B box gene transcriptions: Difference between revisions

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# Negative strand, negative direction: 0.
# Negative strand, negative direction: 0.
# Positive strand, negative direction: 0.
# 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.
# Negative strand, positive direction: 0.
# Negative strand, positive direction: 4, TGGGCA at 4180, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
# Positive strand, positive direction: 0.
# Positive strand, positive direction: 0.
# Inverse complement, negative strand, negative direction: 0.
# Inverse complement, negative strand, negative direction: 0.
# Inverse complement, positive strand, negative direction: 0.
# Inverse complement, positive strand, negative direction: 4, TGCCCA at 4251, TGCCCA at 3883, TGCCCA at 3854, TGCCCA at 1458.
# Inverse complement, negative strand, positive direction: 0.
# Inverse complement, negative strand, positive direction: 2, TGCCCA at 3377, TGCCCA at 3237.
# Inverse complement, positive strand, positive direction: 0.
# Inverse complement, positive strand, positive direction: 1, TGCCCA at 3750.


===B box UTRs===
===B box UTRs===
 
# Positive strand, negative direction: TGCCCA at 4251, TGGGCA at 4191, TGGGCA at 4040, TGCCCA at 3883, TGCCCA at 3854, TGGGCA at 3301.
===B box core promoters===
{{main|Core promoter gene transcriptions}}


===B box proximal promoters===
===B box proximal promoters===
# Positive strand, negative direction: TGGGCA at 2773.


Negative direction: 3'-TGCCCA-5' at 4251 and complement.


Positive direction: 3'-TGGGCA-5' at 4180 and complement.
# Negative strand, positive direction: TGGGCA at 4180.


===B box distal promoters===
===B box distal promoters===
# Positive strand, negative direction: TGGGCA at 2438, TGCCCA at 1458, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462.


Negative direction: 3'-TGGGCA-5' at 4191, 3'-TGGGCA-5' at 4040, 3'-TGCCCA-5' at 3883, 3'-TGCCCA-5' at 3854, 3'-TGGGCA-5' at 3301, 3'-TGGGCA-5' at 2773, 3'-TGGGCA-5' at 2438, 3'-TGCCCA-5' at 1458, 3'-TGGGCA-5' at 1359, 3'-TGGGCA-5' at 1114, 3'-TGGGCA-5' at 902, 3'-TGGGCA-5' at 462, and complements.


Positive direction: 3'-TGCCCA-5' at 3750, 3'-TGCCCA-5' at 3377, 3'-TGCCCA-5' at 3237, 3'-TGGGCA-5' at 2894, 3'-TGGGCA-5' at 1945, 3'-TGGGCA-5' at 27 and complements.
# Negative strand, positive direction: TGCCCA at 3377, TGCCCA at 3237, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
# Positive strand, positive direction: TGCCCA at 3750.


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

Revision as of 01:50, 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.

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=1716824"