ACGT-containing element gene transcriptions: Difference between revisions
Created page with "{{AE}} Henry A. Hoff The "binding affinities of both bZIP proteins were similar to CRE<sup>A/T</sup> (ATGACGTCAT), a CRE sequence with flanking adenine and thymine (A/T) at p..." |
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==Consensus sequences== | |||
"The ABRE contains the core sequence, ACGT, also known as the G‐box (Marcotte et al. 1989; Yamaguchi‐Shinozaki et al. 1990)."<ref name=Watanabe>{{ cite journal | |||
|author=Kenneth A. Watanabe, Arielle Homayouni, Lingkun Gu, Kuan‐Ying Huang, Tuan‐Hua David Ho, Qingxi J. Shen | |||
|title=Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element | |||
|journal=Plant, Cell & Environment | |||
|date=18 June 2017 | |||
|volume=40 | |||
|issue=9 | |||
|pages=2004-2016 | |||
|url=https://onlinelibrary.wiley.com/doi/full/10.1111/pce.13006 | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1111/pce.13006 | |||
|pmid= | |||
|accessdate=5 October 2020 }}</ref> | |||
5'-ACGT-3'.<ref name=Guan/> | |||
The consensus sequence for the ACGT-containing elements (ACEs) is 5'-CACGT-3'.<ref name=Hartmann/> | |||
==Hypotheses== | |||
# A1BG has no ACEs in either promoter. | |||
==Samplings== | |||
# ACGT elements, negative strand, negative direction: 24 between 150 and 4338 nts. | |||
# ACGT elements, negative strand, positive direction: 2, 3'-ACGT-5' at 569, 3'-ACGT-5' at 3254. | |||
# ACGT elements, positive strand, negative direction: 4, 3'-ACGT-5' at 342, 3'-ACGT-5' at 531, 3'-ACGT-5' at 1772, 3'-ACGT-5' at 4236. | |||
# ACGT elements, positive strand, positive direction: 44 between 192 and 4341 nts. | |||
ACGT-containing elements include these metal responsive elements: | |||
# complement, negative strand, negative direction: 6 between 1348 and 4341 nts. | |||
# complement, positive strand, negative direction: 6 between 549 and 3323 nts. | |||
# inverse, negative strand, negative direction: 2, 3'-CTCACGT-5' at 1470, 3'-CACACGT-5' at 2863. | |||
# inverse, positive strand, negative direction: 2, 3'-CACACGT-5' at 531, 3'-CTCACGT-5' at 1772. | |||
# inverse, positive strand, positive direction: 6 between 546 and 3883 nts. | |||
ACGT-containing elements include these cAMP response elements (CRE): | |||
# negative strand in the negative direction (from ZSCAN22 to A1BG): 1, 3'-TGACGTCA-5' at 4317. | |||
==Acknowledgements== | |||
The content on this page was first contributed by: Henry A. Hoff. | |||
==See also== | ==See also== | ||
{{div col|colwidth=20em}} | {{div col|colwidth=20em}} | ||
* [[A1BG gene transcriptions]] | |||
* [[Complex locus A1BG and ZNF497]] | * [[Complex locus A1BG and ZNF497]] | ||
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Revision as of 16:17, 7 October 2020
Associate Editor(s)-in-Chief: Henry A. Hoff
The "binding affinities of both bZIP proteins were similar to CREA/T (ATGACGTCAT), a CRE sequence with flanking adenine and thymine (A/T) at positions -4 and +4. [The] bZIP domains of both STF1 and HY5 have similar binding properties for recognizing ACGT-containing elements (ACEs). [Although] the G-box is a known target site for the HY5 protein, the C-box sequences are the preferred binding sites for both STF1 and HY5."[1]
"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."[2]
"Upstream from the transcriptional start site, several motifs were found [...]. A typical TATA box is located at -43. The CAAT consensus sequence cannot be found between -80 and -120; however, two sequence motifs (GCGCCC, GGGCAG), which are homologous to the consensus sequences for the Spl-binding site, GGGCGG (GC box) [19] were found around -114 and -570. The GC box has been found in promoters of many viral and cellular genes [20], and acts as a binding site of a protein, Spl, which is necessary for transcriptional activity. A pyrimidine box (CCTTT) and Box I (GCAGTG) which are part of the GA response complex [21] were found at -208 and -256. Two 8 bp sequences (CACGTCGC, CACGTAAC) which are similar to an ABA response element (ABRE, CACGTGGC) [22] were located at -308, -648 relative to the + 1 site. The core sequence of the ABA response element (ACGT) is the binding site for basic leucine zipper transcriptional factors or common plant regulatory factors (CPRFs) [23]."[3]
Consensus sequences
"The ABRE contains the core sequence, ACGT, also known as the G‐box (Marcotte et al. 1989; Yamaguchi‐Shinozaki et al. 1990)."[4]
5'-ACGT-3'.[3]
The consensus sequence for the ACGT-containing elements (ACEs) is 5'-CACGT-3'.[2]
Hypotheses
- A1BG has no ACEs in either promoter.
Samplings
- ACGT elements, negative strand, negative direction: 24 between 150 and 4338 nts.
- ACGT elements, negative strand, positive direction: 2, 3'-ACGT-5' at 569, 3'-ACGT-5' at 3254.
- ACGT elements, positive strand, negative direction: 4, 3'-ACGT-5' at 342, 3'-ACGT-5' at 531, 3'-ACGT-5' at 1772, 3'-ACGT-5' at 4236.
- ACGT elements, positive strand, positive direction: 44 between 192 and 4341 nts.
ACGT-containing elements include these metal responsive elements:
- complement, negative strand, negative direction: 6 between 1348 and 4341 nts.
- complement, positive strand, negative direction: 6 between 549 and 3323 nts.
- inverse, negative strand, negative direction: 2, 3'-CTCACGT-5' at 1470, 3'-CACACGT-5' at 2863.
- inverse, positive strand, negative direction: 2, 3'-CACACGT-5' at 531, 3'-CTCACGT-5' at 1772.
- inverse, positive strand, positive direction: 6 between 546 and 3883 nts.
ACGT-containing elements include these cAMP response elements (CRE):
- negative strand in the negative direction (from ZSCAN22 to A1BG): 1, 3'-TGACGTCA-5' at 4317.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 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. Retrieved 26 March 2019.
- ↑ 2.0 2.1 Ulrike Hartmann, Martin Sagasser, Frank Mehrtens, Ralf Stracke and Bernd Weisshaar (January 2005). "Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes" (PDF). Plant Molecular Biology. 57 (2): 155–171. doi:10.1007/s11103-004-6910-0. Retrieved 10 November 2018.
- ↑ 3.0 3.1 Lingqiang Guan, Alexis N. Polidoros and John G. Scandalios (March 1996). "Isolation, characterization and expression of the maize Cat2 catalase gene" (PDF). Plant Molecular Biology. 30 (5): 913–24. doi:10.1007/BF00020803. Retrieved 19 April 2019.
- ↑ Kenneth A. Watanabe, Arielle Homayouni, Lingkun Gu, Kuan‐Ying Huang, Tuan‐Hua David Ho, Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.