Peroxisome proliferator hormone response element gene transcriptions: Difference between revisions

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# inverse negative strand, positive direction, looking for CCCCAGC, 0.
# inverse negative strand, positive direction, looking for CCCCAGC, 0.


===PPARA UTRs===
===PPARA (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
Negative strand, negative direction: CGACCCC at 3037.


===PPARA proximal promoters===
# Negative strand, negative direction: CGACCCC at 3037.
{{main|Proximal promoter gene transcriptions}}
Positive strand, negative direction: CCCCAGC at 2766.


===PPARA distal promoters===
===PPARA negative direction (2811-2596) proximal promoters===
{{main|Distal promoter gene transcriptions}}
 
Positive strand, positive direction: CGACCCC at 279.
# Negative strand, negative direction: GGGGTCG at 2766.
 
===PPARA positive direction (4050-1) distal promoters===
 
# Positive strand, positive direction: CGACCCC at 279.
 
==PPARA random dataset samplings==
 
# 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.
 
===RDr arbitrary (evens) (4560-2846) UTRs===
 
===RDr alternate (odds) (4560-2846) UTRs===
 
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
 
===RDr alternate negative direction (odds) (2846-2811) core promoters===
 
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
 
===RDr alternate positive direction (evens) (4445-4265) core promoters===
 
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
 
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
 
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
 
===RDr alternate negative direction (odds) (2596-1) distal promoters===
 
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
 
===RDr alternate positive direction (evens) (4050-1) distal promoters===
 
==PPARA analysis and results==
{{main|Complex locus A1BG and ZNF497#PPARAs}}
Consensus sequence is CGACCCC.<ref name=Long/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || negative || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || positive || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
 
Comparison:
 
The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.


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

Revision as of 15:12, 25 September 2022

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

"After activation by ligands, PPARs/RXRs heterodimers bind to PPRE consensus sequence (AGGTCANAGGTCA) in the promoter of their target genes."[1]

Peroxisome proliferator hormone response elements (PPREs) consensus sequences are AGGGGA and TCCCCT.[2]

Human genes

Consensus sequences

The DNA consensus sequence is AGGTCANAGGTCA, with N being any nucleotide.

PPRE samplings

For the Basic programs testing consensus sequence AGGTCANAGGTCA (starting with SuccessablesPPRE.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 AGGTCANAGGTCA, 0.
  2. positive strand, negative direction, looking for AGGTCANAGGTCA, 0.
  3. positive strand, positive direction, looking for AGGTCANAGGTCA, 0.
  4. negative strand, positive direction, looking for AGGTCANAGGTCA, 0.
  5. complement, negative strand, negative direction, looking for TCCAGTNTCCAGT, 0.
  6. complement, positive strand, negative direction, looking for TCCAGTNTCCAGT, 0.
  7. complement, positive strand, positive direction, looking for TCCAGTNTCCAGT, 0.
  8. complement, negative strand, positive direction, looking for TCCAGTNTCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCTNTGACCT, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCTNTGACCT, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCTNTGACCT, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCTNTGACCT, 0.
  13. inverse negative strand, negative direction, looking for ACTGGANACTGGA, 0.
  14. inverse positive strand, negative direction, looking for ACTGGANACTGGA, 0.
  15. inverse positive strand, positive direction, looking for ACTGGANACTGGA, 0.
  16. inverse negative strand, positive direction, looking for ACTGGANACTGGA, 0.

PPARA consensus sequences

Consensus sequence is 5'-CGACCCC-3'.[3]

PPARA samplings

Copying the apparent consensus sequence for the PPARA (CGACCCC) and putting it in "⌘F" finds one located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CGACCCC (starting with Successables PPARA.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 CGACCCC, 1, CGACCCC at 3037.
  2. positive strand, negative direction, looking for CGACCCC, 0.
  3. positive strand, positive direction, looking for CGACCCC, 1, CGACCCC at 279.
  4. negative strand, positive direction, looking for CGACCCC, 0.
  5. complement, negative strand, negative direction, looking for GCTGGGG, 0.
  6. complement, positive strand, negative direction, looking for GCTGGGG, 1, GCTGGGG at 3037.
  7. complement, positive strand, positive direction, looking for GCTGGGG, 0.
  8. complement, negative strand, positive direction, looking for GCTGGGG, 1, GCTGGGG at 279.
  9. inverse complement, negative strand, negative direction, looking for GGGGTCG, 1, GGGGTCG at 2766.
  10. inverse complement, positive strand, negative direction, looking for GGGGTCG, 0.
  11. inverse complement, positive strand, positive direction, looking for GGGGTCG, 0.
  12. inverse complement, negative strand, positive direction, looking for GGGGTCG, 0.
  13. inverse negative strand, negative direction, looking for CCCCAGC, 0.
  14. inverse positive strand, negative direction, looking for CCCCAGC, 1, CCCCAGC at 2766.
  15. inverse positive strand, positive direction, looking for CCCCAGC, 0.
  16. inverse negative strand, positive direction, looking for CCCCAGC, 0.

PPARA (4560-2846) UTRs

  1. Negative strand, negative direction: CGACCCC at 3037.

PPARA negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GGGGTCG at 2766.

PPARA positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: CGACCCC at 279.

PPARA 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 arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

PPARA analysis and results

Main article: Complex locus A1BG and ZNF497 § PPARAs

Consensus sequence is CGACCCC.[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

See also

References

  1. ↑ Mengli You, Shuping Yuan, Juanjuan Shi, Yongzhong Hou (1 June 2015). "PPARδ signaling regulates colorectal cancer". Current Pharmaceutical Design. 21 (21): 2956–2959. doi:10.2174/1381612821666150514104035. PMID 26004416. Retrieved 10 September 2020.
  2. ↑ 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.
  3. ↑ 3.0 3.1 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.

External links


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