Antioxidant-electrophile responsive element gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' (starting with SuccessablesAERE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
For the Basic programs testing consensus sequence 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' (starting with SuccessablesAERE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# negative strand, negative direction, looking for 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3', 0.
# negative strand, negative direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
# negative strand, positive direction, looking for 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3', 0.
# negative strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
# positive strand, negative direction, looking for 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3', 2, 5'-GCAGTGTAA-3' at 2087, 5'-GCATTTTAA-3' at 192.
# positive strand, negative direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 2, GCAGTGTAA at 2087, GCATTTTAA at 192.
# positive strand, positive direction, looking for 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3', 0.
# positive strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
# complement, negative strand, negative direction, looking for 5'-CG(A/G/T)(A/C/T)(A/C/T)(A/C/G)A(G/T)T-3', 2, 5'-CGTCACATT-3' at 2087, 5'-CGTAAAATT-3' at 192.
# inverse complement, negative strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 2, TGACTATGC at 3546, TTAATCGGC at 1237.
# complement, negative strand, positive direction, looking for 5'-CG(A/G/T)(A/C/T)(A/C/T)(A/C/G)A(G/T)T-3', 0.
# inverse complement, negative strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGACCAGGC at 2877.
# complement, positive strand, negative direction, looking for 5'-CG(A/G/T)(A/C/T)(A/C/T)(A/C/G)A(G/T)T-3', 0.
# inverse complement, positive strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 3, TGAGTTGGC at 4098, TTAAAAGGC at 3442, TTAGCCAGC at 504.
# complement, positive strand, positive direction, looking for 5'-CG(A/G/T)(A/C/T)(A/C/T)(A/C/G)A(G/T)T-3', 0.
# inverse complement, positive strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGAAAAAGC at 1750.
# inverse complement, negative strand, negative direction, looking for 5'-T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC-3', 2, 5'-TGACTATGC-3' at 3546, 5'-TTAATCGGC-3' at 1237.
 
# inverse complement, negative strand, positive direction, looking for 5'-T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC-3', 1, 5'-TGACCAGGC-3' at 2877.
===AERE (Lacher) UTRs===
# inverse complement, positive strand, negative direction, looking for 5'-T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC-3', 3, 5'-TGAGTTGGC-3' at 4098, 5'-TTAAAAGGC-3' at 3442, 5'-TTAGCCAGC-3' at 504.
# Negative strand, negative direction: TGACTATGC at 3546.
# inverse complement, positive strand, positive direction, looking for 5'-T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC-3', 1, 5'-TGAAAAAGC-3' at 1750.
# Positive strand, negative direction: TGAGTTGGC at 4098, TTAAAAGGC at 3442.
# inverse negative strand, negative direction, looking for 5'-A(A/C)T(C/G/T)(A/G/T)(A/G/T)(A/C/T)CG-3', 3, 5'-ACTCAACCG-3' at 4098, 5'-AATTTTCCG-3' at 3442, 5'-AATCGGTCG-3' at 504.
# inverse negative strand, positive direction, looking for 5'-A(A/C)T(C/G/T)(A/G/T)(A/G/T)(A/C/T)CG-3', 1, 5'-ACTTTTTCG-3' at 1750.
# inverse positive strand, negative direction, looking for 5'-A(A/C)T(C/G/T)(A/G/T)(A/G/T)(A/C/T)CG-3', 2, 5'-ACTGATACG-3' at 3546, 5'-AATTAGCCG-3' at 1237, and complements.
# inverse positive strand, positive direction, looking for 5'-A(A/C)T(C/G/T)(A/G/T)(A/G/T)(A/C/T)CG-3', 1, 5'-ACTGGTCCG-3' at 2877.


===AERE (Lacher) distal promoters===
===AERE (Lacher) distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: 5'-TGACTATGC-3' at 3546, 5'-TTAATCGGC-3' at 1237, and complements.
Negative strand, negative direction: TTAATCGGC at 1237.
Positive strand, negative direction: TGAGTTGGC at 4098, TTAAAAGGC at 3442, GCAGTGTAA at 2087, TTAGCCAGC at 504, GCATTTTAA at 192.
 
 
Negative strand, positive direction: TGACCAGGC at 2877.
Positive strand, positive direction: TGAAAAAGC at 1750.


Positive strand, negative direction: 5'-TGAGTTGGC-3' at 4098, 5'-TTAAAAGGC-3' at 3442, 5'-GCAGTGTAA-3' at 2087, 5'-TTAGCCAGC-3' at 504, 5'-GCATTTTAA-3' at 192 and complements.
==AERE (Lacher) random dataset samplings==


Negative strand, positive direction: 5'-TGACCAGGC-3' at 2877 and complement.
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.


Positive strand, positive direction: 5'-TGAAAAAGC-3' at 1750 and complement.
===RDr UTRs===
{{main|UTR promoter gene transcriptions}}
 
===RDr core promoters===
{{main|Core promoter gene transcriptions}}
 
===RDr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===RDr distal promoters===
{{main|Distal promoter gene transcriptions}}


==See also==
==See also==

Revision as of 16:30, 16 November 2021

Associate Editor(s)-in-Chief: Henry A. Hoff

The "perfect ARE sequence [GCTGAGTCA] is strongly conserved across mammals [...]."[1]

Consensus sequences

5'-GTGAGGTCGC-3'[2]

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'[1], an antioxidant response element (ARE).

Hypotheses

Main article: Hypotheses
  1. A1BG has no Antioxidant-electrophile responsive element in either promoter.
  2. A1BG is not transcribed by an Antioxidant-electrophile responsive element.
  3. Antioxidant-electrophile responsive element does not participate in the transcription of A1BG.

AERE (Otsuki) samplings

Copying an antioxidant-electrophile responsive elements consensus sequence 5'-GTGAGGTCGC-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
  2. negative strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
  3. positive strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
  4. positive strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.

AERE (Lacher) samplings

Copying 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' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' (starting with SuccessablesAERE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  2. negative strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  3. positive strand, negative direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 2, GCAGTGTAA at 2087, GCATTTTAA at 192.
  4. positive strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  5. inverse complement, negative strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 2, TGACTATGC at 3546, TTAATCGGC at 1237.
  6. inverse complement, negative strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGACCAGGC at 2877.
  7. inverse complement, positive strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 3, TGAGTTGGC at 4098, TTAAAAGGC at 3442, TTAGCCAGC at 504.
  8. inverse complement, positive strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGAAAAAGC at 1750.

AERE (Lacher) UTRs

  1. Negative strand, negative direction: TGACTATGC at 3546.
  2. Positive strand, negative direction: TGAGTTGGC at 4098, TTAAAAGGC at 3442.

AERE (Lacher) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTAATCGGC at 1237. Positive strand, negative direction: TGAGTTGGC at 4098, TTAAAAGGC at 3442, GCAGTGTAA at 2087, TTAGCCAGC at 504, GCATTTTAA at 192.


Negative strand, positive direction: TGACCAGGC at 2877. Positive strand, positive direction: TGAAAAAGC at 1750.

AERE (Lacher) random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

See also

References

  1. ↑ 1.0 1.1 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.
  2. ↑ 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.

Acknowledgements

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

External links

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