B box gene transcriptions
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
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
- A1BG has neither a B-box (TGGGCA) nor a box B (or B1 box) (TGTCTCA) in either promoter.
- A1BG is not transcribed by either B box.
- 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.
- Negative 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: 4, TGGGCA at 4180, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
- Positive strand, positive direction: 0.
- Inverse complement, negative 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: 2, TGCCCA at 3377, TGCCCA at 3237.
- Inverse complement, positive strand, positive direction: 1, TGCCCA at 3750.
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 proximal promoters
- Positive strand, negative direction: TGGGCA at 2773.
- Negative strand, positive direction: TGGGCA at 4180.
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 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.
B box random dataset samplings
- RDr0: 0.
- RDr1: 0.
- RDr2: 0.
- RDr3: 0.
- RDr4: 0.
- RDr5: 0.
- RDr6: 0.
- RDr7: 0.
- RDr8: 0.
- RDr9: 0.
- RDr0ci: 0.
- RDr1ci: 0.
- RDr2ci: 0.
- RDr3ci: 0.
- RDr4ci: 0.
- RDr5ci: 0.
- RDr6ci: 0.
- RDr7ci: 0.
- RDr8ci: 0.
- RDr9ci: 0.
RDr UTRs
RDr core promoters
RDr proximal promoters
RDr distal promoters
B1 box proximal promoters
B1 box negative direction: 3'-TGTCTCA-5' at 4373 and complement.
B1 box distal promoters
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
- ↑ 1.0 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.
- ↑ 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.