Downstream TFIIB recognition element gene transcriptions

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

File:Loris lydekkerianus nordicus 003.jpg
This image is of a gray slender loris (Loris lydekkerianus nordicus) from Northern Sri Lanka. Credit: Dr. K.A.I. Nekaris.

The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.[1][2] The BRE is a cis-regulatory element that is found immediately near TATA box, and consists of 7 nucleotides. There are two sets of BREs: one (BREu) found immediately upstream of the TATA box, with the consensus SSRCGCC [(C/G)(C/G)(A/G)CGCC]; the other (BREd) found around 7 nucleotides downstream, with the consensus RTDKKKK [(A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T)].[3][4]

The downstream B recognition element designated as the BREd,[5] or dBRE, is an additional core promoter element that occurs downstream of the TATA box and is recognized by general transcription factor II B.[5]

Consensus sequences

Main article: Consensus sequence gene transcriptions

A consensus sequence is A/G-T-A/G/T-G/T-G/T-G/T-G/T.[5]

Eukaryote genes

Main article: Eukaryote genes

Of 140 promoters from the eukaryotic promoter database, "[S]ix percent ... [contain] at least six out of seven bases of the consensus sequence, 18% contain at least five of seven bases and 37% contain at least four of seven".[5]

Human genes

Main article: Human genes

GeneID: 9555 H2A histone family, member Y (H2AFY)[6] "contains a poor TATA element, but both a consensus Inr and DPE in addition to a six/seven match BREd."[5]

General transcription factor II Bs

Main articles: General transcription factor II B gene transcriptions and General transcription factor II Bs

A TFIIB recognition element (BRE) functions to determine the orientation of the TFIIB-TBP-TATA complex that projects the zinc ribbon of TFIIB toward the TSS.[7]

General transcription factor II B can recognize two distinct sequence elements that flank the TATA box.[5] "The selected sequences contain a strong representation of [ guanine (G) and thymine (T)] bases and a striking preference against [ adenine (A)] (especially between bases -17 and -20)."[5]

"[T]here are ... some weakly conserved features including the TFIIB-Recognition Element (BRE), approximately 5 nucleotides upstream (BREu) and 5 nucleotides downstream (BREd) of the TATA box.[8]"[9]

The TFIIB-DNA contact with the BREd takes place via the minor groove, while that with the upstream B recognition element (BREu) takes place through the major groove.[5]

Transcription start sites

Main articles: Start site gene transcriptions and Transcription start sites

dBRE is cis-TATA box, between the TATA box and the Inr or transcription start site (TSS) and trans-TSS.[5]

Hypotheses

Main article: Hypotheses
  1. The dBRE is not involved in the transcription of A1BG.

dBRE samplings

For the Basic programs (starting with SuccessablesdBRE.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 (+) expanded to 4445 nts from 958, the programs are, are looking for, and found:

  1. Negative strand, negative direction: GTAGGTG at 4458, GTGGGGT at 4446, GTTTTTT at 4378, GTTTTTT at 4218, ATGTTTT at 4216, GTTGTGT at 4196, GTTTTTT at 4068, ATGTTTT at 4066, GTGTTTT at 3767, ATGGTGG at 3740, GTAGTTG at 3523, ATTTGGT at 3484, ATTTGGT at 3365, ATTTGTT at 3338, GTTTTTG at 3328, GTATTTT at 3171, ATTTTTG at 3165, GTGGGTT at 3136, ATTTTTT at 3026, GTAGTTT at 2890, ATATTTG at 2875, GTTGGGT at 2846, GTGGGGT at 2764, ATGTTTT at 2644, ATATGTT at 2642, GTTTGTT at 2488, GTTTGTT at 2484, GTGTGGT at 2419, GTTTTTT at 2309, ATGTTTT at 2307, GTTTTTT at 2184, ATGTTTT at 2182, GTTTTTT at 2038, GTTTTTT at 1882, ATGTTTT at 1880, GTTTGTG at 1540, GTTGGGT at 1516, GTTGGGT at 1409, GTTTTTT at 1396, GTTTGTT at 1392, GTTTTTG at 1386, GTTTTTT at 1230, ATGTTTT at 1228, GTTTTTT at 1094, GTTTTTT at 928, GTGTGGT at 883, GTTTTTT at 773, ATGTTTT at 771, GTTTTTT at 639, ATGTTTT at 637, ATTGGGG at 616, GTTTTTT at 487, ATGTTTT at 485, GTTTTGG at 259, ATATTTT at 222, ATATTTT at 183, GTTTTGT at 166, ATATGTT at 113, ATTTTGT at 68.
  2. Positive strand, negative direction: ATGGTGG at 4110, GTTGGTT at 3944, GTGTTGG at 3942, ATGTGGT at 3811, ATGGGGT at 3802, GTGGTTG at 3605, ATTGGTT at 3531, GTGGGTG at 3195, GTGGTGG at 3192, GTGGTGG at 3189, GTGTGGT at 3187, GTGGTGG at 3050, ATATTTT at 2853, GTGGTGG at 2661, GTGTGGT at 2659, GTGGGTG at 2332, GTGGTGG at 1903, GTGGTGG at 1900, GTGGTGT at 1477, GTGGTGG at 1247, GTGGGTG at 1163, ATTGGGT at 1047, GTGGTGT at 793, GTGGTGG at 790, ATGTGGT at 788, ATGGTGT at 608, ATATGGT at 606, ATGTTTT at 215, ATGGGGT at 204, ATATGGG at 78, ATATGTT at 43.
  3. Negative strand, positive direction: GTGGGGT at 4397, ATGGGGG at 4225, ATTGTTG at 4173, GTGGTTT at 4108, GTGGTGT at 3969, GTGTGGT at 3967, GTGGTGG at 3816, ATGTTTG at 3339, GTGTTGG at 2816, ATTTTTT at 2451, GTGGGGG at 56.
  4. Positive strand, positive direction: GTGGGGT at 4328, GTGGGGT at 4286, GTTTGTG at 4257, GTGTGGT at 3825, GTAGGGT at 3631, ATAGGGT at 3386, GTGTGGG at 2965, ATGGTGG at 2759, GTGTGGT at 2603, ATGGTGT at 2600, ATATGGT at 2591, GTTGGTG at 2122, GTGGGGG at 2020, GTTGGGT at 2015, ATGGGGT at 1891, GTGGTGG at 704, GTAGGTG at 700, GTAGGTG at 631, GTGGGTG at 72.
  5. inverse complement, Negative strand, negative direction: AACCAAC at 3945, CCACTAC at 3798, CACCAAC at 3605, AACCAAC at 3532, CCAAAAT at 3350, CCCACAC at 3185, ACACCAC at 2660, CACCCAC at 2332, CCACCAC at 1902, ACCACAC at 1478, AAAAAAC at 1433, CACCCAC at 1163, AACCCAC at 1048, ACACCAC at 789, ACCACAC at 609, CAAAAAT at 217.
  6. inverse complement, Positive strand, negative direction: AACCCAT at 4454, AAAAAAT at 4219, AAAAAAT at 4069, CCAACAC at 3981, CCCATAC at 3857, ACAAAAT at 3768, CAACTAT at 3526, AAAACAC at 3512, AAACCAC at 3366, CAAAAAC at 3328, AAAACAT at 3167, ACCCCAT at 3152, ACCCAAC at 3137, AAAAAAC at 3027, AAACCAC at 2972, AAAAAAT at 2930, AAAATAT at 2869, AAACAAC at 2843, CAAAAAT at 2646, CCAACAT at 2612, CCAACAC at 2549, AACAAAC at 2511, AACAAAC at 2486, ACACCAC at 2420, AAAATAC at 2303, ACCCCAT at 2288, AAAAAAT at 2185, CCAACAT at 2150, AAAAAAT at 2061, AAAATAC at 1876, ACCCCAT at 1861, AAAATAT at 1740, AACAAAC at 1587, AAAATAC at 1564, CAAACAC at 1540, CAAAAAC at 1386, AAAAAAT at 1231, CCAACAT at 1205, ACACCAT at 884, AAAATAC at 767, AAAATAC at 633, AAAAAAT at 488, AAAACAT at 361, AAACAAT at 230.
  7. inverse complement, Negative strand, positive direction: ACCCCAC at 4287, CAAACAC at 4257, ACCCCAT at 4220, ACCCCAC at 3941, ACACCAT at 3826, ACCAAAC at 3176, AACACAC at 3097, AAACCAC at 2633, ACCACAC at 2601, CAACCAC at 2122, AACCCAC at 2016, AACCTAC at 1283, CCACCAC at 703, CACCCAC at 72.
  8. inverse complement, Positive strand, positive direction: ACCCCAC at 4398, CCAAAAT at 4110, ACACCAC at 3968, AAACCAC at 3949, ACACCAC at 3644, CCAATAC at 3026, CCACAAC at 2815, CACCTAC at 2714, CCAAAAC at 2688, CCCCTAT at 2659, AAAAAAC at 2452, ACCCTAC at 2409, AAAAAAC at 2282, AACCCAC at 1802, ACAAAAT at 148, CCCCTAC at 59.

dBRE (4560-2846) UTRs

  1. Negative strand, negative direction: GTAGGTG at 4458, GTGGGGT at 4446, GTTTTTT at 4378, GTTTTTT at 4218, ATGTTTT at 4216, GTTGTGT at 4196, GTTTTTT at 4068, ATGTTTT at 4066, AACCAAC at 3945, CCACTAC at 3798, GTGTTTT at 3767, ATGGTGG at 3740, CACCAAC at 3605, AACCAAC at 3532, GTAGTTG at 3523, ATTTGGT at 3484, ATTTGGT at 3365, CCAAAAT at 3350, ATTTGTT at 3338, GTTTTTG at 3328, CCCACAC at 3185, GTATTTT at 3171, ATTTTTG at 3165, GTGGGTT at 3136, ATTTTTT at 3026, GTAGTTT at 2890, ATATTTG at 2875, GTTGGGT at 2846.
  2. Positive strand, negative direction: AACCCAT at 4454, AAAAAAT at 4219, ATGGTGG at 4110, AAAAAAT at 4069, CCAACAC at 3981, GTTGGTT at 3944, GTGTTGG at 3942, CCCATAC at 3857, ATGTGGT at 3811, ATGGGGT at 3802, ACAAAAT at 3768, GTGGTTG at 3605, ATTGGTT at 3531, CAACTAT at 3526, AAAACAC at 3512, AAACCAC at 3366, CAAAAAC at 3328, GTGGGTG at 3195, GTGGTGG at 3192, GTGGTGG at 3189, GTGTGGT at 3187, AAAACAT at 3167, ACCCCAT at 3152, ACCCAAC at 3137, GTGGTGG at 3050, AAAAAAC at 3027, AAACCAC at 2972, AAAAAAT at 2930, AAAATAT at 2869, ATATTTT at 2853.

dBRE negative direction (2846-2811) core promoters

  1. Negative strand, negative direction: GTTGGGT at 2846.
  2. Positive strand, negative direction: AAACAAC at 2843.

dBRE positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: GTGGGGT at 4397, ACCCCAC at 4287.
  2. Positive strand, positive direction: ACCCCAC at 4398, GTGGGGT at 4328, GTGGGGT at 4286.

dBRE negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GTGGGGT at 2764, ACACCAC at 2660, ATGTTTT at 2644, ATATGTT at 2642.
  2. Positive strand, negative direction: GTGGTGG at 2661, GTGTGGT at 2659, CAAAAAT at 2646, CCAACAT at 2612.

dBRE positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATGGGGG at 4225, ATTGTTG at 4173, GTGGTTT at 4108.
  2. Positive strand, positive direction: GTTTGTG at 4257.

dBRE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTGTGGT at 2419, CACCCAC at 2332, GTTTTTT at 2309, ATGTTTT at 2307, GTTTTTT at 2184, ATGTTTT at 2182, GTTTTTT at 2038, CCACCAC at 1902, GTTTTTT at 1882, ATGTTTT at 1880, GTTTGTG at 1540, GTTGGGT at 1516, ACCACAC at 1478, AAAAAAC at 1433, GTTGGGT at 1409, GTTTTTT at 1396, GTTTGTT at 1392, GTTTTTG at 1386, GTTTTTT at 1230, ATGTTTT at 1228, CACCCAC at 1163, GTTTTTT at 1094, AACCCAC at 1048, GTTTTTT at 928, GTGTGGT at 883, ACACCAC at 789, GTTTTTT at 773, ATGTTTT at 771, GTTTTTT at 639, ATGTTTT at 637, ATTGGGG at 616, ACCACAC at 609, GTTTTTT at 487, ATGTTTT at 485, GTTTTGG at 259, ATATTTT at 222, CAAAAAT at 217, ATATTTT at 183, GTTTTGT at 166, ATATGTT at 113, ATTTTGT at 68.
  2. Positive strand, negative direction: CCAACAC at 2549, AACAAAC at 2511, AACAAAC at 2486, ACACCAC at 2420, GTGGGTG at 2332, AAAATAC at 2303, ACCCCAT at 2288, AAAAAAT at 2185, CCAACAT at 2150, AAAAAAT at 2061, GTGGTGG at 1903, GTGGTGG at 1900, AAAATAC at 1876, ACCCCAT at 1861, AAAATAT at 1740, AACAAAC at 1587, AAAATAC at 1564, CAAACAC at 1540, GTGGTGT at 1477, CAAAAAC at 1386, GTGGTGG at 1247, AAAAAAT at 1231, CCAACAT at 1205, GTGGGTG at 1163, ATTGGGT at 1047, ACACCAT at 884, GTGGTGT at 793, GTGGTGG at 790, ATGTGGT at 788, AAAATAC at 767, AAAATAC at 633, ATGGTGT at 608, ATATGGT at 606, AAAAAAT at 488, AAAACAT at 361, AAACAAT at 230, ATGTTTT at 215, ATGGGGT at 204, ATATGGG at 78, ATATGTT at 43.

dBRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GTGGTGT at 3969, GTGTGGT at 3967, ACCCCAC at 3941, ACACCAT at 3826, GTGGTGG at 3816, ATGTTTG at 3339, ACCAAAC at 3176, AACACAC at 3097, GTGTTGG at 2816, AAACCAC at 2633, ACCACAC at 2601, ATTTTTT at 2451, CAACCAC at 2122, AACCCAC at 2016, AACCTAC at 1283, CCACCAC at 703, CACCCAC at 72, GTGGGGG at 56.
  2. Positive strand, positive direction: ACACCAC at 3968, AAACCAC at 3949, GTGTGGT at 3825, ACACCAC at 3644, GTAGGGT at 3631, ATAGGGT at 3386, CCAATAC at 3026, GTGTGGG at 2965, CCACAAC at 2815, ATGGTGG at 2759, CACCTAC at 2714, CCAAAAC at 2688, CCCCTAT at 2659, GTGTGGT at 2603, ATGGTGT at 2600, ATATGGT at 2591, AAAAAAC at 2452, ACCCTAC at 2409, AAAAAAC at 2282, GTTGGTG at 2122, GTGGGGG at 2020, GTTGGGT at 2015, ATGGGGT at 1891, AACCCAC at 1802, GTGGTGG at 704, GTAGGTG at 700, GTAGGTG at 631, ACAAAAT at 148, GTGGGTG at 72, CCCCTAC at 59.

dBRE random dataset samplings

  1. dBREr0: 30, GTGGGTG at 4505, GTAGGTT at 4349, ATATTTG at 3311, GTTTGTT at 3180, ATGGTTT at 3177, GTGTTTT at 3080, ATAGGGG at 3014, ATTTGGG at 2497, ATTGTTG at 2236, ATATTTT at 2145, GTTGGTG at 2024, ATGTTTT at 1970, GTGTGTG at 1942, GTGGTGT at 1939, ATGGTTT at 1901, ATGTGGT at 1827, GTTTGTG at 1758, GTTGTTT at 1670, ATTTGGG at 1645, ATTTTTT at 1453, ATGTTTT at 605, GTTTGGG at 566, ATAGTTT at 563, GTGGGGT at 533, ATTGGGT at 381, ATATTGG at 379, GTTTTTG at 303, ATGTTGT at 153, ATTGGTT at 83, GTGTTGT at 17.
  2. dBREr1: 32, GTTTGGG at 4273, ATGGGTG at 4168, ATATGGG at 4166, GTGGGTG at 4151, ATTTGGG at 4053, ATTGTGT at 3975, GTAGTGT at 3511, ATTTTTT at 3455, GTTTGTG at 3401, ATGGTTT at 3342, GTTTTTT at 3032, GTAGGGG at 2820, ATAGGGG at 2512, ATTTGGT at 2428, GTGGGTT at 2342, GTATTTT at 2141, GTTTTTT at 1665, GTGTGTG at 1583, GTTTTTT at 1484, ATTTGTT at 1246, ATGGGGG at 1112, ATATGGG at 1110, ATTGTTG at 1011, GTTTGGG at 925, ATTTTTG at 791, GTGTGGG at 699, ATGGGGG at 489, GTTTGGT at 414, ATGTTGG at 404, GTTTTGT at 281, ATAGGGT at 276, ATGGTGG at 267.
  3. dBREr2: 35, ATTTTGT at 4486, ATGGGTG at 4390, GTGTTTT at 4113, ATAGGGT at 3110, GTTGGGG at 3047, ATAGTTG at 3044, ATAGGGT at 2980, GTTGGGT at 2969, GTTGGTG at 2867, GTTGTTG at 2864, GTTTTTT at 2825, GTGGTGG at 2768, ATGTGGT at 2766, ATGGGGT at 2735, ATTTGTT at 2629, GTTTTGT at 2530, GTGTTGG at 2496, GTGGTTT at 2462, GTGGGGT at 2143, GTGGGTG at 2003, GTGTGGG at 2001, GTAGTTT at 1653, GTATTTT at 1374, ATGTTTG at 1297, GTTGGGT at 1288, ATAGGGG at 1282, GTGGTTT at 1056, GTTTTTG at 1029, GTGGTTT at 1026, ATTGGTG at 757, ATAGGTT at 406, GTATTTT at 262, ATGTTTT at 245, GTGGGTT at 103, GTATGGT at 21.
  4. dBREr3: 37, GTTGTTG at 4515, ATGGGTT at 4412, ATTTTGG at 4352, GTTTTTG at 4103, ATTGTTT at 4004, GTATTGT at 4002, GTGTGGG at 3855, ATTTTTG at 3759, GTTGGTT at 3550, GTGGTTT at 3531, ATTTTTT at 3167, GTTTTTT at 3067, ATAGTTT at 2955, ATTTTTG at 2618, ATTTTTG at 2541, GTTTGTT at 2269, GTTGTTT at 2266, ATGGTGG at 2235, GTAGTGT at 2204, GTTTTTG at 2186, GTGGTTG at 2014, GTGTGGT at 2012, ATTTGGG at 1787, GTAGGTT at 1191, ATATTGG at 1163, GTTTTGG at 1113, GTGGTTT at 1110, GTGTGGT at 1108, ATTTTTG at 927, ATATTGG at 666, GTTGTGG at 641, GTTGTTT at 531, GTGGGGG at 515, GTTTGTT at 452, ATTGTTT at 449, GTGGGTT at 426, GTATTTT at 170.
  5. dBREr4: 37, GTTGGTT at 4422, GTAGGGT at 4127, GTGTTGG at 4076, ATGTGTT at 4074, GTGTGTT at 3606, GTTGTTT at 3532, GTTGGTT at 3528, ATTTTGT at 3517, GTATTTT at 3354, ATGGGTT at 3222, GTTTGTT at 3208, ATGGTTT at 3205, GTAGGTT at 3147, ATTGGGG at 3099, ATTTGTT at 2907, ATTTTTG at 2889, GTGTGGG at 2762, ATGGTTT at 2591, GTGTTGG at 2576, ATAGTGT at 2485, GTTGTTT at 2437, GTTTTTG at 2427, GTAGTTT at 2398, GTGGGTT at 2291, ATTTTGT at 2257, GTATGGG at 1831, ATGTGGG at 1825, GTGGGTG at 1490, GTTTTGG at 1383, GTTTGGG at 1340, GTAGGGT at 1208, ATTTTTT at 844, GTATGTT at 701, GTTTGGT at 430, GTGTTTG at 428, GTGGGTT at 278, GTAGGGT at 29.
  6. dBREr5: 34, ATGTTGG at 4173, ATATGTT at 4171, ATAGTTT at 4108, GTAGGTT at 3892, ATTTGTG at 3880, ATTTTTT at 3706, ATGGGGG at 3403, GTGTGGT at 3375, ATTTTTT at 3356, ATTTGGG at 3283, GTTGGTT at 3268, ATTGGGT at 3174, GTTTTTT at 2954, ATTGTGT at 2837, ATGGTGT at 2732, ATGGGGT at 2570, GTGGGTG at 2217, ATGTTTT at 2074, GTATGTT at 2072, GTTTGTG at 1721, GTTGGGT at 1716, ATGGTTG at 1489, GTTTTTT at 1416, GTTTTTG at 1151, ATGTTTT at 1149, ATGGGGT at 1041, GTGGTTT at 932, ATTGTTG at 888, GTTTTGT at 321, ATAGTTT at 318, GTTGGTT at 256, GTATGGG at 174, GTATTTT at 111, GTTGGGG at 44.
  7. dBREr6: 29, GTTTGTT at 4533, ATTTGGT at 4528, GTGGTTT at 4479, ATATTGG at 4430, GTTTGTG at 4364, ATGGGGG at 4347, GTGGGGG at 3742, ATAGGTT at 3646, ATGGGTT at 3554, ATGGTGT at 2946, GTAGGGT at 2679, ATTTTGT at 2652, GTATTGG at 2516, GTAGGGG at 2111, ATGTTGG at 2012, GTATGTT at 2010, GTTTTGT at 1702, ATAGTTT at 1631, GTTGGTG at 1551, ATGTTGG at 1549, GTAGTTT at 1317, ATATTGG at 1026, ATGTTTG at 910, GTATGTT at 908, GTATTGG at 604, GTTTTGG at 569, GTAGTGG at 533, GTGGGGT at 339, ATTTGGT at 97.
  8. dBREr7: 26, ATAGGGG at 4294, ATGGTTT at 4267, ATTTGTG at 4226, ATATTTG at 4224, ATTTTTT at 3455, ATTGGGG at 3164, GTTGTTG at 2940, GTAGTGG at 2542, ATATTTT at 2517, ATTTGTT at 2448, ATTGTGG at 2154, ATGGGTT at 2136, GTAGTTT at 2118, GTTTGGG at 1849, ATTTGGT at 1179, GTTGGGG at 856, GTGTTGG at 854, ATAGGTT at 733, GTGGTTT at 608, GTGGTGG at 497, ATTTTTG at 491, GTTTTTT at 349, GTAGGGT at 344, GTGGGGT at 135, ATGTGTT at 120, ATTTGGG at 113.
  9. dBREr8: 31, ATAGTGG at 4527, ATTTGGT at 4312, GTTGGTT at 3922, ATTTGGT at 3491, GTATGTT at 3444, GTAGTTT at 3396, ATTGGTT at 3119, GTATTGT at 2967, ATTTTTT at 2543, GTTGTTT at 2382, ATTTTTT at 2291, ATTGGTG at 1979, GTTTTGG at 1835, ATTTTGG at 1814, ATAGGGG at 1737, GTGTTGG at 1597, GTGGTGG at 1409, ATAGTGG at 1324, ATTGTTT at 1230, ATAGTTT at 981, GTTTTTG at 954, ATTGGGG at 857, GTAGGGT at 577, GTATGGG at 571, ATGGTGT at 535, ATGTGGT at 525, ATTTTGG at 485, ATGGGTT at 411, ATTTGGG at 269, ATGGGTG at 97, GTTTGTT at 43.
  10. dBREr9: 33, ATTGTTG at 4560, ATGGGTG at 4531, ATGTGGG at 4391, ATGGTGG at 4358, ATTTTGG at 4273, GTATTTT at 4271, ATAGGTT at 4174, ATTGGTG at 3994, ATATTGG at 3992, ATTGGGT at 3724, GTTTGGG at 3597, ATTTGGG at 3479, GTTTTTT at 3387, GTATGGG at 3178, ATTGGTT at 2891, GTGGTTT at 2706, GTAGTTG at 2635, ATTTTGG at 2527, ATTTTGT at 2513, ATTGTTT at 2248, GTTGTTT at 1734, GTATGTT at 1617, ATTGTTG at 1439, GTGTTTT at 1124, ATGTTTT at 1078, GTATGTT at 1076, ATTTTTT at 836, GTATTTT at 834, ATTTTGT at 469, ATAGGTT at 411, GTTTGTT at 95, GTGTTTG at 21, GTAGTGT at 18.
  11. dBREr0ci: 30, AACACAT at 4435, AAAACAC at 4433, CCAACAT at 4414, CCCATAT at 4385, CCACCAC at 4340, ACCCTAT at 4288, ACCCCAT at 4086, ACCCAAT at 3878, ACAACAC at 3730, ACAAAAT at 3172, AAAATAT at 2698, CCCCAAT at 2614, ACAAAAT at 2334, ACACCAC at 2166, AAAACAT at 2087, CCCATAT at 2040, CCAAAAT at 1812, CACAAAT at 1788, CAAATAC at 1707, AAACAAT at 1577, CACCTAT at 1566, AAACCAT at 1089, ACCAAAC at 1086, ACCCTAC at 1017, AACAAAT at 504, AACCCAC at 440, AAACCAT at 285, CCAAAAT at 195, CCAAAAC at 170, CCCATAC at 40.
  12. dBREr1ci: 29, CAAACAC at 4516, CCCAAAC at 4514, CCCCTAT at 4332, CAACCAT at 4323, CCAAAAT at 3883, AACCCAC at 3730, CCCCCAT at 3631, AAAACAT at 3603, AACCAAC at 3538, AAAAAAT at 3489, AAAATAT at 3365, CCAAAAT at 3363, AAAAAAC at 2856, CCCCTAC at 2416, AACATAT at 2100, CCAACAT at 2098, ACCCCAC at 1920, ACAATAC at 1824, AAACAAT at 1822, AAAACAT at 1710, ACCCCAT at 1315, CCAACAT at 1201, AACCAAT at 786, AACAAAC at 614, ACACTAC at 373, CCAATAC at 298, CACCCAC at 238, AACACAT at 179, AAAATAT at 168.
  13. dBREr2ci: 38, CCACTAT at 4411, CCACCAT at 4404, AAACAAC at 4326, ACAAAAC at 4323, CCCCAAC at 4080, CCCCAAT at 3882, CCACAAC at 3838, ACCAAAT at 3828, ACCCCAC at 3314, AAACCAC at 3211, CAAACAT at 3177, ACCAAAC at 3175, AACAAAC at 3170, ACCCCAT at 2892, ACAACAC at 2833, CACACAT at 2808, CACACAC at 2806, ACCACAC at 2804, CACAAAC at 2685, AAAATAT at 2667, CAAAAAT at 2382, AAACAAC at 2192, CCACTAC at 2150, ACCCTAT at 1947, AACATAT at 1756, CACCCAT at 1705, CCAACAT at 1635, AACCAAC at 1633, CCCCCAT at 1624, ACCCAAT at 1461, CCCCAAT at 1354, AACATAT at 1325, CAAACAT at 1323, AAAAAAC at 940, ACACAAT at 511, AAACTAC at 313, ACACAAC at 61, ACCACAC at 58.
  14. dBREr3ci: 32, AACCCAT at 4456, CCCACAT at 4284, AACCTAC at 4268, CCAATAT at 4254, CCCCAAT at 4252, AAACCAC at 4241, CCCAAAC at 4238, AAAATAC at 4176, ACCAAAT at 4020, CAACTAC at 3787, ACCCTAT at 3678, ACCCTAC at 3561, CCCCTAT at 3353, AACAAAT at 3267, AAAAAAC at 3263, CCACCAT at 3085, AACAAAC at 2925, AAAAAAC at 2921, ACACAAT at 2703, CACACAC at 2700, AAACTAC at 1854, AACCAAT at 1670, CCAACAC at 1596, ACCATAC at 1078, CCCCCAT at 1064, ACCAAAT at 794, CCCCTAT at 781, CCCAAAT at 444, CCCACAC at 435, CCCCAAT at 236, CCCAAAT at 157, CCACCAT at 36.
  15. dBREr4ci: 34, AAAATAT at 4473, ACCCAAT at 4145, AACCAAC at 3909, CAACTAC at 3714, AAACCAT at 3448, AAAAAAC at 3445, CACCTAT at 3281, CCCCCAC at 3157, AACCAAC at 3140, ACACTAC at 3040, CACCAAC at 2658, AAAAAAT at 2515, CCCCAAT at 2480, ACCCAAT at 2325, ACCAAAC at 2135, ACAAAAC at 1972, ACCCAAT at 1784, AAAATAC at 1779, ACAAAAT at 1777, CACATAC at 1256, AACACAT at 1254, AAAACAC at 1252, AAAAAAC at 1250, CCCATAC at 921, CCCCCAT at 919, CCCACAT at 908, CACCCAC at 906, AAACTAT at 603, AACAAAC at 533, CAACAAC at 420, ACCCCAT at 307, CCACAAT at 238, ACCCCAC at 235, CCAAAAC at 54.
  16. dBREr5ci: 33, CCAATAC at 4476, AAAATAT at 4168, AACCAAT at 4156, CCACTAT at 3701, AAACTAT at 3515, CCCAAAC at 3512, CACCCAT at 3210, CCCCTAT at 3140, AAAATAC at 3110, AACCAAC at 2894, AAAAAAC at 2774, CCCATAT at 2627, CCCCCAT at 2625, ACCATAC at 2277, AACCAAC at 1951, CCCATAT at 1778, CAACTAT at 1766, AACACAC at 1641, CCAACAC at 1639, CCCCAAC at 1637, AACATAC at 1619, CCAACAT at 1617, CCCCAAC at 1615, CACCTAT at 1484, AACACAC at 1480, CCAATAC at 1465, CACCAAT at 1463, AACAAAC at 1377, AACAAAT at 1172, AAACAAC at 1168, AAACAAC at 263, CACCAAT at 192, CAAACAT at 140.
  17. dBREr6ci: 49, ACAAAAT at 4523, ACAATAC at 4398, CAACAAT at 4396, CCACAAC at 4393, CCCCTAT at 4342, AACATAC at 4330, AAAACAT at 4328, CCACAAT at 4198, AACCCAC at 4178, CCACCAT at 3918, CAAAAAC at 3848, CCCCTAC at 3780, ACAACAC at 3774, CAAAAAT at 3681, CCCACAC at 3629, CCCCTAC at 3604, CCCAAAT at 3526, CCACCAC at 3360, AACCCAT at 3347, ACCATAC at 3306, AAACCAT at 3304, CACCAAT at 3103, CACAAAT at 3077, CAACCAC at 3073, CCCCAAT at 3037, CACCCAC at 2749, ACCACAT at 2600, AACCCAT at 2459, CCACAAC at 2357, CCCACAT at 2313, CACCCAC at 2311, ACAATAT at 2052, CAACAAT at 2050, CAAAAAT at 1781, CCCACAC at 1671, ACAACAT at 1609, CCCACAT at 1298, CACAAAC at 1169, AAACTAT at 774, AAAAAAC at 771, CCCAAAT at 726, CCCATAT at 625, CACCTAT at 277, ACCATAT at 244, AACATAC at 178, CAAACAT at 176, ACAACAT at 42, CAACAAC at 40, CCACCAT at 29.
  18. dBREr7ci: 34, AACCAAT at 4452, ACCCTAC at 4339, CCCATAT at 4221, ACACTAC at 4117, AAAATAC at 3921, ACCCTAC at 3854, CCCCTAC at 3808, CCAATAC at 3781, CAACCAC at 3690, CCCACAC at 3642, CACCAAT at 3386, CACAAAC at 3269, AAAACAT at 3159, CCAAAAT at 3014, AACCAAT at 2924, AAAATAT at 2514, AAAATAC at 2504, CCAAAAT at 2502, ACCCAAT at 2355, CCCCCAC at 1599, AACCAAT at 1561, CAAATAT at 1411, CCCAAAT at 1409, ACCAAAT at 1210, CCCACAC at 1205, CACCCAT at 1174, CAAAAAC at 938, AAACTAT at 887, CCCAAAC at 884, AACCCAC at 813, CCCCCAC at 679, CAACCAT at 486, ACAAAAT at 430, ACCCAAC at 67.
  19. dBREr8ci: 32, ACACTAC at 4499, ACAAAAC at 4212, CAAAAAC at 4150, AAAAAAC at 4112, ACAAAAC at 4098, AACCTAT at 4004, CACAAAT at 3714, AAAAAAT at 3104, ACCCAAT at 3047, ACCCTAT at 2748, CACCAAT at 2713, AAAAAAC at 2700, ACCAAAT at 2495, AAAACAC at 2410, CCCCCAC at 2177, AAACAAC at 2104, ACACCAC at 1950, ACCACAC at 1947, CCACAAC at 1905, AAAAAAT at 1477, CCCCCAC at 1111, ACCACAC at 1050, AAAAAAC at 1035, ACAATAC at 991, AACAAAT at 962, CAACTAT at 825, CACCAAC at 811, AAACCAC at 559, ACACCAC at 494, AAACAAT at 480, AAAAAAT at 389, ACACTAT at 201.
  20. dBREr9ci: 38, CCCAAAT at 4401, ACCCTAT at 4252, CACAAAT at 4053, CCACTAT at 3831, AAACTAC at 3795, ACAAAAT at 3785, ACCACAC at 3736, CACCCAT at 3474, AACAAAC at 3457, ACACAAC at 3453, CCCACAC at 3450, ACCCAAT at 3429, AAAACAC at 3185, CCCAAAC at 3140, ACCACAT at 3081, ACAATAC at 3076, AACAAAC at 3067, AAAATAC at 2912, CCCCCAT at 2671, ACAAAAC at 2388, CAAATAT at 2095, AACAAAT at 2093, CCCAAAT at 2076, CCACCAT at 1886, ACAAAAC at 1751, CCACAAT at 1676, CCCACAT at 1521, AACCCAC at 1519, ACACAAT at 1098, CAAACAC at 1095, AACAAAC at 1093, CCAACAT at 1062, AAAAAAC at 679, CCCCCAT at 423, AAAAAAT at 406, CACACAC at 305, CAACAAC at 71, CACATAT at 63.

dBREr arbitrary (evens) (4560-2846) UTRs

  1. dBREr0: GTGGGTG at 4505, GTAGGTT at 4349, ATATTTG at 3311, GTTTGTT at 3180, ATGGTTT at 3177, GTGTTTT at 3080, ATAGGGG at 3014.
  2. dBREr2: ATTTTGT at 4486, ATGGGTG at 4390, GTGTTTT at 4113, ATAGGGT at 3110, GTTGGGG at 3047, ATAGTTG at 3044, ATAGGGT at 2980, GTTGGGT at 2969, GTTGGTG at 2867, GTTGTTG at 2864.
  3. dBREr4: GTTGGTT at 4422, GTAGGGT at 4127, GTGTTGG at 4076, ATGTGTT at 4074, GTGTGTT at 3606, GTTGTTT at 3532, GTTGGTT at 3528, ATTTTGT at 3517, GTATTTT at 3354, ATGGGTT at 3222, GTTTGTT at 3208, ATGGTTT at 3205, GTAGGTT at 3147, ATTGGGG at 3099, ATTTGTT at 2907, ATTTTTG at 2889.
  4. dBREr6: GTTTGTT at 4533, ATTTGGT at 4528, GTGGTTT at 4479, ATATTGG at 4430, GTTTGTG at 4364, ATGGGGG at 4347, GTGGGGG at 3742, ATAGGTT at 3646, ATGGGTT at 3554, ATGGTGT at 2946.
  5. dBREr8: ATAGTGG at 4527, ATTTGGT at 4312, GTTGGTT at 3922, ATTTGGT at 3491, GTATGTT at 3444, GTAGTTT at 3396, ATTGGTT at 3119, GTATTGT at 2967.
  6. dBREr0ci: AACACAT at 4435, AAAACAC at 4433, CCAACAT at 4414, CCCATAT at 4385, CCACCAC at 4340, ACCCTAT at 4288, ACCCCAT at 4086, ACCCAAT at 3878, ACAACAC at 3730, ACAAAAT at 3172.
  7. dBREr2ci: CCACTAT at 4411, CCACCAT at 4404, AAACAAC at 4326, ACAAAAC at 4323, CCCCAAC at 4080, CCCCAAT at 3882, CCACAAC at 3838, ACCAAAT at 3828, ACCCCAC at 3314, AAACCAC at 3211, CAAACAT at 3177, ACCAAAC at 3175, AACAAAC at 3170, ACCCCAT at 2892.
  8. dBREr4ci: AAAATAT at 4473, ACCCAAT at 4145, AACCAAC at 3909, CAACTAC at 3714, AAACCAT at 3448, AAAAAAC at 3445, CACCTAT at 3281, CCCCCAC at 3157, AACCAAC at 3140, ACACTAC at 3040.
  9. dBREr6ci: ACAAAAT at 4523, ACAATAC at 4398, CAACAAT at 4396, CCACAAC at 4393, CCCCTAT at 4342, AACATAC at 4330, AAAACAT at 4328, CCACAAT at 4198, AACCCAC at 4178, CCACCAT at 3918, CAAAAAC at 3848, CCCCTAC at 3780, ACAACAC at 3774, CAAAAAT at 3681, CCCACAC at 3629, CCCCTAC at 3604, CCCAAAT at 3526, CCACCAC at 3360, AACCCAT at 3347, ACCATAC at 3306, AAACCAT at 3304, CACCAAT at 3103, CACAAAT at 3077, CAACCAC at 3073, CCCCAAT at 3037.
  10. dBREr8ci: ACACTAC at 4499, ACAAAAC at 4212, CAAAAAC at 4150, AAAAAAC at 4112, ACAAAAC at 4098, AACCTAT at 4004, CACAAAT at 3714, AAAAAAT at 3104, ACCCAAT at 3047.

dBREr alternate (odds) (4560-2846) UTRs

  1. dBREr1: GTTTGGG at 4273, ATGGGTG at 4168, ATATGGG at 4166, GTGGGTG at 4151, ATTTGGG at 4053, ATTGTGT at 3975, GTAGTGT at 3511, ATTTTTT at 3455, GTTTGTG at 3401, ATGGTTT at 3342, GTTTTTT at 3032.
  2. dBREr3: GTTGTTG at 4515, ATGGGTT at 4412, ATTTTGG at 4352, GTTTTTG at 4103, ATTGTTT at 4004, GTATTGT at 4002, GTGTGGG at 3855, ATTTTTG at 3759, GTTGGTT at 3550, GTGGTTT at 3531, ATTTTTT at 3167, GTTTTTT at 3067, ATAGTTT at 2955.
  3. dBREr5: ATGTTGG at 4173, ATATGTT at 4171, ATAGTTT at 4108, GTAGGTT at 3892, ATTTGTG at 3880, ATTTTTT at 3706, ATGGGGG at 3403, GTGTGGT at 3375, ATTTTTT at 3356, ATTTGGG at 3283, GTTGGTT at 3268, ATTGGGT at 3174, GTTTTTT at 2954.
  4. dBREr7: ATAGGGG at 4294, ATGGTTT at 4267, ATTTGTG at 4226, ATATTTG at 4224, ATTTTTT at 3455, ATTGGGG at 3164, GTTGTTG at 2940.
  5. dBREr9: ATTGTTG at 4560, ATGGGTG at 4531, ATGTGGG at 4391, ATGGTGG at 4358, ATTTTGG at 4273, GTATTTT at 4271, ATAGGTT at 4174, ATTGGTG at 3994, ATATTGG at 3992, ATTGGGT at 3724, GTTTGGG at 3597, ATTTGGG at 3479, GTTTTTT at 3387, GTATGGG at 3178, ATTGGTT at 2891.
  6. dBREr1ci: CAAACAC at 4516, CCCAAAC at 4514, CCCCTAT at 4332, CAACCAT at 4323, CCAAAAT at 3883, AACCCAC at 3730, CCCCCAT at 3631, AAAACAT at 3603, AACCAAC at 3538, AAAAAAT at 3489, AAAATAT at 3365, CCAAAAT at 3363, AAAAAAC at 2856.
  7. dBREr3ci: AACCCAT at 4456, CCCACAT at 4284, AACCTAC at 4268, CCAATAT at 4254, CCCCAAT at 4252, AAACCAC at 4241, CCCAAAC at 4238, AAAATAC at 4176, ACCAAAT at 4020, CAACTAC at 3787, ACCCTAT at 3678, ACCCTAC at 3561, CCCCTAT at 3353, AACAAAT at 3267, AAAAAAC at 3263, CCACCAT at 3085, AACAAAC at 2925, AAAAAAC at 2921.
  8. dBREr5ci: CCAATAC at 4476, AAAATAT at 4168, AACCAAT at 4156, CCACTAT at 3701, AAACTAT at 3515, CCCAAAC at 3512, CACCCAT at 3210, CCCCTAT at 3140, AAAATAC at 3110, AACCAAC at 2894.
  9. dBREr7ci: AACCAAT at 4452, ACCCTAC at 4339, CCCATAT at 4221, ACACTAC at 4117, AAAATAC at 3921, ACCCTAC at 3854, CCCCTAC at 3808, CCAATAC at 3781, CAACCAC at 3690, CCCACAC at 3642, CACCAAT at 3386, CACAAAC at 3269, AAAACAT at 3159, CCAAAAT at 3014, AACCAAT at 2924.
  10. dBREr9ci: CCCAAAT at 4401, ACCCTAT at 4252, CACAAAT at 4053, CCACTAT at 3831, AAACTAC at 3795, ACAAAAT at 3785, ACCACAC at 3736, CACCCAT at 3474, AACAAAC at 3457, ACACAAC at 3453, CCCACAC at 3450, ACCCAAT at 3429, AAAACAC at 3185, CCCAAAC at 3140, ACCACAT at 3081, ACAATAC at 3076, AACAAAC at 3067, AAAATAC at 2912.

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

  1. dBREr2: GTTTTTT at 2825.
  2. dBREr2ci: ACAACAC at 2833.

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

  1. dBREr1: GTAGGGG at 2820.
  2. dBREr5: ATTGTGT at 2837.

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

  1. dBREr1: GTTTGGG at 4273.
  2. dBREr3: ATGGGTT at 4412, ATTTTGG at 4352.
  3. dBREr7: ATAGGGG at 4294, ATGGTTT at 4267.
  4. dBREr9: ATGTGGG at 4391, ATGGTGG at 4358, ATTTTGG at 4273, GTATTTT at 4271.
  5. dBREr1ci: CCCCTAT at 4332, CAACCAT at 4323.
  6. dBREr3ci: CCCACAT at 4284, AACCTAC at 4268.
  7. dBREr7ci: ACCCTAC at 4339.
  8. dBREr9ci: CCCAAAT at 4401.

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

  1. dBREr0: GTAGGTT at 4349.
  2. dBREr2: ATGGGTG at 4390.
  3. dBREr4: GTTGGTT at 4422.
  4. dBREr6: ATATTGG at 4430, GTTTGTG at 4364, ATGGGGG at 4347.
  5. dBREr8: ATTTGGT at 4312.
  6. dBREr0ci: AACACAT at 4435, AAAACAC at 4433, CCAACAT at 4414, CCCATAT at 4385, CCACCAC at 4340, ACCCTAT at 4288.
  7. dBREr2ci: CCACTAT at 4411, CCACCAT at 4404, AAACAAC at 4326, ACAAAAC at 4323.
  8. dBREr6ci: ACAATAC at 4398, CAACAAT at 4396, CCACAAC at 4393, CCCCTAT at 4342, AACATAC at 4330, AAAACAT at 4328.

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

  1. dBREr2: GTGGTGG at 2768, ATGTGGT at 2766, ATGGGGT at 2735, ATTTGTT at 2629.
  2. dBREr4: GTGTGGG at 2762.
  3. dBREr6: GTAGGGT at 2679, ATTTTGT at 2652.
  4. dBREr0ci: AAAATAT at 2698, CCCCAAT at 2614.
  5. dBREr2ci: CACACAT at 2808, CACACAC at 2806, ACCACAC at 2804, CACAAAC at 2685, AAAATAT at 2667.
  6. dBREr4ci: CACCAAC at 2658.
  7. dBREr6ci: CACCCAC at 2749, ACCACAT at 2600.
  8. dBREr8ci: ACACTAC at 4499, ACAAAAC at 4212, CAAAAAC at 4150, AAAAAAC at 4112, ACAAAAC at 4098, AACCTAT at 4004, ACCCTAT at 2748, CACCAAT at 2713, AAAAAAC at 2700.

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

  1. dBREr3: ATTTTTG at 2618.
  2. dBREr5: ATGGTGT at 2732.
  3. dBREr9: GTGGTTT at 2706, GTAGTTG at 2635.
  4. dBREr3ci: ACACAAT at 2703, CACACAC at 2700.
  5. dBREr5ci: AAAAAAC at 2774, CCCATAT at 2627, CCCCCAT at 2625.
  6. dBREr9ci: CCCCCAT at 2671.

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

  1. dBREr1: ATGGGTG at 4168, ATATGGG at 4166, GTGGGTG at 4151, ATTTGGG at 4053.
  2. dBREr3: GTTTTTG at 4103.
  3. dBREr5: ATGTTGG at 4173, ATATGTT at 4171, ATAGTTT at 4108.
  4. dBREr7: ATTTGTG at 4226, ATATTTG at 4224.
  5. dBREr9: ATAGGTT at 4174.
  6. dBREr3ci: CCAATAT at 4254, CCCCAAT at 4252, AAACCAC at 4241, CCCAAAC at 4238, AAAATAC at 4176.
  7. dBREr5ci: AAAATAT at 4168, AACCAAT at 4156.
  8. dBREr7ci: CCCATAT at 4221, ACACTAC at 4117.
  9. dBREr9ci: ACCCTAT at 4252, CACAAAT at 4053.

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

  1. dBREr2: GTGTTTT at 4113.
  2. dBREr4: GTAGGGT at 4127, GTGTTGG at 4076, ATGTGTT at 4074.
  3. dBREr0ci: ACCCCAT at 4086.
  4. dBREr2ci: CCCCAAC at 4080.
  5. dBREr4ci: ACCCAAT at 4145.
  6. dBREr6ci: CCACAAT at 4198, AACCCAC at 4178.
  7. dBREr8ci: ACAAAAC at 4212, CAAAAAC at 4150, AAAAAAC at 4112, ACAAAAC at 4098.

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

  1. dBREr0: ATTTGGG at 2497, ATTGTTG at 2236, ATATTTT at 2145, GTTGGTG at 2024, ATGTTTT at 1970, GTGTGTG at 1942, GTGGTGT at 1939, ATGGTTT at 1901, ATGTGGT at 1827, GTTTGTG at 1758, GTTGTTT at 1670, ATTTGGG at 1645, ATTTTTT at 1453, ATGTTTT at 605, GTTTGGG at 566, ATAGTTT at 563, GTGGGGT at 533, ATTGGGT at 381, ATATTGG at 379, GTTTTTG at 303, ATGTTGT at 153, ATTGGTT at 83, GTGTTGT at 17.
  2. dBREr2: GTTTTGT at 2530, GTGTTGG at 2496, GTGGTTT at 2462, GTGGGGT at 2143, GTGGGTG at 2003, GTGTGGG at 2001, GTAGTTT at 1653, GTATTTT at 1374, ATGTTTG at 1297, GTTGGGT at 1288, ATAGGGG at 1282, GTGGTTT at 1056, GTTTTTG at 1029, GTGGTTT at 1026, ATTGGTG at 757, ATAGGTT at 406, GTATTTT at 262, ATGTTTT at 245, GTGGGTT at 103, GTATGGT at 21.
  3. dBREr4: ATGGTTT at 2591, GTGTTGG at 2576, ATAGTGT at 2485, GTTGTTT at 2437, GTTTTTG at 2427, GTAGTTT at 2398, GTGGGTT at 2291, ATTTTGT at 2257, GTATGGG at 1831, ATGTGGG at 1825, GTGGGTG at 1490, GTTTTGG at 1383, GTTTGGG at 1340, GTAGGGT at 1208, ATTTTTT at 844, GTATGTT at 701, GTTTGGT at 430, GTGTTTG at 428, GTGGGTT at 278, GTAGGGT at 29.
  4. dBREr6: GTATTGG at 2516, GTAGGGG at 2111, ATGTTGG at 2012, GTATGTT at 2010, GTTTTGT at 1702, ATAGTTT at 1631, GTTGGTG at 1551, ATGTTGG at 1549, GTAGTTT at 1317, ATATTGG at 1026, ATGTTTG at 910, GTATGTT at 908, GTATTGG at 604, GTTTTGG at 569, GTAGTGG at 533, GTGGGGT at 339, ATTTGGT at 97.
  5. dBREr8: ATTTTTT at 2543, GTTGTTT at 2382, ATTTTTT at 2291, ATTGGTG at 1979, GTTTTGG at 1835, ATTTTGG at 1814, ATAGGGG at 1737, GTGTTGG at 1597, GTGGTGG at 1409, ATAGTGG at 1324, ATTGTTT at 1230, ATAGTTT at 981, GTTTTTG at 954, ATTGGGG at 857, GTAGGGT at 577, GTATGGG at 571, ATGGTGT at 535, ATGTGGT at 525, ATTTTGG at 485, ATGGGTT at 411, ATTTGGG at 269, ATGGGTG at 97, GTTTGTT at 43.
  6. dBREr0ci: ACAAAAT at 2334, ACACCAC at 2166, AAAACAT at 2087, CCCATAT at 2040, CCAAAAT at 1812, CACAAAT at 1788, CAAATAC at 1707, AAACAAT at 1577, CACCTAT at 1566, AAACCAT at 1089, ACCAAAC at 1086, ACCCTAC at 1017, AACAAAT at 504, AACCCAC at 440, AAACCAT at 285, CCAAAAT at 195, CCAAAAC at 170, CCCATAC at 40.
  7. dBREr2ci: CAAAAAT at 2382, AAACAAC at 2192, CCACTAC at 2150, ACCCTAT at 1947, AACATAT at 1756, CACCCAT at 1705, CCAACAT at 1635, AACCAAC at 1633, CCCCCAT at 1624, ACCCAAT at 1461, CCCCAAT at 1354, AACATAT at 1325, CAAACAT at 1323, AAAAAAC at 940, ACACAAT at 511, AAACTAC at 313, ACACAAC at 61, ACCACAC at 58.
  8. dBREr4ci: AAAAAAT at 2515, CCCCAAT at 2480, ACCCAAT at 2325, ACCAAAC at 2135, ACAAAAC at 1972, ACCCAAT at 1784, AAAATAC at 1779, ACAAAAT at 1777, CACATAC at 1256, AACACAT at 1254, AAAACAC at 1252, AAAAAAC at 1250, CCCATAC at 921, CCCCCAT at 919, CCCACAT at 908, CACCCAC at 906, AAACTAT at 603, AACAAAC at 533, CAACAAC at 420, ACCCCAT at 307, CCACAAT at 238, ACCCCAC at 235, CCAAAAC at 54.
  9. dBREr6ci: AACCCAT at 2459, CCACAAC at 2357, CCCACAT at 2313, CACCCAC at 2311, ACAATAT at 2052, CAACAAT at 2050, CAAAAAT at 1781, CCCACAC at 1671, ACAACAT at 1609, CCCACAT at 1298, CACAAAC at 1169, AAACTAT at 774, AAAAAAC at 771, CCCAAAT at 726, CCCATAT at 625, CACCTAT at 277, ACCATAT at 244, AACATAC at 178, CAAACAT at 176, ACAACAT at 42, CAACAAC at 40, CCACCAT at 29.
  10. dBREr8ci: ACCAAAT at 2495, AAAACAC at 2410, CCCCCAC at 2177, AAACAAC at 2104, ACACCAC at 1950, ACCACAC at 1947, CCACAAC at 1905, AAAAAAT at 1477, CCCCCAC at 1111, ACCACAC at 1050, AAAAAAC at 1035, ACAATAC at 991, AACAAAT at 962, CAACTAT at 825, CACCAAC at 811, AAACCAC at 559, ACACCAC at 494, AAACAAT at 480, AAAAAAT at 389, ACACTAT at 201.

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

  1. dBREr1: ATAGGGG at 2512, ATTTGGT at 2428, GTGGGTT at 2342, GTATTTT at 2141, GTTTTTT at 1665, GTGTGTG at 1583, GTTTTTT at 1484, ATTTGTT at 1246, ATGGGGG at 1112, ATATGGG at 1110, ATTGTTG at 1011, GTTTGGG at 925, ATTTTTG at 791, GTGTGGG at 699, ATGGGGG at 489, GTTTGGT at 414, ATGTTGG at 404, GTTTTGT at 281, ATAGGGT at 276, ATGGTGG at 267.
  2. dBREr3: ATTTTTG at 2541, GTTTGTT at 2269, GTTGTTT at 2266, ATGGTGG at 2235, GTAGTGT at 2204, GTTTTTG at 2186, GTGGTTG at 2014, GTGTGGT at 2012, ATTTGGG at 1787, GTAGGTT at 1191, ATATTGG at 1163, GTTTTGG at 1113, GTGGTTT at 1110, GTGTGGT at 1108, ATTTTTG at 927, ATATTGG at 666, GTTGTGG at 641, GTTGTTT at 531, GTGGGGG at 515, GTTTGTT at 452, ATTGTTT at 449, GTGGGTT at 426, GTATTTT at 170.
  3. dBREr5: ATGGGGT at 2570, GTGGGTG at 2217, ATGTTTT at 2074, GTATGTT at 2072, GTTTGTG at 1721, GTTGGGT at 1716, ATGGTTG at 1489, GTTTTTT at 1416, GTTTTTG at 1151, ATGTTTT at 1149, ATGGGGT at 1041, GTGGTTT at 932, ATTGTTG at 888, GTTTTGT at 321, ATAGTTT at 318, GTTGGTT at 256, GTATGGG at 174, GTATTTT at 111, GTTGGGG at 44.
  4. dBREr7: GTAGTGG at 2542, ATATTTT at 2517, ATTTGTT at 2448, ATTGTGG at 2154, ATGGGTT at 2136, GTAGTTT at 2118, GTTTGGG at 1849, ATTTGGT at 1179, GTTGGGG at 856, GTGTTGG at 854, ATAGGTT at 733, GTGGTTT at 608, GTGGTGG at 497, ATTTTTG at 491, GTTTTTT at 349, GTAGGGT at 344, GTGGGGT at 135, ATGTGTT at 120, ATTTGGG at 113.
  5. dBREr9: ATTTTGG at 2527, ATTTTGT at 2513, ATTGTTT at 2248, GTTGTTT at 1734, GTATGTT at 1617, ATTGTTG at 1439, GTGTTTT at 1124, ATGTTTT at 1078, GTATGTT at 1076, ATTTTTT at 836, GTATTTT at 834, ATTTTGT at 469, ATAGGTT at 411, GTTTGTT at 95, GTGTTTG at 21, GTAGTGT at 18.
  6. dBREr1ci: CCCCTAC at 2416, AACATAT at 2100, CCAACAT at 2098, ACCCCAC at 1920, ACAATAC at 1824, AAACAAT at 1822, AAAACAT at 1710, ACCCCAT at 1315, CCAACAT at 1201, AACCAAT at 786, AACAAAC at 614, ACACTAC at 373, CCAATAC at 298, CACCCAC at 238, AACACAT at 179, AAAATAT at 168.
  7. dBREr3ci: AAACTAC at 1854, AACCAAT at 1670, CCAACAC at 1596, ACCATAC at 1078, CCCCCAT at 1064, ACCAAAT at 794, CCCCTAT at 781, CCCAAAT at 444, CCCACAC at 435, CCCCAAT at 236, CCCAAAT at 157, CCACCAT at 36.
  8. dBREr5ci: ACCATAC at 2277, AACCAAC at 1951, CCCATAT at 1778, CAACTAT at 1766, AACACAC at 1641, CCAACAC at 1639, CCCCAAC at 1637, AACATAC at 1619, CCAACAT at 1617, CCCCAAC at 1615, CACCTAT at 1484, AACACAC at 1480, CCAATAC at 1465, CACCAAT at 1463, AACAAAC at 1377, AACAAAT at 1172, AAACAAC at 1168, AAACAAC at 263, CACCAAT at 192, CAAACAT at 140.
  9. dBREr7ci: AAAATAT at 2514, AAAATAC at 2504, CCAAAAT at 2502, ACCCAAT at 2355, CCCCCAC at 1599, AACCAAT at 1561, CAAATAT at 1411, CCCAAAT at 1409, ACCAAAT at 1210, CCCACAC at 1205, CACCCAT at 1174, CAAAAAC at 938, AAACTAT at 887, CCCAAAC at 884, AACCCAC at 813, CCCCCAC at 679, CAACCAT at 486, ACAAAAT at 430, ACCCAAC at 67.
  10. dBREr9ci: ACAAAAC at 2388, CAAATAT at 2095, AACAAAT at 2093, CCCAAAT at 2076, CCACCAT at 1886, ACAAAAC at 1751, CCACAAT at 1676, CCCACAT at 1521, AACCCAC at 1519, ACACAAT at 1098, CAAACAC at 1095, AACAAAC at 1093, CCAACAT at 1062, AAAAAAC at 679, CCCCCAT at 423, AAAAAAT at 406, CACACAC at 305, CAACAAC at 71, CACATAT at 63.

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

  1. dBREr1: ATTGTGT at 3975, GTAGTGT at 3511, ATTTTTT at 3455, GTTTGTG at 3401, ATGGTTT at 3342, GTTTTTT at 3032, GTAGGGG at 2820, ATAGGGG at 2512, ATTTGGT at 2428, GTGGGTT at 2342, GTATTTT at 2141, GTTTTTT at 1665, GTGTGTG at 1583, GTTTTTT at 1484, ATTTGTT at 1246, ATGGGGG at 1112, ATATGGG at 1110, ATTGTTG at 1011, GTTTGGG at 925, ATTTTTG at 791, GTGTGGG at 699, ATGGGGG at 489, GTTTGGT at 414, ATGTTGG at 404, GTTTTGT at 281, ATAGGGT at 276, ATGGTGG at 267.
  2. dBREr3: ATTGTTT at 4004, GTATTGT at 4002, GTGTGGG at 3855, ATTTTTG at 3759, GTTGGTT at 3550, GTGGTTT at 3531, ATTTTTT at 3167, GTTTTTT at 3067, ATAGTTT at 2955, ATTTTTG at 2618, ATTTTTG at 2541, GTTTGTT at 2269, GTTGTTT at 2266, ATGGTGG at 2235, GTAGTGT at 2204, GTTTTTG at 2186, GTGGTTG at 2014, GTGTGGT at 2012, ATTTGGG at 1787, GTAGGTT at 1191, ATATTGG at 1163, GTTTTGG at 1113, GTGGTTT at 1110, GTGTGGT at 1108, ATTTTTG at 927, ATATTGG at 666, GTTGTGG at 641, GTTGTTT at 531, GTGGGGG at 515, GTTTGTT at 452, ATTGTTT at 449, GTGGGTT at 426, GTATTTT at 170.
  3. dBREr5: GTAGGTT at 3892, ATTTGTG at 3880, ATTTTTT at 3706, ATGGGGG at 3403, GTGTGGT at 3375, ATTTTTT at 3356, ATTTGGG at 3283, GTTGGTT at 3268, ATTGGGT at 3174, GTTTTTT at 2954, ATTGTGT at 2837, ATGGTGT at 2732, ATGGGGT at 2570, GTGGGTG at 2217, ATGTTTT at 2074, GTATGTT at 2072, GTTTGTG at 1721, GTTGGGT at 1716, ATGGTTG at 1489, GTTTTTT at 1416, GTTTTTG at 1151, ATGTTTT at 1149, ATGGGGT at 1041, GTGGTTT at 932, ATTGTTG at 888, GTTTTGT at 321, ATAGTTT at 318, GTTGGTT at 256, GTATGGG at 174, GTATTTT at 111, GTTGGGG at 44.
  4. dBREr7: ATTTTTT at 3455, ATTGGGG at 3164, GTTGTTG at 2940, GTAGTGG at 2542, ATATTTT at 2517, ATTTGTT at 2448, ATTGTGG at 2154, ATGGGTT at 2136, GTAGTTT at 2118, GTTTGGG at 1849, ATTTGGT at 1179, GTTGGGG at 856, GTGTTGG at 854, ATAGGTT at 733, GTGGTTT at 608, GTGGTGG at 497, ATTTTTG at 491, GTTTTTT at 349, GTAGGGT at 344, GTGGGGT at 135, ATGTGTT at 120, ATTTGGG at 113.
  5. dBREr9: ATTGGTG at 3994, ATATTGG at 3992, ATTGGGT at 3724, GTTTGGG at 3597, ATTTGGG at 3479, GTTTTTT at 3387, GTATGGG at 3178, ATTGGTT at 2891, GTGGTTT at 2706, GTAGTTG at 2635, ATTTTGG at 2527, ATTTTGT at 2513, ATTGTTT at 2248, GTTGTTT at 1734, GTATGTT at 1617, ATTGTTG at 1439, GTGTTTT at 1124, ATGTTTT at 1078, GTATGTT at 1076, ATTTTTT at 836, GTATTTT at 834, ATTTTGT at 469, ATAGGTT at 411, GTTTGTT at 95, GTGTTTG at 21, GTAGTGT at 18.
  6. dBREr1ci: CCAAAAT at 3883, AACCCAC at 3730, CCCCCAT at 3631, AAAACAT at 3603, AACCAAC at 3538, AAAAAAT at 3489, AAAATAT at 3365, CCAAAAT at 3363, AAAAAAC at 2856, CCCCTAC at 2416, AACATAT at 2100, CCAACAT at 2098, ACCCCAC at 1920, ACAATAC at 1824, AAACAAT at 1822, AAAACAT at 1710, ACCCCAT at 1315, CCAACAT at 1201, AACCAAT at 786, AACAAAC at 614, ACACTAC at 373, CCAATAC at 298, CACCCAC at 238, AACACAT at 179, AAAATAT at 168.
  7. dBREr3ci: ACCAAAT at 4020, CAACTAC at 3787, ACCCTAT at 3678, ACCCTAC at 3561, CCCCTAT at 3353, AACAAAT at 3267, AAAAAAC at 3263, CCACCAT at 3085, AACAAAC at 2925, AAAAAAC at 2921, ACACAAT at 2703, CACACAC at 2700, AAACTAC at 1854, AACCAAT at 1670, CCAACAC at 1596, ACCATAC at 1078, CCCCCAT at 1064, ACCAAAT at 794, CCCCTAT at 781, CCCAAAT at 444, CCCACAC at 435, CCCCAAT at 236, CCCAAAT at 157, CCACCAT at 36.
  8. dBREr5ci: CCACTAT at 3701, AAACTAT at 3515, CCCAAAC at 3512, CACCCAT at 3210, CCCCTAT at 3140, AAAATAC at 3110, AACCAAC at 2894, AAAAAAC at 2774, CCCATAT at 2627, CCCCCAT at 2625, ACCATAC at 2277, AACCAAC at 1951, CCCATAT at 1778, CAACTAT at 1766, AACACAC at 1641, CCAACAC at 1639, CCCCAAC at 1637, AACATAC at 1619, CCAACAT at 1617, CCCCAAC at 1615, CACCTAT at 1484, AACACAC at 1480, CCAATAC at 1465, CACCAAT at 1463, AACAAAC at 1377, AACAAAT at 1172, AAACAAC at 1168, AAACAAC at 263, CACCAAT at 192, CAAACAT at 140.
  9. dBREr7ci: AAAATAC at 3921, ACCCTAC at 3854, CCCCTAC at 3808, CCAATAC at 3781, CAACCAC at 3690, CCCACAC at 3642, CACCAAT at 3386, CACAAAC at 3269, AAAACAT at 3159, CCAAAAT at 3014, AACCAAT at 2924, AAAATAT at 2514, AAAATAC at 2504, CCAAAAT at 2502, ACCCAAT at 2355, CCCCCAC at 1599, AACCAAT at 1561, CAAATAT at 1411, CCCAAAT at 1409, ACCAAAT at 1210, CCCACAC at 1205, CACCCAT at 1174, CAAAAAC at 938, AAACTAT at 887, CCCAAAC at 884, AACCCAC at 813, CCCCCAC at 679, CAACCAT at 486, ACAAAAT at 430, ACCCAAC at 67.
  10. dBREr9ci: CCACTAT at 3831, AAACTAC at 3795, ACAAAAT at 3785, ACCACAC at 3736, CACCCAT at 3474, AACAAAC at 3457, ACACAAC at 3453, CCCACAC at 3450, ACCCAAT at 3429, AAAACAC at 3185, CCCAAAC at 3140, ACCACAT at 3081, ACAATAC at 3076, AACAAAC at 3067, AAAATAC at 2912, CCCCCAT at 2671, ACAAAAC at 2388, CAAATAT at 2095, AACAAAT at 2093, CCCAAAT at 2076, CCACCAT at 1886, ACAAAAC at 1751, CCACAAT at 1676, CCCACAT at 1521, AACCCAC at 1519, ACACAAT at 1098, CAAACAC at 1095, AACAAAC at 1093, CCAACAT at 1062, AAAAAAC at 679, CCCCCAT at 423, AAAAAAT at 406, CACACAC at 305, CAACAAC at 71, CACATAT at 63.

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

  1. dBREr0: ATATTTG at 3311, GTTTGTT at 3180, ATGGTTT at 3177, GTGTTTT at 3080, ATAGGGG at 3014, ATTTGGG at 2497, ATTGTTG at 2236, ATATTTT at 2145, GTTGGTG at 2024, ATGTTTT at 1970, GTGTGTG at 1942, GTGGTGT at 1939, ATGGTTT at 1901, ATGTGGT at 1827, GTTTGTG at 1758, GTTGTTT at 1670, ATTTGGG at 1645, ATTTTTT at 1453, ATGTTTT at 605, GTTTGGG at 566, ATAGTTT at 563, GTGGGGT at 533, ATTGGGT at 381, ATATTGG at 379, GTTTTTG at 303, ATGTTGT at 153, ATTGGTT at 83, GTGTTGT at 17.
  2. dBREr2: ATAGGGT at 3110, GTTGGGG at 3047, ATAGTTG at 3044, ATAGGGT at 2980, GTTGGGT at 2969, GTTGGTG at 2867, GTTGTTG at 2864, GTTTTTT at 2825, GTGGTGG at 2768, ATGTGGT at 2766, ATGGGGT at 2735, ATTTGTT at 2629, GTTTTGT at 2530, GTGTTGG at 2496, GTGGTTT at 2462, GTGGGGT at 2143, GTGGGTG at 2003, GTGTGGG at 2001, GTAGTTT at 1653, GTATTTT at 1374, ATGTTTG at 1297, GTTGGGT at 1288, ATAGGGG at 1282, GTGGTTT at 1056, GTTTTTG at 1029, GTGGTTT at 1026, ATTGGTG at 757, ATAGGTT at 406, GTATTTT at 262, ATGTTTT at 245, GTGGGTT at 103, GTATGGT at 21.
  3. dBREr4: GTGTGTT at 3606, GTTGTTT at 3532, GTTGGTT at 3528, ATTTTGT at 3517, GTATTTT at 3354, ATGGGTT at 3222, GTTTGTT at 3208, ATGGTTT at 3205, GTAGGTT at 3147, ATTGGGG at 3099, ATTTGTT at 2907, ATTTTTG at 2889, GTGTGGG at 2762, ATGGTTT at 2591, GTGTTGG at 2576, ATAGTGT at 2485, GTTGTTT at 2437, GTTTTTG at 2427, GTAGTTT at 2398, GTGGGTT at 2291, ATTTTGT at 2257, GTATGGG at 1831, ATGTGGG at 1825, GTGGGTG at 1490, GTTTTGG at 1383, GTTTGGG at 1340, GTAGGGT at 1208, ATTTTTT at 844, GTATGTT at 701, GTTTGGT at 430, GTGTTTG at 428, GTGGGTT at 278, GTAGGGT at 29.
  4. dBREr6: GTGGGGG at 3742, ATAGGTT at 3646, ATGGGTT at 3554, ATGGTGT at 2946, GTAGGGT at 2679, ATTTTGT at 2652, GTATTGG at 2516, GTAGGGG at 2111, ATGTTGG at 2012, GTATGTT at 2010, GTTTTGT at 1702, ATAGTTT at 1631, GTTGGTG at 1551, ATGTTGG at 1549, GTAGTTT at 1317, ATATTGG at 1026, ATGTTTG at 910, GTATGTT at 908, GTATTGG at 604, GTTTTGG at 569, GTAGTGG at 533, GTGGGGT at 339, ATTTGGT at 97.
  5. dBREr8: GTTGGTT at 3922, ATTTGGT at 3491, GTATGTT at 3444, GTAGTTT at 3396, ATTGGTT at 3119, GTATTGT at 2967, ATTTTTT at 2543, GTTGTTT at 2382, ATTTTTT at 2291, ATTGGTG at 1979, GTTTTGG at 1835, ATTTTGG at 1814, ATAGGGG at 1737, GTGTTGG at 1597, GTGGTGG at 1409, ATAGTGG at 1324, ATTGTTT at 1230, ATAGTTT at 981, GTTTTTG at 954, ATTGGGG at 857, GTAGGGT at 577, GTATGGG at 571, ATGGTGT at 535, ATGTGGT at 525, ATTTTGG at 485, ATGGGTT at 411, ATTTGGG at 269, ATGGGTG at 97, GTTTGTT at 43.
  6. dBREr0ci: ACCCAAT at 3878, ACAACAC at 3730, ACAAAAT at 3172, AAAATAT at 2698, CCCCAAT at 2614, ACAAAAT at 2334, ACACCAC at 2166, AAAACAT at 2087, CCCATAT at 2040, CCAAAAT at 1812, CACAAAT at 1788, CAAATAC at 1707, AAACAAT at 1577, CACCTAT at 1566, AAACCAT at 1089, ACCAAAC at 1086, ACCCTAC at 1017, AACAAAT at 504, AACCCAC at 440, AAACCAT at 285, CCAAAAT at 195, CCAAAAC at 170, CCCATAC at 40.
  7. dBREr2ci: CCCCAAT at 3882, CCACAAC at 3838, ACCAAAT at 3828, ACCCCAC at 3314, AAACCAC at 3211, CAAACAT at 3177, ACCAAAC at 3175, AACAAAC at 3170, ACCCCAT at 2892, ACAACAC at 2833, CACACAT at 2808, CACACAC at 2806, ACCACAC at 2804, CACAAAC at 2685, AAAATAT at 2667, CAAAAAT at 2382, AAACAAC at 2192, CCACTAC at 2150, ACCCTAT at 1947, AACATAT at 1756, CACCCAT at 1705, CCAACAT at 1635, AACCAAC at 1633, CCCCCAT at 1624, ACCCAAT at 1461, CCCCAAT at 1354, AACATAT at 1325, CAAACAT at 1323, AAAAAAC at 940, ACACAAT at 511, AAACTAC at 313, ACACAAC at 61, ACCACAC at 58.
  8. dBREr4ci: AACCAAC at 3909, CAACTAC at 3714, AAACCAT at 3448, AAAAAAC at 3445, CACCTAT at 3281, CCCCCAC at 3157, AACCAAC at 3140, ACACTAC at 3040, CACCAAC at 2658, AAAAAAT at 2515, CCCCAAT at 2480, ACCCAAT at 2325, ACCAAAC at 2135, ACAAAAC at 1972, ACCCAAT at 1784, AAAATAC at 1779, ACAAAAT at 1777, CACATAC at 1256, AACACAT at 1254, AAAACAC at 1252, AAAAAAC at 1250, CCCATAC at 921, CCCCCAT at 919, CCCACAT at 908, CACCCAC at 906, AAACTAT at 603, AACAAAC at 533, CAACAAC at 420, ACCCCAT at 307, CCACAAT at 238, ACCCCAC at 235, CCAAAAC at 54.
  9. dBREr6ci: CCACCAT at 3918, CAAAAAC at 3848, CCCCTAC at 3780, ACAACAC at 3774, CAAAAAT at 3681, CCCACAC at 3629, CCCCTAC at 3604, CCCAAAT at 3526, CCACCAC at 3360, AACCCAT at 3347, ACCATAC at 3306, AAACCAT at 3304, CACCAAT at 3103, CACAAAT at 3077, CAACCAC at 3073, CCCCAAT at 3037, CACCCAC at 2749, ACCACAT at 2600, AACCCAT at 2459, CCACAAC at 2357, CCCACAT at 2313, CACCCAC at 2311, ACAATAT at 2052, CAACAAT at 2050, CAAAAAT at 1781, CCCACAC at 1671, ACAACAT at 1609, CCCACAT at 1298, CACAAAC at 1169, AAACTAT at 774, AAAAAAC at 771, CCCAAAT at 726, CCCATAT at 625, CACCTAT at 277, ACCATAT at 244, AACATAC at 178, CAAACAT at 176, ACAACAT at 42, CAACAAC at 40, CCACCAT at 29.
  10. dBREr8ci: AACCTAT at 4004, CACAAAT at 3714, AAAAAAT at 3104, ACCCAAT at 3047, ACCCTAT at 2748, CACCAAT at 2713, AAAAAAC at 2700, ACCAAAT at 2495, AAAACAC at 2410, CCCCCAC at 2177, AAACAAC at 2104, ACACCAC at 1950, ACCACAC at 1947, CCACAAC at 1905, AAAAAAT at 1477, CCCCCAC at 1111, ACCACAC at 1050, AAAAAAC at 1035, ACAATAC at 991, AACAAAT at 962, CAACTAT at 825, CACCAAC at 811, AAACCAC at 559, ACACCAC at 494, AAACAAT at 480, AAAAAAT at 389, ACACTAT at 201.

dBRE analysis and results

Main article: Complex locus A1BG and ZNF497 § dBRE

There are two sets of BREs: one (BREu) found immediately upstream of the TATA box, with the consensus SSRCGCC [(C/G)(C/G)(A/G)CGCC]; the other (BREd) found around 7 nucleotides downstream, with the consensus RTDKKKK [(A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T)].[3][4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 58 2 29 29 ± 1 (--28,+-30)
Randoms UTR arbitrary negative 119 10 11.9 12.6 ± 0.7
Randoms UTR alternate negative 133 10 13.3 12.6 ± 0.7
Reals Core negative 2 2 1 1 ± 0 (--1,+-1)
Randoms Core arbitrary negative 2 10 0.2 0.2
Randoms Core alternate negative 2 10 0.2 0.2
Reals Core positive 5 2 2.5 2.5 ± 0.5 (-+2,++3)
Randoms Core arbitrary positive 15 10 1.5 1.9 ± 0.4
Randoms Core alternate positive 23 10 2.3 1.9 ± 0.4
Reals Proximal negative 8 2 4 4 ± 0 (--4,+-4)
Randoms Proximal arbitrary negative 26 10 2.6 1.8
Randoms Proximal alternate negative 10 10 1.0 1.8
Reals Proximal positive 4 2 2 2 ± 1 (-+3,++1)
Randoms Proximal arbitrary positive 22 10 2.2 1.75 ± 0.45
Randoms Proximal alternate positive 13 10 1.3 1.75 ± 0.45
Reals Distal negative 83 2 41.5 41.5 ± (--43,+-40)
Randoms Distal arbitrary negative 204 10 20.4 19.35 ± 1.05
Randoms Distal alternate negative 183 10 18.3 19.35 ± 1.05
Reals Distal positive 48 2 24 24 ± 6 (-+18,++30)
Randoms Distal arbitrary positive 283 10 28.3 29.15 ± 0.85
Randoms Distal alternate positive 300 10 30.0 29.15 ± 0.85

Comparison:

The occurrences of real dBREs are greater than the randoms, positive cores overlap high randoms, positive proximals are outside the randoms, positive distals overlap randoms at the high end. This suggests that the real dBREs are likely active or activable.

Comparing the distal promoters, the negative direction is higher than the randoms, whereas the positive direction is comparable to the randoms. This suggests that as least in the negative direction the reals are likely active or activable, but in the positive direction the core and proximal promoter are likely active or activable, but the distal promoter sequences may be random.

Comparisons of negative direction promoter elements

Butler (2002) Watson (2014) Wilson (2019)
~-37 to -32 BREu SSRCGCC ~-31 to -26 TATAWAW ~-19 to -12 BREd RTDKKKK
UTR nn(4560-2846) UTR nn(4560-2846) UTR nn(4560-2846)
- - GTAGGTG at 4458
- - GTGGGGT at 4446
- - GTTTTTT at 4378
- - GTTTTTT at 4218
- - ATGTTTT at 4216
- - GTTGTGT at 4196
- - GTTTTTT at 4068
- - ATGTTTT at 4066
- - ciAACCAAC at 3945
- - ciCCACTAC at 3798
- - GTGTTTT at 3767
- - ATGGTGG at 3740
- - ciCACCAAC at 3605
- - ciAACCAAC at 3532
- - GTAGTTG at 3523
- TATAAT at 3468 Christensen (1982) -
- TATAAT at 3454 Christensen (1982) ATTTGGT at 3484
- - ATTTGGT at 3365
- - ciCCAAAAT at 3350
- - ATTTGTT at 3338
- - GTTTTTG at 3328
- - ciCCCACAC at 3185
- - GTATTTT at 3171
- - ATTTTTG at 3165
CCACGCC at 3047 - GTGGGTT at 3136
- - ATTTTTT at 3026
- - GTAGTTT at 2890
- ciTTTATA at 2869 Butler (2002) ATATTTG at 2875
- - GTTGGGT at 2846
- TATAAA at 2852 Butler (2002) -
Core nn(2846-2811) Core nn(2846-2811) Core nn(2846-2811)
- - GTTGGGT at 2846
Proximal nn(2811-2596) Proximal nn(2811-2596) Proximal nn(2811-2596)
- - GTGGGGT at 2764
- ciTTTATA at 2638 ciACACCAC at 2660
- - ATGTTTT at 2644
- - ATATGTT at 2642
Distal nn(2596-1) Distal nn(2596-1) Distal nn(2596-1)
- - GTTTGTT at 2488
- - GTTTGTT at 2484
- - GTGTGGT at 2419
- - ciCACCCAC at 2332
- - GTTTTTT at 2309
CCACGCC at 2197 - ATGTTTT at 2307
- - GTTTTTT at 2184
- - ATGTTTT at 2182
- - GTTTTTT at 2038
- - ciCCACCAC at 1902
- - GTTTTTT at 1882
- - ATGTTTT at 1880
CCGCGCC at 1762 - -
- ciTTTATA at 1740 -
- TATAAA at 1602 -
- - GTTTGTG at 1540
- - GTTGGGT at 1516
- - ciACCACAC at 1478
- - ciAAAAAAC at 1433
- - GTTGGGT at 1409
- - GTTTTTT at 1396
- - GTTTGTT at 1392
- - GTTTTTG at 1386
- - GTTTTTT at 1230
- - ATGTTTT at 1228
- - ciCACCCAC at 1163
- - GTTTTTT at 1094
- - ciAACCCAC at 1048
- - GTTTTTT at 928
- - GTGTGGT at 883
- - ciACACCAC at 789
- - GTTTTTT at 773
- - ATGTTTT at 771
- - GTTTTTT at 639
- ciATTATA at 603 Christensen (1982) ATGTTTT at 637
- - ATTGGGG at 616
- - ciACCACAC at 609
- - GTTTTTT at 487
CCACGCC at 380 - ATGTTTT at 485
- ciATTATA at 272 Christensen (1982) -
- - GTTTTGG at 259
- - ATATTTT at 222
- - ciCAAAAAT at 217
- - ATATTTT at 183
- - GTTTTGT at 166
- - ATATGTT at 113
- - ATTTTGT at 68
UTR pn(4560-2846) UTR pn(4560-2846) UTR pn(4560-2846)
- - ciAACCCAT at 4454
- - ciAAAAAAT at 4219
- - ATGGTGG at 4110
- - ciAAAAAAT at 4069
- - ciCCAACAC at 3981
- - GTTGGTT at 3944
- - GTGTTGG at 3942
- - ciCCCATAC at 3857
- - ATGTGGT at 3811
- - ATGGGGT at 3802
- - ciACAAAAT at 3768
- - GTGGTTG at 3605
- - ATTGGTT at 3531
- - ciCAACTAT at 3526
- - ciAAAACAC at 3512
- - ciAAACCAC at 3366
- - ciCAAAAAC at 3328
- - GTGGGTG at 3195
- - GTGGTGG at 3192
- - GTGGTGG at 3189
- - GTGTGGT at 3187
- - ciAAAACAT at 3167
- - ciACCCCAT at 3152
- - ciACCCAAC at 3137
- - GTGGTGG at 3050
- - ciAAAAAAC at 3027
- - ciAAACCAC at 2972
- TATAAA at 2874 Butler (2002) ciAAAAAAT at 2930
- - ciAAAATAT at 2869
- - ciATATTTT at 2853
Core pn(2846-2811) Core pn(2846-2811) Core pn(2846-2811)
- - ciAAACAAC at 2843
Proximal pn(2811-2596) Proximal pn(2811-2596) Proximal pn(2811-2596)
- - GTGGTGG at 2661
- - GTGTGGT at 2659
- - ciCAAAAAT at 2646
- - ciCCAACAT at 2612
Distal pn(2596-1) Distal pn(2596-1) Distal pn(2596-1)
- - ciCCAACAC at 2549
- - ciAACAAAC at 2511
- - ciAACAAAC at 2486
- - ciACACCAC at 2420
- - GTGGGTG at 2332
- - ciAAAATAC at 2303
- - ciACCCCAT at 2288
- - ciAAAAAAT at 2185
- - ciCCAACAT at 2150
- - ciAAAAAAT at 2061
- - GTGGTGG at 1903
ciGGCGTGG at 1897 - GTGGTGG at 1900
- - ciAAAATAC at 1876
- - ciACCCCAT at 1861
- TATATAT at 1600 Watson (2014) ciAAAATAT at 1740
- ciATATATA at 1599 Watson (2014) ciAAAATAT at 1740
- - ciAACAAAC at 1587
- - ciAAAATAC at 1564
- - ciCAAACAC at 1540
- - GTGGTGT at 1477
- - ciCAAAAAC at 1386
ciGGCGTGG at 1244 - GTGGTGG at 1247
- - ciAAAAAAT at 1231
- - ciCCAACAT at 1205
GGACGCC at 1153 - GTGGGTG at 1163
- - ATTGGGT at 1047
- - ciACACCAT at 884
- - GTGGTGT at 793
- - GTGGTGG at 790
- - ATGTGGT at 788
- - ciAAAATAC at 767
- - ciAAAATAC at 633
- - ATGGTGT at 608
- - ATATGGT at 606
- - ciAAAAAAT at 488
- - ciAAAACAT at 361
- TATAAAAG at 223 Juven-Gershon (2010) ciAAACAAT at 230
- TATAAAA at 222 Carninci (2006) ciAAACAAT at 230
- TATAAA at 221 Butler (2002) ciAAACAAT at 230
- ciTTTATA at 219 Butler (2002) ciAAACAAT at 230
- TATAAAAG at 184 Juven-Gershon (2010) ATGTTTT at 215
- TATAAAA at 183 Carninci (2006) ATGTTTT at 215
- TATAAA at 182 Butler (2002) ATGGGGT at 204
- - ATATGGG at 78
- - ATATGTT at 43

Comparisons of positive direction promoter elements

Butler (2002) Watson (2014) Wilson (2019)
~-37 to -32 BREu SSRCGCC ~-31 to -26 TATAWAW ~-19 to -12 BREd RTDKKKK
Core np(4445-4265) Core np(4445-4265) Core np(4445-4265)
- - GTGGGGT at 4397
Proximal np(4265-4050) Proximal np(4265-4050) Proximal np(4265-4050)
- - ATGGGGG at 4225
- - ATTGTTG at 4173
- - GTGGTTT at 4108
Distal np(4050-1) Distal np(4050-1) Distal np(4050-1)
- - GTGGTGT at 3969
- - GTGTGGT at 3967
- - GTGGTGG at 3816
- - ATGTTTG at 3339
- - GTGTTGG at 2816
- ciTTTATA at 2588 -
- - ATTTTTT at 2451
ciGGCGCCC at 1770 - -
GGGCGCC at 1769 - -
GGACGCC at 1672 - -
GCACGCC at 1302 - -
- TATAAT at 729 Christensen (1982) -
- ciATTATA at 727 Christensen (1982) -
- - GTGGGGG at 56
Core pp(4445-4265) Core pp(4445-4265) Core pp(4445-4265)
- - ciACCCCAC at 4398
- - GTGGGGT at 4328
- - GTGGGGT at 4286
Proximal pp(4265-4050) Proximal pp(4265-4050) Proximal pp(4265-4050)
- - GTTTGTG at 4257
- - ciCCAAAAT at 4110
Distal pp(4050-1) Distal pp(4050-1) pp(4050-1)
- - ciACACCAC at 3968
- - ciAAACCAC at 3949
- - GTGTGGT at 3825
- - ciACACCAC at 3644
- - GTAGGGT at 3631
- - ATAGGGT at 3386
- - ciCCAATAC at 3026
- - GTGTGGG at 2965
- - ciCCACAAC at 2815
- - ATGGTGG at 2759
- - ciCACCTAC at 2714
- - ciCCAAAAC at 2688
- - ciCCCCTAT at 2659
- - GTGTGGT at 2603
- - ATGGTGT at 2600
ciGGCGTGG at 2566 - ATATGGT at 2591
- - ciAAAAAAC at 2452
- - ciACCCTAC at 2409
- - ciAAAAAAC at 2282
- - GTTGGTG at 2122
- - GTGGGGG at 2020
- - GTTGGGT at 2015
- - ATGGGGT at 1891
CCACGCC at 1764 - ciAACCCAC at 1802
ciGGCGCCG at 1438 - -
ciGGCGCCG at 1338 - -
CGACGCC at 1033 - -
ciGGCGCGC at 682 - GTGGTGG at 704
- - GTAGGTG at 700
- - GTAGGTG at 631
CCACGCC at 489 - -
- - ciACAAAAT at 148
- - GTGGGTG at 72
- - ciCCCCTAC at 59

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. ↑ Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998). "New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB". Genes & Development. 12 (1): 34–44. doi:10.1101/gad.12.1.34. PMC 316406. PMID 9420329.
  2. ↑ Littlefield O, Korkhin Y, Sigler PB (1999). "The structural basis for the oriented assembly of a TBP/TFB/promoter complex". Proceedings of the National Academy of Sciences of the USA. 96 (24): 13668–13673. Bibcode:1999PNAS...9613668L. doi:10.1073/pnas.96.24.13668. PMC 24122. PMID 10570130.
  3. ↑ 3.0 3.1 Wilson, David B. "Drosophila Core Promoter Motifs". Retrieved 2 April 2019.
  4. ↑ 4.0 4.1 Juven-Gershon, T; Kadonaga, JT (15 March 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.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 Wensheng Deng, Stefan G.E. Roberts (October 15, 2005). "A core promoter element downstream of the TATA box that is recognized by TFIIB". Genes & Development. 19 (20): 2418–23. doi:10.1101/gad.342405. PMID 16230532.
  6. ↑ HGNC (February 10, 2013). "H2AFY H2A histone family, member Y [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-11.
  7. ↑ Tsai FTP, Sigler PB (2000). "Structural basis of preinitiation complex assembly on human Pol II promoters". EMBO J. 19: 25–36.
  8. ↑ "Polymerase II".
  9. ↑ "RNA polymerase II holoenzyme, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 19, 2013. Retrieved 2013-02-11.

Further reading

External links


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