Downstream core element gene transcriptions

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Editor-In-Chief: Henry A. Hoff

Template:TOCright 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.

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.

Downstream core element SIII samplings

  1. negative strand, negative direction, looking for DCE SIII: 3'-AGC-5', 11, 3'-AGC-5' at 157, 3'-AGC-5' at 720, 3'-AGC-5' at 838, 3'-AGC-5' at 1065, 3'-AGC-5' at 1446, 3'-AGC-5' at 2453, 3'-AGC-5' at 2709, 3'-AGC-5' at 3501, 3'-AGC-5' at 3595, 3'-AGC-5' at 3813, 3'-AGC-5' at 4289.
  2. negative strand, positive direction, looking for DCE SIII: 3'-AGC-5', 109, 3'-AGC-5' at 64, 3'-AGC-5' at 329, 3'-AGC-5' at 335, 3'-AGC-5' at 339, 3'-AGC-5' at 383, 3'-AGC-5' at 427, 3'-AGC-5' at 431, 3'-AGC-5' at 473, 3'-AGC-5' at 511, 3'-AGC-5' at 533, 3'-AGC-5' at 560, 3'-AGC-5' at 601, 3'-AGC-5' at 613, 3'-AGC-5' at 617, 3'-AGC-5' at 623, 3'-AGC-5' at 634, 3'-AGC-5' at 644, 3'-AGC-5' at 692, 3'-AGC-5' at 718, 3'-AGC-5' at 728, 3'-AGC-5' at 769, 3'-AGC-5' at 785, 3'-AGC-5' at 831, 3'-AGC-5' at 837, 3'-AGC-5' at 853, 3'-AGC-5' at 931, 3'-AGC-5' at 937, 3'-AGC-5' at 953, 3'-AGC-5' at 1037, 3'-AGC-5' at 1054, 3'-AGC-5' at 1057, 3'-AGC-5' at 1064, 3'-AGC-5' at 1105, 3'-AGC-5' at 1112, 3'-AGC-5' at 1121, 3'-AGC-5' at 1127, 3'-AGC-5' at 1145, 3'-AGC-5' at 1205, 3'-AGC-5' at 1232, 3'-AGC-5' at 1267, 3'-AGC-5' at 1271, 3'-AGC-5' at 1288, 3'-AGC-5' at 1341, 3'-AGC-5' at 1348, 3'-AGC-5' at 1357, 3'-AGC-5' at 1363, 3'-AGC-5' at 1441, 3'-AGC-5' at 1448, 3'-AGC-5' at 1457, 3'-AGC-5' at 1463, 3'-AGC-5' at 1507, 3'-AGC-5' at 1532, 3'-AGC-5' at 1540, 3'-AGC-5' at 1595, 3'-AGC-5' at 1603, 3'-AGC-5' at 1625, 3'-AGC-5' at 1634, 3'-AGC-5' at 1678, 3'-AGC-5' at 2005, 3'-AGC-5' at 2008, 3'-AGC-5' at 2052, 3'-AGC-5' at 2102, 3'-AGC-5' at 2193, 3'-AGC-5' at 2198, 3'-AGC-5' at 2352, 3'-AGC-5' at 2390, 3'-AGC-5' at 2399, 3'-AGC-5' at 2402, 3'-AGC-5' at 2526, 3'-AGC-5' at 2536, 3'-AGC-5' at 2557, 3'-AGC-5' at 2703, 3'-AGC-5' at 2731, 3'-AGC-5' at 2749, 3'-AGC-5' at 2785, 3'-AGC-5' at 2845, 3'-AGC-5' at 2896, 3'-AGC-5' at 2970, 3'-AGC-5' at 3041, 3'-AGC-5' at 3100, 3'-AGC-5' at 3125, 3'-AGC-5' at 3137, 3'-AGC-5' at 3144, 3'-AGC-5' at 3155, 3'-AGC-5' at 3194, 3'-AGC-5' at 3211, 3'-AGC-5' at 3217, 3'-AGC-5' at 3223, 3'-AGC-5' at 3239, 3'-AGC-5' at 3262, 3'-AGC-5' at 3513, 3'-AGC-5' at 3518, 3'-AGC-5' at 3598, 3'-AGC-5' at 3668, 3'-AGC-5' at 3691, 3'-AGC-5' at 3701, 3'-AGC-5' at 3720, 3'-AGC-5' at 3723, 3'-AGC-5' at 3737, 3'-AGC-5' at 3763, 3'-AGC-5' at 3775, 3'-AGC-5' at 3808, 3'-AGC-5' at 3895, 3'-AGC-5' at 3997, 3'-AGC-5' at 4023, 3'-AGC-5' at 4026, 3'-AGC-5' at 4052, 3'-AGC-5' at 4279.
  3. positive strand, negative direction, looking for DCE DCE SIII: 3'-AGC-5', 91, 3'-AGC-5' at 35, 3'-AGC-5' at 137, 3'-AGC-5' at 146, 3'-AGC-5' at 185, 3'-AGC-5' at 403, 3'-AGC-5' at 455, 3'-AGC-5' at 500, 3'-AGC-5' at 504, 3'-AGC-5' at 540, 3'-AGC-5' at 676, 3'-AGC-5' at 728, 3'-AGC-5' at 737, 3'-AGC-5' at 778, 3'-AGC-5' at 810, 3'-AGC-5' at 870, 3'-AGC-5' at 895, 3'-AGC-5' at 909, 3'-AGC-5' at 944, 3'-AGC-5' at 976, 3'-AGC-5' at 1036, 3'-AGC-5' at 1061, 3'-AGC-5' at 1140, 3'-AGC-5' at 1194, 3'-AGC-5' at 1235, 3'-AGC-5' at 1267, 3'-AGC-5' at 1327, 3'-AGC-5' at 1367, 3'-AGC-5' at 1486, 3'-AGC-5' at 1497, 3'-AGC-5' at 1611, 3'-AGC-5' at 1678, 3'-AGC-5' at 1785, 3'-AGC-5' at 1888, 3'-AGC-5' at 1920, 3'-AGC-5' at 1969, 3'-AGC-5' at 1980, 3'-AGC-5' at 2005, 3'-AGC-5' at 2019, 3'-AGC-5' at 2094, 3'-AGC-5' at 2129, 3'-AGC-5' at 2264, 3'-AGC-5' at 2273, 3'-AGC-5' at 2314, 3'-AGC-5' at 2346, 3'-AGC-5' at 2406, 3'-AGC-5' at 2431, 3'-AGC-5' at 2472, 3'-AGC-5' at 2478, 3'-AGC-5' at 2650, 3'-AGC-5' at 2681, 3'-AGC-5' at 2741, 3'-AGC-5' at 2766, 3'-AGC-5' at 2780, 3'-AGC-5' at 2915, 3'-AGC-5' at 3032, 3'-AGC-5' at 3070, 3'-AGC-5' at 3105, 3'-AGC-5' at 3124, 3'-AGC-5' at 3177, 3'-AGC-5' at 3204, 3'-AGC-5' at 3209, 3'-AGC-5' at 3269, 3'-AGC-5' at 3294, 3'-AGC-5' at 3309, 3'-AGC-5' at 3370, 3'-AGC-5' at 3494, 3'-AGC-5' at 3646, 3'-AGC-5' at 3682, 3'-AGC-5' at 3694, 3'-AGC-5' at 3701, 3'-AGC-5' at 3726, 3'-AGC-5' at 3731, 3'-AGC-5' at 3773, 3'-AGC-5' at 3838, 3'-AGC-5' at 3845, 3'-AGC-5' at 3899, 3'-AGC-5' at 3912, 3'-AGC-5' at 4014, 3'-AGC-5' at 4033, 3'-AGC-5' at 4130, 3'-AGC-5' at 4184, 3'-AGC-5' at 4229, 3'-AGC-5' at 4261, 3'-AGC-5' at 4296, 3'-AGC-5' at 4321, 3'-AGC-5' at 4345, 3'-AGC-5' at 4411, 3'-AGC-5' at 4439.
  4. positive strand, positive direction, looking for DCE SIII: 3'-AGC-5', 26, 3'-AGC-5' at 77, 3'-AGC-5' at 457, 3'-AGC-5' at 537, 3'-AGC-5' at 593, 3'-AGC-5' at 688, 3'-AGC-5' at 761, 3'-AGC-5' at 1013, 3'-AGC-5' at 1108, 3'-AGC-5' at 1154, 3'-AGC-5' at 1181, 3'-AGC-5' at 1306, 3'-AGC-5' at 1390, 3'-AGC-5' at 1406, 3'-AGC-5' at 1490, 3'-AGC-5' at 1517, 3'-AGC-5' at 1528, 3'-AGC-5' at 1687, 3'-AGC-5' at 1713, 3'-AGC-5' at 1750, 3'-AGC-5' at 1915, 3'-AGC-5' at 1927, 3'-AGC-5' at 2091, 3'-AGC-5' at 3272, 3'-AGC-5' at 3283, 3'-AGC-5' at 3509, 3'-AGC-5' at 3985.

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: 3'-GCT-5', 23, 3'-GCT-5' at 310, 3'-GCT-5' at 434, 3'-GCT-5' at 448, 3'-GCT-5' at 492, 3'-GCT-5' at 571, 3'-GCT-5' at 707, 3'-GCT-5' at 721, 3'-GCT-5' at 911, 3'-GCT-5' at 1039, 3'-GCT-5' at 1066, 3'-GCT-5' at 1155, 3'-GCT-5' at 1181, 3'-GCT-5' at 1189, 3'-GCT-5' at 1330, 3'-GCT-5' at 1553, 3'-GCT-5' at 1983, 3'-GCT-5' at 2013, 3'-GCT-5' at 2155, 3'-GCT-5' at 2409, 3'-GCT-5' at 3231, 3'-GCT-5' at 3814, 3'-GCT-5' at 3875, 3'-GCT-5' at 4241.
  2. negative strand, positive direction, looking for DCE SIIIci: 3'-GCT-5', 87, 3'-GCT-5' at 3, 3'-GCT-5' at 10, 3'-GCT-5' at 262, 3'-GCT-5' at 275, 3'-GCT-5' at 384, 3'-GCT-5' at 415, 3'-GCT-5' at 479, 3'-GCT-5' at 518, 3'-GCT-5' at 528, 3'-GCT-5' at 602, 3'-GCT-5' at 652, 3'-GCT-5' at 693, 3'-GCT-5' at 737, 3'-GCT-5' at 777, 3'-GCT-5' at 838, 3'-GCT-5' at 938, 3'-GCT-5' at 1029, 3'-GCT-5' at 1093, 3'-GCT-5' at 1106, 3'-GCT-5' at 1113, 3'-GCT-5' at 1177, 3'-GCT-5' at 1190, 3'-GCT-5' at 1274, 3'-GCT-5' at 1342, 3'-GCT-5' at 1349, 3'-GCT-5' at 1442, 3'-GCT-5' at 1449, 3'-GCT-5' at 1533, 3'-GCT-5' at 1576, 3'-GCT-5' at 1651, 3'-GCT-5' at 1727, 3'-GCT-5' at 1734, 3'-GCT-5' at 1777, 3'-GCT-5' at 1817, 3'-GCT-5' at 1882, 3'-GCT-5' at 1907, 3'-GCT-5' at 1973, 3'-GCT-5' at 2043, 3'-GCT-5' at 2046, 3'-GCT-5' at 2053, 3'-GCT-5' at 2056, 3'-GCT-5' at 2089, 3'-GCT-5' at 2093, 3'-GCT-5' at 2155, 3'-GCT-5' at 2161, 3'-GCT-5' at 2194, 3'-GCT-5' at 2318, 3'-GCT-5' at 2368, 3'-GCT-5' at 2403, 3'-GCT-5' at 2435, 3'-GCT-5' at 2504, 3'-GCT-5' at 2695, 3'-GCT-5' at 2732, 3'-GCT-5' at 2750, 3'-GCT-5' at 2753, 3'-GCT-5' at 2768, 3'-GCT-5' at 2786, 3'-GCT-5' at 2808, 3'-GCT-5' at 2846, 3'-GCT-5' at 2885, 3'-GCT-5' at 2913, 3'-GCT-5' at 2971, 3'-GCT-5' at 2976, 3'-GCT-5' at 3119, 3'-GCT-5' at 3151, 3'-GCT-5' at 3195, 3'-GCT-5' at 3227, 3'-GCT-5' at 3240, 3'-GCT-5' at 3263, 3'-GCT-5' at 3274, 3'-GCT-5' at 3307, 3'-GCT-5' at 3347, 3'-GCT-5' at 3368, 3'-GCT-5' at 3420, 3'-GCT-5' at 3481, 3'-GCT-5' at 3519, 3'-GCT-5' at 3524, 3'-GCT-5' at 3586, 3'-GCT-5' at 3638, 3'-GCT-5' at 3696, 3'-GCT-5' at 3724, 3'-GCT-5' at 3776, 3'-GCT-5' at 3983, 3'-GCT-5' at 3987, 3'-GCT-5' at 3992, 3'-GCT-5' at 4027, 3'-GCT-5' at 4175.
  3. positive strand, negative direction, looking for DCE SIIIci: 3'-GCT-5', 78, 3'-GCT-5' at 138, 3'-GCT-5' at 147, 3'-GCT-5' at 335, 3'-GCT-5' at 385, 3'-GCT-5' at 598, 3'-GCT-5' at 658, 3'-GCT-5' at 779, 3'-GCT-5' at 811, 3'-GCT-5' at 823, 3'-GCT-5' at 840, 3'-GCT-5' at 890, 3'-GCT-5' at 977, 3'-GCT-5' at 989, 3'-GCT-5' at 1006, 3'-GCT-5' at 1109, 3'-GCT-5' at 1122, 3'-GCT-5' at 1268, 3'-GCT-5' at 1280, 3'-GCT-5' at 1448, 3'-GCT-5' at 1462, 3'-GCT-5' at 1487, 3'-GCT-5' at 1498, 3'-GCT-5' at 1744, 3'-GCT-5' at 1754, 3'-GCT-5' at 1767, 3'-GCT-5' at 1798, 3'-GCT-5' at 1843, 3'-GCT-5' at 1889, 3'-GCT-5' at 1906, 3'-GCT-5' at 1921, 3'-GCT-5' at 1970, 3'-GCT-5' at 2067, 3'-GCT-5' at 2107, 3'-GCT-5' at 2130, 3'-GCT-5' at 2202, 3'-GCT-5' at 2224, 3'-GCT-5' at 2324, 3'-GCT-5' at 2347, 3'-GCT-5' at 2359, 3'-GCT-5' at 2376, 3'-GCT-5' at 2529, 3'-GCT-5' at 2560, 3'-GCT-5' at 2682, 3'-GCT-5' at 2694, 3'-GCT-5' at 2711, 3'-GCT-5' at 2742, 3'-GCT-5' at 2896, 3'-GCT-5' at 2933, 3'-GCT-5' at 3006, 3'-GCT-5' at 3033, 3'-GCT-5' at 3039, 3'-GCT-5' at 3052, 3'-GCT-5' at 3083, 3'-GCT-5' at 3106, 3'-GCT-5' at 3178, 3'-GCT-5' at 3210, 3'-GCT-5' at 3222, 3'-GCT-5' at 3263, 3'-GCT-5' at 3398, 3'-GCT-5' at 3580, 3'-GCT-5' at 3647, 3'-GCT-5' at 3702, 3'-GCT-5' at 3707, 3'-GCT-5' at 3717, 3'-GCT-5' at 3774, 3'-GCT-5' at 3862, 3'-GCT-5' at 3955, 3'-GCT-5' at 3961, 3'-GCT-5' at 3992, 3'-GCT-5' at 4112, 3'-GCT-5' at 4131, 3'-GCT-5' at 4143, 3'-GCT-5' at 4185, 3'-GCT-5' at 4255, 3'-GCT-5' at 4262, 3'-GCT-5' at 4274, 3'-GCT-5' at 4291, 3'-GCT-5' at 4402.
  4. positive strand, positive direction, looking for DCE SIIIci: 3'-GCT-5', 36, 3'-GCT-5' at 162, 3'-GCT-5' at 242, 3'-GCT-5' at 308, 3'-GCT-5' at 360, 3'-GCT-5' at 429, 3'-GCT-5' at 555, 3'-GCT-5' at 576, 3'-GCT-5' at 639, 3'-GCT-5' at 766, 3'-GCT-5' at 790, 3'-GCT-5' at 851, 3'-GCT-5' at 896, 3'-GCT-5' at 951, 3'-GCT-5' at 996, 3'-GCT-5' at 1059, 3'-GCT-5' at 1080, 3'-GCT-5' at 1101, 3'-GCT-5' at 1155, 3'-GCT-5' at 1164, 3'-GCT-5' at 1227, 3'-GCT-5' at 1346, 3'-GCT-5' at 1379, 3'-GCT-5' at 1446, 3'-GCT-5' at 1479, 3'-GCT-5' at 1563, 3'-GCT-5' at 1584, 3'-GCT-5' at 1623, 3'-GCT-5' at 1665, 3'-GCT-5' at 1835, 3'-GCT-5' at 1919, 3'-GCT-5' at 1962, 3'-GCT-5' at 2215, 3'-GCT-5' at 2357, 3'-GCT-5' at 2804, 3'-GCT-5' at 3799, 3'-GCT-5' at 4277.

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.

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 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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