Downstream promoter element gene transcriptions: Difference between revisions

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# complement, positive strand, negative direction is SuccessablesDPEJc+-.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 63, 5'-CCTGTA-3' at 395, 5'-CCAGCA-3' at 404, 5'-CCAAGA-3' at 420, 5'-TCAGGA-3' at 442, 5'-TCTACA-3' at 482, 5'-CCAGCA-3' at 541, 5'-CCAAGA-3' at 557, 5'-TCAGGA-3' at 579, 5'-CCTGTA-3' at 668, 5'-CCAGCA-3' at 677, 5'-TCAGGA-3' at 715, 5'-CCTGTA-3' at 802, 5'-CCAGGA-3' at 851, 5'-CCAAGA-3' at 875, 5'-CCTGTA-3' at 968, 5'-TCAGGA-3' at 985, 5'-CCTGTA-3' at 1132, 5'-CCAGCA-3' at 1141, 5'-CCAACA-3' at 1204, 5'-TCTACA-3' at 1225, 5'-CCTGTA-3' at 1259, 5'-TCAGGA-3' at 1276, 5'-TCTATA-3' at 1526, 5'-CCAGCA-3' at 1612, 5'-TCTGTA-3' at 1777, 5'-CCAGCA-3' at 1786, 5'-CCTGTA-3' at 1912, 5'-TCAGGA-3' at 2135, 5'-CCAACA-3' at 2149, 5'-CCAGTA-3' at 2212, 5'-TCAGGA-3' at 2251, 5'-CCTGGA-3' at 2269, 5'-CCTGTA-3' at 2338, 5'-TCAATA-3' at 2497, 5'-CCTGTA-3' at 2539, 5'-CCAACA-3' at 2548, 5'-TCAGGA-3' at 2588, 5'-CCAACA-3' at 2611, 5'-CCTGTA-3' at 2673, 5'-CCAATA-3' at 2849, 5'-TCTACA-3' at 2989, 5'-CCTGTA-3' at 3062, 5'-CCAGCA-3' at 3071, 5'-TCAGGA-3' at 3111, 5'-CCAACA-3' at 3138, 5'-TCAGGA-3' at 3218, 5'-CCAGGA-3' at 3250, 5'-CCAAGA-3' at 3274, 5'-CCAGCA-3' at 3732, 5'-CCTGGA-3' at 3745, 5'-TCTGGA-3' at 3836, 5'-CCTGGA-3' at 3907, 5'-CCTGTA-3' at 3971, 5'-CCAACA-3' at 3980, 5'-CCAAGA-3' at 4020, 5'-TCAAGA-3' at 4028, 5'-TCTACA-3' at 4063, 5'-CCTGTA-3' at 4122, 5'-TCAGGA-3' at 4139, 5'-CCAGGA-3' at 4171, 5'-TCAAGA-3' at 4179, 5'-TCTACA-3' at 4213, 5'-TCAGGA-3' at 4437.
# complement, positive strand, negative direction is SuccessablesDPEJc+-.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 63, 5'-CCTGTA-3' at 395, 5'-CCAGCA-3' at 404, 5'-CCAAGA-3' at 420, 5'-TCAGGA-3' at 442, 5'-TCTACA-3' at 482, 5'-CCAGCA-3' at 541, 5'-CCAAGA-3' at 557, 5'-TCAGGA-3' at 579, 5'-CCTGTA-3' at 668, 5'-CCAGCA-3' at 677, 5'-TCAGGA-3' at 715, 5'-CCTGTA-3' at 802, 5'-CCAGGA-3' at 851, 5'-CCAAGA-3' at 875, 5'-CCTGTA-3' at 968, 5'-TCAGGA-3' at 985, 5'-CCTGTA-3' at 1132, 5'-CCAGCA-3' at 1141, 5'-CCAACA-3' at 1204, 5'-TCTACA-3' at 1225, 5'-CCTGTA-3' at 1259, 5'-TCAGGA-3' at 1276, 5'-TCTATA-3' at 1526, 5'-CCAGCA-3' at 1612, 5'-TCTGTA-3' at 1777, 5'-CCAGCA-3' at 1786, 5'-CCTGTA-3' at 1912, 5'-TCAGGA-3' at 2135, 5'-CCAACA-3' at 2149, 5'-CCAGTA-3' at 2212, 5'-TCAGGA-3' at 2251, 5'-CCTGGA-3' at 2269, 5'-CCTGTA-3' at 2338, 5'-TCAATA-3' at 2497, 5'-CCTGTA-3' at 2539, 5'-CCAACA-3' at 2548, 5'-TCAGGA-3' at 2588, 5'-CCAACA-3' at 2611, 5'-CCTGTA-3' at 2673, 5'-CCAATA-3' at 2849, 5'-TCTACA-3' at 2989, 5'-CCTGTA-3' at 3062, 5'-CCAGCA-3' at 3071, 5'-TCAGGA-3' at 3111, 5'-CCAACA-3' at 3138, 5'-TCAGGA-3' at 3218, 5'-CCAGGA-3' at 3250, 5'-CCAAGA-3' at 3274, 5'-CCAGCA-3' at 3732, 5'-CCTGGA-3' at 3745, 5'-TCTGGA-3' at 3836, 5'-CCTGGA-3' at 3907, 5'-CCTGTA-3' at 3971, 5'-CCAACA-3' at 3980, 5'-CCAAGA-3' at 4020, 5'-TCAAGA-3' at 4028, 5'-TCTACA-3' at 4063, 5'-CCTGTA-3' at 4122, 5'-TCAGGA-3' at 4139, 5'-CCAGGA-3' at 4171, 5'-TCAAGA-3' at 4179, 5'-TCTACA-3' at 4213, 5'-TCAGGA-3' at 4437.
# complement, positive strand, positive direction is SuccessablesDPEJc++.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 18, 5'-CCTGGA-3' at 38, 5'-CCAGGA-3' at 219, 5'-TCAGGA-3' at 758, 5'-CCTGTA-3' at 1870, 5'-TCAAGA-3' at 1988, 5'-CCTATA-3' at 2660, 5'-CCTACA-3' at 2715, 5'-TCTGGA-3' at 2862, 5'-CCAAGA-3' at 2923, 5'-TCAAGA-3' at 2955, 5'-TCAGGA-3' at 2999, 5'-CCAATA-3' at 3025, 5'-CCAACA-3' at 3051, 5'-TCAATA-3' at 3382, 5'-TCTGGA-3' at 3551, 5'-CCTACA-3' at 3575, 5'-TCAGGA-3' at 3864, 5'-CCAAGA-3' at 4074.
# complement, positive strand, positive direction is SuccessablesDPEJc++.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 18, 5'-CCTGGA-3' at 38, 5'-CCAGGA-3' at 219, 5'-TCAGGA-3' at 758, 5'-CCTGTA-3' at 1870, 5'-TCAAGA-3' at 1988, 5'-CCTATA-3' at 2660, 5'-CCTACA-3' at 2715, 5'-TCTGGA-3' at 2862, 5'-CCAAGA-3' at 2923, 5'-TCAAGA-3' at 2955, 5'-TCAGGA-3' at 2999, 5'-CCAATA-3' at 3025, 5'-CCAACA-3' at 3051, 5'-TCAATA-3' at 3382, 5'-TCTGGA-3' at 3551, 5'-CCTACA-3' at 3575, 5'-TCAGGA-3' at 3864, 5'-CCAAGA-3' at 4074.
# inverse complement, negative strand, negative direction is SuccessablesDPEci--.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 174, 3'-TGTCT-5', 13, 3'-TGACT-5', 17, 3'-CAACT-5', 85, 3'-TATCT-5', 100, 3'-CATCC-5', 119, 3'-TGACT-5', 130, 3'-CGACT-5', 140, 3'-TGTCT-5', 168, 3'-GGTCC-5', 262, 3'-CATCT-5', 284, 3'-TGTCT-5', 289, 3'-TGACT-5', 307, 3'-GAACC-5', 328, 3'-TATCT-5', 355, 3'-TGTCC-5', 424, 3'-GGACC-5', 459, 3'-GGACC-5', 508, 3'-TGTCC-5', 561, 3'-CGTCC-5', 565, 3'-TAACT-5', 585, 3'-GGACC-5', 596, 3'-TAACC-5', 643, 3'-GGTCC-5', 648, 3'-CGTCC-5', 697, 3'-GGACT-5', 732, 3'-CGACC-5', 781, 3'-CGACT-5', 825, 3'-CGTCC-5', 831, 3'-GAACT-5', 843, 3'-GGTCC-5', 850, 3'-GGACC-5', 899, 3'-TGTCT-5', 907, 3'-GGTCC-5', 948, 3'-CATCT-5', 970, 3'-CGACT-5', 991, 3'-CGTCC-5', 997, 3'-GAACT-5', 1009, 3'-GGACC-5', 1015, 3'-CGTCT-5', 1023, 3'-TAACC-5', 1045, 3'-TGTCT-5', 1073, 3'-CGACC-5', 1111, 3'-GGACT-5', 1173, 3'-GGACC-5', 1198, 3'-CGACT-5', 1282, 3'-CGTCC-5', 1288, 3'-GAACT-5', 1300, 3'-GATCC-5', 1307, 3'-CGTCT-5', 1314, 3'-GGTCT-5', 1411, 3'-GGTCC-5', 1460, 3'-CGACC-5', 1464, 3'-GGTCT-5', 1518, 3'-TGTCT-5', 1567, 3'-CGTCT-5', 1614, 3'-GGACT-5', 1623, 3'-GAACC-5', 1649, 3'-CATCT-5', 1653, 3'-GGTCT-5', 1670, 3'-TATCT-5', 1710, 3'-CGACC-5', 1746, 3'-CGACC-5', 1756, 3'-CGACT-5', 1800, 3'-CGTCC-5', 1823, 3'-GGACC-5', 1841, 3'-CAACT-5', 1853, 3'-CGACC-5', 1891, 3'-GAACC-5', 1927, 3'-TGACT-5', 1935, 3'-CGTCC-5', 1941, 3'-GGACC-5', 1959, 3'-CGTCT-5', 1967, 3'-GGACC-5', 2009, 3'-TGTCT-5', 2017, 3'-CGACC-5', 2069, 3'-GGTCC-5', 2077, 3'-CGACT-5', 2109, 3'-TGTCT-5', 2119, 3'-GAACT-5', 2127, 3'-CGACT-5', 2226, 3'-CAACC-5', 2235, 3'-GGACC-5', 2268, 3'-CGACC-5', 2326, 3'-CGACT-5', 2361, 3'-CGTCC-5', 2367, 3'-GAACT-5', 2379, 3'-GGACC-5', 2385, 3'-CGTCC-5', 2389, 3'-GGACC-5', 2435, 3'-TGTCT-5', 2443, 3'-TGTCC-5', 2514, 3'-GGTCC-5', 2519, 3'-CGACT-5', 2562, 3'-CGTCC-5', 2568, 3'-GAACT-5', 2580, 3'-CAACT-5', 2593, 3'-TGTCC-5', 2689, 3'-CGACT-5', 2696, 3'-CAACT-5', 2705, 3'-GAACT-5', 2714, 3'-GGACC-5', 2720, 3'-CGACT-5', 2744, 3'-GGACC-5', 2770, 3'-TGTCT-5', 2778, 3'-TGTCT-5', 2878, 3'-TATCT-5', 2903, 3'-GAACC-5', 2921, 3'-CGACC-5', 3035, 3'-CGACC-5', 3041, 3'-CGACT-5', 3085, 3'-GAACT-5', 3103, 3'-CAACC-5', 3116, 3'-GGACC-5', 3128, 3'-CGACC-5', 3180, 3'-CGACT-5', 3224, 3'-GAACT-5', 3242, 3'-GGTCC-5', 3249, 3'-CATCT-5', 3256, 3'-GGACC-5', 3298, 3'-TAACT-5', 3358, 3'-GAACT-5', 3401, 3'-TATCT-5', 3422, 3'-CGTCT-5', 3431, 3'-TATCC-5', 3447, 3'-GATCT-5', 3463, 3'-GGTCT-5', 3486, 3'-CAACT-5', 3505, 3'-TAACC-5', 3529, 3'-CAACT-5', 3533, 3'-TGACT-5', 3542, 3'-GGTCC-5', 3564, 3'-GAACT-5', 3571, 3'-GGTCC-5', 3585, 3'-CGTCT-5', 3589, 3'-CAACC-5', 3606, 3'-CGACT-5', 3649, 3'-TGTCT-5', 3672, 3'-CGACC-5', 3719, 3'-GGACC-5', 3744, 3'-TGACC-5', 3749, 3'-GGACT-5', 3781, 3'-GAACC-5', 3793, 3'-CAACT-5', 3805, 3'-CATCT-5', 3820, 3'-CGACC-5', 3864, 3'-GGTCC-5', 3871, 3'-GGTCC-5', 3885, 3'-GGACC-5', 3906, 3'-TGTCT-5', 3917, 3'-GGACT-5', 3932, 3'-CAACC-5', 3942, 3'-CAACC-5', 3946, 3'-GGTCC-5', 3951, 3'-CGACT-5', 3994, 3'-GAACT-5', 4012, 3'-GGACC-5', 4037, 3'-TATCT-5', 4079, 3'-CAACC-5', 4097, 3'-GGTCC-5', 4102, 3'-CGACT-5', 4145, 3'-GGTCC-5', 4170, 3'-GAACC-5', 4188, 3'-GGTCT-5', 4233, 3'-GGTCC-5', 4253, 3'-GAACC-5', 4268, 3'-CGACT-5', 4276, 3'-CGTCC-5', 4282, 3'-GAACT-5', 4294, 3'-GGACC-5', 4300, 3'-GGACC-5', 4349, 3'-GGTCT-5', 4448, 3'-GGACC-5', 4494, 3'-TGTCT-5', 4518, 3'-GGACC-5', 4546,
# inverse complement, negative strand, negative direction is SuccessablesDPEci--.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 18, 5'-ACATCT-3' at 284, 5'-AGGACC-3' at 596, 5'-ACATCT-3' at 970, 5'-ATGTCT-3' at 1567, 5'-AGAACC-3' at 1649, 5'-AGGACC-3' at 1841, 5'-ACAACT-3' at 1853, 5'-ACGACC-3' at 2326, 5'-ATATCT-3' at 2903, 5'-ACGTCT-3' at 3431, 5'-ATAACC-3' at 3529, 5'-ATGACT-3' at 3542, 5'-AGGTCC-3' at 3585, 5'-AGAACC-3' at 3793, 5'-ACGACC-3' at 3864, 5'-AGGACC-3' at 3906, 5'-ACAACC-3' at 3942, 5'-AGGACC-3' at 4546, and complements.
# inverse complement, negative strand, positive direction is SuccessablesDPEci-+.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 95, 3'-CATCC-5' at 30, 3'-GGACC-5' at 37, 3'-TGTCC-5' at 82, 3'-TGTCT-5' at 100, 3'-GGACC-5' at 187, 3'-GGTCC-5' at 218, 3'-TGTCT-5' at 268, 3'-CAACC-5' at 608, 3'-CATCC-5' at 629, 3'-CATCC-5' at 698, 3'-GGACT-5' at 746, 3'-GGACT-5' at 814, 3'-CAACC-5' at 844, 3'-GATCC-5' at 865, 3'-TGTCC-5' at 893, 3'-CGACT-5' at 898, 3'-GGACT-5' at 914, 3'-CAACC-5' at 944, 3'-GATCC-5' at 965, 3'-TGTCC-5' at 993, 3'-CGACT-5' at 998, 3'-CAACC-5' at 1280, 3'-CGTCT-5' at 1393, 3'-CGTCT-5' at 1493, 3'-CAACC-5' at 1616, 3'-TGACC-5' at 1662, 3'-GGTCT-5' at 1711, 3'-TGTCT-5' at 1731, 3'-GAACC-5' at 1811, 3'-TGTCT-5' at 1862, 3'-CGTCC-5' at 1930, 3'-GAACT-5' at 1951, 3'-GGTCT-5' at 1958, 3'-CAACC-5' at 2013, 3'-TGTCT-5' at 2078, 3'-CATCT-5' at 2111, 3'-CAACC-5' at 2120, 3'-TGTCT-5' at 2172, 3'-TGACC-5' at 2213, 3'-GAACC-5' at 2225, 3'-GGTCT-5' at 2258, 3'-GGACT-5' at 2271, 3'-CGACT-5' at 2359, 3'-GATCC-5' at 2378, 3'-TGTCT-5' at 2466, 3'-GGTCT-5' at 2489, 3'-GATCC-5' at 2514, 3'-GAACC-5' at 2579, 3'-GGACT-5' at 2672, 3'-GAACC-5' at 2776, 3'-GGACT-5' at 2820, 3'-CATCT-5' at 2852, 3'-TGACC-5' at 2873, 3'-GGTCT-5' at 2941, 3'-TGACT-5' at 2945, 3'-TGTCT-5' at 3004, 3'-GGTCT-5' at 3019, 3'-TGACT-5' at 3029, 3'-TGTCT-5' at 3053, 3'-CATCC-5' at 3108, 3'-GGACC-5' at 3172, 3'-CGTCC-5' at 3203, 3'-GGTCT-5' at 3245, 3'-CGTCT-5' at 3256, 3'-CAACT-5' at 3291, 3'-GGTCT-5' at 3299, 3'-CATCT-5' at 3329, 3'-TATCC-5' at 3384, 3'-TGTCT-5' at 3392, 3'-CATCT-5' at 3403, 3'-GGACC-5' at 3545, 3'-TGTCC-5' at 3577, 3'-GGTCT-5' at 3608, 3'-TGTCC-5' at 3619, 3'-CATCC-5' at 3629, 3'-TGACC-5' at 3714, 3'-TAACT-5' at 3733, 3'-GGTCT-5' at 3771, 3'-TGACC-5' at 3784, 3'-CGACT-5' at 3801, 3'-GAACC-5' at 3838, 3'-GAACC-5' at 3856, 3'-CAACC-5' at 3911, 3'-GAACC-5' at 3937, 3'-TGACC-5' at 4018, 3'-GAACT-5' at 4048, 3'-CGTCT-5' at 4056, 3'-GATCC-5' at 4081, 3'-CATCC-5' at 4183, 3'-TGACC-5' at 4216, 3'-CGACC-5' at 4358, 3'-TGTCC-5' at 4367, 3'-GGTCT-5' at 4380, 3'-GGTCT-5' at 4414, 3'-GGTCC-5' at 4420.
# inverse complement, negative strand, positive direction is SuccessablesDPEci-+.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 16, 5'-AGGTCC-3' at 218, 5'-AGATCC-3' at 865, 5'-AGATCC-3' at 965, 5'-AGAACC-3' at 1811, 5'-AGAACT-3' at 1951, 5'-AGAACC-3' at 2225, 5'-AGGTCT-3' at 2258, 5'-AGAACC-3' at 2776, 5'-AGGTCT-3' at 3019, 5'-ATGACT-3' at 3029, 5'-ACGTCT-3' at 3256, 5'-ATGTCC-3' at 3577, 5'-AGGTCT-3' at 3771, 5'-ATGACC-3' at 3784, 5'-AGAACT-3' at 4048, 5'-ATGTCC-3' at 4367, and complements.
# inverse complement, positive strand, negative direction is SuccessablesDPEci+-.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 58, 3'-GGACC-5', 32, 3'-TGTCT-5', 479, 3'-CATCC-5', 593, 3'-TAACC-5', 614, 3'-TGACC-5', 734, 3'-CGTCT-5', 754, 3'-GAACC-5', 846, 3'-TGTCT-5', 921, 3'-GATCC-5', 973, 3'-GAACC-5', 1012, 3'-TGACT-5', 1051, 3'-TGTCT-5', 1087, 3'-CGACC-5', 1191, 3'-TGTCT-5', 1222, 3'-GAACC-5', 1303, 3'-CAACC-5', 1407, 3'-GATCT-5', 1482, 3'-CAACC-5', 1514, 3'-TATCC-5', 1529, 3'-CATCC-5', 1572, 3'-GAACT-5', 1685, 3'-TATCT-5', 1731, 3'-CGTCT-5', 1774, 3'-GATCC-5', 1813, 3'-CATCC-5', 1838, 3'-CATCT-5', 1863, 3'-GAACC-5', 1956, 3'-TGTCT-5', 2031, 3'-TGTCT-5', 2165, 3'-TGACC-5', 2189, 3'-CATCT-5', 2290, 3'-GAACC-5', 2382, 3'-GAACC-5', 2717, 3'-TGACT-5', 2786, 3'-CAACC-5', 2844, 3'-CAACT-5', 2911, 3'-TGTCT-5', 2986, 3'-CATCT-5', 3154, 3'-GAACC-5', 3245, 3'-TGTCT-5', 3321, 3'-GAACT-5', 3460, 3'-CAACT-5', 3524, 3'-CATCT-5', 3551, 3'-GGACT-5', 3640, 3'-CGTCC-5', 3698, 3'-GGACT-5', 3747, 3'-GAACC-5', 3784, 3'-TGTCT-5', 3833, 3'-CAACT-5', 3849, 3'-GGACC-5', 3868, 3'-CATCC-5', 3903, 3'-CATCT-5', 4058, 3'-TGTCT-5', 4210, 3'-GGACT-5', 4327, 3'-TGTCT-5', 4371, 3'-GAACC-5', 4451, 3'-CATCC-5', 4456, 3'-GATCC-5', 4476,
# inverse complement, positive strand, negative direction is SuccessablesDPEci+-.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 58, 3'-GGACC-5', 32, 3'-TGTCT-5', 479, 3'-CATCC-5', 593, 3'-TAACC-5', 614, 3'-TGACC-5', 734, 3'-CGTCT-5', 754, 3'-GAACC-5', 846, 3'-TGTCT-5', 921, 3'-GATCC-5', 973, 3'-GAACC-5', 1012, 3'-TGACT-5', 1051, 3'-TGTCT-5', 1087, 3'-CGACC-5', 1191, 3'-TGTCT-5', 1222, 3'-GAACC-5', 1303, 3'-CAACC-5', 1407, 3'-GATCT-5', 1482, 3'-CAACC-5', 1514, 3'-TATCC-5', 1529, 3'-CATCC-5', 1572, 3'-GAACT-5', 1685, 3'-TATCT-5', 1731, 3'-CGTCT-5', 1774, 3'-GATCC-5', 1813, 3'-CATCC-5', 1838, 3'-CATCT-5', 1863, 3'-GAACC-5', 1956, 3'-TGTCT-5', 2031, 3'-TGTCT-5', 2165, 3'-TGACC-5', 2189, 3'-CATCT-5', 2290, 3'-GAACC-5', 2382, 3'-GAACC-5', 2717, 3'-TGACT-5', 2786, 3'-CAACC-5', 2844, 3'-CAACT-5', 2911, 3'-TGTCT-5', 2986, 3'-CATCT-5', 3154, 3'-GAACC-5', 3245, 3'-TGTCT-5', 3321, 3'-GAACT-5', 3460, 3'-CAACT-5', 3524, 3'-CATCT-5', 3551, 3'-GGACT-5', 3640, 3'-CGTCC-5', 3698, 3'-GGACT-5', 3747, 3'-GAACC-5', 3784, 3'-TGTCT-5', 3833, 3'-CAACT-5', 3849, 3'-GGACC-5', 3868, 3'-CATCC-5', 3903, 3'-CATCT-5', 4058, 3'-TGTCT-5', 4210, 3'-GGACT-5', 4327, 3'-TGTCT-5', 4371, 3'-GAACC-5', 4451, 3'-CATCC-5', 4456, 3'-GATCC-5', 4476,
# inverse complement, positive strand, positive direction is SuccessablesDPEci++.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 152, 3'-GGTCC-5' at 8, 3'-GGTCT-5' at 15, 3'-TAACC-5' at 24, 3'-GGTCC-5' at 33, 3'-GGACC-5' at 40, 3'-TGTCC-5' at 157, 3'-CGTCC-5' at 194, 3'-GGTCT-5' at 204, 3'-GGTCC-5' at 215, 3'-CGACC-5' at 277, 3'-GGACC-5' at 286, 3'-CGTCC-5' at 318, 3'-TGACC-5' at 347, 3'-TGTCC-5' at 365, 3'-CGTCC-5' at 379, 3'-CGACC-5' at 386, 3'-CGTCT-5' at 396, 3'-CGACC-5' at 417, 3'-GGTCC-5' at 424, 3'-CGTCT-5' at 438, 3'-GGTCT-5' at 468, 3'-GGTCC-5' at 515, 3'-TGTCC-5' at 552, 3'-GGACC-5' at 598, 3'-CGTCC-5' at 658, 3'-GGTCC-5' at 707, 3'-GGACT-5' at 725, 3'-CGACC-5' at 779, 3'-GGTCT-5' at 835, 3'-GGACC-5' at 847, 3'-GGACT-5' at 859, 3'-GGTCT-5' at 935, 3'-GGACC-5' at 947, 3'-GGACT-5' at 959, 3'-TGACC-5' at 1140, 3'-GGTCC-5' at 1175, 3'-GGACC-5' at 1199, 3'-TGACT-5' at 1286, 3'-CGTCT-5' at 1316, 3'-CGTCT-5' at 1416, 3'-GGTCT-5' at 1631, 3'-GGACT-5' at 1660, 3'-GGACT-5' at 1676, 3'-CGACC-5' at 1736, 3'-GGTCT-5' at 1742, 3'-CGACC-5' at 1779, 3'-CGTCC-5' at 1788, 3'-GAACC-5' at 1799, 3'-GGACC-5' at 1815, 3'-GGTCC-5' at 1855, 3'-CATCC-5' at 1875, 3'-GGTCC-5' at 1893, 3'-CGTCC-5' at 1905, 3'-CGTCT-5' at 1937, 3'-TGACC-5' at 1953, 3'-TGTCC-5' at 1966, 3'-TGTCC-5' at 2125, 3'-CAACC-5' at 2185, 3'-GGACT-5' at 2211, 3'-GGTCT-5' at 2228, 3'-CATCC-5' at 2255, 3'-CGTCC-5' at 2296, 3'-GGTCC-5' at 2316, 3'-CGACC-5' at 2320, 3'-CGACC-5' at 2405, 3'-TGTCT-5' at 2414, 3'-GGACC-5' at 2433, 3'-GATCC-5' at 2482, 3'-GGACC-5' at 2501, 3'-CAACC-5' at 2541, 3'-TATCC-5' at 2550, 3'-GGACC-5' at 2569, 3'-GGTCC-5' at 2574, 3'-TATCT-5' at 2627, 3'-GATCC-5' at 2639, 3'-TGTCT-5' at 2652, 3'-TGACT-5' at 2674, 3'-CGTCC-5' at 2683, 3'-CGTCT-5' at 2721, 3'-CGACC-5' at 2734, 3'-CGTCC-5' at 2745, 3'-CGACC-5' at 2770, 3'-GGTCC-5' at 2780, 3'-CGACC-5' at 2810, 3'-CAACC-5' at 2816, 3'-TGTCT-5' at 2837, 3'-CGTCT-5' at 2859, 3'-GGTCC-5' at 2876, 3'-GGACC-5' at 2891, 3'-CGACT-5' at 2915, 3'-GGACT-5' at 2968, 3'-GGACC-5' at 2988, 3'-GGTCC-5' at 3016, 3'-GGACC-5' at 3047, 3'-GGTCT-5' at 3091, 3'-GGTCC-5' at 3111, 3'-TGACC-5' at 3117, 3'-CGTCC-5' at 3128, 3'-TGTCT-5' at 3133, 3'-CGTCC-5' at 3147, 3'-TGTCT-5' at 3179, 3'-CGTCT-5' at 3214, 3'-GGTCT-5' at 3221, 3'-CGACC-5' at 3242, 3'-GGACC-5' at 3296, 3'-TGACC-5' at 3345, 3'-GGACC-5' at 3362, 3'-CATCT-5' at 3416, 3'-CGTCC-5' at 3466, 3'-CGTCT-5' at 3473, 3'-GATCC-5' at 3484, 3'-GGACC-5' at 3496, 3'-GATCC-5' at 3522, 3'-CGACC-5' at 3526, 3'-GGTCC-5' at 3536, 3'-GGTCT-5' at 3548, 3'-TGTCC-5' at 3571, 3'-CGACT-5' at 3588, 3'-TGTCC-5' at 3636, 3'-CGTCC-5' at 3662, 3'-GGACC-5' at 3679, 3'-GGTCC-5' at 3687, 3'-CGTCC-5' at 3694, 3'-TGACT-5' at 3735, 3'-CATCC-5' at 3753, 3'-GGACC-5' at 3758, 3'-CGTCC-5' at 3768, 3'-CGACT-5' at 3778, 3'-GGACC-5' at 3787, 3'-GGTCT-5' at 3806, 3'-CGTCT-5' at 3831, 3'-GGTCT-5' at 3891, 3'-CGTCT-5' at 3916, 3'-TGTCC-5' at 3975, 3'-CGACC-5' at 3989, 3'-GAACT-5' at 4016, 3'-GGTCC-5' at 4032, 3'-CATCT-5' at 4036, 3'-GATCT-5' at 4065, 3'-TGTCC-5' at 4070, 3'-GATCC-5' at 4077, 3'-TGACT-5' at 4089, 3'-GAACT-5' at 4131, 3'-TAACT-5' at 4161, 3'-CGACC-5' at 4177, 3'-GGACT-5' at 4186, 3'-GGACT-5' at 4214, 3'-GAACC-5' at 4300, 3'-CGTCT-5' at 4317, 3'-GGTCT-5' at 4330, 3'-GGACC-5' at 4409, 3'-GGACC-5' at 4424.
# inverse complement, positive strand, positive direction is SuccessablesDPEci++.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 152, 3'-GGTCC-5' at 8, 3'-GGTCT-5' at 15, 3'-TAACC-5' at 24, 3'-GGTCC-5' at 33, 3'-GGACC-5' at 40, 3'-TGTCC-5' at 157, 3'-CGTCC-5' at 194, 3'-GGTCT-5' at 204, 3'-GGTCC-5' at 215, 3'-CGACC-5' at 277, 3'-GGACC-5' at 286, 3'-CGTCC-5' at 318, 3'-TGACC-5' at 347, 3'-TGTCC-5' at 365, 3'-CGTCC-5' at 379, 3'-CGACC-5' at 386, 3'-CGTCT-5' at 396, 3'-CGACC-5' at 417, 3'-GGTCC-5' at 424, 3'-CGTCT-5' at 438, 3'-GGTCT-5' at 468, 3'-GGTCC-5' at 515, 3'-TGTCC-5' at 552, 3'-GGACC-5' at 598, 3'-CGTCC-5' at 658, 3'-GGTCC-5' at 707, 3'-GGACT-5' at 725, 3'-CGACC-5' at 779, 3'-GGTCT-5' at 835, 3'-GGACC-5' at 847, 3'-GGACT-5' at 859, 3'-GGTCT-5' at 935, 3'-GGACC-5' at 947, 3'-GGACT-5' at 959, 3'-TGACC-5' at 1140, 3'-GGTCC-5' at 1175, 3'-GGACC-5' at 1199, 3'-TGACT-5' at 1286, 3'-CGTCT-5' at 1316, 3'-CGTCT-5' at 1416, 3'-GGTCT-5' at 1631, 3'-GGACT-5' at 1660, 3'-GGACT-5' at 1676, 3'-CGACC-5' at 1736, 3'-GGTCT-5' at 1742, 3'-CGACC-5' at 1779, 3'-CGTCC-5' at 1788, 3'-GAACC-5' at 1799, 3'-GGACC-5' at 1815, 3'-GGTCC-5' at 1855, 3'-CATCC-5' at 1875, 3'-GGTCC-5' at 1893, 3'-CGTCC-5' at 1905, 3'-CGTCT-5' at 1937, 3'-TGACC-5' at 1953, 3'-TGTCC-5' at 1966, 3'-TGTCC-5' at 2125, 3'-CAACC-5' at 2185, 3'-GGACT-5' at 2211, 3'-GGTCT-5' at 2228, 3'-CATCC-5' at 2255, 3'-CGTCC-5' at 2296, 3'-GGTCC-5' at 2316, 3'-CGACC-5' at 2320, 3'-CGACC-5' at 2405, 3'-TGTCT-5' at 2414, 3'-GGACC-5' at 2433, 3'-GATCC-5' at 2482, 3'-GGACC-5' at 2501, 3'-CAACC-5' at 2541, 3'-TATCC-5' at 2550, 3'-GGACC-5' at 2569, 3'-GGTCC-5' at 2574, 3'-TATCT-5' at 2627, 3'-GATCC-5' at 2639, 3'-TGTCT-5' at 2652, 3'-TGACT-5' at 2674, 3'-CGTCC-5' at 2683, 3'-CGTCT-5' at 2721, 3'-CGACC-5' at 2734, 3'-CGTCC-5' at 2745, 3'-CGACC-5' at 2770, 3'-GGTCC-5' at 2780, 3'-CGACC-5' at 2810, 3'-CAACC-5' at 2816, 3'-TGTCT-5' at 2837, 3'-CGTCT-5' at 2859, 3'-GGTCC-5' at 2876, 3'-GGACC-5' at 2891, 3'-CGACT-5' at 2915, 3'-GGACT-5' at 2968, 3'-GGACC-5' at 2988, 3'-GGTCC-5' at 3016, 3'-GGACC-5' at 3047, 3'-GGTCT-5' at 3091, 3'-GGTCC-5' at 3111, 3'-TGACC-5' at 3117, 3'-CGTCC-5' at 3128, 3'-TGTCT-5' at 3133, 3'-CGTCC-5' at 3147, 3'-TGTCT-5' at 3179, 3'-CGTCT-5' at 3214, 3'-GGTCT-5' at 3221, 3'-CGACC-5' at 3242, 3'-GGACC-5' at 3296, 3'-TGACC-5' at 3345, 3'-GGACC-5' at 3362, 3'-CATCT-5' at 3416, 3'-CGTCC-5' at 3466, 3'-CGTCT-5' at 3473, 3'-GATCC-5' at 3484, 3'-GGACC-5' at 3496, 3'-GATCC-5' at 3522, 3'-CGACC-5' at 3526, 3'-GGTCC-5' at 3536, 3'-GGTCT-5' at 3548, 3'-TGTCC-5' at 3571, 3'-CGACT-5' at 3588, 3'-TGTCC-5' at 3636, 3'-CGTCC-5' at 3662, 3'-GGACC-5' at 3679, 3'-GGTCC-5' at 3687, 3'-CGTCC-5' at 3694, 3'-TGACT-5' at 3735, 3'-CATCC-5' at 3753, 3'-GGACC-5' at 3758, 3'-CGTCC-5' at 3768, 3'-CGACT-5' at 3778, 3'-GGACC-5' at 3787, 3'-GGTCT-5' at 3806, 3'-CGTCT-5' at 3831, 3'-GGTCT-5' at 3891, 3'-CGTCT-5' at 3916, 3'-TGTCC-5' at 3975, 3'-CGACC-5' at 3989, 3'-GAACT-5' at 4016, 3'-GGTCC-5' at 4032, 3'-CATCT-5' at 4036, 3'-GATCT-5' at 4065, 3'-TGTCC-5' at 4070, 3'-GATCC-5' at 4077, 3'-TGACT-5' at 4089, 3'-GAACT-5' at 4131, 3'-TAACT-5' at 4161, 3'-CGACC-5' at 4177, 3'-GGACT-5' at 4186, 3'-GGACT-5' at 4214, 3'-GAACC-5' at 4300, 3'-CGTCT-5' at 4317, 3'-GGTCT-5' at 4330, 3'-GGACC-5' at 4409, 3'-GGACC-5' at 4424.

Revision as of 12:22, 15 December 2020

Editor-In-Chief: Henry A. Hoff

File:Core promoter elements.svg
The diagram is an overview of four core promoter elements. Credit: Jennifer E.F. Butler & James T. Kadonaga.

The figure on the right is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.[1]

"The downstream promoter element (DPE) is a core promoter element ... present in other species including humans and excluding Saccharomyces cerevisiae.[2]"[3]

"Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II."[3]

Gene transcriptions

Main article: Gene transcriptions

"Transcription by RNA polymerase II is directed by cis-acting [close-acting] DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers [trans-acting, or distant-acting, protein factors], that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins."[4]

Core promoters

Main articles: Core promoter gene transcriptions and Core promoters

"[T]he core promoter [consists of] the DNA sequences, which encompass the transcription start site (within about -40 and +40 [nucleotides] relative to the +1 start site"[4].

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A+1 nucleotide in the Inr"[5]. It is located about 28–33 nucleotides downstream of the transcription start site.[2]

"DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements.[6][4][7]"[8]

Initiator elements

Main articles: Initiator element gene transcriptions and Initiator elements

"There is a strict requirement for spacing between the [Initiator element] Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID."[4]

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences

The early DPE consensus sequence was RGWCGTG.[6][9]

The DPE consensus sequence is the more general sequence RGWYVT, or (A/G)G(A/T)(C/T)(A/C/G)T.[2]

The DPE in "the ATP‐binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" is 5'-AGTCTC-3'.[10]

DPE-containing promoters

"The ... Drosophila Antennapedia P2 (Antp P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus"[4]. GeneID: 40835 Antp Antennapedia [Drosophila melanogaster] is also known as Antp P2.[11] GeneID: 3204 HOXA7 homeobox A7 [ Homo sapiens ] is also known as ANTP and "[t]his gene is highly similar to the antennapedia (Antp) gene of Drosophila."[12] As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of Drosophila"[12], it may have a DPE like the Drosophila gene core promoter does.

"[T]he TATA-less Drosophila Abdominal-B (Abd-B) promoter [has a] partial DPE sequence"[4]. GeneID: 3205 HOXA9 homeobox A9 [ Homo sapiens] is also known as ABD-B and "[t]his gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila."[13] GeneID: 3205 may also be TATA-less and have a DPE.

General transcription factor II Ds

Main articles: General transcription factor II D gene transcriptions and General transcription factor II Ds

The DPE "is required for the binding of purified [general transcription factor II D] TFIID to a subset of TATA-less promoters"[5].

"Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 [TAF6 GeneID: 6878] and dTAFII40 [TAF11 GeneID: 6882] to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE."[4]

Hypotheses

Main article: Hypotheses
  1. The DPE is not used to transcribe A1BG.

Samplings

Main article: A1BG gene transcription core promoters

For the Basic programs (starting with SuccessablesDPE.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 expanded in the positive direction from 958 to 4445, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDPEJ--.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 63, 5'-GGACAT-3' at 395, 5'-GGTCGT-3' at 404, 5'-GGTTCT-3' at 420, 5'-AGTCCT-3' at 442, 5'-AGATGT-3' at 482, 5'-GGTCGT-3' at 541, 5'-GGTTCT-3' at 557, 5'-AGTCCT-3' at 579, 5'-GGACAT-3' at 668, 5'-GGTCGT-3' at 677, 5'-AGTCCT-3' at 715, 5'-GGACAT-3' at 802, 5'-GGTCCT-3' at 851, 5'-GGTTCT-3' at 875, 5'-GGACAT-3' at 968, 5'-AGTCCT-3' at 985, 5'-GGACAT-3' at 1132, 5'-GGTCGT-3' at 1141, 5'-GGTTGT-3' at 1204, 5'-AGATGT-3' at 1225, 5'-GGACAT-3' at 1259, 5'-AGTCCT-3' at 1276, 5'-AGATAT-3' at 1526, 5'-GGTCGT-3' at 1612, 5'-AGACAT-3' at 1777, 5'-GGTCGT-3' at 1786, 5'-GGACAT-3' at 1912, 5'-AGTCCT-3' at 2135, 5'-GGTTGT-3' at 2149, 5'-GGTCAT-3' at 2212, 5'-AGTCCT-3' at 2251, 5'-GGACCT-3' at 2269, 5'-GGACAT-3' at 2338, 5'-AGTTAT-3' at 2497, 5'-GGACAT-3' at 2539, 5'-GGTTGT-3' at 2548, 5'-AGTCCT-3' at 2588, 5'-GGTTGT-3' at 2611, 5'-GGACAT-3' at 2673, 5'-GGTTAT-3' at 2849, 5'-AGATGT-3' at 2989, 5'-GGACAT-3' at 3062, 5'-GGTCGT-3' at 3071, 5'-AGTCCT-3' at 3111, 5'-GGTTGT-3' at 3138, 5'-AGTCCT-3' at 3218, 5'-GGTCCT-3' at 3250, 5'-GGTTCT-3' at 3274, 5'-GGTCGT-3' at 3732, 5'-GGACCT-3' at 3745, 5'-AGACCT-3' at 3836, 5'-GGACCT-3' at 3907, 5'-GGACAT-3' at 3971, 5'-GGTTGT-3' at 3980, 5'-GGTTCT-3' at 4020, 5'-AGTTCT-3' at 4028, 5'-AGATGT-3' at 4063, 5'-GGACAT-3' at 4122, 5'-AGTCCT-3' at 4139, 5'-GGTCCT-3' at 4171, 5'-AGTTCT-3' at 4179, 5'-AGATGT-3' at 4213, 5'-AGTCCT-3' at 4437, and complements.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDPEJ-+.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 18, 5'-GGACCT-3' at 38, 5'-GGTCCT-3' at 219, 5'-AGTCCT-3' at 758, 5'-GGACAT-3' at 1870, 5'-AGTTCT-3' at 1988, 5'-GGATAT-3' at 2660, 5'-GGATGT-3' at 2715, 5'-AGACCT-3' at 2862, 5'-GGTTCT-3' at 2923, 5'-AGTTCT-3' at 2955, 5'-AGTCCT-3' at 2999, 5'-GGTTAT-3' at 3025, 5'-GGTTGT-3' at 3051, 5'-AGTTAT-3' at 3382, 5'-AGACCT-3' at 3551, 5'-GGATGT-3' at 3575, 5'-AGTCCT-3' at 3864, 5'-GGTTCT-3' at 4074, and complements.
  3. positive strand in the negative direction is SuccessablesDPEJ+-.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 16, 5'-GGATAT-3' at 75, 5'-GGATAT-3' at 109, 5'-AGACAT-3' at 171, 5'-AGATGT-3' at 245, 5'-GGATGT-3' at 785, 5'-AGACAT-3' at 1570, 5'-AGATAT-3' at 1596, 5'-AGACAT-3' at 2881, 5'-AGACAT-3' at 2949, 5'-AGATAT-3' at 2982, 5'-AGACAT-3' at 3434, 5'-AGATAT-3' at 3466, 5'-AGATGT-3' at 3621, 5'-AGACGT-3' at 4236, 5'-AGTTCT-3' at 4418, 5'-AGACAT-3' at 4508, and complements.
  4. positive strand in the positive direction is SuccessablesDPEJ++.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 31, 5'-GGACCT-3' at 41, 5'-GGTTCT-3' at 178, 5'-GGACGT-3' at 192, 5'-AGACGT-3' at 224, 5'-AGACCT-3' at 271, 5'-GGTCCT-3' at 425, 5'-GGACGT-3' at 436, 5'-GGACCT-3' at 599, 5'-GGTCGT-3' at 618, 5'-GGTCCT-3' at 708, 5'-GGACGT-3' at 1119, 5'-GGTCGT-3' at 1358, 5'-GGACGT-3' at 1370, 5'-GGTCGT-3' at 1458, 5'-GGACGT-3' at 1470, 5'-AGTCGT-3' at 2103, 5'-AGTCGT-3' at 2199, 5'-AGTCCT-3' at 2621, 5'-AGACGT-3' at 2857, 5'-AGTCGT-3' at 3042, 5'-AGACGT-3' at 3061, 5'-AGTCGT-3' at 3156, 5'-AGACGT-3' at 3268, 5'-AGACGT-3' at 3279, 5'-GGACCT-3' at 3363, 5'-AGTTAT-3' at 3425, 5'-GGTTGT-3' at 3634, 5'-GGTCGT-3' at 3721, 5'-AGTCCT-3' at 3869, 5'-AGTCGT-3' at 4024, 5'-AGATCT-3' at 4065, and complements.
  5. complement, negative strand, negative direction is SuccessablesDPEJc--.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 16, 5'-CCTATA-3' at 75, 5'-CCTATA-3' at 109, 5'-TCTGTA-3' at 171, 5'-TCTACA-3' at 245, 5'-CCTACA-3' at 785, 5'-TCTGTA-3' at 1570, 5'-TCTATA-3' at 1596, 5'-TCTGTA-3' at 2881, 5'-TCTGTA-3' at 2949, 5'-TCTATA-3' at 2982, 5'-TCTGTA-3' at 3434, 5'-TCTATA-3' at 3466, 5'-TCTACA-3' at 3621, 5'-TCTGCA-3' at 4236, 5'-TCAAGA-3' at 4418, 5'-TCTGTA-3' at 4508.
  6. complement, negative strand, positive direction is SuccessablesDPEJc-+.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 31, 5'-CCTGGA-3' at 41, 5'-CCAAGA-3' at 178, 5'-CCTGCA-3' at 192, 5'-TCTGCA-3' at 224, 5'-TCTGGA-3' at 271, 5'-CCAGGA-3' at 425, 5'-CCTGCA-3' at 436, 5'-CCTGGA-3' at 599, 5'-CCAGCA-3' at 618, 5'-CCAGGA-3' at 708, 5'-CCTGCA-3' at 1119, 5'-CCAGCA-3' at 1358, 5'-CCTGCA-3' at 1370, 5'-CCAGCA-3' at 1458, 5'-CCTGCA-3' at 1470, 5'-TCAGCA-3' at 2103, 5'-TCAGCA-3' at 2199, 5'-TCAGGA-3' at 2621, 5'-TCTGCA-3' at 2857, 5'-TCAGCA-3' at 3042, 5'-TCTGCA-3' at 3061, 5'-TCAGCA-3' at 3156, 5'-TCTGCA-3' at 3268, 5'-TCTGCA-3' at 3279, 5'-CCTGGA-3' at 3363, 5'-TCAATA-3' at 3425, 5'-CCAACA-3' at 3634, 5'-CCAGCA-3' at 3721, 5'-TCAGGA-3' at 3869, 5'-TCAGCA-3' at 4024, 5'-TCTAGA-3' at 4065.
  7. complement, positive strand, negative direction is SuccessablesDPEJc+-.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 63, 5'-CCTGTA-3' at 395, 5'-CCAGCA-3' at 404, 5'-CCAAGA-3' at 420, 5'-TCAGGA-3' at 442, 5'-TCTACA-3' at 482, 5'-CCAGCA-3' at 541, 5'-CCAAGA-3' at 557, 5'-TCAGGA-3' at 579, 5'-CCTGTA-3' at 668, 5'-CCAGCA-3' at 677, 5'-TCAGGA-3' at 715, 5'-CCTGTA-3' at 802, 5'-CCAGGA-3' at 851, 5'-CCAAGA-3' at 875, 5'-CCTGTA-3' at 968, 5'-TCAGGA-3' at 985, 5'-CCTGTA-3' at 1132, 5'-CCAGCA-3' at 1141, 5'-CCAACA-3' at 1204, 5'-TCTACA-3' at 1225, 5'-CCTGTA-3' at 1259, 5'-TCAGGA-3' at 1276, 5'-TCTATA-3' at 1526, 5'-CCAGCA-3' at 1612, 5'-TCTGTA-3' at 1777, 5'-CCAGCA-3' at 1786, 5'-CCTGTA-3' at 1912, 5'-TCAGGA-3' at 2135, 5'-CCAACA-3' at 2149, 5'-CCAGTA-3' at 2212, 5'-TCAGGA-3' at 2251, 5'-CCTGGA-3' at 2269, 5'-CCTGTA-3' at 2338, 5'-TCAATA-3' at 2497, 5'-CCTGTA-3' at 2539, 5'-CCAACA-3' at 2548, 5'-TCAGGA-3' at 2588, 5'-CCAACA-3' at 2611, 5'-CCTGTA-3' at 2673, 5'-CCAATA-3' at 2849, 5'-TCTACA-3' at 2989, 5'-CCTGTA-3' at 3062, 5'-CCAGCA-3' at 3071, 5'-TCAGGA-3' at 3111, 5'-CCAACA-3' at 3138, 5'-TCAGGA-3' at 3218, 5'-CCAGGA-3' at 3250, 5'-CCAAGA-3' at 3274, 5'-CCAGCA-3' at 3732, 5'-CCTGGA-3' at 3745, 5'-TCTGGA-3' at 3836, 5'-CCTGGA-3' at 3907, 5'-CCTGTA-3' at 3971, 5'-CCAACA-3' at 3980, 5'-CCAAGA-3' at 4020, 5'-TCAAGA-3' at 4028, 5'-TCTACA-3' at 4063, 5'-CCTGTA-3' at 4122, 5'-TCAGGA-3' at 4139, 5'-CCAGGA-3' at 4171, 5'-TCAAGA-3' at 4179, 5'-TCTACA-3' at 4213, 5'-TCAGGA-3' at 4437.
  8. complement, positive strand, positive direction is SuccessablesDPEJc++.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 18, 5'-CCTGGA-3' at 38, 5'-CCAGGA-3' at 219, 5'-TCAGGA-3' at 758, 5'-CCTGTA-3' at 1870, 5'-TCAAGA-3' at 1988, 5'-CCTATA-3' at 2660, 5'-CCTACA-3' at 2715, 5'-TCTGGA-3' at 2862, 5'-CCAAGA-3' at 2923, 5'-TCAAGA-3' at 2955, 5'-TCAGGA-3' at 2999, 5'-CCAATA-3' at 3025, 5'-CCAACA-3' at 3051, 5'-TCAATA-3' at 3382, 5'-TCTGGA-3' at 3551, 5'-CCTACA-3' at 3575, 5'-TCAGGA-3' at 3864, 5'-CCAAGA-3' at 4074.
  9. inverse complement, negative strand, negative direction is SuccessablesDPEci--.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 18, 5'-ACATCT-3' at 284, 5'-AGGACC-3' at 596, 5'-ACATCT-3' at 970, 5'-ATGTCT-3' at 1567, 5'-AGAACC-3' at 1649, 5'-AGGACC-3' at 1841, 5'-ACAACT-3' at 1853, 5'-ACGACC-3' at 2326, 5'-ATATCT-3' at 2903, 5'-ACGTCT-3' at 3431, 5'-ATAACC-3' at 3529, 5'-ATGACT-3' at 3542, 5'-AGGTCC-3' at 3585, 5'-AGAACC-3' at 3793, 5'-ACGACC-3' at 3864, 5'-AGGACC-3' at 3906, 5'-ACAACC-3' at 3942, 5'-AGGACC-3' at 4546, and complements.
  10. inverse complement, negative strand, positive direction is SuccessablesDPEci-+.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 16, 5'-AGGTCC-3' at 218, 5'-AGATCC-3' at 865, 5'-AGATCC-3' at 965, 5'-AGAACC-3' at 1811, 5'-AGAACT-3' at 1951, 5'-AGAACC-3' at 2225, 5'-AGGTCT-3' at 2258, 5'-AGAACC-3' at 2776, 5'-AGGTCT-3' at 3019, 5'-ATGACT-3' at 3029, 5'-ACGTCT-3' at 3256, 5'-ATGTCC-3' at 3577, 5'-AGGTCT-3' at 3771, 5'-ATGACC-3' at 3784, 5'-AGAACT-3' at 4048, 5'-ATGTCC-3' at 4367, and complements.
  11. inverse complement, positive strand, negative direction is SuccessablesDPEci+-.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 58, 3'-GGACC-5', 32, 3'-TGTCT-5', 479, 3'-CATCC-5', 593, 3'-TAACC-5', 614, 3'-TGACC-5', 734, 3'-CGTCT-5', 754, 3'-GAACC-5', 846, 3'-TGTCT-5', 921, 3'-GATCC-5', 973, 3'-GAACC-5', 1012, 3'-TGACT-5', 1051, 3'-TGTCT-5', 1087, 3'-CGACC-5', 1191, 3'-TGTCT-5', 1222, 3'-GAACC-5', 1303, 3'-CAACC-5', 1407, 3'-GATCT-5', 1482, 3'-CAACC-5', 1514, 3'-TATCC-5', 1529, 3'-CATCC-5', 1572, 3'-GAACT-5', 1685, 3'-TATCT-5', 1731, 3'-CGTCT-5', 1774, 3'-GATCC-5', 1813, 3'-CATCC-5', 1838, 3'-CATCT-5', 1863, 3'-GAACC-5', 1956, 3'-TGTCT-5', 2031, 3'-TGTCT-5', 2165, 3'-TGACC-5', 2189, 3'-CATCT-5', 2290, 3'-GAACC-5', 2382, 3'-GAACC-5', 2717, 3'-TGACT-5', 2786, 3'-CAACC-5', 2844, 3'-CAACT-5', 2911, 3'-TGTCT-5', 2986, 3'-CATCT-5', 3154, 3'-GAACC-5', 3245, 3'-TGTCT-5', 3321, 3'-GAACT-5', 3460, 3'-CAACT-5', 3524, 3'-CATCT-5', 3551, 3'-GGACT-5', 3640, 3'-CGTCC-5', 3698, 3'-GGACT-5', 3747, 3'-GAACC-5', 3784, 3'-TGTCT-5', 3833, 3'-CAACT-5', 3849, 3'-GGACC-5', 3868, 3'-CATCC-5', 3903, 3'-CATCT-5', 4058, 3'-TGTCT-5', 4210, 3'-GGACT-5', 4327, 3'-TGTCT-5', 4371, 3'-GAACC-5', 4451, 3'-CATCC-5', 4456, 3'-GATCC-5', 4476,
  12. inverse complement, positive strand, positive direction is SuccessablesDPEci++.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 152, 3'-GGTCC-5' at 8, 3'-GGTCT-5' at 15, 3'-TAACC-5' at 24, 3'-GGTCC-5' at 33, 3'-GGACC-5' at 40, 3'-TGTCC-5' at 157, 3'-CGTCC-5' at 194, 3'-GGTCT-5' at 204, 3'-GGTCC-5' at 215, 3'-CGACC-5' at 277, 3'-GGACC-5' at 286, 3'-CGTCC-5' at 318, 3'-TGACC-5' at 347, 3'-TGTCC-5' at 365, 3'-CGTCC-5' at 379, 3'-CGACC-5' at 386, 3'-CGTCT-5' at 396, 3'-CGACC-5' at 417, 3'-GGTCC-5' at 424, 3'-CGTCT-5' at 438, 3'-GGTCT-5' at 468, 3'-GGTCC-5' at 515, 3'-TGTCC-5' at 552, 3'-GGACC-5' at 598, 3'-CGTCC-5' at 658, 3'-GGTCC-5' at 707, 3'-GGACT-5' at 725, 3'-CGACC-5' at 779, 3'-GGTCT-5' at 835, 3'-GGACC-5' at 847, 3'-GGACT-5' at 859, 3'-GGTCT-5' at 935, 3'-GGACC-5' at 947, 3'-GGACT-5' at 959, 3'-TGACC-5' at 1140, 3'-GGTCC-5' at 1175, 3'-GGACC-5' at 1199, 3'-TGACT-5' at 1286, 3'-CGTCT-5' at 1316, 3'-CGTCT-5' at 1416, 3'-GGTCT-5' at 1631, 3'-GGACT-5' at 1660, 3'-GGACT-5' at 1676, 3'-CGACC-5' at 1736, 3'-GGTCT-5' at 1742, 3'-CGACC-5' at 1779, 3'-CGTCC-5' at 1788, 3'-GAACC-5' at 1799, 3'-GGACC-5' at 1815, 3'-GGTCC-5' at 1855, 3'-CATCC-5' at 1875, 3'-GGTCC-5' at 1893, 3'-CGTCC-5' at 1905, 3'-CGTCT-5' at 1937, 3'-TGACC-5' at 1953, 3'-TGTCC-5' at 1966, 3'-TGTCC-5' at 2125, 3'-CAACC-5' at 2185, 3'-GGACT-5' at 2211, 3'-GGTCT-5' at 2228, 3'-CATCC-5' at 2255, 3'-CGTCC-5' at 2296, 3'-GGTCC-5' at 2316, 3'-CGACC-5' at 2320, 3'-CGACC-5' at 2405, 3'-TGTCT-5' at 2414, 3'-GGACC-5' at 2433, 3'-GATCC-5' at 2482, 3'-GGACC-5' at 2501, 3'-CAACC-5' at 2541, 3'-TATCC-5' at 2550, 3'-GGACC-5' at 2569, 3'-GGTCC-5' at 2574, 3'-TATCT-5' at 2627, 3'-GATCC-5' at 2639, 3'-TGTCT-5' at 2652, 3'-TGACT-5' at 2674, 3'-CGTCC-5' at 2683, 3'-CGTCT-5' at 2721, 3'-CGACC-5' at 2734, 3'-CGTCC-5' at 2745, 3'-CGACC-5' at 2770, 3'-GGTCC-5' at 2780, 3'-CGACC-5' at 2810, 3'-CAACC-5' at 2816, 3'-TGTCT-5' at 2837, 3'-CGTCT-5' at 2859, 3'-GGTCC-5' at 2876, 3'-GGACC-5' at 2891, 3'-CGACT-5' at 2915, 3'-GGACT-5' at 2968, 3'-GGACC-5' at 2988, 3'-GGTCC-5' at 3016, 3'-GGACC-5' at 3047, 3'-GGTCT-5' at 3091, 3'-GGTCC-5' at 3111, 3'-TGACC-5' at 3117, 3'-CGTCC-5' at 3128, 3'-TGTCT-5' at 3133, 3'-CGTCC-5' at 3147, 3'-TGTCT-5' at 3179, 3'-CGTCT-5' at 3214, 3'-GGTCT-5' at 3221, 3'-CGACC-5' at 3242, 3'-GGACC-5' at 3296, 3'-TGACC-5' at 3345, 3'-GGACC-5' at 3362, 3'-CATCT-5' at 3416, 3'-CGTCC-5' at 3466, 3'-CGTCT-5' at 3473, 3'-GATCC-5' at 3484, 3'-GGACC-5' at 3496, 3'-GATCC-5' at 3522, 3'-CGACC-5' at 3526, 3'-GGTCC-5' at 3536, 3'-GGTCT-5' at 3548, 3'-TGTCC-5' at 3571, 3'-CGACT-5' at 3588, 3'-TGTCC-5' at 3636, 3'-CGTCC-5' at 3662, 3'-GGACC-5' at 3679, 3'-GGTCC-5' at 3687, 3'-CGTCC-5' at 3694, 3'-TGACT-5' at 3735, 3'-CATCC-5' at 3753, 3'-GGACC-5' at 3758, 3'-CGTCC-5' at 3768, 3'-CGACT-5' at 3778, 3'-GGACC-5' at 3787, 3'-GGTCT-5' at 3806, 3'-CGTCT-5' at 3831, 3'-GGTCT-5' at 3891, 3'-CGTCT-5' at 3916, 3'-TGTCC-5' at 3975, 3'-CGACC-5' at 3989, 3'-GAACT-5' at 4016, 3'-GGTCC-5' at 4032, 3'-CATCT-5' at 4036, 3'-GATCT-5' at 4065, 3'-TGTCC-5' at 4070, 3'-GATCC-5' at 4077, 3'-TGACT-5' at 4089, 3'-GAACT-5' at 4131, 3'-TAACT-5' at 4161, 3'-CGACC-5' at 4177, 3'-GGACT-5' at 4186, 3'-GGACT-5' at 4214, 3'-GAACC-5' at 4300, 3'-CGTCT-5' at 4317, 3'-GGTCT-5' at 4330, 3'-GGACC-5' at 4409, 3'-GGACC-5' at 4424.
  13. inverse, negative strand, negative direction, is SuccessablesDPEi--.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 58, 3'-CCTGG-5', 32, 3'-ACAGA-5', 479, 3'-GTAGG-5', 593, 3'-ATTGG-5', 614, 3'-ACTGG-5', 734, 3'-GCAGA-5', 754, 3'-CTTGG-5', 846, 3'-ACAGA-5', 921, 3'-CTAGG-5', 973, 3'-CTTGG-5', 1012, 3'-ACTGA-5', 1051, 3'-ACAGA-5', 1087, 3'-GCTGG-5', 1191, 3'-ACAGA-5', 1222, 3'-CTTGG-5', 1303, 3'-GTTGG-5', 1407, 3'-CTAGA-5', 1482, 3'-GTTGG-5', 1514, 3'-ATAGG-5', 1529, 3'-GTAGG-5', 1572, 3'-CTTGA-5', 1685, 3'-ATAGA-5', 1731, 3'-GCAGA-5', 1774, 3'-CTAGG-5', 1813, 3'-GTAGG-5', 1838, 3'-GTAGA-5', 1863, 3'-CTTGG-5', 1956, 3'-ACAGA-5', 2031, 3'-ACAGA-5', 2165, 3'-ACTGG-5', 2189, 3'-GTAGA-5', 2290, 3'-CTTGG-5', 2382, 3'-CTTGG-5', 2717, 3'-ACTGA-5', 2786, 3'-GTTGG-5', 2844, 3'-GTTGA-5', 2911, 3'-ACAGA-5', 2986, 3'-GTAGA-5', 3154, 3'-CTTGG-5', 3245, 3'-ACAGA-5', 3321, 3'-CTTGA-5', 3460, 3'-GTTGA-5', 3524, 3'-GTAGA-5', 3551, 3'-CCTGA-5', 3640, 3'-GCAGG-5', 3698, 3'-CCTGA-5', 3747, 3'-CTTGG-5', 3784, 3'-ACAGA-5', 3833, 3'-GTTGA-5', 3849, 3'-CCTGG-5', 3868, 3'-GTAGG-5', 3903, 3'-GTAGA-5', 4058, 3'-ACAGA-5', 4210, 3'-CCTGA-5', 4327, 3'-ACAGA-5', 4371, 3'-CTTGG-5', 4451, 3'-GTAGG-5', 4456, 3'-CTAGG-5', 4476,
  14. inverse, negative strand, positive direction, is SuccessablesDPEi-+.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 152 , 3'-CCAGG-5' at 8 , 3'-CCAGA-5' at 15 , 3'-ATTGG-5' at 24 , 3'-CCAGG-5' at 33 , 3'-CCTGG-5' at 40 , 3'-ACAGG-5' at 157 , 3'-GCAGG-5' at 194 , 3'-CCAGA-5' at 204 , 3'-CCAGG-5' at 215 , 3'-GCTGG-5' at 277 , 3'-CCTGG-5' at 286 , 3'-GCAGG-5' at 318 , 3'-ACTGG-5' at 347 , 3'-ACAGG-5' at 365 , 3'-GCAGG-5' at 379 , 3'-GCTGG-5' at 386 , 3'-GCAGA-5' at 396 , 3'-GCTGG-5' at 417 , 3'-CCAGG-5' at 424 , 3'-GCAGA-5' at 438 , 3'-CCAGA-5' at 468 , 3'-CCAGG-5' at 515 , 3'-ACAGG-5' at 552 , 3'-CCTGG-5' at 598 , 3'-GCAGG-5' at 658 , 3'-CCAGG-5' at 707 , 3'-CCTGA-5' at 725 , 3'-GCTGG-5' at 779 , 3'-CCAGA-5' at 835 , 3'-CCTGG-5' at 847 , 3'-CCTGA-5' at 859 , 3'-CCAGA-5' at 935 , 3'-CCTGG-5' at 947 , 3'-CCTGA-5' at 959 , 3'-ACTGG-5' at 1140 , 3'-CCAGG-5' at 1175 , 3'-CCTGG-5' at 1199 , 3'-ACTGA-5' at 1286 , 3'-GCAGA-5' at 1316 , 3'-GCAGA-5' at 1416 , 3'-CCAGA-5' at 1631 , 3'-CCTGA-5' at 1660 , 3'-CCTGA-5' at 1676 , 3'-GCTGG-5' at 1736 , 3'-CCAGA-5' at 1742 , 3'-GCTGG-5' at 1779 , 3'-GCAGG-5' at 1788 , 3'-CTTGG-5' at 1799 , 3'-CCTGG-5' at 1815 , 3'-CCAGG-5' at 1855 , 3'-GTAGG-5' at 1875 , 3'-CCAGG-5' at 1893 , 3'-GCAGG-5' at 1905 , 3'-GCAGA-5' at 1937 , 3'-ACTGG-5' at 1953 , 3'-ACAGG-5' at 1966 , 3'-ACAGG-5' at 2125 , 3'-GTTGG-5' at 2185 , 3'-CCTGA-5' at 2211 , 3'-CCAGA-5' at 2228 , 3'-GTAGG-5' at 2255 , 3'-GCAGG-5' at 2296 , 3'-CCAGG-5' at 2316 , 3'-GCTGG-5' at 2320 , 3'-GCTGG-5' at 2405 , 3'-ACAGA-5' at 2414 , 3'-CCTGG-5' at 2433 , 3'-CTAGG-5' at 2482 , 3'-CCTGG-5' at 2501 , 3'-GTTGG-5' at 2541 , 3'-ATAGG-5' at 2550 , 3'-CCTGG-5' at 2569 , 3'-CCAGG-5' at 2574 , 3'-ATAGA-5' at 2627 , 3'-CTAGG-5' at 2639 , 3'-ACAGA-5' at 2652 , 3'-ACTGA-5' at 2674 , 3'-GCAGG-5' at 2683 , 3'-GCAGA-5' at 2721 , 3'-GCTGG-5' at 2734 , 3'-GCAGG-5' at 2745 , 3'-GCTGG-5' at 2770 , 3'-CCAGG-5' at 2780 , 3'-GCTGG-5' at 2810 , 3'-GTTGG-5' at 2816 , 3'-ACAGA-5' at 2837 , 3'-GCAGA-5' at 2859 , 3'-CCAGG-5' at 2876 , 3'-CCTGG-5' at 2891 , 3'-GCTGA-5' at 2915 , 3'-CCTGA-5' at 2968 , 3'-CCTGG-5' at 2988 , 3'-CCAGG-5' at 3016 , 3'-CCTGG-5' at 3047 , 3'-CCAGA-5' at 3091 , 3'-CCAGG-5' at 3111 , 3'-ACTGG-5' at 3117 , 3'-GCAGG-5' at 3128 , 3'-ACAGA-5' at 3133 , 3'-GCAGG-5' at 3147 , 3'-ACAGA-5' at 3179 , 3'-GCAGA-5' at 3214 , 3'-CCAGA-5' at 3221 , 3'-GCTGG-5' at 3242 , 3'-CCTGG-5' at 3296 , 3'-ACTGG-5' at 3345 , 3'-CCTGG-5' at 3362 , 3'-GTAGA-5' at 3416 , 3'-GCAGG-5' at 3466 , 3'-GCAGA-5' at 3473 , 3'-CTAGG-5' at 3484 , 3'-CCTGG-5' at 3496 , 3'-CTAGG-5' at 3522 , 3'-GCTGG-5' at 3526 , 3'-CCAGG-5' at 3536 , 3'-CCAGA-5' at 3548 , 3'-ACAGG-5' at 3571 , 3'-GCTGA-5' at 3588 , 3'-ACAGG-5' at 3636 , 3'-GCAGG-5' at 3662 , 3'-CCTGG-5' at 3679 , 3'-CCAGG-5' at 3687 , 3'-GCAGG-5' at 3694 , 3'-ACTGA-5' at 3735 , 3'-GTAGG-5' at 3753 , 3'-CCTGG-5' at 3758 , 3'-GCAGG-5' at 3768 , 3'-GCTGA-5' at 3778 , 3'-CCTGG-5' at 3787 , 3'-CCAGA-5' at 3806 , 3'-GCAGA-5' at 3831 , 3'-CCAGA-5' at 3891 , 3'-GCAGA-5' at 3916 , 3'-ACAGG-5' at 3975 , 3'-GCTGG-5' at 3989 , 3'-CTTGA-5' at 4016 , 3'-CCAGG-5' at 4032 , 3'-GTAGA-5' at 4036 , 3'-CTAGA-5' at 4065 , 3'-ACAGG-5' at 4070 , 3'-CTAGG-5' at 4077 , 3'-ACTGA-5' at 4089 , 3'-CTTGA-5' at 4131 , 3'-ATTGA-5' at 4161 , 3'-GCTGG-5' at 4177 , 3'-CCTGA-5' at 4186 , 3'-CCTGA-5' at 4214 , 3'-CTTGG-5' at 4300 , 3'-GCAGA-5' at 4317 , 3'-CCAGA-5' at 4330 , 3'-CCTGG-5' at 4409 , 3'-CCTGG-5' at 4424.
  15. inverse, positive strand, negative direction, is SuccessablesDPEi+-.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 174, 3'-ACAGA-5', 13, 3'-ACTGA-5', 17, 3'-GTTGA-5', 85, 3'-ATAGA-5', 100, 3'-GTAGG-5', 119, 3'-ACTGA-5', 130, 3'-GCTGA-5', 140, 3'-ACAGA-5', 168, 3'-CCAGG-5', 262, 3'-GTAGA-5', 284, 3'-ACAGA-5', 289, 3'-ACTGA-5', 307, 3'-CTTGG-5', 328, 3'-ATAGA-5', 355, 3'-ACAGG-5', 424, 3'-CCTGG-5', 459, 3'-CCTGG-5', 508, 3'-ACAGG-5', 561, 3'-GCAGG-5', 565, 3'-ATTGA-5', 585, 3'-CCTGG-5', 596, 3'-ATTGG-5', 643, 3'-CCAGG-5', 648, 3'-GCAGG-5', 697, 3'-CCTGA-5', 732, 3'-GCTGG-5', 781, 3'-GCTGA-5', 825, 3'-GCAGG-5', 831, 3'-CTTGA-5', 843, 3'-CCAGG-5', 850, 3'-CCTGG-5', 899, 3'-ACAGA-5', 907, 3'-CCAGG-5', 948, 3'-GTAGA-5', 970, 3'-GCTGA-5', 991, 3'-GCAGG-5', 997, 3'-CTTGA-5', 1009, 3'-CCTGG-5', 1015, 3'-GCAGA-5', 1023, 3'-ATTGG-5', 1045, 3'-ACAGA-5', 1073, 3'-GCTGG-5', 1111, 3'-CCTGA-5', 1173, 3'-CCTGG-5', 1198, 3'-GCTGA-5', 1282, 3'-GCAGG-5', 1288, 3'-CTTGA-5', 1300, 3'-CTAGG-5', 1307, 3'-GCAGA-5', 1314, 3'-CCAGA-5', 1411, 3'-CCAGG-5', 1460, 3'-GCTGG-5', 1464, 3'-CCAGA-5', 1518, 3'-ACAGA-5', 1567, 3'-GCAGA-5', 1614, 3'-CCTGA-5', 1623, 3'-CTTGG-5', 1649, 3'-GTAGA-5', 1653, 3'-CCAGA-5', 1670, 3'-ATAGA-5', 1710, 3'-GCTGG-5', 1746, 3'-GCTGG-5', 1756, 3'-GCTGA-5', 1800, 3'-GCAGG-5', 1823, 3'-CCTGG-5', 1841, 3'-GTTGA-5', 1853, 3'-GCTGG-5', 1891, 3'-CTTGG-5', 1927, 3'-ACTGA-5', 1935, 3'-GCAGG-5', 1941, 3'-CCTGG-5', 1959, 3'-GCAGA-5', 1967, 3'-CCTGG-5', 2009, 3'-ACAGA-5', 2017, 3'-GCTGG-5', 2069, 3'-CCAGG-5', 2077, 3'-GCTGA-5', 2109, 3'-ACAGA-5', 2119, 3'-CTTGA-5', 2127, 3'-GCTGA-5', 2226, 3'-GTTGG-5', 2235, 3'-CCTGG-5', 2268, 3'-GCTGG-5', 2326, 3'-GCTGA-5', 2361, 3'-GCAGG-5', 2367, 3'-CTTGA-5', 2379, 3'-CCTGG-5', 2385, 3'-GCAGG-5', 2389, 3'-CCTGG-5', 2435, 3'-ACAGA-5', 2443, 3'-ACAGG-5', 2514, 3'-CCAGG-5', 2519, 3'-GCTGA-5', 2562, 3'-GCAGG-5', 2568, 3'-CTTGA-5', 2580, 3'-GTTGA-5', 2593, 3'-ACAGG-5', 2689, 3'-GCTGA-5', 2696, 3'-GTTGA-5', 2705, 3'-CTTGA-5', 2714, 3'-CCTGG-5', 2720, 3'-GCTGA-5', 2744, 3'-CCTGG-5', 2770, 3'-ACAGA-5', 2778, 3'-ACAGA-5', 2878, 3'-ATAGA-5', 2903, 3'-CTTGG-5', 2921, 3'-GCTGG-5', 3035, 3'-GCTGG-5', 3041, 3'-GCTGA-5', 3085, 3'-CTTGA-5', 3103, 3'-GTTGG-5', 3116, 3'-CCTGG-5', 3128, 3'-GCTGG-5', 3180, 3'-GCTGA-5', 3224, 3'-CTTGA-5', 3242, 3'-CCAGG-5', 3249, 3'-GTAGA-5', 3256, 3'-CCTGG-5', 3298, 3'-ATTGA-5', 3358, 3'-CTTGA-5', 3401, 3'-ATAGA-5', 3422, 3'-GCAGA-5', 3431, 3'-ATAGG-5', 3447, 3'-CTAGA-5', 3463, 3'-CCAGA-5', 3486, 3'-GTTGA-5', 3505, 3'-ATTGG-5', 3529, 3'-GTTGA-5', 3533, 3'-ACTGA-5', 3542, 3'-CCAGG-5', 3564, 3'-CTTGA-5', 3571, 3'-CCAGG-5', 3585, 3'-GCAGA-5', 3589, 3'-GTTGG-5', 3606, 3'-GCTGA-5', 3649, 3'-ACAGA-5', 3672, 3'-GCTGG-5', 3719, 3'-CCTGG-5', 3744, 3'-ACTGG-5', 3749, 3'-CCTGA-5', 3781, 3'-CTTGG-5', 3793, 3'-GTTGA-5', 3805, 3'-GTAGA-5', 3820, 3'-GCTGG-5', 3864, 3'-CCAGG-5', 3871, 3'-CCAGG-5', 3885, 3'-CCTGG-5', 3906, 3'-ACAGA-5', 3917, 3'-CCTGA-5', 3932, 3'-GTTGG-5', 3942, 3'-GTTGG-5', 3946, 3'-CCAGG-5', 3951, 3'-GCTGA-5', 3994, 3'-CTTGA-5', 4012, 3'-CCTGG-5', 4037, 3'-ATAGA-5', 4079, 3'-GTTGG-5', 4097, 3'-CCAGG-5', 4102, 3'-GCTGA-5', 4145, 3'-CCAGG-5', 4170, 3'-CTTGG-5', 4188, 3'-CCAGA-5', 4233, 3'-CCAGG-5', 4253, 3'-CTTGG-5', 4268, 3'-GCTGA-5', 4276, 3'-GCAGG-5', 4282, 3'-CTTGA-5', 4294, 3'-CCTGG-5', 4300, 3'-CCTGG-5', 4349, 3'-CCAGA-5', 4448, 3'-CCTGG-5', 4494, 3'-ACAGA-5', 4518, 3'-CCTGG-5', 4546,
  16. inverse, positive strand, positive direction, is SuccessablesDPEi++.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 95, 3'-GTAGG-5' at 30, 3'-CCTGG-5' at 37, 3'-ACAGG-5' at 82, 3'-ACAGA-5' at 100, 3'-CCTGG-5' at 187, 3'-CCAGG-5' at 218, 3'-ACAGA-5' at 268, 3'-GTTGG-5' at 608, 3'-GTAGG-5' at 629, 3'-GTAGG-5' at 698, 3'-CCTGA-5' at 746, 3'-CCTGA-5' at 814, 3'-GTTGG-5' at 844, 3'-CTAGG-5' at 865, 3'-ACAGG-5' at 893, 3'-GCTGA-5' at 898, 3'-CCTGA-5' at 914, 3'-GTTGG-5' at 944, 3'-CTAGG-5' at 965, 3'-ACAGG-5' at 993, 3'-GCTGA-5' at 998, 3'-GTTGG-5' at 1280, 3'-GCAGA-5' at 1393, 3'-GCAGA-5' at 1493, 3'-GTTGG-5' at 1616, 3'-ACTGG-5' at 1662, 3'-CCAGA-5' at 1711, 3'-ACAGA-5' at 1731, 3'-CTTGG-5' at 1811, 3'-ACAGA-5' at 1862, 3'-GCAGG-5' at 1930, 3'-CTTGA-5' at 1951, 3'-CCAGA-5' at 1958, 3'-GTTGG-5' at 2013, 3'-ACAGA-5' at 2078, 3'-GTAGA-5' at 2111, 3'-GTTGG-5' at 2120, 3'-ACAGA-5' at 2172, 3'-ACTGG-5' at 2213, 3'-CTTGG-5' at 2225, 3'-CCAGA-5' at 2258, 3'-CCTGA-5' at 2271, 3'-GCTGA-5' at 2359, 3'-CTAGG-5' at 2378, 3'-ACAGA-5' at 2466, 3'-CCAGA-5' at 2489, 3'-CTAGG-5' at 2514, 3'-CTTGG-5' at 2579, 3'-CCTGA-5' at 2672, 3'-CTTGG-5' at 2776, 3'-CCTGA-5' at 2820, 3'-GTAGA-5' at 2852, 3'-ACTGG-5' at 2873, 3'-CCAGA-5' at 2941, 3'-ACTGA-5' at 2945, 3'-ACAGA-5' at 3004, 3'-CCAGA-5' at 3019, 3'-ACTGA-5' at 3029, 3'-ACAGA-5' at 3053, 3'-GTAGG-5' at 3108, 3'-CCTGG-5' at 3172, 3'-GCAGG-5' at 3203, 3'-CCAGA-5' at 3245, 3'-GCAGA-5' at 3256, 3'-GTTGA-5' at 3291, 3'-CCAGA-5' at 3299, 3'-GTAGA-5' at 3329, 3'-ATAGG-5' at 3384, 3'-ACAGA-5' at 3392, 3'-GTAGA-5' at 3403, 3'-CCTGG-5' at 3545, 3'-ACAGG-5' at 3577, 3'-CCAGA-5' at 3608, 3'-ACAGG-5' at 3619, 3'-GTAGG-5' at 3629, 3'-ACTGG-5' at 3714, 3'-ATTGA-5' at 3733, 3'-CCAGA-5' at 3771, 3'-ACTGG-5' at 3784, 3'-GCTGA-5' at 3801, 3'-CTTGG-5' at 3838, 3'-CTTGG-5' at 3856, 3'-GTTGG-5' at 3911, 3'-CTTGG-5' at 3937, 3'-ACTGG-5' at 4018, 3'-CTTGA-5' at 4048, 3'-GCAGA-5' at 4056, 3'-CTAGG-5' at 4081, 3'-GTAGG-5' at 4183, 3'-ACTGG-5' at 4216, 3'-GCTGG-5' at 4358, 3'-ACAGG-5' at 4367, 3'-CCAGA-5' at 4380, 3'-CCAGA-5' at 4414, 3'-CCAGG-5' at 4420.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Jennifer E.F. Butler, James T. Kadonaga (October 15, 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development. 16 (20): 2583–92. doi:10.1101/gad.1026202. PMID 12381658.
  2. ↑ 2.0 2.1 2.2 Tamar Juven-Gershon, James T. Kadonaga (March 15, 2010). "Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMC 2830304. PMID 19682982.
  3. ↑ 3.0 3.1 "Downstream promoter element". San Francisco, California: Wikimedia Foundation, Inc. May 6, 2012. Retrieved 2012-05-20.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 Thomas W. Burke and James T. Kadonaga (November 15, 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development. 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMC 316699. PMID 9367984.
  5. ↑ 5.0 5.1 Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  6. ↑ 6.0 6.1 T.W. Burke and James T. Kadonaga (15 March 1996). "Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters" (PDF). Genes & Development. 10 (6): 711–724. doi:10.1101/gad.10.6.711. PMID 8598298.
  7. ↑ Kutach, Alan K.; Kadonaga, James T. (July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology. 20 (13): 4754–4764. doi:10.1128/MCB.20.13.4754-4764.2000. PMC 85905. PMID 10848601.
  8. ↑ "Downstream promoter element". San Francisco, California: Wikimedia Foundation, Inc. November 8, 2012. Retrieved 2013-01-23.
  9. ↑ James T. Kadonaga (September 2002). "The DPE, a core promoter element for transcription by RNA polymerase II" (PDF). Experimental & Molecular Medicine. 34 (4): 259–264. PMID 12515390.
  10. ↑ Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  11. ↑ FlyBase (February 3, 2013). "Antp Antennapedia [ Drosophila melanogaster ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  12. ↑ 12.0 12.1 HGNC (February 5, 2013). "HOXA7 homeobox A7 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  13. ↑ HGNC (February 5, 2013). "HOXA9 homeobox A9 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.

Further reading

External links

{{Phosphate biochemistry}}

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