B box gene transcriptions: Difference between revisions

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# Neither B box participates in the transcription of A1BG.
# Neither B box participates in the transcription of A1BG.


==B box samplings==
==B box (Johnson) samplings==


Copying the above consensus B box and putting the sequences in "⌘F" locates any consensus sequences in any nucleotide positions as may be found by the computer programs.
Copying the above consensus B box and putting the sequences in "⌘F" locates any consensus sequences in any nucleotide positions as may be found by the computer programs.
Line 72: Line 72:
# Positive strand, positive direction: TGCCCA at 3750.
# Positive strand, positive direction: TGCCCA at 3750.


==B box random dataset samplings==
==B box (Johnson) random dataset samplings==


# Bboxr0: 1, TGGGCA at 1253.
# Bboxr0: 1, TGGGCA at 1253.
Line 127: Line 127:
# Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.
# Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.


==B1 box samplings==
==B1 box (Sanchez) samplings==
# Negative strand, negative direction: 2, TGTCTCA at 2445, TGTCTCA at 1075.
# Negative strand, negative direction: 2, TGTCTCA at 2445, TGTCTCA at 1075.
# Positive strand, negative direction: 5, TGTCTCA at 4373, TGTCTCA at 3323, TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.
# Positive strand, negative direction: 5, TGTCTCA at 4373, TGTCTCA at 3323, TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.
Line 149: Line 149:
# Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.
# Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.


==B1 box random dataset samplings==
==B1 box (Sanchez) random dataset samplings==


# B1boxr0: 0.
# B1boxr0: 0.

Revision as of 15:25, 4 December 2021

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

"The mP2 EB fragment used for binding was the 118 nucleotide fragment extending from the Dde I site at position -140 to the Dde I site at position -23 [...]. This fragment contains the GC, E, B, CAAT, and TATA boxes."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

TGGGCA is a B-box.[1]

"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]

Hypotheses

  1. A1BG has neither a B-box (TGGGCA) nor a box B (or B1 box) (TGTCTCA) in either promoter.
  2. A1BG is not transcribed by either B box.
  3. Neither B box participates in the transcription of A1BG.

B box (Johnson) samplings

Copying the above consensus B box and putting the sequences in "⌘F" locates any consensus sequences in any nucleotide positions as may be found by the computer programs.

One 3'-TGGGCA-5' shows up at about -600 nucleotides from the TSS between ZSCAN22 and A1BG as A1BG is approached from ZSCAN22 on the positive strand. This warrants testing with the computer programs.

  1. Negative strand, negative direction: 0.
  2. Positive strand, negative direction: 9, TGGGCA at 4191, TGGGCA at 4040, TGGGCA at 3301, TGGGCA at 2773, TGGGCA at 2438, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462.
  3. Negative strand, positive direction: 4, TGGGCA at 4180, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
  4. Positive strand, positive direction: 0.
  5. Inverse complement, negative strand, negative direction: 0.
  6. Inverse complement, positive strand, negative direction: 4, TGCCCA at 4251, TGCCCA at 3883, TGCCCA at 3854, TGCCCA at 1458.
  7. Inverse complement, negative strand, positive direction: 2, TGCCCA at 3377, TGCCCA at 3237.
  8. Inverse complement, positive strand, positive direction: 1, TGCCCA at 3750.

B box UTRs

  1. Positive strand, negative direction: TGCCCA at 4251, TGGGCA at 4191, TGGGCA at 4040, TGCCCA at 3883, TGCCCA at 3854, TGGGCA at 3301.

B box proximal promoters

  1. Positive strand, negative direction: TGGGCA at 2773.


  1. Negative strand, positive direction: TGGGCA at 4180.

B box distal promoters

  1. Positive strand, negative direction: TGGGCA at 2438, TGCCCA at 1458, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462.


  1. Negative strand, positive direction: TGCCCA at 3377, TGCCCA at 3237, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
  2. Positive strand, positive direction: TGCCCA at 3750.

B box (Johnson) random dataset samplings

  1. Bboxr0: 1, TGGGCA at 1253.
  2. Bboxr1: 2, TGGGCA at 3675, TGGGCA at 2650.
  3. Bboxr2: 0.
  4. Bboxr3: 3, TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
  5. Bboxr4: 1, TGGGCA at 4228.
  6. Bboxr5: 0.
  7. Bboxr6: 0.
  8. Bboxr7: 1, TGGGCA at 2615.
  9. Bboxr8: 2, TGGGCA at 2952, TGGGCA at 1018.
  10. Bboxr9: 1, TGGGCA at 3599.
  11. Bboxr0ci: 2, TGCCCA at 1080, TGCCCA at 245.
  12. Bboxr1ci: 0.
  13. Bboxr2ci: 0.
  14. Bboxr3ci: 5, TGCCCA at 4519, TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
  15. Bboxr4ci: 0.
  16. Bboxr5ci: 1, TGCCCA at 2606.
  17. Bboxr6ci: 1, TGCCCA at 956.
  18. Bboxr7ci: 4, TGCCCA at 4059, TGCCCA at 3010, TGCCCA at 1406, TGCCCA at 1338.
  19. Bboxr8ci: 3, TGCCCA at 4140, TGCCCA at 1901, TGCCCA at 1380.
  20. Bboxr9ci: 2, TGCCCA at 1672, TGCCCA at 732.

Bboxr UTRs

Main article: UTR promoter gene transcriptions
  1. Bboxr4: TGGGCA at 4228.
  2. Bboxr8: TGGGCA at 2952.
  3. Bboxr8ci: TGCCCA at 4140.

Bboxr core promoters

Main article: Core promoter gene transcriptions
  1. Bboxr3ci: TGCCCA at 4519.

Bboxr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. Bboxr7ci: TGCCCA at 4059.

Bboxr distal promoters

Main article: Distal promoter gene transcriptions
  1. Bboxr0: TGGGCA at 1253.
  2. Bboxr8: TGGGCA at 1018.
  3. Bboxr0ci: TGCCCA at 1080, TGCCCA at 245.
  4. Bboxr6ci: TGCCCA at 956.
  5. Bboxr8ci: TGCCCA at 1901, TGCCCA at 1380.


  1. Bboxr1: TGGGCA at 3675, TGGGCA at 2650.
  2. Bboxr3: TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
  3. Bboxr7: TGGGCA at 2615.
  4. Bboxr9: TGGGCA at 3599.
  5. Bboxr3ci: TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
  6. Bboxr5ci: TGCCCA at 2606.
  7. Bboxr7ci: TGCCCA at 3010, TGCCCA at 1406, TGCCCA at 1338.
  8. Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.

B1 box (Sanchez) samplings

  1. Negative strand, negative direction: 2, TGTCTCA at 2445, TGTCTCA at 1075.
  2. Positive strand, negative direction: 5, TGTCTCA at 4373, TGTCTCA at 3323, TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.
  3. Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.
  4. Positive strand, positive direction: 0.

B1 box UTRs

  1. Positive strand, negative direction: TGTCTCA at 4373, TGTCTCA at 3323.

B1 box proximal promoters

Main article: Proximal promoter gene transcriptions

B1 box distal promoters

Main article: Distal promoter gene transcriptions
  1. Negative strand, negative direction: TGTCTCA at 2445, TGTCTCA at 1075.
  2. Positive strand, negative direction: TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.

B1 box negative direction: 3'-TGTCTCA-5' at 3323, 3'-TGTCTCA-5' at 2445, 3'-TGTCTCA-5' at 2033, 3'-TGAGACA-5' at 2029, 3'-TGTCTCA-5' at 1089, 3'-TGAGACA-5' at 1085, 3'-TGTCTCA-5' at 1075, 3'-TGTCTCA-5' at 923, 3'-TGAGACA-5' at 919 and complements.

B1 box positive direction: 3'-TGTCTCA-5' at 2468, 3'-TGAGACA-5' at 2308, 3'-TGTCTCA-5' at 2174 and complements.

  1. Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.

B1 box (Sanchez) random dataset samplings

  1. B1boxr0: 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 UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 PA Johnson, D Bunick, NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. Retrieved 6 April 2019.
  2. ↑ Amber Paratore Sanchez and Kumar Sharma (July 2009). "Transcription factors in the pathogenesis of diabetic nephropathy". Expert Reviews in Molecular Medicine. 11: e13. doi:10.1017/S1462399409001057. Retrieved 1 October 2018.

External links


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