P box gene transcriptions

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

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)".[1]

"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)]."[2]

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′."[1]

"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)."[1]

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."[3]

"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)."[3]

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)."[4]

"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)."[4]

P-boxes

P-box (TGAGTTCA).[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

P box consensus sequence is 3'-GTAA(T/C)-5'.[4]

P box consensus sequence is 3'-(T/A)AAAG-5'.[1]

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 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 3'-(A/G)T(A/T)(A/T)(T/C)-5', 84, 3'-ATTTT-5', 66, 3'-GTTTC-5', 93, 3'-GTAAT-5', 153, 3'-GTTTT-5', 164, 3'-GTAAT-5', 173, 3'-ATATT-5', 181, 3'-ATTTT-5', 183, 3'-ATATT-5', 220, 3'-ATTTT-5', 222, 3'-ATAAT-5', 236, 3'-ATTAT-5', 249, 3'-GTTTT-5', 257, 3'-GTATT-5', 269, 3'-ATTAT-5', 271, 3'-GTATC-5', 468, 3'-GTTTT-5', 485, 3'-ATTAT-5', 602, 3'-ATTTT-5', 629, 3'-GTTTT-5', 637, 3'-ATTTT-5', 763, 3'-GTTTT-5', 771, 3'-GTAAC-5', 886, 3'-GTTTT-5', 926, 3'-GTTTT-5', 1092, 3'-GTTTT-5', 1228, 3'-GTAAC-5', 1343, 3'-GTTAT-5', 1362, 3'-GTTTT-5', 1371, 3'-GTTTT-5', 1384, 3'-GTTTT-5', 1394, 3'-ATTTC-5', 1548, 3'-GTTTT-5', 1561, 3'-GTTTC-5', 1638, 3'-ATTAT-5', 1708, 3'-ATTTT-5', 1737, 3'-ATTTT-5', 1872, 3'-GTTTT-5', 1880, 3'-GTTTT-5', 2036, 3'-ATTTC-5', 2174, 3'-GTTTT-5', 2182, 3'-ATTTT-5', 2299, 3'-GTTTT-5', 2307, 3'-GTTTT-5', 2476, 3'-GTTTT-5', 2490, 3'-GTTAT-5', 2497, 3'-GTTTT-5', 2644, 3'-GTTTT-5', 2795, 3'-GTTAT-5', 2849, 3'-ATTTC-5', 2857, 3'-GTTTT-5', 2866, 3'-ATATT-5', 2873, 3'-GTTTC-5', 2891, 3'-ATATC-5', 2902, 3'-GTAAT-5', 2951, 3'-ATAAT-5', 2977, 3'-ATAAT-5', 2998, 3'-ATTTT-5', 3010, 3'-ATTTT-5', 3024, 3'-ATTTT-5', 3163, 3'-GTATT-5', 3169, 3'-ATTTT-5', 3171, 3'-GTAAC-5', 3285, 3'-GTTTT-5', 3313, 3'-GTTTT-5', 3326, 3'-ATTTT-5', 3353, 3'-GTATC-5', 3421, 3'-GTAAT-5', 3436, 3'-ATTTT-5', 3439, 3'-GTATC-5', 3446, 3'-ATAAT-5', 3454, 3'-ATAAT-5', 3468, 3'-ATAAC-5', 3528, 3'-ATTAT-5', 3538, 3'-ATTAC-5', 3658, 3'-GTTTT-5', 3767, 3'-GTATC-5', 4046, 3'-GTTTT-5', 4066, 3'-ATTAT-5', 4077, 3'-GTTTT-5', 4216, 3'-ATTAT-5', 4223, 3'-GTTTT-5', 4310, 3'-GTTTT-5', 4376, 3'-GTTTC-5', 4504, 3'-ATAAT-5', 4538,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPbox-+.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 6, 3'-GTAAC-5', 293, 3'-GTTTT-5', 670, 3'-ATTTT-5', 681, 3'-ATTAT-5', 719, 3'-ATTAT-5', 726, 3'-ATAAT-5', 729,
  3. positive strand in the negative direction is SuccessablesPbox+-.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 40, 3'-ATTTC-5', 22, 3'-ATTTT-5', 190, 3'-GTTTT-5', 215, 3'-GTAAT-5', 248, 3'-ATAAT-5', 270, 3'-GTAAT-5', 397, 3'-GTAAT-5', 534, 3'-GTAAC-5', 613, 3'-GTAAT-5', 670, 3'-GTAAT-5', 804, 3'-GTAAT-5', 1134, 3'-GTAAT-5', 1261, 3'-ATTAC-5', 1296, 3'-ATTTC-5', 1380, 3'-ATATC-5', 1528, 3'-ATATT-5', 1601, 3'-ATTTC-5', 1603, 3'-GTAAT-5', 1707, 3'-ATTAT-5', 1724, 3'-ATTTT-5', 1727, 3'-GTAAT-5', 1779, 3'-GTAAT-5', 1914, 3'-GTAAT-5', 2088, 3'-GTAAT-5', 2675, 3'-ATATT-5', 2851, 3'-ATTTT-5', 2853, 3'-ATTTC-5', 2884, 3'-GTAAT-5', 3064, 3'-GTTTT-5', 3349, 3'-ATATT-5', 3453, 3'-ATATT-5', 3467, 3'-ATTAC-5', 3469, 3'-ATAAT-5', 3537, 3'-ATAAT-5', 3657, 3'-ATTTC-5', 3688, 3'-GTAAT-5', 3973, 3'-ATAAT-5', 4076, 3'-ATAAT-5', 4222, 3'-ATAAT-5', 4225, 3'-ATTTT-5', 4511,
  4. positive strand in the positive direction is SuccessablesPbox++.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 5, 3'-ATATC-5', 261, 3'-ATAAT-5', 704, 3'-ATAAC-5', 721, 3'-ATATT-5', 728, 3'-GTAAC-5', 871,
  5. complement, negative strand, negative direction is SuccessablesPboxc--.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 40, 3'-TAAAG-5', 22, 3'-TAAAA-5', 190, 3'-CAAAA-5', 215, 3'-CATTA-5', 248, 3'-TATTA-5', 270, 3'-CATTA-5', 397, 3'-CATTA-5', 534, 3'-CATTG-5', 613, 3'-CATTA-5', 670, 3'-CATTA-5', 804, 3'-CATTA-5', 1134, 3'-CATTA-5', 1261, 3'-TAATG-5', 1296, 3'-TAAAG-5', 1380, 3'-TATAG-5', 1528, 3'-TATAA-5', 1601, 3'-TAAAG-5', 1603, 3'-CATTA-5', 1707, 3'-TAATA-5', 1724, 3'-TAAAA-5', 1727, 3'-CATTA-5', 1779, 3'-CATTA-5', 1914, 3'-CATTA-5', 2088, 3'-CATTA-5', 2675, 3'-TATAA-5', 2851, 3'-TAAAA-5', 2853, 3'-TAAAG-5', 2884, 3'-CATTA-5', 3064, 3'-CAAAA-5', 3349, 3'-TATAA-5', 3453, 3'-TATAA-5', 3467, 3'-TAATG-5', 3469, 3'-TATTA-5', 3537, 3'-TATTA-5', 3657, 3'-TAAAG-5', 3688, 3'-CATTA-5', 3973, 3'-TATTA-5', 4076, 3'-TATTA-5', 4222, 3'-TATTA-5', 4225, 3'-TAAAA-5', 4511,
  6. complement, negative strand, positive direction is SuccessablesPboxc-+.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 5, 3'-TATAG-5', 261, 3'-TATTA-5', 704, 3'-TATTG-5', 721, 3'-TATAA-5', 728, 3'-CATTG-5', 871,
  7. complement, positive strand, negative direction is SuccessablesPboxc+-.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 84, 3'-TAAAA-5', 66, 3'-CAAAG-5', 93, 3'-CATTA-5', 153, 3'-CAAAA-5', 164, 3'-CATTA-5', 173, 3'-TATAA-5', 181, 3'-TAAAA-5', 183, 3'-TATAA-5', 220, 3'-TAAAA-5', 222, 3'-TATTA-5', 236, 3'-TAATA-5', 249, 3'-CAAAA-5', 257, 3'-CATAA-5', 269, 3'-TAATA-5', 271, 3'-CATAG-5', 468, 3'-CAAAA-5', 485, 3'-TAATA-5', 602, 3'-TAAAA-5', 629, 3'-CAAAA-5', 637, 3'-TAAAA-5', 763, 3'-CAAAA-5', 771, 3'-CATTG-5', 886, 3'-CAAAA-5', 926, 3'-CAAAA-5', 1092, 3'-CAAAA-5', 1228, 3'-CATTG-5', 1343, 3'-CAATA-5', 1362, 3'-CAAAA-5', 1371, 3'-CAAAA-5', 1384, 3'-CAAAA-5', 1394, 3'-TAAAG-5', 1548, 3'-CAAAA-5', 1561, 3'-CAAAG-5', 1638, 3'-TAATA-5', 1708, 3'-TAAAA-5', 1737, 3'-TAAAA-5', 1872, 3'-CAAAA-5', 1880, 3'-CAAAA-5', 2036, 3'-TAAAG-5', 2174, 3'-CAAAA-5', 2182, 3'-TAAAA-5', 2299, 3'-CAAAA-5', 2307, 3'-CAAAA-5', 2476, 3'-CAAAA-5', 2490, 3'-CAATA-5', 2497, 3'-CAAAA-5', 2644, 3'-CAAAA-5', 2795, 3'-CAATA-5', 2849, 3'-TAAAG-5', 2857, 3'-CAAAA-5', 2866, 3'-TATAA-5', 2873, 3'-CAAAG-5', 2891, 3'-TATAG-5', 2902, 3'-CATTA-5', 2951, 3'-TATTA-5', 2977, 3'-TATTA-5', 2998, 3'-TAAAA-5', 3010, 3'-TAAAA-5', 3024, 3'-TAAAA-5', 3163, 3'-CATAA-5', 3169, 3'-TAAAA-5', 3171, 3'-CATTG-5', 3285, 3'-CAAAA-5', 3313, 3'-CAAAA-5', 3326, 3'-TAAAA-5', 3353, 3'-CATAG-5', 3421, 3'-CATTA-5', 3436, 3'-TAAAA-5', 3439, 3'-CATAG-5', 3446, 3'-TATTA-5', 3454, 3'-TATTA-5', 3468, 3'-TATTG-5', 3528, 3'-TAATA-5', 3538, 3'-TAATG-5', 3658, 3'-CAAAA-5', 3767, 3'-CATAG-5', 4046, 3'-CAAAA-5', 4066, 3'-TAATA-5', 4077, 3'-CAAAA-5', 4216, 3'-TAATA-5', 4223, 3'-CAAAA-5', 4310, 3'-CAAAA-5', 4376, 3'-CAAAG-5', 4504, 3'-TATTA-5', 4538,
  8. complement, positive strand, positive direction is SuccessablesPboxc++.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 6, 3'-CATTG-5', 293, 3'-CAAAA-5', 670, 3'-TAAAA-5', 681, 3'-TAATA-5', 719, 3'-TAATA-5', 726, 3'-TATTA-5', 729,
  9. inverse complement, negative strand, negative direction is SuccessablesPboxci--.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 54, 3'-AAAAC-5', 28, 3'-GAAAT-5', 48, 3'-GTAAT-5', 153, 3'-GTAAT-5', 173, 3'-AAAAT-5', 191, 3'-GATAC-5', 211, 3'-AAAAT-5', 217, 3'-AATAT-5', 219, 3'-ATAAT-5', 236, 3'-ATTAT-5', 249, 3'-ATTAT-5', 271, 3'-GAAAT-5', 348, 3'-AATAC-5', 350, 3'-GAAAC-5', 409, 3'-GAAAC-5', 546, 3'-ATTAT-5', 602, 3'-GAAAC-5', 682, 3'-GTAAC-5', 886, 3'-GAAAC-5', 1146, 3'-GTAAC-5', 1343, 3'-GTTAT-5', 1362, 3'-AAAAC-5', 1433, 3'-GATAT-5', 1526, 3'-GAAAC-5', 1688, 3'-ATTAT-5', 1708, 3'-AAAAT-5', 1728, 3'-GAAAT-5', 1734, 3'-GAAAC-5', 1791, 3'-GAAAC-5', 2100, 3'-GAAAC-5', 2217, 3'-GTTAT-5', 2497, 3'-GAAAC-5', 2553, 3'-GTTAT-5', 2849, 3'-AAAAT-5', 2854, 3'-GATAT-5', 2899, 3'-GTAAT-5', 2951, 3'-ATAAT-5', 2977, 3'-ATAAT-5', 2998, 3'-AAAAT-5', 3021, 3'-GAAAC-5', 3076, 3'-GTAAC-5', 3285, 3'-AAAAT-5', 3350, 3'-GTAAT-5', 3436, 3'-ATAAT-5', 3454, 3'-ATAAT-5', 3468, 3'-ATAAC-5', 3528, 3'-ATTAT-5', 3538, 3'-ATTAC-5', 3658, 3'-GAAAC-5', 3985, 3'-ATTAT-5', 4077, 3'-ATTAT-5', 4223, 3'-GAAAC-5', 4462, 3'-AAAAT-5', 4512, 3'-ATAAT-5', 4538,
  10. inverse complement, negative strand, positive direction is SuccessablesPboxci-+.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 6, 3'-GTAAC-5', 293, 3'-GAAAT-5', 356, 3'-GAAAT-5', 653, 3'-ATTAT-5', 719, 3'-ATTAT-5', 726, 3'-ATAAT-5', 729,
  11. inverse complement, positive strand, negative direction is SuccessablesPboxci+-.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 107, 3'-GATAC-5', 58, 3'-AAAAC-5', 67, 3'-GATAT-5', 75, 3'-GATAT-5', 109, 3'-GAAAC-5', 127, 3'-AAAAC-5', 165, 3'-GAAAC-5', 227, 3'-GTAAT-5', 248, 3'-AAAAC-5', 258, 3'-ATAAT-5', 270, 3'-AATAT-5', 272, 3'-GAAAC-5', 304, 3'-GAAAC-5', 313, 3'-AAAAC-5', 359, 3'-GTAAT-5', 397, 3'-GAAAC-5', 474, 3'-AAAAT-5', 488, 3'-AATAC-5', 490, 3'-AAAAT-5', 496, 3'-GTAAT-5', 534, 3'-AATAT-5', 603, 3'-GTAAC-5', 613, 3'-AAAAT-5', 631, 3'-AATAC-5', 633, 3'-AAAAT-5', 640, 3'-GTAAT-5', 670, 3'-AAAAT-5', 765, 3'-AATAC-5', 767, 3'-AAAAT-5', 774, 3'-GTAAT-5', 804, 3'-GTAAT-5', 1134, 3'-GAAAC-5', 1213, 3'-AAAAT-5', 1231, 3'-GTAAT-5', 1261, 3'-ATTAC-5', 1296, 3'-AAAAC-5', 1372, 3'-AAAAC-5', 1386, 3'-AAAAT-5', 1562, 3'-AATAC-5', 1564, 3'-GAAAC-5', 1583, 3'-GATAT-5', 1596, 3'-GAAAT-5', 1631, 3'-GAAAC-5', 1643, 3'-GAAAT-5', 1661, 3'-GATAC-5', 1666, 3'-GTAAT-5', 1707, 3'-ATTAT-5', 1724, 3'-AAAAT-5', 1738, 3'-AATAT-5', 1740, 3'-GTAAT-5', 1779, 3'-GAAAC-5', 1856, 3'-AAAAT-5', 1874, 3'-AATAC-5', 1876, 3'-AAAAT-5', 1884, 3'-GTAAT-5', 1914, 3'-AAAAT-5', 2061, 3'-GTAAT-5', 2088, 3'-GAAAT-5', 2158, 3'-AATAC-5', 2160, 3'-GATAC-5', 2178, 3'-AAAAT-5', 2185, 3'-GAAAC-5', 2283, 3'-AAAAT-5', 2301, 3'-AATAC-5', 2303, 3'-AAAAC-5', 2310, 3'-AAAAC-5', 2491, 3'-AAAAC-5', 2507, 3'-GAAAC-5', 2620, 3'-AATAT-5', 2638, 3'-AAAAT-5', 2646, 3'-GTAAT-5', 2675, 3'-GAAAT-5', 2747, 3'-AAAAC-5', 2840, 3'-AATAT-5', 2850, 3'-AAAAT-5', 2867, 3'-AATAT-5', 2869, 3'-AAAAT-5', 2930, 3'-GAAAC-5', 2958, 3'-AAAAC-5', 2969, 3'-GATAT-5', 2982, 3'-AAAAT-5', 3011, 3'-AAAAC-5', 3027, 3'-GTAAT-5', 3064, 3'-GAAAC-5', 3147, 3'-AAAAC-5', 3165, 3'-AAAAT-5', 3173, 3'-AAAAT-5', 3314, 3'-AAAAC-5', 3328, 3'-AAAAT-5', 3355, 3'-GATAT-5', 3466, 3'-ATTAC-5', 3469, 3'-AAAAC-5', 3510, 3'-ATAAT-5', 3537, 3'-AATAC-5', 3539, 3'-GATAC-5', 3545, 3'-GAAAC-5', 3592, 3'-ATAAT-5', 3657, 3'-AAAAT-5', 3768, 3'-GTAAT-5', 3973, 3'-AAAAT-5', 4069, 3'-ATAAT-5', 4076, 3'-AAAAT-5', 4088, 3'-AAAAT-5', 4219, 3'-ATAAT-5', 4222, 3'-ATAAT-5', 4225, 3'-AAAAC-5', 4311, 3'-AAAAC-5', 4396,
  12. inverse complement, positive strand, positive direction is SuccessablesPboxci++.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 9, 3'-GATAT-5', 260, 3'-GAAAC-5', 507, 3'-AAAAT-5', 671, 3'-AAAAT-5', 682, 3'-ATAAT-5', 704, 3'-ATAAC-5', 721, 3'-AATAT-5', 727, 3'-GAAAC-5', 769, 3'-GTAAC-5', 871,
  13. inverse, negative strand, negative direction, is SuccessablesPboxi--.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 107, 3'-CTATG-5', 58, 3'-TTTTG-5', 67, 3'-CTATA-5', 75, 3'-CTATA-5', 109, 3'-CTTTG-5', 127, 3'-TTTTG-5', 165, 3'-CTTTG-5', 227, 3'-CATTA-5', 248, 3'-TTTTG-5', 258, 3'-TATTA-5', 270, 3'-TTATA-5', 272, 3'-CTTTG-5', 304, 3'-CTTTG-5', 313, 3'-TTTTG-5', 359, 3'-CATTA-5', 397, 3'-CTTTG-5', 474, 3'-TTTTA-5', 488, 3'-TTATG-5', 490, 3'-TTTTA-5', 496, 3'-CATTA-5', 534, 3'-TTATA-5', 603, 3'-CATTG-5', 613, 3'-TTTTA-5', 631, 3'-TTATG-5', 633, 3'-TTTTA-5', 640, 3'-CATTA-5', 670, 3'-TTTTA-5', 765, 3'-TTATG-5', 767, 3'-TTTTA-5', 774, 3'-CATTA-5', 804, 3'-CATTA-5', 1134, 3'-CTTTG-5', 1213, 3'-TTTTA-5', 1231, 3'-CATTA-5', 1261, 3'-TAATG-5', 1296, 3'-TTTTG-5', 1372, 3'-TTTTG-5', 1386, 3'-TTTTA-5', 1562, 3'-TTATG-5', 1564, 3'-CTTTG-5', 1583, 3'-CTATA-5', 1596, 3'-CTTTA-5', 1631, 3'-CTTTG-5', 1643, 3'-CTTTA-5', 1661, 3'-CTATG-5', 1666, 3'-CATTA-5', 1707, 3'-TAATA-5', 1724, 3'-TTTTA-5', 1738, 3'-TTATA-5', 1740, 3'-CATTA-5', 1779, 3'-CTTTG-5', 1856, 3'-TTTTA-5', 1874, 3'-TTATG-5', 1876, 3'-TTTTA-5', 1884, 3'-CATTA-5', 1914, 3'-TTTTA-5', 2061, 3'-CATTA-5', 2088, 3'-CTTTA-5', 2158, 3'-TTATG-5', 2160, 3'-CTATG-5', 2178, 3'-TTTTA-5', 2185, 3'-CTTTG-5', 2283, 3'-TTTTA-5', 2301, 3'-TTATG-5', 2303, 3'-TTTTG-5', 2310, 3'-TTTTG-5', 2491, 3'-TTTTG-5', 2507, 3'-CTTTG-5', 2620, 3'-TTATA-5', 2638, 3'-TTTTA-5', 2646, 3'-CATTA-5', 2675, 3'-CTTTA-5', 2747, 3'-TTTTG-5', 2840, 3'-TTATA-5', 2850, 3'-TTTTA-5', 2867, 3'-TTATA-5', 2869, 3'-TTTTA-5', 2930, 3'-CTTTG-5', 2958, 3'-TTTTG-5', 2969, 3'-CTATA-5', 2982, 3'-TTTTA-5', 3011, 3'-TTTTG-5', 3027, 3'-CATTA-5', 3064, 3'-CTTTG-5', 3147, 3'-TTTTG-5', 3165, 3'-TTTTA-5', 3173, 3'-TTTTA-5', 3314, 3'-TTTTG-5', 3328, 3'-TTTTA-5', 3355, 3'-CTATA-5', 3466, 3'-TAATG-5', 3469, 3'-TTTTG-5', 3510, 3'-TATTA-5', 3537, 3'-TTATG-5', 3539, 3'-CTATG-5', 3545, 3'-CTTTG-5', 3592, 3'-TATTA-5', 3657, 3'-TTTTA-5', 3768, 3'-CATTA-5', 3973, 3'-TTTTA-5', 4069, 3'-TATTA-5', 4076, 3'-TTTTA-5', 4088, 3'-TTTTA-5', 4219, 3'-TATTA-5', 4222, 3'-TATTA-5', 4225, 3'-TTTTG-5', 4311, 3'-TTTTG-5', 4396,
  14. inverse, negative strand, positive direction, is SuccessablesPboxi-+.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 9, 3'-CTATA-5', 260, 3'-CTTTG-5', 507, 3'-TTTTA-5', 671, 3'-TTTTA-5', 682, 3'-TATTA-5', 704, 3'-TATTG-5', 721, 3'-TTATA-5', 727, 3'-CTTTG-5', 769, 3'-CATTG-5', 871,
  15. inverse, positive strand, negative direction, is SuccessablesPboxi+-.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 54, 3'-TTTTG-5', 28, 3'-CTTTA-5', 48, 3'-CATTA-5', 153, 3'-CATTA-5', 173, 3'-TTTTA-5', 191, 3'-CTATG-5', 211, 3'-TTTTA-5', 217, 3'-TTATA-5', 219, 3'-TATTA-5', 236, 3'-TAATA-5', 249, 3'-TAATA-5', 271, 3'-CTTTA-5', 348, 3'-TTATG-5', 350, 3'-CTTTG-5', 409, 3'-CTTTG-5', 546, 3'-TAATA-5', 602, 3'-CTTTG-5', 682, 3'-CATTG-5', 886, 3'-CTTTG-5', 1146, 3'-CATTG-5', 1343, 3'-CAATA-5', 1362, 3'-TTTTG-5', 1433, 3'-CTATA-5', 1526, 3'-CTTTG-5', 1688, 3'-TAATA-5', 1708, 3'-TTTTA-5', 1728, 3'-CTTTA-5', 1734, 3'-CTTTG-5', 1791, 3'-CTTTG-5', 2100, 3'-CTTTG-5', 2217, 3'-CAATA-5', 2497, 3'-CTTTG-5', 2553, 3'-CAATA-5', 2849, 3'-TTTTA-5', 2854, 3'-CTATA-5', 2899, 3'-CATTA-5', 2951, 3'-TATTA-5', 2977, 3'-TATTA-5', 2998, 3'-TTTTA-5', 3021, 3'-CTTTG-5', 3076, 3'-CATTG-5', 3285, 3'-TTTTA-5', 3350, 3'-CATTA-5', 3436, 3'-TATTA-5', 3454, 3'-TATTA-5', 3468, 3'-TATTG-5', 3528, 3'-TAATA-5', 3538, 3'-TAATG-5', 3658, 3'-CTTTG-5', 3985, 3'-TAATA-5', 4077, 3'-TAATA-5', 4223, 3'-CTTTG-5', 4462, 3'-TTTTA-5', 4512, 3'-TATTA-5', 4538,
  16. inverse, positive strand, positive direction, is SuccessablesPboxi++.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 6, 3'-CATTG-5', 293, 3'-CTTTA-5', 356, 3'-CTTTA-5', 653, 3'-TAATA-5', 719, 3'-TAATA-5', 726, 3'-TATTA-5', 729.

P-box samplings

Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (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 AAAAAAAA, 0.
  2. negative strand, positive direction, looking for AAAAAAAA, 0.
  3. positive strand, negative direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  8. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  12. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse negative strand, positive direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  16. inverse positive strand, positive direction, looking for AAAAAAAA, 0.

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 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.
  2. ↑ 2.0 2.1 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.
  3. ↑ 3.0 3.1 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.
  4. ↑ 4.0 4.1 4.2 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.

External links

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