W box gene transcriptions
"Consistent with its role as a transcriptional repressor, OsWRKY71 binds specifically to functionally defined TGAC-containing W boxes of the Amy32b promoter in electrophoretic mobility shift assays (Zhang et al. 2004)."
"Details of auto-regulation or cross-regulation by WRKY factors were provided for the parsley group I member PcWRKY1 and its ortholog AtWRKY33 . In response to PAMP treatment PcWRKY1 transcripts accumulate rapidly and transiently . AtWRKY33 is activated with similar kinetics by defense-related stimuli . This rapid response is mediated by a conserved arrangement of three synergistically acting W boxes (WABC). Chromatin immunoprecipitation (ChIP) revealed that in vivo these orthologous W boxes are constitutively occupied by WRKY proteins ."
"The synthesis of SA and the expression of NPR1, a key regulator of some PAMP-triggered responses, appear to be partly controlled by WRKY factors. NPR1 is regulated by WRKY TFs interacting with two W box elements in its 50UTR . Defense-associated SA production is strongly dependent on pathogen-inducible expression of ICS1 . This gene is a likely target of WRKY TFs, as its promoter is enriched for W boxes."
A "missense mutation within its WRKY domain results in conditional activation of defense responses and loss of in vitro binding to W boxes suggesting a negative role of this factor in defense signaling ."
Functionality and conservation of the W-box element across plant species shown by gel shift experiments, random binding site selection, yeast one-hybrid screens and co-transfection assays performed with many different WRKY proteins and In silico-based studies have identified clusters of W-boxes in stress-inducible promoters, where the binding of WRKY proteins to W-boxes is a feature of both biotic and abiotic stress responses, together with other plant processes such as germination. It has also been shown that multiple W-boxes have a synergistic effect on transcription.
Almost all WRKY transcription factors bind preferentially to W-boxes, and since their discovery, this has raised the question as to how they show specificity for the promoters of their target genes. Although the W-box core is required, adjacent sequences also play a role in determining binding-site preference. Recent evidence suggests that the TGAC core is more degenerate, composed of a guanine adenine cytosine (GAC) core, and the upstream thymine and downstream pyrimidine flanking sequences help dictate recognition by specific WRKY factors. Basic residues of the WRKY protein domain also are believed to recognize the phosphate backbone of the cis-element.
The solution structure of the C-terminal WRKY domain of Arabidopsis WRKY4 in complex with the W-box DNA has been determined by NMR. A four-stranded -sheet enters the major groove of DNA in a structure called the -wedge, where the sheet is nearly perpendicular to the DNA helical ais: as predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA.

# WRKY
WRKY family of genes contain the common degenerate nucleotide sequence: WRKY, or W = A or T (U) , R = A or G , K = G or T (U) , Y = C or T (U) .
"Plant immune responses are associated with the concerted modulation of a large number of different WRKY transcripts and proteins . Upon triggering of SA-dependent defenses, at least 49 AtWRKY genes exhibited differential regulation representing separate waves of transcript accumulation or repression . Their promoters are statistically enriched for W boxes, suggesting that they are autoregulated or controlled by other WRKY proteins ."
"Some architectural features of the WRKY web are emerging. As motif D containing group I WRKY TFs can be phosphorylated by MAP-kinases, they are likely to serve as the first WRKY proteins activated in response to PAMP-triggered MAPK signaling. Their targets may include the IIe WRKY genes AtWRKY22 and AtWRKY29, which are upregulated by a PAMP-induced MAPK cascade and contain multiple W boxes within their respective promoters ."

# Consensus sequences
The "presence of WRKY TF binding sites (C/TTGACC/T, W boxes) in numerous co-regulated Arabidopsis defense gene promoters provided circumstantial evidence that zinc-finger-type WRKY factors play a broad and pivotal role in regulating defenses ."
The W box is a DNA cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of WRKY transcription factors.

# W box samplings
For the Basic programs (starting with SuccessablesWbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
- negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesWbox--.bas, looking for 3'-(C/T)TGAC(C/T)-5', 5, 3'-CTGACT-5', 17, 3'-TTGACT-5', 130, 3'-TTGACT-5', 307, 3'-CTGACT-5', 1935, 3'-CTGACC-5', 3749,
- positive strand in the negative direction is SuccessablesWbox+-.bas, looking for 3'-(C/T)TGAC(C/T)-5', 1, 3'-CTGACC-5', 734,
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesWbox-+.bas, looking for 3'-(C/T)TGAC(C/T)-5', 6, 3'-CTGACC-5', 1662, 3'-CTGACC-5', 2213, 3'-TTGACC-5', 2873, 3'-CTGACT-5', 2945, 3'-TTGACC-5', 4018, 3'-CTGACC-5', 4216,
- positive strand in the positive direction is SuccessablesWbox++.bas, looking for 3'-(C/T)TGAC(C/T)-5', 3, 3'-TTGACC-5', 1953, 3'-CTGACT-5', 2674, 3'-TTGACT-5', 3735,
- complement, negative strand, negative direction is SuccessablesWboxc--.bas, looking for 3'-(A/G)ACTG(A/G)-5', 1, 3'-GACTGG-5', 734,
- complement, negative strand, positive direction is SuccessablesWboxc-+.bas, looking for 3'-(A/G)ACTG(A/G)-5', 3, 3'-AACTGG-5', 1953, 3'-GACTGA-5', 2674, 3'-AACTGA-5', 3735,
- complement, positive strand, negative direction is SuccessablesWboxc+-.bas, looking for 3'-(A/G)ACTG(A/G)-5', 5, 3'-GACTGA-5', 17, 3'-AACTGA-5', 130, 3'-AACTGA-5', 307, 3'-GACTGA-5', 1935, 3'-GACTGG-5', 3749,
- complement, positive strand, positive direction is SuccessablesWboxc++.bas, looking for 3'-(A/G)ACTG(A/G)-5', 6, 3'-GACTGG-5', 1662, 3'-GACTGG-5', 2213, 3'-AACTGG-5', 2873, 3'-GACTGA-5', 2945, 3'-AACTGG-5', 4018, 3'-GACTGG-5', 4216,
- inverse complement, negative strand, negative direction is SuccessablesWboxci--.bas, looking for 3'-(A/G)GTCA(A/G)-5', 2, 3'-GGTCAG-5', 1353, 3'-GGTCAA-5', 4416,
- inverse complement, negative strand, positive direction is SuccessablesWboxci-+.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-AGTCAG-5', 2101, 3'-GGTCAG-5', 2221, 3'-AGTCAG-5', 2608, 3'-AGTCAA-5', 2614, 3'-AGTCAG-5', 2619, 3'-GGTCAG-5', 4270,
- inverse complement, positive strand, negative direction is SuccessablesWboxci+-.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-GGTCAG-5', 440, 3'-GGTCAG-5', 577, 3'-GGTCAG-5', 713, 3'-GGTCAG-5', 2249, 3'-GGTCAG-5', 2586, 3'-GGTCAA-5', 4308,
- inverse complement, positive strand, positive direction is SuccessablesWboxci++.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-GGTCAG-5', 2025, 3'-AGTCAG-5', 2099, 3'-GGTCAG-5', 2606, 3'-GGTCAG-5', 2997, 3'-GGTCAG-5', 3083, 3'-GGTCAA-5', 3380,
- inverse, negative strand, negative direction, is SuccessablesWboxi--.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-CCAGTC-5', 440, 3'-CCAGTC-5', 577, 3'-CCAGTC-5', 713, 3'-CCAGTC-5', 2249, 3'-CCAGTC-5', 2586, 3'-CCAGTT-5', 4308,
- inverse, negative strand, positive direction, is SuccessablesWboxi-+.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-CCAGTC-5', 2025, 3'-TCAGTC-5', 2099, 3'-CCAGTC-5', 2606, 3'-CCAGTC-5', 2997, 3'-CCAGTC-5', 3083, 3'-CCAGTT-5', 3380,
- inverse, positive strand, negative direction, is SuccessablesWboxi+-.bas, looking for 3'-(C/T)CAGT(C/T)-5', 2, 3'-CCAGTC-5', 1353, 3'-CCAGTT-5', 4416,
- inverse, positive strand, positive direction, is SuccessablesWboxi++.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-TCAGTC-5', 2101, 3'-CCAGTC-5', 2221, 3'-TCAGTC-5', 2608, 3'-TCAGTT-5', 2614, 3'-TCAGTC-5', 2619, 3'-CCAGTC-5', 4270.

## Wbox (4560-2846) UTRs
- Negative strand, negative direction: CTGACC at 3749.
- Negative strand, negative direction: GGTCAA at 4416.
- Positive strand, negative direction: GGTCAA at 4308.

## Wbox positive direction (4445-4265) core promoters
- Negative strand, positive direction: GGTCAG at 4270.

## Wbox positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: CTGACC at 4216.

## Wbox negative direction (2596-1) distal promoters
- Negative strand, negative direction: CTGACT at 1935, TTGACT at 307, TTGACT at 130, CTGACT at 17.
- Negative strand, negative direction: GGTCAG at 1353.
- Positive strand, negative direction: CTGACC at 734.
- Positive strand, negative direction: GGTCAG at 2586, GGTCAG at 2249, GGTCAG at 713, GGTCAG at 577, GGTCAG at 440.

## Wbox positive direction (4050-1) distal promoters
- Negative strand, positive direction: TTGACC at 4018, CTGACT at 2945, TTGACC at 2873, CTGACC at 2213, CTGACC at 1662.
- Negative strand, positive direction: AGTCAG at 2619, AGTCAA at 2614, AGTCAG at 2608, GGTCAG at 2221, AGTCAG at 2101.
- Positive strand, positive direction: TTGACT at 3735, CTGACT at 2674, TTGACC at 1953.
- Positive strand, positive direction: GGTCAA at 3380, GGTCAG at 3083, GGTCAG at 2997, GGTCAG at 2606, AGTCAG at 2099, GGTCAG at 2025.

# W box random dataset samplings
- Wboxr0: 6, TTGACC at 4380, TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
- Wboxr1: 5, TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.
- Wboxr2: 4, CTGACC at 3755, CTGACC at 3580, TTGACT at 1736, TTGACC at 853.
- Wboxr3: 4, TTGACT at 4479, CTGACC at 4438, TTGACC at 3102, CTGACT at 1141.
- Wboxr4: 7, TTGACT at 2961, TTGACC at 2892, TTGACT at 2539, TTGACC at 2131, CTGACT at 1980, CTGACT at 1922, TTGACC at 344.
- Wboxr5: 1, TTGACT at 1914.
- Wboxr6: 3, CTGACT at 4233, TTGACC at 2398, TTGACT at 2043.
- Wboxr7: 2, CTGACC at 3140, TTGACC at 898.
- Wboxr8: 2, TTGACC at 1241, TTGACC at 776.
- Wboxr9: 3, CTGACC at 4209, TTGACT at 4205, CTGACT at 3521.
- Wboxr0ci: 3, AGTCAA at 4044, GGTCAA at 1985, GGTCAG at 846.
- Wboxr1ci: 4, GGTCAA at 4484, AGTCAA at 3855, GGTCAA at 2778, GGTCAG at 1751.
- Wboxr2ci: 9, AGTCAA at 4375, GGTCAG at 3906, AGTCAA at 3850, GGTCAA at 3164, AGTCAG at 2900, GGTCAA at 2186, GGTCAG at 468, GGTCAA at 142, GGTCAG at 24.
- Wboxr3ci: 4, GGTCAG at 3506, GGTCAG at 2239, GGTCAA at 1052, GGTCAA at 601.
- Wboxr4ci: 3, AGTCAA at 3240, AGTCAA at 3119, AGTCAA at 986.
- Wboxr5ci: 3, AGTCAA at 3608, AGTCAG at 1920, AGTCAG at 1355.
- Wboxr6ci: 6, AGTCAA at 4504, AGTCAA at 4450, GGTCAA at 2737, AGTCAG at 2125, GGTCAA at 1833, AGTCAG at 394.
- Wboxr7ci: 1, GGTCAA at 4458.
- Wboxr8ci: 4, AGTCAA at 4172, GGTCAA at 3494, GGTCAA at 3434, GGTCAA at 2695.
- Wboxr9ci: 7, GGTCAA at 4380, AGTCAA at 3950, AGTCAG at 3359, GGTCAA at 3056, AGTCAA at 2475, GGTCAG at 2057, AGTCAG at 107.

## Wboxr arbitrary (evens) (4560-2846) UTRs
- Wboxr0: TTGACC at 4380, TTGACT at 4031, CTGACT at 3270.
- Wboxr2: CTGACC at 3755, CTGACC at 3580.
- Wboxr6: CTGACT at 4233.
- Wboxr4: TTGACT at 2961, TTGACC at 2892.
- Wboxr0ci: AGTCAA at 4044.
- Wboxr2ci: AGTCAA at 4375, GGTCAG at 3906, AGTCAA at 3850, GGTCAA at 3164, AGTCAG at 2900.
- Wboxr4ci: AGTCAA at 3240, AGTCAA at 3119.
- Wboxr6ci: AGTCAA at 4504, AGTCAA at 4450.
- Wboxr8ci: AGTCAA at 4172, GGTCAA at 3494, GGTCAA at 3434.

## Wboxr alternate (odds) (4560-2846) UTRs
- Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937.
- Wboxr3: TTGACT at 4479, CTGACC at 4438, TTGACC at 3102.
- Wboxr7: CTGACC at 3140.
- Wboxr9: CTGACC at 4209, TTGACT at 4205, CTGACT at 3521.
- Wboxr1ci: GGTCAA at 4484, AGTCAA at 3855.
- Wboxr3ci: GGTCAG at 3506.
- Wboxr5ci: AGTCAA at 3608.
- Wboxr7ci: GGTCAA at 4458.
- Wboxr9ci: GGTCAA at 4380, AGTCAA at 3950, AGTCAG at 3359, GGTCAA at 3056.

## Wboxr arbitrary positive direction (odds) (4445-4265) core promoters
- Wboxr3: CTGACC at 4438.
- Wboxr9ci: GGTCAA at 4380.

## Wboxr alternate positive direction (evens) (4445-4265) core promoters
- Wboxr0: TTGACC at 4380.
- Wboxr2ci: AGTCAA at 4375.

## Wboxr arbitrary negative direction (evens) (2811-2596) proximal promoters
- Wboxr6ci: GGTCAA at 2737.
- Wboxr8ci: GGTCAA at 2695.

## Wboxr alternate negative direction (odds) (2811-2596) proximal promoters
- Wboxr1ci: GGTCAA at 2778.

## Wboxr arbitrary positive direction (odds) (4265-4050) proximal promoters
- Wboxr9: CTGACC at 4209, TTGACT at 4205.

## Wboxr alternate positive direction (evens) (4265-4050) proximal promoters
- Wboxr6: CTGACT at 4233.
- Wboxr8ci: AGTCAA at 4172.

## Wboxr arbitrary negative direction (evens) (2596-1) distal promoters
- Wboxr0: CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
- Wboxr2: TTGACT at 1736, TTGACC at 853.
- Wboxr4: TTGACT at 2539, TTGACC at 2131, CTGACT at 1980, CTGACT at 1922, TTGACC at 344.
- Wboxr6: TTGACC at 2398, TTGACT at 2043.
- Wboxr8: TTGACC at 1241, TTGACC at 776.
- Wboxr0ci: GGTCAA at 1985, GGTCAG at 846.
- Wboxr2ci: GGTCAA at 2186, GGTCAG at 468, GGTCAA at 142, GGTCAG at 24.
- Wboxr4ci: AGTCAA at 986.
- Wboxr6ci: AGTCAG at 2125, GGTCAA at 1833, AGTCAG at 394.

## Wboxr alternate negative direction (odds) (2596-1) distal promoters
- Wboxr1: CTGACC at 1160, CTGACC at 154.
- Wboxr3: CTGACT at 1141.
- Wboxr5: TTGACT at 1914.
- Wboxr7: TTGACC at 898.
- Wboxr1ci: GGTCAG at 1751.
- Wboxr3ci: GGTCAG at 2239, GGTCAA at 1052, GGTCAA at 601.
- Wboxr5ci: AGTCAG at 1920, AGTCAG at 1355.
- Wboxr9ci: AGTCAA at 2475, GGTCAG at 2057, AGTCAG at 107.

## Wboxr arbitrary positive direction (odds) (4050-1) distal promoters
- Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.
- Wboxr3: TTGACC at 3102, CTGACT at 1141.
- Wboxr5: TTGACT at 1914.
- Wboxr7: CTGACC at 3140, TTGACC at 898.
- Wboxr9: CTGACT at 3521.
- Wboxr1ci: AGTCAA at 3855, GGTCAA at 2778, GGTCAG at 1751.
- Wboxr3ci: GGTCAG at 3506, GGTCAG at 2239, GGTCAA at 1052, GGTCAA at 601.
- Wboxr5ci: AGTCAA at 3608, AGTCAG at 1920, AGTCAG at 1355.
- Wboxr9ci: AGTCAA at 3950, AGTCAG at 3359, GGTCAA at 3056, AGTCAA at 2475, GGTCAG at 2057, AGTCAG at 107.

## Wboxr alternate positive direction (evens) (4050-1) distal promoters
- Wboxr0: TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
- Wboxr2: CTGACC at 3755, CTGACC at 3580, TTGACT at 1736, TTGACC at 853.
- Wboxr4: TTGACT at 2961, TTGACC at 2892, TTGACT at 2539, TTGACC at 2131, CTGACT at 1980, CTGACT at 1922, TTGACC at 344.
- Wboxr6: TTGACC at 2398, TTGACT at 2043.
- Wboxr8: TTGACC at 1241, TTGACC at 776.
- Wboxr0ci: AGTCAA at 4044, GGTCAA at 1985, GGTCAG at 846.
- Wboxr2ci: GGTCAG at 3906, AGTCAA at 3850, GGTCAA at 3164, AGTCAG at 2900, GGTCAA at 2186, GGTCAG at 468, GGTCAA at 142, GGTCAG at 24.
- Wboxr4ci: AGTCAA at 3240, AGTCAA at 3119, AGTCAA at 986.
- Wboxr6ci: GGTCAA at 2737, AGTCAG at 2125, GGTCAA at 1833, AGTCAG at 394.
- Wboxr8ci: GGTCAA at 3494, GGTCAA at 3434, GGTCAA at 2695.

# Wbox analysis and results
The "presence of WRKY TF binding sites (C/TTGACC/T, W boxes) in numerous co-regulated Arabidopsis defense gene promoters provided circumstantial evidence that zinc-finger-type WRKY factors play a broad and pivotal role in regulating defenses ."
Comparison:
The occurrences of real W-box UTRs are  randoms, cores, proximals and distals are greater than the randoms. This suggests that the real W boxes are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.