ACGT-containing element gene transcriptions
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.  bZIP domains of both STF1 and HY5 have similar binding properties for recognizing ACGT-containing elements (ACEs).  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."
"The combination of an  ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."
"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)  were found around -114 and -570. The GC box has been found in promoters of many viral and cellular genes , 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  were found at -208 and -256. Two 8 bp sequences (CACGTCGC, CACGTAAC) which are similar to an ABA response element (ABRE, CACGTGGC)  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) ."
"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; Nijhawan et al., 2008)."

# ABA-response elements
"The ABA responsive element (ABRE) is a key cisregulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABAinduced genes in rice aleurone cells, suggesting other ABREs may exist."
"Many ABAinducible genes in various species contain a conserved cisregulatory ABA responsive element (ABRE) with the consensus sequence ACGTG(G/T)C (Hattori et al. 2002; Shen et al. 2004)."
"The ABRE contains the core sequence, ACGT, also known as the Gbox (Marcotte et al. 1989; YamaguchiShinozaki et al. 1990)."

## ABRE Core promoters
Positive strand, positive direction: 5'-ACGTGGC-3' at 4344 and complement.

## ABRE Proximal promoters
Positive strand, negative direction: 5'-ACGTGGC-3' at 4239 and complement.

## ABRE Distal promoters
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
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include  TACGTA (A box) ."

## A box proximal promoters
Negative direction: 5'-TACGTA-3' at 4246 and complement.

## A box distal promoters
Positive direction: 5'-TACGTA-3' at 3071 and complement.

# Abscisic acid-responsive elements
Abscisic acid-responsive elements (CACGTG).
"The  motif is bound by the transcription factor Pho4,  class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."
The Pho4 homodimer binds to DNA sequences containing the bHLH binding site 5'-CACGTG-3'.
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 .

## Pho4 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, and 5'-CACGTG-3' at 547 and complements.

## Phop distal promoters
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
"The putative ChREBP binding sites  ChoRE1 (CACGTGACCGGATCTTG, -324 to -308) and ChoRE2 (TCCGCCCCCATCACGTG, -298 to - 282) , where the 5-nt spacer  between the two E-boxes in ChoRE motifs ."

## 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
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include  GACGTC (C box) ."
Analysis "of the recombinant (soybean  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 . 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 ."

# C-boxes
Analysis "of the recombinant (soybean  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 . 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 ."
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.

# CRE boxes
"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."
The upstream activating sequence (UAS) for the Aca1p, the basic "leucine zipper (bZIP) transcription factor  involved in carbon source utilization" is 5'-TGACGTCA-3' the same as a CRE.
The upstream activating sequence (UAS) for the Sko1p, involved "in osmotic and oxidative stress responses" is 5'-TGACGTCA-3' the same as a CRE.

## CRE box proximal promoters
Negative strand, negative direction: 5'-TGACGTCA-3', 4317, and complement.

# Enhancer boxes

## 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
"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  4-CA."
The "perfect palindrome 5'-GCCACGTGGC-3' which is also known as the G-box motif."
"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".
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box) ."
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 ."

# GCN4 motifs
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include  a GCN4 motif, namely TGA(G/C)TCA ."

# Hex sequences
The Hex sequence is (TGACGTGGC).

# Hybrids
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
"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."

# 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
"hree potential metal response elements (MREs)  the E-boxes in the repeats, (TGCACGT with TGCRCNC being the consensus sequence; 17,18)."

## MRE proximal promoters
Negative strand, negative direction: 5'-ACGTGAG-3' at 4341 and complement.

## MRE distal promoters
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
"As a transcription factor, ORE1 was reported to bind to consensus DNA sequences of GTN{5,6}AC  or TCGT ."
Consensus sequences are 5'-(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G)-3' or 5'-T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)-3'.
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
Abscisic acid-responsive elements (CACGTG).
"The  motif is bound by the transcription factor Pho4,  class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."
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 .

## 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
Root specific elements (TGACGTCA).

# 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."
"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."

# T boxes
"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."
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include  AACGTT (T box) ."
"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)."

# Unfolded protein response elements
X-box binding protein 1s "XBP1s binds to the  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)."

# Z boxes
"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)."

## 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 Gbox (Marcotte et al. 1989; YamaguchiShinozaki et al. 1990)."
5'-ACGT-3'.
The consensus sequence for the ACGT-containing elements (ACEs) is 5'-CACGT-3'.

# Hypotheses
- A1BG has no ACEs in either promoter.

# ACE samplings
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
- Positive strand, positive direction: ACGTG at 4342.

## ACE proximal promoters
- Negative strand, negative direction: ACGTG at 2760.

## ACE distal promoters
- 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
"The combination of an  ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."
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 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 .

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