Sucrose box gene transcriptions

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

Manual "scanning was also done to identify the presence of sugar responsive elements such as sucrose box (NNAATCA) (Chen et al., 2002; Fillion et al., 1999) and pyrimidine box (CCTTTT, TTTTTTCC) (Washio, 2003)."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Sucrose box (NNAATCA) (Chen et al., 2002; Fillion et al., 1999).[1]

Binding site for

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

Sucrose box samplings

Copying a responsive elements consensus sequence NNAATCA 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 NNAATCA (starting with SuccessablesSucrose.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 NNAATCA, 1, GTAATCA at 155.
  2. positive strand, negative direction, looking for NNAATCA, 6, AGAATCA at 3237, GAAATCA at 2749, AAAATCA at 2648, CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.
  3. positive strand, positive direction, looking for NNAATCA, 1, TAAATCA at 4137.
  4. negative strand, positive direction, looking for NNAATCA, 2, TTAATCA at 4147, GCAATCA at 2338.
  5. complement, negative strand, negative direction, looking for NNTTAGT, 6, TCTTAGT at 3237, CTTTAGT at 2749, TTTTAGT at 2648, GATTAGT at 982, TCTTAGT at 293, TCTTAGT at 198.
  6. complement, positive strand, negative direction, looking for NNTTAGT, 1, CATTAGT at 155.
  7. complement, positive strand, positive direction, looking for NNTTAGT, 2, AATTAGT at 4147, CGTTAGT at 2338.
  8. complement, negative strand, positive direction, looking for NNTTAGT, 1, ATTTAGT at 4137.
  9. inverse complement, negative strand, negative direction, looking for TGATTNN, 11, TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915, TGATTTA at 2636, TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629.
  10. inverse complement, positive strand, negative direction, looking for TGATTNN, 0.
  11. inverse complement, positive strand, positive direction, looking for TGATTNN, 0.
  12. inverse complement, negative strand, positive direction, looking for TGATTNN, 4, TGATTAT at 4165, TGATTAT at 4158, TGATTTA at 4135, TGATTGT at 2678.
  13. inverse negative strand, negative direction, looking for ACTAANN, 0.
  14. inverse positive strand, negative direction, looking for ACTAANN, 11, ACTAAGG at 3474, ACTAAAA at 3163, ACTAAGC at 3032, ACTAAGC at 2915, ACTAAAT at 2636, ACTAAAA at 2299, ACTAAAG at 2174, ACTAAAA at 1872, ACTAAGG at 818, ACTAAAA at 763, ACTAAAA at 629.
  15. inverse positive strand, positive direction, looking for ACTAANN, 4, ACTAATA at 4165, ACTAATA at 4158, ACTAAAT at 4135, ACTAACA at 2678.
  16. inverse negative strand, positive direction, looking for ACTAANN, 0.

Sucrose (4560-2846) UTRs

  1. Negative strand, negative direction: TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915.
  2. Positive strand, negative direction: AGAATCA at 3237.

Sucrose negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: TGATTTA at 2636.
  2. Positive strand, negative direction: GAAATCA at 2749, AAAATCA at 2648.

Sucrose positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: TTAATCA at 4147.
  2. Negative strand, positive direction: TGATTAT at 4165, TGATTAT at 4158, TGATTTA at 4135.
  3. Positive strand, positive direction: TAAATCA at 4137.

Sucrose negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GTAATCA at 155.
  2. Negative strand, negative direction: TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629.
  3. Positive strand, negative direction: CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.

Sucrose positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GCAATCA at 2338.
  2. Negative strand, positive direction: TGATTGT at 2678.

Sucrose box random dataset samplings

  1. Sucroser0: 3, GTAATCA at 4153, GCAATCA at 2962, CAAATCA at 2809.
  2. Sucroser1: 3, TTAATCA at 3460, CGAATCA at 3229, TAAATCA at 3170.
  3. Sucroser2: 5, CAAATCA at 4311, GTAATCA at 3449, AAAATCA at 2384, CCAATCA at 1356, TCAATCA at 71.
  4. Sucroser3: 4, AAAATCA at 1837, TCAATCA at 1655, TGAATCA at 1555, TTAATCA at 1352.
  5. Sucroser4: 4, TAAATCA at 4186, ATAATCA at 4118, CGAATCA at 3347, CCAATCA at 2109.
  6. Sucroser5: 5, ATAATCA at 3215, GTAATCA at 3205, CCAATCA at 2637, GGAATCA at 2158, CAAATCA at 135.
  7. Sucroser6: 4, CTAATCA at 3129, CGAATCA at 2622, TCAATCA at 1836, TTAATCA at 35.
  8. Sucroser7: 2, GGAATCA at 2946, TCAATCA at 1137.
  9. Sucroser8: 4, AAAATCA at 2981, GCAATCA at 2359, ATAATCA at 1749, TAAATCA at 141.
  10. Sucroser9: 3, CCAATCA at 3564, TTAATCA at 3367, CCAATCA at 1528.
  11. Sucroser0ci: 4, TGATTTT at 3024, TGATTTC at 2826, TGATTTT at 1820, TGATTTT at 1460.
  12. Sucroser1ci: 3, TGATTTC at 4035, TGATTAA at 2851, TGATTCC at 708.
  13. Sucroser2ci: 4, TGATTTA at 4144, TGATTCG at 3772, TGATTTC at 1246, TGATTCA at 489.
  14. Sucroser3ci: 2, TGATTTC at 2019, TGATTTA at 1088.
  15. Sucroser4ci: 3, TGATTGT at 3795, TGATTAC at 2647, TGATTGG at 651.
  16. Sucroser5ci: 5, TGATTCG at 4378, TGATTAA at 4204, TGATTTC at 4196, TGATTTT at 1448, TGATTAC at 893.
  17. Sucroser6ci: 3, TGATTCT at 3178, TGATTCA at 283, TGATTCT at 260.
  18. Sucroser7ci: 2, TGATTCG at 2468, TGATTTG at 111.
  19. Sucroser8ci: 3, TGATTAG at 4362, TGATTTT at 2541, TGATTGA at 1177.
  20. Sucroser9ci: 3, TGATTGA at 4264, TGATTTA at 3116, TGATTTG at 1742.

Sucroser arbitrary (evens) (4560-2846) UTRs

  1. Sucroser0: GTAATCA at 4153, GCAATCA at 2962, CAAATCA at 2809.
  2. Sucroser2: CAAATCA at 4311, GTAATCA at 3449.
  3. Sucroser4: TAAATCA at 4186, ATAATCA at 4118, CGAATCA at 3347.
  4. Sucroser6: CTAATCA at 3129.
  5. Sucroser8: AAAATCA at 2981.
  6. Sucroser0ci: TGATTTT at 3024.
  7. Sucroser2ci: TGATTTA at 4144, TGATTCG at 3772.
  8. Sucroser4ci: TGATTGT at 3795.
  9. Sucroser6ci: TGATTCT at 3178.
  10. Sucroser8ci: TGATTAG at 4362.

Sucroser alternate (odds) (4560-2846) UTRs

  1. Sucroser1: TTAATCA at 3460, CGAATCA at 3229, TAAATCA at 3170.
  2. Sucroser5: ATAATCA at 3215, GTAATCA at 3205.
  3. Sucroser7: GGAATCA at 2946.
  4. Sucroser9: CCAATCA at 3564, TTAATCA at 3367.
  5. Sucroser1ci: TGATTTC at 4035, TGATTAA at 2851.
  6. Sucroser9ci: TGATTGA at 4264, TGATTTA at 3116.

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

  1. Sucroser0ci: TGATTTC at 2826.

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

  1. Sucroser2: CAAATCA at 4311.
  2. Sucroser8ci: TGATTAG at 4362.

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

  1. Sucroser0: CAAATCA at 2809.
  2. Sucroser6: CGAATCA at 2622.
  3. Sucroser4ci: TGATTAC at 2647.

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

  1. Sucroser5: CCAATCA at 2637.

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

  1. Sucroser9ci: TGATTGA at 4264.

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

  1. Sucroser0: GTAATCA at 4153.
  2. Sucroser4: TAAATCA at 4186, ATAATCA at 4118.
  3. Sucroser2ci: TGATTTA at 4144.

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

  1. Sucroser2: AAAATCA at 2384, CCAATCA at 1356, TCAATCA at 71.
  2. Sucroser4: CCAATCA at 2109.
  3. Sucroser6: TCAATCA at 1836, TTAATCA at 35.
  4. Sucroser8: GCAATCA at 2359, ATAATCA at 1749, TAAATCA at 141.
  5. Sucroser0ci: TGATTTT at 1820, TGATTTT at 1460.
  6. Sucroser2ci: TGATTTC at 1246, TGATTCA at 489.
  7. Sucroser4ci: TGATTGG at 651.
  8. Sucroser6ci: TGATTCA at 283, TGATTCT at 260.
  9. Sucroser8ci: TGATTTT at 2541, TGATTGA at 1177.

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

  1. Sucroser3: AAAATCA at 1837, TCAATCA at 1655, TGAATCA at 1555, TTAATCA at 1352.
  2. Sucroser5: GGAATCA at 2158, CAAATCA at 135.
  3. Sucroser7: TCAATCA at 1137.
  4. Sucroser9: CCAATCA at 1528.
  5. Sucroser1ci: TGATTCC at 708.
  6. Sucroser3ci: TGATTTC at 2019, TGATTTA at 1088.
  7. Sucroser7ci: TGATTCG at 2468, TGATTTG at 111.
  8. Sucroser9ci: TGATTTG at 1742.

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

  1. Sucroser1: TTAATCA at 3460, CGAATCA at 3229, TAAATCA at 3170.
  2. Sucroser3: AAAATCA at 1837, TCAATCA at 1655, TGAATCA at 1555, TTAATCA at 1352.
  3. Sucroser5: ATAATCA at 3215, GTAATCA at 3205, CCAATCA at 2637, GGAATCA at 2158, CAAATCA at 135.
  4. Sucroser7: GGAATCA at 2946, TCAATCA at 1137.
  5. Sucroser9: CCAATCA at 3564, TTAATCA at 3367, CCAATCA at 1528.
  6. Sucroser1ci: TGATTTC at 4035, TGATTAA at 2851, TGATTCC at 708.
  7. Sucroser3ci: TGATTTC at 2019, TGATTTA at 1088.
  8. Sucroser7ci: TGATTCG at 2468, TGATTTG at 111.
  9. Sucroser9ci: TGATTTA at 3116, TGATTTG at 1742.

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

  1. Sucroser0: GCAATCA at 2962, CAAATCA at 2809.
  2. Sucroser2: GTAATCA at 3449, AAAATCA at 2384, CCAATCA at 1356, TCAATCA at 71.
  3. Sucroser4: CGAATCA at 3347, CCAATCA at 2109.
  4. Sucroser6: CTAATCA at 3129, CGAATCA at 2622, TCAATCA at 1836, TTAATCA at 35.
  5. Sucroser8: AAAATCA at 2981, GCAATCA at 2359, ATAATCA at 1749, TAAATCA at 141.
  6. Sucroser0ci: TGATTTT at 3024, TGATTTC at 2826, TGATTTT at 1820, TGATTTT at 1460.
  7. Sucroser2ci: TGATTCG at 3772, TGATTTC at 1246, TGATTCA at 489.
  8. Sucroser4ci: TGATTGT at 3795, TGATTAC at 2647, TGATTGG at 651.
  9. Sucroser6ci: TGATTCT at 3178, TGATTCA at 283, TGATTCT at 260.
  10. Sucroser8ci: TGATTTT at 2541, TGATTGA at 1177.

Sucrose box analysis and results

Main article: Complex locus A1BG and ZNF497 § Sucroses

Manual "scanning was also done to identify the presence of sugar responsive elements such as sucrose box (NNAATCA) (Chen et al., 2002; Fillion et al., 1999) and pyrimidine box (CCTTTT, TTTTTTCC) (Washio, 2003)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 1.5 (--4,+-1)
Randoms UTR arbitrary negative 16 10 1.6 1.4
Randoms UTR alternate negative 12 10 1.2 1.4
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.05
Randoms Core alternate negative 0 10 0 0.05
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.1
Randoms Core alternate positive 2 10 0.2 0.1
Reals Proximal negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms Proximal arbitrary negative 3 10 0.3 0.2
Randoms Proximal alternate negative 1 10 0.1 0.2
Reals Proximal positive 5 2 2.5 2.5 ± 1.5 (-+4,++1)
Randoms Proximal arbitrary positive 1 10 0.1 0.25
Randoms Proximal alternate positive 4 10 0.4 0.25
Reals Distal negative 10 2 5 5 ± 2 (--7,+-3)
Randoms Distal arbitrary negative 18 10 1.8 1.6
Randoms Distal alternate negative 14 10 1.4 1.6
Reals Distal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Distal arbitrary positive 26 10 2.6 2.85
Randoms Distal alternate positive 31 10 3.1 2.85

Comparison:

The occurrences of real sucrose box UTRs are outside the randoms, the proximals and negative distals are greater than the randoms, and the positive distals are less than the randoms. This suggests that the real sucrose boxes 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 M. Abiramavalli and B. Usha (7 July 2020). "Identification, characterization and expression analysis of sucrose transporters in the model plant Nicotiana tabacum cv.petit havana" (PDF). Journal of Environmental Biology. 41: 803–811. doi:10.22438/jeb/41/4/MRN-1233. Retrieved 7 January 2021.

External links

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