Downstream promoter element gene transcriptions

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Editor-In-Chief: Henry A. Hoff

File:Core promoter elements.svg
The diagram is an overview of four core promoter elements. Credit: Jennifer E.F. Butler & James T. Kadonaga.

The figure on the right is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.[1]

The downstream promoter element (DPE) is a core promoter element present in other species including humans and excluding Saccharomyces cerevisiae.[2]

Gene transcriptions

Main article: Gene transcriptions

"Transcription by RNA polymerase II is directed by cis-acting [close-acting] DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers [trans-acting, or distant-acting, protein factors], that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins."[3]

Core promoters

Main articles: Core promoter gene transcriptions and Core promoters

"[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"[3].

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A+1 nucleotide in the Inr"[4]. It is located about 28–33 nucleotides downstream of the transcription start site.[2]

DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements.[5][3][6]

Initiator elements

Main articles: Initiator element gene transcriptions and Initiator elements

"There is a strict requirement for spacing between the [Initiator element] Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID."[3]

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences

The early DPE consensus sequence was RGWCGTG.[5][7]

The DPE consensus sequence is the more general sequence RGWYVT, or (A/G)G(A/T)(C/T)(A/C/G)T.[2]

The DPE in "the ATP‐binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" is 5'-AGTCTC-3'.[8]

DPE-containing promoters

"The ... Drosophila Antennapedia P2 (Antp P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus"[3]. GeneID: 40835 Antp Antennapedia [Drosophila melanogaster] is also known as Antp P2.[9] GeneID: 3204 HOXA7 homeobox A7 [ Homo sapiens ] is also known as ANTP and "[t]his gene is highly similar to the antennapedia (Antp) gene of Drosophila."[10] As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of Drosophila"[10], it may have a DPE like the Drosophila gene core promoter does.

"[T]he TATA-less Drosophila Abdominal-B (Abd-B) promoter [has a] partial DPE sequence"[3]. GeneID: 3205 HOXA9 homeobox A9 [ Homo sapiens] is also known as ABD-B and "[t]his gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila."[11] GeneID: 3205 may also be TATA-less and have a DPE.

General transcription factor II Ds

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

The DPE "is required for the binding of purified [general transcription factor II D] TFIID to a subset of TATA-less promoters"[4].

"Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 [TAF6 GeneID: 6878] and dTAFII40 [TAF11 GeneID: 6882] to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE."[3]

Hypotheses

Main article: Hypotheses
  1. The DPE is not used to transcribe A1BG.

Samplings

Main article: A1BG gene transcription core promoters

For the Basic programs (starting with SuccessablesDPE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are expanded in the positive direction from 958 to 4445, are looking for, and found:

  1. Negative strand, negative direction: 163, GGACC at 4546, GGACC at 4494, AGTCG at 4489, GGTCG at 4480, AGTCC at 4436, AGATG at 4430, GGTCA at 4415, GGACA at 4369, GGACC at 4349, GGTCG at 4345, GGACC at 4300, GGTCG at 4261, GGTCC at 4253, AGATG at 4212, GGACA at 4208, AGTTC at 4178, GGTCC at 4170, AGTCC at 4138, GGTCG at 4130, GGACA at 4121, GGTCC at 4102, AGATG at 4062, GGACC at 4037, GGTCG at 4033, AGTTC at 4027, GGTTC at 4019, GGTTG at 3979, GGACA at 3970, GGTCC at 3951, GGACC at 3906, GGTCC at 3885, GGTCC at 3871, GGACG at 3861, AGTTC at 3844, AGACC at 3835, GGACC at 3744, GGTCG at 3731, AGACG at 3706, GGTCG at 3701, GGTCG at 3682, GGTCC at 3585, GGACG at 3579, GGTCC at 3564, AGACA at 3556, AGTTG at 3523, AGTCC at 3396, AGACA at 3319, GGACC at 3298, GGTCG at 3294, GGTTC at 3273, GGTCC at 3249, AGTCC at 3217, GGTCG at 3209, AGTCG at 3204, GGACA at 3200, AGATG at 3158, GGTTG at 3137, GGACC at 3128, GGTCG at 3124, AGTCC at 3110, GGTCG at 3070, GGACA at 3061, GGATA at 2996, AGATG at 2988, GGTTA at 2848, GGACC at 2770, GGTCG at 2766, GGACC at 2720, GGTCG at 2681, GGACA at 2672, GGTCA at 2654, AGTCG at 2650, GGTTG at 2610, GGTCA at 2601, AGTCC at 2587, GGTTG at 2547, GGACA at 2538, GGTCC at 2519, AGTTA at 2496, GGACC at 2435, GGTCG at 2431, GGACC at 2385, GGTCG at 2346, GGACA at 2337, AGATG at 2294, GGACC at 2268, GGTCG at 2264, AGTCC at 2250, GGTCA at 2211, AGATG at 2169, GGTTG at 2148, AGTCC at 2134, GGATC at 2093, GGTCC at 2077, AGACA at 2029, GGACC at 2009, GGTCG at 2005, GGACC at 1959, GGTCG at 1920, GGACA at 1911, AGATG at 1867, GGACC at 1841, GGTTC at 1817, GGTCG at 1785, AGACA at 1776, GGTCG at 1611, GGTCA at 1532, AGATA at 1525, AGTTG at 1513, AGTCG at 1486, GGTCC at 1460, AGACA at 1452, AGTTG at 1406, AGACC at 1356, GGTCA at 1352, GGATC at 1306, AGTCC at 1275, GGTCG at 1267, GGACA at 1258, AGATG at 1224, GGTTG at 1203, GGACC at 1198, GGTCG at 1194, GGTCG at 1140, GGACA at 1131, AGACA at 1085, GGTCG at 1061, GGACC at 1015, AGTCC at 984, GGTCG at 976, GGACA at 967, GGTCC at 948, AGACA at 919, GGACC at 899, GGTCG at 895, GGTTC at 874, GGTCC at 850, GGTCG at 810, GGACA at 801, AGATG at 758, GGTCG at 737, GGTCG at 728, AGTCC at 714, GGTTC at 692, GGTCG at 676, GGACA at 667, GGTCC at 648, AGATG at 624, GGACC at 596, AGTCC at 578, GGTTC at 556, GGTCG at 540, GGACC at 508, GGTCG at 504, AGATG at 481, GGACC at 459, AGTCC at 441, GGTTC at 419, GGTCG at 403, GGACA at 394, GGTCC at 262, AGATA at 234, GGTCG at 35.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDPEJ-+.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 18, 5'-GGACCT-3' at 38, 5'-GGTCCT-3' at 219, 5'-AGTCCT-3' at 758, 5'-GGACAT-3' at 1870, 5'-AGTTCT-3' at 1988, 5'-GGATAT-3' at 2660, 5'-GGATGT-3' at 2715, 5'-AGACCT-3' at 2862, 5'-GGTTCT-3' at 2923, 5'-AGTTCT-3' at 2955, 5'-AGTCCT-3' at 2999, 5'-GGTTAT-3' at 3025, 5'-GGTTGT-3' at 3051, 5'-AGTTAT-3' at 3382, 5'-AGACCT-3' at 3551, 5'-GGATGT-3' at 3575, 5'-AGTCCT-3' at 3864, 5'-GGTTCT-3' at 4074, and complements.
  3. Positive strand, negative direction:16, AGACAT at 4508, AGTTCT at 4418, AGACGT at 4236, AGATGT at 3621, AGATAT at 3466, AGACAT at 3434, AGATAT at 2982, AGACAT at 2949, AGACAT at 2881, AGATAT at 1596, AGACAT at 1570, GGATGT at 785, AGATGT at 245, AGACAT at 171, GGATAT at 109, GGATAT at 75.
  4. positive strand in the positive direction is SuccessablesDPEJ++.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 31, 5'-GGACCT-3' at 41, 5'-GGTTCT-3' at 178, 5'-GGACGT-3' at 192, 5'-AGACGT-3' at 224, 5'-AGACCT-3' at 271, 5'-GGTCCT-3' at 425, 5'-GGACGT-3' at 436, 5'-GGACCT-3' at 599, 5'-GGTCGT-3' at 618, 5'-GGTCCT-3' at 708, 5'-GGACGT-3' at 1119, 5'-GGTCGT-3' at 1358, 5'-GGACGT-3' at 1370, 5'-GGTCGT-3' at 1458, 5'-GGACGT-3' at 1470, 5'-AGTCGT-3' at 2103, 5'-AGTCGT-3' at 2199, 5'-AGTCCT-3' at 2621, 5'-AGACGT-3' at 2857, 5'-AGTCGT-3' at 3042, 5'-AGACGT-3' at 3061, 5'-AGTCGT-3' at 3156, 5'-AGACGT-3' at 3268, 5'-AGACGT-3' at 3279, 5'-GGACCT-3' at 3363, 5'-AGTTAT-3' at 3425, 5'-GGTTGT-3' at 3634, 5'-GGTCGT-3' at 3721, 5'-AGTCCT-3' at 3869, 5'-AGTCGT-3' at 4024, 5'-AGATCT-3' at 4065, and complements.
  5. complement, negative strand, negative direction is SuccessablesDPEJc--.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 16, 5'-CCTATA-3' at 75, 5'-CCTATA-3' at 109, 5'-TCTGTA-3' at 171, 5'-TCTACA-3' at 245, 5'-CCTACA-3' at 785, 5'-TCTGTA-3' at 1570, 5'-TCTATA-3' at 1596, 5'-TCTGTA-3' at 2881, 5'-TCTGTA-3' at 2949, 5'-TCTATA-3' at 2982, 5'-TCTGTA-3' at 3434, 5'-TCTATA-3' at 3466, 5'-TCTACA-3' at 3621, 5'-TCTGCA-3' at 4236, 5'-TCAAGA-3' at 4418, 5'-TCTGTA-3' at 4508.
  6. complement, negative strand, positive direction is SuccessablesDPEJc-+.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 31, 5'-CCTGGA-3' at 41, 5'-CCAAGA-3' at 178, 5'-CCTGCA-3' at 192, 5'-TCTGCA-3' at 224, 5'-TCTGGA-3' at 271, 5'-CCAGGA-3' at 425, 5'-CCTGCA-3' at 436, 5'-CCTGGA-3' at 599, 5'-CCAGCA-3' at 618, 5'-CCAGGA-3' at 708, 5'-CCTGCA-3' at 1119, 5'-CCAGCA-3' at 1358, 5'-CCTGCA-3' at 1370, 5'-CCAGCA-3' at 1458, 5'-CCTGCA-3' at 1470, 5'-TCAGCA-3' at 2103, 5'-TCAGCA-3' at 2199, 5'-TCAGGA-3' at 2621, 5'-TCTGCA-3' at 2857, 5'-TCAGCA-3' at 3042, 5'-TCTGCA-3' at 3061, 5'-TCAGCA-3' at 3156, 5'-TCTGCA-3' at 3268, 5'-TCTGCA-3' at 3279, 5'-CCTGGA-3' at 3363, 5'-TCAATA-3' at 3425, 5'-CCAACA-3' at 3634, 5'-CCAGCA-3' at 3721, 5'-TCAGGA-3' at 3869, 5'-TCAGCA-3' at 4024, 5'-TCTAGA-3' at 4065.
  7. complement, positive strand, negative direction is SuccessablesDPEJc+-.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 63, 5'-CCTGTA-3' at 395, 5'-CCAGCA-3' at 404, 5'-CCAAGA-3' at 420, 5'-TCAGGA-3' at 442, 5'-TCTACA-3' at 482, 5'-CCAGCA-3' at 541, 5'-CCAAGA-3' at 557, 5'-TCAGGA-3' at 579, 5'-CCTGTA-3' at 668, 5'-CCAGCA-3' at 677, 5'-TCAGGA-3' at 715, 5'-CCTGTA-3' at 802, 5'-CCAGGA-3' at 851, 5'-CCAAGA-3' at 875, 5'-CCTGTA-3' at 968, 5'-TCAGGA-3' at 985, 5'-CCTGTA-3' at 1132, 5'-CCAGCA-3' at 1141, 5'-CCAACA-3' at 1204, 5'-TCTACA-3' at 1225, 5'-CCTGTA-3' at 1259, 5'-TCAGGA-3' at 1276, 5'-TCTATA-3' at 1526, 5'-CCAGCA-3' at 1612, 5'-TCTGTA-3' at 1777, 5'-CCAGCA-3' at 1786, 5'-CCTGTA-3' at 1912, 5'-TCAGGA-3' at 2135, 5'-CCAACA-3' at 2149, 5'-CCAGTA-3' at 2212, 5'-TCAGGA-3' at 2251, 5'-CCTGGA-3' at 2269, 5'-CCTGTA-3' at 2338, 5'-TCAATA-3' at 2497, 5'-CCTGTA-3' at 2539, 5'-CCAACA-3' at 2548, 5'-TCAGGA-3' at 2588, 5'-CCAACA-3' at 2611, 5'-CCTGTA-3' at 2673, 5'-CCAATA-3' at 2849, 5'-TCTACA-3' at 2989, 5'-CCTGTA-3' at 3062, 5'-CCAGCA-3' at 3071, 5'-TCAGGA-3' at 3111, 5'-CCAACA-3' at 3138, 5'-TCAGGA-3' at 3218, 5'-CCAGGA-3' at 3250, 5'-CCAAGA-3' at 3274, 5'-CCAGCA-3' at 3732, 5'-CCTGGA-3' at 3745, 5'-TCTGGA-3' at 3836, 5'-CCTGGA-3' at 3907, 5'-CCTGTA-3' at 3971, 5'-CCAACA-3' at 3980, 5'-CCAAGA-3' at 4020, 5'-TCAAGA-3' at 4028, 5'-TCTACA-3' at 4063, 5'-CCTGTA-3' at 4122, 5'-TCAGGA-3' at 4139, 5'-CCAGGA-3' at 4171, 5'-TCAAGA-3' at 4179, 5'-TCTACA-3' at 4213, 5'-TCAGGA-3' at 4437.
  8. complement, positive strand, positive direction is SuccessablesDPEJc++.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 18, 5'-CCTGGA-3' at 38, 5'-CCAGGA-3' at 219, 5'-TCAGGA-3' at 758, 5'-CCTGTA-3' at 1870, 5'-TCAAGA-3' at 1988, 5'-CCTATA-3' at 2660, 5'-CCTACA-3' at 2715, 5'-TCTGGA-3' at 2862, 5'-CCAAGA-3' at 2923, 5'-TCAAGA-3' at 2955, 5'-TCAGGA-3' at 2999, 5'-CCAATA-3' at 3025, 5'-CCAACA-3' at 3051, 5'-TCAATA-3' at 3382, 5'-TCTGGA-3' at 3551, 5'-CCTACA-3' at 3575, 5'-TCAGGA-3' at 3864, 5'-CCAAGA-3' at 4074.
  9. inverse complement, negative strand, negative direction is SuccessablesDPEJci--.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 18, 5'-ACATCT-3' at 284, 5'-AGGACC-3' at 596, 5'-ACATCT-3' at 970, 5'-ATGTCT-3' at 1567, 5'-AGAACC-3' at 1649, 5'-AGGACC-3' at 1841, 5'-ACAACT-3' at 1853, 5'-ACGACC-3' at 2326, 5'-ATATCT-3' at 2903, 5'-ACGTCT-3' at 3431, 5'-ATAACC-3' at 3529, 5'-ATGACT-3' at 3542, 5'-AGGTCC-3' at 3585, 5'-AGAACC-3' at 3793, 5'-ACGACC-3' at 3864, 5'-AGGACC-3' at 3906, 5'-ACAACC-3' at 3942, 5'-AGGACC-3' at 4546, and complements.
  10. inverse complement, negative strand, positive direction is SuccessablesDPEJci-+.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 16, 5'-AGGTCC-3' at 218, 5'-AGATCC-3' at 865, 5'-AGATCC-3' at 965, 5'-AGAACC-3' at 1811, 5'-AGAACT-3' at 1951, 5'-AGAACC-3' at 2225, 5'-AGGTCT-3' at 2258, 5'-AGAACC-3' at 2776, 5'-AGGTCT-3' at 3019, 5'-ATGACT-3' at 3029, 5'-ACGTCT-3' at 3256, 5'-ATGTCC-3' at 3577, 5'-AGGTCT-3' at 3771, 5'-ATGACC-3' at 3784, 5'-AGAACT-3' at 4048, 5'-ATGTCC-3' at 4367, and complements.
  11. inverse complement, positive strand, negative direction is SuccessablesDPEJci+-.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 12, 5'-AGATCC-3' at 973, 5'-ATATCC-3' at 1529, 5'-ACATCC-3' at 1572, 5'-ACGTCT-3' at 1774, 5'-ATGACC-3' at 2189, 5'-ATGACT-3' at 2786, 5'-ACAACC-3' at 2844, 5'-ATGTCT-3' at 2986, 5'-AGGACT-3' at 3640, 5'-ATGTCT-3' at 3833, 5'-AGAACC-3' at 4451, 5'-AGATCC-3' at 4476, and complements.
  12. inverse complement, positive strand, positive direction is SuccessablesDPEJci++.bas, looking for 5'-A(C/G/T)(A/G)(A/T)C(C/T)-3', 39, 5'-AGGTCC-3' at 8, 5'-AGGTCT-3' at 15, 5'-AGGTCC-3' at 33, 5'-ACGTCC-3' at 194, 5'-ACGTCT-3' at 438, 5'-ACGTCC-3' at 658, 5'-ATGACT-3' at 1286, 5'-ACGACC-3' at 1736, 5'-ACGACC-3' at 1779, 5'-ACGTCC-3' at 1788, 5'-ACATCC-3' at 1875, 5'-ACGTCT-3' at 1937, 5'-ACAACC-3' at 2185, 5'-AGGACT-3' at 2211, 5'-ACATCC-3' at 2255, 5'-AGGACC-3' at 2501, 5'-ATATCC-3' at 2550, 5'-ACGTCC-3' at 2683, 5'-ACGTCT-3' at 2721, 5'-ACGTCC-3' at 2745, 5'-ACAACC-3' at 2816, 5'-ACGTCT-3' at 2859, 5'-AGGTCC-3' at 3111, 5'-ATGACC-3' at 3117, 5'-AGGACC-3' at 3296, 5'-ACGTCC-3' at 3466, 5'-AGGTCC-3' at 3687, 5'-AGGTCT-3' at 3806, 5'-ACGTCT-3' at 3831, 5'-AGGTCT-3' at 3891, 5'-AGGTCC-3' at 4032, 5'-AGATCT-3' at 4065, 5'-AGATCC-3' at 4077, 5'-AGAACT-3' at 4131, 5'-ATAACT-3' at 4161, 5'-ACGACC-3' at 4177, 5'-AGGACT-3' at 4186, 5'-ACGTCT-3' at 4317, 5'-AGGACC-3' at 4409, and complements.
  13. inverse, negative strand, negative direction, is SuccessablesDPEJi--.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 12, 5'-TCTAGG-3' at 973, 5'-TATAGG-3' at 1529, 5'-TGTAGG-3' at 1572, 5'-TGCAGA-3' at 1774, 5'-TACTGG-3' at 2189, 5'-TACTGA-3' at 2786, 5'-TGTTGG-3' at 2844, 5'-TACAGA-3' at 2986, 5'-TCCTGA-3' at 3640, 5'-TACAGA-3' at 3833, 5'-TCTTGG-3' at 4451, 5'-TCTAGG-3' at 4476.
  14. inverse, negative strand, positive direction, is SuccessablesDPEJi-+.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 39, 5'-TCCAGG-3' at 8, 5'-TCCAGA-3' at 15, 5'-TCCAGG-3' at 33, 5'-TGCAGG-3' at 194, 5'-TGCAGA-3' at 438, 5'-TGCAGG-3' at 658, 5'-TACTGA-3' at 1286, 5'-TGCTGG-3' at 1736, 5'-TGCTGG-3' at 1779, 5'-TGCAGG-3' at 1788, 5'-TGTAGG-3' at 1875, 5'-TGCAGA-3' at 1937, 5'-TGTTGG-3' at 2185, 5'-TCCTGA-3' at 2211, 5'-TGTAGG-3' at 2255, 5'-TCCTGG-3' at 2501, 5'-TATAGG-3' at 2550, 5'-TGCAGG-3' at 2683, 5'-TGCAGA-3' at 2721, 5'-TGCAGG-3' at 2745, 5'-TGTTGG-3' at 2816, 5'-TGCAGA-3' at 2859, 5'-TCCAGG-3' at 3111, 5'-TACTGG-3' at 3117, 5'-TCCTGG-3' at 3296, 5'-TGCAGG-3' at 3466, 5'-TCCAGG-3' at 3687, 5'-TCCAGA-3' at 3806, 5'-TGCAGA-3' at 3831, 5'-TCCAGA-3' at 3891, 5'-TCCAGG-3' at 4032, 5'-TCTAGA-3' at 4065, 5'-TCTAGG-3' at 4077, 5'-TCTTGA-3' at 4131, 5'-TATTGA-3' at 4161, 5'-TGCTGG-3' at 4177, 5'-TCCTGA-3' at 4186, 5'-TGCAGA-3' at 4317, 5'-TCCTGG-3' at 4409.
  15. inverse, positive strand, negative direction, is SuccessablesDPEJi+-.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 18, 5'-TGTAGA-3' at 284, 5'-TCCTGG-3' at 596, 5'-TGTAGA-3' at 970, 5'-TACAGA-3' at 1567, 5'-TCTTGG-3' at 1649, 5'-TCCTGG-3' at 1841, 5'-TGTTGA-3' at 1853, 5'-TGCTGG-3' at 2326, 5'-TATAGA-3' at 2903, 5'-TGCAGA-3' at 3431, 5'-TATTGG-3' at 3529, 5'-TACTGA-3' at 3542, 5'-TCCAGG-3' at 3585, 5'-TCTTGG-3' at 3793, 5'-TGCTGG-3' at 3864, 5'-TCCTGG-3' at 3906, 5'-TGTTGG-3' at 3942, 5'-TCCTGG-3' at 4546.
  16. inverse, positive strand, positive direction, is SuccessablesDPEJi++.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 16, 5'-TCCAGG-3' at 218, 5'-TCTAGG-3' at 865, 5'-TCTAGG-3' at 965, 5'-TCTTGG-3' at 1811, 5'-TCTTGA-3' at 1951, 5'-TCTTGG-3' at 2225, 5'-TCCAGA-3' at 2258, 5'-TCTTGG-3' at 2776, 5'-TCCAGA-3' at 3019, 5'-TACTGA-3' at 3029, 5'-TGCAGA-3' at 3256, 5'-TACAGG-3' at 3577, 5'-TCCAGA-3' at 3771, 5'-TACTGG-3' at 3784, 5'-TCTTGA-3' at 4048, 5'-TACAGG-3' at 4367.

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. ↑ Jennifer E.F. Butler, James T. Kadonaga (October 15, 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development. 16 (20): 2583–92. doi:10.1101/gad.1026202. PMID 12381658.
  2. ↑ 2.0 2.1 2.2 Tamar Juven-Gershon, James T. Kadonaga (March 15, 2010). "Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMC 2830304. PMID 19682982.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 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.
  4. ↑ 4.0 4.1 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.
  5. ↑ 5.0 5.1 T.W. Burke and James T. Kadonaga (15 March 1996). "Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters" (PDF). Genes & Development. 10 (6): 711–724. doi:10.1101/gad.10.6.711. PMID 8598298.
  6. ↑ Kutach, Alan K.; Kadonaga, James T. (July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology. 20 (13): 4754–4764. doi:10.1128/MCB.20.13.4754-4764.2000. PMC 85905. PMID 10848601.
  7. ↑ James T. Kadonaga (September 2002). "The DPE, a core promoter element for transcription by RNA polymerase II" (PDF). Experimental & Molecular Medicine. 34 (4): 259–264. PMID 12515390.
  8. ↑ Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  9. ↑ FlyBase (February 3, 2013). "Antp Antennapedia [ Drosophila melanogaster ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  10. ↑ 10.0 10.1 HGNC (February 5, 2013). "HOXA7 homeobox A7 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  11. ↑ HGNC (February 5, 2013). "HOXA9 homeobox A9 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.

Further reading

External links

{{Phosphate biochemistry}}

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