Downstream core element gene transcriptions

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Editor-In-Chief: Henry A. Hoff

The downstream core element (DCE) is a transcription core promoter sequence that is within the transcribed portion of a gene.

Downstream

Def. lower "down, in relation to a river or stream ... [f]ollowing the path of a river or stream"[1] is called downstream.

By analogy, gene transcription follows a path along the human DNA template strand once the RNA polymerase II holoenzyme locates the transcription start site (TSS).

Cores

Main articles: Core promoter gene transcriptions and Core promoters

Def. the "central part ... heart ... center or inner part ... [t]he most important part of a thing",[2] an "inside"[3] is called a core.

Consensus sequences

Main article: Consensus sequences

The consensus sequence for the DCE is CTTC...CTGT...AGC.[4] These three consensus elements are referred to as subelements: "SI is CTTC, SII is CTGT, and SIII is AGC."[4]

The number of nucleotides between each subelement can apparently vary down to none.

Core promoters

Main articles: Core promoter gene transcriptions and Core promoters
File:Preinitiation complex.png
The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: ArneLH.

The core promoter is the minimal portion of the promoter required to properly initiate gene transcription.[5]

It contains a binding site for RNA polymerase (RNA polymerase I, RNA polymerase II, or RNA polymerase III).

"[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"[6].

"Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)"[7][8].

A core promoter that contains all three subelements of the downstream core element may be much less common than one containing only one or two.[4] "SI resides approximately from +6 to +11, SII from +16 to +21, and SIII from +30 to +34."[4]

Transcription start sites

Main articles: Start site gene transcriptions and Transcription start sites

Notation: let the subscript (+1) indicate the specific nucleobase (nucleotide) along the template strand that is a transcription start site. For example, A+1.

The transcription start site (TSS) is the location on the DNA template strand where transcription begins at the 3'-end of a gene.[9] This location corresponds to the 5'-end of the mRNA which by convention is used to designate DNA locations.[9]

Nucleotides downstream from the TSS (N+1, where N stands for any nucleotide) are numbered increasing from +1.

TSS location

One method to perform a TSS location is to test for portions of the downstream core element (DCE) within the about to be transcribed portion of the gene.

SI as 3'-CTTC-5' can occur as 3 of 4 (CTT, TTC) or 4 of 4 (CTTC). SII as 3'-CTGT-5' can also occur as 3 of 4 (CTG, TGT) or 4 of 4 (CTGT). SIII as AGC is not known to vary.

DCE SIII can function independently of SI and SII.[4]

General transcription factor II Ds

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

Transcription factor II D (TFIID), a transcription factor that is part of the RNA polymerase II holoenzyme, interacts with promoters containing only SIII of the DCE suggesting a critical spacing parameter between SIII and the TATA box, initiator element, or some combination of the two.[4] TFIID probably serves as a core promoter recognition complex.[4]

TAF1 interacts with the DCE in a sequence-dependent manner.[4]

The differences between core promoters with downstream elements may be explained by

  1. "TATA- and DPE-dependent promoters are specific for particular enhancers"[4],
  2. "preferences of activators for specific core promoter architectures"[4], and
  3. "the presence of a DCE or [downstream core promoter element (DPE)] might be indicative of an architecture designed for specific regulatory networks, such as the regulation of housekeeping promoters versus tissue-specific promoters (or other highly regulated promoters) or the regulation of subsets of viral promoters."[4]

Hypotheses

Main article: Hypotheses
  1. The downstream core element is not involved in the transcription of A1BG.

Downstream core element SI samplings

  1. negative strand, negative direction, looking for DCE SI: CTTC, 16, CTTC at 3936, CTTC at 3909, CTTC at 3610, CTTC at 3407, CTTC at 2828, CTTC at 2811, CTTC at 2730, CTTC at 2595, CTTC at 2557, CTTC at 1655, CTTC at 1555, CTTC at 367, CTTC at 331, CTTC at 241, CTTC at 132, CTTC at 81.
  2. negative strand, positive direction, looking for DCE SI: CTTC, 30, CTTC at 4241, CTTC at 4061, CTTC at 3994, CTTC at 3394, CTTC at 3312, CTTC at 3247, CTTC at 3057, CTTC at 3031, CTTC at 2947, CTTC at 2582, CTTC at 2361, CTTC at 2107, CTTC at 2095, CTTC at 1914, CTTC at 1516, CTTC at 1432, CTTC at 1405, CTTC at 1332, CTTC at 1305, CTTC at 1264, CTTC at 1153, CTTC at 1069, CTTC at 1012, CTTC at 928, CTTC at 828, CTTC at 760, CTTC at 733, CTTC at 676, CTTC at 592, CTTC at 456.
  3. positive strand, negative direction, looking for DCE SI: CTTC, 5, CTTC at 4528, CTTC at 3776, CTTC at 3553, CTTC at 1053, CTTC at 619.
  4. positive strand, positive direction, looking for DCE SI: CTTC, 24, CTTC at 4263, CTTC at 4248, CTTC at 4197, CTTC at 3871, CTTC at 3851, CTTC at 3762, CTTC at 3667, CTTC at 3216, CTTC at 2784, CTTC at 2748, CTTC at 2192, CTTC at 1633, CTTC at 1594, CTTC at 1231, CTTC at 1063, CTTC at 961, CTTC at 861, CTTC at 768, CTTC at 727, CTTC at 643, CTTC at 559, CTTC at 232, CTTC at 209, CTTC at 48.

Downstream core element SI complements

  1. negative strand, negative direction, looking for DCE SIc: 3'-GAAG-5', 4, 3'-GAAG-5' at 619, 3'-GAAG-5' at 1053, 3'-GAAG-5' at 3553, 3'-GAAG-5' at 3776.
  2. negative strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 24, 3'-GAAG-5' at 48, 3'-GAAG-5' at 209, 3'-GAAG-5' at 232, 3'-GAAG-5' at 559, 3'-GAAG-5' at 643, 3'-GAAG-5' at 727, 3'-GAAG-5' at 768, 3'-GAAG-5' at 861, 3'-GAAG-5' at 961, 3'-GAAG-5' at 1063, 3'-GAAG-5' at 1231, 3'-GAAG-5' at 1594, 3'-GAAG-5' at 1633, 3'-GAAG-5' at 2192, 3'-GAAG-5' at 2748, 3'-GAAG-5' at 2784, 3'-GAAG-5' at 3216, 3'-GAAG-5' at 3667, 3'-GAAG-5' at 3762, 3'-GAAG-5' at 3851, 3'-GAAG-5' at 3871, 3'-GAAG-5' at 4197, 3'-GAAG-5' at 4248, 3'-GAAG-5' at 4263.
  3. positive strand, negative direction, looking for DCE SIc: 3'-GAAG-5', 16, 3'-GAAG-5' at 81, 3'-GAAG-5' at 132, 3'-GAAG-5' at 241, 3'-GAAG-5' at 331, 3'-GAAG-5' at 367, 3'-GAAG-5' at 1555, 3'-GAAG-5' at 1655, 3'-GAAG-5' at 2557, 3'-GAAG-5' at 2595, 3'-GAAG-5' at 2730, 3'-GAAG-5' at 2811, 3'-GAAG-5' at 2828, 3'-GAAG-5' at 3407, 3'-GAAG-5' at 3610, 3'-GAAG-5' at 3909, 3'-GAAG-5' at 3936.
  4. positive strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 30, 3'-GAAG-5' at 456, 3'-GAAG-5' at 592, 3'-GAAG-5' at 676, 3'-GAAG-5' at 733, 3'-GAAG-5' at 760, 3'-GAAG-5' at 828, 3'-GAAG-5' at 928, 3'-GAAG-5' at 1012, 3'-GAAG-5' at 1069, 3'-GAAG-5' at 1153, 3'-GAAG-5' at 1264, 3'-GAAG-5' at 1305, 3'-GAAG-5' at 1332, 3'-GAAG-5' at 1405, 3'-GAAG-5' at 1432, 3'-GAAG-5' at 1516, 3'-GAAG-5' at 1914, 3'-GAAG-5' at 2095, 3'-GAAG-5' at 2107, 3'-GAAG-5' at 2361, 3'-GAAG-5' at 2582, 3'-GAAG-5' at 2947, 3'-GAAG-5' at 3031, 3'-GAAG-5' at 3057, 3'-GAAG-5' at 3247, 3'-GAAG-5' at 3312, 3'-GAAG-5' at 3394, 3'-GAAG-5' at 3994, 3'-GAAG-5' at 4061, 3'-GAAG-5' at 4241.

Downstream core element SI Inverse complements

  1. looking for DCE SIci: 3'-GAAG-5', same as the complements.

Downstream core element SI Inverses

  1. looking for DCE SIi: 3'-CTTC-5', same as the direct.

DCE SI UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CTTC at 3936, CTTC at 3909, CTTC at 3610, CTTC at 3407.

Positive strand, negative direction: CTTC at 4528, CTTC at 3776, CTTC at 3553.

DCE SI core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: CTTC at 2828, CTTC at 2811.

DCE SI proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: CTTC at 2811, CTTC at 2730.

Negative strand, positive direction: CTTC at 4241, CTTC at 4061.

Positive strand, positive direction: CTTC at 4263, CTTC at 4248, CTTC at 4197.

DCE SI distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CTTC at 2595, CTTC at 2557, CTTC at 1655, CTTC at 1555, CTTC at 367, CTTC at 331, CTTC at 241, CTTC at 132, CTTC at 81.

Positive strand, negative direction: CTTC at 1053, CTTC at 619.

Negative strand, positive direction: CTTC at 3994, CTTC at 3394, CTTC at 3312, CTTC at 3247, CTTC at 3057, CTTC at 3031, CTTC at 2947, CTTC at 2582, CTTC at 2361, CTTC at 2107, CTTC at 2095, CTTC at 1914, CTTC at 1516, CTTC at 1432, CTTC at 1405, CTTC at 1332, CTTC at 1305, CTTC at 1264, CTTC at 1153, CTTC at 1069, CTTC at 1012, CTTC at 928, CTTC at 828, CTTC at 760, CTTC at 733, CTTC at 676, CTTC at 592, CTTC at 456.

Positive strand, positive direction: CTTC at 3871, CTTC at 3851, CTTC at 3762, CTTC at 3667, CTTC at 3216, CTTC at 2784, CTTC at 2748, CTTC at 2192, CTTC at 1633, CTTC at 1594, CTTC at 1231, CTTC at 1063, CTTC at 961, CTTC at 861, CTTC at 768, CTTC at 727, CTTC at 643, CTTC at 559, CTTC at 232, CTTC at 209, CTTC at 48.

DCE SI random dataset samplings

  1. DCESIr0: 15, CTTC at 4095, CTTC at 3518, CTTC at 3462, CTTC at 3334, CTTC at 3265, CTTC at 3091, CTTC at 2829, CTTC at 2541, CTTC at 2117, CTTC at 1763, CTTC at 1593, CTTC at 1118, CTTC at 691, CTTC at 310, CTTC at 121.
  2. DCESIr1: 18, CTTC at 4074, CTTC at 4066, CTTC at 3895, CTTC at 3248, CTTC at 2863, CTTC at 2706, CTTC at 2092, CTTC at 2062, CTTC at 1990, CTTC at 1952, CTTC at 1793, CTTC at 1563, CTTC at 1528, CTTC at 1210, CTTC at 761, CTTC at 731, CTTC at 649, CTTC at 292.
  3. DCESIr2: 21, CTTC at 4277, CTTC at 4263, CTTC at 3969, CTTC at 3569, CTTC at 3394, CTTC at 2857, CTTC at 2709, CTTC at 2290, CTTC at 2100, CTTC at 2049, CTTC at 1994, CTTC at 1901, CTTC at 1794, CTTC at 1738, CTTC at 922, CTTC at 820, CTTC at 747, CTTC at 713, CTTC at 695, CTTC at 645, CTTC at 160.
  4. DCESIr3: 19, CTTC at 3953, CTTC at 3564, CTTC at 3418, CTTC at 2928, CTTC at 2891, CTTC at 2524, CTTC at 1860, CTTC at 1843, CTTC at 1821, CTTC at 1599, CTTC at 1268, CTTC at 1180, CTTC at 1034, CTTC at 1021, CTTC at 987, CTTC at 984, CTTC at 681, CTTC at 331, CTTC at 271.
  5. DCESIr4: 23, CTTC at 4546, CTTC at 4477, CTTC at 4193, CTTC at 3986, CTTC at 3846, CTTC at 3691, CTTC at 3503, CTTC at 3275, CTTC at 3051, CTTC at 2148, CTTC at 2081, CTTC at 1718, CTTC at 1700, CTTC at 1585, CTTC at 1460, CTTC at 1190, CTTC at 962, CTTC at 823, CTTC at 760, CTTC at 589, CTTC at 581, CTTC at 468, CTTC at 312.
  6. DCESIr5: 14, CTTC at 3444, CTTC at 3219, CTTC at 3194, CTTC at 3056, CTTC at 2914, CTTC at 2849, CTTC at 2524, CTTC at 2448, CTTC at 2189, CTTC at 2016, CTTC at 1667, CTTC at 1645, CTTC at 1471, CTTC at 1279.
  7. DCESIr6: 16, CTTC at 4320, CTTC at 4241, CTTC at 4001, CTTC at 3591, CTTC at 3479, CTTC at 2754, CTTC at 2441, CTTC at 2304, CTTC at 2148, CTTC at 1987, CTTC at 1961, CTTC at 1730, CTTC at 1355, CTTC at 1040, CTTC at 696, CTTC at 504.
  8. DCESIr7: 18, CTTC at 4125, CTTC at 3083, CTTC at 3069, CTTC at 3043, CTTC at 3002, CTTC at 2707, CTTC at 2365, CTTC at 2310, CTTC at 2202, CTTC at 1899, CTTC at 1800, CTTC at 1358, CTTC at 1199, CTTC at 1020, CTTC at 600, CTTC at 440, CTTC at 218, CTTC at 77.
  9. DCESIr8: 26, CTTC at 4445, CTTC at 4332, CTTC at 4251, CTTC at 4177, CTTC at 3949, CTTC at 3521, CTTC at 3389, CTTC at 3294, CTTC at 3291, CTTC at 3065, CTTC at 2627, CTTC at 2614, CTTC at 2507, CTTC at 2346, CTTC at 2320, CTTC at 2309, CTTC at 1823, CTTC at 1610, CTTC at 1466, CTTC at 1396, CTTC at 1355, CTTC at 1303, CTTC at 648, CTTC at 632, CTTC at 261, CTTC at 189.
  10. DCESIr9: 25, CTTC at 3528, CTTC at 3337, CTTC at 3133, CTTC at 3105, CTTC at 2837, CTTC at 2823, CTTC at 2770, CTTC at 2715, CTTC at 2398, CTTC at 1993, CTTC at 1979, CTTC at 1957, CTTC at 1854, CTTC at 1536, CTTC at 1199, CTTC at 1049, CTTC at 1013, CTTC at 711, CTTC at 698, CTTC at 695, CTTC at 611, CTTC at 478, CTTC at 308, CTTC at 142, CTTC at 125.

DCESIr UTRs

Main article: UTR promoter gene transcriptions
  1. DCESIr0: CTTC at 4095, CTTC at 3518, CTTC at 3462, CTTC at 3334, CTTC at 3265, CTTC at 3091.
  2. DCESIr2: CTTC at 4277, CTTC at 4263, CTTC at 3969, CTTC at 3569, CTTC at 3394, CTTC at 2857.
  3. DCESIr4: CTTC at 4546, CTTC at 4477, CTTC at 4193, CTTC at 3986, CTTC at 3846, CTTC at 3691, CTTC at 3503, CTTC at 3275, CTTC at 3051.
  4. DCESIr6: CTTC at 4320, CTTC at 4241, CTTC at 4001, CTTC at 3591, CTTC at 3479.
  5. DCESIr8: CTTC at 4445, CTTC at 4332, CTTC at 4251, CTTC at 4177, CTTC at 3949, CTTC at 3521, CTTC at 3389, CTTC at 3294, CTTC at 3291, CTTC at 3065.

DCESIr core promoters

Main article: Core promoter gene transcriptions
  1. DCESIr0: CTTC at 2829.

DCESIr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. DCESIr2: CTTC at 2709.
  2. DCESIr6: CTTC at 2754.
  3. DCESIr8: CTTC at 2627, CTTC at 2614.


  1. DCESIr1: CTTC at 4074, CTTC at 4066.
  2. DCESIr7: CTTC at 4125.

DCESIr distal promoters

Main article: Distal promoter gene transcriptions
  1. DCESIr0: CTTC at 2541, CTTC at 2117, CTTC at 1763, CTTC at 1593, CTTC at 1118, CTTC at 691, CTTC at 310, CTTC at 121.
  2. DCESIr2: CTTC at 2290, CTTC at 2100, CTTC at 2049, CTTC at 1994, CTTC at 1901, CTTC at 1794, CTTC at 1738, CTTC at 922, CTTC at 820, CTTC at 747, CTTC at 713, CTTC at 695, CTTC at 645, CTTC at 160.
  3. DCESIr4: CTTC at 2148, CTTC at 2081, CTTC at 1718, CTTC at 1700, CTTC at 1585, CTTC at 1460, CTTC at 1190, CTTC at 962, CTTC at 823, CTTC at 760, CTTC at 589, CTTC at 581, CTTC at 468, CTTC at 312.
  4. DCESIr6: CTTC at 2441, CTTC at 2304, CTTC at 2148, CTTC at 1987, CTTC at 1961, CTTC at 1730, CTTC at 1355, CTTC at 1040, CTTC at 696, CTTC at 504.
  5. DCESIr8: CTTC at 2507, CTTC at 2346, CTTC at 2320, CTTC at 2309, CTTC at 1823, CTTC at 1610, CTTC at 1466, CTTC at 1396, CTTC at 1355, CTTC at 1303, CTTC at 648, CTTC at 632, CTTC at 261, CTTC at 189.


  1. DCESIr1: CTTC at 3895, CTTC at 3248, CTTC at 2863, CTTC at 2706, CTTC at 2092, CTTC at 2062, CTTC at 1990, CTTC at 1952, CTTC at 1793, CTTC at 1563, CTTC at 1528, CTTC at 1210, CTTC at 761, CTTC at 731, CTTC at 649, CTTC at 292.
  2. DCESIr3: CTTC at 3953, CTTC at 3564, CTTC at 3418, CTTC at 2928, CTTC at 2891, CTTC at 2524, CTTC at 1860, CTTC at 1843, CTTC at 1821, CTTC at 1599, CTTC at 1268, CTTC at 1180, CTTC at 1034, CTTC at 1021, CTTC at 987, CTTC at 984, CTTC at 681, CTTC at 331, CTTC at 271.
  3. DCESIr5: CTTC at 3444, CTTC at 3219, CTTC at 3194, CTTC at 3056, CTTC at 2914, CTTC at 2849, CTTC at 2524, CTTC at 2448, CTTC at 2189, CTTC at 2016, CTTC at 1667, CTTC at 1645, CTTC at 1471, CTTC at 1279.
  4. DCESIr7: CTTC at 3083, CTTC at 3069, CTTC at 3043, CTTC at 3002, CTTC at 2707, CTTC at 2365, CTTC at 2310, CTTC at 2202, CTTC at 1899, CTTC at 1800, CTTC at 1358, CTTC at 1199, CTTC at 1020, CTTC at 600, CTTC at 440, CTTC at 218, CTTC at 77.
  5. DCESIr9: CTTC at 3528, CTTC at 3337, CTTC at 3133, CTTC at 3105, CTTC at 2837, CTTC at 2823, CTTC at 2770, CTTC at 2715, CTTC at 2398, CTTC at 1993, CTTC at 1979, CTTC at 1957, CTTC at 1854, CTTC at 1536, CTTC at 1199, CTTC at 1049, CTTC at 1013, CTTC at 711, CTTC at 698, CTTC at 695, CTTC at 611, CTTC at 478, CTTC at 308, CTTC at 142, CTTC at 125.

DCESI analysis and results

Main article: Complex locus A1BG and ZNF497 § DCE SI

The consensus sequence for the DCE is CTTC...CTGT...AGC.[4] These three consensus elements are referred to as subelements: "SI is CTTC, SII is CTGT, and SIII is AGC."[4]

The real downstream core elements in the UTR between ZSCAN22 and A1BG have seven sequences for an occurrence of 3.5. The random data sets had thirty-six sequences for an occurrence of 7.0.

The real DCE in the core promoters (two) have an occurrence of 0.5. The random data sets had one for an occurrence of 0.2.

The real DCE in the proximal promoters (seven) have an occurrence of 1.75. The randoms had seven for an occurrence of 0.7.

The real DCE in the distal promoters (sixty) have an occurrence of 15. The randoms had one hundred and fifty-one for an occurrence of 5.1.

The disparity between the reals and randoms was often as much as a factor of 2 which suggests that the real DCE SI is likely active or activable.

Downstream core element SII samplings

  1. Negative strand, negative direction, looking for DCE SII: CTGT, 19, CTGT at 4507, CTGT at 4468, CTGT at 4355, CTGT at 4181, CTGT at 3756, CTGT at 3433, CTGT at 3412, CTGT at 3389, CTGT at 2948, CTGT at 2880, CTGT at 2271, CTGT at 2117, CTGT at 2015, CTGT at 1569, CTGT at 1068, CTGT at 746, CTGT at 559, CTGT at 422, CTGT at 170.
  2. Negative strand, positive direction, looking for DCE SII: CTGT, 26, CTGT at 4392, CTGT at 3640, CTGT at 3622, CTGT at 3617, CTGT at 3434, CTGT at 3390, CTGT at 3349, CTGT at 2957, CTGT at 2931, CTGT at 2925, CTGT at 2342, CTGT at 2308, CTGT at 2260, CTGT at 2250, CTGT at 2182, CTGT at 2074, CTGT at 1998, CTGT at 1860, CTGT at 1729, CTGT at 991, CTGT at 916, CTGT at 891, CTGT at 816, CTGT at 264, CTGT at 144, CTGT at 98.
  3. Positive strand, negative direction, looking for DCE SII: CTGT, 30, CTGT at 4399, CTGT at 4369, CTGT at 4208, CTGT at 4121, CTGT at 3970, CTGT at 3957, CTGT at 3709, CTGT at 3556, CTGT at 3426, CTGT at 3319, CTGT at 3265, CTGT at 3200, CTGT at 3061, CTGT at 2672, CTGT at 2538, CTGT at 2337, CTGT at 2163, CTGT at 2029, CTGT at 1911, CTGT at 1776, CTGT at 1452, CTGT at 1258, CTGT at 1131, CTGT at 1085, CTGT at 967, CTGT at 919, CTGT at 801, CTGT at 667, CTGT at 477, CTGT at 394.
  4. Positive strand, positive direction, looking for DCE SII: CTGT, 16, CTGT at 4332, CTGT at 4252, CTGT at 3973, CTGT at 3893, CTGT at 3569, CTGT at 3530, CTGT at 3131, CTGT at 2843, CTGT at 2460, CTGT at 2412, CTGT at 2130, CTGT at 1964, CTGT at 1869, CTGT at 1693, CTGT at 712, CTGT at 62.

Downstream core element SII Complements

  1. negative strand, negative direction, looking for DCE SIIc: 3'-GACA-5', 30, 3'-GACA-5' at 394, 3'-GACA-5' at 477, 3'-GACA-5' at 667, 3'-GACA-5' at 801, 3'-GACA-5' at 919, 3'-GACA-5' at 967, 3'-GACA-5' at 1085, 3'-GACA-5' at 1131, 3'-GACA-5' at 1258, 3'-GACA-5' at 1452, 3'-GACA-5' at 1776, 3'-GACA-5' at 1911, 3'-GACA-5' at 2029, 3'-GACA-5' at 2163, 3'-GACA-5' at 2337, 3'-GACA-5' at 2538, 3'-GACA-5' at 2672, 3'-GACA-5' at 3061, 3'-GACA-5' at 3200, 3'-GACA-5' at 3265, 3'-GACA-5' at 3319, 3'-GACA-5' at 3426, 3'-GACA-5' at 3556, 3'-GACA-5' at 3709, 3'-GACA-5' at 3957, 3'-GACA-5' at 3970, 3'-GACA-5' at 4121, 3'-GACA-5' at 4208, 3'-GACA-5' at 4369, 3'-GACA-5' at 4399.
  2. negative strand, positive direction, looking for DCE SIIc: 3'-GACA-5', 15, 3'-GACA-5' at 62, 3'-GACA-5' at 712, 3'-GACA-5' at 1693, 3'-GACA-5' at 1869, 3'-GACA-5' at 1964, 3'-GACA-5' at 2130, 3'-GACA-5' at 2412, 3'-GACA-5' at 2460, 3'-GACA-5' at 2843, 3'-GACA-5' at 3131, 3'-GACA-5' at 3530, 3'-GACA-5' at 3569, 3'-GACA-5' at 3893, 3'-GACA-5' at 3973, 3'-GACA-5' at 4252.
  3. positive strand, negative direction, looking for DCE SIIc: 3'-GACA-5', 17, 3'-GACA-5' at 170, 3'-GACA-5' at 422, 3'-GACA-5' at 559, 3'-GACA-5' at 746, 3'-GACA-5' at 1068, 3'-GACA-5' at 1569, 3'-GACA-5' at 2015, 3'-GACA-5' at 2117, 3'-GACA-5' at 2271, 3'-GACA-5' at 2880, 3'-GACA-5' at 2948, 3'-GACA-5' at 3389, 3'-GACA-5' at 3412, 3'-GACA-5' at 3433, 3'-GACA-5' at 3756, 3'-GACA-5' at 4181, 3'-GACA-5' at 4355.
  4. positive strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 25, 3'-GACA-5' at 98, 3'-GACA-5' at 144, 3'-GACA-5' at 264, 3'-GACA-5' at 816, 3'-GACA-5' at 891, 3'-GACA-5' at 916, 3'-GACA-5' at 991, 3'-GACA-5' at 1729, 3'-GACA-5' at 1860, 3'-GACA-5' at 1998, 3'-GACA-5' at 2074, 3'-GACA-5' at 2182, 3'-GACA-5' at 2250, 3'-GACA-5' at 2260, 3'-GACA-5' at 2308, 3'-GACA-5' at 2342, 3'-GACA-5' at 2925, 3'-GACA-5' at 2931, 3'-GACA-5' at 2957, 3'-GACA-5' at 3349, 3'-GACA-5' at 3390, 3'-GACA-5' at 3434, 3'-GACA-5' at 3617, 3'-GACA-5' at 3622, 3'-GACA-5' at 3640.

Downstream core element SII Inverse complements

  1. Negative strand, negative direction, looking for DCE SIIci: ACAG, 13, ACAG at 4370, ACAG at 4209, ACAG at 3832, ACAG at 3622, ACAG at 3320, ACAG at 3201, ACAG at 2985, ACAG at 2164, ACAG at 2030, ACAG at 1221, ACAG at 1086, ACAG at 920, ACAG at 478.
  2. Negative strand, positive direction, looking for DCE SIIci: ACAG, 28, ACAG at 4069, ACAG at 3974, ACAG at 3894, ACAG at 3860, ACAG at 3635, ACAG at 3570, ACAG at 3412, ACAG at 3210, ACAG at 3193, ACAG at 3178, ACAG at 3132, ACAG at 3099, ACAG at 2844, ACAG at 2836, ACAG at 2651, ACAG at 2461, ACAG at 2413, ACAG at 2131, ACAG at 2124, ACAG at 1965, ACAG at 1823, ACAG at 1053, ACAG at 717, ACAG at 633, ACAG at 551, ACAG at 364, ACAG at 156, ACAG at 63.
  3. Positive strand, negative direction, looking for DCE SIIci: ACAG, 26, ACAG at 4517, ACAG at 4356, ACAG at 4197, ACAG at 3916, ACAG at 3725, ACAG at 3693, ACAG at 3671, ACAG at 2877, ACAG at 2777, ACAG at 2688, ACAG at 2513, ACAG at 2442, ACAG at 2272, ACAG at 2118, ACAG at 2016, ACAG at 1566, ACAG at 1117, ACAG at 1072, ACAG at 906, ACAG at 560, ACAG at 519, ACAG at 423, ACAG at 296, ACAG at 288, ACAG at 167, ACAG at 12.
  4. Positive strand, positive direction, looking for DCE SIIci: ACAG, 21, ACAG at 4366, ACAG at 3951, ACAG at 3744, ACAG at 3618, ACAG at 3576, ACAG at 3391, ACAG at 3052, ACAG at 3003, ACAG at 2926, ACAG at 2465, ACAG at 2309, ACAG at 2171, ACAG at 2077, ACAG at 1999, ACAG at 1861, ACAG at 1730, ACAG at 992, ACAG at 892, ACAG at 267, ACAG at 99, ACAG at 81.
  5. Positive strand, negative direction, looking for DCE SIIi: ACAG, 13, ACAG at 4370, ACAG at 4209, ACAG at 3832, ACAG at 3622, ACAG at 3320, ACAG at 3201, ACAG at 2985, ACAG at 2164, ACAG at 2030, ACAG at 1221, ACAG at 1086, ACAG at 920, ACAG at 478.

Downstream core element SII Inverses

  1. Negative strand, negative direction, looking for DCE SIIi: TGTC, 26, TGTC at 4517, TGTC at 4356, TGTC at 4197, TGTC at 3916, TGTC at 3725, TGTC at 3693, TGTC at 3671, TGTC at 2877, TGTC at 2777, TGTC at 2688, TGTC at 2513, TGTC at 2442, TGTC at 2272, TGTC at 2118, TGTC at 2016, TGTC at 1566, TGTC at 1117, TGTC at 1072, TGTC at 906, TGTC at 560, TGTC at 519, TGTC at 423, TGTC at 296, TGTC at 288, TGTC at 167, TGTC at 12.
  2. Negative strand, positive direction, looking for DCE SIIi: TGTC, 21, TGTC at 4366, TGTC at 3951, TGTC at 3744, TGTC at 3618, TGTC at 3576, TGTC at 3391, TGTC at 3052, TGTC at 3003, TGTC at 2926, TGTC at 2465, TGTC at 2309, TGTC at 2171, TGTC at 2077, TGTC at 1999, TGTC at 1861, TGTC at 1730, TGTC at 992, TGTC at 892, TGTC at 267, TGTC at 99, TGTC at 81.
  3. Positive strand, negative direction, looking for DCE SIIi: TGTC, 13, TGTC at 4370, TGTC at 4209, TGTC at 3832, TGTC at 3622, TGTC at 3320, TGTC at 3201, TGTC at 2985, TGTC at 2164, TGTC at 2030, TGTC at 1221, TGTC at 1086, TGTC at 920, TGTC at 478.
  4. Positive strand, positive direction, looking for DCE SIIi: TGTC, 28, TGTC at 4069, TGTC at 3974, TGTC at 3894, TGTC at 3860, TGTC at 3635, TGTC at 3570, TGTC at 3412, TGTC at 3210, TGTC at 3193, TGTC at 3178, TGTC at 3132, TGTC at 3099, TGTC at 2844, TGTC at 2836, TGTC at 2651, TGTC at 2461, TGTC at 2413, TGTC at 2131, TGTC at 2124, TGTC at 1965, TGTC at 1823, TGTC at 1053, TGTC at 717, TGTC at 633, TGTC at 551, TGTC at 364, TGTC at 156, TGTC at 63.

DCE SII UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CTGT at 4507, CTGT at 4468, ACAG at 4370, CTGT at 4355, ACAG at 4209, CTGT at 4181, ACAG at 3832, CTGT at 3756, ACAG at 3622, CTGT at 3433, CTGT at 3412, CTGT at 3389, ACAG at 3320, ACAG at 3201, ACAG at 2985, CTGT at 2948, CTGT at 2880.

Positive strand, negative direction: ACAG at 4517, CTGT at 4399, CTGT at 4369, ACAG at 4356, CTGT at 4208, ACAG at 4197, CTGT at 4121, CTGT at 3970, CTGT at 3957, ACAG at 3916, ACAG at 3725, CTGT at 3709, ACAG at 3693, ACAG at 3671, CTGT at 3556, CTGT at 3426, CTGT at 3319, CTGT at 3265, CTGT at 3200, CTGT at 3061, ACAG at 2877.

DCE SII core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: CTGT at 4392.

Positive strand, positive direction: ACAG at 4366, CTGT at 4332.

DCE SII proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: ACAG at 2777, ACAG at 2688, CTGT at 2672.

Negative strand, positive direction: ACAG at 4069.

Positive strand, positive direction: CTGT at 4252.

DCE SII distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CTGT at 2271, ACAG at 2164, CTGT at 2117, ACAG at 2030, CTGT at 2015, CTGT at 1569, ACAG at 1221, ACAG at 1086, CTGT at 1068, ACAG at 920, CTGT at 746, CTGT at 559, ACAG at 478, CTGT at 422, CTGT at 170.

Positive strand, negative direction: CTGT at 2538, ACAG at 2513, ACAG at 2442, CTGT at 2337, ACAG at 2272, CTGT at 2163, ACAG at 2118, CTGT at 2029, ACAG at 2016, CTGT at 1911, CTGT at 1776, ACAG at 1566, CTGT at 1452, CTGT at 1258, CTGT at 1131, ACAG at 1117, CTGT at 1085, ACAG at 1072, CTGT at 967, CTGT at 919, ACAG at 906, CTGT at 801, CTGT at 667, ACAG at 560, ACAG at 519, CTGT at 477, ACAG at 423, CTGT at 394, ACAG at 296, ACAG at 288, ACAG at 167, ACAG at 12.

Negative strand, positive direction: ACAG at 3974, ACAG at 3894, ACAG at 3860, CTGT at 3640, ACAG at 3635, CTGT at 3622, CTGT at 3617, ACAG at 3570, CTGT at 3434, ACAG at 3412, CTGT at 3390, CTGT at 3349, ACAG at 3210, ACAG at 3193, ACAG at 3178, ACAG at 3132, ACAG at 3099, CTGT at 2957, CTGT at 2931, CTGT at 2925, ACAG at 2844, ACAG at 2836, ACAG at 2651, ACAG at 2461, ACAG at 2413, CTGT at 2342, CTGT at 2308, CTGT at 2260, CTGT at 2250, CTGT at 2182, ACAG at 2131, ACAG at 2124, CTGT at 2074, CTGT at 1998, ACAG at 1965, CTGT at 1860, ACAG at 1823, CTGT at 1729, ACAG at 1053, CTGT at 991, CTGT at 916, CTGT at 891, CTGT at 816, ACAG at 717, ACAG at 633, ACAG at 551, ACAG at 364, CTGT at 264, ACAG at 156, CTGT at 144, CTGT at 98, ACAG at 63.

Positive strand, positive direction: ACAG at 3951, CTGT at 3973, CTGT at 3893, ACAG at 3744, ACAG at 3618, ACAG at 3576, CTGT at 3569, CTGT at 3530, ACAG at 3391, CTGT at 3131, ACAG at 3052, ACAG at 3003, ACAG at 2926, CTGT at 2843, ACAG at 2465, CTGT at 2460, CTGT at 2412, ACAG at 2309, ACAG at 2171, CTGT at 2130, ACAG at 2077, ACAG at 1999, ACAG at 1861, ACAG at 1730, ACAG at 992, ACAG at 892, ACAG at 267, ACAG at 99, ACAG at 81.

DCE SII random dataset samplings

  1. DCESIIr0: 16, CTGT at 4533, CTGT at 4373, CTGT at 4143, CTGT at 3930, CTGT at 3668, CTGT at 3620, CTGT at 3590, CTGT at 3468, CTGT at 2841, CTGT at 2514, CTGT at 2253, CTGT at 1976, CTGT at 1551, CTGT at 1009, CTGT at 460, CTGT at 344.
  2. DCESIIr1: 8, CTGT at 3618, CTGT at 3520, CTGT at 2753, CTGT at 2389, CTGT at 1802, CTGT at 1215, CTGT at 862, CTGT at 639.
  3. DCESIIr2: 18, CTGT at 4213, CTGT at 4060, CTGT at 3893, CTGT at 3475, CTGT at 2964, CTGT at 2944, CTGT at 2879, CTGT at 2688, CTGT at 1513, CTGT at 1369, CTGT at 1313, CTGT at 1204, CTGT at 1096, CTGT at 1051, CTGT at 725, CTGT at 596, CTGT at 457, CTGT at 342.
  4. DCESIIr3: 13, CTGT at 4335, CTGT at 3609, CTGT at 3545, CTGT at 3499, CTGT at 2668, CTGT at 2445, CTGT at 2397, CTGT at 1744, CTGT at 1214, CTGT at 636, CTGT at 510, CTGT at 350, CTGT at 334.
  5. DCESIIr4: 15, CTGT at 4180, CTGT at 4080, CTGT at 4039, CTGT at 3992, CTGT at 3523, CTGT at 3287, CTGT at 3073, CTGT at 2416, CTGT at 2361, CTGT at 2025, CTGT at 1959, CTGT at 1368, CTGT at 1355, CTGT at 1310, CTGT at 801.
  6. DCESIIr5: 11, CTGT at 4242, CTGT at 3550, CTGT at 2096, CTGT at 1898, CTGT at 1546, CTGT at 828, CTGT at 724, CTGT at 424, CTGT at 169, CTGT at 164, CTGT at 21.
  7. DCESIIr6: 14, CTGT at 4483, CTGT at 4474, CTGT at 4359, CTGT at 3566, CTGT at 3057, CTGT at 2929, CTGT at 2882, CTGT at 2849, CTGT at 1460, CTGT at 1312, CTGT at 997, CTGT at 942, CTGT at 824, CTGT at 262.
  8. DCESIIr7: 12, CTGT at 4507, CTGT at 4272, CTGT at 4129, CTGT at 3124, CTGT at 2818, CTGT at 2196, CTGT at 916, CTGT at 876, CTGT at 714, CTGT at 471, CTGT at 369, CTGT at 21.
  9. DCESIIr8: 12, CTGT at 4233, CTGT at 3449, CTGT at 2815, CTGT at 2146, CTGT at 1886, CTGT at 1712, CTGT at 1283, CTGT at 1114, CTGT at 765, CTGT at 588, CTGT at 450, CTGT at 29.
  10. DCESIIr9: 9, CTGT at 4082, CTGT at 3571, CTGT at 3291, CTGT at 3006, CTGT at 2253, CTGT at 1899, CTGT at 1818, CTGT at 714, CTGT at 551.
  11. DCESIIr0ci: 15, ACAG at 3995, ACAG at 3653, ACAG at 3395, ACAG at 3072, ACAG at 3036, ACAG at 2884, ACAG at 2454, ACAG at 2223, ACAG at 1955, ACAG at 1709, ACAG at 1534, ACAG at 1284, ACAG at 713, ACAG at 577, ACAG at 185.
  12. DCESIIr1ci: 20, ACAG at 4350, ACAG at 4236, ACAG at 4193, ACAG at 4139, ACAG at 3385, ACAG at 3353, ACAG at 3273, ACAG at 3239, ACAG at 3039, ACAG at 2868, ACAG at 2608, ACAG at 2594, ACAG at 2496, ACAG at 2439, ACAG at 1054, ACAG at 743, ACAG at 443, ACAG at 318, ACAG at 74, ACAG at 34.
  13. DCESIIr2ci: 12, ACAG at 4533, ACAG at 4328, ACAG at 3620, ACAG at 1892, ACAG at 1857, ACAG at 1830, ACAG at 1823, ACAG at 1798, ACAG at 1088, ACAG at 1040, ACAG at 948, ACAG at 942.
  14. DCESIIr3ci: 9, ACAG at 4084, ACAG at 3921, ACAG at 2738, ACAG at 2402, ACAG at 1893, ACAG at 1342, ACAG at 456, ACAG at 242, ACAG at 197.
  15. DCESIIr4ci: 7, ACAG at 4358, ACAG at 4199, ACAG at 3951, ACAG at 3832, ACAG at 3477, ACAG at 694, ACAG at 75.
  16. DCESIIr5ci: 13, ACAG at 4073, ACAG at 3433, ACAG at 3390, ACAG at 3297, ACAG at 2613, ACAG at 1830, ACAG at 1518, ACAG at 1283, ACAG at 1197, ACAG at 980, ACAG at 895, ACAG at 694, ACAG at 366.
  17. DCESIIr6ci: 14, ACAG at 4400, ACAG at 4043, ACAG at 3207, ACAG at 2988, ACAG at 2933, ACAG at 2591, ACAG at 2565, ACAG at 2378, ACAG at 2296, ACAG at 2245, ACAG at 1942, ACAG at 1100, ACAG at 647, ACAG at 581.
  18. DCESIIr7ci: 17, ACAG at 4461, ACAG at 3897, ACAG at 3756, ACAG at 3717, ACAG at 3406, ACAG at 2897, ACAG at 2882, ACAG at 2791, ACAG at 2681, ACAG at 2421, ACAG at 2278, ACAG at 1126, ACAG at 1058, ACAG at 1011, ACAG at 909, ACAG at 513, ACAG at 199.
  19. DCESIIr8ci: 7, ACAG at 4260, ACAG at 1754, ACAG at 1289, ACAG at 1180, ACAG at 659, ACAG at 583, ACAG at 67.
  20. DCESIIr9ci: 14, ACAG at 4422, ACAG at 4282, ACAG at 4119, ACAG at 4108, ACAG at 4005, ACAG at 3939, ACAG at 3125, ACAG at 2914, ACAG at 2260, ACAG at 2016, ACAG at 1252, ACAG at 416, ACAG at 73, ACAG at 12.

DCESIIr UTRs

Main article: UTR promoter gene transcriptions
  1. DCESIIr0: CTGT at 4533, CTGT at 4373, CTGT at 4143, CTGT at 3930, CTGT at 3668, CTGT at 3620, CTGT at 3590, CTGT at 3468.
  2. DCESIIr2: CTGT at 4213, CTGT at 4060, CTGT at 3893, CTGT at 3475, CTGT at 2964, CTGT at 2944, CTGT at 2879.
  3. DCESIIr4: CTGT at 4180, CTGT at 4080, CTGT at 4039, CTGT at 3992, CTGT at 3523, CTGT at 3287, CTGT at 3073.
  4. DCESIIr6: CTGT at 4483, CTGT at 4474, CTGT at 4359, CTGT at 3566, CTGT at 3057, CTGT at 2929, CTGT at 2882, CTGT at 2849.
  5. DCESIIr8: CTGT at 4233, CTGT at 3449.
  6. DCESIIr0ci: ACAG at 3995, ACAG at 3653, ACAG at 3395, ACAG at 3072, ACAG at 3036, ACAG at 2884.
  7. DCESIIr2ci: ACAG at 4533, ACAG at 4328, ACAG at 3620.
  8. DCESIIr4ci: ACAG at 4358, ACAG at 4199, ACAG at 3951, ACAG at 3832, ACAG at 3477.
  9. DCESIIr6ci: ACAG at 4400, ACAG at 4043, ACAG at 3207, ACAG at 2988, ACAG at 2933.
  10. DCESIIr8ci: ACAG at 4260.

DCESIIr core promoters

Main article: Core promoter gene transcriptions
  1. DCESIIr0: CTGT at 2841.
  2. DCESIIr8: CTGT at 2815.


  1. DCESIIr3: CTGT at 4335.
  2. DCESIIr7: CTGT at 4507, CTGT at 4272.
  3. DCESIIr1ci: ACAG at 4350.
  4. DCESIIr7ci: ACAG at 4461.
  5. DCESIIr9ci: ACAG at 4422, ACAG at 4282.

DCESIIr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. DCESIIr2: CTGT at 2688.


  1. DCESIIr5: CTGT at 4242.
  2. DCESIIr7: CTGT at 4129.
  3. DCESIIr9: CTGT at 4082.
  4. DCESIIr1ci: ACAG at 4236, ACAG at 4193, ACAG at 4139.
  5. DCESIIr3ci: ACAG at 4084.
  6. DCESIIr5ci: ACAG at 4073.
  7. DCESIIr9ci: ACAG at 4119, ACAG at 4108.

DCESIIr distal promoters

Main article: Distal promoter gene transcriptions
  1. DCESIIr0: CTGT at 2514, CTGT at 2253, CTGT at 1976, CTGT at 1551, CTGT at 1009, CTGT at 460, CTGT at 344.
  2. DCESIIr2: CTGT at 1513, CTGT at 1369, CTGT at 1313, CTGT at 1204, CTGT at 1096, CTGT at 1051, CTGT at 725, CTGT at 596, CTGT at 457, CTGT at 342.
  3. DCESIIr4: CTGT at 2416, CTGT at 2361, CTGT at 2025, CTGT at 1959, CTGT at 1368, CTGT at 1355, CTGT at 1310, CTGT at 801.
  4. DCESIIr6: CTGT at 1460, CTGT at 1312, CTGT at 997, CTGT at 942, CTGT at 824, CTGT at 262.
  5. DCESIIr8: CTGT at 2146, CTGT at 1886, CTGT at 1712, CTGT at 1283, CTGT at 1114, CTGT at 765, CTGT at 588, CTGT at 450, CTGT at 29.
  6. DCESIIr0ci: ACAG at 2454, ACAG at 2223, ACAG at 1955, ACAG at 1709, ACAG at 1534, ACAG at 1284, ACAG at 713, ACAG at 577, ACAG at 185.
  7. DCESIIr2ci: ACAG at 1892, ACAG at 1857, ACAG at 1830, ACAG at 1823, ACAG at 1798, ACAG at 1088, ACAG at 1040, ACAG at 948, ACAG at 942.
  8. DCESIIr4ci: ACAG at 694, ACAG at 75.
  9. DCESIIr6ci: ACAG at 2591, ACAG at 2565, ACAG at 2378, ACAG at 2296, ACAG at 2245, ACAG at 1942, ACAG at 1100, ACAG at 647, ACAG at 581.
  10. DCESIIr8ci: ACAG at 1754, ACAG at 1289, ACAG at 1180, ACAG at 659, ACAG at 583, ACAG at 67.


  1. DCESIIr1: CTGT at 3618, CTGT at 3520, CTGT at 2753, CTGT at 2389, CTGT at 1802, CTGT at 1215, CTGT at 862, CTGT at 639.
  2. DCESIIr3: CTGT at 3609, CTGT at 3545, CTGT at 3499, CTGT at 2668, CTGT at 2445, CTGT at 2397, CTGT at 1744, CTGT at 1214, CTGT at 636, CTGT at 510, CTGT at 350, CTGT at 334.
  3. DCESIIr5: CTGT at 3550, CTGT at 2096, CTGT at 1898, CTGT at 1546, CTGT at 828, CTGT at 724, CTGT at 424, CTGT at 169, CTGT at 164, CTGT at 21.
  4. DCESIIr7: CTGT at 3124, CTGT at 2818, CTGT at 2196, CTGT at 916, CTGT at 876, CTGT at 714, CTGT at 471, CTGT at 369, CTGT at 21.
  5. DCESIIr9: CTGT at 3571, CTGT at 3291, CTGT at 3006, CTGT at 2253, CTGT at 1899, CTGT at 1818, CTGT at 714, CTGT at 551.
  6. DCESIIr1ci: ACAG at 3385, ACAG at 3353, ACAG at 3273, ACAG at 3239, ACAG at 3039, ACAG at 2868, ACAG at 2608, ACAG at 2594, ACAG at 2496, ACAG at 2439, ACAG at 1054, ACAG at 743, ACAG at 443, ACAG at 318, ACAG at 74, ACAG at 34.
  7. DCESIIr3ci: ACAG at 3921, ACAG at 2738, ACAG at 2402, ACAG at 1893, ACAG at 1342, ACAG at 456, ACAG at 242, ACAG at 197.
  8. DCESIIr5ci: ACAG at 3433, ACAG at 3390, ACAG at 3297, ACAG at 2613, ACAG at 1830, ACAG at 1518, ACAG at 1283, ACAG at 1197, ACAG at 980, ACAG at 895, ACAG at 694, ACAG at 366.
  9. DCESIIr7ci: ACAG at 3897, ACAG at 3756, ACAG at 3717, ACAG at 3406, ACAG at 2897, ACAG at 2882, ACAG at 2791, ACAG at 2681, ACAG at 2421, ACAG at 2278, ACAG at 1126, ACAG at 1058, ACAG at 1011, ACAG at 909, ACAG at 513, ACAG at 199.
  10. DCESIIr9ci: ACAG at 4005, ACAG at 3939, ACAG at 3125, ACAG at 2914, ACAG at 2260, ACAG at 2016, ACAG at 1252, ACAG at 416, ACAG at 73, ACAG at 12.

DCE SII analysis and results

Main article: Complex locus A1BG and ZNF497 § DCE SII

The reals have seventeen on the negative strand, in the negative direction in the UTR and twenty-one on the positive strand, in the negative direction, for an average occurrence of 19.0.

The randoms had fifty-two in the UTR for an occurrence of 5.2.

The reals have three in the positive direction only for an average occurrence of 1.5. But, reals could have been present in the negative direction core promoter, so the total average occurrence is 0.75.

The randoms had two in the arbitrary negative direction in the core promoter for an occurrence of 0.2 and seven in the arbitrary positive direction for an average occurrence of 0.7.

For the proximal promoters, the reals have three in the negative direction for an average occurrence of 1.5 and two in the positive direction for an average occurrence of 1.0.

The randoms had one in the arbitrary negative direction for an occurrence of 0.1 and ten in the positive direction for an average occurrence of 1.0, for an average occurrence of 0.55.

For the distal promoters, the reals have fifteen on the negative strand, in the negative direction, and thirty-two on the positive strand, in the negative direction for an average occurrence of 23.5. The randoms have seventy-five in the arbitrary negative direction for an average occurrence of 7.5.

The reals have fifty-two on the negative strand, in the positive direction and twenty-nine on the positive strand, positive direction, for an average occurrence of 40.5. The randoms had one hundred and nine for an average occurrence of 10.9.

Comparatively, the reals in the UTR between ZSCAN22 and A1BG are likely active or activable. For the core promoters, the randoms are close in occurrences but lower than the reals to suggest that the reals are likely active or activable.

For the proximal promoters, again the occurrences for the randoms are at or on average below that of the reals suggesting that the reals are likely active or activable.

The distal promoters in the real promoters have systematically much higher occurrences than the randoms suggesting that the reals are likely active or activable.

Downstream core element SIII samplings

  1. Negative strand, negative direction, looking for DCE SIII: AGC, 11, AGC at 4289, AGC at 3813, AGC at 3595, AGC at 3501, AGC at 2709, AGC at 2453, AGC at 1446, AGC at 1065, AGC at 838, AGC at 720, AGC at 157.
  2. Negative strand, positive direction, looking for DCE SIII: AGC, 109, AGC at 4352, AGC at 4279, AGC at 4052, AGC at 4026, AGC at 4023, AGC at 3997, AGC at 3895, AGC at 3808, AGC at 3775, AGC at 3763, AGC at 3737, AGC at 3723, AGC at 3720, AGC at 3701, AGC at 3691, AGC at 3668, AGC at 3598, AGC at 3518, AGC at 3513, AGC at 3262, AGC at 3239, AGC at 3223, AGC at 3217, AGC at 3211, AGC at 3194, AGC at 3155, AGC at 3144, AGC at 3137, AGC at 3125, AGC at 3100, AGC at 3041, AGC at 2970, AGC at 2896, AGC at 2845, AGC at 2785, AGC at 2749, AGC at 2731, AGC at 2703, AGC at 2557, AGC at 2536, AGC at 2526, AGC at 2402, AGC at 2399, AGC at 2390, AGC at 2352, AGC at 2198, AGC at 2193, AGC at 2102, AGC at 2052, AGC at 2008, AGC at 2005, AGC at 1678, AGC at 1634, AGC at 1625, AGC at 1603, AGC at 1595, AGC at 1540, AGC at 1532, AGC at 1507, AGC at 1463, AGC at 1457, AGC at 1448, AGC at 1441, AGC at 1363, AGC at 1357, AGC at 1348, AGC at 1341, AGC at 1288, AGC at 1271, AGC at 1267, AGC at 1232, AGC at 1205, AGC at 1145, AGC at 1127, AGC at 1121, AGC at 1112, AGC at 1105, AGC at 1064, AGC at 1057, AGC at 1054, AGC at 1037, AGC at 953, AGC at 937, AGC at 931, AGC at 853, AGC at 837, AGC at 831, AGC at 785, AGC at 769, AGC at 728, AGC at 718, AGC at 692, AGC at 644, AGC at 634, AGC at 623, AGC at 617, AGC at 613, AGC at 601, AGC at 560, AGC at 533, AGC at 511, AGC at 473, AGC at 431, AGC at 427, AGC at 383, AGC at 339, AGC at 335, AGC at 329, AGC at 64.
  3. Positive strand, negative direction, looking for DCE DCE SIII: AGC, 91, AGC at 4520, AGC at 4489, AGC at 4480, AGC at 4439, AGC at 4411, AGC at 4345, AGC at 4321, AGC at 4296, AGC at 4261, AGC at 4229, AGC at 4184, AGC at 4130, AGC at 4033, AGC at 4014, AGC at 3912, AGC at 3899, AGC at 3845, AGC at 3838, AGC at 3773, AGC at 3731, AGC at 3726, AGC at 3701, AGC at 3694, AGC at 3682, AGC at 3646, AGC at 3494, AGC at 3370, AGC at 3309, AGC at 3294, AGC at 3269, AGC at 3209, AGC at 3204, AGC at 3177, AGC at 3124, AGC at 3105, AGC at 3070, AGC at 3032, AGC at 2915, AGC at 2780, AGC at 2766, AGC at 2741, AGC at 2681, AGC at 2650, AGC at 2478, AGC at 2472, AGC at 2431, AGC at 2406, AGC at 2346, AGC at 2314, AGC at 2273, AGC at 2264, AGC at 2129, AGC at 2094, AGC at 2019, AGC at 2005, AGC at 1980, AGC at 1969, AGC at 1920, AGC at 1888, AGC at 1785, AGC at 1678, AGC at 1611, AGC at 1497, AGC at 1486, AGC at 1367, AGC at 1327, AGC at 1267, AGC at 1235, AGC at 1194, AGC at 1140, AGC at 1061, AGC at 1036, AGC at 976, AGC at 944, AGC at 909, AGC at 895, AGC at 870, AGC at 810, AGC at 778, AGC at 737, AGC at 728, AGC at 676, AGC at 540, AGC at 504, AGC at 500, AGC at 455, AGC at 403, AGC at 185, AGC at 146, AGC at 137, AGC at 35.
  4. Positive strand, positive direction, looking for DCE SIII: AGC, 27, AGC at 4374, AGC at 3985, AGC at 3509, AGC at 3283, AGC at 3272, AGC at 2091, AGC at 1927, AGC at 1915, AGC at 1750, AGC at 1713, AGC at 1687, AGC at 1528, AGC at 1517, AGC at 1490, AGC at 1406, AGC at 1390, AGC at 1306, AGC at 1181, AGC at 1154, AGC at 1108, AGC at 1013, AGC at 761, AGC at 688, AGC at 593, AGC at 537, AGC at 457, AGC at 77.

Downstream core element SIII Complements

  1. negative strand, negative direction, looking for DCE SIIIc: 3'-TCG-5', 88, 3'-TCG-5' at 35, 3'-TCG-5' at 137, 3'-TCG-5' at 146, 3'-TCG-5' at 185, 3'-TCG-5' at 403, 3'-TCG-5' at 455, 3'-TCG-5' at 500, 3'-TCG-5' at 504, 3'-TCG-5' at 540, 3'-TCG-5' at 676, 3'-TCG-5' at 728, 3'-TCG-5' at 737, 3'-TCG-5' at 778, 3'-TCG-5' at 810, 3'-TCG-5' at 870, 3'-TCG-5' at 895, 3'-TCG-5' at 909, 3'-TCG-5' at 944, 3'-TCG-5' at 976, 3'-TCG-5' at 1036, 3'-TCG-5' at 1061, 3'-TCG-5' at 1140, 3'-TCG-5' at 1194, 3'-TCG-5' at 1235, 3'-TCG-5' at 1267, 3'-TCG-5' at 1327, 3'-TCG-5' at 1367, 3'-TCG-5' at 1486, 3'-TCG-5' at 1497, 3'-TCG-5' at 1611, 3'-TCG-5' at 1678, 3'-TCG-5' at 1785, 3'-TCG-5' at 1888, 3'-TCG-5' at 1920, 3'-TCG-5' at 1969, 3'-TCG-5' at 1980, 3'-TCG-5' at 2005, 3'-TCG-5' at 2019, 3'-TCG-5' at 2094, 3'-TCG-5' at 2129, 3'-TCG-5' at 2264, 3'-TCG-5' at 2273, 3'-TCG-5' at 2314, 3'-TCG-5' at 2346, 3'-TCG-5' at 2406, 3'-TCG-5' at 2431, 3'-TCG-5' at 2472, 3'-TCG-5' at 2478, 3'-TCG-5' at 2650, 3'-TCG-5' at 2681, 3'-TCG-5' at 2741, 3'-TCG-5' at 2766, 3'-TCG-5' at 2780, 3'-TCG-5' at 2915, 3'-TCG-5' at 3032, 3'-TCG-5' at 3070, 3'-TCG-5' at 3105, 3'-TCG-5' at 3124, 3'-TCG-5' at 3177, 3'-TCG-5' at 3204, 3'-TCG-5' at 3209, 3'-TCG-5' at 3269, 3'-TCG-5' at 3294, 3'-TCG-5' at 3309, 3'-TCG-5' at 3370, 3'-TCG-5' at 3494, 3'-TCG-5' at 3646, 3'-TCG-5' at 3682, 3'-TCG-5' at 3694, 3'-TCG-5' at 3701, 3'-TCG-5' at 3726, 3'-TCG-5' at 3731, 3'-TCG-5' at 3773, 3'-TCG-5' at 3838, 3'-TCG-5' at 3845, 3'-TCG-5' at 3899, 3'-TCG-5' at 3912, 3'-TCG-5' at 4014, 3'-TCG-5' at 4033, 3'-TCG-5' at 4130, 3'-TCG-5' at 4184, 3'-TCG-5' at 4229, 3'-TCG-5' at 4261, 3'-TCG-5' at 4296, 3'-TCG-5' at 4321, 3'-TCG-5' at 4345, 3'-TCG-5' at 4411, 3'-TCG-5' at 4439.
  2. negative strand, positive direction, looking for DCE SIIIc: 3'-TCG-5', 26, 3'-TCG-5' at 77, 3'-TCG-5' at 457, 3'-TCG-5' at 537, 3'-TCG-5' at 593, 3'-TCG-5' at 688, 3'-TCG-5' at 761, 3'-TCG-5' at 1013, 3'-TCG-5' at 1108, 3'-TCG-5' at 1154, 3'-TCG-5' at 1181, 3'-TCG-5' at 1306, 3'-TCG-5' at 1390, 3'-TCG-5' at 1406, 3'-TCG-5' at 1490, 3'-TCG-5' at 1517, 3'-TCG-5' at 1528, 3'-TCG-5' at 1687, 3'-TCG-5' at 1713, 3'-TCG-5' at 1750, 3'-TCG-5' at 1915, 3'-TCG-5' at 1927, 3'-TCG-5' at 2091, 3'-TCG-5' at 3272, 3'-TCG-5' at 3283, 3'-TCG-5' at 3509, 3'-TCG-5' at 3985.
  3. positive strand, negative direction, looking for DCE SIIIc: 3'-TCG-5', 11, 3'-TCG-5' at 157, 3'-TCG-5' at 720, 3'-TCG-5' at 838, 3'-TCG-5' at 1065, 3'-TCG-5' at 1446, 3'-TCG-5' at 2453, 3'-TCG-5' at 2709, 3'-TCG-5' at 3501, 3'-TCG-5' at 3595, 3'-TCG-5' at 3813, 3'-TCG-5' at 4289.
  4. positive strand, positive direction, looking for DCE SIIIc: 3'-TCG-5', 109, 3'-TCG-5' at 64, 3'-TCG-5' at 329, 3'-TCG-5' at 335, 3'-TCG-5' at 339, 3'-TCG-5' at 383, 3'-TCG-5' at 427, 3'-TCG-5' at 431, 3'-TCG-5' at 473, 3'-TCG-5' at 511, 3'-TCG-5' at 533, 3'-TCG-5' at 560, 3'-TCG-5' at 601, 3'-TCG-5' at 613, 3'-TCG-5' at 617, 3'-TCG-5' at 623, 3'-TCG-5' at 634, 3'-TCG-5' at 644, 3'-TCG-5' at 692, 3'-TCG-5' at 718, 3'-TCG-5' at 728, 3'-TCG-5' at 769, 3'-TCG-5' at 785, 3'-TCG-5' at 831, 3'-TCG-5' at 837, 3'-TCG-5' at 853, 3'-TCG-5' at 931, 3'-TCG-5' at 937, 3'-TCG-5' at 953, 3'-TCG-5' at 1037, 3'-TCG-5' at 1054, 3'-TCG-5' at 1057, 3'-TCG-5' at 1064, 3'-TCG-5' at 1105, 3'-TCG-5' at 1112, 3'-TCG-5' at 1121, 3'-TCG-5' at 1127, 3'-TCG-5' at 1145, 3'-TCG-5' at 1205, 3'-TCG-5' at 1232, 3'-TCG-5' at 1267, 3'-TCG-5' at 1271, 3'-TCG-5' at 1288, 3'-TCG-5' at 1341, 3'-TCG-5' at 1348, 3'-TCG-5' at 1357, 3'-TCG-5' at 1363, 3'-TCG-5' at 1441, 3'-TCG-5' at 1448, 3'-TCG-5' at 1457, 3'-TCG-5' at 1463, 3'-TCG-5' at 1507, 3'-TCG-5' at 1532, 3'-TCG-5' at 1540, 3'-TCG-5' at 1595, 3'-TCG-5' at 1603, 3'-TCG-5' at 1625, 3'-TCG-5' at 1634, 3'-TCG-5' at 1678, 3'-TCG-5' at 2005, 3'-TCG-5' at 2008, 3'-TCG-5' at 2052, 3'-TCG-5' at 2102, 3'-TCG-5' at 2193, 3'-TCG-5' at 2198, 3'-TCG-5' at 2352, 3'-TCG-5' at 2390, 3'-TCG-5' at 2399, 3'-TCG-5' at 2402, 3'-TCG-5' at 2526, 3'-TCG-5' at 2536, 3'-TCG-5' at 2557, 3'-TCG-5' at 2703, 3'-TCG-5' at 2731, 3'-TCG-5' at 2749, 3'-TCG-5' at 2785, 3'-TCG-5' at 2845, 3'-TCG-5' at 2896, 3'-TCG-5' at 2970, 3'-TCG-5' at 3041, 3'-TCG-5' at 3100, 3'-TCG-5' at 3125, 3'-TCG-5' at 3137, 3'-TCG-5' at 3144, 3'-TCG-5' at 3155, 3'-TCG-5' at 3194, 3'-TCG-5' at 3211, 3'-TCG-5' at 3217, 3'-TCG-5' at 3223, 3'-TCG-5' at 3239, 3'-TCG-5' at 3262, 3'-TCG-5' at 3513, 3'-TCG-5' at 3518, 3'-TCG-5' at 3598, 3'-TCG-5' at 3668, 3'-TCG-5' at 3691, 3'-TCG-5' at 3701, 3'-TCG-5' at 3720, 3'-TCG-5' at 3723, 3'-TCG-5' at 3737, 3'-TCG-5' at 3763, 3'-TCG-5' at 3775, 3'-TCG-5' at 3808, 3'-TCG-5' at 3895, 3'-TCG-5' at 3997, 3'-TCG-5' at 4023, 3'-TCG-5' at 4026, 3'-TCG-5' at 4052, 3'-TCG-5' at 4279.

Downstream core element SIII Inverse complements

  1. Negative strand, negative direction, looking for DCE SIIIci: GCT, 24, GCT at 4471, GCT at 4241, GCT at 3875, GCT at 3814, GCT at 3231, GCT at 2409, GCT at 2155, GCT at 2013, GCT at 1983, GCT at 1553, GCT at 1330, GCT at 1189, GCT at 1181, GCT at 1155, GCT at 1066, GCT at 1039, GCT at 911, GCT at 721, GCT at 707, GCT at 571, GCT at 492, GCT at 448, GCT at 434, GCT at 310.
  2. Negative strand, positive direction, looking for DCE SIIIci: GCT, 91, GCT at 4390, GCT at 4372, GCT at 4321, GCT at 4312, GCT at 4175, GCT at 4027, GCT at 3992, GCT at 3987, GCT at 3983, GCT at 3776, GCT at 3724, GCT at 3696, GCT at 3638, GCT at 3586, GCT at 3524, GCT at 3519, GCT at 3481, GCT at 3420, GCT at 3368, GCT at 3347, GCT at 3307, GCT at 3274, GCT at 3263, GCT at 3240, GCT at 3227, GCT at 3195, GCT at 3151, GCT at 3119, GCT at 2976, GCT at 2971, GCT at 2913, GCT at 2885, GCT at 2846, GCT at 2808, GCT at 2786, GCT at 2768, GCT at 2753, GCT at 2750, GCT at 2732, GCT at 2695, GCT at 2504, GCT at 2435, GCT at 2403, GCT at 2368, GCT at 2318, GCT at 2194, GCT at 2161, GCT at 2155, GCT at 2093, GCT at 2089, GCT at 2056, GCT at 2053, GCT at 2046, GCT at 2043, GCT at 1973, GCT at 1907, GCT at 1882, GCT at 1817, GCT at 1777, GCT at 1734, GCT at 1727, GCT at 1651, GCT at 1576, GCT at 1533, GCT at 1449, GCT at 1442, GCT at 1349, GCT at 1342, GCT at 1274, GCT at 1190, GCT at 1177, GCT at 1113, GCT at 1106, GCT at 1093, GCT at 1029, GCT at 938, GCT at 838, GCT at 777, GCT at 737, GCT at 693, GCT at 652, GCT at 602, GCT at 528, GCT at 518, GCT at 479, GCT at 415, GCT at 384, GCT at 275, GCT at 262, GCT at 10, GCT at 3.
  3. Positive strand, negative direction, looking for DCE SIIIci: GCT, 78, GCT at 4402, GCT at 4291, GCT at 4274, GCT at 4262, GCT at 4255, GCT at 4185, GCT at 4143, GCT at 4131, GCT at 4112, GCT at 3992, GCT at 3961, GCT at 3955, GCT at 3862, GCT at 3774, GCT at 3717, GCT at 3707, GCT at 3702, GCT at 3647, GCT at 3580, GCT at 3398, GCT at 3263, GCT at 3222, GCT at 3210, GCT at 3178, GCT at 3106, GCT at 3083, GCT at 3052, GCT at 3039, GCT at 3033, GCT at 3006, GCT at 2933, GCT at 2896, GCT at 2742, GCT at 2711, GCT at 2694, GCT at 2682, GCT at 2560, GCT at 2529, GCT at 2376, GCT at 2359, GCT at 2347, GCT at 2324, GCT at 2224, GCT at 2202, GCT at 2130, GCT at 2107, GCT at 2067, GCT at 1970, GCT at 1921, GCT at 1906, GCT at 1889, GCT at 1843, GCT at 1798, GCT at 1767, GCT at 1754, GCT at 1744, GCT at 1498, GCT at 1487, GCT at 1462, GCT at 1448, GCT at 1280, GCT at 1268, GCT at 1122, GCT at 1109, GCT at 1006, GCT at 989, GCT at 977, GCT at 890, GCT at 840, GCT at 823, GCT at 811, GCT at 779, GCT at 658, GCT at 598, GCT at 385, GCT at 335, GCT at 147, GCT at 138.
  4. Positive strand, positive direction, looking for DCE SIIIci: GCT, 37, GCT at 4356, GCT at 4277, GCT at 3799, GCT at 2804, GCT at 2357, GCT at 2215, GCT at 1962, GCT at 1919, GCT at 1835, GCT at 1665, GCT at 1623, GCT at 1584, GCT at 1563, GCT at 1479, GCT at 1446, GCT at 1379, GCT at 1346, GCT at 1227, GCT at 1164, GCT at 1155, GCT at 1101, GCT at 1080, GCT at 1059, GCT at 996, GCT at 951, GCT at 896, GCT at 851, GCT at 790, GCT at 766, GCT at 639, GCT at 576, GCT at 555, GCT at 429, GCT at 360, GCT at 308, GCT at 242, GCT at 162.

Downstream core element SIII Inverses

  1. negative strand, negative direction, looking for DCE SIIIi: 3'-CGA-5', 78, 3'-CGA-5' at 138, 3'-CGA-5' at 147, 3'-CGA-5' at 335, 3'-CGA-5' at 385, 3'-CGA-5' at 598, 3'-CGA-5' at 658, 3'-CGA-5' at 779, 3'-CGA-5' at 811, 3'-CGA-5' at 823, 3'-CGA-5' at 840, 3'-CGA-5' at 890, 3'-CGA-5' at 977, 3'-CGA-5' at 989, 3'-CGA-5' at 1006, 3'-CGA-5' at 1109, 3'-CGA-5' at 1122, 3'-CGA-5' at 1268, 3'-CGA-5' at 1280, 3'-CGA-5' at 1448, 3'-CGA-5' at 1462, 3'-CGA-5' at 1487, 3'-CGA-5' at 1498, 3'-CGA-5' at 1744, 3'-CGA-5' at 1754, 3'-CGA-5' at 1767, 3'-CGA-5' at 1798, 3'-CGA-5' at 1843, 3'-CGA-5' at 1889, 3'-CGA-5' at 1906, 3'-CGA-5' at 1921, 3'-CGA-5' at 1970, 3'-CGA-5' at 2067, 3'-CGA-5' at 2107, 3'-CGA-5' at 2130, 3'-CGA-5' at 2202, 3'-CGA-5' at 2224, 3'-CGA-5' at 2324, 3'-CGA-5' at 2347, 3'-CGA-5' at 2359, 3'-CGA-5' at 2376, 3'-CGA-5' at 2529, 3'-CGA-5' at 2560, 3'-CGA-5' at 2682, 3'-CGA-5' at 2694, 3'-CGA-5' at 2711, 3'-CGA-5' at 2742, 3'-CGA-5' at 2896, 3'-CGA-5' at 2933, 3'-CGA-5' at 3006, 3'-CGA-5' at 3033, 3'-CGA-5' at 3039, 3'-CGA-5' at 3052, 3'-CGA-5' at 3083, 3'-CGA-5' at 3106, 3'-CGA-5' at 3178, 3'-CGA-5' at 3210, 3'-CGA-5' at 3222, 3'-CGA-5' at 3263, 3'-CGA-5' at 3398, 3'-CGA-5' at 3580, 3'-CGA-5' at 3647, 3'-CGA-5' at 3702, 3'-CGA-5' at 3707, 3'-CGA-5' at 3717, 3'-CGA-5' at 3774, 3'-CGA-5' at 3862, 3'-CGA-5' at 3955, 3'-CGA-5' at 3961, 3'-CGA-5' at 3992, 3'-CGA-5' at 4112, 3'-CGA-5' at 4131, 3'-CGA-5' at 4143, 3'-CGA-5' at 4185, 3'-CGA-5' at 4255, 3'-CGA-5' at 4262, 3'-CGA-5' at 4274, 3'-CGA-5' at 4291, 3'-CGA-5' at 4402.
  2. negative strand, positive direction, looking for DCE SIIIi: 3'-CGA-5', 36, 3'-CGA-5' at 162, 3'-CGA-5' at 242, 3'-CGA-5' at 308, 3'-CGA-5' at 360, 3'-CGA-5' at 429, 3'-CGA-5' at 555, 3'-CGA-5' at 576, 3'-CGA-5' at 639, 3'-CGA-5' at 766, 3'-CGA-5' at 790, 3'-CGA-5' at 851, 3'-CGA-5' at 896, 3'-CGA-5' at 951, 3'-CGA-5' at 996, 3'-CGA-5' at 1059, 3'-CGA-5' at 1080, 3'-CGA-5' at 1101, 3'-CGA-5' at 1155, 3'-CGA-5' at 1164, 3'-CGA-5' at 1227, 3'-CGA-5' at 1346, 3'-CGA-5' at 1379, 3'-CGA-5' at 1446, 3'-CGA-5' at 1479, 3'-CGA-5' at 1563, 3'-CGA-5' at 1584, 3'-CGA-5' at 1623, 3'-CGA-5' at 1665, 3'-CGA-5' at 1835, 3'-CGA-5' at 1919, 3'-CGA-5' at 1962, 3'-CGA-5' at 2215, 3'-CGA-5' at 2357, 3'-CGA-5' at 2804, 3'-CGA-5' at 3799, 3'-CGA-5' at 4277.
  3. positive strand, negative direction, looking for DCE SIIIi: 3'-CGA-5', 24, 3'-CGA-5' at 310, 3'-CGA-5' at 434, 3'-CGA-5' at 448, 3'-CGA-5' at 492, 3'-CGA-5' at 571, 3'-CGA-5' at 707, 3'-CGA-5' at 721, 3'-CGA-5' at 911, 3'-CGA-5' at 1039, 3'-CGA-5' at 1066, 3'-CGA-5' at 1155, 3'-CGA-5' at 1181, 3'-CGA-5' at 1189, 3'-CGA-5' at 1330, 3'-CGA-5' at 1553, 3'-CGA-5' at 1983, 3'-CGA-5' at 2013, 3'-CGA-5' at 2155, 3'-CGA-5' at 2409, 3'-CGA-5' at 3231, 3'-CGA-5' at 3814, 3'-CGA-5' at 3875, 3'-CGA-5' at 4241.
  4. positive strand, positive direction, looking for DCE SIIIi: 3'-CGA-5', 87, 3'-CGA-5' at 3, 3'-CGA-5' at 10, 3'-CGA-5' at 262, 3'-CGA-5' at 275, 3'-CGA-5' at 384, 3'-CGA-5' at 415, 3'-CGA-5' at 479, 3'-CGA-5' at 518, 3'-CGA-5' at 528, 3'-CGA-5' at 602, 3'-CGA-5' at 652, 3'-CGA-5' at 693, 3'-CGA-5' at 737, 3'-CGA-5' at 777, 3'-CGA-5' at 838, 3'-CGA-5' at 938, 3'-CGA-5' at 1029, 3'-CGA-5' at 1093, 3'-CGA-5' at 1106, 3'-CGA-5' at 1113, 3'-CGA-5' at 1177, 3'-CGA-5' at 1190, 3'-CGA-5' at 1274, 3'-CGA-5' at 1342, 3'-CGA-5' at 1349, 3'-CGA-5' at 1442, 3'-CGA-5' at 1449, 3'-CGA-5' at 1533, 3'-CGA-5' at 1576, 3'-CGA-5' at 1651, 3'-CGA-5' at 1727, 3'-CGA-5' at 1734, 3'-CGA-5' at 1777, 3'-CGA-5' at 1817, 3'-CGA-5' at 1882, 3'-CGA-5' at 1907, 3'-CGA-5' at 1973, 3'-CGA-5' at 2043, 3'-CGA-5' at 2046, 3'-CGA-5' at 2053, 3'-CGA-5' at 2056, 3'-CGA-5' at 2089, 3'-CGA-5' at 2093, 3'-CGA-5' at 2155, 3'-CGA-5' at 2161, 3'-CGA-5' at 2194, 3'-CGA-5' at 2318, 3'-CGA-5' at 2368, 3'-CGA-5' at 2403, 3'-CGA-5' at 2435, 3'-CGA-5' at 2504, 3'-CGA-5' at 2695, 3'-CGA-5' at 2732, 3'-CGA-5' at 2750, 3'-CGA-5' at 2753, 3'-CGA-5' at 2768, 3'-CGA-5' at 2786, 3'-CGA-5' at 2808, 3'-CGA-5' at 2846, 3'-CGA-5' at 2885, 3'-CGA-5' at 2913, 3'-CGA-5' at 2971, 3'-CGA-5' at 2976, 3'-CGA-5' at 3119, 3'-CGA-5' at 3151, 3'-CGA-5' at 3195, 3'-CGA-5' at 3227, 3'-CGA-5' at 3240, 3'-CGA-5' at 3263, 3'-CGA-5' at 3274, 3'-CGA-5' at 3307, 3'-CGA-5' at 3347, 3'-CGA-5' at 3368, 3'-CGA-5' at 3420, 3'-CGA-5' at 3481, 3'-CGA-5' at 3519, 3'-CGA-5' at 3524, 3'-CGA-5' at 3586, 3'-CGA-5' at 3638, 3'-CGA-5' at 3696, 3'-CGA-5' at 3724, 3'-CGA-5' at 3776, 3'-CGA-5' at 3983, 3'-CGA-5' at 3987, 3'-CGA-5' at 3992, 3'-CGA-5' at 4027, 3'-CGA-5' at 4175.

DCE SIII UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GCT at 4471, AGC at 4289, GCT at 4241, GCT at 3875, GCT at 3814, AGC at 3813, AGC at 3595, AGC at 3501, GCT at 3231.

Positive strand, negative direction: AGC at 4520, AGC at 4489, AGC at 4480, AGC at 4439, AGC at 4411, GCT at 4402, AGC at 4345, AGC at 4321, AGC at 4296, GCT at 4291, GCT at 4274, GCT at 4262, AGC at 4261, GCT at 4255, AGC at 4229, GCT at 4185, AGC at 4184, GCT at 4143, GCT at 4131, AGC at 4130, GCT at 4112, AGC at 4033, AGC at 4014, GCT at 3992, GCT at 3961, GCT at 3955, AGC at 3912, AGC at 3899, GCT at 3862, AGC at 3845, AGC at 3838, GCT at 3774, AGC at 3773, AGC at 3731, AGC at 3726, GCT at 3717, GCT at 3707, GCT at 3702, AGC at 3701, AGC at 3694, AGC at 3682, GCT at 3647, AGC at 3646, GCT at 3580, AGC at 3494, GCT at 3398, AGC at 3370, AGC at 3309, AGC at 3294, AGC at 3269, GCT at 3263, GCT at 3222, GCT at 3210, AGC at 3209, AGC at 3204, GCT at 3178, AGC at 3177, AGC at 3124, GCT at 3106, AGC at 3105, GCT at 3083, AGC at 3070, GCT at 3052, GCT at 3039, GCT at 3033, AGC at 3032, GCT at 3006, GCT at 2933, AGC at 2915, GCT at 2896.

DCE SIII core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: GCT at 4390, GCT at 4372, AGC at 4352, GCT at 4321, GCT at 4312, AGC at 4279.

Positive strand, positive direction: AGC at 4374, GCT at 4356, GCT at 4277.

DCE SIII proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: AGC at 2709.

Positive strand, negative direction: AGC at 2780, AGC at 2766, GCT at 2742, AGC at 2741, GCT at 2711, GCT at 2694, GCT at 2682, AGC at 2681, AGC at 2650.

Negative strand, positive direction: AGC at 4052.

DCE SIII distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: AGC at 2453, GCT at 2409, GCT at 2155, GCT at 2013, GCT at 1983, GCT at 1553, AGC at 1446, GCT at 1330, GCT at 1189, GCT at 1181, GCT at 1155, GCT at 1066, AGC at 1065, GCT at 1039, GCT at 911, AGC at 838, GCT at 721, AGC at 720, GCT at 707, GCT at 571, GCT at 492, GCT at 448, GCT at 434, GCT at 310, AGC at 157.

Positive strand, negative direction: GCT at 2560, GCT at 2529, AGC at 2478, AGC at 2472, AGC at 2431, AGC at 2406, GCT at 2376, GCT at 2359, GCT at 2347, AGC at 2346, GCT at 2324, AGC at 2314, AGC at 2273, AGC at 2264, GCT at 2224, GCT at 2202, GCT at 2130, AGC at 2129, GCT at 2107, AGC at 2094, GCT at 2067, AGC at 2019, AGC at 2005, AGC at 1980, GCT at 1970, AGC at 1969, GCT at 1921, AGC at 1920, GCT at 1906, GCT at 1889, AGC at 1888, GCT at 1843, GCT at 1798, AGC at 1785, GCT at 1767, GCT at 1754, GCT at 1744, AGC at 1678, AGC at 1611, GCT at 1498, AGC at 1497, GCT at 1487, AGC at 1486, GCT at 1462, GCT at 1448, AGC at 1367, AGC at 1327, GCT at 1280, GCT at 1268, AGC at 1267, AGC at 1235, AGC at 1194, AGC at 1140, GCT at 1122, GCT at 1109, AGC at 1061, AGC at 1036, GCT at 1006, GCT at 989, GCT at 977, AGC at 976, AGC at 944, AGC at 909, AGC at 895, GCT at 890, AGC at 870, GCT at 840, GCT at 823, GCT at 811, AGC at 810, GCT at 779, AGC at 778, AGC at 737, AGC at 728, AGC at 676, GCT at 658, GCT at 598, AGC at 540, AGC at 504, AGC at 500, AGC at 455, AGC at 403, GCT at 385, GCT at 335, AGC at 185, GCT at 147, AGC at 146, GCT at 138, AGC at 137, AGC at 35.

Negative strand, positive direction: GCT at 4027, AGC at 4026, AGC at 4023, AGC at 3997, GCT at 3992, GCT at 3987, GCT at 3983, AGC at 3895, AGC at 3808, GCT at 3776, AGC at 3775, AGC at 3763, AGC at 3737, GCT at 3724, AGC at 3723, AGC at 3720, AGC at 3701, GCT at 3696, AGC at 3691, AGC at 3668, GCT at 3638, AGC at 3598, GCT at 3586, GCT at 3524, GCT at 3519, AGC at 3518, AGC at 3513, GCT at 3481, GCT at 3420, GCT at 3368, GCT at 3347, GCT at 3307, GCT at 3274, GCT at 3263, AGC at 3262, GCT at 3240, AGC at 3239, GCT at 3227, AGC at 3223, AGC at 3217, AGC at 3211, GCT at 3195, AGC at 3194, AGC at 3155, GCT at 3151, AGC at 3144, AGC at 3137, AGC at 3125, GCT at 3119, AGC at 3100, AGC at 3041, GCT at 2976, GCT at 2971, AGC at 2970, GCT at 2913, AGC at 2896, GCT at 2885, GCT at 2846, AGC at 2845, GCT at 2808, GCT at 2786, AGC at 2785, GCT at 2768, GCT at 2753, GCT at 2750, AGC at 2749, GCT at 2732, AGC at 2731, AGC at 2703, GCT at 2695, AGC at 2557, AGC at 2536, AGC at 2526, GCT at 2504, GCT at 2435, GCT at 2403, AGC at 2402, AGC at 2399, AGC at 2390, GCT at 2368, AGC at 2352, GCT at 2318, AGC at 2198, GCT at 2194, AGC at 2193, GCT at 2161, GCT at 2155, AGC at 2102, GCT at 2093, GCT at 2089, GCT at 2056, GCT at 2053, AGC at 2052, GCT at 2046, GCT at 2043, AGC at 2008, AGC at 2005, GCT at 1973, GCT at 1907, GCT at 1882, GCT at 1817, GCT at 1777, GCT at 1734, GCT at 1727, AGC at 1678, GCT at 1651, AGC at 1634, AGC at 1625, AGC at 1603, AGC at 1595, GCT at 1576, AGC at 1540, GCT at 1533, AGC at 1532, AGC at 1507, AGC at 1463, AGC at 1457, GCT at 1449, AGC at 1448, GCT at 1442, AGC at 1441, AGC at 1363, AGC at 1357, GCT at 1349, AGC at 1348, GCT at 1342, AGC at 1341, AGC at 1288, GCT at 1274, AGC at 1271, AGC at 1267, AGC at 1232, AGC at 1205, GCT at 1190, GCT at 1177, AGC at 1145, AGC at 1127, AGC at 1121, GCT at 1113, AGC at 1112, GCT at 1106, AGC at 1105, GCT at 1093, AGC at 1064, AGC at 1057, AGC at 1054, AGC at 1037, GCT at 1029, AGC at 953, GCT at 938, AGC at 937, AGC at 931, AGC at 853, GCT at 838, AGC at 837, AGC at 831, AGC at 785, GCT at 777, AGC at 769, GCT at 737, AGC at 728, AGC at 718, GCT at 693, AGC at 692, GCT at 652, AGC at 644, AGC at 634, AGC at 623, AGC at 617, AGC at 613, GCT at 602, AGC at 601, AGC at 560, AGC at 533, GCT at 528, GCT at 518, AGC at 511, GCT at 479, AGC at 473, AGC at 431, AGC at 427, GCT at 415, GCT at 384, AGC at 383, AGC at 339, AGC at 335, AGC at 329, GCT at 275, GCT at 262, AGC at 64, GCT at 10, GCT at 3.

Positive strand, positive direction: AGC at 3985, GCT at 3799, AGC at 3509, AGC at 3283, AGC at 3272, GCT at 2804, GCT at 2357, GCT at 2215, AGC at 2091, GCT at 1962, AGC at 1927, GCT at 1919, AGC at 1915, GCT at 1835, AGC at 1750, AGC at 1713, AGC at 1687, GCT at 1665, GCT at 1623, GCT at 1584, GCT at 1563, AGC at 1528, AGC at 1517, AGC at 1490, GCT at 1479, GCT at 1446, AGC at 1406, AGC at 1390, GCT at 1379, GCT at 1346, AGC at 1306, GCT at 1227, AGC at 1181, GCT at 1164, GCT at 1155, AGC at 1154, AGC at 1108, GCT at 1101, GCT at 1080, GCT at 1059, AGC at 1013, GCT at 996, GCT at 951, GCT at 896, GCT at 851, GCT at 790, GCT at 766, AGC at 761, AGC at 688, GCT at 639, AGC at 593, GCT at 576, GCT at 555, AGC at 537, AGC at 457, GCT at 429, GCT at 360, GCT at 308, GCT at 242, GCT at 162, AGC at 77.

DCE SIII random dataset samplings

  1. DCESIIIr0: 54, AGC at 4527, AGC at 4511, AGC at 4487, AGC at 4275, AGC at 4245, AGC at 4140, AGC at 3792, AGC at 3785, AGC at 3596, AGC at 3435, AGC at 3382, AGC at 3358, AGC at 3327, AGC at 3299, AGC at 3277, AGC at 3073, AGC at 2927, AGC at 2876, AGC at 2868, AGC at 2781, AGC at 2756, AGC at 2531, AGC at 2376, AGC at 2288, AGC at 2265, AGC at 2215, AGC at 2211, AGC at 2191, AGC at 1887, AGC at 1874, AGC at 1799, AGC at 1796, AGC at 1729, AGC at 1710, AGC at 1479, AGC at 1295, AGC at 1222, AGC at 1208, AGC at 1180, AGC at 1113, AGC at 958, AGC at 714, AGC at 578, AGC at 519, AGC at 516, AGC at 507, AGC at 457, AGC at 444, AGC at 324, AGC at 292, AGC at 271, AGC at 258, AGC at 163, AGC at 32.
  2. DCESIIIr1: 74, AGC at 4556, AGC at 4526, AGC at 4503, AGC at 4458, AGC at 4444, AGC at 4422, AGC at 4364, AGC at 4311, AGC at 4286, AGC at 4257, AGC at 4180, AGC at 4130, AGC at 3997, AGC at 3928, AGC at 3886, AGC at 3848, AGC at 3745, AGC at 3684, AGC at 3563, AGC at 3548, AGC at 3517, AGC at 3496, AGC at 3420, AGC at 3394, AGC at 3293, AGC at 3240, AGC at 3218, AGC at 3196, AGC at 3127, AGC at 3040, AGC at 2925, AGC at 2889, AGC at 2877, AGC at 2838, AGC at 2805, AGC at 2800, AGC at 2787, AGC at 2731, AGC at 2595, AGC at 2440, AGC at 2256, AGC at 2222, AGC at 2219, AGC at 2215, AGC at 2183, AGC at 2044, AGC at 1960, AGC at 1925, AGC at 1904, AGC at 1874, AGC at 1809, AGC at 1782, AGC at 1611, AGC at 1554, AGC at 1522, AGC at 1518, AGC at 1432, AGC at 1287, AGC at 1236, AGC at 1195, AGC at 1155, AGC at 1086, AGC at 1055, AGC at 1040, AGC at 929, AGC at 883, AGC at 795, AGC at 777, AGC at 744, AGC at 544, AGC at 254, AGC at 227, AGC at 186, AGC at 35.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  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
  1. DCESIIIr0: AGC at 4527, AGC at 4511, AGC at 4487, AGC at 4275, AGC at 4245, AGC at 4140, AGC at 3792, AGC at 3785, AGC at 3596, AGC at 3435, AGC at 3382, AGC at 3358, AGC at 3327, AGC at 3299, AGC at 3277, AGC at 3073, AGC at 2927, AGC at 2876, AGC at 2868.

RDr core promoters

Main article: Core promoter gene transcriptions

DCESIIIr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. DCESIIIr0: AGC at 2781, AGC at 2756.

DCESIIIr distal promoters

Main article: Distal promoter gene transcriptions
  1. DCESIIIr0: AGC at 2531, AGC at 2376, AGC at 2288, AGC at 2265, AGC at 2215, AGC at 2211, AGC at 2191, AGC at 1887, AGC at 1874, AGC at 1799, AGC at 1796, AGC at 1729, AGC at 1710, AGC at 1479, AGC at 1295, AGC at 1222, AGC at 1208, AGC at 1180, AGC at 1113, AGC at 958, AGC at 714, AGC at 578, AGC at 519, AGC at 516, AGC at 507, AGC at 457, AGC at 444, AGC at 324, AGC at 292, AGC at 271, AGC at 258, AGC at 163, AGC at 32.

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § DCE SIII

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. ↑ Wonderfool (25 March 2006). "downstream". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  2. ↑ Poccil (20 October 2004). "core". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  3. ↑ SemperBlotto (5 August 2012). "core". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 Dong-Hoon Lee, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg and Brian A. Lewis (November 2005). "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1". Molecular and Cellular Biology. 25 (21): 9674–86. doi:10.1128/MCB.25.21.9674-9686.2005. PMID 16227614. Retrieved 2010-10-23.
  5. ↑ 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. ↑ 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.
  7. ↑ Gillian E. Chalkley and C. Peter Verrijzer (September 1, 1999). "DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator" (PDF). The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26.
  8. ↑ S. T. Smale (1997). "Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes". Biochim. Biophys. Acta. 1351: 73–88. |access-date= requires |url= (help)
  9. ↑ 9.0 9.1 Marketa J. Zvelebil, Jeremy O. Baum (2008). Dom Holdsworth, ed. Understanding bioinformatics. New York: Garland Science. p. 772. ISBN 978-0815340249.

Further reading

External links

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