A1BG response element negative results: Difference between revisions
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| [[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]] || 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 | ||
|author=Kenneth A. Watanabe | |author=Kenneth A. Watanabe | ||
|author2=Arielle Homayouni | |||
|author3=Lingkun Gu | |||
|author4=Kuan‐Ying Huang | |||
|author5=Tuan‐Hua David Ho | |||
|author6=Qingxi J. Shen | |||
|title=Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element | |title=Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element | ||
|journal=Plant, Cell & Environment | |journal=Plant, Cell & Environment | ||
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| [[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]] || 5'-CGTCCTCTACG-3' || 16 || 5'-CGTNNNNNACGAT-3'<ref name=Rossi>{{ cite journal | ||
|author=Matthew J. Rossi | |author=Matthew J. Rossi | ||
|author2=William K.M. Lai | |||
|author3=B. Franklin Pugh | |||
|title=Genome-wide determinants of sequence-specific DNA binding of general regulatory factors | |title=Genome-wide determinants of sequence-specific DNA binding of general regulatory factors | ||
|journal=Genome Research | |journal=Genome Research | ||
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| [[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]] || 5'-GCCCACGGG-3' || 16 || Activating protein 2 (AP-2)<ref name=Murata>{{ cite journal | ||
|author=Takayuki Murata | |author=Takayuki Murata | ||
|author2=Chieko Noda | |||
|author3=Yohei Narita1 | |||
|author4=Takahiro Watanabe | |||
|author5=Masahiro Yoshida | |||
|author6=Keiji Ashio | |||
|author7=Yoshitaka Sato | |||
|author8=Fumi Goshima | |||
|author9=Teru Kanda | |||
|author10=Hironori Yoshiyama | |||
|author11=Tatsuya Tsurumi | |||
|author12=Hiroshi Kimura | |||
|title=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) | |title=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) | ||
|journal=Journal of Virology | |journal=Journal of Virology | ||
| Line 71: | Line 89: | ||
|- | |- | ||
| [[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]] || 5'-TATCCA-3' || 16 || 5'-TATCCATCCATCC-3'<ref name=Sharma>{{ cite journal | ||
|author=Bhaskar Sharma | |author=Bhaskar Sharma | ||
|author2=Joemar Taganna | |||
|title=Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato | |title=Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato | ||
|journal=Scientific Reports | |journal=Scientific Reports | ||
| Line 88: | Line 107: | ||
|- | |- | ||
| [[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]] || 5'-TTTGCATCA-3' || 16 || 5'-TTTGCATCA-3'.<ref name=Broer>{{ cite journal | ||
|author=Angelika Bröer | |author=Angelika Bröer | ||
|author2=Gregory Gauthier-Coles | |||
|author3=Farid Rahimi | |||
|author4=Michelle van Geldermalsen | |||
|author5=Dieter Dorsch | |||
|author6=Ansgar Wegener | |||
|author7=Jeff Holst | |||
|author8=Stefan Bröer | |||
|title=Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells | |title=Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells | ||
|journal=Journal of Biological Chemistry | |journal=Journal of Biological Chemistry | ||
| Line 101: | Line 127: | ||
|pmid= | |pmid= | ||
|accessdate=4 October 2020 }}</ref><ref name=Garaeva>{{ cite journal | |accessdate=4 October 2020 }}</ref><ref name=Garaeva>{{ cite journal | ||
|author=Alisa A. Garaeva | |author=Alisa A. Garaeva | ||
|author2=Irina E. Kovaleva | |||
|author3=Peter M. Chumakov | |||
|author4=Alexandra G. Evstafieva | |||
|title=Mitochondrial dysfunction induces ''SESN2'' gene expression through Activating Transcription Factor 4 | |title=Mitochondrial dysfunction induces ''SESN2'' gene expression through Activating Transcription Factor 4 | ||
|journal=Cell Cycle | |journal=Cell Cycle | ||
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|- | |- | ||
| [[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]] || 5'-TGGTGAAAG-3' || 16 || AARE-like sequence (5′- TGGTGAAAG-3′, named AARE3)<ref name=Maruyama>{{ cite journal | ||
|author=Ryuto Maruyama | |author=Ryuto Maruyama | ||
|author2=Makoto Shimizu | |||
|author3=Juan Li, Jun Inoue | |||
|author4=Ryuichiro Sato | |||
|title=''Fibroblast growth factor 21'' induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region | |title=''Fibroblast growth factor 21'' induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region | ||
|journal=Bioscience, Biotechnology, and Biochemistry | |journal=Bioscience, Biotechnology, and Biochemistry | ||
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| [[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]] || 5'-GGTACANNNTGTTCT-3'<ref name=Kouhpayeh/> || 16 || 5′-GGTACACGGTGTTCT-3′<ref name=Kouhpayeh>{{ cite journal | ||
|author=S Kouhpayeh | |author=S Kouhpayeh | ||
|author2=AR Einizadeh | |||
|author3=Z Hejazi | |||
|author4=M Boshtam | |||
|author5=L Shariati | |||
|author6=M Mirian | |||
|author7=L Darzi | |||
|author8=M Sojoudi | |||
|author9=H Khanahmad | |||
|author10=A Rezaei | |||
|title=Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line | |title=Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line | ||
|journal=Cancer Gene Therapy | |journal=Cancer Gene Therapy | ||
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| [[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]] || 5'-TGATTCGTGAG-3' || 16 || 5'-AGAACANNNTGTTCT-3'<ref name=Wilson>{{ cite journal | ||
|author=Stephen Wilson | |author=Stephen Wilson | ||
|author2=Jianfei Qi | |||
|author3=Fabian V. Filipp | |||
|title=Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines | |title=Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines | ||
|journal=Scientific Reports | |journal=Scientific Reports | ||
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|- | |- | ||
| [[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]] || 5'-GTGAGGTCGC-3' || 16 || 5'-GTGAGGTCGC-3'<ref name=Otsuki>{{ cite journal | ||
|author=Akihito Otsuki | |author=Akihito Otsuki | ||
|author2=Mikiko Suzuki | |||
|author3=Fumiki Katsuoka | |||
|author4=Kouhei Tsuchida | |||
|author5=Hiromi Suda | |||
|author6=Masanobu Morita | |||
|author7=Ritsuko Shimizu | |||
|author8=Masayuki Yamamoto | |||
|title=Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection | |title=Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection | ||
|journal=Free Radical Biology and Medicine | |journal=Free Radical Biology and Medicine | ||
| Line 174: | Line 224: | ||
|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 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 | ||
|author=Sarah E. Lacher | |author=Sarah E. Lacher | ||
|author2=Daniel C. Levings | |||
|author3=Samuel Freeman | |||
|author4=Matthew Slattery | |||
|title=Identification of a functional antioxidant response element at the HIF1A locus | |title=Identification of a functional antioxidant response element at the HIF1A locus | ||
|journal=Redox Biology | |journal=Redox Biology | ||
| Line 191: | Line 244: | ||
|- | |- | ||
| [[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]] || 5'-CTATTTCGAG-3' || 16 || CaRE1 5'-CTATTTCGAG-3'<ref name=Tao>{{ cite journal | ||
|author=Xu Tao | |author=Xu Tao | ||
|author2=Anne E. West | |||
|author3=Wen G. Chen | |||
|author4=Gabriel Corfas | |||
|author5=Michael E. Greenberg | |||
|title=A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF | |title=A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF | ||
|journal=Neuron | |journal=Neuron | ||
| Line 206: | Line 263: | ||
|- | |- | ||
| [[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]] || 5'-CACGTGACCGGATCTTG-3', 5'-TCCGCCCCCATCACGTG-3' || 16 || ChoRE1, ChoRE2<ref name=Long>{{ cite journal | ||
|author=Jianyin Long | |author=Jianyin Long | ||
|author2=Daniel L. Galvan | |||
|author3=Koki Mise | |||
|author4=Yashpal S. Kanwar | |||
|author5=Li Li | |||
|author6=Naravat Poungavrin | |||
|author7=Paul A. Overbeek | |||
|author8=Benny H. Chang | |||
|author9=Farhad R. Danesh | |||
|title=Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1 | |title=Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1 | ||
|journal=Journal of Biological Chemistry | |journal=Journal of Biological Chemistry | ||
| Line 223: | Line 288: | ||
|- | |- | ||
| [[C box gene transcriptions|C-boxes]] || 5'-GAGGCCATCT-3' || 16 || 5'-GAGGCCATCT-3'<ref name=Johnson>{{ cite journal | | [[C box gene transcriptions|C-boxes]] || 5'-GAGGCCATCT-3' || 16 || 5'-GAGGCCATCT-3'<ref name=Johnson>{{ cite journal | ||
|author=PA Johnson | |author=PA Johnson | ||
|author2=D Bunick | |||
|author3=NB Hecht | |||
|title=Protein Binding Regions in the Mouse and Rat Protamine-2 Genes | |title=Protein Binding Regions in the Mouse and Rat Protamine-2 Genes | ||
|journal=Biology of Reproduction | |journal=Biology of Reproduction | ||
| Line 238: | Line 305: | ||
|- | |- | ||
| [[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]] || 5'-TGACGTAT-3' || 16 || 5'-TGACGTAT-3'<ref name=Song>{{ cite journal | ||
|author=Young Hun Song | |author=Young Hun Song | ||
|author2=Cheol Min Yoo | |||
|author3=An Pio Hong | |||
|author4=Seong Hee Kim | |||
|author5=Hee Jeong Jeong | |||
|author6=Su Young Shin | |||
|author7=Hye Jin Kim | |||
|author8=Dae-Jin Yun | |||
|author9=Chae Oh Lim | |||
|author10=Jeong Dong Bahk | |||
|author11=Sang Yeol Lee | |||
|author12=Ron T. Nagao | |||
|author13=Joe L. Key | |||
|author14=Jong Chan Hong | |||
|title=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 | |title=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 | ||
|journal=Plant Physiology | |journal=Plant Physiology | ||
| Line 255: | Line 335: | ||
|- | |- | ||
| [[C-EBP box gene transcriptions|C/EBP boxes]] || 5'-TTAGGACAT-3',<ref name=Misra>{{ cite journal | | [[C-EBP box gene transcriptions|C/EBP boxes]] || 5'-TTAGGACAT-3',<ref name=Misra>{{ cite journal | ||
|author=Ravi P. Misra | |author=Ravi P. Misra | ||
|author2=Azad Bonni | |||
|author3=Cindy K. Miranti | |||
|author4=Victor M. Rivera | |||
|author5=Morgan Sheng | |||
|author6=Michael E.Greenberg | |||
|title=L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway | |title=L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway | ||
|journal=The Journal of Biological Chemistry | |journal=The Journal of Biological Chemistry | ||
| Line 268: | Line 353: | ||
|pmid=7929249 | |pmid=7929249 | ||
|accessdate=7 December 2019 }}</ref> or 5'-TAGCATT-3'<ref name=Yao>{{ cite journal | |accessdate=7 December 2019 }}</ref> or 5'-TAGCATT-3'<ref name=Yao>{{ cite journal | ||
| | | author = Yao EF | ||
|author2=Denison MS | |||
| title = DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer | | title = DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer | ||
| journal = Biochemistry | | journal = Biochemistry | ||
| Line 285: | Line 371: | ||
|- | |- | ||
| [[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)]] || 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 | ||
|author=Hideharu Hashimoto | |author=Hideharu Hashimoto | ||
|author2=Dongxue Wang | |||
|author3=John R. Horton | |||
|author4=Xing Zhang | |||
|author5=Victor G. Corces | |||
|author6=Xiaodong Cheng | |||
|title=Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA | |title=Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA | ||
|journal=Molecular Cell | |journal=Molecular Cell | ||
| Line 300: | Line 391: | ||
|- | |- | ||
| [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] || 5'-TGATAAG-3' || ⌘F || DAF-16-associated element (DAE)<ref name=Li>{{ cite journal | | [[DAF-16-associated element gene transcriptions|DAF-16-associated elements]] || 5'-TGATAAG-3' || ⌘F || DAF-16-associated element (DAE)<ref name=Li>{{ cite journal | ||
|author=Yan-Hui Li | |author=Yan-Hui Li | ||
|author2=Gai-Gai Zhang | |||
|title=Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in ''Caenorhabditis elegans'' | |title=Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in ''Caenorhabditis elegans'' | ||
|journal=Oncotarget | |journal=Oncotarget | ||
| Line 317: | Line 409: | ||
|- | |- | ||
| [[D box gene transcriptions|D boxes]] || 5'-GTTGTATAAC-3' || ⌘F || 5′-CTTATGTAAA-3′<ref name=Mracek>{{ cite journal | | [[D box gene transcriptions|D boxes]] || 5'-GTTGTATAAC-3' || ⌘F || 5′-CTTATGTAAA-3′<ref name=Mracek>{{ cite journal | ||
|author=Philipp Mracek | |author=Philipp Mracek | ||
|author2=Cristina Santoriello | |||
|author3=M. Laura Idda | |||
|author4=Cristina Pagano | |||
|author5=Zohar Ben-Moshe | |||
|author6=Yoav Gothilf | |||
|author7=Daniela Vallone | |||
|author8=Nicholas S. Foulkes | |||
|title=Regulation of ''per'' and ''cry'' Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression | |title=Regulation of ''per'' and ''cry'' Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression | ||
|journal=PLoS ONE | |journal=PLoS ONE | ||
| Line 338: | Line 437: | ||
|- | |- | ||
| [[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]] || 5'-TATCGATA-3' || ⌘F || DNA replication-related element (DRE)<ref name=Hirose>{{ cite journal | ||
|author=Fumiko Hirose | |author=Fumiko Hirose | ||
|author2=Masamitsu Yamaguchi | |||
|author3=Akio Matsukage | |||
|title=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 | |title=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 | ||
|journal=Molecular and Cellular Biology | |journal=Molecular and Cellular Biology | ||
Revision as of 01:02, 28 November 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
- A1BG has no response elements in either promoter.
- A1BG is not transcribed by a response element.
- Each response element does not participate in the transcription of A1BG.
Response element negative results
| Name of elements | Consensus sequences | Testing | Notes |
|---|---|---|---|
| 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.[2] |
| Abf1 regulatory factors | 5'-CGTCCTCTACG-3' | 16 | 5'-CGTNNNNNACGAT-3'[3] |
| Activating proteins | 5'-GCCCACGGG-3' | 16 | Activating protein 2 (AP-2)[4] |
| Activating proteins | 5'-GGCCAA-3' | 16 | Activating protein 2 (AP-2)[5] |
| Alpha-amylase conserved elements | 5'-TATCCA-3' | 16 | 5'-TATCCATCCATCC-3'[6] |
| Amino acid response elements | 5'-ATTGCATCA-3' | 16 | AARE1 (5'-ATTGCATCA-3')[7] |
| Amino acid response elements | 5'-TTTGCATCA-3' | 16 | 5'-TTTGCATCA-3'.[8][9] |
| AARE-like | 5'-TGGTGAAAG-3' | 16 | AARE-like sequence (5′- TGGTGAAAG-3′, named AARE3)[7] |
| Androgen response elements | 5'-GGTACANNNTGTTCT-3'[10] | 16 | 5′-GGTACACGGTGTTCT-3′[10] |
| Androgen response elements | 5'-TGATTCGTGAG-3' | 16 | 5'-AGAACANNNTGTTCT-3'[11] |
| Antioxidant-electrophile responsive elements | 5'-GTGAGGTCGC-3' | 16 | 5'-GTGAGGTCGC-3'[12] 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'[13], an antioxidant response element (ARE) |
| 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 |
| Calcium-response elements | 5'-CTATTTCGAG-3' | 16 | CaRE1 5'-CTATTTCGAG-3'[14] |
| Carbohydrate response elements | 5'-CACGTGACCGGATCTTG-3', 5'-TCCGCCCCCATCACGTG-3' | 16 | ChoRE1, ChoRE2[15] |
| 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 |
| C-boxes | 5'-GAGGCCATCT-3' | 16 | 5'-GAGGCCATCT-3'[16] |
| C/A hybrid boxes | 5'-TGACGTAT-3' | 16 | 5'-TGACGTAT-3'[17] |
| C/T hybrid boxes | 5'-TGACGTTA-3' | 16 | 5'-TGACGTTA-3'[17] |
| C/EBP boxes | 5'-TTAGGACAT-3',[18] or 5'-TAGCATT-3'[5] | 16 | CCAAT-enhancer-binding site (C/EBP) is TAGCATT |
| Cell cycle regulation | 5'-CCCAACGGT-3'[6] | 16 | tomato genome-wide analysis |
| CENP-B boxes | 5'-TTTCGTTGGAAGCGGGA-3' | 16 | specifically localized at the centromere |
| Circadian control elements | 5'-CAACTTTA-3' | ⌘F | CCE |
| 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′[19] |
| DAF-16-associated elements | 5'-TGATAAG-3' | ⌘F | DAF-16-associated element (DAE)[20] |
| DAF-16 binding elements | 5'-GTAAACA-3' | ⌘F | DAF-16 binding element (DBE)[20] |
| D boxes | 5'-GTTGTATAAC-3' | ⌘F | 5′-CTTATGTAAA-3′[21] |
| D-boxes | 5'-TCTCACA-3' | ⌘F | TCTCACATT(A/C)AATAAGTCA is a D-box.[16] |
| Defense and stress-responsive elements | 5'-ATTTTCTTCA-3' | ⌘F | Defense and stress-responsive elements (DREs) |
| DNA damage response elements (DREs) | 5'-TAGCCGCCG-3' or 5'-TTTCAAT-3' | ⌘F | in the upstream repression sequence (URS) |
| DNA replication-related elements | 5'-TATCGATA-3' | ⌘F | DNA replication-related element (DRE)[22] |
| DREB boxes | 5'-TACCGACAT-3' | 16 | CRT/DREB box |
| EIF4E basal elements | 5'-TTACCCCCCCTT-3' | 16 | poly(C) motif |
| Endoplasmic reticulum stress response elements | 5'-CCAAT-3' | ⌘F | 5'-CCAATGGGCTGAAAC-3' between ZNF497 and A1BG |
| Estrogen response elements | 5'-AGGTTA-3' or 5'-GGTCAGGAT-3' | ⌘F | 5'-AGGTTATTGCCTCCT-3' or 5'-GGTCAGGATGAC-3' |
| Forkhead boxes | 5'-(A/G)(C/T)AAA(C/T)A-3' | ⌘F | 5'-GTAAACAA-3' FOXO1 |
| Gal4ps | 5'-CGGACCGC-3' | ⌘F | 5'-CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG-3' |
| G boxes | 5'-(G/T)CCACGTG(G/T)C-3' | ⌘F | no "perfect palindrome" G boxes in either promoter |
| GCN4 motifs | 5'-TGACTCA-3', 5'-TGAGTCA-3' | ⌘F | ACGT motif |
| Gcn4ps | 5'-ATGACTCTT-3' | ⌘F | GCN4 motifs |
| GLM boxes | 5′-(G/A)TGA(G/C)TCA(T/C)-3′ | 16 | GCN4-like motif |
| γ-interferon activated sequences (GAS) | 5'-TTCCTAGAA-3' | ⌘F | ALS-GAS1 between nt −633 and nt −625 |
| Grainy head transcription factor binding sites | 5'-AACCGGTT-3' | ⌘F | also 5'-GACTGGTT-3' |
| GT boxes | 5'-GGGGTGGGG-3' | ⌘F | (-78 to -69) |
| Hac1ps | 5'-CAGCGTG-3' | ⌘F | Regulates the unfolded protein response |
| Heat-responsive elements | 5'-AAAAAATTTC-3' | ⌘F | four nGAAn motifs |
| Hex sequences | 5'-TGACGTGGC-3' | ⌘F | the Hex sequence (TGACGTGGC)[17] |
| HMG boxes | 5'-(A/T)(A/T)CAAAG-3' | ⌘F | two or more HMG boxes |
| Hybrid C, A boxes | 5'-TGACGTAT-3' | ⌘F | A at the 12 position |
| Hybrid C, G boxes | 5'-TGACGTGT-3' | ⌘F | G at the 12 position |
| Hybrid C, T boxes | 5'-TGACGTTA-3' | ⌘F | T at the 12 position |
| Hypoxia-inducible factors | 5'-GCCCTACGT-3' | ⌘F | composed of HIF-1α and HIF-1β |
| I boxes | 5'-GATAAG-3' | ⌘F | 5'-GGATGAGATAAGA-3' |
| Inositol, choline-responsive element | 5'-TYTTCACATGY-3' | ⌘F | 5'-TCTTCAC, TCTTCACAT-3' |
| Kozak sequences | 5'-(GCC)GCC(A/G)CCATGG-3' | ⌘F | 5'-GAAAATGG-3'[23] |
| L boxes | 5'-TAAATG(A/C/G)A-3' | ⌘F | L1 box |
| MAREs | 5'-TGCTGA(G/C)TCAGCA-3' | ⌘F | and 5'-TGCTGA(GC/CG)TCAGCA-3' |
| M boxes | 5'-GTCATGTGCT-3' | ⌘F | upstream of the TATA box |
| 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 |
| Met31ps | 5'-AAACTGTGG-3' | ⌘F | Sulfur amino acid metabolism [72] |
| Middle sporulation elements | 5'-C(A/G)CAAA(A/T)-3' | ⌘F | 5'-ACACAAA-3' (2017) |
| 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 |
| Ndt80ps | 5'-TCCGCA-3' | ⌘F | 5'-DNCRCAAAW-3' |
| Nuclear factor Y | 5'-TACCGACAT-3' | ⌘F | NF-Y is a trimeric complex |
| Nutrient-sensing response element 1 | 5'-GTTTCATCA-3' | ⌘F | only one nucleotide difference between the SESN2 CARE and the ASNS |
| 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)3T(A/C/G/T)A(A/C/G/T)9-12CCG-3' |
| Pdr1p/Pdr3ps | 5'-TCCGCGGA-3' | ⌘F | Pdr1p/Pdr3p response element (PDRE) |
| Polycomb response elements | 5'-CGCCATTT-3' | ⌘F | closely resembles the extended Pho-Phol consensus sequence |
| 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 |
| Rgt1ps | 5'-CGGACCA-3' | ⌘F | Glucose-responsive transcription factor |
| Rlm1ps | 5'-CTATATATAG-3' | ⌘F | CTA(T/A)4TAG |
| Rox1ps | 5'-GGGTAA-3' | ⌘F | Heme-dependent repressor of hypoxic genes [78] |
| Rpn4ps | 5'-GGTGGCAAA-3' | ⌘F | proteasome genes |
| Seed-specific elements | 5'-CATGCATG-3' | ⌘F | SRE consensus: 5'-CAGCAGATTGCG-3' is none |
| Shoot specific elements | 5'-GATAATGATG-3' | ⌘F | SRE consensus: 5'-CAGCAGATTGCG-3' is none |
| Sip4ps | 5'-CCGTCCGT-3' | ⌘F | 5'-CC(C/G)T(C/T)C(C/G)TCCG-3' |
| Smp1ps | 5'-ACTACTA-3' | ⌘F | 5-ACTACTA(T/A)4TAG-3' |
| Sterol response elements | 5'-TCGTATA-3' | ⌘F | perhaps plant specific |
| TATCCAC boxes | 5'-TATCCAC-3' | 16 | GA responsive complex component |
| TCCACCATA elements | 5'-TCCACCATA-3' | ⌘F | adjacent co-dependent regulatory element of POLLEN1 |
| Tec1ps | 5'-GAATGT-3' | ⌘F | Ste12p cofactor |
| 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 |
| TGF-β control elements (TCEs) | 5'-GAGTGGGGCG-3' | ⌘F | in mouse and rat, 5'-GCGTGGGGGA-3' in humans |
| TGF-β inhibitory elements (TIEs) | 5'-GAGTGGTGA-3' | 16 | in the rat transin/stromelysin promoter |
| Thyroid hormone response elements (TREs) | 5'-AGGTCA-3' | ⌘F | See VDREs, X boxes |
| TCCACCATA elements | 5'-TCCACCATA-3' | ⌘F | adjacent co-dependent regulatory element of POLLEN1 |
| Tec1ps | 5'-GAATGT-3' | ⌘F | Ste12p cofactor |
| 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 |
| TGF-β control elements (TCEs) | 5'-GAGTGGGGCG-3' | ⌘F | in mouse and rat, 5'-GCGTGGGGGA-3' in humans |
| TGF-β inhibitory elements (TIEs) | 5'-GAGTGGTGA-3' | 16 | in the rat transin/stromelysin promoter |
| Thyroid hormone response elements (TREs) | 5'-AGGTCA-3' | ⌘F | See VDREs, X boxes |
| Unfolded protein response elements (UPREs) | 5'-TGACGTG(G/A)-3' | ⌘F | XBP1 binds to UPRE |
| Vhr1ps | 5'-AATCA-N8-TGA(C/T)T-3' | ⌘F | Response to low biotin [71] concentrations |
| Vitamin D response elements (VDREs) | 5'-(A/G)G(G/T)(G/T)CA-3' | ⌘F | 5'-AGGTCA-3' not ⌘F |
| X boxes | 5'-GTTGGCATGGCAAC-3' | 16 | X2 box is 5'-AGGTCCA-3' not ⌘F |
| Xbp1ps | 5'-GcCTCGA(G/A)G(C/A)g(a/g)-3' | ⌘F | Transcriptional repressor |
| Xenobiotic response elements (XREs) | 5'-(T/G)NGCGTG(A/C)(G/C)A-3' | ⌘F | contains the core sequence 5'-GCGTG-3' |
| Yap1p,2ps | 5'-TTACTAA-3' | ⌘F | Yap1p binding sites |
| Y boxes | 5'-(A/G)CTAACC(A/G)(A/G)(C/T)-3' | 16 | inverted CAAT box |
| Zap1ps | 5'-ACCCTCA-3' | ⌘F | 5'-ACC(C/T)(C/T)(A/C/G/T)AAGGT-3' |
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
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