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 (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.

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 (Johnson) random dataset samplings

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

Bboxr UTRs

Bboxr4: TGGGCA at 4228.
Bboxr8: TGGGCA at 2952.
Bboxr8ci: TGCCCA at 4140.

Bboxr core promoters

Bboxr3ci: TGCCCA at 4519.

Bboxr proximal promoters

Bboxr7ci: TGCCCA at 4059.

Bboxr distal promoters

Bboxr0: TGGGCA at 1253.
Bboxr8: TGGGCA at 1018.
Bboxr0ci: TGCCCA at 1080, TGCCCA at 245.
Bboxr6ci: TGCCCA at 956.
Bboxr8ci: TGCCCA at 1901, TGCCCA at 1380.

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.
Bboxr3ci: TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
Bboxr5ci: TGCCCA at 2606.
Bboxr7ci: TGCCCA at 3010, TGCCCA at 1406, TGCCCA at 1338.
Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.

B1 box (Sanchez) samplings

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.
Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.
Positive strand, positive direction: 0.
Negative strand, negative direction, inverse complement: 3, TGAGACA at 2029, TGAGACA at 1085, TGAGACA at 919.
Positive strand, negative direction, inverse complement: 0.
Positive strand, positive direction, inverse complement: 1, TGAGACA at 2308.
Negative strand, positive direction, inverse complement: 0.

B1 box UTRs

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

B1 box distal promoters

Negative strand, negative direction: TGTCTCA at 2445, TGAGACA at 2029, TGAGACA at 1085, TGTCTCA at 1075, TGAGACA at 919.
Positive strand, negative direction: TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.

Negative strand, positive direction: TGTCTCA at 2468, TGTCTCA at 2174.
Positive strand, positive direction, inverse complement: TGAGACA at 2308.

B1 box (Sanchez) random dataset samplings

B1boxr0: 0.
B1boxr1: 0.
B1boxr2: 0.
B1boxr3: 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

Acknowledgements

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

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

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.

External links

[Johnson-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.

[Paratore-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.

[1]

[2]

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions