View source for ACGT-containing element gene transcriptions

{{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 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."<ref name=Song>{{ cite journal
|author=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
|title=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
|journal=Plant Physiology
|date=April 2008
|volume=146
|issue=4
|pages=1862–1877
|url=http://www.plantphysiol.org/content/plantphysiol/146/4/1862.full.pdf
|arxiv=
|bibcode=
|doi=10.1104/pp.107.113217
|pmid=
|accessdate=26 March 2019 }}</ref>

"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."<ref name=Hartmann>{{ cite journal
|author=Ulrike Hartmann, Martin Sagasser, Frank Mehrtens, Ralf Stracke and Bernd Weisshaar
|title=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
|journal=Plant Molecular Biology
|date=January 2005
|volume=57
|issue=2
|pages=155–171
|url=http://pubman.mpdl.mpg.de/pubman/item/escidoc:1222162/component/escidoc:1222161/hartmann_weisshaar_pmb_2005.pdf
|arxiv=
|bibcode=
|doi=10.1007/s11103-004-6910-0
|pmid=
|accessdate=10 November 2018 }}</ref>

"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]."<ref name=Guan>{{ cite journal
|author=Lingqiang Guan, Alexis N. Polidoros and John G. Scandalios
|title=Isolation, characterization and expression of the maize ''Cat2'' catalase gene
|journal=Plant Molecular Biology
|date=March 1996
|volume=30
|issue=5
|pages=913-24
|url=http://users.auth.gr/~palexios/Publications/Pdf-SCI/Public-Polidoros-1-10.pdf
|arxiv=
|bibcode=
|doi=10.1007/BF00020803
|pmid=
|accessdate=19 April 2019 }}</ref>

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box), GACGTC (C box), TACGTA (A box), AACGTT (T box), and a GCN4 motif, namely TGA(G/C)TCA (Landschulz et al., 1988;<ref name=Landschulz>{{ cite journal
| authors = Landschulz WH, Johnson PF, McKnight SL | title = The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins | journal = Science | volume = 240 | issue = 4860 | pages = 1759–64 | date = June 1988 | pmid = 3289117
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref> Nijhawan et al., 2008<ref name=Nijhawan>{{ cite journal | authors = Nijhawan A, Jain M, Tyagi AK, Khurana JP
| title = Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice
| journal = Plant Physiology
| volume = 146
| issue = 2
| pages = 333–50
| date = February 2008
| pmid = 18065552
| doi = 10.1104/pp.107.112821 }}</ref>)."<ref name=Zhang2014>{{ cite journal
| authors = Z.G. E, Y.P. Zhang, J.H. Zhou and L. Wang
| title = Roles of the bZIP gene family in rice
| journal = Genetics and Molecular Research
| volume = 13
| issue = 2
| pages = 3025–36
| date = 16 April 2014
| pmid = 24782137
| doi = 10.4238/2014.April.16.11 }}</ref>

==ABA-response elements==
{{main|ABA-response element gene transcriptions}}
"The ABA responsive element (ABRE) is a key cis‐regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA‐induced genes in rice aleurone cells, suggesting other ABREs may exist."<ref name=Watanabe/> ABA responsive element, Table 2, number 3, order 29, present, ACGTG(G/T)C[3].

"Many ABA‐inducible genes in various species contain a conserved cis‐regulatory ABA responsive element (ABRE) with the consensus sequence ACGTG(G/T)C (Hattori et al. 2002; Shen et al. 2004)."<ref name=Watanabe/>

"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/>

===ABRE Core promoters===
{{main|Core promoter gene transcriptions}}
Positive strand, positive direction: 5'-ACGTGGC-3' at 4344 and complement.

===ABRE Proximal promoters===
{{main|Proximal promoter gene transcriptions}}
Positive strand, negative direction: 5'-ACGTGGC-3' at 4239 and complement.

===ABRE Distal promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: 5'-GACACGT-3' at 3429 and complement.

Positive strand, positive direction: 5'-GACACGT-3' at 2960, 5'-ACGTGTC-3' at 1823 and complements.

==A boxes==
{{main|A box gene transcriptions}}
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...]."<ref name=Zhang2014/> A-box, Table 2, number 5, order 26, present, TACGTA[15].

===A box proximal promoters===
{{main|Proximal promoter gene transcriptions}}
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.

==Abscisic acid-responsive elements==
{{main|Phosphate starvation-response transcription factor gene transcriptions}}
Abscisic acid-responsive elements (CACGTG).<ref name=Sharma/> Abscisic acid-responsive element, Table 2, number 6, order 126, present, CACGTG[8].

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."<ref name=Rossi/>

The Pho4 homodimer binds to DNA sequences containing the bHLH binding site 5'-CACGTG-3'.<ref name=Shao>{{ cite journal
|author=Dalei Shao, Caretha L. Creasy, Lawrence W. Bergman
|title = A cysteine residue in helixII of the bHLH domain is essential for homodimerization of the yeast transcription factor Pho4p
|journal = Nucleic Acids Research
|volume = 26
|issue = 3
|pages = 710–4
|date= 1 February 1998
|pmid = 9443961
|pmc = 147311
|doi = 10.1093/nar/26.3.710
|url = https://academic.oup.com/nar/article/26/3/710/1052045 }}</ref>

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of ''HIS4'' and ''PHO5'' regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].<ref name=Tang/>

===Pho4 distal promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 1219, and 5'-CACGTG-3' at 547 and complements.

===Phop distal promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: 5'-TTACAC-3' at 4091, 5'-AACGTG-3' at 3288, 3'-CACGTT-5' at 2864, 3'-CACATT-5' at 2087, 5'-TTACAC-3' at 2064, 5'-AACGTG-3' at 1718, 3'-CACGTT-5' at 1536, 5'-AACGTG-3' at 1346, 5'-AACGTG-3' at 1338, 3'-CACATG-5' at 797, 3'-CACATT-5' at 612, and 3'-CACATG-5' at 324 and complements.

Positive strand, negative direction: 5'-CACATG-3' at 2667, 5'-CACGTT-3' at 343 and complements.

Negative strand, positive direction: 5'-CATGTG-3' at 3958, 5'-CACATG-3' at 3956, 5'-CATGTG-3' at 3902, 5'-CACATG-3' at 3742, 5'-CACATG-3' at 3707, 5'-CACATG-3' at 2031, 5'-CACGTG-3' at 570, 5'-AATGTG-3' at 229 and complements.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTT-3' at 2801, 5'-CACGTT-3' at 2335, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547 and complements.

==Activating transcription factors==

===Activating transcription factor (Burton) distal promoters===

Negative strand, positive direction: 5'-TGACGTAAG-3' at 2207 and complement.

==Carbohydrate response elements==
{{main|Carbohydrate response element gene transcriptions}}
"The putative ChREBP binding sites [are] ChoRE1 (CACGTG<u>ACCGG</u>ATCTTG, -324 to -308) and ChoRE2 (TCCGCC<u>CCCAT</u>CACGTG, -298 to - 282) [...], where the 5-nt spacer [Carb and Carb1 is] between the two E-boxes in ChoRE motifs [CarbE1, CarbE2 and CarbE3]."<ref name=Long>{{ cite journal
|author=Jianyin Long, Daniel L. Galvan, Koki Mise, Yashpal S. Kanwar, Li Li, Naravat Poungavrin, Paul A. Overbeek, Benny H. Chang, and Farhad R. Danesh
|title=Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1
|journal=Journal of Biological Chemistry
|date=28 May 2020
|volume=5
|issue=28
|pages=
|url=https://www.jbc.org/content/early/2020/05/28/jbc.RA120.013228.full.pdf
|arxiv=
|bibcode=
|doi=10.1074/jbc.RA120.013228
|pmid=
|accessdate=6 October 2020 }}</ref> Carbohydrate response element, Table 2, number 60, order 43, absent, CACGTGACCGGATCTTG, TCCGCCCCCATCACGTG[6]. Carbohydrate response element, Table 2, number 64, order 207, present, CACGTG[6].

===ChoRE distal promoters===

Negative strand, positive direction: 5'-CACGTG-3' at 570, and complement (CarbE2).

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547, and complements (CarbE2).

==C boxes==
{{main|C box gene transcriptions}}
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] GACGTC (C box) [...]."<ref name=Zhang2014/> C box, Table 2, number 78, order 218, present, GACGTC[9].

Analysis "of the recombinant (soybean [''Glycine max''] TGACG-motif binding factor 1) STF1 protein revealed the C-box (nGACGTCn) to be a high-affinity binding site (Cheong et al., 1998). [...] To test whether STF1 and HY5 have similar DNA-binding properties, the binding properties of each were compared with eight different DNA sequences that represent G-, C-, and C/G-box motifs [TGACGTGT]. C-box sequences carrying the mammalian cAMP responsive element (CRE; TGACGTCA) motif and the Hex sequence (TGACGTGGC), a hybrid C/G-box (Cheong et al., 1998), were high-affinity binding sites for both proteins [...]."<ref name=Song>{{ cite journal
|author=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
|title=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
|journal=Plant Physiology
|date=April 2008
|volume=146
|issue=4
|pages=1862–1877
|url=http://www.plantphysiol.org/content/plantphysiol/146/4/1862.full.pdf
|arxiv=
|bibcode=
|doi=10.1104/pp.107.113217
|pmid=18287490
|accessdate=26 March 2019 }}</ref>

==C-boxes==
{{main|C box gene transcriptions}}
Analysis "of the recombinant (soybean [''Glycine max''] TGACG-motif binding factor 1) STF1 protein revealed the C-box (nGACGTCn) to be a high-affinity binding site (Cheong et al., 1998). [...] To test whether STF1 and HY5 have similar DNA-binding properties, the binding properties of each were compared with eight different DNA sequences that represent G-, C-, and C/G-box motifs [TGACGTGT]. C-box sequences carrying the mammalian cAMP responsive element (CRE; TGACGTCA) motif and the Hex sequence (TGACGTGGC), a hybrid C/G-box (Cheong et al., 1998), were high-affinity binding sites for both proteins [...]."<ref name=Song/>

Copying the C-box consensus sequence 5'-nGACGTCn-3' (Cheong et al., 1998) and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG or no locations between ZSCAN22 and A1BG as can be found by the computer programs.

===C-box (Song) core promoters===

Positive strand, positive direction: 5'-GACGTC-3' at 4316, and complement.

===C-box (Song) proximal promoters===

Negative strand, negative direction: 5'-GACGTC-3', 4316 and complement.

===C-box (Song) distal promoters===

Positive strand, positive direction: 5'-GACGTC-3' at 3280, 5'-GACGTC-3' at 3231, 5'-GACGTC-3' at 2858, 5'-GACGTC-3' at 1506, 5'-GACGTC-3' at 1120, 5'-GACGTC-3' at 532, 5'-GACGTC-3' at 437, 5'-GACGTC-3' at 193, and complements.

===C/G-box hybrid (Song) distal promoters===

Positive strand, positive direction: 5'-ACACGTCA-3' at 3962 and complement. C/A hybrid box, Table 2, number 79, order 32, absent, TGACGTAT[9]. C/G hybrid box, Table 2, number 80, order 244, present, TGACGTGT[9]. C/T hybrid boxes is Table 2, number 81, order 34, absent, TGACGTTA.[9]

==CRE boxes==
{{main|CRE box gene transcriptions}}
"Within the cAMP-responsive element of the somatostatin gene, we observed an 8-base palindrome, 5'-TGACGTCA-3', which is highly conserved in many other genes whose expression is regulated by cAMP."<ref name=Montminy>{{ cite journal
|author=Marc R. Montminy, Kevin A. Sevarino, John A. Wagner, Gail Mandel, and Richard H. Goodman
|title=Identification of a cyclic-AMP-responsive element within the rat somatostatin gene
|journal=Proceedings of the National Academy of Sciences of the USA
|date=September 1986
|volume=83
|issue=18
|pages=6382-6
|url=http://www.pnas.org/content/pnas/83/18/6682.full.pdf
|arxiv=
|bibcode=
|doi=
|pmid=2875459
|accessdate=17 September 2018 }}</ref> Cyclic-AMP-responsive element, Table 2, number 102, order 274, present, TGACGTCA[127].

The upstream activating sequence (UAS) for the Aca1p, the basic "leucine zipper (bZIP) transcription factor [55] involved in carbon source utilization" is 5'-TGACGTCA-3'<ref name=Tang>{{ cite journal
|author=Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling
|title=Promoter Architecture and Promoter Engineering in ''Saccharomyces cerevisiae''
|journal=Metabolites
|date=6 August 2020
|volume=10
|issue=8
|pages=320-39
|url=https://www.mdpi.com/2218-1989/10/8/320/pdf
|arxiv=
|bibcode=
|doi=10.3390/metabo10080320
|pmid=32781665
|accessdate=18 September 2020 }}</ref> the same as a CRE.

The upstream activating sequence (UAS) for the Sko1p, involved "in osmotic and oxidative stress responses" is 5'-TGACGTCA-3'<ref name=Tang/> the same as a CRE.

===CRE box proximal promoters===

Negative strand, negative direction: 5'-TGACGTCA-3', 4317, and complement.

==Enhancer boxes==

E-box, Table 2, number 141, order 7, present, CACGTG [7].

===Enhancer box distal promoters===

Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547, and complements.

==G boxes==
{{main|G box gene transcriptions}}
"Two distinct sequence elements, the H-box (consensus CCTACC(N)<sub>7</sub>CT) and the G-box (CACGTG), are required for stimulation of the ''chsl5'' promoter by [p-coumaric acid] 4-CA."<ref name=Loake>{{ cite journal
|author=Gary J. Loake, Ouriel Faktor, Christopher J. Lamb, and Richard A. Dixon
|title=Combination of H-box [CCTACC(N)<sub>7</sub>CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate ''p''-coumaricacid
|journal=Proceedings of the National Academy of Sciences USA
|date=October 1992
|volume=89
|issue=
|pages=9230-4
|url=https://www.pnas.org/content/pnas/89/19/9230.full.pdf
|arxiv=
|bibcode=
|doi=
|pmid=
|accessdate=5 May 2020 }}</ref> G-box, Table 2, number 6, order 126, present, CACGTG[5].

The "perfect palindrome 5'-GCCACGTGGC-3' which is also known as the G-box motif."<ref name=Oeda>{{ cite journal
|author=K Oeda, J Salinas, and N H Chua
|title=A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes
|journal=The EMBO Journal
|date=July 1991
|volume=10
|issue=7
|pages=1793–1802
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC452853/
|arxiv=
|bibcode=
|doi=
|pmid=2050116
|accessdate=2017-02-13 }}</ref> G box, Table 2, number 157, order 115, absent, (G/T)CCACGTG(G/T)C[9].

"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".<ref name=Oeda/>

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box) [...]."<ref name=Zhang2014/>

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 [...]."<ref name=Song/>

==GCN4 motifs==
{{main|GLM box gene transcriptions#GCN4 motifs}}
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] a GCN4 motif, namely TGA(G/C)TCA [...]."<ref name=Zhang2014/>

==Hex sequences==
{{main|Hex sequence gene transcriptions}}
The Hex sequence is (TGACGTGGC).<ref name=Song/> Hex sequence, Table 2, number 201, order 134, present, TGACGTGGC[9].

==Hybrids==
{{main|C box gene transcriptions}}
Hybrid C, A boxes 5'-TGACGTAT-3' have A at the 12 position, hybrid C, G boxes 5'-TGACGTGT-3' have G at the 12 position, and hybrid C, T boxes 5'-TGACGTTA-3' have T at the 12 position.

==Hypoxia response elements==
{{main|ABA-response element gene transcriptions}}
"The hypoxia response element (HRE) and estrogen response element (ERE) were located on −154 to −150 "ACGTG", and −94 to −80 "AGGTTATTGCCTCCT" on the transcript, respectively."<ref name=Matsumoto>{{ cite journal
|author=Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima
|title=Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish ''Takifugu rubripes''
|journal=Fisheries Science
|date=9 August 2020
|volume=86
|issue=
|pages=873-887
|url=https://researchmap.jp/hiroyukiharada/published_papers/29953426/attachment_file.pdf
|arxiv=
|bibcode=
|doi=10.1007/s12562-020-01451-z
|pmid=
|accessdate=27 September 2020 }}</ref> Hypoxia-inducible factor, Table 2, number 206, order 65, absent, GCCCTACGTGCTGTCTCA[11].

Hypoxia-inducible factor, Table 2, number 207, order 37, present, ACGTG[12].

==Initiator elements==

===Initiator element (YYANWYY) core promoters===

Positive strand, positive direction: 5'-GACGTGG-3' at 4343 and complement.

===Initiator element (YYANWYY) proximal promoters===

Negative strand, negative direction: 5'-GACGTGA-3' at 4340, and complement.

===Initiator element (YYANWYY) distal promoters===

Negative strand, negative direction: 5'-TTACGTC-3' at 3772, 5'-AACGTGA-3' at 3289, 5'-GACGTGG-3' at 2761, 5'-GACGTGA-3' at 2426, 5'-CCACGTC-3' at 2082, 5'-GACGTGA-3' at 2000, 5'-TCACGTT-5' at 1536, 5'-TCACGTC-3' at 1471, 5'-AACGTGA-3' at 1347, 5'-AACGTGG-3' at 1339, 5'-GACGTAA-3' at 152, and complements.

Positive strand, negative direction: 5'-GACGTGG-3' at 4238, 5'-TCACGTC-3' at 1773, and complements.

Negative strand, positive direction: 5'-TCACGTC-3' at 3255, and complement.

Positive strand, positive direction: 5'-TCACGTC-3' at 3465, 5'-CTACGTC-3' at 3460, 5'-AACGTAG-3' at 3402, 5'-AACGTGA-3' at 3343, 5'-GACGTGG-3' at 3322, 5'-CCACGTT-3' at 2801, 5'-CCACGTT-3' at 2335, 5'-TCACGTC-3' at 2327, 5'-TCACGTC-3' at 2064, 5'-GACGTAA-3' at 2206, 5'-TCACGTC-3' at 1787, 5'-GACGTGA-3' at 1472, 5'-GACGTGA-3' at 1372, 5'-CCACGTC-3' at 784, and complement.

===Initiator element (BBCABW) core promoters===

Positive strand, positive direction: 5'-TGACGT-3' at 4341, 5'-TGACGT-3' at 4338, 5'-TGACGT-3' at 4330, 5'-ACGTCT-3' at 4317, and complements.

===Initiator element (BBCABW) proximal promoters===

Negative strand, negative direction: 5'-ACGTGA-3' at 4340, 5'-ACGTCA-3' at 4317, 5'-TGACGT-3' at 4315, and complements.

===Initiator element (BBCABW) distal promoters===

Negative strand, negative direction: 5'-TTACGT-3', 3771, 5'-ACGTCT-3' at 3431, 5'-ACACGT-3' at 3429, 5'-ACGTGA-3' at 3289, 5'-ACACGT-3' at 2863, 5'-TGACGT-3' at 2759, 53'-ACGTCA-3' at 2737, 5'-ACGTGA-3' at 2426, 5'-TGACGT-3' at 2424, 5'-ACGTCA-3' at 2402, 5'-ACGTCA-3' at 2083, 5'-ACGTGA-3' at 2000, 5'-TGACGT-3' at 1998, 5'-ACGTCA-3' at 1976, 5'-ACGTGT-3' at 1719, 5'-TCACGT-3' at 1535, 5'-TGACGT-3' at 1494, 5'-ACGTCA-3' at 1472, 5'-ACGTGA-3' at 1347, 5'-ACGTCA-3' at 1323, 5'-ACGTCA-3' at 1032, 5'-ACGTAA-3' at 152, and complements.

Positive strand, negative direction: 5'-AGACGT-3' at 4236, 5'-ACGTCT-3' at 1774, 5'-TCACGT-3' at 1772, 5'-ACGTAA-3' at 533, 5'-ACACGT-3' at 531, 5'-ACACGT-3' at 342, and complements.

Negative strand, positive direction: 5'-ACGTCT-3' at 3256, 5'-TCACGT-3' at 3254, 5'-ACACGT-3' at 569, and complements.

Positive strand, positive direction: 5'-ACGTCA-3' at 3962, 5'-ACACGT-3' at 3960, 5'-ACGTCT-3' at 3831, 5'-TCACGT-3' at 3464, 5'-ACGTCA-3' at 3461, 5'-ACGTGA-3' at 3343, 5'-TGACGT-3' at 3320, 5'-ACGTCA-3' at 3281, 5'-AGACGT-3' at 3279, 5'-AGACGT-3' at 3268, 5'-ACGTCA-3' at 3232, 5'-ACGTAA-3' at 3072, 5'-TTACGT-3' at 3070, 5'-AGACGT-3' at 3061, 5'-ACGTGT-3' at 2962, 5'-ACACGT-3' at 2960, 5'-ACGTCT-3' at 2859, 5'-AGACGT-3' at 2857, 5'-ACGTCT-3' at 2721, 5'-ACACGT-3' at 2681, 5'-ACGTCA-3' at 2328, 5'-TCACGT-3' at 2326, 5'-ACGTAA-3' at 2206, 5'-TGACGT-3' at 2204, 5'-ACGTCA-3' at 2065, 5'-TCACGT-3' at 2063, 5'-ACGTCT-3' at 1937, 5'-ACGTGT-3' at 1822, 5'-TCACGT-3' at 1786, 5'-TGACGT-3' at 1505, 5'-ACGTGA-3' at 1472, 5'-ACGTGA-3' at 1372, 5'-ACGTGT-3' at 1220, 5'-ACGTGT-3' at 548, 5'-ACGTCT-3' at 438, 5'-AGACGT-3' at 224, and complements.

==Metal responsive elements==
{{main|Metal responsive element gene transcriptions}}
"[T]hree potential metal response elements (MREs) [overlap] the E-boxes in the repeats, (TGCACGT with TGCRCNC being the consensus sequence; 17,18)."<ref name=Levinson>{{ cite journal
|author=Barbara Levinson, Rebecca Conant, Rhonda Schnur, Soma Das, Seymour Packman and Jane Gitschier
|title=A Repeated Element in the Regulatory Region of the ''MNK'' Gene and Its Deletion in A Patient With Occipital Horn Syndrome
|journal=Human Molecular Genetics
|month=
|year=1996
|volume=5
|issue=11
|pages=1737-42
|url=http://hmg.oxfordjournals.org/content/5/11/1737.full
|arxiv=
|bibcode=
|doi=10.1093/hmg/5.11.1737
|pmid=
|accessdate=2013-04-15 }}</ref>

===MRE proximal promoters===
{{main|Proximal promoter gene transcriptions}}
Negative strand, negative direction: 5'-ACGTGAG-3' at 4341 and complement.

===MRE distal promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: 5'-ACGTGAG-3' at 3290, 5'-CACACGT-3' at 2863, 5'-ACGTGGG-3' at 2762, 5'-ACGTGAG-3' at 2427, 5'-ACGTGAG-3' at 2001, 5'-CTCACGT-3' at 1470, 5'-ACGTGAG-3' at 1348, and complements.

Positive strand, negative direction: 5'-ACGTGGG-3' at 3323, 5'-ACGTGTG-3' at 2963, 5'-CTCACGT-3' at 1772, 5'-ACGTGAG-3' at 1473, 5'-ACGTGAG-3' at 1373, 5'-ACGTGTG-3' at 1221, 5'-ACGTGTG-3' at 549, 5'-CACACGT-3' at 531, and complements.

Positive strand, positive direction: 5'-CCCACGT-3' at 3883, 5'-CCCACGT-3' at 2800, 5'-CTCACGT-3' at 2326, 5'-CTCACGT-3' at 1786, 5'-CGCACGT-3' at 1218, 5'-CGCACGT-3' at 546, and complements.

==ORE1 binding sites==
{{main|ORE1 binding site gene transcriptions}}
"As a transcription factor, ORE1 was reported to bind to consensus DNA sequences of [ACG][CA]GT[AG]N{5,6}[CT]AC[AG] [29] or T[TAG][GA]CGT[GA][TCA][TAG] [37]."<ref name=Qiu>{{ cite journal
|author=Kai Qiu, Zhongpeng Li, Zhen Yang, Junyi Chen, Shouxin Wu, Xiaoyu Zhu, Shan Gao, Jiong Gao, Guodong Ren, Benke Kuai, and Xin Zhou
|title=EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in ''Arabidopsis''
|journal=PLoS Genetics
|date=July 2015
|volume=11
|issue=7
|pages=e1005399
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517869/
|arxiv=
|bibcode=
|doi=10.1371/journal.pgen.1005399
|pmid=26218222
|accessdate=4 October 2020 }}</ref>

Consensus sequences are 5'-(A/C/G)(A/C)GT(A/G)N<sub>5,6</sub>(C/T)AC(A/G)-3' or 5'-T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)-3'.<ref name=Qiu/>

Copying 5'-TTACGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

==Phosphate starvation-response transcription factors==
{{main|Phosphate starvation-response transcription factor gene transcriptions}}
Abscisic acid-responsive elements (CACGTG).<ref name=Sharma>{{ cite journal
|author=Bhaskar Sharma & Joemar Taganna 
|title=Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
|journal=Scientific Reports
|date=12 June 2020
|volume=10
|issue=9581
|pages=
|url=https://www.nature.com/articles/s41598-020-66553-1
|arxiv=
|bibcode=
|doi=10.1038/s41598-020-66553-1
|pmid=32533036
|accessdate=27 August 2020 }}</ref>

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."<ref name=Rossi>{{ cite journal
|author=Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh
|title=Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
|journal=Genome Research
|date=21 March 2018
|volume=28
|issue=
|pages=497-508
|url=https://genome.cshlp.org/content/28/4/497.full
|arxiv=
|bibcode=
|doi=10.1101/gr.229518.117
|pmid=29563167
|accessdate=31 August 2020 }}</ref>

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of ''HIS4'' and ''PHO5'' regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].<ref name=Tang/>

===Phop distal promoters===

Negative strand, negative direction: 5'-AACGTG-3' at 3288, 3'-CACGTT-5' at 2864, 5'-AACGTG-3' at 1718, 3'-CACGTT-5' at 1536, 5'-AACGTG-3' at 1346, 5'-AACGTG-3' at 1338 and complements.

Positive strand, negative direction: 5'-CACGTT-3' at 343 and complements.

Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTT-3' at 2801, 5'-CACGTT-3' at 2335, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547 and complements.

==Root specific elements==
{{main|Root specific element gene transcriptions}}
Root specific elements (TGACGTCA).<ref name=Sharma/> Cyclic-AMP-responsive element, Table 2, number 102, order 274, present, TGACGTCA[127].

==Synaptic Activity-Responsive Elements==
{{main|Synaptic Activity-Responsive Elements}}
"A unique synaptic activity-responsive element (SARE) sequence, composed of the consensus binding sites for SRF, MEF2 and CREB, is necessary for control of transcriptional upregulation of the Arc gene in response to synaptic activity."<ref name=Tornos>{{ cite journal
|author=Fernanda M. Rodríguez-Tornos, Iñigo San Aniceto, Beatriz Cubelos, Marta Nieto
|title=Enrichment of Conserved Synaptic Activity-Responsive Element in Neuronal Genes Predicts a Coordinated Response of MEF2, CREB and SRF
|journal=PLoS ONE
|date=31 January 2013
|volume=8
|issue=1
|pages=e53848
|url=https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0053848&type=printable
|arxiv=
|bibcode=
|doi=10.1371/journal.pone.0053848
|pmid=23382855
|accessdate=12 November 2018 }}</ref>

"Within the cAMP-responsive element of the somatostatin gene, we observed an 8-base palindrome, 5'-TGACGTCA-3', which is highly conserved in many other genes whose expression is regulated by cAMP."<ref name=Montminy/>

==T boxes==
{{main|T box gene transcriptions}}
"The different inducing activities of Xbra, VegT and Eomesodermin suggest that the proteins might recognise different DNA target sequences. [...] All three proteins prove to recognise the same core sequence of TCACACCT with some differences in flanking nucleotides."<ref name=Conlon>{{ cite journal
|author=Frank L. Conlon, Lynne Fairclough, Brenda M. J. Price, Elena S. Casey and J. C. Smith
|title=Determinants of T box protein specificity
|journal=Development
|date=2001
|volume=128
|issue=19
|pages=3749-3758
|url=http://dev.biologists.org/content/develop/128/19/3749.full.pdf?download=true
|arxiv=
|bibcode=
|doi=
|pmid=11585801
|accessdate=17 November 2018 }}</ref>

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] AACGTT (T box) [...]."<ref name=Zhang2014/> T box, Table 2, number 335, order 247, present, AACGTT[228].

"Despite sequence variations within the Tbox DBD between family members, all members of the family appear to bind to the same DNA consensus sequence, TCACACCT. In several in vitro binding-site selection studies, members of the Tbox family were found to bind preferentially sequences containing two or more of these core motifs arranged in various orientations; however, the significance of such double sites in vivo is uncertain, as most Tbox target gene sites have been found to contain only a single consensus motif (18)."<ref name=Liu>{{ cite journal
|author=Ce Feng Liu, Gabriel S. Brandt, Quyen Q. Hoang, Natalia Naumova, Vanja Lazarevic, Eun Sook Hwang, Job Dekker, Laurie H. Glimcher, Dagmar Ringe, and Gregory A. Petsko
|title=Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites
|journal=Proceedings of the National Academy of Sciences of the USA
|date=25 October 2016
|volume=113
|issue=43
|pages=E6572-E6581
|url=https://www.pnas.org/content/113/43/E6572
|arxiv=
|bibcode=
|doi=10.1073/pnas.1613914113
|pmid=27791029
|accessdate=28 August 2020 }}</ref>

==Unfolded protein response elements==
{{main|Unfolded protein response element gene transcriptions}}
X-box binding protein 1s "XBP1s binds to the [unfolded protein response] UPR element (UPRE) containing the consensus sequence TGACGTGG/A and regulates the transcription of target genes in a cell type- and condition-specific manner (Yamamoto et al., 2004)."<ref name=So>{{ cite journal
|author=Jae-Seon So
|title=Roles of Endoplasmic Reticulum Stress in Immune Responses
|journal=Molecules and Cells
|date=31 August 2018
|volume=41
|issue=8
|pages=705-16
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125421/
|arxiv=
|bibcode=
|doi=10.14348/molcells.2018.0241
|pmid=30078231
|accessdate=5 September 2020 }}</ref> Unfolded protein response element, Table 2, number 348, order 33, TGACGTG(G/A)[14].

==Z boxes==
{{main|Z box gene transcriptions}}
"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of ''RbcS1A'' (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."<ref name=Song/> Z-box, Table 2, number 371, order 252, absent, ATACGTGT[9].

===Z box distal promoters===

Positive strand, positive direction: 5'-ACACGTGT-3' at 2962 and complement.

==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.

==ACE samplings==

Myeloblastosis, Table 2, number 252, order 159, present, CACGT[289].

For the Basic programs (starting with SuccessablesACE.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, negative direction, is SuccessablesACE--.bas, looking for CACGT, 5, CACGT at 3429, CACGT at 2863, CACGT at 2081, CACGT at 1535, CACGT at 1470,
# positive strand, negative direction, is SuccessablesACE+-.bas, looking for CACGT, 3, CACGT at 1772, CACGT at 531, CACGT at 342,
# negative strand, positive direction, is SuccessablesACE-+.bas, looking for CACGT, 2, CACGT at 3254, CACGT at 569,
# positive strand, positive direction, is SuccessablesACE++.bas, looking for CACGT, 13, CACGT at 3960, CACGT at 3883, CACGT at 3464, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, CACGT at 1786, CACGT at 1218, CACGT at 783, CACGT at 546,
# inverse complement, negative strand, negative direction, is SuccessablesACEci--.bas, looking for ACGTG, 8, ACGTG at 4339, ACGTG at 3288, ACGTG at 2760, ACGTG at 2425, ACGTG at 1999, ACGTG at 1718, ACGTG at 1346, ACGTG at 1338.
# inverse complement, negative strand, positive direction, is SuccessablesACEci-+.bas, looking for ACGTG, 1, ACGTG at 570.
# inverse complement, positive strand, negative direction, is SuccessablesACEci+-.bas, looking for ACGTG, 1, ACGTG at 4237.
# inverse complement, positive strand, positive direction, is SuccessablesACEci++.bas, looking for ACGTG, 10, ACGTG at 4342, ACGTG at 3884, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, ACGTG at 1821, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, ACGTG at 547.

===ACE UTR promoters===
# Negative strand, negative direction: ACGTG at 4339, CACGT at 3429, ACGTG at 3288, CACGT at 2863.
# Positive strand, negative direction: ACGTG at 4237.

===ACE core promoters===
{{main|Core promoter gene transcriptions}}
# Positive strand, positive direction: ACGTG at 4342.

===ACE proximal promoters===
{{main|Proximal promoter gene transcriptions}}
# Negative strand, negative direction: ACGTG at 2760.

===ACE distal promoters===
{{main|Distal promoter gene transcriptions}}
# Negative strand, negative direction: ACGTG at 2425, ACGTG at 1999, ACGTG at 1718, CACGT at 2081, CACGT at 1535, CACGT at 1470, ACGTG at 1346, ACGTG at 1338.
# Positive strand, negative direction: CACGT at 1772, CACGT at 531, CACGT at 342.


# Negative strand, positive direction: CACGT at 3254, ACGTG at 570, CACGT at 569.
# Positive strand, positive direction: CACGT at 3960, ACGTG at 3884, CACGT at 3883, CACGT at 3464, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, ACGTG at 1821, CACGT at 1786, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, CACGT at 1218, CACGT at 783, ACGTG at 547, CACGT at 546.

==ACGT samplings==

# Negative strand, negative direction: 24, ACGT at 4338, ACGT at 4330, ACGT at 4315, ACGT at 4245, ACGT at 3771, ACGT at 3429, ACGT at 3287, ACGT at 2863, ACGT at 2759, ACGT at 2735, ACGT at 2424, ACGT at 2400, ACGT at 2081, ACGT at 1998, ACGT at 1974, ACGT at 1717, ACGT at 1535, ACGT at 1494, ACGT at 1470, ACGT at 1345, ACGT at 1337, ACGT at 1321, ACGT at 1030, ACGT at 150.
# Positive strand, negative direction: 4, ACGT at 4236, ACGT at 1772, ACGT at 531, ACGT at 342.
# Negative strand, positive direction: 2, ACGT at 3254, ACGT at 569.
# Positive strand, positive direction: 44, ACGT at 4341, ACGT at 4315, ACGT at 3960, ACGT at 3883, ACGT at 3829, ACGT at 3464, ACGT at 3459, ACGT at 3400, ACGT at 3341, ACGT at 3320, ACGT at 3279, ACGT at 3268, ACGT at 3230, ACGT at 3142, ACGT at 3070, ACGT at 3061, ACGT at 2960, ACGT at 2857, ACGT at 2800, ACGT at 2743, ACGT at 2719, ACGT at 2690, ACGT at 2681, ACGT at 2350, ACGT at 2334, ACGT at 2326, ACGT at 2204, ACGT at 2063, ACGT at 1935, ACGT at 1820, ACGT at 1786, ACGT at 1613, ACGT at 1505, ACGT at 1470, ACGT at 1370, ACGT at 1218, ACGT at 1119, ACGT at 783, ACGT at 656, ACGT at 546, ACGT at 531, ACGT at 436, ACGT at 224, ACGT at 192.

Complement inverse of ACGT is ACGT.

===ACGT (4560-2846) UTRs===

# Negative strand, negative direction: ACGT at 4338, ACGT at 4330, ACGT at 4315, ACGT at 4245, ACGT at 3771, ACGT at 3429, ACGT at 3287, ACGT at 2863.
# Positive strand, negative direction: ACGT at 4236.

===ACGT positive direction (4445-4265) core promoters===

# Positive strand, positive direction: ACGT at 4341, ACGT at 4315.

===ACGT negative direction (2811-2596) proximal promoters===

# Negative strand, negative direction: ACGT at 2759, ACGT at 2735.

===ACGT negative direction (2596-1) distal promoters===

# Negative strand, negative direction: ACGT at 2424, ACGT at 2400, ACGT at 2081, ACGT at 1998, ACGT at 1974, ACGT at 1717, ACGT at 1535, ACGT at 1494, ACGT at 1470, ACGT at 1345, ACGT at 1337, ACGT at 1321, ACGT at 1030, ACGT at 150.
# Positive strand, negative direction: 4ACGT at 1772, ACGT at 531, ACGT at 342.

===ACGT positive direction (4050-1) distal promoters===

# Negative strand, positive direction: ACGT at 3254, ACGT at 569.
# Positive strand, positive direction: ACGT at 3960, ACGT at 3883, ACGT at 3829, ACGT at 3464, ACGT at 3459, ACGT at 3400, ACGT at 3341, ACGT at 3320, ACGT at 3279, ACGT at 3268, ACGT at 3230, ACGT at 3142, ACGT at 3070, ACGT at 3061, ACGT at 2960, ACGT at 2857, ACGT at 2800, ACGT at 2743, ACGT at 2719, ACGT at 2690, ACGT at 2681, ACGT at 2350, ACGT at 2334, ACGT at 2326, ACGT at 2204, ACGT at 2063, ACGT at 1935, ACGT at 1820, ACGT at 1786, ACGT at 1613, ACGT at 1505, ACGT at 1470, ACGT at 1370, ACGT at 1218, ACGT at 1119, ACGT at 783, ACGT at 656, ACGT at 546, ACGT at 531, ACGT at 436, ACGT at 224, ACGT at 192.

==ACGT random samplings==

# ACGTr0: 19, ACGT at 4342, ACGT at 3683, ACGT at 3208, ACGT at 3106, ACGT at 3065, ACGT at 2914, ACGT at 2891, ACGT at 2636, ACGT at 2592, ACGT at 2537, ACGT at 2398, ACGT at 2168, ACGT at 1934, ACGT at 1737, ACGT at 1356, ACGT at 904, ACGT at 840, ACGT at 419, ACGT at 397.
# ACGTr1: 17, ACGT at 4489, ACGT at 4174, ACGT at 4029, ACGT at 3788, ACGT at 3715, ACGT at 3428, ACGT at 3298, ACGT at 3164, ACGT at 3027, ACGT at 2263, ACGT at 1856, ACGT at 1594, ACGT at 1511, ACGT at 1457, ACGT at 1184, ACGT at 495, ACGT at 191.
# ACGTr2: 16, ACGT at 4460, ACGT at 4187, ACGT at 3708, ACGT at 3409, ACGT at 3194, ACGT at 1861, ACGT at 1696, ACGT at 1659, ACGT at 1603, ACGT at 1593, ACGT at 1343, ACGT at 931, ACGT at 483, ACGT at 434, ACGT at 98, ACGT at 63.
# ACGTr3: 12, ACGT at 4448, ACGT at 4080, ACGT at 3768, ACGT at 3246, ACGT at 3204, ACGT at 2750, ACGT at 2638, ACGT at 2583, ACGT at 1933, ACGT at 1482, ACGT at 1436, ACGT at 629.
# ACGTr4: 20, ACGT at 4503, ACGT at 4410, ACGT at 4365, ACGT at 4332, ACGT at 3911, ACGT at 3507, ACGT at 3142, ACGT at 2729, ACGT at 2660, ACGT at 2637, ACGT at 2403, ACGT at 2313, ACGT at 2286, ACGT at 1605, ACGT at 1452, ACGT at 899, ACGT at 659, ACGT at 546, ACGT at 385, ACGT at 291.
# ACGTr5: 12, ACGT at 4478, ACGT at 4401, ACGT at 4067, ACGT at 3665, ACGT at 3125, ACGT at 1586, ACGT at 1537, ACGT at 903, ACGT at 843, ACGT at 711, ACGT at 265, ACGT at 58.
# ACGTr6: 17, ACGT at 4422, ACGT at 4081, ACGT at 3444, ACGT at 3433, ACGT at 3380, ACGT at 2925, ACGT at 2904, ACGT at 2674, ACGT at 2528, ACGT at 2279, ACGT at 2106, ACGT at 1863, ACGT at 1636, ACGT at 836, ACGT at 653, ACGT at 609, ACGT at 564.
# ACGTr7: 19, ACGT at 4257, ACGT at 4032, ACGT at 3830, ACGT at 3810, ACGT at 3533, ACGT at 3402, ACGT at 2858, ACGT at 2805, ACGT at 2703, ACGT at 1855, ACGT at 1717, ACGT at 1574, ACGT at 1396, ACGT at 1391, ACGT at 1331, ACGT at 944, ACGT at 849, ACGT at 696, ACGT at 402.
# ACGTr8: 12, ACGT at 4533, ACGT at 4065, ACGT at 3927, ACGT at 3750, ACGT at 3601, ACGT at 3567, ACGT at 3542, ACGT at 3226, ACGT at 2984, ACGT at 2150, ACGT at 913, ACGT at 897.
# ACGTr9: 9, ACGT at 3687, ACGT at 3509, ACGT at 2965, ACGT at 2698, ACGT at 1858, ACGT at 1186, ACGT at 874, ACGT at 796, ACGT at 246.

===ACGTr arbitrary (evens) (4560-2846) UTRs===

# ACGTr0: ACGT at 4342, ACGT at 3683, ACGT at 3208, ACGT at 3106, ACGT at 3065, ACGT at 2914, ACGT at 2891.
# ACGTr2: ACGT at 4460, ACGT at 4187, ACGT at 3708, ACGT at 3409, ACGT at 3194.
# ACGTr4: ACGT at 4503, ACGT at 4410, ACGT at 4365, ACGT at 4332, ACGT at 3911, ACGT at 3507, ACGT at 3142.
# ACGTr6: ACGT at 4422, ACGT at 4081, ACGT at 3444, ACGT at 3433, ACGT at 3380, ACGT at 2925, ACGT at 2904.
# ACGTr8: ACGT at 4533, ACGT at 4065, ACGT at 3927, ACGT at 3750, ACGT at 3601, ACGT at 3567, ACGT at 3542, ACGT at 3226, ACGT at 2984.

===ACGTr alternate (odds) (4560-2846) UTRs===

# ACGTr1: ACGT at 4489, ACGT at 4174, ACGT at 4029, ACGT at 3788, ACGT at 3715, ACGT at 3428, ACGT at 3298, ACGT at 3164, ACGT at 3027.
# ACGTr3: ACGT at 4448, ACGT at 4080, ACGT at 3768, ACGT at 3246, ACGT at 3204
# ACGTr5: ACGT at 4478, ACGT at 4401, ACGT at 4067, ACGT at 3665, ACGT at 3125.
# ACGTr7: ACGT at 4257, ACGT at 4032, ACGT at 3830, ACGT at 3810, ACGT at 3533, ACGT at 3402, ACGT at 2858.
# ACGTr9: ACGT at 3687, ACGT at 3509, ACGT at 2965.

===ACGTr arbitrary positive direction (odds) (4445-4265) core promoters===

# ACGTr5: ACGT at 4401.

===ACGTr alternate positive direction (evens) (4445-4265) core promoters===

# ACGTr0: ACGT at 4342.
# ACGTr4: ACGT at 4410, ACGT at 4365, ACGT at 4332.
# ACGTr6: ACGT at 4422.

===ACGTr arbitrary negative direction (evens) (2811-2596) proximal promoters===

# ACGTr0: ACGT at 2636.
# ACGTr4: ACGT at 2729, ACGT at 2660, ACGT at 2637.
# ACGTr6: ACGT at 2674.

===ACGTr alternate negative direction (odds) (2811-2596) proximal promoters===

# ACGTr3: ACGT at 2750, ACGT at 2638.
# ACGTr7: ACGT at 2805, ACGT at 2703.
# ACGTr9: ACGT at 2698.

===ACGTr arbitrary positive direction (odds) (4265-4050) proximal promoters===

# ACGTr1: ACGT at 4174.
# ACGTr3: ACGT at 4080.
# ACGTr5: ACGT at 4067.
# ACGTr7: ACGT at 4257.

===ACGTr alternate positive direction (evens) (4265-4050) proximal promoters===

# ACGTr2: ACGT at 4187.
# ACGTr6: ACGT at 4081.
# ACGTr8: ACGT at 4065.

===ACGTr arbitrary negative direction (evens) (2596-1) distal promoters===

# ACGTr0: ACGT at 2592, ACGT at 2537, ACGT at 2398, ACGT at 2168, ACGT at 1934, ACGT at 1737, ACGT at 1356, ACGT at 904, ACGT at 840, ACGT at 419, ACGT at 397.
# ACGTr2: ACGT at 1861, ACGT at 1696, ACGT at 1659, ACGT at 1603, ACGT at 1593, ACGT at 1343, ACGT at 931, ACGT at 483, ACGT at 434, ACGT at 98, ACGT at 63.
# ACGTr4: ACGT at 2403, ACGT at 2313, ACGT at 2286, ACGT at 1605, ACGT at 1452, ACGT at 899, ACGT at 659, ACGT at 546, ACGT at 385, ACGT at 291.
# ACGTr6: ACGT at 2528, ACGT at 2279, ACGT at 2106, ACGT at 1863, ACGT at 1636, ACGT at 836, ACGT at 653, ACGT at 609, ACGT at 564.
# ACGTr8: ACGT at 2150, ACGT at 913, ACGT at 897.

===ACGTr alternate negative direction (odds) (2596-1) distal promoters===

# ACGTr1: ACGT at 2263, ACGT at 1856, ACGT at 1594, ACGT at 1511, ACGT at 1457, ACGT at 1184, ACGT at 495, ACGT at 191.
# ACGTr3: ACGT at 2583, ACGT at 1933, ACGT at 1482, ACGT at 1436, ACGT at 629.
# ACGTr5: ACGT at 1586, ACGT at 1537, ACGT at 903, ACGT at 843, ACGT at 711, ACGT at 265, ACGT at 58.
# ACGTr7: ACGT at 1855, ACGT at 1717, ACGT at 1574, ACGT at 1396, ACGT at 1391, ACGT at 1331, ACGT at 944, ACGT at 849, ACGT at 696, ACGT at 402.
# ACGTr9: ACGT at 1858, ACGT at 1186, ACGT at 874, ACGT at 796, ACGT at 246.

===ACGTr arbitrary positive direction (odds) (4050-1) distal promoters===

# ACGTr1: ACGT at 4029, ACGT at 3788, ACGT at 3715, ACGT at 3428, ACGT at 3298, ACGT at 3164, ACGT at 3027, ACGT at 2263, ACGT at 1856, ACGT at 1594, ACGT at 1511, ACGT at 1457, ACGT at 1184, ACGT at 495, ACGT at 191.
# ACGTr3: ACGT at 3768, ACGT at 3246, ACGT at 3204, ACGT at 2750, ACGT at 2638, ACGT at 2583, ACGT at 1933, ACGT at 1482, ACGT at 1436, ACGT at 629.
# ACGTr5: ACGT at 3665, ACGT at 3125, ACGT at 1586, ACGT at 1537, ACGT at 903, ACGT at 843, ACGT at 711, ACGT at 265, ACGT at 58.
# ACGTr7: ACGT at 4032, ACGT at 3830, ACGT at 3810, ACGT at 3533, ACGT at 3402, ACGT at 2858, ACGT at 2805, ACGT at 2703, ACGT at 1855, ACGT at 1717, ACGT at 1574, ACGT at 1396, ACGT at 1391, ACGT at 1331, ACGT at 944, ACGT at 849, ACGT at 696, ACGT at 402.
# ACGTr9: ACGT at 3687, ACGT at 3509, ACGT at 2965, ACGT at 2698, ACGT at 1858, ACGT at 1186, ACGT at 874, ACGT at 796, ACGT at 246.

===ACGTr alternate positive direction (evens) (4050-1) distal promoters===

# ACGTr0: ACGT at 3683, ACGT at 3208, ACGT at 3106, ACGT at 3065, ACGT at 2914, ACGT at 2891, ACGT at 2636, ACGT at 2592, ACGT at 2537, ACGT at 2398, ACGT at 2168, ACGT at 1934, ACGT at 1737, ACGT at 1356, ACGT at 904, ACGT at 840, ACGT at 419, ACGT at 397.
# ACGTr2: ACGT at 3708, ACGT at 3409, ACGT at 3194, ACGT at 1861, ACGT at 1696, ACGT at 1659, ACGT at 1603, ACGT at 1593, ACGT at 1343, ACGT at 931, ACGT at 483, ACGT at 434, ACGT at 98, ACGT at 63.
# ACGTr4: ACGT at 3911, ACGT at 3507, ACGT at 3142, ACGT at 2729, ACGT at 2660, ACGT at 2637, ACGT at 2403, ACGT at 2313, ACGT at 2286, ACGT at 1605, ACGT at 1452, ACGT at 899, ACGT at 659, ACGT at 546, ACGT at 385, ACGT at 291.
# ACGTr6: ACGT at 3444, ACGT at 3433, ACGT at 3380, ACGT at 2925, ACGT at 2904, ACGT at 2674, ACGT at 2528, ACGT at 2279, ACGT at 2106, ACGT at 1863, ACGT at 1636, ACGT at 836, ACGT at 653, ACGT at 609, ACGT at 564.
# ACGTr8: ACGT at 3927, ACGT at 3750, ACGT at 3601, ACGT at 3567, ACGT at 3542, ACGT at 3226, ACGT at 2984, ACGT at 2150, ACGT at 913, ACGT at 897.

==ACGT analysis and results==
{{main|Complex locus A1BG and ZNF497#ACGTs}}
"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."<ref name=Hartmann/>

{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1) 
|-
| Reals || UTR || negative || 9 || 2 || 4.5 || 4.5 ± 3.5 (--8,+-1) 
|-
| Randoms || UTR || arbitrary negative || 35 || 10 || 3.5 || 3.2 ± 0.3 
|-
| Randoms || UTR || alternate negative || 29 || 10 || 2.9 || 3.2 ± 0.3 
|-
| Reals || Core || negative || 0 || 2 || 0 || 0 
|-
| Randoms || Core || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0 
|-
| Reals || Core || positive || 2 || 2 || 1 || 1 
|-
| Randoms || Core || arbitrary positive || 1 || 10 || 0.1 || 0.3
|-
| Randoms || Core || alternate positive || 5 || 10 || 0.5 || 0.3 
|-
| Reals || Proximal || negative || 2 || 2 || 1 || 1 
|-
| Randoms || Proximal || arbitrary negative || 5 || 10 || 0.5 || 0.5 
|-
| Randoms || Proximal || alternate negative || 5 || 10 || 0.5 || 0.5 
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0 
|-
| Randoms || Proximal || arbitrary positive || 4 || 10 || 0.4 || 0.35 
|-
| Randoms || Proximal || alternate positive || 3 || 10 || 0.3 || 0.35 
|-
| Reals || Distal || negative || 17 || 2 || 8.5 || 8.5 ± 5.5 (--14, -+3) 
|-
| Randoms || Distal || arbitrary negative || 44 || 10 || 4.4 || 3.95 ± 0.45
|-
| Randoms || Distal || alternate negative || 35 || 10 || 3.5 || 3.95 ± 0.45 
|-
| Reals || Distal || positive || 44 || 2 || 22 || 22 ± 20 (-+2,++42) 
|-
| Randoms || Distal || arbitrary positive || 61 || 10 || 6.1 || 6.7 ± 0.6 
|-
| Randoms || Distal || alternate positive || 73 || 10 || 7.3 || 6.7 ± 0.6 
|}

Comparison:

The occurrences of real ACGT cores and proximals are greater than the randoms, the UTRs and distal promoters overlap the randoms at the low occurrence ends. This suggests that the real ACGT cores and proximals are likely active or activable, but a few of the UTRs and distal promoters may be random.

==Conclusions==

An [[ACGT-containing element gene transcriptions|ACGT element]] is its own inverse complement. Random datasets had 5 to 9 elements (ACGT) per dataset in the UTR negative direction toward A1BG. The real dataset had 8 in the UTR for the negative strand and one on the positive strand. This suggests that the negative strand, negative direction real occurrences could be random, but the occurrence of only one on the positive strand is likely real.

The real positive direction core promoter from ZNF497 toward A1BG has two ACGT strands. In the positive transcription direction three of five random datasets had 1 or 2 ACGT sequences. But, the real sequences are at or within 4445 nucleotides from ZNF497, whereas the three random datasets are between 4445 and 4560: at 4489, 4448, and 4478 with the transcription start site at 4300 nts. The real promoters on the positive direction were only tested to 4445 nts from ZNF497. So the random datasets kept to the same constraint as the real tests only produced one core promoter at 4401. This excess of real core promoters in the positive direction suggests they are real.

Regarding proximal promoters, only two exist both in the negative direction. The random datasets (3) had five proximal promoters in the negative direction for an average just over one each. One had three sequences suggesting that only two real sequences could be random.

For distal promoters in the negative direction there are 17 real sequences. The random datasets had between 3 and 11 ACGT sequences in the arbitrary negative direction. For the arbitrary positive direction there were between 9 and 15 sequences.

The positive direction had 44 sequences. Both sides of A1BG are not included in the random results suggesting they are real.

For total ACGT occurrences: negative direction between ZSCAN22 and A1BG is 28 and positive direction is 44, but the random datasets had between 9 and 20. The excessive occurrences of ACGT in both directions suggests they are real.

==Purine and histidine biosynthesis pathways==

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of ''HIS4'' and ''PHO5'' regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].<ref name=Tang/>

==Acknowledgements==

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

==See also==
{{div col|colwidth=20em}}
* [[A1BG gene transcriptions]]
* [[Complex locus A1BG and ZNF497]]
{{Div col end}}

==References==
{{reflist|2}}

==External links==

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{{Gene project}}

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