View source for Downstream promoter element gene transcriptions

'''Editor-In-Chief:''' Henry A. Hoff
[[Image:Core_promoter_elements.svg|thumb|right|250px|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]].<ref name=Butler2002>{{ cite journal
| author = Jennifer E.F. Butler, James T. Kadonaga
| date = October 15, 2002
| title = The RNA polymerase II core promoter: a key component in the regulation of gene expression
| journal = Genes & Development
| volume = 16
| issue = 20
| pages = 2583–92
| doi = 10.1101/gad.1026202
| pmid = 12381658
| url = http://genesdev.cshlp.org/content/16/20/2583.full }}</ref>

"The '''downstream promoter element (DPE)''' is a [[core promoter]] element ... present in other species including humans and excluding ''Saccharomyces cerevisiae''.<ref name=Juven-Gershon2010>{{ cite journal
| author = Tamar Juven-Gershon, James T. Kadonaga
| date = March 15, 2010
| title = Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery
| journal = Developmental Biology
| volume = 339
| issue = 2
| pages = 225–9
| doi = 10.1016/j.ydbio.2009.08.009
| pmid = 19682982
| pmc = 2830304 }}</ref>"<ref name=Downstreampromoterelement/>

"Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II."<ref name=Downstreampromoterelement>{{ cite web
|title=Downstream promoter element
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=May 6, 2012
|url=http://en.wikipedia.org/wiki/Downstream_promoter_element
|accessdate=2012-05-20 }}</ref>
{{clear}}

==Gene transcriptions==
{{main|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."<ref name=Burke1997/>

==Core promoters==
{{main|Core promoter gene transcriptions|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"<ref name=Burke1997/>.

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A<sub>+1</sub> nucleotide in the Inr"<ref name=Smale03/>. It is located about 28–33 [[w:nucleotide|nucleotide]]s downstream of the [[Transcription (genetics)|transcription]] start site.<ref name=Juven-Gershon2010/>

"DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements.<ref name=Burke1996/><ref name=Burke1997>{{ cite journal
| author = Thomas W. Burke and James T. Kadonaga
| title = The downstream core promoter element, DPE, is conserved from ''Drosophila'' to humans and is recognized by TAF<sub>II</sub>60 of ''Drosophila''
| date = November 15, 1997
| journal = Genes & Development
| volume = 11
| issue = 22
| pages = 3020–31
| url=http://genesdev.cshlp.org/content/11/22/3020.long
| doi = 10.1101/gad.11.22.3020
| pmid = 9367984
| pmc = 316699 }}</ref><ref name=Kutach2000>{{cite journal
| last1 = Kutach
| first1 = Alan K.
| last2 = Kadonaga
| first2 = James T.
| date = July 2000
| title = The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters
| journal = Molecular and Cellular Biology
| volume = 20
| issue = 13
| pages = 4754–4764
| doi = 10.1128/MCB.20.13.4754-4764.2000
| pmid = 10848601
| pmc = 85905}}</ref>"<ref name=DownstreamPromoterElement>{{ cite web
|title=Downstream promoter element
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=November 8, 2012
|url=http://en.wikipedia.org/wiki/Downstream_promoter_element
|accessdate=2013-01-23 }}</ref>

==Initiator elements==
{{main|Initiator element gene transcriptions|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."<ref name=Burke1997/>

==Consensus sequences==
{{main|Consensus sequence gene transcriptions|Consensus sequences}}
The early DPE consensus sequence was RGWCGTG.<ref name=Burke1996>{{ cite journal
| author = T.W. Burke and James T. Kadonaga
| date = 15 March 1996
| title = Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters
| journal = Genes & Development
| volume = 10
| issue = 6
| pages = 711–724
| doi = 10.1101/gad.10.6.711
| pmid = 8598298
| url = http://genesdev.cshlp.org/content/10/6/711.full.pdf }}</ref><ref name=Kadonaga2002>{{ cite journal
| author = James T. Kadonaga
| date = September 2002
| title = The DPE, a core promoter element for transcription by RNA polymerase II
| journal = Experimental & Molecular Medicine
| volume = 34
| issue = 4
| pages = 259–264
| doi = 
| pmid = 12515390
| url = http://www.e-emm.or.kr/article/article_files/emm34-4-1.pdf }}</ref>

The DPE consensus sequence is the more general sequence RGWYVT, or (A/G)G(A/T)(C/T)(A/C/G)T.<ref name=Juven-Gershon2010/>

The DPE in "the ATP‐binding cassette subfamily G member 2 gene in the marine pufferfish ''Takifugu rubripes''" is 5'-AGTCTC-3'.<ref name=Matsumoto>{{ cite journal
|author=Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima
|title=Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish ''Takifugu rubripes''
|journal=Fisheries Science
|date=9 August 2020
|volume=86
|issue=
|pages=873-887
|url=https://researchmap.jp/hiroyukiharada/published_papers/29953426/attachment_file.pdf
|arxiv=
|bibcode=
|doi=10.1007/s12562-020-01451-z
|pmid=
|accessdate=27 September 2020 }}</ref>

==DPE-containing promoters==

"The ... ''Drosophila Antennapedia'' P2 (''Antp'' P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus"<ref name=Burke1997/>. GeneID: 40835 Antp Antennapedia [''Drosophila melanogaster''] is also known as Antp P2.<ref name=FlyBase>{{ cite web
|author=FlyBase
|title=Antp Antennapedia [ ''Drosophila melanogaster'' ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=February 3, 2013
|url=http://www.ncbi.nlm.nih.gov/gene/?term=Drosophila+Antennapedia+P2
|accessdate=2013-02-07 }}</ref> 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."<ref name=HGNC>{{ cite web
|author=HGNC
|title=HOXA7 homeobox A7 [ Homo sapiens ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=February 5, 2013
|url=http://www.ncbi.nlm.nih.gov/gene/3204
|accessdate=2013-02-07 }}</ref> As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of ''Drosophila''"<ref name=HGNC/>, 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"<ref name=Burke1997/>. 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."<ref name=HGNC3205>{{ cite web
|author=HGNC
|title=HOXA9 homeobox A9 [ Homo sapiens ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=February 5, 2013
|url=http://www.ncbi.nlm.nih.gov/gene/3205
|accessdate=2013-02-07 }}</ref> GeneID: 3205 may also be TATA-less and have a DPE.

==General transcription factor II Ds==
{{main|General transcription factor II D gene transcriptions|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"<ref name=Smale03>{{ cite journal
|author=Stephen T. Smale and James T. Kadonaga
|title=The RNA Polymerase II Core Promoter
|journal=Annual Review of Biochemistry
|date=July 2003
|volume=72
|issue=1
|pages=449-79
|url=http://www.lps.ens.fr/~monasson/Houches/Kadonaga/CorePromoterAnnuRev2003.pdf
|arxiv=
|bibcode=
|doi=10.1146/annurev.biochem.72.121801.161520
|pmid=12651739
|accessdate=2012-05-07 }}</ref>.

"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."<ref name=Burke1997/>

==Hypotheses==
{{main|Hypotheses}}
# The DPE is not used to transcribe A1BG.

==Samplings==
{{main|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:
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDPEJ--.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 63, 5'-GGACAT-3' at 395, 5'-GGTCGT-3' at 404, 5'-GGTTCT-3' at 420, 5'-AGTCCT-3' at 442, 5'-AGATGT-3' at 482, 5'-GGTCGT-3' at 541, 5'-GGTTCT-3' at 557, 5'-AGTCCT-3' at 579, 5'-GGACAT-3' at 668, 5'-GGTCGT-3' at 677, 5'-AGTCCT-3' at 715, 5'-GGACAT-3' at 802, 5'-GGTCCT-3' at 851, 5'-GGTTCT-3' at 875, 5'-GGACAT-3' at 968, 5'-AGTCCT-3' at 985, 5'-GGACAT-3' at 1132, 5'-GGTCGT-3' at 1141, 5'-GGTTGT-3' at 1204, 5'-AGATGT-3' at 1225, 5'-GGACAT-3' at 1259, 5'-AGTCCT-3' at 1276, 5'-AGATAT-3' at 1526, 5'-GGTCGT-3' at 1612, 5'-AGACAT-3' at 1777, 5'-GGTCGT-3' at 1786, 5'-GGACAT-3' at 1912, 5'-AGTCCT-3' at 2135, 5'-GGTTGT-3' at 2149, 5'-GGTCAT-3' at 2212, 5'-AGTCCT-3' at 2251, 5'-GGACCT-3' at 2269, 5'-GGACAT-3' at 2338, 5'-AGTTAT-3' at 2497, 5'-GGACAT-3' at 2539, 5'-GGTTGT-3' at 2548, 5'-AGTCCT-3' at 2588, 5'-GGTTGT-3' at 2611, 5'-GGACAT-3' at 2673, 5'-GGTTAT-3' at 2849, 5'-AGATGT-3' at 2989, 5'-GGACAT-3' at 3062, 5'-GGTCGT-3' at 3071, 5'-AGTCCT-3' at 3111, 5'-GGTTGT-3' at 3138, 5'-AGTCCT-3' at 3218, 5'-GGTCCT-3' at 3250, 5'-GGTTCT-3' at 3274, 5'-GGTCGT-3' at 3732, 5'-GGACCT-3' at 3745, 5'-AGACCT-3' at 3836, 5'-GGACCT-3' at 3907, 5'-GGACAT-3' at 3971, 5'-GGTTGT-3' at 3980, 5'-GGTTCT-3' at 4020, 5'-AGTTCT-3' at 4028, 5'-AGATGT-3' at 4063, 5'-GGACAT-3' at 4122, 5'-AGTCCT-3' at 4139, 5'-GGTCCT-3' at 4171, 5'-AGTTCT-3' at 4179, 5'-AGATGT-3' at 4213, 5'-AGTCCT-3' at 4437, and complements.
# 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.
# positive strand in the negative direction is SuccessablesDPEJ+-.bas, looking for 5'-(A/G)G(A/T)(C/T)(A/C/G)T-3', 16, 5'-GGATAT-3' at 75, 5'-GGATAT-3' at 109, 5'-AGACAT-3' at 171, 5'-AGATGT-3' at 245, 5'-GGATGT-3' at 785, 5'-AGACAT-3' at 1570, 5'-AGATAT-3' at 1596, 5'-AGACAT-3' at 2881, 5'-AGACAT-3' at 2949, 5'-AGATAT-3' at 2982, 5'-AGACAT-3' at 3434, 5'-AGATAT-3' at 3466, 5'-AGATGT-3' at 3621, 5'-AGACGT-3' at 4236, 5'-AGTTCT-3' at 4418, 5'-AGACAT-3' at 4508, and complements.
# 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.
# 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.
# 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.
# complement, positive strand, negative direction is SuccessablesDPEc+-.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 101, 3'-GGACC-5', 32, 3'-AGATA-5', 57, 3'-GGATA-5', 74, 3'-AGTTG-5', 84, 3'-GGATA-5', 98, 3'-GGATA-5', 108, 3'-AGTCG-5', 157, 3'-AGACA-5', 170, 3'-GGTCA-5', 206, 3'-AGATG-5', 244, 3'-AGTTC-5', 253, 3'-AGACA-5', 422, 3'-GGATC-5', 430, 3'-GGTCA-5', 439, 3'-GGATC-5', 525, 3'-AGACA-5', 559, 3'-GGTCA-5', 568, 3'-GGTCA-5', 576, 3'-AGATC-5', 589, 3'-GGATC-5', 703, 3'-GGTCA-5', 712, 3'-AGTTC-5', 719, 3'-AGACC-5', 725, 3'-GGATG-5', 784, 3'-GGTTG-5', 862, 3'-AGATC-5', 877, 3'-AGATC-5', 972, 3'-GGTTG-5', 1028, 3'-GGACG-5', 1151, 3'-GGATC-5', 1167, 3'-AGTTC-5', 1177, 3'-GGTTG-5', 1319, 3'-AGATG-5', 1438, 3'-AGACA-5', 1569, 3'-AGATA-5', 1595, 3'-GGATC-5', 1812, 3'-AGATG-5', 1828, 3'-AGACC-5', 1834, 3'-AGATC-5', 1987, 3'-GGACA-5', 2117, 3'-AGACC-5', 2121, 3'-AGACC-5', 2145, 3'-AGATA-5', 2177, 3'-GGTTG-5', 2234, 3'-GGATC-5', 2239, 3'-GGTCA-5', 2248, 3'-AGACC-5', 2261, 3'-GGACA-5', 2271, 3'-GGTTG-5', 2398, 3'-AGATC-5', 2413, 3'-AGTCC-5', 2543, 3'-GGATC-5', 2574, 3'-GGTCA-5', 2585, 3'-AGTTG-5', 2592, 3'-AGACC-5', 2598, 3'-AGTTG-5', 2704, 3'-AGTTG-5', 2733, 3'-AGACA-5', 2880, 3'-AGATG-5', 2894, 3'-AGATG-5', 2905, 3'-AGACA-5', 2948, 3'-AGATA-5', 2981, 3'-GGATC-5', 3097, 3'-AGTTG-5', 3115, 3'-AGACC-5', 3121, 3'-GGTTG-5', 3261, 3'-AGATC-5', 3276, 3'-GGACA-5', 3389, 3'-AGACA-5', 3433, 3'-AGATA-5', 3465, 3'-AGATC-5', 3488, 3'-GGTTG-5', 3532, 3'-GGTTG-5', 3605, 3'-AGATG-5', 3620, 3'-AGATG-5', 3627, 3'-GGATA-5', 3655, 3'-GGACA-5', 3756, 3'-AGACC-5', 3761, 3'-GGTTG-5', 3804, 3'-GGTCG-5', 3813, 3'-GGACC-5', 3868, 3'-AGATG-5', 3919, 3'-GGTTG-5', 3945, 3'-GGATC-5', 4006, 3'-AGTTC-5', 4024, 3'-AGACC-5', 4030, 3'-AGTTG-5', 4096, 3'-AGTCC-5', 4126, 3'-GGATC-5', 4157, 3'-AGTTC-5', 4175, 3'-AGACA-5', 4181, 3'-AGACC-5', 4204, 3'-AGACG-5', 4235, 3'-GGATC-5', 4288, 3'-GGTCA-5', 4307, 3'-AGACC-5', 4365, 3'-AGTTC-5', 4417, 3'-GGACA-5', 4468, 3'-AGATC-5', 4475, 3'-AGTCC-5', 4500, 3'-AGACA-5', 4507,
# complement, positive strand, positive direction is SuccessablesDPEc++.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 73, 3'-CCTGG-5' at 37, 3'-CCTAC-5' at 59, 3'-CCAGT-5' at 153, 3'-TCTAC-5' at 166, 3'-TCAGG-5' at 172, 3'-CCTGG-5' at 187, 3'-CCAGG-5' at 218, 3'-CCAAG-5' at 305, 3'-CCTGC-5' at 323, 3'-CCTGC-5' at 359, 3'-TCTGC-5' at 398, 3'-CCTGC-5' at 410, 3'-TCTGG-5' at 440, 3'-TCTGT-5' at 712, 3'-TCAGG-5' at 757, 3'-TCTAG-5' at 864, 3'-TCTAG-5' at 964, 3'-TCAGC-5' at 1528, 3'-CCTGC-5' at 1670, 3'-CCAGC-5' at 1687, 3'-CCTGT-5' at 1693, 3'-TCAGG-5' at 1826, 3'-TCAGG-5' at 1841, 3'-CCTGT-5' at 1869, 3'-CCTAC-5' at 1878, 3'-CCAAG-5' at 1926, 3'-TCAAG-5' at 1987, 3'-TCAGG-5' at 2026, 3'-CCAGT-5' at 2035, 3'-TCAGT-5' at 2100, 3'-TCAAT-5' at 2134, 3'-CCAGT-5' at 2220, 3'-TCTAG-5' at 2230, 3'-CCTAC-5' at 2409, 3'-CCTGT-5' at 2460, 3'-TCAGT-5' at 2607, 3'-TCAGT-5' at 2613, 3'-TCAGT-5' at 2618, 3'-CCTAT-5' at 2659, 3'-TCAAT-5' at 2666, 3'-CCTAC-5' at 2714, 3'-CCTAT-5' at 2737, 3'-TCTGG-5' at 2861, 3'-CCAAG-5' at 2922, 3'-TCAAG-5' at 2954, 3'-TCAGG-5' at 2998, 3'-CCAAT-5' at 3024, 3'-CCAAC-5' at 3050, 3'-TCAGG-5' at 3084, 3'-CCTGT-5' at 3131, 3'-CCTGG-5' at 3172, 3'-TCAGC-5' at 3283, 3'-TCAAT-5' at 3381, 3'-TCTAC-5' at 3418, 3'-CCTAC-5' at 3457, 3'-TCTAC-5' at 3475, 3'-CCAAC-5' at 3490, 3'-CCTGT-5' at 3530, 3'-CCTGG-5' at 3545, 3'-TCTGG-5' at 3550, 3'-CCTAC-5' at 3574, 3'-CCAGT-5' at 3820, 3'-TCAGG-5' at 3863, 3'-TCTGT-5' at 3893, 3'-CCAAG-5' at 4073, 3'-CCTAG-5' at 4080, 3'-CCTAC-5' at 4099, 3'-TCAAG-5' at 4200, 3'-CCTGT-5' at 4252, 3'-CCAGT-5' at 4269, 3'-TCTGC-5' at 4319, 3'-TCTGT-5' at 4332, 3'-CCAGG-5' at 4420.
# inverse complement, negative strand, negative direction is SuccessablesDPEci--.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 174, 3'-TGTCT-5', 13, 3'-TGACT-5', 17, 3'-CAACT-5', 85, 3'-TATCT-5', 100, 3'-CATCC-5', 119, 3'-TGACT-5', 130, 3'-CGACT-5', 140, 3'-TGTCT-5', 168, 3'-GGTCC-5', 262, 3'-CATCT-5', 284, 3'-TGTCT-5', 289, 3'-TGACT-5', 307, 3'-GAACC-5', 328, 3'-TATCT-5', 355, 3'-TGTCC-5', 424, 3'-GGACC-5', 459, 3'-GGACC-5', 508, 3'-TGTCC-5', 561, 3'-CGTCC-5', 565, 3'-TAACT-5', 585, 3'-GGACC-5', 596, 3'-TAACC-5', 643, 3'-GGTCC-5', 648, 3'-CGTCC-5', 697, 3'-GGACT-5', 732, 3'-CGACC-5', 781, 3'-CGACT-5', 825, 3'-CGTCC-5', 831, 3'-GAACT-5', 843, 3'-GGTCC-5', 850, 3'-GGACC-5', 899, 3'-TGTCT-5', 907, 3'-GGTCC-5', 948, 3'-CATCT-5', 970, 3'-CGACT-5', 991, 3'-CGTCC-5', 997, 3'-GAACT-5', 1009, 3'-GGACC-5', 1015, 3'-CGTCT-5', 1023, 3'-TAACC-5', 1045, 3'-TGTCT-5', 1073, 3'-CGACC-5', 1111, 3'-GGACT-5', 1173, 3'-GGACC-5', 1198, 3'-CGACT-5', 1282, 3'-CGTCC-5', 1288, 3'-GAACT-5', 1300, 3'-GATCC-5', 1307, 3'-CGTCT-5', 1314, 3'-GGTCT-5', 1411, 3'-GGTCC-5', 1460, 3'-CGACC-5', 1464, 3'-GGTCT-5', 1518, 3'-TGTCT-5', 1567, 3'-CGTCT-5', 1614, 3'-GGACT-5', 1623, 3'-GAACC-5', 1649, 3'-CATCT-5', 1653, 3'-GGTCT-5', 1670, 3'-TATCT-5', 1710, 3'-CGACC-5', 1746, 3'-CGACC-5', 1756, 3'-CGACT-5', 1800, 3'-CGTCC-5', 1823, 3'-GGACC-5', 1841, 3'-CAACT-5', 1853, 3'-CGACC-5', 1891, 3'-GAACC-5', 1927, 3'-TGACT-5', 1935, 3'-CGTCC-5', 1941, 3'-GGACC-5', 1959, 3'-CGTCT-5', 1967, 3'-GGACC-5', 2009, 3'-TGTCT-5', 2017, 3'-CGACC-5', 2069, 3'-GGTCC-5', 2077, 3'-CGACT-5', 2109, 3'-TGTCT-5', 2119, 3'-GAACT-5', 2127, 3'-CGACT-5', 2226, 3'-CAACC-5', 2235, 3'-GGACC-5', 2268, 3'-CGACC-5', 2326, 3'-CGACT-5', 2361, 3'-CGTCC-5', 2367, 3'-GAACT-5', 2379, 3'-GGACC-5', 2385, 3'-CGTCC-5', 2389, 3'-GGACC-5', 2435, 3'-TGTCT-5', 2443, 3'-TGTCC-5', 2514, 3'-GGTCC-5', 2519, 3'-CGACT-5', 2562, 3'-CGTCC-5', 2568, 3'-GAACT-5', 2580, 3'-CAACT-5', 2593, 3'-TGTCC-5', 2689, 3'-CGACT-5', 2696, 3'-CAACT-5', 2705, 3'-GAACT-5', 2714, 3'-GGACC-5', 2720, 3'-CGACT-5', 2744, 3'-GGACC-5', 2770, 3'-TGTCT-5', 2778, 3'-TGTCT-5', 2878, 3'-TATCT-5', 2903, 3'-GAACC-5', 2921, 3'-CGACC-5', 3035, 3'-CGACC-5', 3041, 3'-CGACT-5', 3085, 3'-GAACT-5', 3103, 3'-CAACC-5', 3116, 3'-GGACC-5', 3128, 3'-CGACC-5', 3180, 3'-CGACT-5', 3224, 3'-GAACT-5', 3242, 3'-GGTCC-5', 3249, 3'-CATCT-5', 3256, 3'-GGACC-5', 3298, 3'-TAACT-5', 3358, 3'-GAACT-5', 3401, 3'-TATCT-5', 3422, 3'-CGTCT-5', 3431, 3'-TATCC-5', 3447, 3'-GATCT-5', 3463, 3'-GGTCT-5', 3486, 3'-CAACT-5', 3505, 3'-TAACC-5', 3529, 3'-CAACT-5', 3533, 3'-TGACT-5', 3542, 3'-GGTCC-5', 3564, 3'-GAACT-5', 3571, 3'-GGTCC-5', 3585, 3'-CGTCT-5', 3589, 3'-CAACC-5', 3606, 3'-CGACT-5', 3649, 3'-TGTCT-5', 3672, 3'-CGACC-5', 3719, 3'-GGACC-5', 3744, 3'-TGACC-5', 3749, 3'-GGACT-5', 3781, 3'-GAACC-5', 3793, 3'-CAACT-5', 3805, 3'-CATCT-5', 3820, 3'-CGACC-5', 3864, 3'-GGTCC-5', 3871, 3'-GGTCC-5', 3885, 3'-GGACC-5', 3906, 3'-TGTCT-5', 3917, 3'-GGACT-5', 3932, 3'-CAACC-5', 3942, 3'-CAACC-5', 3946, 3'-GGTCC-5', 3951, 3'-CGACT-5', 3994, 3'-GAACT-5', 4012, 3'-GGACC-5', 4037, 3'-TATCT-5', 4079, 3'-CAACC-5', 4097, 3'-GGTCC-5', 4102, 3'-CGACT-5', 4145, 3'-GGTCC-5', 4170, 3'-GAACC-5', 4188, 3'-GGTCT-5', 4233, 3'-GGTCC-5', 4253, 3'-GAACC-5', 4268, 3'-CGACT-5', 4276, 3'-CGTCC-5', 4282, 3'-GAACT-5', 4294, 3'-GGACC-5', 4300, 3'-GGACC-5', 4349, 3'-GGTCT-5', 4448, 3'-GGACC-5', 4494, 3'-TGTCT-5', 4518, 3'-GGACC-5', 4546,
# inverse complement, negative strand, positive direction is SuccessablesDPEci-+.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 95, 3'-CATCC-5' at 30, 3'-GGACC-5' at 37, 3'-TGTCC-5' at 82, 3'-TGTCT-5' at 100, 3'-GGACC-5' at 187, 3'-GGTCC-5' at 218, 3'-TGTCT-5' at 268, 3'-CAACC-5' at 608, 3'-CATCC-5' at 629, 3'-CATCC-5' at 698, 3'-GGACT-5' at 746, 3'-GGACT-5' at 814, 3'-CAACC-5' at 844, 3'-GATCC-5' at 865, 3'-TGTCC-5' at 893, 3'-CGACT-5' at 898, 3'-GGACT-5' at 914, 3'-CAACC-5' at 944, 3'-GATCC-5' at 965, 3'-TGTCC-5' at 993, 3'-CGACT-5' at 998, 3'-CAACC-5' at 1280, 3'-CGTCT-5' at 1393, 3'-CGTCT-5' at 1493, 3'-CAACC-5' at 1616, 3'-TGACC-5' at 1662, 3'-GGTCT-5' at 1711, 3'-TGTCT-5' at 1731, 3'-GAACC-5' at 1811, 3'-TGTCT-5' at 1862, 3'-CGTCC-5' at 1930, 3'-GAACT-5' at 1951, 3'-GGTCT-5' at 1958, 3'-CAACC-5' at 2013, 3'-TGTCT-5' at 2078, 3'-CATCT-5' at 2111, 3'-CAACC-5' at 2120, 3'-TGTCT-5' at 2172, 3'-TGACC-5' at 2213, 3'-GAACC-5' at 2225, 3'-GGTCT-5' at 2258, 3'-GGACT-5' at 2271, 3'-CGACT-5' at 2359, 3'-GATCC-5' at 2378, 3'-TGTCT-5' at 2466, 3'-GGTCT-5' at 2489, 3'-GATCC-5' at 2514, 3'-GAACC-5' at 2579, 3'-GGACT-5' at 2672, 3'-GAACC-5' at 2776, 3'-GGACT-5' at 2820, 3'-CATCT-5' at 2852, 3'-TGACC-5' at 2873, 3'-GGTCT-5' at 2941, 3'-TGACT-5' at 2945, 3'-TGTCT-5' at 3004, 3'-GGTCT-5' at 3019, 3'-TGACT-5' at 3029, 3'-TGTCT-5' at 3053, 3'-CATCC-5' at 3108, 3'-GGACC-5' at 3172, 3'-CGTCC-5' at 3203, 3'-GGTCT-5' at 3245, 3'-CGTCT-5' at 3256, 3'-CAACT-5' at 3291, 3'-GGTCT-5' at 3299, 3'-CATCT-5' at 3329, 3'-TATCC-5' at 3384, 3'-TGTCT-5' at 3392, 3'-CATCT-5' at 3403, 3'-GGACC-5' at 3545, 3'-TGTCC-5' at 3577, 3'-GGTCT-5' at 3608, 3'-TGTCC-5' at 3619, 3'-CATCC-5' at 3629, 3'-TGACC-5' at 3714, 3'-TAACT-5' at 3733, 3'-GGTCT-5' at 3771, 3'-TGACC-5' at 3784, 3'-CGACT-5' at 3801, 3'-GAACC-5' at 3838, 3'-GAACC-5' at 3856, 3'-CAACC-5' at 3911, 3'-GAACC-5' at 3937, 3'-TGACC-5' at 4018, 3'-GAACT-5' at 4048, 3'-CGTCT-5' at 4056, 3'-GATCC-5' at 4081, 3'-CATCC-5' at 4183, 3'-TGACC-5' at 4216, 3'-CGACC-5' at 4358, 3'-TGTCC-5' at 4367, 3'-GGTCT-5' at 4380, 3'-GGTCT-5' at 4414, 3'-GGTCC-5' at 4420.
# inverse complement, positive strand, negative direction is SuccessablesDPEci+-.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 58, 3'-GGACC-5', 32, 3'-TGTCT-5', 479, 3'-CATCC-5', 593, 3'-TAACC-5', 614, 3'-TGACC-5', 734, 3'-CGTCT-5', 754, 3'-GAACC-5', 846, 3'-TGTCT-5', 921, 3'-GATCC-5', 973, 3'-GAACC-5', 1012, 3'-TGACT-5', 1051, 3'-TGTCT-5', 1087, 3'-CGACC-5', 1191, 3'-TGTCT-5', 1222, 3'-GAACC-5', 1303, 3'-CAACC-5', 1407, 3'-GATCT-5', 1482, 3'-CAACC-5', 1514, 3'-TATCC-5', 1529, 3'-CATCC-5', 1572, 3'-GAACT-5', 1685, 3'-TATCT-5', 1731, 3'-CGTCT-5', 1774, 3'-GATCC-5', 1813, 3'-CATCC-5', 1838, 3'-CATCT-5', 1863, 3'-GAACC-5', 1956, 3'-TGTCT-5', 2031, 3'-TGTCT-5', 2165, 3'-TGACC-5', 2189, 3'-CATCT-5', 2290, 3'-GAACC-5', 2382, 3'-GAACC-5', 2717, 3'-TGACT-5', 2786, 3'-CAACC-5', 2844, 3'-CAACT-5', 2911, 3'-TGTCT-5', 2986, 3'-CATCT-5', 3154, 3'-GAACC-5', 3245, 3'-TGTCT-5', 3321, 3'-GAACT-5', 3460, 3'-CAACT-5', 3524, 3'-CATCT-5', 3551, 3'-GGACT-5', 3640, 3'-CGTCC-5', 3698, 3'-GGACT-5', 3747, 3'-GAACC-5', 3784, 3'-TGTCT-5', 3833, 3'-CAACT-5', 3849, 3'-GGACC-5', 3868, 3'-CATCC-5', 3903, 3'-CATCT-5', 4058, 3'-TGTCT-5', 4210, 3'-GGACT-5', 4327, 3'-TGTCT-5', 4371, 3'-GAACC-5', 4451, 3'-CATCC-5', 4456, 3'-GATCC-5', 4476,
# inverse complement, positive strand, positive direction is SuccessablesDPEci++.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 152, 3'-GGTCC-5' at 8, 3'-GGTCT-5' at 15, 3'-TAACC-5' at 24, 3'-GGTCC-5' at 33, 3'-GGACC-5' at 40, 3'-TGTCC-5' at 157, 3'-CGTCC-5' at 194, 3'-GGTCT-5' at 204, 3'-GGTCC-5' at 215, 3'-CGACC-5' at 277, 3'-GGACC-5' at 286, 3'-CGTCC-5' at 318, 3'-TGACC-5' at 347, 3'-TGTCC-5' at 365, 3'-CGTCC-5' at 379, 3'-CGACC-5' at 386, 3'-CGTCT-5' at 396, 3'-CGACC-5' at 417, 3'-GGTCC-5' at 424, 3'-CGTCT-5' at 438, 3'-GGTCT-5' at 468, 3'-GGTCC-5' at 515, 3'-TGTCC-5' at 552, 3'-GGACC-5' at 598, 3'-CGTCC-5' at 658, 3'-GGTCC-5' at 707, 3'-GGACT-5' at 725, 3'-CGACC-5' at 779, 3'-GGTCT-5' at 835, 3'-GGACC-5' at 847, 3'-GGACT-5' at 859, 3'-GGTCT-5' at 935, 3'-GGACC-5' at 947, 3'-GGACT-5' at 959, 3'-TGACC-5' at 1140, 3'-GGTCC-5' at 1175, 3'-GGACC-5' at 1199, 3'-TGACT-5' at 1286, 3'-CGTCT-5' at 1316, 3'-CGTCT-5' at 1416, 3'-GGTCT-5' at 1631, 3'-GGACT-5' at 1660, 3'-GGACT-5' at 1676, 3'-CGACC-5' at 1736, 3'-GGTCT-5' at 1742, 3'-CGACC-5' at 1779, 3'-CGTCC-5' at 1788, 3'-GAACC-5' at 1799, 3'-GGACC-5' at 1815, 3'-GGTCC-5' at 1855, 3'-CATCC-5' at 1875, 3'-GGTCC-5' at 1893, 3'-CGTCC-5' at 1905, 3'-CGTCT-5' at 1937, 3'-TGACC-5' at 1953, 3'-TGTCC-5' at 1966, 3'-TGTCC-5' at 2125, 3'-CAACC-5' at 2185, 3'-GGACT-5' at 2211, 3'-GGTCT-5' at 2228, 3'-CATCC-5' at 2255, 3'-CGTCC-5' at 2296, 3'-GGTCC-5' at 2316, 3'-CGACC-5' at 2320, 3'-CGACC-5' at 2405, 3'-TGTCT-5' at 2414, 3'-GGACC-5' at 2433, 3'-GATCC-5' at 2482, 3'-GGACC-5' at 2501, 3'-CAACC-5' at 2541, 3'-TATCC-5' at 2550, 3'-GGACC-5' at 2569, 3'-GGTCC-5' at 2574, 3'-TATCT-5' at 2627, 3'-GATCC-5' at 2639, 3'-TGTCT-5' at 2652, 3'-TGACT-5' at 2674, 3'-CGTCC-5' at 2683, 3'-CGTCT-5' at 2721, 3'-CGACC-5' at 2734, 3'-CGTCC-5' at 2745, 3'-CGACC-5' at 2770, 3'-GGTCC-5' at 2780, 3'-CGACC-5' at 2810, 3'-CAACC-5' at 2816, 3'-TGTCT-5' at 2837, 3'-CGTCT-5' at 2859, 3'-GGTCC-5' at 2876, 3'-GGACC-5' at 2891, 3'-CGACT-5' at 2915, 3'-GGACT-5' at 2968, 3'-GGACC-5' at 2988, 3'-GGTCC-5' at 3016, 3'-GGACC-5' at 3047, 3'-GGTCT-5' at 3091, 3'-GGTCC-5' at 3111, 3'-TGACC-5' at 3117, 3'-CGTCC-5' at 3128, 3'-TGTCT-5' at 3133, 3'-CGTCC-5' at 3147, 3'-TGTCT-5' at 3179, 3'-CGTCT-5' at 3214, 3'-GGTCT-5' at 3221, 3'-CGACC-5' at 3242, 3'-GGACC-5' at 3296, 3'-TGACC-5' at 3345, 3'-GGACC-5' at 3362, 3'-CATCT-5' at 3416, 3'-CGTCC-5' at 3466, 3'-CGTCT-5' at 3473, 3'-GATCC-5' at 3484, 3'-GGACC-5' at 3496, 3'-GATCC-5' at 3522, 3'-CGACC-5' at 3526, 3'-GGTCC-5' at 3536, 3'-GGTCT-5' at 3548, 3'-TGTCC-5' at 3571, 3'-CGACT-5' at 3588, 3'-TGTCC-5' at 3636, 3'-CGTCC-5' at 3662, 3'-GGACC-5' at 3679, 3'-GGTCC-5' at 3687, 3'-CGTCC-5' at 3694, 3'-TGACT-5' at 3735, 3'-CATCC-5' at 3753, 3'-GGACC-5' at 3758, 3'-CGTCC-5' at 3768, 3'-CGACT-5' at 3778, 3'-GGACC-5' at 3787, 3'-GGTCT-5' at 3806, 3'-CGTCT-5' at 3831, 3'-GGTCT-5' at 3891, 3'-CGTCT-5' at 3916, 3'-TGTCC-5' at 3975, 3'-CGACC-5' at 3989, 3'-GAACT-5' at 4016, 3'-GGTCC-5' at 4032, 3'-CATCT-5' at 4036, 3'-GATCT-5' at 4065, 3'-TGTCC-5' at 4070, 3'-GATCC-5' at 4077, 3'-TGACT-5' at 4089, 3'-GAACT-5' at 4131, 3'-TAACT-5' at 4161, 3'-CGACC-5' at 4177, 3'-GGACT-5' at 4186, 3'-GGACT-5' at 4214, 3'-GAACC-5' at 4300, 3'-CGTCT-5' at 4317, 3'-GGTCT-5' at 4330, 3'-GGACC-5' at 4409, 3'-GGACC-5' at 4424.
# inverse, negative strand, negative direction, is SuccessablesDPEi--.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 58, 3'-CCTGG-5', 32, 3'-ACAGA-5', 479, 3'-GTAGG-5', 593, 3'-ATTGG-5', 614, 3'-ACTGG-5', 734, 3'-GCAGA-5', 754, 3'-CTTGG-5', 846, 3'-ACAGA-5', 921, 3'-CTAGG-5', 973, 3'-CTTGG-5', 1012, 3'-ACTGA-5', 1051, 3'-ACAGA-5', 1087, 3'-GCTGG-5', 1191, 3'-ACAGA-5', 1222, 3'-CTTGG-5', 1303, 3'-GTTGG-5', 1407, 3'-CTAGA-5', 1482, 3'-GTTGG-5', 1514, 3'-ATAGG-5', 1529, 3'-GTAGG-5', 1572, 3'-CTTGA-5', 1685, 3'-ATAGA-5', 1731, 3'-GCAGA-5', 1774, 3'-CTAGG-5', 1813, 3'-GTAGG-5', 1838, 3'-GTAGA-5', 1863, 3'-CTTGG-5', 1956, 3'-ACAGA-5', 2031, 3'-ACAGA-5', 2165, 3'-ACTGG-5', 2189, 3'-GTAGA-5', 2290, 3'-CTTGG-5', 2382, 3'-CTTGG-5', 2717, 3'-ACTGA-5', 2786, 3'-GTTGG-5', 2844, 3'-GTTGA-5', 2911, 3'-ACAGA-5', 2986, 3'-GTAGA-5', 3154, 3'-CTTGG-5', 3245, 3'-ACAGA-5', 3321, 3'-CTTGA-5', 3460, 3'-GTTGA-5', 3524, 3'-GTAGA-5', 3551, 3'-CCTGA-5', 3640, 3'-GCAGG-5', 3698, 3'-CCTGA-5', 3747, 3'-CTTGG-5', 3784, 3'-ACAGA-5', 3833, 3'-GTTGA-5', 3849, 3'-CCTGG-5', 3868, 3'-GTAGG-5', 3903, 3'-GTAGA-5', 4058, 3'-ACAGA-5', 4210, 3'-CCTGA-5', 4327, 3'-ACAGA-5', 4371, 3'-CTTGG-5', 4451, 3'-GTAGG-5', 4456, 3'-CTAGG-5', 4476,
# inverse, negative strand, positive direction, is SuccessablesDPEi-+.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 152 , 3'-CCAGG-5' at 8 , 3'-CCAGA-5' at 15 , 3'-ATTGG-5' at 24 , 3'-CCAGG-5' at 33 , 3'-CCTGG-5' at 40 , 3'-ACAGG-5' at 157 , 3'-GCAGG-5' at 194 , 3'-CCAGA-5' at 204 , 3'-CCAGG-5' at 215 , 3'-GCTGG-5' at 277 , 3'-CCTGG-5' at 286 , 3'-GCAGG-5' at 318 , 3'-ACTGG-5' at 347 , 3'-ACAGG-5' at 365 , 3'-GCAGG-5' at 379 , 3'-GCTGG-5' at 386 , 3'-GCAGA-5' at 396 , 3'-GCTGG-5' at 417 , 3'-CCAGG-5' at 424 , 3'-GCAGA-5' at 438 , 3'-CCAGA-5' at 468 , 3'-CCAGG-5' at 515 , 3'-ACAGG-5' at 552 , 3'-CCTGG-5' at 598 , 3'-GCAGG-5' at 658 , 3'-CCAGG-5' at 707 , 3'-CCTGA-5' at 725 , 3'-GCTGG-5' at 779 , 3'-CCAGA-5' at 835 , 3'-CCTGG-5' at 847 , 3'-CCTGA-5' at 859 , 3'-CCAGA-5' at 935 , 3'-CCTGG-5' at 947 , 3'-CCTGA-5' at 959 , 3'-ACTGG-5' at 1140 , 3'-CCAGG-5' at 1175 , 3'-CCTGG-5' at 1199 , 3'-ACTGA-5' at 1286 , 3'-GCAGA-5' at 1316 , 3'-GCAGA-5' at 1416 , 3'-CCAGA-5' at 1631 , 3'-CCTGA-5' at 1660 , 3'-CCTGA-5' at 1676 , 3'-GCTGG-5' at 1736 , 3'-CCAGA-5' at 1742 , 3'-GCTGG-5' at 1779 , 3'-GCAGG-5' at 1788 , 3'-CTTGG-5' at 1799 , 3'-CCTGG-5' at 1815 , 3'-CCAGG-5' at 1855 , 3'-GTAGG-5' at 1875 , 3'-CCAGG-5' at 1893 , 3'-GCAGG-5' at 1905 , 3'-GCAGA-5' at 1937 , 3'-ACTGG-5' at 1953 , 3'-ACAGG-5' at 1966 , 3'-ACAGG-5' at 2125 , 3'-GTTGG-5' at 2185 , 3'-CCTGA-5' at 2211 , 3'-CCAGA-5' at 2228 , 3'-GTAGG-5' at 2255 , 3'-GCAGG-5' at 2296 , 3'-CCAGG-5' at 2316 , 3'-GCTGG-5' at 2320 , 3'-GCTGG-5' at 2405 , 3'-ACAGA-5' at 2414 , 3'-CCTGG-5' at 2433 , 3'-CTAGG-5' at 2482 , 3'-CCTGG-5' at 2501 , 3'-GTTGG-5' at 2541 , 3'-ATAGG-5' at 2550 , 3'-CCTGG-5' at 2569 , 3'-CCAGG-5' at 2574 , 3'-ATAGA-5' at 2627 , 3'-CTAGG-5' at 2639 , 3'-ACAGA-5' at 2652 , 3'-ACTGA-5' at 2674 , 3'-GCAGG-5' at 2683 , 3'-GCAGA-5' at 2721 , 3'-GCTGG-5' at 2734 , 3'-GCAGG-5' at 2745 , 3'-GCTGG-5' at 2770 , 3'-CCAGG-5' at 2780 , 3'-GCTGG-5' at 2810 , 3'-GTTGG-5' at 2816 , 3'-ACAGA-5' at 2837 , 3'-GCAGA-5' at 2859 , 3'-CCAGG-5' at 2876 , 3'-CCTGG-5' at 2891 , 3'-GCTGA-5' at 2915 , 3'-CCTGA-5' at 2968 , 3'-CCTGG-5' at 2988 , 3'-CCAGG-5' at 3016 , 3'-CCTGG-5' at 3047 , 3'-CCAGA-5' at 3091 , 3'-CCAGG-5' at 3111 , 3'-ACTGG-5' at 3117 , 3'-GCAGG-5' at 3128 , 3'-ACAGA-5' at 3133 , 3'-GCAGG-5' at 3147 , 3'-ACAGA-5' at 3179 , 3'-GCAGA-5' at 3214 , 3'-CCAGA-5' at 3221 , 3'-GCTGG-5' at 3242 , 3'-CCTGG-5' at 3296 , 3'-ACTGG-5' at 3345 , 3'-CCTGG-5' at 3362 , 3'-GTAGA-5' at 3416 , 3'-GCAGG-5' at 3466 , 3'-GCAGA-5' at 3473 , 3'-CTAGG-5' at 3484 , 3'-CCTGG-5' at 3496 , 3'-CTAGG-5' at 3522 , 3'-GCTGG-5' at 3526 , 3'-CCAGG-5' at 3536 , 3'-CCAGA-5' at 3548 , 3'-ACAGG-5' at 3571 , 3'-GCTGA-5' at 3588 , 3'-ACAGG-5' at 3636 , 3'-GCAGG-5' at 3662 , 3'-CCTGG-5' at 3679 , 3'-CCAGG-5' at 3687 , 3'-GCAGG-5' at 3694 , 3'-ACTGA-5' at 3735 , 3'-GTAGG-5' at 3753 , 3'-CCTGG-5' at 3758 , 3'-GCAGG-5' at 3768 , 3'-GCTGA-5' at 3778 , 3'-CCTGG-5' at 3787 , 3'-CCAGA-5' at 3806 , 3'-GCAGA-5' at 3831 , 3'-CCAGA-5' at 3891 , 3'-GCAGA-5' at 3916 , 3'-ACAGG-5' at 3975 , 3'-GCTGG-5' at 3989 , 3'-CTTGA-5' at 4016 , 3'-CCAGG-5' at 4032 , 3'-GTAGA-5' at 4036 , 3'-CTAGA-5' at 4065 , 3'-ACAGG-5' at 4070 , 3'-CTAGG-5' at 4077 , 3'-ACTGA-5' at 4089 , 3'-CTTGA-5' at 4131 , 3'-ATTGA-5' at 4161 , 3'-GCTGG-5' at 4177 , 3'-CCTGA-5' at 4186 , 3'-CCTGA-5' at 4214 , 3'-CTTGG-5' at 4300 , 3'-GCAGA-5' at 4317 , 3'-CCAGA-5' at 4330 , 3'-CCTGG-5' at 4409 , 3'-CCTGG-5' at 4424.
# inverse, positive strand, negative direction, is SuccessablesDPEi+-.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 174, 3'-ACAGA-5', 13, 3'-ACTGA-5', 17, 3'-GTTGA-5', 85, 3'-ATAGA-5', 100, 3'-GTAGG-5', 119, 3'-ACTGA-5', 130, 3'-GCTGA-5', 140, 3'-ACAGA-5', 168, 3'-CCAGG-5', 262, 3'-GTAGA-5', 284, 3'-ACAGA-5', 289, 3'-ACTGA-5', 307, 3'-CTTGG-5', 328, 3'-ATAGA-5', 355, 3'-ACAGG-5', 424, 3'-CCTGG-5', 459, 3'-CCTGG-5', 508, 3'-ACAGG-5', 561, 3'-GCAGG-5', 565, 3'-ATTGA-5', 585, 3'-CCTGG-5', 596, 3'-ATTGG-5', 643, 3'-CCAGG-5', 648, 3'-GCAGG-5', 697, 3'-CCTGA-5', 732, 3'-GCTGG-5', 781, 3'-GCTGA-5', 825, 3'-GCAGG-5', 831, 3'-CTTGA-5', 843, 3'-CCAGG-5', 850, 3'-CCTGG-5', 899, 3'-ACAGA-5', 907, 3'-CCAGG-5', 948, 3'-GTAGA-5', 970, 3'-GCTGA-5', 991, 3'-GCAGG-5', 997, 3'-CTTGA-5', 1009, 3'-CCTGG-5', 1015, 3'-GCAGA-5', 1023, 3'-ATTGG-5', 1045, 3'-ACAGA-5', 1073, 3'-GCTGG-5', 1111, 3'-CCTGA-5', 1173, 3'-CCTGG-5', 1198, 3'-GCTGA-5', 1282, 3'-GCAGG-5', 1288, 3'-CTTGA-5', 1300, 3'-CTAGG-5', 1307, 3'-GCAGA-5', 1314, 3'-CCAGA-5', 1411, 3'-CCAGG-5', 1460, 3'-GCTGG-5', 1464, 3'-CCAGA-5', 1518, 3'-ACAGA-5', 1567, 3'-GCAGA-5', 1614, 3'-CCTGA-5', 1623, 3'-CTTGG-5', 1649, 3'-GTAGA-5', 1653, 3'-CCAGA-5', 1670, 3'-ATAGA-5', 1710, 3'-GCTGG-5', 1746, 3'-GCTGG-5', 1756, 3'-GCTGA-5', 1800, 3'-GCAGG-5', 1823, 3'-CCTGG-5', 1841, 3'-GTTGA-5', 1853, 3'-GCTGG-5', 1891, 3'-CTTGG-5', 1927, 3'-ACTGA-5', 1935, 3'-GCAGG-5', 1941, 3'-CCTGG-5', 1959, 3'-GCAGA-5', 1967, 3'-CCTGG-5', 2009, 3'-ACAGA-5', 2017, 3'-GCTGG-5', 2069, 3'-CCAGG-5', 2077, 3'-GCTGA-5', 2109, 3'-ACAGA-5', 2119, 3'-CTTGA-5', 2127, 3'-GCTGA-5', 2226, 3'-GTTGG-5', 2235, 3'-CCTGG-5', 2268, 3'-GCTGG-5', 2326, 3'-GCTGA-5', 2361, 3'-GCAGG-5', 2367, 3'-CTTGA-5', 2379, 3'-CCTGG-5', 2385, 3'-GCAGG-5', 2389, 3'-CCTGG-5', 2435, 3'-ACAGA-5', 2443, 3'-ACAGG-5', 2514, 3'-CCAGG-5', 2519, 3'-GCTGA-5', 2562, 3'-GCAGG-5', 2568, 3'-CTTGA-5', 2580, 3'-GTTGA-5', 2593, 3'-ACAGG-5', 2689, 3'-GCTGA-5', 2696, 3'-GTTGA-5', 2705, 3'-CTTGA-5', 2714, 3'-CCTGG-5', 2720, 3'-GCTGA-5', 2744, 3'-CCTGG-5', 2770, 3'-ACAGA-5', 2778, 3'-ACAGA-5', 2878, 3'-ATAGA-5', 2903, 3'-CTTGG-5', 2921, 3'-GCTGG-5', 3035, 3'-GCTGG-5', 3041, 3'-GCTGA-5', 3085, 3'-CTTGA-5', 3103, 3'-GTTGG-5', 3116, 3'-CCTGG-5', 3128, 3'-GCTGG-5', 3180, 3'-GCTGA-5', 3224, 3'-CTTGA-5', 3242, 3'-CCAGG-5', 3249, 3'-GTAGA-5', 3256, 3'-CCTGG-5', 3298, 3'-ATTGA-5', 3358, 3'-CTTGA-5', 3401, 3'-ATAGA-5', 3422, 3'-GCAGA-5', 3431, 3'-ATAGG-5', 3447, 3'-CTAGA-5', 3463, 3'-CCAGA-5', 3486, 3'-GTTGA-5', 3505, 3'-ATTGG-5', 3529, 3'-GTTGA-5', 3533, 3'-ACTGA-5', 3542, 3'-CCAGG-5', 3564, 3'-CTTGA-5', 3571, 3'-CCAGG-5', 3585, 3'-GCAGA-5', 3589, 3'-GTTGG-5', 3606, 3'-GCTGA-5', 3649, 3'-ACAGA-5', 3672, 3'-GCTGG-5', 3719, 3'-CCTGG-5', 3744, 3'-ACTGG-5', 3749, 3'-CCTGA-5', 3781, 3'-CTTGG-5', 3793, 3'-GTTGA-5', 3805, 3'-GTAGA-5', 3820, 3'-GCTGG-5', 3864, 3'-CCAGG-5', 3871, 3'-CCAGG-5', 3885, 3'-CCTGG-5', 3906, 3'-ACAGA-5', 3917, 3'-CCTGA-5', 3932, 3'-GTTGG-5', 3942, 3'-GTTGG-5', 3946, 3'-CCAGG-5', 3951, 3'-GCTGA-5', 3994, 3'-CTTGA-5', 4012, 3'-CCTGG-5', 4037, 3'-ATAGA-5', 4079, 3'-GTTGG-5', 4097, 3'-CCAGG-5', 4102, 3'-GCTGA-5', 4145, 3'-CCAGG-5', 4170, 3'-CTTGG-5', 4188, 3'-CCAGA-5', 4233, 3'-CCAGG-5', 4253, 3'-CTTGG-5', 4268, 3'-GCTGA-5', 4276, 3'-GCAGG-5', 4282, 3'-CTTGA-5', 4294, 3'-CCTGG-5', 4300, 3'-CCTGG-5', 4349, 3'-CCAGA-5', 4448, 3'-CCTGG-5', 4494, 3'-ACAGA-5', 4518, 3'-CCTGG-5', 4546,
# inverse, positive strand, positive direction, is SuccessablesDPEi++.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 95, 3'-GTAGG-5' at 30, 3'-CCTGG-5' at 37, 3'-ACAGG-5' at 82, 3'-ACAGA-5' at 100, 3'-CCTGG-5' at 187, 3'-CCAGG-5' at 218, 3'-ACAGA-5' at 268, 3'-GTTGG-5' at 608, 3'-GTAGG-5' at 629, 3'-GTAGG-5' at 698, 3'-CCTGA-5' at 746, 3'-CCTGA-5' at 814, 3'-GTTGG-5' at 844, 3'-CTAGG-5' at 865, 3'-ACAGG-5' at 893, 3'-GCTGA-5' at 898, 3'-CCTGA-5' at 914, 3'-GTTGG-5' at 944, 3'-CTAGG-5' at 965, 3'-ACAGG-5' at 993, 3'-GCTGA-5' at 998, 3'-GTTGG-5' at 1280, 3'-GCAGA-5' at 1393, 3'-GCAGA-5' at 1493, 3'-GTTGG-5' at 1616, 3'-ACTGG-5' at 1662, 3'-CCAGA-5' at 1711, 3'-ACAGA-5' at 1731, 3'-CTTGG-5' at 1811, 3'-ACAGA-5' at 1862, 3'-GCAGG-5' at 1930, 3'-CTTGA-5' at 1951, 3'-CCAGA-5' at 1958, 3'-GTTGG-5' at 2013, 3'-ACAGA-5' at 2078, 3'-GTAGA-5' at 2111, 3'-GTTGG-5' at 2120, 3'-ACAGA-5' at 2172, 3'-ACTGG-5' at 2213, 3'-CTTGG-5' at 2225, 3'-CCAGA-5' at 2258, 3'-CCTGA-5' at 2271, 3'-GCTGA-5' at 2359, 3'-CTAGG-5' at 2378, 3'-ACAGA-5' at 2466, 3'-CCAGA-5' at 2489, 3'-CTAGG-5' at 2514, 3'-CTTGG-5' at 2579, 3'-CCTGA-5' at 2672, 3'-CTTGG-5' at 2776, 3'-CCTGA-5' at 2820, 3'-GTAGA-5' at 2852, 3'-ACTGG-5' at 2873, 3'-CCAGA-5' at 2941, 3'-ACTGA-5' at 2945, 3'-ACAGA-5' at 3004, 3'-CCAGA-5' at 3019, 3'-ACTGA-5' at 3029, 3'-ACAGA-5' at 3053, 3'-GTAGG-5' at 3108, 3'-CCTGG-5' at 3172, 3'-GCAGG-5' at 3203, 3'-CCAGA-5' at 3245, 3'-GCAGA-5' at 3256, 3'-GTTGA-5' at 3291, 3'-CCAGA-5' at 3299, 3'-GTAGA-5' at 3329, 3'-ATAGG-5' at 3384, 3'-ACAGA-5' at 3392, 3'-GTAGA-5' at 3403, 3'-CCTGG-5' at 3545, 3'-ACAGG-5' at 3577, 3'-CCAGA-5' at 3608, 3'-ACAGG-5' at 3619, 3'-GTAGG-5' at 3629, 3'-ACTGG-5' at 3714, 3'-ATTGA-5' at 3733, 3'-CCAGA-5' at 3771, 3'-ACTGG-5' at 3784, 3'-GCTGA-5' at 3801, 3'-CTTGG-5' at 3838, 3'-CTTGG-5' at 3856, 3'-GTTGG-5' at 3911, 3'-CTTGG-5' at 3937, 3'-ACTGG-5' at 4018, 3'-CTTGA-5' at 4048, 3'-GCAGA-5' at 4056, 3'-CTAGG-5' at 4081, 3'-GTAGG-5' at 4183, 3'-ACTGG-5' at 4216, 3'-GCTGG-5' at 4358, 3'-ACAGG-5' at 4367, 3'-CCAGA-5' at 4380, 3'-CCAGA-5' at 4414, 3'-CCAGG-5' at 4420.
{{clear}}

==Acknowledgements==

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from [http://www.wikiversity.org Wikiversity].

==See also==
{{div col|colwidth=20em}}
* [[Core promoter gene transcriptions]]
* [[Downstream core element gene transcriptions]]
* [[A1BG gene transcriptions|Transcription of A1BG]]
{{Div col end}}

==References==
{{reflist|2}}

==Further reading==
* {{ cite journal
| author = Jennifer E.F. Butler, James T. Kadonaga
| date = October 15, 2002
| title = The RNA polymerase II core promoter: a key component in the regulation of gene expression
| journal = Genes & Development
| volume = 16
| issue = 20
| pages = 2583–92
| doi = 10.1101/gad.1026202
| pmid = 12381658
| url = http://genesdev.cshlp.org/content/16/20/2583.full }}

==External links==
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
* [http://www.osti.gov/ Office of Scientific & Technical Information]
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]

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