Antioxidant-electrophile responsive element gene transcriptions: Difference between revisions

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==AERE (Lacher) random dataset samplings==
==AERE (Lacher) random dataset samplings==


# RDr0: 0.
# AEREr0: 2, GCATATTCA at 3451, GCCATTTAA at 2392.
# RDr1: 0.
# AEREr1: 4, GCTTACTAA at 4451, GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.
# RDr2: 0.
# AEREr2: 2, GCTAAGTCA at 4374, GCTGAGTAA at 3017.
# RDr3: 0.
# RDr3: 0.
# RDr4: 0.
# RDr4: 0.
Line 115: Line 115:
# RDr9ci: 0.
# RDr9ci: 0.


===RDr UTRs===
===AEREr UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
# AEREr0: GCATATTCA at 3451.
# AEREr2: GCTAAGTCA at 4374, GCTGAGTAA at 3017.


===RDr core promoters===
===AEREr core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}
# AEREr1: GCTTACTAA at 4451.


===RDr proximal promoters===
===RDr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}


===RDr distal promoters===
===AEREr distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
# AEREr0: GCCATTTAA at 2392.
# AEREr1: GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.


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

Revision as of 07:53, 17 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. The predominant consensus sequence for Human, Chimp, Gorilla, Rhesus, Mouse, and Rat is TGCTGAGTCAT.[1]

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: 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. AEREr0: 2, GCATATTCA at 3451, GCCATTTAA at 2392.
  2. AEREr1: 4, GCTTACTAA at 4451, GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.
  3. AEREr2: 2, GCTAAGTCA at 4374, GCTGAGTAA at 3017.
  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.

AEREr UTRs

Main article: UTR promoter gene transcriptions
  1. AEREr0: GCATATTCA at 3451.
  2. AEREr2: GCTAAGTCA at 4374, GCTGAGTAA at 3017.

AEREr core promoters

Main article: Core promoter gene transcriptions
  1. AEREr1: GCTTACTAA at 4451.

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

AEREr distal promoters

Main article: Distal promoter gene transcriptions
  1. AEREr0: GCCATTTAA at 2392.


  1. AEREr1: GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.

See also

References

  1. ↑ 1.0 1.1 1.2 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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