Gibberellin responsive element gene transcriptions: Difference between revisions

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# GREr0: 1, AAACAGA at 3654.
# GREr0: 1, AAACAGA at 3654.
# RDr1: 0.
# GREr1: 1, AAACAGA at 4351.
# RDr2: 0.
# GREr2: 2, AAACAGA at 1858, AAACAGA at 943.
# RDr3: 0.
# GREr3: 0.
# RDr4: 0.
# GREr4: 0.
# RDr5: 0.
# GREr5: 0.
# RDr6: 0.
# GREr6: 2, AAACAGA at 2566, AAACAGA at 1101.
# RDr7: 0.
# GREr7: 0.
# RDr8: 0.
# GREr8: 0.
# RDr9: 0.
# GREr9: 0.
# RDr0ci: 0.
# GREr0ci: 1, TCTGTTT at 4375.
# RDr1ci: 0.
# GREr1ci: 0.
# RDr2ci: 0.
# GREr2ci: 0.
# RDr3ci: 0.
# GREr3ci: 1, TCTGTTT at 336.
# RDr4ci: 0.
# GREr4ci: 0.
# RDr5ci: 0.
# GREr5ci: 0.
# RDr6ci: 0.
# GREr6ci: 0.
# RDr7ci: 0.
# GREr7ci: 0.
# RDr8ci: 0.
# GREr8ci: 0.
# RDr9ci: 0.
# GREr9ci: 1, TCTGTTT at 716.


===GREr arbitrary (evens) (4560-2846) UTRs===
===GREr arbitrary (evens) (4560-2846) UTRs===


# GREr0: AAACAGA at 3654.
# GREr0: AAACAGA at 3654.
# GREr0ci: TCTGTTT at 4375.


===RDr alternate (odds) (4560-2846) UTRs===
===GREr alternate (odds) (4560-2846) UTRs===


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
# GREr1: AAACAGA at 4351.


===RDr alternate negative direction (odds) (2846-2811) core promoters===
===GREr arbitrary positive direction (odds) (4445-4265) core promoters===


===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
# GREr1: AAACAGA at 4351.


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


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
# GREr0ci: TCTGTTT at 4375.


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
===GREr arbitrary negative direction (evens) (2596-1) distal promoters===


===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
# GREr2: AAACAGA at 1858, AAACAGA at 943.
# GREr6: AAACAGA at 2566, AAACAGA at 1101.


===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
===GREr alternate negative direction (odds) (2596-1) distal promoters===


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
# GREr3ci: TCTGTTT at 336.
# GREr9ci: TCTGTTT at 716.


===RDr alternate negative direction (odds) (2596-1) distal promoters===
===GREr arbitrary positive direction (odds) (4050-1) distal promoters===


===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
# GREr3ci: TCTGTTT at 336.
# GREr9ci: TCTGTTT at 716.


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


# GREr0: AAACAGA at 3654.
# GREr0: AAACAGA at 3654.
# GREr2: AAACAGA at 1858, AAACAGA at 943.
# GREr6: AAACAGA at 2566, AAACAGA at 1101.


==GRE analysis and results==
==GRE analysis and results==
Line 122: Line 128:
| Reals || UTR || negative || 2 || 2 || 1 || 1  
| Reals || UTR || negative || 2 || 2 || 1 || 1  
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 2 || 10 || 0.2 || 0.15
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 1 || 10 || 0.1 || 0.15
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
Line 134: Line 140:
| Reals || Core || positive || 0 || 2 || 0 || 0  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 1 || 10 || 0.1 || 0.1
|-
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Core || alternate positive || 1 || 10 || 0.1 || 0.1
|-
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
Line 152: Line 158:
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5  
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5  
|-
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
| Randoms || Distal || arbitrary negative || 4 || 10 || 0.4 || 0.3
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate negative || 2 || 10 || 0.2 || 0.3
|-
|-
| Reals || Distal || positive || 3 || 2 || 1.5 || 1.5 ± 0.5 (-+2,++1)  
| Reals || Distal || positive || 3 || 2 || 1.5 || 1.5 ± 0.5 (-+2,++1)  
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary positive || 2 || 10 || 0.2 || 0.35
|-
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 5 || 10 || 0.5 || 0.35
|}
|}


Comparison:
Comparison:


The occurrences of real GREs are greater than the randoms. This suggests that the real GREs are likely active or activable.
The occurrences of real GRE UTRs and distals are greater than the randoms. This suggests that the real GREs are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Latest revision as of 01:19, 8 January 2023

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

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Gibberellin responsive elements (CCTTTTG, AAACAGA).[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no GREs in either promoter.
  2. A1BG is not transcribed by a GRE.
  3. GRE does not participate in the transcription of A1BG.

GRE samplings

Copying an apparent consensus sequence of CCTTTTG, AAACAGA and putting it in "⌘F" finds one located between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AAACAGA (starting with SuccessablesGib.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 AAACAGA, 0.
  2. positive strand, negative direction, looking for AAACAGA, 3, AAACAGA at 4518, AAACAGA at 2878, AAACAGA at 168.
  3. negative strand, positive direction, looking for AAACAGA, 2, AAACAGA at 3179, AAACAGA at 2652.
  4. positive strand, positive direction, looking for AAACAGA, 0.
  5. inverse complement, negative strand, negative direction, looking for TCTGTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TCTGTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TCTGTTT, 1, TCTGTTT at 2262.
  8. inverse complement, positive strand, positive direction, looking for TCTGTTT, 0.

GRE (4560-2846) UTRs

  1. Positive strand, negative direction: AAACAGA at 4518, AAACAGA at 2878.

GRE negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: AAACAGA at 168.

GRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AAACAGA at 3179, AAACAGA at 2652.
  2. Negative strand, positive direction: TCTGTTT at 2262.

GRE random dataset samplings

  1. GREr0: 1, AAACAGA at 3654.
  2. GREr1: 1, AAACAGA at 4351.
  3. GREr2: 2, AAACAGA at 1858, AAACAGA at 943.
  4. GREr3: 0.
  5. GREr4: 0.
  6. GREr5: 0.
  7. GREr6: 2, AAACAGA at 2566, AAACAGA at 1101.
  8. GREr7: 0.
  9. GREr8: 0.
  10. GREr9: 0.
  11. GREr0ci: 1, TCTGTTT at 4375.
  12. GREr1ci: 0.
  13. GREr2ci: 0.
  14. GREr3ci: 1, TCTGTTT at 336.
  15. GREr4ci: 0.
  16. GREr5ci: 0.
  17. GREr6ci: 0.
  18. GREr7ci: 0.
  19. GREr8ci: 0.
  20. GREr9ci: 1, TCTGTTT at 716.

GREr arbitrary (evens) (4560-2846) UTRs

  1. GREr0: AAACAGA at 3654.
  2. GREr0ci: TCTGTTT at 4375.

GREr alternate (odds) (4560-2846) UTRs

  1. GREr1: AAACAGA at 4351.

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

  1. GREr1: AAACAGA at 4351.

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

  1. GREr0ci: TCTGTTT at 4375.

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

  1. GREr2: AAACAGA at 1858, AAACAGA at 943.
  2. GREr6: AAACAGA at 2566, AAACAGA at 1101.

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

  1. GREr3ci: TCTGTTT at 336.
  2. GREr9ci: TCTGTTT at 716.

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

  1. GREr3ci: TCTGTTT at 336.
  2. GREr9ci: TCTGTTT at 716.

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

  1. GREr0: AAACAGA at 3654.
  2. GREr2: AAACAGA at 1858, AAACAGA at 943.
  3. GREr6: AAACAGA at 2566, AAACAGA at 1101.

GRE analysis and results

Main article: Complex locus A1BG and ZNF497 § GREs

Gibberellin responsive elements (CCTTTTG, AAACAGA).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 2 10 0.2 0.15
Randoms UTR alternate negative 1 10 0.1 0.15
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 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
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 4 10 0.4 0.3
Randoms Distal alternate negative 2 10 0.2 0.3
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+2,++1)
Randoms Distal arbitrary positive 2 10 0.2 0.35
Randoms Distal alternate positive 5 10 0.5 0.35

Comparison:

The occurrences of real GRE UTRs and distals are greater than the randoms. This suggests that the real GREs 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 Bhaskar Sharma & Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

External links

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