B box gene transcriptions: Difference between revisions

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.

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.

Core promoters

Proximal promoters

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

Positive direction: 3'-TGGGCA-5' at 4180 and complement.

Distal promoters

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.

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.

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

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B 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gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Factor II B recognition element gene transcriptions F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes 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 transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene 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

@@ Line 1: / Line 1: @@
 {{AE}} 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."<ref name=Johnson/>
+==Consensus sequences==
+{{main|Consensus sequence gene transcriptions}}
 TGGGCA is a B-box.<ref name=Johnson>{{ cite journal
 |author=PA Johnson, D Bunick, NB Hecht
@@ Line 15: / Line 19: @@
 |pmid=
 |accessdate=6 April 2019 }}</ref>
-"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."<ref name=Johnson/>
 "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)."<ref name=Paratore>{{ cite journal
@@ Line 35: / Line 37: @@
 ==Hypotheses==
-# A1BG has no B boxes in either promoter.
+# 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.
 ==Samplings==
@@ Line 42: / Line 46: @@
 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.
+==Core promoters==
+{{main|Core promoter gene transcriptions}}
+==Proximal promoters==
+Negative direction: 3'-TGCCCA-5' at 4251 and complement.
+Positive direction: 3'-TGGGCA-5' at 4180 and complement.
+==Distal promoters==
+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.
+==B1 box proximal promoters==
+{{main|Proximal promoter gene transcriptions}}
+B1 box negative direction: 3'-TGTCTCA-5' at 4373 and complement.
+==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.
 ==Acknowledgements==
@@ Line 52: / Line 81: @@
 {{div col|colwidth=20em}}
 * [[A1BG gene transcriptions]]
-* [[CAAT box gene transcriptions]]
+* [[Complex locus A1BG and ZNF497]]
-* [[Enhancer box gene transcriptions|E box gene transcriptions]]
-* [[GC box gene transcriptions]]
-* [[TATA box gene transcriptions]]
 {{Div col end}}
 ==References==
 {{reflist|2}}
+==External links==
+* [http://www.genome.jp/ GenomeNet KEGG database]
+* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
+* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
+* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
+* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
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