B box gene transcriptions: Difference between revisions

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==B box random dataset samplings==
==B box random dataset samplings==


# RDr0: 0.
# Bboxr0: 1, TGGGCA at 1253.
# RDr1: 0.
# Bboxr1: 2, TGGGCA at 3675, TGGGCA at 2650.
# RDr2: 0.
# Bboxr2: 0.
# RDr3: 0.
# Bboxr3: 3, TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
# RDr4: 0.
# Bboxr4: 1, TGGGCA at 4228.
# RDr5: 0.
# Bboxr5: 0.
# RDr6: 0.
# Bboxr6: 0.
# RDr7: 0.
# Bboxr7: 1, TGGGCA at 2615.
# RDr8: 0.
# Bboxr8: 2, TGGGCA at 2952, TGGGCA at 1018.
# RDr9: 0.
# Bboxr9: 1, TGGGCA at 3599.
# RDr0ci: 0.
# Bboxr0ci: 2, TGCCCA at 1080, TGCCCA at 245.
# RDr1ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr2ci: 0.
Line 95: Line 95:
# RDr9ci: 0.
# RDr9ci: 0.


===RDr UTRs===
===Bboxr UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
# Bboxr4: TGGGCA at 4228.
# Bboxr8: TGGGCA at 2952.


===RDr core promoters===
===RDr core promoters===
Line 104: Line 106:
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}


===RDr distal promoters===
===Bboxr distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
# Bboxr0: TGGGCA at 1253.
# Bboxr8: TGGGCA at 1018.
# Bboxr0ci: TGCCCA at 1080, TGCCCA at 245.
# Bboxr1: TGGGCA at 3675, TGGGCA at 2650.
# Bboxr3: TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
# Bboxr7: TGGGCA at 2615.
# Bboxr9: TGGGCA at 3599.


==B1 box proximal promoters==
==B1 box proximal promoters==

Revision as of 06:34, 2 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 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 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. 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.

Bboxr UTRs

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

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

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.


  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.

B1 box proximal promoters

Main article: Proximal promoter gene transcriptions

B1 box negative direction: 3'-TGTCTCA-5' at 4373 and complement.

B1 box distal promoters

Main article: Distal promoter gene transcriptions

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.

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

Retrieved from "https://www.wikidoc.org/index.php?title=B_box_gene_transcriptions&oldid=1716840"