Downstream TFIIB recognition element gene transcriptions: Difference between revisions

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# 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.
# 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.
# 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.
# 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.
# RDr3: 0.
# 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.
# RDr4: 0.
# 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.
# RDr5: 0.
# 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.
# RDr6: 0.
# RDr6: 0.
# RDr7: 0.
# RDr7: 0.

Revision as of 00:41, 4 March 2022

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 UTRs

Main article: UTR promoter gene transcriptions
  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 core promoters

Main article: Core promoter gene transcriptions
  1. Positive strand, negative direction: AAACAAC at 2843.


  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 proximal promoters

Main article: Proximal promoter gene transcriptions
  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.


  1. Negative strand, positive direction: CAAACAC at 4257, ATGGGGG at 4225, ACCCCAT at 4220, ATTGTTG at 4173, GTGGTTT at 4108.
  2. Positive strand, positive direction: GTTTGTG at 4257, CCAAAAT at 4110.

dBRE distal promoters

Main article: Distal promoter gene transcriptions
  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.


  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. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

dBRE analysis and results

Main article: Complex locus A1BG and ZNF497 § dBRE

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. ↑ Wilson, David B. "Drosophila Core Promoter Motifs". Retrieved 2 April 2019.
  4. ↑ 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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