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.

Samplings

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.

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 SIIs

  1. negative strand, negative direction, looking for DCE SII: 3'-CTGT-5', 19, 3'-CTGT-5' at 170 , 3'-CTGT-5' at 422 , 3'-CTGT-5' at 559 , 3'-CTGT-5' at 746 , 3'-CTGT-5' at 1068 , 3'-CTGT-5' at 1569 , 3'-CTGT-5' at 2015 , 3'-CTGT-5' at 2117 , 3'-CTGT-5' at 2271 , 3'-CTGT-5' at 2880 , 3'-CTGT-5' at 2948 , 3'-CTGT-5' at 3389 , 3'-CTGT-5' at 3412 , 3'-CTGT-5' at 3433 , 3'-CTGT-5' at 3756 , 3'-CTGT-5' at 4181 , 3'-CTGT-5' at 4355.
  2. negative strand, positive direction, looking for DCE SII: 3'-CTGT-5', 26, 3'-CTGT-5' at 98, 3'-CTGT-5' at 144, 3'-CTGT-5' at 264, 3'-CTGT-5' at 816, 3'-CTGT-5' at 891, 3'-CTGT-5' at 916, 3'-CTGT-5' at 991, 3'-CTGT-5' at 1729, 3'-CTGT-5' at 1860, 3'-CTGT-5' at 1998, 3'-CTGT-5' at 2074, 3'-CTGT-5' at 2182, 3'-CTGT-5' at 2250, 3'-CTGT-5' at 2260, 3'-CTGT-5' at 2308, 3'-CTGT-5' at 2342, 3'-CTGT-5' at 2925, 3'-CTGT-5' at 2931, 3'-CTGT-5' at 2957, 3'-CTGT-5' at 3349, 3'-CTGT-5' at 3390, 3'-CTGT-5' at 3434, 3'-CTGT-5' at 3617, 3'-CTGT-5' at 3622, 3'-CTGT-5' at 3640, 3'-CTGT-5' at 4392.
  3. positive strand, negative direction, looking for DCE SII: 3'-CTGT-5', 30, 3'-CTGT-5' at 394, 3'-CTGT-5' at 477, 3'-CTGT-5' at 667, 3'-CTGT-5' at 801, 3'-CTGT-5' at 919, 3'-CTGT-5' at 967, 3'-CTGT-5' at 1085, 3'-CTGT-5' at 1131, 3'-CTGT-5' at 1258, 3'-CTGT-5' at 1452, 3'-CTGT-5' at 1776, 3'-CTGT-5' at 1911, 3'-CTGT-5' at 2029, 3'-CTGT-5' at 2163, 3'-CTGT-5' at 2337, 3'-CTGT-5' at 2538, 3'-CTGT-5' at 2672, 3'-CTGT-5' at 3061, 3'-CTGT-5' at 3200, 3'-CTGT-5' at 3265, 3'-CTGT-5' at 3319, 3'-CTGT-5' at 3426, 3'-CTGT-5' at 3556, 3'-CTGT-5' at 3709, 3'-CTGT-5' at 3957, 3'-CTGT-5' at 3970, 3'-CTGT-5' at 4121, 3'-CTGT-5' at 4208, 3'-CTGT-5' at 4369, 3'-CTGT-5' at 4399.
  4. positive strand, positive direction, looking for DCE SII: 3'-CTGT-5', 15, 3'-CTGT-5' at 62, 3'-CTGT-5' at 712, 3'-CTGT-5' at 1693, 3'-CTGT-5' at 1869, 3'-CTGT-5' at 1964, 3'-CTGT-5' at 2130, 3'-CTGT-5' at 2412, 3'-CTGT-5' at 2460, 3'-CTGT-5' at 2843, 3'-CTGT-5' at 3131, 3'-CTGT-5' at 3530, 3'-CTGT-5' at 3569, 3'-CTGT-5' at 3893, 3'-CTGT-5' at 3973, 3'-CTGT-5' at 4252.

Downstream core element SIIIs

  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 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 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 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 SI Inverse complements

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

Downstream core element SII Inverse complements

  1. negative strand, negative direction, looking for DCE SIIci: 3'-ACAG-5', 13, 3'-ACAG-5' at 478, 3'-ACAG-5' at 920, 3'-ACAG-5' at 1086, 3'-ACAG-5' at 1221, 3'-ACAG-5' at 2030, 3'-ACAG-5' at 2164, 3'-ACAG-5' at 2985, 3'-ACAG-5' at 3201, 3'-ACAG-5' at 3320, 3'-ACAG-5' at 3622, 3'-ACAG-5' at 3832, 3'-ACAG-5' at 4209, 3'-ACAG-5' at 4370.
  2. negative strand, positive direction, looking for DCE SIIci: 3'-ACAG-5', 28, 3'-ACAG-5' at 63, 3'-ACAG-5' at 156, 3'-ACAG-5' at 364, 3'-ACAG-5' at 551, 3'-ACAG-5' at 633, 3'-ACAG-5' at 717, 3'-ACAG-5' at 1053, 3'-ACAG-5' at 1823, 3'-ACAG-5' at 1965, 3'-ACAG-5' at 2124, 3'-ACAG-5' at 2131, 3'-ACAG-5' at 2413, 3'-ACAG-5' at 2461, 3'-ACAG-5' at 2651, 3'-ACAG-5' at 2836, 3'-ACAG-5' at 2844, 3'-ACAG-5' at 3099, 3'-ACAG-5' at 3132, 3'-ACAG-5' at 3178, 3'-ACAG-5' at 3193, 3'-ACAG-5' at 3210, 3'-ACAG-5' at 3412, 3'-ACAG-5' at 3570, 3'-ACAG-5' at 3635, 3'-ACAG-5' at 3860, 3'-ACAG-5' at 3894, 3'-ACAG-5' at 3974, 3'-ACAG-5' at 4069.
  3. positive strand, negative direction, looking for DCE SIIci: 3'-ACAG-5', 25, 3'-ACAG-5' at 12, 3'-ACAG-5' at 167, 3'-ACAG-5' at 288, 3'-ACAG-5' at 296, 3'-ACAG-5' at 423, 3'-ACAG-5' at 519, 3'-ACAG-5' at 560, 3'-ACAG-5' at 906, 3'-ACAG-5' at 1072, 3'-ACAG-5' at 1117, 3'-ACAG-5' at 1566, 3'-ACAG-5' at 2016, 3'-ACAG-5' at 2118, 3'-ACAG-5' at 2272, 3'-ACAG-5' at 2442, 3'-ACAG-5' at 2513, 3'-ACAG-5' at 2688, 3'-ACAG-5' at 2777, 3'-ACAG-5' at 2877, 3'-ACAG-5' at 3671, 3'-ACAG-5' at 3693, 3'-ACAG-5' at 3725, 3'-ACAG-5' at 3916, 3'-ACAG-5' at 4197, 3'-ACAG-5' at 4356.
  4. positive strand, positive direction, looking for DCE SIIci: 3'-ACAG-5', 20, 3'-ACAG-5' at 81, 3'-ACAG-5' at 99, 3'-ACAG-5' at 267, 3'-ACAG-5' at 892, 3'-ACAG-5' at 992, 3'-ACAG-5' at 1730, 3'-ACAG-5' at 1861, 3'-ACAG-5' at 1999, 3'-ACAG-5' at 2077, 3'-ACAG-5' at 2171, 3'-ACAG-5' at 2309, 3'-ACAG-5' at 2465, 3'-ACAG-5' at 2926, 3'-ACAG-5' at 3003, 3'-ACAG-5' at 3052, 3'-ACAG-5' at 3391, 3'-ACAG-5' at 3576, 3'-ACAG-5' at 3618, 3'-ACAG-5' at 3744, 3'-ACAG-5' at 3951.

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 SI Inverses

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

Downstream core element SII Inverses

  1. negative strand, negative direction, looking for DCE SIIi: 3'-TGTC-5', 25, 3'-TGTC-5' at 12, 3'-TGTC-5' at 167, 3'-TGTC-5' at 288, 3'-TGTC-5' at 296, 3'-TGTC-5' at 423, 3'-TGTC-5' at 519, 3'-TGTC-5' at 560, 3'-TGTC-5' at 906, 3'-TGTC-5' at 1072, 3'-TGTC-5' at 1117, 3'-TGTC-5' at 1566, 3'-TGTC-5' at 2016, 3'-TGTC-5' at 2118, 3'-TGTC-5' at 2272, 3'-TGTC-5' at 2442, 3'-TGTC-5' at 2513, 3'-TGTC-5' at 2688, 3'-TGTC-5' at 2777, 3'-TGTC-5' at 2877, 3'-TGTC-5' at 3671, 3'-TGTC-5' at 3693, 3'-TGTC-5' at 3725, 3'-TGTC-5' at 3916, 3'-TGTC-5' at 4197, 3'-TGTC-5' at 4356.
  2. negative strand, positive direction, looking for DCE SIIi: 3'-TGTC-5', 20, 3'-TGTC-5' at 81, 3'-TGTC-5' at 99, 3'-TGTC-5' at 267, 3'-TGTC-5' at 892, 3'-TGTC-5' at 992, 3'-TGTC-5' at 1730, 3'-TGTC-5' at 1861, 3'-TGTC-5' at 1999, 3'-TGTC-5' at 2077, 3'-TGTC-5' at 2171, 3'-TGTC-5' at 2309, 3'-TGTC-5' at 2465, 3'-TGTC-5' at 2926, 3'-TGTC-5' at 3003, 3'-TGTC-5' at 3052, 3'-TGTC-5' at 3391, 3'-TGTC-5' at 3576, 3'-TGTC-5' at 3618, 3'-TGTC-5' at 3744, 3'-TGTC-5' at 3951.
  3. positive strand, negative direction, looking for DCE SIIi: 3'-TGTC-5', 13, 3'-TGTC-5' at 478, 3'-TGTC-5' at 920, 3'-TGTC-5' at 1086, 3'-TGTC-5' at 1221, 3'-TGTC-5' at 2030, 3'-TGTC-5' at 2164, 3'-TGTC-5' at 2985, 3'-TGTC-5' at 3201, 3'-TGTC-5' at 3320, 3'-TGTC-5' at 3622, 3'-TGTC-5' at 3832, 3'-TGTC-5' at 4209, 3'-TGTC-5' at 4370.
  4. positive strand, positive direction, looking for DCE SIIi: 3'-TGTC-5', 28, 3'-TGTC-5' at 63, 3'-TGTC-5' at 156, 3'-TGTC-5' at 364, 3'-TGTC-5' at 551, 3'-TGTC-5' at 633, 3'-TGTC-5' at 717, 3'-TGTC-5' at 1053, 3'-TGTC-5' at 1823, 3'-TGTC-5' at 1965, 3'-TGTC-5' at 2124, 3'-TGTC-5' at 2131, 3'-TGTC-5' at 2413, 3'-TGTC-5' at 2461, 3'-TGTC-5' at 2651, 3'-TGTC-5' at 2836, 3'-TGTC-5' at 2844, 3'-TGTC-5' at 3099, 3'-TGTC-5' at 3132, 3'-TGTC-5' at 3178, 3'-TGTC-5' at 3193, 3'-TGTC-5' at 3210, 3'-TGTC-5' at 3412, 3'-TGTC-5' at 3570, 3'-TGTC-5' at 3635, 3'-TGTC-5' at 3860, 3'-TGTC-5' at 3894, 3'-TGTC-5' at 3974, 3'-TGTC-5' at 4069.

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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