A1BG response element negative results: Difference between revisions

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| [[Coupling element gene transcriptions|Coupling elements]] || 5'-TGCCACCGG-3'<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
| [[Coupling element gene transcriptions|Coupling elements]] || 5'-TGCCACCGG-3'<ref name=Watanabe/> || 16 || CE1 (Watanabe)  
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| [[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' || 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

Revision as of 00:46, 4 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

  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

Response elements not occurring in promoters near A1BG
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]
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′[18]
C/EBP boxes 5'-TTAGGACAT-3',[19] 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
Coupling elements 5'-TGCCACCGG-3'[2] 16 CE1 (Watanabe)
DAF-16-associated elements 5'-TGATAAG-3' 16 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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External links

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