A box gene transcriptions
The GC boxes are not apparently associated with the A box, B box, C box, and D box.
"AS/T, serine/threonine-rich subdomain within the A box". "AQ, glutamine-rich subdomain within the A box".

# Consensus sequences

## Box A
"The human  TGFB1 promoter region contains two binding sequences for  AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."
"The human TGF-1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after  HG stimulation."

## A-box
"Because of their sessile lifestyle, plants have developed advanced mechanisms to cope with many forms of environmental stress conditions. Under changing environmental conditions, the adaptive responses of plants largely depend on the proper integration of light signaling and stress response pathways. Plants are equipped with multiple photoreceptors, including red/far-red light-absorbing phytochromes, blue/UV (UV)-A light-absorbing cryptochromes and phototropins, and the UV-B light-absorbing UV RESISTANCE LOCUS 8 (1, 2). The downstream component ELONGATED HYPOCOTYL 5 (HY5), a basic leucine zipper (bZIP) transcription factor (TF), mediates photoreceptor responses to promote photomorphogenesis (3). Recently, genome-wide gene expression analyses and chromatin immunoprecipitation (ChIP) studies have shown that HY5 is a higher hierarchical regulator of transcriptional networks for photomorphogenesis (4, 5). In particular, HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."
"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)."
"A majority of the plant bZIP proteins isolated to date recognize elements with an ACGT core (Foster et al., 1994)."
"Most recombinant bZIP proteins can interact with ACGT elements derived from different plant genes, albeit with different affinity. Systematic protein/DNA binding studies have shown that sequences flanking the ACGT core affect bZIP protein binding specificity. These studies have provided the basis for a concise ACGT nomenclature and defined high- affinity A-box, C-box, and G-box elements."
TACGTA is the A-box.

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

# Box A samplings
Box A 3-TGACTCT-5' was not found using "F" to locate any consensus sequences.
Hypothesis 1: A1BG is not transcribed by box A.
For the Basic programs testing consensus sequence 3'-TGACTCT-5' (starting with SuccessablesAbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox--.bas, looking for 3'-TGACTCT-5', 0.
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox-+.bas, looking for 3'-TGACTCT-5', 0.
- positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox+-.bas, looking for 3'-TGACTCT-5', 1, 3'-TGACTCT-5' at 2788.
- positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox++.bas, looking for 3'-TGACTCT-5', 0.
- complement, negative strand, negative direction is SuccessablesAboxc--.bas, looking for 3'-ACTGAGA-5', 1, 3'-ACTGAGA-5' at 2788.
- complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc-+.bas, looking for 3'-ACTGAGA-5', 0.
- complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxc+-.bas, looking for 3'-ACTGAGA-5', 0.
- complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc++.bas, looking for 3'-ACTGAGA-5', 0.
- inverse complement, negative strand, negative direction is SuccessablesAboxci--.bas, looking for 3'-AGAGTCA-5', 0.
- inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci-+.bas, looking for 3'-AGAGTCA-5', 1, 3'-AGAGTCA-5' at 2613.
- inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxci+-.bas, looking for 3'-AGAGTCA-5', 0.
- inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci++.bas, looking for 3'-AGAGTCA-5', 0.
- inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi--.bas, looking for 3'-TCTCAGT-5', 0.
- inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi-+.bas, looking for 3'-TCTCAGT-5', 0.
- inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0.
- inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613.

## Box A distal promoters
Positive strand, negative direction: TGACTCT at 2788.
Positive strand, positive direction: TCTCAGT at 2613.

# Box A random dataset samplings
- Aboxr0: 0.
- Aboxr1: 0.
- Aboxr2: 0.
- Aboxr3: 2, TGACTCT at 4481, TGACTCT at 2451.
- Aboxr4: 0.
- Aboxr5: 0.
- Aboxr6: 0.
- Aboxr7: 0.
- Aboxr8: 0.
- Aboxr9: 1, TGACTCT at 3523.
- Aboxr0ci: 0.
- Aboxr1ci: 0.
- Aboxr2ci: 0.
- Aboxr3ci: 0.
- Aboxr4ci: 0.
- Aboxr5ci: 0.
- Aboxr6ci: 3, AGAGTCA at 4503, AGAGTCA at 4449, AGAGTCA at 1109.
- Aboxr7ci: 0.
- Aboxr8ci: 0.
- Aboxr9ci: 0.

## Aboxr UTRs
- Aboxr6ci: AGAGTCA at 4503, AGAGTCA at 4449.

## Aboxr core promoters
- Aboxr3: TGACTCT at 4481.

## Aboxr distal promoters
- Aboxr6ci: AGAGTCA at 1109.
- Aboxr3: TGACTCT at 2451.
- Aboxr9: TGACTCT at 3523.

# Box A analysis and results
"The human TGF-1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after  HG stimulation."
Comparison:
The occurrences of box A consensus sequences are greater than the randoms. This suggests that the real box A consensus sequences are likely active or activable.

# A-boxes samplings
A box 5'-TACGTA-3' using "F" has one location between ZSCAN22 and A1BG and none between ZNF497 and A1BG.
Hypothesis 1: A1BG is not transcribed by an A-box.
For the Basic programs testing consensus sequence 3'-TACGTA-5' (starting with SuccessablesAbox1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- Negative strand, negative direction: 1, TACGTA at 4246.
- Negative strand, positive direction: 0.
- Positive strand, negative direction: 0.
- Positive strand, positive direction: 1, TACGTA at 3071.
- complement inverse is TACGTA.

## A-box UTRs
Negative strand, negative direction: TACGTA at 4246.

## A-box distal promoters
Positive strand, positive direction: TACGTA at 3071.

## A-box random dataset samplings
- Aboxr0: 1, TACGTA at 398.
- Aboxr1: 0.
- Aboxr2: 0.
- Aboxr3: 0.
- Aboxr4: 0.
- Aboxr5: 1, TACGTA at 3126.
- Aboxr6: 1, TACGTA at 2107.
- Aboxr7: 0.
- Aboxr8: 0.
- Aboxr9: 1, TACGTA at 3688.

## Aboxr distal promoters
- Aboxr0: TACGTA at 398.
- Aboxr6: TACGTA at 2107.
- Aboxr5: TACGTA at 3126.
- Aboxr9: TACGTA at 3688.

# Discussion
For box A (TGACTCT) there is a consensus sequence on either side of A1BG whereas the random datasets have only 0.3 on either side.
In the A1BG promoters, the consensus sequence for A box: TACGTA occurs in the negative direction UTR at 4246 nucleotides from ZSCAN22 and the positive direction distal promoter at 3071 nucleotides from ZNF497.
For the random datasets, it occurs only in the distal promoters at 398 or 2107 (two out of ten datasets) of the assigned negative direction and at 3126 or 3688 (two out of ten datasets) of the assigned positive direction.
The real promoters have twice as many consensus sequences relative to any random dataset with a result and the real promoters have them located in the UTR or distal promoter instead of just the distal promoter, which suggests they are real rather than random.

# A-boxes analysis and results
In particular, HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."
Comparison:
The occurrences of real A-boxes are greater than the randoms. This suggests that the real A-boxes are likely active or activable.

# Light signaling and stress response pathways
"Under changing environmental conditions, the adaptive responses of plants largely depend on the proper integration of light signaling and stress response pathways."
"In particular, HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."

# PKC-dependent pathway
"The human  TGFB1 promoter region contains two binding sequences for  AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."

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