P box gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

"The proximal promoter region (bp -87 to -45) of the human PAI-1 gene contains several potent binding sites for transcription factors [two phorbol-ester-response-element (TRE)-like sequences; D-box (-82 to -76) and P-box (-61 to 54), and one Sp1 binding site-like sequence, Sp1-box 1 (-72 to -67)]."[1]

Pyrimidine boxes

Main article: Pyrimidine box gene transcriptions

"Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5′-CCTTTT-3′."[2]

"Although this GARC [GA responsive complex] may not always be tripartite, most often it includes three sequence motifs, the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994)."[2]

"REV-ERBα and RORa are nuclear receptors rather than bZIP transcription factors like VRI and PDP1ϵ, and they regulate transcription by binding RORE elements rather than V/P-boxes (Bell-Pedersen et al., 2005)."[3]

P-boxes

The "complementary strand of the pyrimidine box element (5′-CTTTT-3′) in GA-induced hydrolase gene promoters was identical to the core sequence (5′-AAAAG-3′) recognized by PBF in prolamin gene promoters (P-box: 5′-T/AAAAG-3′; Vicente-Carbajosa et al., 1997; Mena et al., 1998; Yanagisawa and Schmidt, 1999)".[2]

Prolamin boxes

Main article: Prolamin box gene transcriptions

"The BPBF [barley prolamin-box (P-box) binding factor] expressed in bacteria as a GST-fusion binds a P-box 5′-TGTAAAG-3′ containing oligonucleotide derived from the promoter region of anHor2gene."[4]

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995). The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."[4]

V and P-boxes

Main article: V and P box gene transcriptions

"As VRI [target gene: vrille (VRI)] accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[3]

Consensus sequences

Main article: Consensus sequence gene transcriptions

The P box is actually the prolamin box.[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no P-box in either promoter.
  2. A1BG is not transcribed by a P-box.
  3. No P-box participates in the transcription of A1BG.

P-box (Yu) samplings

Copying the apparent consensus sequence for the P box GTAA(T/C) and putting it in "⌘F" finds seven located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs (starting with SuccessablesPbox.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:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPbox--.bas, looking for GTAA(C/T), 7, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951, GTAAC at 1343, GTAAC at 886, GTAAT at 173, GTAAT at 153, and complements.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPbox-+.bas, looking for GTAA(C/T), 1, GTAAC at 3732, and complement.
  3. positive strand in the negative direction is SuccessablesPbox+-.bas, looking for GTAA(C/T), 15, GTAAT at 3973, GTAAT at 3064, GTAAT at 2675, GTAAT at 2088, GTAAT at 1914, GTAAT at 1779, GTAAT at 1707, GTAAT at 1261, GTAAT at 1134, GTAAT at 804, GTAAT at 670, GTAAC at 613, GTAAT at 534, GTAAT at 397, GTAAT at 248, and complements.
  4. positive strand in the positive direction is SuccessablesPbox++.bas, looking for GTAA(C/T), 4, GTAAC at 4310, GTAAC at 2903, GTAAC at 1703, GTAAC at 23, and complements.
  5. complement, negative strand, negative direction is SuccessablesPboxc--.bas, looking for CATT(A/G), 15, CATTA at 3973, CATTA at 3064, CATTA at 2675, CATTA at 2088, CATTA at 1914, CATTA at 1779, CATTA at 1707, CATTA at 1261, CATTA at 1134, CATTA at 804, CATTA at 670, CATTG at 613, CATTA at 534, CATTA at 397, CATTA at 248.
  6. complement, negative strand, positive direction is SuccessablesPboxc-+.bas, looking for CATT(A/G), 4, CATTG at 4310, CATTG at 2903, CATTG at 1703, CATTG at 23.
  7. complement, positive strand, negative direction is SuccessablesPboxc+-.bas, looking for CATT(A/G), 7, CATTA at 3436, CATTG at 3285, CATTA at 2951, CATTG at 1343, CATTG at 886, CATTA at 173, CATTA at 153.
  8. complement, positive strand, positive direction is SuccessablesPboxc++.bas, looking for CATT(A/G), 1, CATTG at 3732.
  9. inverse complement, negative strand, negative direction is SuccessablesPboxci--.bas, looking for (A/G)TTAC, 1, ATTAC at 3658, and complement.
  10. inverse complement, negative strand, positive direction is SuccessablesPboxci-+.bas, looking for (A/G)TTAC, 0.
  11. inverse complement, positive strand, negative direction is SuccessablesPboxci+-.bas, looking for (A/G)TTAC, 2, ATTAC at 3469, ATTAC at 1296, and complements.
  12. inverse complement, positive strand, positive direction is SuccessablesPboxci++.bas, looking for (A/G)TTAC, 2, GTTAC at 2909, GTTAC at 227, and complements.
  13. inverse, negative strand, negative direction, is SuccessablesPboxi--.bas, looking for (C/T)AATG, 2, TAATG at 3469, TAATG at 1296.
  14. inverse, negative strand, positive direction, is SuccessablesPboxi-+.bas, looking for (C/T)AATG, 2, CAATG at 2909, CAATG at 227.
  15. inverse, positive strand, negative direction, is SuccessablesPboxi+-.bas, looking for (C/T)AATG, 1, TAATG at 3658.
  16. inverse, positive strand, positive direction, is SuccessablesPboxi++.bas, looking for (C/T)AATG, 0.

P-box (Yu) (4560-2846) UTRs

  1. Negative strand, negative direction: ATTAC at 3658, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951.
  2. Positive strand, negative direction: GTAAT at 3973, ATTAC at 3469, GTAAT at 3064.

P-box (Yu) positive direction (4445-4265) core promoters

  1. Positive strand, positive direction: GTAAC at 4310.

P-box (Yu) negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: GTAAT at 2675.

P-box (Yu) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GTAAC at 1343, GTAAC at 886, GTAAT at 173, GTAAT at 153.
  2. Positive strand, negative direction: GTAAT at 2088, GTAAT at 1914, GTAAT at 1779, GTAAT at 1707, ATTAC at 1296, GTAAT at 1261, GTAAT at 1134, GTAAT at 804, GTAAT at 670, GTAAC at 613, GTAAT at 534, GTAAT at 397, GTAAT at 248.

P-box (Yu) positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GTAAC at 3732.
  2. Positive strand, positive direction: GTTAC at 2909, GTAAC at 2903, GTAAC at 1703, GTTAC at 227, GTAAC at 23.

P-box (Yu) random dataset samplings

  1. PboxYr0: 7, GTAAT at 4151, GTAAC at 2624, GTAAC at 2608, GTAAC at 2410, GTAAC at 2221, GTAAC at 2131, GTAAC at 183.
  2. PboxYr1: 8, GTAAC at 4317, GTAAC at 4172, GTAAC at 4027, GTAAT at 3330, GTAAC at 2491, GTAAC at 1725, GTAAT at 805, GTAAT at 538.
  3. PboxYr2: 8, GTAAT at 4025, GTAAT at 3980, GTAAT at 3447, GTAAT at 3113, GTAAC at 3018, GTAAC at 2947, GTAAT at 845, GTAAT at 826.
  4. PboxYr3: 15, GTAAT at 4367, GTAAT at 4114, GTAAC at 3602, GTAAT at 2591, GTAAC at 2400, GTAAT at 2230, GTAAC at 2214, GTAAT at 1794, GTAAT at 1695, GTAAC at 1565, GTAAT at 1217, GTAAT at 917, GTAAT at 824, GTAAC at 742, GTAAC at 497.
  5. PboxYr4: 9, GTAAC at 3934, GTAAC at 3589, GTAAC at 3520, GTAAC at 3481, GTAAT at 3404, GTAAC at 2713, GTAAC at 2302, GTAAT at 1313, GTAAT at 1211.
  6. PboxYr5: 9, GTAAT at 3203, GTAAT at 2089, GTAAT at 2060, GTAAT at 2011, GTAAC at 1369, GTAAT at 1243, GTAAC at 978, GTAAT at 645, GTAAT at 467.
  7. PboxYr6: 7, GTAAT at 4425, GTAAC at 3977, GTAAC at 3145, GTAAT at 3002, GTAAC at 2547, GTAAC at 414, GTAAT at 400.
  8. PboxYr7: 8, GTAAC at 4448, GTAAT at 3911, GTAAT at 3842, GTAAC at 2546, GTAAC at 1056, GTAAC at 642, GTAAT at 372, GTAAC at 318.
  9. PboxYr8: 10, GTAAC at 4536, GTAAC at 4481, GTAAC at 3310, GTAAT at 2925, GTAAT at 2818, GTAAT at 2619, GTAAC at 1967, GTAAT at 1431, GTAAC at 958, GTAAT at 922.
  10. PboxYr9: 3, GTAAC at 3512, GTAAT at 3294, GTAAC at 2206.
  11. PboxYr0ci: 8, ATTAC at 3777, GTTAC at 3681, ATTAC at 3606, GTTAC at 2097, GTTAC at 1053, GTTAC at 1012, ATTAC at 547, GTTAC at 189.
  12. PboxYr1ci: 6, GTTAC at 4413, GTTAC at 4385, GTTAC at 3718, GTTAC at 2962, GTTAC at 2344, ATTAC at 368.
  13. PboxYr2ci: 7, GTTAC at 4332, GTTAC at 4303, ATTAC at 4033, GTTAC at 2591, GTTAC at 2310, GTTAC at 2248, GTTAC at 481.
  14. PboxYr3ci: 7, ATTAC at 3919, GTTAC at 3297, GTTAC at 3202, ATTAC at 2974, ATTAC at 2733, GTTAC at 1380, GTTAC at 454.
  15. PboxYr4ci: 8, GTTAC at 4520, ATTAC at 3753, ATTAC at 2647, ATTAC at 2235, GTTAC at 1935, ATTAC at 951, GTTAC at 887, ATTAC at 621.
  16. PboxYr5ci: 6, ATTAC at 4063, GTTAC at 3292, ATTAC at 2510, ATTAC at 1066, ATTAC at 893, ATTAC at 692.
  17. PboxYr6ci: 9, ATTAC at 4495, ATTAC at 3684, ATTAC at 2526, ATTAC at 2462, ATTAC at 2294, GTTAC at 2117, GTTAC at 1889, ATTAC at 1784, GTTAC at 1420.
  18. PboxYr7ci: 7, ATTAC at 3376, ATTAC at 2404, ATTAC at 2335, GTTAC at 2199, GTTAC at 2033, ATTAC at 1572, GTTAC at 1394.
  19. PboxYr8ci: 7, GTTAC at 4369, ATTAC at 3967, GTTAC at 3229, ATTAC at 2091, ATTAC at 1820, ATTAC at 1723, ATTAC at 228.
  20. PboxYr9ci: 10, GTTAC at 4247, GTTAC at 3731, GTTAC at 3685, GTTAC at 2357, GTTAC at 2010, GTTAC at 1704, ATTAC at 1168, GTTAC at 917, GTTAC at 548, GTTAC at 172.

PboxYr arbitrary (evens) (4560-2846) UTRs

  1. PboxYr0: GTAAT at 4151.
  2. PboxYr2: GTAAT at 4025, GTAAT at 3980, GTAAT at 3447, GTAAT at 3113, GTAAC at 3018, GTAAC at 2947.
  3. PboxYr4: GTAAC at 3934, GTAAC at 3589, GTAAC at 3520, GTAAC at 3481, GTAAT at 3404.
  4. PboxYr6: GTAAT at 4425, GTAAC at 3977, GTAAC at 3145, GTAAT at 3002.
  5. PboxYr0ci: ATTAC at 3777, GTTAC at 3681, ATTAC at 3606.
  6. PboxYr2ci: GTTAC at 4332, GTTAC at 4303, ATTAC at 4033.
  7. PboxYr4ci: GTTAC at 4520, ATTAC at 3753.
  8. PboxYr6ci: ATTAC at 4495, ATTAC at 3684.
  9. PboxYr8ci: GTTAC at 4369, ATTAC at 3967, GTTAC at 3229.

PboxYr alternate (odds) (4560-2846) UTRs

  1. PboxYr1: GTAAC at 4317, GTAAC at 4172, GTAAC at 4027, GTAAT at 3330.
  2. PboxYr3: GTAAT at 4367, GTAAT at 4114, GTAAC at 3602.
  3. PboxYr5: GTAAT at 3203.
  4. PboxYr7: GTAAC at 4448, GTAAT at 3911, GTAAT at 3842.
  5. PboxYr9: GTAAC at 3512, GTAAT at 3294.
  6. PboxYr1ci: GTTAC at 4413, GTTAC at 4385, GTTAC at 3718, GTTAC at 2962.
  7. PboxYr3ci: ATTAC at 3919, GTTAC at 3297, GTTAC at 3202, ATTAC at 2974.
  8. PboxYr5ci: ATTAC at 4063, GTTAC at 3292.
  9. PboxYr7ci: ATTAC at 3376.
  10. PboxYr9ci: GTTAC at 4247, GTTAC at 3731, GTTAC at 3685.

PboxYr arbitrary positive direction (odds) (4445-4265) core promoters

  1. PboxYr3: GTAAT at 4367.
  2. PboxYr1ci: GTTAC at 4413, GTTAC at 4385.

PboxYr alternate positive direction (evens) (4445-4265) core promoters

  1. PboxYr6: GTAAT at 4425.
  2. PboxYr2ci: GTTAC at 4332, GTTAC at 4303.
  3. PboxYr8ci: GTTAC at 4369.

PboxYr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. PboxYr0: GTAAC at 2624, GTAAC at 2608.
  2. PboxYr4: GTAAC at 2713.
  3. PboxYr4ci: ATTAC at 2647.

PboxYr alternate negative direction (odds) (2811-2596) proximal promoters

  1. PboxYr3ci: ATTAC at 2733.

PboxYr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. PboxYr3: GTAAT at 4114.
  2. PboxYr5ci: ATTAC at 4063.
  3. PboxYr9ci: GTTAC at 4247.

PboxYr alternate positive direction (evens) (4265-4050) proximal promoters

  1. PboxYr0: GTAAT at 4151.

PboxYr arbitrary negative direction (evens) (2596-1) distal promoters

  1. PboxYr0: GTAAC at 2410, GTAAC at 2221, GTAAC at 2131, GTAAC at 183.
  2. PboxYr2: GTAAT at 845, GTAAT at 826.
  3. PboxYr4: GTAAC at 2302, GTAAT at 1313, GTAAT at 1211.
  4. PboxYr6: GTAAC at 2547, GTAAC at 414, GTAAT at 400.
  5. PboxYr0ci: GTTAC at 2097, GTTAC at 1053, GTTAC at 1012, ATTAC at 547, GTTAC at 189.
  6. PboxYr2ci: GTTAC at 2591, GTTAC at 2310, GTTAC at 2248, GTTAC at 481.
  7. PboxYr4ci: ATTAC at 2235, GTTAC at 1935, ATTAC at 951, GTTAC at 887, ATTAC at 621.
  8. PboxYr6ci: ATTAC at 2526, ATTAC at 2462, ATTAC at 2294, GTTAC at 2117, GTTAC at 1889, ATTAC at 1784, GTTAC at 1420.
  9. PboxYr8ci: ATTAC at 2091, ATTAC at 1820, ATTAC at 1723, ATTAC at 228.

PboxYr alternate negative direction (odds) (2596-1) distal promoters

  1. PboxYr1: GTAAC at 2491, GTAAC at 1725, GTAAT at 805, GTAAT at 538.
  2. PboxYr3: GTAAT at 2591, GTAAC at 2400, GTAAT at 2230, GTAAC at 2214, GTAAT at 1794, GTAAT at 1695, GTAAC at 1565, GTAAT at 1217, GTAAT at 917, GTAAT at 824, GTAAC at 742, GTAAC at 497.
  3. PboxYr5: GTAAT at 2089, GTAAT at 2060, GTAAT at 2011, GTAAC at 1369, GTAAT at 1243, GTAAC at 978, GTAAT at 645, GTAAT at 467.
  4. PboxYr7: GTAAC at 2546, GTAAC at 1056, GTAAC at 642, GTAAT at 372, GTAAC at 318.
  5. PboxYr9: GTAAC at 2206.
  6. PboxYr1ci: GTTAC at 2344, ATTAC at 368.
  7. PboxYr3ci: GTTAC at 1380, GTTAC at 454.
  8. PboxYr5ci: ATTAC at 2510, ATTAC at 1066, ATTAC at 893, ATTAC at 692.
  9. PboxYr7ci: ATTAC at 2404, ATTAC at 2335, GTTAC at 2199, GTTAC at 2033, ATTAC at 1572, GTTAC at 1394.
  10. PboxYr9ci: GTTAC at 2357, GTTAC at 2010, GTTAC at 1704, ATTAC at 1168, GTTAC at 917, GTTAC at 548, GTTAC at 172.

PboxYr arbitrary positive direction (odds) (4050-1) distal promoters

  1. PboxYr1: GTAAC at 4027, GTAAT at 3330, GTAAC at 2491, GTAAC at 1725, GTAAT at 805, GTAAT at 538.
  2. PboxYr3: GTAAC at 3602, GTAAT at 2591, GTAAC at 2400, GTAAT at 2230, GTAAC at 2214, GTAAT at 1794, GTAAT at 1695, GTAAC at 1565, GTAAT at 1217, GTAAT at 917, GTAAT at 824, GTAAC at 742, GTAAC at 497.
  3. PboxYr5: GTAAT at 3203, GTAAT at 2089, GTAAT at 2060, GTAAT at 2011, GTAAC at 1369, GTAAT at 1243, GTAAC at 978, GTAAT at 645, GTAAT at 467.
  4. PboxYr7: GTAAT at 3911, GTAAT at 3842, GTAAC at 2546, GTAAC at 1056, GTAAC at 642, GTAAT at 372, GTAAC at 318.
  5. PboxYr9: GTAAC at 3512, GTAAT at 3294, GTAAC at 2206.
  6. PboxYr1ci: GTTAC at 3718, GTTAC at 2962, GTTAC at 2344, ATTAC at 368.
  7. PboxYr3ci: ATTAC at 3919, GTTAC at 3297, GTTAC at 3202, ATTAC at 2974, ATTAC at 2733, GTTAC at 1380, GTTAC at 454.
  8. PboxYr5ci: GTTAC at 3292, ATTAC at 2510, ATTAC at 1066, ATTAC at 893, ATTAC at 692.
  9. PboxYr7ci: ATTAC at 3376, ATTAC at 2404, ATTAC at 2335, GTTAC at 2199, GTTAC at 2033, ATTAC at 1572, GTTAC at 1394.
  10. PboxYr9ci: GTTAC at 3731, GTTAC at 3685, GTTAC at 2357, GTTAC at 2010, GTTAC at 1704, ATTAC at 1168, GTTAC at 917, GTTAC at 548, GTTAC at 172.

PboxYr alternate positive direction (evens) (4050-1) distal promoters

  1. PboxYr0: GTAAC at 2624, GTAAC at 2608, GTAAC at 2410, GTAAC at 2221, GTAAC at 2131, GTAAC at 183.
  2. PboxYr2: GTAAT at 4025, GTAAT at 3980, GTAAT at 3447, GTAAT at 3113, GTAAC at 3018, GTAAC at 2947, GTAAT at 845, GTAAT at 826.
  3. PboxYr6: GTAAC at 3977, GTAAC at 3145, GTAAT at 3002, GTAAC at 2547, GTAAC at 414, GTAAT at 400.
  4. PboxYr0ci: ATTAC at 3777, GTTAC at 3681, ATTAC at 3606, GTTAC at 2097, GTTAC at 1053, GTTAC at 1012, ATTAC at 547, GTTAC at 189.
  5. PboxYr2ci: ATTAC at 4033, GTTAC at 2591, GTTAC at 2310, GTTAC at 2248, GTTAC at 481.
  6. PboxYr4ci: ATTAC at 3753, ATTAC at 2647, ATTAC at 2235, GTTAC at 1935, ATTAC at 951, GTTAC at 887, ATTAC at 621.
  7. PboxYr6ci: ATTAC at 3684, ATTAC at 2526, ATTAC at 2462, ATTAC at 2294, GTTAC at 2117, GTTAC at 1889, ATTAC at 1784, GTTAC at 1420.
  8. PboxYr8ci: ATTAC at 3967, GTTAC at 3229, ATTAC at 2091, ATTAC at 1820, ATTAC at 1723, ATTAC at 228.

P-box (Yu) analysis and results

Main article: Complex locus A1BG and ZNF497 § P-box (Yu)s

"As VRI [target gene: vrille (VRI)] accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 7 2 3.5 3.5 ± 0.5 (--4,+-3)
Randoms UTR arbitrary negative 28 10 2.8 3.05
Randoms UTR alternate negative 33 10 3.3 3.05
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 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Core arbitrary positive 3 10 0.3 0.35
Randoms Core alternate positive 4 10 0.4 0.35
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 4 10 0.4 0.25
Randoms Proximal alternate negative 1 10 0.1 0.25
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 3 10 0.3 0.2
Randoms Proximal alternate positive 1 10 0.1 0.2
Reals Distal negative 17 2 8.5 8.5 ± 4.5 (--4,+-13)
Randoms Distal arbitrary negative 37 10 3.7 4.4
Randoms Distal alternate negative 51 10 5.1 4.4
Reals Distal positive 6 2 3 3 ± 2 (-+1,++5)
Randoms Distal arbitrary positive 70 10 7.0 6.2
Randoms Distal alternate positive 54 10 5.4 6.2

Comparison:

The occurrences of real P-box (Yu) cores and proximals are greater than the randoms, the UTRs and negative distals overlap the high randoms, the positive distals are less than the randoms. This suggests that the real P-box (Yu)s are likely active or activable with some overlapping the randoms.

Consensus sequences

Main article: Consensus sequence gene transcriptions

P-box: 5′-(T/A)AAAG-3′.[2]

P-box (TGAGTTCA).[1]

P-box (Mena) samplings

Copying a responsive elements consensus sequence (T/A)AAAG and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (T/A)AAAG (starting with SuccessablesPbMe.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:

  1. Negative strand, negative direction, looking for (T/A)AAAG, 5, TAAAG at 3688, TAAAG at 2884, TAAAG at 1603, TAAAG at 1380, TAAAG at 22.
  2. Negative strand, positive direction, looking for (T/A)AAAG, 3, AAAAG at 3928, AAAAG at 2708, AAAAG at 2004.
  3. Positive strand, negative direction, looking for (T/A)AAAG, 24, AAAAG at 4391, AAAAG at 4386, AAAAG at 4379, AAAAG at 3440, AAAAG at 3344, TAAAG at 2857, AAAAG at 2835, AAAAG at 2823, AAAAG at 2818, AAAAG at 2806, AAAAG at 2797, AAAAG at 2477, AAAAG at 2471, TAAAG at 2174, AAAAG at 2052, AAAAG at 1627, TAAAG at 1548, AAAAG at 1399, AAAAG at 1106, AAAAG at 943, AAAAG at 223, AAAAG at 184, AAAAG at 104, AAAAG at 54.
  4. Positive strand, positive direction, looking for (T/A)AAAG, 5, TAAAG at 2645, AAAAG at 2275, TAAAG at 1978, AAAAG at 1749, AAAAG at 136.
  5. complement, negative strand, negative direction, looking for (A/T)TTTC, 24, TTTTC at 4391, TTTTC at 4386, TTTTC at 4379, TTTTC at 3440, TTTTC at 3344, ATTTC at 2857, TTTTC at 2835, TTTTC at 2823, TTTTC at 2818, TTTTC at 2806, TTTTC at 2797, TTTTC at 2477, TTTTC at 2471, ATTTC at 2174, TTTTC at 2052, TTTTC at 1627, ATTTC at 1548, TTTTC at 1399, TTTTC at 1106, TTTTC at 943, TTTTC at 223, TTTTC at 184, TTTTC at 104, TTTTC at 54.
  6. complement, negative strand, positive direction, looking for (A/T)TTTC, 5, ATTTC at 2645, TTTTC at 2275, ATTTC at 1978, TTTTC at 1749, TTTTC at 136.
  7. complement, positive strand, negative direction, looking for (A/T)TTTC, 5, ATTTC at 3688, ATTTC at 2884, ATTTC at 1603, ATTTC at 1380, ATTTC at 22.
  8. complement, positive strand, positive direction, looking for (A/T)TTTC, 3, TTTTC at 3928, TTTTC at 2708, TTTTC at 2004.
  9. inverse complement, negative strand, negative direction, looking for CTTT(A/T), 23, CTTTT at 4395, CTTTT at 4390, CTTTT at 4383, CTTTT at 3508, CTTTT at 3343, CTTTT at 2968, CTTTT at 2927, CTTTT at 2839, CTTTT at 2832, CTTTT at 2822, CTTTT at 2815, CTTTA at 2747, CTTTT at 2506, CTTTT at 2459, CTTTA at 2158, CTTTT at 2056, CTTTA at 1661, CTTTA at 1631, CTTTT at 1626, CTTTT at 495, CTTTT at 358, CTTTT at 103, CTTTT at 53.
  10. inverse complement, negative strand, positive direction, looking for CTTT(A/T), 5, CTTTA at 2586, CTTTT at 2279, CTTTT at 2274, CTTTT at 1747, CTTTT at 135.
  11. inverse complement, positive strand, negative direction, looking for CTTT(A/T), 6, CTTTT at 3019, CTTTA at 1734, CTTTT at 1419, CTTTA at 348, CTTTA at 48, CTTTT at 26.
  12. inverse complement, positive strand, positive direction, looking for CTTT(A/T), 6, CTTTA at 4092, CTTTT at 3927, CTTTA at 3795, CTTTA at 3166, CTTTA at 2624, CTTTT at 291.
  13. inverse negative strand, negative direction, looking for GAAA(T/A), 6, GAAAA at 3019, GAAAT at 1734, GAAAA at 1419, GAAAT at 348, GAAAT at 48, GAAAA at 26.
  14. inverse negative strand, positive direction, looking for GAAA(T/A), 6, GAAAT at 4092, GAAAA at 3927, GAAAT at 3795, GAAAT at 3166, GAAAT at 2624, GAAAA at 291.
  15. inverse positive strand, negative direction, looking for GAAA(T/A), 23, GAAAA at 4395, GAAAA at 4390, GAAAA at 4383, GAAAA at 3508, GAAAA at 3343, GAAAA at 2968, GAAAA at 2927, GAAAA at 2839, GAAAA at 2832, GAAAA at 2822, GAAAA at 2815, GAAAT at 2747, GAAAA at 2506, GAAAA at 2459, GAAAT at 2158, GAAAA at 2056, GAAAT at 1661, GAAAT at 1631, GAAAA at 1626, GAAAA at 495, GAAAA at 358, GAAAA at 103, GAAAA at 53.
  16. inverse positive strand, positive direction, looking for GAAA(T/A), 5, GAAAT at 2586, GAAAA at 2279, GAAAA at 2274, GAAAA at 1747, GAAAA at 135.

P-box (Mena) (4560-2846) UTRs

  1. Negative strand, negative direction: CTTTT at 4395, CTTTT at 4390, CTTTT at 4383, TAAAG at 3688, CTTTT at 3508, CTTTT at 3343, CTTTT at 2968, CTTTT at 2927, TAAAG at 2884.
  2. Positive strand, negative direction: AAAAG at 4391, AAAAG at 4386, AAAAG at 4379, AAAAG at 3440, AAAAG at 3344, CTTTT at 3019, TAAAG at 2857.

P-box (Mena) negative direction (2846-2811) core promoters

  1. Negative strand, negative direction: CTTTT at 2839, CTTTT at 2832, CTTTT at 2822, CTTTT at 2815.
  2. Positive strand, negative direction: AAAAG at 2835, AAAAG at 2823, AAAAG at 2818.

P-box (Mena) negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: CTTTA at 2747.
  2. Positive strand, negative direction: AAAAG at 2806, AAAAG at 2797.

P-box (Mena) positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: CTTTA at 4092.

P-box (Mena) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CTTTT at 2506, CTTTT at 2459, CTTTA at 2158, CTTTT at 2056, CTTTA at 1661, CTTTA at 1631, CTTTT at 1626, TAAAG at 1603, TAAAG at 1380, CTTTT at 495, CTTTT at 358, CTTTT at 103, CTTTT at 53, TAAAG at 22.
  2. Positive strand, negative direction: AAAAG at 2477, AAAAG at 2471, TAAAG at 2174, AAAAG at 2052, CTTTA at 1734, AAAAG at 1627, TAAAG at 1548, CTTTT at 1419, AAAAG at 1399, AAAAG at 1106, AAAAG at 943, CTTTA at 348, AAAAG at 223, AAAAG at 184, AAAAG at 104, AAAAG at 54, CTTTA at 48, CTTTT at 26.

P-box (Mena) positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AAAAG at 3928, AAAAG at 2708, TAAAG at 2645, CTTTA at 2586, CTTTT at 2279, CTTTT at 2274, AAAAG at 2004, CTTTT at 1747, CTTTT at 135.
  2. Positive strand, positive direction: CTTTT at 3927, CTTTA at 3795, CTTTA at 3166, TAAAG at 2645, CTTTA at 2624, AAAAG at 2275, TAAAG at 1978, AAAAG at 1749, CTTTT at 291, AAAAG at 136.

P-box (Mena) random dataset samplings

  1. PbMer0: 15, AAAAG at 4526, TAAAG at 3784, TAAAG at 3756, AAAAG at 3658, AAAAG at 3482, TAAAG at 2018, TAAAG at 1728, TAAAG at 1587, TAAAG at 1233, TAAAG at 630, AAAAG at 592, TAAAG at 323, TAAAG at 316, AAAAG at 100, TAAAG at 7.
  2. PbMer1: 16, AAAAG at 4555, AAAAG at 4409, AAAAG at 4356, AAAAG at 4012, AAAAG at 3823, TAAAG at 3447, AAAAG at 3176, TAAAG at 3124, AAAAG at 3065, AAAAG at 2799, AAAAG at 1776, AAAAG at 1517, AAAAG at 1442, TAAAG at 1305, TAAAG at 911, AAAAG at 882.
  3. PbMer2: 20, AAAAG at 4366, AAAAG at 4315, TAAAG at 4291, AAAAG at 4154, TAAAG at 4147, TAAAG at 3857, AAAAG at 3655, TAAAG at 3149, AAAAG at 3123, TAAAG at 2913, AAAAG at 2340, AAAAG at 1845, AAAAG at 1439, AAAAG at 1264, TAAAG at 1080, TAAAG at 1020, AAAAG at 473, TAAAG at 387, AAAAG at 251, AAAAG at 109.
  4. PbMer3: 15, TAAAG at 3734, TAAAG at 3712, AAAAG at 3595, TAAAG at 3061, TAAAG at 3052, AAAAG at 2599, AAAAG at 2463, AAAAG at 2275, AAAAG at 2080, TAAAG at 1938, TAAAG at 1711, AAAAG at 570, AAAAG at 552, TAAAG at 211, TAAAG at 128.
  5. PbMer4: 11, AAAAG at 3880, TAAAG at 3739, TAAAG at 2949, TAAAG at 2696, AAAAG at 2340, AAAAG at 2180, AAAAG at 1997, TAAAG at 1641, TAAAG at 1108, TAAAG at 734, TAAAG at 214.
  6. PbMer5: 16, AAAAG at 4336, AAAAG at 4322, TAAAG at 3765, TAAAG at 3361, TAAAG at 3348, TAAAG at 2948, TAAAG at 2292, TAAAG at 2049, TAAAG at 1806, TAAAG at 1656, TAAAG at 1501, TAAAG at 1139, AAAAG at 1034, AAAAG at 636, TAAAG at 419, AAAAG at 226.
  7. PbMer6: 14, AAAAG at 4453, AAAAG at 4019, TAAAG at 3792, AAAAG at 3485, AAAAG at 3422, AAAAG at 2862, TAAAG at 2630, TAAAG at 2181, AAAAG at 2132, AAAAG at 1442, AAAAG at 1238, TAAAG at 1125, AAAAG at 971, AAAAG at 227.
  8. PbMer7: 16, AAAAG at 4548, AAAAG at 4394, TAAAG at 4067, AAAAG at 3884, AAAAG at 3791, TAAAG at 2960, AAAAG at 2890, TAAAG at 2769, TAAAG at 2568, TAAAG at 2374, AAAAG at 1932, TAAAG at 1674, AAAAG at 1537, AAAAG at 1276, AAAAG at 360, TAAAG at 285.
  9. PbMer8: 19, AAAAG at 3683, TAAAG at 3574, AAAAG at 3344, AAAAG at 3192, TAAAG at 3096, AAAAG at 2389, TAAAG at 2269, AAAAG at 2165, AAAAG at 2133, AAAAG at 2112, TAAAG at 1928, AAAAG at 1684, TAAAG at 1521, AAAAG at 1218, AAAAG at 891, TAAAG at 881, AAAAG at 709, AAAAG at 503, AAAAG at 310.
  10. PbMer9: 13, TAAAG at 4220, AAAAG at 3855, AAAAG at 2492, TAAAG at 2376, TAAAG at 1666, AAAAG at 1409, TAAAG at 1381, AAAAG at 1305, TAAAG at 1259, TAAAG at 1109, TAAAG at 665, AAAAG at 587, AAAAG at 32.
  11. PbMer0ci: 14, CTTTA at 4422, CTTTT at 3942, CTTTA at 3789, CTTTA at 3372, CTTTT at 2953, CTTTA at 2110, CTTTT at 1275, CTTTA at 1137, CTTTT at 1021, CTTTT at 654, CTTTA at 407, CTTTT at 358, CTTTT at 221, CTTTA at 206.
  12. PbMer1ci: 12, CTTTT at 4226, CTTTT at 3646, CTTTA at 3578, CTTTT at 3044, CTTTT at 2673, CTTTT at 2407, CTTTT at 2288, CTTTT at 2195, CTTTA at 1279, CTTTT at 1273, CTTTT at 654, CTTTA at 524.
  13. PbMer2ci: 9, CTTTT at 4103, CTTTT at 3664, CTTTA at 3573, CTTTT at 3219, CTTTA at 2055, CTTTT at 1732, CTTTT at 1679, CTTTA at 1184, CTTTT at 858.
  14. PbMer3ci: 21, CTTTT at 4323, CTTTT at 4187, CTTTT at 4070, CTTTT at 3693, CTTTA at 3639, CTTTT at 3538, CTTTT at 2811, CTTTT at 2470, CTTTA at 2456, CTTTT at 2358, CTTTT at 2224, CTTTT at 1911, CTTTA at 1848, CTTTT at 1704, CTTTA at 1239, CTTTT at 1025, CTTTA at 912, CTTTT at 841, CTTTA at 317, CTTTA at 288, CTTTT at 148.
  15. PbMer4ci: 21, CTTTT at 4524, CTTTA at 4157, CTTTT at 3941, CTTTT at 3926, CTTTA at 3014, CTTTT at 3001, CTTTT at 2834, CTTTA at 2278, CTTTT at 2203, CTTTA at 2019, CTTTT at 2013, CTTTA at 1947, CTTTT at 1790, CTTTT at 1732, CTTTT at 1423, CTTTT at 1404, CTTTT at 1345, CTTTA at 828, CTTTT at 594, CTTTT at 472, CTTTA at 191.
  16. PbMer5ci: 10, CTTTT at 4531, CTTTT at 3096, CTTTA at 2368, CTTTT at 2355, CTTTA at 2176, CTTTT at 1976, CTTTT at 1793, CTTTT at 1344, CTTTT at 1265, CTTTT at 219.
  17. PbMer6ci: 17, CTTTT at 4236, CTTTT at 4226, CTTTT at 4182, CTTTA at 3957, CTTTT at 3924, CTTTT at 3672, CTTTT at 3353, CTTTT at 3289, CTTTT at 3282, CTTTA at 2501, CTTTT at 2394, CTTTA at 2340, CTTTA at 2253, CTTTA at 1994, CTTTA at 1531, CTTTT at 1372, CTTTA at 1286.
  18. PbMer7ci: 14, CTTTA at 4250, CTTTT at 3928, CTTTT at 3580, CTTTT at 3257, CTTTT at 3174, CTTTT at 2838, CTTTT at 2831, CTTTT at 2590, CTTTT at 1990, CTTTA at 1555, CTTTA at 1432, CTTTA at 843, CTTTA at 757, CTTTT at 97.
  19. PbMer8ci: 12, CTTTA at 3802, CTTTT at 3414, CTTTA at 3381, CTTTT at 3060, CTTTT at 3011, CTTTT at 2253, CTTTA at 2056, CTTTT at 1862, CTTTA at 652, CTTTA at 474, CTTTA at 224, CTTTT at 74.
  20. PbMer9ci: 14, CTTTT at 4332, CTTTA at 3955, CTTTA at 3874, CTTTT at 3256, CTTTT at 2868, CTTTT at 2693, CTTTT at 2684, CTTTA at 1943, CTTTT at 1908, CTTTA at 1396, CTTTT at 1030, CTTTA at 964, CTTTT at 900, CTTTT at 134.

PbMer arbitrary (evens) (4560-2846) UTRs

  1. PbMer0: AAAAG at 4526, TAAAG at 3784, TAAAG at 3756, AAAAG at 3658, AAAAG at 3482.
  2. PbMer2: AAAAG at 4366, AAAAG at 4315, TAAAG at 4291, AAAAG at 4154, TAAAG at 4147, TAAAG at 3857, AAAAG at 3655, TAAAG at 3149, AAAAG at 3123, TAAAG at 2913.
  3. PbMer4: AAAAG at 3880, TAAAG at 3739, TAAAG at 2949.
  4. PbMer6: AAAAG at 4453, AAAAG at 4019, TAAAG at 3792, AAAAG at 3485, AAAAG at 3422, AAAAG at 2862.
  5. PbMer8: AAAAG at 3683, TAAAG at 3574, AAAAG at 3344, AAAAG at 3192, TAAAG at 3096.
  6. PbMer0ci: CTTTA at 4422, CTTTT at 3942, CTTTA at 3789, CTTTA at 3372, CTTTT at 2953.
  7. PbMer2ci: CTTTT at 4103, CTTTT at 3664, CTTTA at 3573, CTTTT at 3219.
  8. PbMer4ci: CTTTT at 4524, CTTTA at 4157, CTTTT at 3941, CTTTT at 3926, CTTTA at 3014, CTTTT at 3001.
  9. PbMer6ci: CTTTT at 4236, CTTTT at 4226, CTTTT at 4182, CTTTA at 3957, CTTTT at 3924, CTTTT at 3672, CTTTT at 3353, CTTTT at 3289, CTTTT at 3282.
  10. PbMer8ci: CTTTA at 3802, CTTTT at 3414, CTTTA at 3381, CTTTT at 3060, CTTTT at 3011.

PbMer alternate (odds) (4560-2846) UTRs

  1. PbMer1: AAAAG at 4555, AAAAG at 4409, AAAAG at 4356, AAAAG at 4012, AAAAG at 3823, TAAAG at 3447, AAAAG at 3176, TAAAG at 3124, AAAAG at 3065.
  2. PbMer3: TAAAG at 3734, TAAAG at 3712, AAAAG at 3595, TAAAG at 3061, TAAAG at 3052.
  3. PbMer5: AAAAG at 4336, AAAAG at 4322, TAAAG at 3765, TAAAG at 3361, TAAAG at 3348, TAAAG at 2948.
  4. PbMer7: AAAAG at 4548, AAAAG at 4394, TAAAG at 4067, AAAAG at 3884, AAAAG at 3791, TAAAG at 2960, AAAAG at 2890.
  5. PbMer9: TAAAG at 4220, AAAAG at 3855.
  6. PbMer1ci: CTTTT at 4226, CTTTT at 3646, CTTTA at 3578, CTTTT at 3044.
  7. PbMer3ci: CTTTT at 4323, CTTTT at 4187, CTTTT at 4070, CTTTT at 3693, CTTTA at 3639, CTTTT at 3538.
  8. PbMer5ci: CTTTT at 4531, CTTTT at 3096.
  9. PbMer7ci: CTTTA at 4250, CTTTT at 3928, CTTTT at 3580, CTTTT at 3257, CTTTT at 3174.
  10. PbMer9ci: CTTTT at 4332, CTTTA at 3955, CTTTA at 3874, CTTTT at 3256, CTTTT at 2868.

PbMer arbitrary negative direction (evens) (2846-2811) core promoters

  1. PbMer4ci: CTTTT at 2834.

PbMer alternate negative direction (odds) (2846-2811) core promoters

  1. PbMer3ci: CTTTT at 2811.
  2. PbMer7ci: CTTTT at 2838, CTTTT at 2831.

PbMer arbitrary positive direction (odds) (4445-4265) core promoters

  1. PbMer1: AAAAG at 4409, AAAAG at 4356.
  2. PbMer5: AAAAG at 4336, AAAAG at 4322.
  3. PbMer7: AAAAG at 4394.
  4. PbMer3ci: CTTTT at 4323.
  5. PbMer9ci: CTTTT at 4332.

PbMer alternate positive direction (evens) (4445-4265) core promoters

  1. PbMer2: AAAAG at 4366, AAAAG at 4315, TAAAG at 4291.
  2. PbMer0ci: CTTTA at 4422.

PbMer arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. PbMer4: TAAAG at 2696.

PbMer alternate negative direction (odds) (2811-2596) proximal promoters

  1. PbMer1: AAAAG at 2799.
  2. PbMer7: TAAAG at 2769.
  3. PbMer1ci: CTTTT at 2673.
  4. PbMer3ci: CTTTT at 2811.
  5. PbMer9ci: CTTTT at 2693, CTTTT at 2684.

PbMer arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. PbMer7: TAAAG at 4067.
  2. PbMer1ci: CTTTT at 4226.
  3. PbMer3ci: CTTTT at 4187, CTTTT at 4070.
  4. PbMer7ci: CTTTA at 4250.

PbMer alternate positive direction (evens) (4265-4050) proximal promoters

  1. PbMer2: AAAAG at 4154, TAAAG at 4147.
  2. PbMer2ci: CTTTT at 4103.
  3. PbMer4ci: CTTTA at 4157.
  4. PbMer6ci: CTTTT at 4236, CTTTT at 4226, CTTTT at 4182.

PbMer arbitrary negative direction (evens) (2596-1) distal promoters

  1. PbMer0: TAAAG at 2018, TAAAG at 1728, TAAAG at 1587, TAAAG at 1233, TAAAG at 630, AAAAG at 592, TAAAG at 323, TAAAG at 316, AAAAG at 100, TAAAG at 7.
  2. PbMer2: TAAAG at 2913, AAAAG at 2340, AAAAG at 1845, AAAAG at 1439, AAAAG at 1264, TAAAG at 1080, TAAAG at 1020, AAAAG at 473, TAAAG at 387, AAAAG at 251, AAAAG at 109.
  3. PbMer4: AAAAG at 2340, AAAAG at 2180, AAAAG at 1997, TAAAG at 1641, TAAAG at 1108, TAAAG at 734, TAAAG at 214.
  4. PbMer6: TAAAG at 2181, AAAAG at 2132, AAAAG at 1442, AAAAG at 1238, TAAAG at 1125, AAAAG at 971, AAAAG at 227.
  5. PbMer8: AAAAG at 2389, TAAAG at 2269, AAAAG at 2165, AAAAG at 2133, AAAAG at 2112, TAAAG at 1928, AAAAG at 1684, TAAAG at 1521, AAAAG at 1218, AAAAG at 891, TAAAG at 881, AAAAG at 709, AAAAG at 503, AAAAG at 310.
  6. PbMer0ci: CTTTA at 2110, CTTTT at 1275, CTTTA at 1137, CTTTT at 1021, CTTTT at 654, CTTTA at 407, CTTTT at 358, CTTTT at 221, CTTTA at 206.
  7. PbMer2ci: CTTTA at 2055, CTTTT at 1732, CTTTT at 1679, CTTTA at 1184, CTTTT at 858.
  8. PbMer4ci: CTTTA at 2278, CTTTT at 2203, CTTTA at 2019, CTTTT at 2013, CTTTA at 1947, CTTTT at 1790, CTTTT at 1732, CTTTT at 1423, CTTTT at 1404, CTTTT at 1345, CTTTA at 828, CTTTT at 594, CTTTT at 472, CTTTA at 191.
  9. PbMer6ci: CTTTA at 2501, CTTTT at 2394, CTTTA at 2340, CTTTA at 2253, CTTTA at 1994, CTTTA at 1531, CTTTT at 1372, CTTTA at 1286.
  10. PbMer8ci: CTTTT at 2253, CTTTA at 2056, CTTTT at 1862, CTTTA at 652, CTTTA at 474, CTTTA at 224, CTTTT at 74.

PbMer alternate negative direction (odds) (2596-1) distal promoters

  1. PbMer1: AAAAG at 1776, AAAAG at 1517, AAAAG at 1442, TAAAG at 1305, TAAAG at 911, AAAAG at 882.
  2. PbMer3: AAAAG at 2463, AAAAG at 2275, AAAAG at 2080, TAAAG at 1938, TAAAG at 1711, AAAAG at 570, AAAAG at 552, TAAAG at 211, TAAAG at 128.
  3. PbMer5: TAAAG at 2292, TAAAG at 2049, TAAAG at 1806, TAAAG at 1656, TAAAG at 1501, TAAAG at 1139, AAAAG at 1034, AAAAG at 636, TAAAG at 419, AAAAG at 226.
  4. PbMer7: TAAAG at 2568, TAAAG at 2374, AAAAG at 1932, TAAAG at 1674, AAAAG at 1537, AAAAG at 1276, AAAAG at 360, TAAAG at 285.
  5. PbMer9: AAAAG at 2492, TAAAG at 2376, TAAAG at 1666, AAAAG at 1409, TAAAG at 1381, AAAAG at 1305, TAAAG at 1259, TAAAG at 1109, TAAAG at 665, AAAAG at 587, AAAAG at 32.
  6. PbMer1ci: CTTTT at 2407, CTTTT at 2288, CTTTT at 2195, CTTTA at 1279, CTTTT at 1273, CTTTT at 654, CTTTA at 524.
  7. PbMer3ci: CTTTT at 2470, CTTTA at 2456, CTTTT at 2358, CTTTT at 2224, CTTTT at 1911, CTTTA at 1848, CTTTT at 1704, CTTTA at 1239, CTTTT at 1025, CTTTA at 912, CTTTT at 841, CTTTA at 317, CTTTA at 288, CTTTT at 148.
  8. PbMer5ci: CTTTA at 2368, CTTTT at 2355, CTTTA at 2176, CTTTT at 1976, CTTTT at 1793, CTTTT at 1344, CTTTT at 1265, CTTTT at 219.
  9. PbMer7ci: CTTTT at 2590, CTTTT at 1990, CTTTA at 1555, CTTTA at 1432, CTTTA at 843, CTTTA at 757, CTTTT at 97.
  10. PbMer9ci: CTTTA at 1943, CTTTT at 1908, CTTTA at 1396, CTTTT at 1030, CTTTA at 964, CTTTT at 900, CTTTT at 134.

PbMer arbitrary positive direction (odds) (4050-1) distal promoters

  1. PbMer1: AAAAG at 4012, AAAAG at 3823, TAAAG at 3447, AAAAG at 3176, TAAAG at 3124, AAAAG at 3065, AAAAG at 2799, AAAAG at 1776, AAAAG at 1517, AAAAG at 1442, TAAAG at 1305, TAAAG at 911, AAAAG at 882.
  2. PbMer3: TAAAG at 3734, TAAAG at 3712, AAAAG at 3595, TAAAG at 3061, TAAAG at 3052, AAAAG at 2599, AAAAG at 2463, AAAAG at 2275, AAAAG at 2080, TAAAG at 1938, TAAAG at 1711, AAAAG at 570, AAAAG at 552, TAAAG at 211, TAAAG at 128.
  3. PbMer5: TAAAG at 3765, TAAAG at 3361, TAAAG at 3348, TAAAG at 2948, TAAAG at 2292, TAAAG at 2049, TAAAG at 1806, TAAAG at 1656, TAAAG at 1501, TAAAG at 1139, AAAAG at 1034, AAAAG at 636, TAAAG at 419, AAAAG at 226.
  4. PbMer7: AAAAG at 3884, AAAAG at 3791, TAAAG at 2960, AAAAG at 2890, TAAAG at 2769, TAAAG at 2568, TAAAG at 2374, AAAAG at 1932, TAAAG at 1674, AAAAG at 1537, AAAAG at 1276, AAAAG at 360, TAAAG at 285.
  5. PbMer9: AAAAG at 3855, AAAAG at 2492, TAAAG at 2376, TAAAG at 1666, AAAAG at 1409, TAAAG at 1381, AAAAG at 1305, TAAAG at 1259, TAAAG at 1109, TAAAG at 665, AAAAG at 587, AAAAG at 32.
  6. PbMer1ci: CTTTT at 3646, CTTTA at 3578, CTTTT at 3044, CTTTT at 2673, CTTTT at 2407, CTTTT at 2288, CTTTT at 2195, CTTTA at 1279, CTTTT at 1273, CTTTT at 654, CTTTA at 524.
  7. PbMer3ci: CTTTT at 3693, CTTTA at 3639, CTTTT at 3538, CTTTT at 2811, CTTTT at 2470, CTTTA at 2456, CTTTT at 2358, CTTTT at 2224, CTTTT at 1911, CTTTA at 1848, CTTTT at 1704, CTTTA at 1239, CTTTT at 1025, CTTTA at 912, CTTTT at 841, CTTTA at 317, CTTTA at 288, CTTTT at 148.
  8. PbMer5ci: CTTTT at 3096, CTTTA at 2368, CTTTT at 2355, CTTTA at 2176, CTTTT at 1976, CTTTT at 1793, CTTTT at 1344, CTTTT at 1265, CTTTT at 219.
  9. PbMer7ci: CTTTT at 3928, CTTTT at 3580, CTTTT at 3257, CTTTT at 3174, CTTTT at 2838, CTTTT at 2831, CTTTT at 2590, CTTTT at 1990, CTTTA at 1555, CTTTA at 1432, CTTTA at 843, CTTTA at 757, CTTTT at 97.
  10. PbMer9ci: CTTTA at 3955, CTTTA at 3874, CTTTT at 3256, CTTTT at 2868, CTTTT at 2693, CTTTT at 2684, CTTTA at 1943, CTTTT at 1908, CTTTA at 1396, CTTTT at 1030, CTTTA at 964, CTTTT at 900, CTTTT at 134.

PbMer alternate positive direction (evens) (4050-1) distal promoters

  1. PbMer0: TAAAG at 3784, TAAAG at 3756, AAAAG at 3658, AAAAG at 3482, TAAAG at 2018, TAAAG at 1728, TAAAG at 1587, TAAAG at 1233, TAAAG at 630, AAAAG at 592, TAAAG at 323, TAAAG at 316, AAAAG at 100, TAAAG at 7.
  2. PbMer2: TAAAG at 3857, AAAAG at 3655, TAAAG at 3149, AAAAG at 3123, TAAAG at 2913, AAAAG at 2340, AAAAG at 1845, AAAAG at 1439, AAAAG at 1264, TAAAG at 1080, TAAAG at 1020, AAAAG at 473, TAAAG at 387, AAAAG at 251, AAAAG at 109.
  3. PbMer4: AAAAG at 3880, TAAAG at 3739, TAAAG at 2949, TAAAG at 2696, AAAAG at 2340, AAAAG at 2180, AAAAG at 1997, TAAAG at 1641, TAAAG at 1108, TAAAG at 734, TAAAG at 214.
  4. PbMer6: AAAAG at 4019, TAAAG at 3792, AAAAG at 3485, AAAAG at 3422, AAAAG at 2862, TAAAG at 2630, TAAAG at 2181, AAAAG at 2132, AAAAG at 1442, AAAAG at 1238, TAAAG at 1125, AAAAG at 971, AAAAG at 227.
  5. PbMer8: AAAAG at 3683, TAAAG at 3574, AAAAG at 3344, AAAAG at 3192, TAAAG at 3096, AAAAG at 2389, TAAAG at 2269, AAAAG at 2165, AAAAG at 2133, AAAAG at 2112, TAAAG at 1928, AAAAG at 1684, TAAAG at 1521, AAAAG at 1218, AAAAG at 891, TAAAG at 881, AAAAG at 709, AAAAG at 503, AAAAG at 310.
  6. PbMer0ci: CTTTT at 3942, CTTTA at 3789, CTTTA at 3372, CTTTT at 2953, CTTTA at 2110, CTTTT at 1275, CTTTA at 1137, CTTTT at 1021, CTTTT at 654, CTTTA at 407, CTTTT at 358, CTTTT at 221, CTTTA at 206.
  7. PbMer2ci: CTTTT at 3664, CTTTA at 3573, CTTTT at 3219, CTTTA at 2055, CTTTT at 1732, CTTTT at 1679, CTTTA at 1184, CTTTT at 858.
  8. PbMer4ci: CTTTT at 3941, CTTTT at 3926, CTTTA at 3014, CTTTT at 3001, CTTTT at 2834, CTTTA at 2278, CTTTT at 2203, CTTTA at 2019, CTTTT at 2013, CTTTA at 1947, CTTTT at 1790, CTTTT at 1732, CTTTT at 1423, CTTTT at 1404, CTTTT at 1345, CTTTA at 828, CTTTT at 594, CTTTT at 472, CTTTA at 191.
  9. PbMer6ci: CTTTA at 3957, CTTTT at 3924, CTTTT at 3672, CTTTT at 3353, CTTTT at 3289, CTTTT at 3282, CTTTA at 2501, CTTTT at 2394, CTTTA at 2340, CTTTA at 2253, CTTTA at 1994, CTTTA at 1531, CTTTT at 1372, CTTTA at 1286.
  10. PbMer8ci: CTTTA at 3802, CTTTT at 3414, CTTTA at 3381, CTTTT at 3060, CTTTT at 3011, CTTTT at 2253, CTTTA at 2056, CTTTT at 1862, CTTTA at 652, CTTTA at 474, CTTTA at 224, CTTTT at 74.

P-box (Mena) analysis and results

Main article: Complex locus A1BG and ZNF497 § P-box (Mena)s

P-box: 5′-(T/A)AAAG-3′.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 16 2 8 8 ± 1 (--9,+-7)
Randoms UTR arbitrary negative 58 10 5.8 5.45 ± 0.35
Randoms UTR alternate negative 51 10 5.1 5.45 ± 0.35
Reals Core negative 7 2 3.5 3.5 ± 0.5 (--4,+-3)
Randoms Core arbitrary negative 1 10 0.1 0.2 ± 0.1
Randoms Core alternate negative 3 10 0.3 0.2 ± 0.1
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 7 10 0.7 0.55 ± 0.15
Randoms Core alternate positive 4 10 0.4 0.55 ± 0.15
Reals Proximal negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms Proximal arbitrary negative 1 10 0.1 0.35 ± 0.25
Randoms Proximal alternate negative 6 10 0.6 0.35 ± 0.25
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Proximal arbitrary positive 5 10 0.5 0.6 ± 0.1
Randoms Proximal alternate positive 7 10 0.7 0.6 ± 0.1
Reals Distal negative 32 2 16 16 ± 2 (--14,+-18)
Randoms Distal arbitrary negative 92 10 9.2 8.95 ± 0.25
Randoms Distal alternate negative 87 10 8.7 8.95 ± 0.25
Reals Distal positive 19 2 9.5 9.5 ± 0.5 (-+9,++10)
Randoms Distal arbitrary positive 131 10 13.1 13.45 ± 0.35
Randoms Distal alternate positive 138 10 13.8 13.45 ± 0.35

Comparison:

The occurrences of real P-box (Mena) UTRs, cores, proximals, and negative distals are greater than the randoms, the positive proximals are less than the randoms. This suggests that the real P-box (Mena)s are likely active or activable.

P-box (Motojima) samplings

Copying a responsive elements consensus sequence TGAGTTCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TGAGTTCA (starting with SuccessablesAAA.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:

  1. negative strand, negative direction, looking for TGAGTTCA, 0.
  2. negative strand, positive direction, looking for TGAGTTCA, 0.
  3. positive strand, negative direction, looking for TGAGTTCA, 1, TGAGTTCA at 1178.
  4. positive strand, positive direction, looking for TGAGTTCA, 0.
  5. inverse complement, negative strand, negative direction, looking for TGAACTCA, 0.
  6. inverse complement, negative strand, positive direction, looking for TGAACTCA, 0.
  7. inverse complement, positive strand, negative direction, looking for TGAACTCA, 0.
  8. inverse complement, positive strand, positive direction, looking for TGAACTCA, 0.

PbMo negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TGAGTTCA at 1178.

P-box (Motojima) random dataset samplings

  1. PbMor0: 0.
  2. PbMor1: 0.
  3. PbMor2: 0.
  4. PbMor3: 0.
  5. PbMor4: 0.
  6. PbMor5: 0.
  7. PbMor6: 0.
  8. PbMor7: 0.
  9. PbMor8: 0.
  10. PbMor9: 0.
  11. PbMor0ci: 0.
  12. PbMor1ci: 0.
  13. PbMor2ci: 0.
  14. PbMor3ci: 0.
  15. PbMor4ci: 0.
  16. PbMor5ci: 1, TGAACTCA at 3800.
  17. PbMor6ci: 1, TGAACTCA at 3098.
  18. PbMor7ci: 0.
  19. PbMor8ci: 0.
  20. PbMor9ci: 0.

PbMor arbitrary (evens) (4560-2846) UTRs

  1. PbMor6ci: TGAACTCA at 3098.

PbMor alternate (odds) (4560-2846) UTRs

  1. PbMor5ci: TGAACTCA at 3800.

PbMor arbitrary positive direction (odds) (4050-1) distal promoters

  1. PbMor5ci: TGAACTCA at 3800.

PbMor alternate positive direction (evens) (4050-1) distal promoters

  1. PbMor6ci: TGAACTCA at 3098.

P-box (Motojima) analysis and results

Main article: Complex locus A1BG and ZNF497 § P-box (Motojima)s

P-box (TGAGTTCA).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
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 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 1 10 0.1 0.1
Randoms Distal alternate positive 1 10 0.1 0.1

Comparison:

The occurrences of real P-box (Motojima)s are greater than the randoms. This suggests that the real P-box (Motojima)s are likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Masaru Motojima, Takao Ando and Toshimasa Yoshioka (10 July 2000). "Sp1-like activity mediates angiotensin-II-induced plasminogen-activator inhibitor type-1 (PAI-1) gene expression in mesangial cells" (PDF). Biomedical Journal. 349 (2): 435–441. doi:10.1042/0264-6021:3490435. PMID 10880342. Retrieved 13 August 2020.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Montaña Mena, Francisco Javier Cejudo, Ines Isabel-Lamoneda and Pilar Carbonero (1 September 2002). "A Role for the DOF Transcription Factor BPBF in the Regulation of Gibberellin-Responsive Genes in Barley Aleurone". Plant Physiology. 130 (1): 111–9. doi:10.1104/pp.0005561. Retrieved 2017-02-19.
  3. ↑ 3.0 3.1 3.2 Wangjie Yu and Paul E. Hardin (2006). "Circadian oscillators of Drosophila and mammals". Journal of Cell Science. 119: 4793–5. doi:10.1242/jcs.03174. Retrieved 2017-02-19.
  4. ↑ 4.0 4.1 Montaña Mena, Jesus Vicente-Carbajosa, Robert J. Schmidt and Pilar Carbonero (October 1998). "An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm". The Plant Journal. 16 (1): 53–62. doi:10.1046/j.1365-313x.1998.00275.x. Retrieved 2017-02-19.

External links

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