ROR-response element gene transcriptions: Difference between revisions

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==VROR random dataset samplings==
==VROR random dataset samplings==


# RDr0: 0.
# VRORr0: 0.
# RDr1: 0.
# VRORr1: 3, CTGGGCCA at 3661, CAAGGGCA at 3203, CTGGGACA at 1892.
# RDr2: 0.
# VRORr2: 1, CAGGGCCA at 2277.
# RDr3: 0.
# VRORr3: 2, CAGGGCCA at 1592, CAGGGCCA at 1479.
# RDr4: 0.
# VRORr4: 0.
# RDr5: 0.
# VRORr5: 2, CTAGGCCA at 1994, CAGGGACA at 1517.
# RDr6: 0.
# VRORr6: 1, CAAGGACA at 791.
# RDr7: 0.
# VRORr7: 0.
# RDr8: 0.
# RDr8: 0.
# RDr9: 0.
# RDr9: 0.
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===RDr arbitrary (evens) (4560-2846) UTRs===
===RDr arbitrary (evens) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===
===VRORr alternate (odds) (4560-2846) UTRs===
 
# VRORr1: CTGGGCCA at 3661, CAAGGGCA at 3203.


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


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


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


===RDr alternate positive direction (evens) (4445-4265) core promoters===
===RDr alternate positive direction (evens) (4445-4265) core promoters===
Line 201: Line 205:


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


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


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


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===VRORr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# VRORr2: CAGGGCCA at 2277.
# VRORr6: CAAGGACA at 791.
 
===VRORr alternate negative direction (odds) (2596-1) distal promoters===
 
# VRORr1: CTGGGACA at 1892.
# VRORr3: CAGGGCCA at 1592, CAGGGCCA at 1479.
# VRORr5: CTAGGCCA at 1994, CAGGGACA at 1517.
 
===VRORr arbitrary positive direction (odds) (4050-1) distal promoters===


===RDr alternate negative direction (odds) (2596-1) distal promoters===
# VRORr1: CTGGGCCA at 3661, CAAGGGCA at 3203, CTGGGACA at 1892.
# VRORr3: CAGGGCCA at 1592, CAGGGCCA at 1479.
# VRORr5: CTAGGCCA at 1994, CAGGGACA at 1517.


===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===VRORr alternate positive direction (evens) (4050-1) distal promoters===


===RDr alternate positive direction (evens) (4050-1) distal promoters===
# VRORr2: CAGGGCCA at 2277.
# VRORr6: CAAGGACA at 791.


==VRORE analysis and results==
==VRORE analysis and results==

Revision as of 03:59, 23 January 2023

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

RAR-related orphan receptor "ROR-γ binds DNA with specific sequence motifs AA/TNTAGGTCA (the classic RORE motif) or CT/AG/AGGNCA (the variant RORE motif)13, 31."[1]

Human genes

Consensus sequences

The consensus sequences for the ROR-response elements are 5'-A(A/T)NTAGGTCA-3' (classic RORE motif) and 5'-C(T/A)(G/A)GGNCA-3' (variant RORE).[1]

RORE samplings

Main article: Model samplings

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

Copying the apparent consensus sequence for the variant RORE (CTGGGACA) and putting it in "⌘F" finds two located between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence A(A/T)NTAGGTCA (starting with SuccessablesRORE.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 A(A/T)NTAGGTCA, 1, ATATAGGTCA at 1532.
  2. positive strand, negative direction, looking for A(A/T)NTAGGTCA, 0.
  3. positive strand, positive direction, looking for A(A/T)NTAGGTCA, 0.
  4. negative strand, positive direction, looking for A(A/T)NTAGGTCA, 0.
  5. complement, negative strand, negative direction, looking for T(A/T)NATCCAGT, 0.
  6. complement, positive strand, negative direction, looking for T(A/T)NATCCAGT, 1, ATATAGGTCA at 1532.
  7. complement, positive strand, positive direction, looking for T(A/T)NATCCAGT, 0.
  8. complement, negative strand, positive direction, looking for T(A/T)NATCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCTAN(A/T)T, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCTAN(A/T)T, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCTAN(A/T)T, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCTAN(A/T)T, 0.
  13. inverse negative strand, negative direction, looking for ACTGGATN(A/T)A, 0.
  14. inverse positive strand, negative direction, looking for ACTGGATN(A/T)A, 0.
  15. inverse positive strand, positive direction, looking for ACTGGATN(A/T)A, 0.
  16. inverse negative strand, positive direction, looking for ACTGGATN(A/T)A, 0.

ROR negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATATAGGTCA at 1532.

RORE dataset samplings

  1. ROREr0: 0.
  2. ROREr1: 0.
  3. ROREr2: 0.
  4. ROREr3: 0.
  5. ROREr4: 0.
  6. ROREr5: 0.
  7. ROREr6: 0.
  8. ROREr7: 0.
  9. ROREr8: 0.
  10. ROREr9: 0.
  11. ROREr0ci: 0.
  12. ROREr1ci: 0.
  13. ROREr2ci: 0.
  14. ROREr3ci: 0.
  15. ROREr4ci: 0.
  16. ROREr5ci: 0.
  17. ROREr6ci: 0.
  18. ROREr7ci: 0.
  19. ROREr8ci: 0.
  20. ROREr9ci: 0.

RORE analysis and results

Main article: Complex locus A1BG and ZNF497 § ROREs

"ROR-γ binds DNA with specific sequence motifs AA/TNTAGGTCA (the classic RORE motif) or CT/AG/AGGNCA (the variant RORE motif)13, 31."[1]

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 1 2 0.5 0.5
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 ROREs are greater than the randoms. This suggests that the real ROREs are likely active or activable.

RORE variant samplings

Main article: Model samplings

Copying a responsive elements consensus sequence C(T/A)(G/A)GGNCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence C(T/A)(G/A)GGNCA (starting with SuccessablesVRORE.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 C(T/A)(G/A)GGNCA, 2, CTGGGACA at 4369, CTGGGACA at 4208.
  2. positive strand, negative direction, looking for C(T/A)(G/A)GGNCA, 2, CAAGGTCA at 2248, CAAGGGCA at 1821.
  3. positive strand, positive direction, looking for C(T/A)(G/A)GGNCA, 0.
  4. negative strand, positive direction, looking for C(T/A)(G/A)GGNCA, 1, CTGGGACA at 3530.
  5. complement, negative strand, negative direction, looking for G(T/A)(C/T)CCNGT, 2, GTTCCAGT at 2248, GTTCCCGT at 1821.
  6. complement, positive strand, negative direction, looking for G(T/A)(C/T)CCNGT, 2, GACCCTGT at 4369, GACCCTGT at 4208.
  7. complement, positive strand, positive direction, looking for G(T/A)(C/T)CCNGT, 1, GACCCTGT at 3530.
  8. complement, negative strand, positive direction, looking for G(T/A)(C/T)CCNGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGNCC(C/T)(A/T)G, 0.
  10. inverse complement, positive strand, negative direction, looking for TGNCC(C/T)(A/T)G, 0.
  11. inverse complement, positive strand, positive direction, looking for TGNCC(C/T)(A/T)G, 0.
  12. inverse complement, negative strand, positive direction, looking for TGNCC(C/T)(A/T)G, 2, TGCCCCAG at 3015, TGGCCCAG at 1741.
  13. inverse negative strand, negative direction, looking for ACNGG(A/G)(A/T)C, 0.
  14. inverse positive strand, negative direction, looking for ACNGG(A/G)(A/T)C, 0.
  15. inverse positive strand, positive direction, looking for ACNGG(A/G)(A/T)C, 2, ACGGGGTC at 3015, ACCGGGTC at 1741.
  16. inverse negative strand, positive direction, looking for ACNGG(A/G)(A/T)C, 0.

VROR (4560-2846) UTRs

  1. Negative strand, negative direction: CTGGGACA at 4369, CTGGGACA at 4208.

VROR negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: CAAGGTCA at 2248, CAAGGGCA at 1821.

VROR positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CTGGGACA at 3530.
  2. Negative strand, positive direction: TGCCCCAG at 3015, TGGCCCAG at 1741.

VROR random dataset samplings

  1. VRORr0: 0.
  2. VRORr1: 3, CTGGGCCA at 3661, CAAGGGCA at 3203, CTGGGACA at 1892.
  3. VRORr2: 1, CAGGGCCA at 2277.
  4. VRORr3: 2, CAGGGCCA at 1592, CAGGGCCA at 1479.
  5. VRORr4: 0.
  6. VRORr5: 2, CTAGGCCA at 1994, CAGGGACA at 1517.
  7. VRORr6: 1, CAAGGACA at 791.
  8. VRORr7: 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

VRORr alternate (odds) (4560-2846) UTRs

  1. VRORr1: CTGGGCCA at 3661, CAAGGGCA at 3203.

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

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

  1. VRORr2: CAGGGCCA at 2277.
  2. VRORr6: CAAGGACA at 791.

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

  1. VRORr1: CTGGGACA at 1892.
  2. VRORr3: CAGGGCCA at 1592, CAGGGCCA at 1479.
  3. VRORr5: CTAGGCCA at 1994, CAGGGACA at 1517.

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

  1. VRORr1: CTGGGCCA at 3661, CAAGGGCA at 3203, CTGGGACA at 1892.
  2. VRORr3: CAGGGCCA at 1592, CAGGGCCA at 1479.
  3. VRORr5: CTAGGCCA at 1994, CAGGGACA at 1517.

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

  1. VRORr2: CAGGGCCA at 2277.
  2. VRORr6: CAAGGACA at 791.

VRORE analysis and results

Main article: Complex locus A1BG and ZNF497 § VROREs

"ROR-γ binds DNA with specific sequence motifs AA/TNTAGGTCA (the classic RORE motif) or CT/AG/AGGNCA (the variant RORE motif)13, 31."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
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 2 2 1 1
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 3 2 1.5 1.5
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real VRORs are greater than the randoms. This suggests that the real VRORs are likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Junjian Wang, June X. Zou, Xiaoqian Xue, Demin Cai, Yan Zhang, Zhijian Duan, Qiuping Xiang, Joy C. Yang, Maggie C. Louie, Alexander D. Borowsky, Allen C. Gao, Christopher P. Evans, Kit S. Lam, Jianzhen Xu, Hsing-Jien Kung, Ronald M. Evans, Yong Xu, and Hong-Wu Chen (May 2016). "ROR-γ drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer". Nature Medicine. 22 (5): 488–496. doi:10.1038/nm.4070. PMID 27019329. Retrieved 6 September 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=ROR-response_element_gene_transcriptions&oldid=1732816"