Jasmonic acid-responsive element gene transcriptions

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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. JAREr0: 4, TGACG at 2913, TGACG at 2860, TGACG at 2483, TGACG at 1698.
  2. JAREr1: 1, TGACG at 1175.
  3. JAREr2: 4, TGACG at 3071, TGACG at 2573, TGACG at 1920, TGACG at 1342.
  4. JAREr3: 5, TGACG at 3961, TGACG at 2637, TGACG at 2582, TGACG at 2208, TGACG at 1760.
  5. JAREr4: 3, TGACG at 2779, TGACG at 658, TGACG at 335.
  6. JAREr5: 1, TGACG at 3310.
  7. JAREr6: 1, TGACG at 1873.
  8. JAREr7: 3, TGACG at 2360, TGACG at 1330, TGACG at 1027.
  9. JAREr8: 4, TGACG at 2235, TGACG at 1667, TGACG at 912, TGACG at 110.
  10. JAREr9: 5, TGACG at 3333, TGACG at 2233, TGACG at 1590, TGACG at 1442, TGACG at 785.
  11. JAREr0ci: 2, CGTCA at 3260, CGTCA at 784.
  12. JAREr1ci: 1, CGTCA at 357.
  13. JAREr2ci: 4, CGTCA at 4189, CGTCA at 3328, CGTCA at 2429, CGTCA at 1494.
  14. JAREr3ci: 5, CGTCA at 3523, CGTCA at 2756, CGTCA at 2689, CGTCA at 2382, CGTCA at 1675.
  15. JAREr4ci: 5, CGTCA at 3913, CGTCA at 3496, CGTCA at 2405, CGTCA at 901, CGTCA at 436.
  16. JAREr5ci: 4, CGTCA at 1818, CGTCA at 1025, CGTCA at 623, CGTCA at 361.
  17. JAREr6ci: 5, CGTCA at 3711, CGTCA at 3491, CGTCA at 2645, CGTCA at 1638, CGTCA at 838.
  18. JAREr7ci: 6, CGTCA at 4344, CGTCA at 3144, CGTCA at 2471, CGTCA at 2324, CGTCA at 1719, CGTCA at 16.
  19. JAREr8ci: 5, CGTCA at 4067, CGTCA at 4036, CGTCA at 3544, CGTCA at 319, CGTCA at 249.
  20. JAREr9ci: 2, CGTCA at 1860, CGTCA at 1800.

JAREr arbitrary (evens) (4560-2846) UTRs

  1. JAREr0: TGACG at 2913, TGACG at 2860.
  2. JAREr2: TGACG at 3071.
  3. JAREr0ci: CGTCA at 3260.
  4. JAREr2ci: CGTCA at 4189, CGTCA at 3328.
  5. JAREr4ci: CGTCA at 3913, CGTCA at 3496.
  6. JAREr6ci: CGTCA at 3711, CGTCA at 3491.
  7. JAREr8ci: CGTCA at 4067, CGTCA at 4036, CGTCA at 3544.

JAREr alternate (odds) (4560-2846) UTRs

  1. JAREr3: TGACG at 3961.
  2. JAREr5: TGACG at 3310.
  3. JAREr9: TGACG at 3333.
  4. JAREr3ci: CGTCA at 3523.
  5. JAREr7ci: CGTCA at 4344, CGTCA at 3144.

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

  1. JAREr7ci: CGTCA at 4344.

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

  1. JAREr4: TGACG at 2779.
  2. JAREr6ci: CGTCA at 2645.

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

  1. JAREr3: TGACG at 2637.
  2. JAREr3ci: CGTCA at 2756, CGTCA at 2689.

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

  1. JAREr2ci: CGTCA at 4189.
  2. JAREr8ci: CGTCA at 4067.

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

  1. JAREr0: TGACG at 2483, TGACG at 1698.
  2. JAREr2: TGACG at 2573, TGACG at 1920, TGACG at 1342.
  3. JAREr4: TGACG at 658, TGACG at 335.
  4. JAREr8: TGACG at 2235, TGACG at 1667, TGACG at 912, TGACG at 110.
  5. JAREr0ci: CGTCA at 784.
  6. JAREr2ci: CGTCA at 2429, CGTCA at 1494.
  7. JAREr4ci: CGTCA at 2405, CGTCA at 901, CGTCA at 436.
  8. JAREr6ci: CGTCA at 1638, CGTCA at 838.
  9. JAREr8ci: CGTCA at 319, CGTCA at 249.

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

  1. JAREr1: TGACG at 1175.
  2. JAREr3: TGACG at 2582, TGACG at 2208, TGACG at 1760.
  3. JAREr7: TGACG at 2360, TGACG at 1330, TGACG at 1027.
  4. JAREr9: TGACG at 2233, TGACG at 1590, TGACG at 1442, TGACG at 785.
  5. JAREr1ci: CGTCA at 357.
  6. JAREr3ci: CGTCA at 2382, CGTCA at 1675.
  7. JAREr5ci: CGTCA at 1818, CGTCA at 1025, CGTCA at 623, CGTCA at 361.
  8. JAREr7ci: CGTCA at 2471, CGTCA at 2324, CGTCA at 1719, CGTCA at 16.
  9. JAREr9ci: CGTCA at 1860, CGTCA at 1800.

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

  1. JAREr1: TGACG at 1175.
  2. JAREr3: TGACG at 3961, TGACG at 2637, TGACG at 2582, TGACG at 2208, TGACG at 1760.
  3. JAREr5: TGACG at 3310.
  4. JAREr7: TGACG at 2360, TGACG at 1330, TGACG at 1027.
  5. JAREr9: TGACG at 3333, TGACG at 2233, TGACG at 1590, TGACG at 1442, TGACG at 785.
  6. JAREr1ci: CGTCA at 357.
  7. JAREr3ci: CGTCA at 3523, CGTCA at 2756, CGTCA at 2689, CGTCA at 2382, CGTCA at 1675.
  8. JAREr5ci: CGTCA at 1818, CGTCA at 1025, CGTCA at 623, CGTCA at 361.
  9. JAREr7ci: CGTCA at 3144, CGTCA at 2471, CGTCA at 2324, CGTCA at 1719, CGTCA at 16.
  10. JAREr9ci: CGTCA at 1860, CGTCA at 1800.

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

  1. JAREr0: TGACG at 2913, TGACG at 2860, TGACG at 2483, TGACG at 1698.
  2. JAREr2: TGACG at 3071, TGACG at 2573, TGACG at 1920, TGACG at 1342.
  3. JAREr4: TGACG at 2779, TGACG at 658, TGACG at 335.
  4. JAREr8: TGACG at 2235, TGACG at 1667, TGACG at 912, TGACG at 110.
  5. JAREr0ci: CGTCA at 784.
  6. JAREr2ci: CGTCA at 3328, CGTCA at 2429, CGTCA at 1494.
  7. JAREr4ci: CGTCA at 3913, CGTCA at 3496, CGTCA at 2405, CGTCA at 901, CGTCA at 436.
  8. JAREr6ci: CGTCA at 3711, CGTCA at 3491, CGTCA at 2645, CGTCA at 1638, CGTCA at 838.
  9. JAREr8ci: CGTCA at 4036, CGTCA at 3544, CGTCA at 319, CGTCA at 249.

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 13 10 1.3 0.95
Randoms UTR alternate negative 6 10 0.6 0.95
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 2 2 1 1
Randoms Proximal arbitrary negative 2 10 0.2 0.25
Randoms Proximal alternate negative 3 10 0.3 0.25
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.1
Randoms Proximal alternate positive 2 10 0.2 0.1
Reals Distal negative 11 2 5.5 5.5 ± 3.5 (--9,+-2)
Randoms Distal arbitrary negative 21 10 2.1 2.25
Randoms Distal alternate negative 24 10 2.4 2.25
Reals Distal positive 18 2 9 9 ± 6 (-+3,++15)
Randoms Distal arbitrary positive 36 10 3.6 3.45
Randoms Distal alternate positive 33 10 3.3 3.45

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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