B box gene transcriptions: Difference between revisions

Revision as of 03:12, 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

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

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 samplings

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.

B1 box random dataset samplings

B1boxr0: 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

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]

@@ Line 127: / Line 127: @@
 # Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.
-==B1 box proximal promoters==
+==B1 box samplings==
+===B1 box proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
 B1 box negative direction: 3'-TGTCTCA-5' at 4373 and complement.
-==B1 box distal promoters==
+===B1 box distal promoters===
 {{main|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.
+==B1 box random dataset samplings==
+# B1boxr0: 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===
+{{main|UTR promoter gene transcriptions}}
+===RDr core promoters===
+{{main|Core promoter gene transcriptions}}
+===RDr proximal promoters===
+{{main|Proximal promoter gene transcriptions}}
+===RDr distal promoters===
+{{main|Distal promoter gene transcriptions}}
 ==Acknowledgements==
@@ Line 163: / Line 200: @@
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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene 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 Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene 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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