Jasmonic acid-responsive element gene transcriptions: Difference between revisions

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Positive strand, positive direction: CGTCA at 3962, CGTCA at 3461, TGACG at 3319, CGTCA at 3281, CGTCA at 3232, TGACG at 2822, CGTCA at 2328, TGACG at 2203, CGTCA at 2065, TGACG at 2042, TGACG at 1504, TGACG at 1000, TGACG at 900, TGACG at 748, TGACG at 237.
Positive strand, positive direction: CGTCA at 3962, CGTCA at 3461, TGACG at 3319, CGTCA at 3281, CGTCA at 3232, TGACG at 2822, CGTCA at 2328, TGACG at 2203, CGTCA at 2065, TGACG at 2042, TGACG at 1504, TGACG at 1000, TGACG at 900, TGACG at 748, TGACG at 237.
==JARE 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 UTRs===
===RDr alternate UTRs===
===RDr arbitrary negative direction core promoters===
===RDr alternate negative direction core promoters===
===RDr arbitrary positive direction core promoters===
===RDr alternate positive direction core promoters===
===RDr arbitrary negative direction proximal promoters===
===RDr alternate negative direction proximal promoters===
===RDr arbitrary positive direction proximal promoters===
===RDr alternate positive direction proximal promoters===
===RDr arbitrary negative direction distal promoters===
===RDr alternate negative direction distal promoters===
===RDr arbitrary positive direction distal promoters===
===RDr alternate positive direction distal promoters===
==JARE analysis and results==
{{main|Complex locus A1BG and ZNF497#JAREs}}
Jasmonic acid-responsive elements (TGACG, CGTCA).<ref name=Sharma/>
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 7 || 2 || 3.5 || 3.5 (4,3)
|-
| 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 || 1 || 2 || 0.5 || 0.5
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 2 || 2 || 1 || 1
|-
| 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 || 11 || 2 || 5.5 || 5.5 ± 3.5 (--9,+-2)
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 18 || 2 || 9 || 9 ± 6 (-+3,++15)
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
Comparison:
The occurrences of real JAREs are greater than the randoms. This suggests that the real JAREs are likely active or activable.


==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element gene transcriptions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
{{Div col end}}
{{Div col end}}


Revision as of 15:22, 18 June 2022

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

Jasmonic acid-responsive elements (TGACG, CGTCA).[1]

Human genes

Interactions

Consensus sequences

Apparent consensus sequence for the JARE is TGACG.[2]

JARE samplings

Copying an apparent consensus sequence for the jasmonic acid-responsive element (JARE)[2] of TGACG and putting it in "⌘F" finds eight 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 TGACG (starting with SuccessablesJARE.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 TGACG, 8, TGACG at 4337, TGACG at 4329, TGACG at 4314, TGACG at 3851, TGACG at 2758, TGACG at 2423, TGACG at 1997, TGACG at 1493.
  2. negative strand, positive direction, looking for TGACG, 1, TGACG at 1834.
  3. positive strand, negative direction, looking for TGACG, 1, TGACG at 309.
  4. positive strand, positive direction, looking for TGACG, 10, TGACG at 4340, TGACG at 3319, TGACG at 2822, TGACG at 2203, TGACG at 2042, TGACG at 1504, TGACG at 1000, TGACG at 900, TGACG at 748, TGACG at 237.
  5. complement, negative strand, negative direction, looking for ACTGC, 1, ACTGC at 309.
  6. complement, negative strand, positive direction, looking for ACTGC, 10, ACTGC at 4340, ACTGC at 3319, ACTGC at 2822, ACTGC at 2203, ACTGC at 2042, ACTGC at 1504, ACTGC at 1000, ACTGC at 900, ACTGC at 748, ACTGC at 237.
  7. complement, positive strand, negative direction, looking for ACTGC, 8, ACTGC at 4337, ACTGC at 4329, ACTGC at 4314, ACTGC at 3851, ACTGC at 2758, ACTGC at 2423, ACTGC at 1997, ACTGC at 1493.
  8. complement, positive strand, positive direction, looking for ACTGC, 1, ACTGC at 1834.
  9. inverse complement, negative strand, negative direction, looking for CGTCA, 10, CGTCA at 4317, CGTCA at 3600, CGTCA at 3478, CGTCA at 2737, CGTCA at 2402, CGTCA at 2083, CGTCA at 1976, CGTCA at 1472, CGTCA at 1323, CGTCA at 1032.
  10. inverse complement, negative strand, positive direction, looking for CGTCA, 2, CGTCA at 2423, CGTCA at 1184.
  11. inverse complement, positive strand, negative direction, looking for CGTCA, 1, CGTCA at 1511.
  12. inverse complement, positive strand, positive direction, looking for CGTCA, 6, CGTCA at 3962, CGTCA at 3461, CGTCA at 3281, CGTCA at 3232, CGTCA at 2328, CGTCA at 2065.
  13. inverse negative strand, negative direction, looking for GCAGT, 1, GCAGT at 1511.
  14. inverse negative strand, positive direction, looking for GCAGT, 6, GCAGT at 3962, GCAGT at 3461, GCAGT at 3281, GCAGT at 3232, GCAGT at 2328, GCAGT at 2065.
  15. inverse positive strand, negative direction, looking for GCAGT, 10, GCAGT at 4317, GCAGT at 3600, GCAGT at 3478, GCAGT at 2737, GCAGT at 2402, GCAGT at 2083, GCAGT at 1976, GCAGT at 1472, GCAGT at 1323, GCAGT at 1032.
  16. inverse positive strand, positive direction, looking for GCAGT, 2, GCAGT at 2423, GCAGT at 1184.

JARE UTR gene transcriptions

Main article: UTR gene transcriptions

Negative strand, negative direction: TGACG at 4337, TGACG at 4329, CGTCA at 4317, TGACG at 4314, TGACG at 3851, CGTCA at 3600, CGTCA at 3478.

JARE core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: TGACG at 4340.

JARE proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: TGACG at 2758, CGTCA at 2737.

JARE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TGACG at 2423, CGTCA at 2402, CGTCA at 2083, TGACG at 1997, CGTCA at 1976, TGACG at 1493, CGTCA at 1472, CGTCA at 1323, CGTCA at 1032.

Positive strand, negative direction: CGTCA at 1511, TGACG at 309.

Negative strand, positive direction: CGTCA at 2423, TGACG at 1834, CGTCA at 1184.

Positive strand, positive direction: CGTCA at 3962, CGTCA at 3461, TGACG at 3319, CGTCA at 3281, CGTCA at 3232, TGACG at 2822, CGTCA at 2328, TGACG at 2203, CGTCA at 2065, TGACG at 2042, TGACG at 1504, TGACG at 1000, TGACG at 900, TGACG at 748, TGACG at 237.

JARE 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 UTRs

RDr alternate UTRs

RDr arbitrary negative direction core promoters

RDr alternate negative direction core promoters

RDr arbitrary positive direction core promoters

RDr alternate positive direction core promoters

RDr arbitrary negative direction proximal promoters

RDr alternate negative direction proximal promoters

RDr arbitrary positive direction proximal promoters

RDr alternate positive direction proximal promoters

RDr arbitrary negative direction distal promoters

RDr alternate negative direction distal promoters

RDr arbitrary positive direction distal promoters

RDr alternate positive direction distal promoters

JARE analysis and results

Main article: Complex locus A1BG and ZNF497 § JAREs

Jasmonic acid-responsive elements (TGACG, CGTCA).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 7 2 3.5 3.5 (4,3)
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 1 2 0.5 0.5
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 2 2 1 1
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 11 2 5.5 5.5 ± 3.5 (--9,+-2)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 18 2 9 9 ± 6 (-+3,++15)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

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

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.
  2. ↑ 2.0 2.1 Young Jin Kim, Dong Gwan Kim, Sun Hi Lee and Incheol Lee (February 2006). "Wound-induced expression of the ferulate 5-hydroxylase gene in Camptotheca acuminata". Biochimica et Biophysica Acta (BBA) - General Subjects. 1760 (2): 182–190. doi:10.1016/j.bbagen.2005.08.015. PMID 16332414. Retrieved 9 September 2020.

External links

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