A box gene transcriptions: Difference between revisions

Revision as of 03:05, 28 November 2020

Associate Editor(s)-in-Chief: Henry A. Hoff

The GC boxes are not apparently associated with the A box, B box, C box, and D box.^[1]

"A^S/T, serine/threonine-rich subdomain within the A box".^[1] "A^Q, glutamine-rich subdomain within the A box".^[1]

Consensus sequences

"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]

Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].^[3]^[4]^[5]

"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."^[6]

Hypotheses

A1BG has no A boxes in either promoter.
A1BG is not transcribed by an A box.
An A box does not participate in the transcription of A1BG.

Samplings

Box A 3-TGACTCT-5' was not found using "⌘F" to locate any consensus sequences.

Hypothesis 1: A1BG is not transcribed by box A.

For the Basic programs testing consensus sequence 3'-TGACTCT-5' (starting with SuccessablesAbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox--.bas, looking for 3'-TGACTCT-5', 0.
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox-+.bas, looking for 3'-TGACTCT-5', 0.
positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox+-.bas, looking for 3'-TGACTCT-5', 1, 3'-TGACTCT-5' at 2788.
positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox++.bas, looking for 3'-TGACTCT-5', 0.
complement, negative strand, negative direction is SuccessablesAboxc--.bas, looking for 3'-ACTGAGA-5', 1, 3'-ACTGAGA-5' at 2788.
complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc-+.bas, looking for 3'-ACTGAGA-5', 0.
complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxc+-.bas, looking for 3'-ACTGAGA-5', 0.
complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc++.bas, looking for 3'-ACTGAGA-5', 0.
inverse complement, negative strand, negative direction is SuccessablesAboxci--.bas, looking for 3'-AGAGTCA-5', 0.
inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci-+.bas, looking for 3'-AGAGTCA-5', 1, 3'-AGAGTCA-5' at 2613.
inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxci+-.bas, looking for 3'-AGAGTCA-5', 0.
inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci++.bas, looking for 3'-AGAGTCA-5', 0.
inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi--.bas, looking for 3'-TCTCAGT-5', 0.
inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi-+.bas, looking for 3'-TCTCAGT-5', 0.
inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0.
inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613.

A box 5'-TACGTA-3' using "⌘F" has one location between ZSCAN22 and A1BG and none between ZNF497 and A1BG.

Hypothesis 1: A1BG is not transcribed by an A box.

For the Basic programs testing consensus sequence 3'-TACGTA-5' (starting with SuccessablesAbox1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1--.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5' at 4246.
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1-+.bas, looking for 3'-TACGTA-5', 0.
positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1+-.bas, looking for 3'-TACGTA-5', 0.
positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1++.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5', 3071.
complement, negative strand, negative direction is SuccessablesAbox1c--.bas, looking for 3'-ATGCAT-5', 0.
complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c-+.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 3071.
complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1c+-.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 4246.
complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c++.bas, looking for 3'-ACTGAGA-5', 0.

A box proximal promoters

Negative strand, negative direction: 5'-TACGTA-3' at 4246 and complement.

A box distal promoters

Positive strand, positiver direction: 5'-TACGTA-3' at 3071 and complement.

Box A distal promoters

Positive strand, negative direction: 5'-TGACTCT-3' at 2788 and complement.

Positive strand, positive direction: 5'-TCTCAGT-3' at 2613 and complement.

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 Huajun Jin, Arthi Kanthasamy, Dilshan S. Harischandra, Naveen Kondru, Anamitra Ghosh, Nikhil Panicker, Vellareddy Anantharam, Ajay Rana, and Anumantha G. Kanthasamy (December 12, 2014). "Histone Hyperacetylation Up-regulates Protein Kinase C􏰀 in Dopaminergic Neurons to Induce Cell Death RELEVANCE TO EPIGENETIC MECHANISMS OF NEURODEGENERATION IN PARKINSON DISEASE" (PDF). 289 (50): 34743–34767. doi:10.1074/jbc.M114.576702. Retrieved 10 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.
↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
↑ Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: name (help)
↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.

External links

[Jin-1] 1.0 ^1.1 ^1.2 Huajun Jin, Arthi Kanthasamy, Dilshan S. Harischandra, Naveen Kondru, Anamitra Ghosh, Nikhil Panicker, Vellareddy Anantharam, Ajay Rana, and Anumantha G. Kanthasamy (December 12, 2014). "Histone Hyperacetylation Up-regulates Protein Kinase C􏰀 in Dopaminergic Neurons to Induce Cell Death RELEVANCE TO EPIGENETIC MECHANISMS OF NEURODEGENERATION IN PARKINSON DISEASE" (PDF). 289 (50): 34743–34767. doi:10.1074/jbc.M114.576702. Retrieved 10 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.

[Landschulz-3] Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.

[Zhang2014-4] Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: name (help)

[Nijhawan-5] Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.

[Kokoroishi-6] Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 117: / Line 117: @@
 ===A box proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
-Negative direction: 5'-TACGTA-3' at 4246 and complement.
+Negative strand, negative direction: 5'-TACGTA-3' at 4246 and complement.
 ===A box distal promoters===
 {{main|Distal promoter gene transcriptions}}
-Positive direction: 5'-TACGTA-3' at 3071 and complement.
+Positive strand, positiver direction: 5'-TACGTA-3' at 3071 and complement.
 ===Box A distal promoters===
-Negative direction: 5'-TGACTCT-3' at 2788 and complement.
+Positive strand, negative direction: 5'-TGACTCT-3' at 2788 and complement.
-Positive direction: 5'-TCTCAGT-3' at 2613 and complement.
+Positive strand, positive direction: 5'-TCTCAGT-3' at 2613 and complement.
 ==Acknowledgements==

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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 Abscisic acid-responsive elements 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 AP-2 (Roesler) elements ATA box gene 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Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element 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 Families of TATA box genes 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 Heat shock elements 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 Immunoglobulin like domain containing family 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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 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 Nanos/Pumilio response element 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 Shue boxes Sip4p gene transcriptions Smp1p gene transcriptions Sp1 (Berberich) elements 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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 Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream repressor site 1 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

A box gene transcriptions: Difference between revisions

Revision as of 03:05, 28 November 2020

Contents

Consensus sequences

Hypotheses

Samplings

A box proximal promoters

A box distal promoters

Box A distal promoters

Acknowledgements

See also

References

External links

Navigation menu

A box gene transcriptions: Difference between revisions

Revision as of 03:05, 28 November 2020

Consensus sequences

Hypotheses

Samplings

A box proximal promoters

A box distal promoters

Box A distal promoters

Acknowledgements

See also

References

External links

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