATGAGATAAGA  
|-
|-
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive element]] || 5'-TYTTCACATGY-3' || ⌘F || 5'-TCTTCAC, TCTTCACAT-3'
| [[Inositol, choline-responsive element gene transcriptions|Inositol, choline-responsive element]] || TYTTCACATGY || ⌘F || TCTTCAC, TCTTCACAT  
|-
|-
| [[Kozak sequence gene transcriptions|Kozak sequences]] || 5'-(GCC)GCC(A/G)CCATGG-3' || ⌘F || 5'-GAAAATGG-3'<ref name=Matsumoto>{{ cite journal
| [[Kozak sequence gene transcriptions|Kozak sequences]] || (GCC)GCC(A/G)CCATGG || ⌘F || GAAAATGG<ref name=Matsumoto>{{ cite journal
|author=Takuya Matsumoto
|author=Takuya Matsumoto
|author2=Saemi Kitajima
|author2=Saemi Kitajima
Line 520: Line 548:
|accessdate=27 September 2020 }}</ref>  
|accessdate=27 September 2020 }}</ref>  
|-
|-
| [[L box gene transcriptions|L boxes]] || 5'-TAAATG(A/C/G)A-3' || ⌘F || L1 box  
| [[L box gene transcriptions|L boxes]] || TAAATG(A/C/G)A || ⌘F || L1 box  
|-
|-
| [[Maf recognition element gene transcriptions|MAREs]] || 5'-TGCTGA(G/C)TCAGCA-3' || ⌘F || and 5'-TGCTGA(GC/CG)TCAGCA-3'
| [[Maf recognition element gene transcriptions|MAREs]] || TGCTGA(G/C)TCAGCA || ⌘F || and TGCTGA(GC/CG)TCAGCA  
|-
|-
| [[M box gene transcriptions|M boxes]] || 5'-GTCATGTGCT-3' || ⌘F || upstream of the TATA box  
| [[M box gene transcriptions|M boxes]] || GTCATGTGCT || ⌘F || upstream of the TATA box  
|-
|-
| [[Mcm1 regulatory factor gene transcriptions|Mcm1 regulatory factors]] || 5'-(A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T)-3' || ⌘F || Genome-wide determinant search  
| [[Mcm1 regulatory factor gene transcriptions|Mcm1 regulatory factors]] || (A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T) || ⌘F || Genome-wide determinant search  
|-
|-
| [[Met31p box gene transcriptions|Met31ps]] || 5'-AAACTGTGG-3' || ⌘F || Sulfur amino acid metabolism [72]  
| [[Met31p box gene transcriptions|Met31ps]] || AAACTGTGG || ⌘F || Sulfur amino acid metabolism [72]  
|-
|-
| [[Middle sporulation element gene transcriptions|Middle sporulation elements]] || 5'-C(A/G)CAAA(A/T)-3' || ⌘F || 5'-ACACAAA-3' (2017)  
| [[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]] || 5'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-3' || 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  
|-
|-
| [[Ndt80p gene transcriptions|Ndt80ps]] || 5'-TCCGCA-3' || ⌘F || 5'-DNCRCAAAW-3'
| [[Ndt80p gene transcriptions|Ndt80ps]] || TCCGCA || ⌘F || DNCRCAAAW  
|-
|-
| [[Nuclear factor Y gene transcriptions|Nuclear factor Y]] || 5'-TACCGACAT-3' || ⌘F || NF-Y is a trimeric complex  
| [[Nuclear factor Y gene transcriptions|Nuclear factor Y]] || TACCGACAT || ⌘F || NF-Y is a trimeric complex  
|-
|-
| [[Nutrient-sensing response element gene transcriptions|Nutrient-sensing response element 1]] || 5'-GTTTCATCA-3' || ⌘F || only one nucleotide difference between the ''SESN2'' CARE and the ''ASNS''  
| [[Nutrient-sensing response element gene transcriptions|Nutrient-sensing response element 1]] || GTTTCATCA || ⌘F || only one nucleotide difference between the ''SESN2'' CARE and the ''ASNS''  
|-
|-
| [[Oaf1p gene transcriptions|Oaf1ps]] || 5'-(A/C/G/T)(A/C/G/T)(A/C/G/T)T(A/C/G/T)A(A/C/G/T)-3' || ⌘F || 5'-CGG(A/C/G/T)<sub>3</sub>T(A/C/G/T)A(A/C/G/T)<sub>9-12</sub>CCG-3'
| [[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]] || 5'-TCCGCGGA-3' || ⌘F || Pdr1p/Pdr3p response element (PDRE)  
| [[Pdr1,3p gene transcriptions|Pdr1p/Pdr3ps]] || TCCGCGGA || ⌘F || Pdr1p/Pdr3p response element (PDRE)  
|-
|-
| [[Polycomb response element gene transcriptions|Polycomb response elements]] || 5'-CGCCATTT-3' || ⌘F || closely resembles the extended Pho-Phol consensus sequence  
| [[Polycomb response element gene transcriptions|Polycomb response elements]] || CGCCATTT || ⌘F || closely resembles the extended Pho-Phol consensus sequence  
|-
|-
| [[Rap1 regulatory factor gene transcriptions|Rap1 regulatory factors]] || 5'-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)-3' || ⌘F || Rap1 (CCCACCAACAAAA) none  
| [[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  
|-
|-
| [[Rgt1p gene transcriptions|Rgt1ps]] || 5'-CGGACCA-3' || ⌘F || Glucose-responsive transcription factor  
| [[Rgt1p gene transcriptions|Rgt1ps]] || CGGACCA || ⌘F || Glucose-responsive transcription factor  
|-
|-
| [[Rlm1p gene transcriptions|Rlm1ps]] || 5'-CTATATATAG-3' || ⌘F || CTA(T/A)<sub>4</sub>TAG  
| [[Rlm1p gene transcriptions|Rlm1ps]] || CTATATATAG || ⌘F || CTA(T/A)<sub>4</sub>TAG  
|-
|-
| [[Rox1p gene transcriptions|Rox1ps]] || 5'-GGGTAA-3' || ⌘F || Heme-dependent repressor of hypoxic genes [78]  
| [[Rox1p gene transcriptions|Rox1ps]] || GGGTAA || ⌘F || Heme-dependent repressor of hypoxic genes [78]  
|-
|-
| [[Rpn4p gene transcriptions|Rpn4ps]] || 5'-GGTGGCAAA-3' || ⌘F || proteasome genes  
| [[Rpn4p gene transcriptions|Rpn4ps]] || GGTGGCAAA || ⌘F || proteasome genes  
|-
|-
| [[Seed-specific element gene transcriptions|Seed-specific elements]] || 5'-CATGCATG-3' || ⌘F || SRE consensus: 5'-CAGCAGATTGCG-3' is none  
| [[Seed-specific element gene transcriptions|Seed-specific elements]] || CATGCATG || ⌘F || SRE consensus: CAGCAGATTGCG is none  
|-
|-
| [[Shoot specific element gene transcriptions|Shoot specific elements]] || 5'-GATAATGATG-3' || ⌘F || SRE consensus: 5'-CAGCAGATTGCG-3' is none  
| [[Shoot specific element gene transcriptions|Shoot specific elements]] || GATAATGATG || ⌘F || SRE consensus: CAGCAGATTGCG is none  
|-
|-
| [[Sip4p gene transcriptions|Sip4ps]] || 5'-CCGTCCGT-3' || ⌘F || 5'-CC(C/G)T(C/T)C(C/G)TCCG-3'
| [[Sip4p gene transcriptions|Sip4ps]] || CCGTCCGT || ⌘F || CC(C/G)T(C/T)C(C/G)TCCG  
|-
|-
| [[Smp1p gene transcriptions|Smp1ps]] || 5'-ACTACTA-3' || ⌘F || 5-ACTACTA(T/A)4TAG-3'
| [[Smp1p gene transcriptions|Smp1ps]] || ACTACTA || ⌘F || 5-ACTACTA(T/A)4TAG  
|-
|-
| [[Sterol response element gene transcriptions|Sterol response elements]] || 5'-TCGTATA-3' || ⌘F || perhaps plant specific  
| [[Sterol response element gene transcriptions|Sterol response elements]] || TCGTATA || ⌘F || perhaps plant specific  
|-
|-
| [[TATC box gene transcriptions|TATCCAC boxes]] || 5'-TATCCAC-3' || 16 || GA responsive complex component  
| [[TATC box gene transcriptions|TATCCAC boxes]] || TATCCAC || 16 || GA responsive complex component  
|-
|-
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || 5'-TCCACCATA-3' || ⌘F || adjacent co-dependent regulatory element of POLLEN1  
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || TCCACCATA || ⌘F || adjacent co-dependent regulatory element of POLLEN1  
|-
|-
| [[Tec1p gene transcriptions|Tec1ps]] || 5'-GAATGT-3' || ⌘F || Ste12p cofactor  
| [[Tec1p gene transcriptions|Tec1ps]] || GAATGT || ⌘F || Ste12p cofactor  
|-
|-
| [[Tetradecanoylphorbol-13-acetate response element gene transcriptions|Tetradecanoylphorbol-13-acetate response elements (TREs)]] || 5'-TGA(G/C)TCA-3' || 16 || ''cis''-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40  
| [[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  
|-
|-
| [[TC element gene transcriptions|TGF-β control elements (TCEs)]] || 5'-GAGTGGGGCG-3' || ⌘F || in mouse and rat, 5'-GCGTGGGGGA-3' in humans  
| [[TC element gene transcriptions|TGF-β control elements (TCEs)]] || GAGTGGGGCG || ⌘F || in mouse and rat, GCGTGGGGGA in humans  
|-
|-
| [[TC element gene transcriptions|TGF-β inhibitory elements (TIEs)]] || 5'-GAGTGGTGA-3' || 16 || in the rat transin/stromelysin promoter  
| [[TC element gene transcriptions|TGF-β inhibitory elements (TIEs)]] || GAGTGGTGA || 16 || in the rat transin/stromelysin promoter  
|-
|-
| [[Thyroid hormone response element gene transcriptions|Thyroid hormone response elements (TREs)]] || 5'-AGGTCA-3' || ⌘F || See VDREs, X boxes  
| [[Thyroid hormone response element gene transcriptions|Thyroid hormone response elements (TREs)]] || AGGTCA || ⌘F || See VDREs, X boxes  
|-
|-
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || 5'-TCCACCATA-3' || ⌘F || adjacent co-dependent regulatory element of POLLEN1  
| [[TCCACCATA element gene transcriptions|TCCACCATA elements]] || TCCACCATA || ⌘F || adjacent co-dependent regulatory element of POLLEN1  
|-
|-
| [[Tec1p gene transcriptions|Tec1ps]] || 5'-GAATGT-3' || ⌘F || Ste12p cofactor  
| [[Tec1p gene transcriptions|Tec1ps]] || GAATGT || ⌘F || Ste12p cofactor  
|-
|-
| [[Tetradecanoylphorbol-13-acetate response element gene transcriptions|Tetradecanoylphorbol-13-acetate response elements (TREs)]] || 5'-TGA(G/C)TCA-3' || 16 || ''cis''-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40  
| [[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  
|-
|-
| [[TC element gene transcriptions|TGF-β control elements (TCEs)]] || 5'-GAGTGGGGCG-3' || ⌘F || in mouse and rat, 5'-GCGTGGGGGA-3' in humans  
| [[TC element gene transcriptions|TGF-β control elements (TCEs)]] || GAGTGGGGCG || ⌘F || in mouse and rat, GCGTGGGGGA in humans  
|-
|-
| [[TC element gene transcriptions|TGF-β inhibitory elements (TIEs)]] || 5'-GAGTGGTGA-3' || 16 || in the rat transin/stromelysin promoter  
| [[TC element gene transcriptions|TGF-β inhibitory elements (TIEs)]] || GAGTGGTGA || 16 || in the rat transin/stromelysin promoter  
|-
|-
| [[Thyroid hormone response element gene transcriptions|Thyroid hormone response elements (TREs)]] || 5'-AGGTCA-3' || ⌘F || See VDREs, X boxes  
| [[Thyroid hormone response element gene transcriptions|Thyroid hormone response elements (TREs)]] || AGGTCA || ⌘F || See VDREs, X boxes  
|-
|-
| [[Unfolded protein response element gene transcriptions|Unfolded protein response elements (UPREs)]] || 5'-TGACGTG(G/A)-3' || ⌘F || XBP1 binds to UPRE  
| [[Unfolded protein response element gene transcriptions|Unfolded protein response elements (UPREs)]] || TGACGTG(G/A) || ⌘F || XBP1 binds to UPRE  
|-
|-
| [[Vhr1p gene transcriptions|Vhr1ps]] || 5'-AATCA-N<sub>8</sub>-TGA(C/T)T-3' || ⌘F || Response to low biotin [71] concentrations  
| [[Vhr1p gene transcriptions|Vhr1ps]] || AATCA-N<sub>8</sub>-TGA(C/T)T || ⌘F || Response to low biotin [71] concentrations  
|-
|-
| [[Vitamin D response element gene transcriptions|Vitamin D response elements (VDREs)]] || 5'-(A/G)G(G/T)(G/T)CA-3' || ⌘F || 5'-AGGTCA-3' not ⌘F  
| [[Vitamin D response element gene transcriptions|Vitamin D response elements (VDREs)]] || (A/G)G(G/T)(G/T)CA || ⌘F || AGGTCA not ⌘F  
|-
|-
| [[X box gene transcriptions|X boxes]] || 5'-GTTGGCATGGCAAC-3' || 16 || X2 box is 5'-AGGTCCA-3' not ⌘F  
| [[X box gene transcriptions|X boxes]] || GTTGGCATGGCAAC || 16 || X2 box is AGGTCCA not ⌘F  
|-
|-
| [[Xbp1p gene transcriptions|Xbp1ps]] || 5'-GcCTCGA(G/A)G(C/A)g(a/g)-3' || ⌘F || Transcriptional repressor  
| [[Xbp1p gene transcriptions|Xbp1ps]] || GcCTCGA(G/A)G(C/A)g(a/g) || ⌘F || Transcriptional repressor  
|-
|-
| [[Xenobiotic response element gene transcriptions|Xenobiotic response elements (XREs)]] || 5'-(T/G)NGCGTG(A/C)(G/C)A-3' || ⌘F || contains the core sequence 5'-GCGTG-3'
| [[Xenobiotic response element gene transcriptions|Xenobiotic response elements (XREs)]] || (T/G)NGCGTG(A/C)(G/C)A || ⌘F || contains the core sequence GCGTG  
|-
|-
| [[Yap1p,2p gene transcriptions|Yap1p,2ps]] || 5'-TTACTAA-3' || ⌘F || Yap1p binding sites  
| [[Yap1p,2p gene transcriptions|Yap1p,2ps]] || TTACTAA || ⌘F || Yap1p binding sites  
|-
|-
| [[Y box gene transcriptions|Y boxes]] || 5'-(A/G)CTAACC(A/G)(A/G)(C/T)-3' || 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]] || 5'-ACCCTCA-3' || ⌘F || 5'-ACC(C/T)(C/T)(A/C/G/T)AAGGT-3'
| [[Zap1p gene transcriptions|Zap1ps]] || ACCCTCA || ⌘F || ACC(C/T)(C/T)(A/C/G/T)AAGGT  
|-
|-
|}
|}

Revision as of 22:48, 18 December 2020

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
ABA-response elements GATCGATC, CGATCGAT, ACGTGTCC, GATCGAT 16 ABREN, CGATCGAT motif, ABRE, and core of ABREN and CGATCGAT motif.[2]
Abf1 regulatory factors CGTCCTCTACG 16 CGTNNNNNACGAT[3]
Activating proteins GCCCACGGG 16 Activating protein 2 (AP-2)[4]
Activating proteins GGCCAA 16 Activating protein 2 (AP-2)[5]
Alpha-amylase conserved elements TATCCA 16 TATCCATCCATCC[6]
Amino acid response elements ATTGCATCA 16 AARE1 (ATTGCATCA)[7]
Amino acid response elements TTTGCATCA 16 TTTGCATCA.[8][9]
AARE-like TGGTGAAAG 16 AARE-like sequence (TGGTGAAAG, named AARE3)[7]
Androgen response elements GGTACANNNTGTTCT[10] 16 GGTACACGGTGTTCT[10]
Androgen response elements 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 CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG 16 ChoRE1, ChoRE2[15]
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[16]
C/A hybrid boxes TGACGTAT 16 TGACGTAT[17]
C/T hybrid boxes TGACGTTA 16 TGACGTTA[17]
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)[18]
C/EBP boxes TTAGGACAT,[19] or TAGCATT[5] 16 CCAAT-enhancer-binding site (C/EBP) is TAGCATT
Cell cycle regulation CCCAACGGT[6] 16 tomato genome-wide analysis
CENP-B boxes TTTCGTTGGAAGCGGGA 16 specifically localized at the centromere
Coupling elements TGCCACCGG[2] 16 CE1 (Watanabe)
DAF-16-associated elements TGATAAG 16 DAF-16-associated element (DAE)[20]
D-box GTTGTATAAC (Mracek1) 16 GTTGTATAAC[21]
D-box CTTATGTAAA (Mracek2) 16 CTTATGTAAA[21]
D-box TCTCACA 16 TCTCACATT(A/C)AATAAGTCA is a D-box.[16]
Defense and stress-responsive elements ATTTTCTTCA 16 (ATTTTCTTCA)[6]
DNA damage response elements (DREs) TTTCAAT[22] 16 in the upstream repression sequence (URS)
DNA damage response elements (DREs) TAGCCGCCG of TAGCCGCCGRRRR[23] ⌘F in the upstream repression sequence (URS)
DNA replication-related elements TATCGATA ⌘F DNA replication-related element (DRE)[24]
DREB boxes TACCGACAT 16 CRT/DREB box
EIF4E basal elements TTACCCCCCCTT 16 poly(C) motif
Endoplasmic reticulum stress response elements CCAAT ⌘F CCAATGGGCTGAAAC between ZNF497 and A1BG
Estrogen response elements AGGTTA or GGTCAGGAT ⌘F AGGTTATTGCCTCCT or GGTCAGGATGAC
Forkhead boxes (A/G)(C/T)AAA(C/T)A ⌘F GTAAACAA FOXO1
Gal4ps CGGACCGC ⌘F CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG
G boxes (G/T)CCACGTG(G/T)C ⌘F no "perfect palindrome" G boxes in either promoter
GCN4 motifs TGACTCA, TGAGTCA ⌘F ACGT motif
Gcn4ps ATGACTCTT ⌘F GCN4 motifs
GLM boxes (G/A)TGA(G/C)TCA(T/C) 16 GCN4-like motif
γ-interferon activated sequences (GAS) TTCCTAGAA ⌘F ALS-GAS1 between nt −633 and nt −625
Grainy head transcription factor binding sites AACCGGTT ⌘F also GACTGGTT
GT boxes GGGGTGGGG ⌘F (-78 to -69)
Hac1ps CAGCGTG ⌘F Regulates the unfolded protein response
Heat-responsive elements AAAAAATTTC ⌘F four nGAAn motifs
Hex sequences TGACGTGGC ⌘F the Hex sequence (TGACGTGGC)[17]
HMG boxes (A/T)(A/T)CAAAG ⌘F two or more HMG boxes
Hybrid C, A boxes TGACGTAT ⌘F A at the 12 position
Hybrid C, G boxes TGACGTGT ⌘F G at the 12 position
Hybrid C, T boxes TGACGTTA ⌘F T at the 12 position
Hypoxia-inducible factors GCCCTACGT ⌘F composed of HIF-1α and HIF-1β
I boxes GATAAG ⌘F GGATGAGATAAGA
Inositol, choline-responsive element TYTTCACATGY ⌘F TCTTCAC, TCTTCACAT
Kozak sequences (GCC)GCC(A/G)CCATGG ⌘F GAAAATGG[25]
L boxes TAAATG(A/C/G)A ⌘F L1 box
MAREs TGCTGA(G/C)TCAGCA ⌘F and TGCTGA(GC/CG)TCAGCA
M boxes GTCATGTGCT ⌘F upstream of the TATA box
Mcm1 regulatory factors (A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T) ⌘F Genome-wide determinant search
Met31ps AAACTGTGG ⌘F Sulfur amino acid metabolism [72]
Middle sporulation elements C(A/G)CAAA(A/T) ⌘F ACACAAA (2017)
Motif ten elements C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G 16 Gene ID: 6309
Ndt80ps TCCGCA ⌘F DNCRCAAAW
Nuclear factor Y TACCGACAT ⌘F NF-Y is a trimeric complex
Nutrient-sensing response element 1 GTTTCATCA ⌘F only one nucleotide difference between the SESN2 CARE and the ASNS
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)3T(A/C/G/T)A(A/C/G/T)9-12CCG
Pdr1p/Pdr3ps TCCGCGGA ⌘F Pdr1p/Pdr3p response element (PDRE)
Polycomb response elements CGCCATTT ⌘F closely resembles the extended Pho-Phol consensus sequence
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
Rgt1ps CGGACCA ⌘F Glucose-responsive transcription factor
Rlm1ps CTATATATAG ⌘F CTA(T/A)4TAG
Rox1ps GGGTAA ⌘F Heme-dependent repressor of hypoxic genes [78]
Rpn4ps GGTGGCAAA ⌘F proteasome genes
Seed-specific elements CATGCATG ⌘F SRE consensus: CAGCAGATTGCG is none
Shoot specific elements GATAATGATG ⌘F SRE consensus: CAGCAGATTGCG is none
Sip4ps CCGTCCGT ⌘F CC(C/G)T(C/T)C(C/G)TCCG
Smp1ps ACTACTA ⌘F 5-ACTACTA(T/A)4TAG
Sterol response elements TCGTATA ⌘F perhaps plant specific
TATCCAC boxes TATCCAC 16 GA responsive complex component
TCCACCATA elements TCCACCATA ⌘F adjacent co-dependent regulatory element of POLLEN1
Tec1ps GAATGT ⌘F Ste12p cofactor
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 ⌘F in mouse and rat, GCGTGGGGGA in humans
TGF-β inhibitory elements (TIEs) GAGTGGTGA 16 in the rat transin/stromelysin promoter
Thyroid hormone response elements (TREs) AGGTCA ⌘F See VDREs, X boxes
TCCACCATA elements TCCACCATA ⌘F adjacent co-dependent regulatory element of POLLEN1
Tec1ps GAATGT ⌘F Ste12p cofactor
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 ⌘F in mouse and rat, GCGTGGGGGA in humans
TGF-β inhibitory elements (TIEs) GAGTGGTGA 16 in the rat transin/stromelysin promoter
Thyroid hormone response elements (TREs) AGGTCA ⌘F See VDREs, X boxes
Unfolded protein response elements (UPREs) TGACGTG(G/A) ⌘F XBP1 binds to UPRE
Vhr1ps AATCA-N8-TGA(C/T)T ⌘F Response to low biotin [71] concentrations
Vitamin D response elements (VDREs) (A/G)G(G/T)(G/T)CA ⌘F AGGTCA not ⌘F
X boxes GTTGGCATGGCAAC 16 X2 box is AGGTCCA not ⌘F
Xbp1ps GcCTCGA(G/A)G(C/A)g(a/g) ⌘F Transcriptional repressor
Xenobiotic response elements (XREs) (T/G)NGCGTG(A/C)(G/C)A ⌘F contains the core sequence GCGTG
Yap1p,2ps TTACTAA ⌘F Yap1p binding sites
Y boxes (A/G)CTAACC(A/G)(A/G)(C/T) 16 inverted CAAT box
Zap1ps ACCCTCA ⌘F 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 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. ↑ 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.
  9. ↑ 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.
  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. ↑ 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. ↑ 16.0 16.1 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.
  17. ↑ 17.0 17.1 17.2 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.
  18. ↑ 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.
  19. ↑ 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.
  20. ↑ Yan-Hui Li; Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.
  21. ↑ 21.0 21.1 Philipp Mracek; Cristina Santoriello; M. Laura Idda; Cristina Pagano; Zohar Ben-Moshe; Yoav Gothilf; Daniela Vallone; Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.
  22. ↑ Joshua J. Smith, Eric S. Cole, Daniel P. Romero (15 July 2004). "Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila". Nucleic Acids Research. 32 (14): 4313–4321. doi:10.1093/nar/gkh771. PMID 15304567. Retrieved 4 September 2020.
  23. ↑ Roberta A. Sumrada and Terrance G. Cooper (June 1987). "Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast" (PDF). Proceedings of the National Academy of Sciences USA. 84: 3997–4001. doi:10.1073/pnas.84.12.3997. PMID 3295874. Retrieved 6 September 2020.
  24. ↑ 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.
  25. ↑ 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.

External links

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