G box gene transcriptions: Difference between revisions

Revision as of 03:19, 25 July 2021

Editor-In-Chief: Henry A. Hoff

"Two distinct sequence elements, the H-box (consensus CCTACC(N)₇CT) and the G-box (CACGTG), are required for stimulation of the chsl5 promoter by [p-coumaric acid] 4-CA."^[1]

G boxes

The "perfect palindrome 5'-GCCACGTGGC-3' which is also known as the G-box motif."^[2]

"TAF-1 can bind to the G-box and related motifs and that it functions as a transcription activator."^[2]

"A G-box-related motif, containing the core sequence CACGTG is also present in the 5' regions of two other classes of light-responsive genes".^[2]

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

"Binding to the palindromic G-box (PA G-box, GCCACGTGGC) was moderate. However, binding activity to the G-box of the light-responsive unit 1 (U1) region of the parsley (Petroselinum crispum) CHS promoter (CHS-U1: TCCACGTGGC; Schulze-Lefert et al., 1989) or the G-box of GmAux28 (TCCACGTGTC) was much weaker than to the PA G-box [...]."^[6]

(G/T)CCACGTG(G/T)C combines the PA G-box (GCCACGTGGC) with the G-box of GmAux28 (TCCACGTGTC) for testing both.

Oeda samplings

For the Basic programs (starting with SuccessablesGbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGbox--.bas, looking for GCCACGTGGC, 0,
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGbox-+.bas, looking for GCCACGTGGC, 0,
positive strand in the negative direction is SuccessablesGbox+-.bas, looking for GCCACGTGGC, 0,
positive strand in the positive direction is SuccessablesGbox++.bas, looking for GCCACGTGGC, 0,
inverse complement, negative strand, negative direction is SuccessablesGboxci--.bas, looking for GCCACGTGGC, 0,
inverse complement, negative strand, positive direction is SuccessablesGboxci-+.bas, looking for GCCACGTGGC, 0,
inverse complement, positive strand, negative direction is SuccessablesGboxci+-.bas, looking for GCCACGTGGC, 0,
inverse complement, positive strand, positive direction is SuccessablesGboxci++.bas, looking for GCCACGTGGC, 0,

GObox random dataset samplings

GOboxr0: 0.
GOboxr1: 0.
GOboxr2: 0.
GOboxr3: 0.
GOboxr4: 0.
GOboxr5: 0.
GOboxr6: 0.
GOboxr7: 0.
GOboxr8: 0.
GOboxr9: 0.

Song samplings

Copying a responsive elements consensus sequence (G/T)CCACGTG(G/T)C and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/T)CCACGTG(G/T)C (starting with SuccessablesGSbox.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, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
positive strand, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
positive strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
negative strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
inverse complement, negative strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
inverse complement, positive strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
inverse complement, positive strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
inverse complement, negative strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.

GSbox random dataset samplings

GSboxr0: 0.
GSboxr1: 0.
GSboxr2: 0.
GSboxr3: 0.
GSboxr4: 0.
GSboxr5: 0.
GSboxr6: 1, TCCACGTGTC at 2907.
GSboxr7: 0.
GSboxr8: 0.
GSboxr9: 0.
GSboxr0ci: 0.
GSboxr1ci: 0.
GSboxr2ci: 0.
GSboxr3ci: 0.
GSboxr4ci: 0.
GSboxr5ci: 0.
GSboxr6ci: 0.
GSboxr7ci: 0.
GSboxr8ci: 0.
GSboxr9ci: 0.

GSboxr UTRs

GSboxr6: TCCACGTGTC at 2907.

GSboxr core promoters

GSboxr proximal promoters

GSboxr 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

↑ Gary J. Loake, Ouriel Faktor, Christopher J. Lamb, and Richard A. Dixon (October 1992). "Combination of H-box [CCTACC(N)₇CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate p-coumaricacid" (PDF). Proceedings of the National Academy of Sciences USA. 89: 9230–4. Retrieved 5 May 2020.
↑ ^2.0 ^2.1 ^2.2 K Oeda, J Salinas, and N H Chua (July 1991). "A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes". The EMBO Journal. 10 (7): 1793–1802. PMID 2050116. Retrieved 2017-02-13.
↑ 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.
↑ Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.

External links

Template:Sisterlinks

[Loake-1] Gary J. Loake, Ouriel Faktor, Christopher J. Lamb, and Richard A. Dixon (October 1992). "Combination of H-box [CCTACC(N)₇CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate p-coumaricacid" (PDF). Proceedings of the National Academy of Sciences USA. 89: 9230–4. Retrieved 5 May 2020.

[Oeda-2] 2.0 ^2.1 ^2.2 K Oeda, J Salinas, and N H Chua (July 1991). "A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes". The EMBO Journal. 10 (7): 1793–1802. PMID 2050116. Retrieved 2017-02-13.

[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.

[Zhang-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.

[Song-6] Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.

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[2]

[3]

[4]

[5]

[6]

@@ Line 139: / Line 139: @@
 ===GSboxr UTRs===
 {{main|UTR promoter gene transcriptions}}
+# GSboxr6: TCCACGTGTC at 2907.
 ===GSboxr core promoters===

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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 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 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 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 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