LOCUS       sequence-311756-        6276 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Tests for the impacts 4 uracils in a poly-uracil tract in 
            conjunctiuon with an immediately upstream hairpin have on human 
            polymerase III transcription elongation from a U6 promoter. .
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6276)
  AUTHORS   Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, 
            Lucks JB
  TITLE     RNA Sequence and Structure Determinants of Pol III Transcriptional 
            Termination in Human Cells.
  JOURNAL   J Mol Biol. 2021 Jun 25;433(13):166978. doi: 
            10.1016/j.jmb.2021.166978. Epub 2021 Apr 1.
  PUBMED    33811918
REFERENCE   2  (bases 1 to 6276)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "J Mol 
            Biol."; date: "2021-06-25"; volume: "433(13):166978. doi"; pages: " 
            10.1016/j.jmb.2021.166978. Epub 2021 Apr 1"
COMMENT     Sequence Label: 
            pAV-U6+27-Linear-3_PolyU(4)_HairpinDistance(0)nts_Tornado-Corn
FEATURES             Location/Qualifiers
     source          1..6276
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(111..566)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(248..269)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     460..479
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     promoter        593..697
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(698..766,767..1558)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(916..935)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      1729..2317
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     2218..2237
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     polyA_signal    2586..2720
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     CDS             complement(3145..3165)
                     /codon_start=1
                     /product="nuclear localization signal of SV40 (simian virus
                     40) large T antigen"
                     /label=SV40 NLS
                     /translation="PKKKRKV"
     intron          3295..3360
                     /label=small t intron
                     /note="SV40 (simian virus 40) small t antigen intron"
     CDS             complement(3780..4574)
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(3891..3910)
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     4501..4520
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     promoter        complement(4931..5260)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      4945..5080
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     5245..5265
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        5293..5541
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     5293..5313
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     5464..5483
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     polyA_signal    5994..6115
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     repeat_region   join(6164..6276,1..17)
                     /label=AAV2 ITR
ORIGIN
        1 agcgagcgag cgcgcagaga gggacagatc tgcagatctg ctggcgtaat agcgaagagg
       61 cccgcaccga tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg aaattgtaag
      121 cgttaatatt ttgttaaaat tcgcgttaaa tttttgttaa atcagctcat tttttaacca
      181 ataggccgaa atcggcaaaa tcccttataa atcaaaagaa tagaccgaga tagggttgag
      241 tgttgttcca gtttggaaca agagtccact attaaagaac gtggactcca acgtcaaagg
      301 gcgaaaaacc gtctatcagg gcgatggccc actacgtgaa ccatcaccct aatcaagttt
      361 tttggggtcg aggtgccgta aagcactaaa tcggaaccct aaagggagcc cccgatttag
      421 agcttgacgg ggaaagccgg cgaacgtggc gagaaaggaa gggaagaaag cgaaaggagc
      481 gggcgctagg gcgctggcaa gtgtagcggt cacgctgcgc gtaaccacca cacccgccgc
      541 gcttaatgcg ccgctacagg gcgcgtcagg tggcactttt cggggaaatg tgcgcggaac
      601 ccctatttgt ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc
      661 ctgataaatg cttcaataat attgaaaaag gaagagtatg agtattcaac atttccgtgt
      721 cgcccttatt cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct
      781 ggtgaaagta aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga
      841 tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc caatgatgag
      901 cacttttaaa gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca
      961 actcggtcgc cgcatacact attctcagaa tgacttggtt gagtactcac cagtcacaga
     1021 aaagcatctt acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag
     1081 tgataacact gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc
     1141 ttttttgcac aacatggggg atcatgtaac tcgccttgat cgttgggaac cggagctgaa
     1201 tgaagccata ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt
     1261 gcgcaaacta ttaactggcg aactacttac tctagcttcc cggcaacaat taatagactg
     1321 gatggaggcg gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt
     1381 tattgctgat aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg
     1441 gccagatggt aagccctccc gtatcgtagt tatctacacg acggggagtc aggcaactat
     1501 ggatgaacga aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact
     1561 gtcagaccaa gtttactcat atatacttta gattgattta aaacttcatt tttaatttaa
     1621 aaggatctag gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt
     1681 ttcgttccac tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt
     1741 ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag cggtggtttg
     1801 tttgccggat caagagctac caactctttt tccgaaggta actggcttca gcagagcgca
     1861 gataccaaat actgttcttc tagtgtagcc gtagttaggc caccacttca agaactctgt
     1921 agcaccgcct acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga
     1981 taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc
     2041 gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaact
     2101 gagataccta cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga
     2161 caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg
     2221 aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt
     2281 tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt
     2341 acggttcctg gccttttgct ggccttttgc tcacatgttc tttcctgcgt tatcccctga
     2401 ttctgtggat aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac
     2461 gaccgagcgc agcgagtcag tgagcgagcg cgcagagagg gagtggccaa ctccatcact
     2521 aggggttcct ggaggggtgg agtcgtgacg tgaattacgt catagggtta gggaggtcct
     2581 ggatcgatcc agacatgata agatacattg atgagtttgg acaaaccaca actagaatgc
     2641 agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat tgctttattt gtaaccatta
     2701 taagctgcaa taaacaagtt aacaacaaca attgcattca ttttatgttt caggttcagg
     2761 gggaggtgtg ggaggttttt taaagcaagt aaaacctcta caaatgtggt atggctgatt
     2821 atgatctcta gtcaaggcac tatacatcaa atattcctta ttaacccctt tacaaattaa
     2881 aaagctaaag gtacacaatt tttgagcata gttattaata gcagacactc tatgcctgtg
     2941 tggagtaaga aaaaacagta tgttatgatt ataactgtta tgcctactta taaaggttac
     3001 agaatatttt tccataattt tcttgtatag cagtgcagct ttttcctttg tggtgtaaat
     3061 agcaaagcaa gcaagagttc tattactaaa cacagcatga ctcaaaaaac ttagcaattc
     3121 tgaaggaaag tccttggggt cttctacctt tctcttcttt tttggaggag tagaatgttg
     3181 agagtcagca gtagcctcat catcactaga tggcatttct tctgagcaaa acaggttttc
     3241 ctcattaaag gcattccacc actgctccca ttcatcagtt ccataggttg gaatctaaaa
     3301 tacacaaaca attagaatca gtagtttaac acattataca cttaaaaatt ttatatttac
     3361 cttagagctt taaatctctg taggtagttt gtccaattat gtcacaccac agaagtaagg
     3421 ttccttcaca aagatccgga ccaaagcggc catcgtgcct ccccactcct gcagttcggg
     3481 ggcatggatg cgcggatagc cgctgctggt ttcctggatg ccgacggatt tgcactgccg
     3541 gtagaactcc gcgaggtcgt ccagcctcag gcagcagctg aaccaactcg cgaggggatc
     3601 gagcccgggg tgggcgaaga actccagcat gagatccccg cgctggagga tcatccagcc
     3661 ggcgtcccgg aaaacgattc cgaagcccaa cctttcatag aaggcggcgg tggaatcgaa
     3721 atctcgtgat ggcaggttgg gcgtcgcttg gtcggtcatt tcgaacccca gagtcccgct
     3781 cagaagaact cgtcaagaag gcgatagaag gcgatgcgct gcgaatcggg agcggcgata
     3841 ccgtaaagca cgaggaagcg gtcagcccat tcgccgccaa gctcttcagc aatatcacgg
     3901 gtagccaacg ctatgtcctg atagcggtcc gccacaccca gccggccaca gtcgatgaat
     3961 ccagaaaagc ggccattttc caccatgata ttcggcaagc aggcatcgcc atgggtcacg
     4021 acgagatcct cgccgtcggg catgcgcgcc ttgagcctgg cgaacagttc ggctggcgcg
     4081 agcccctgat gctcttcgtc cagatcatcc tgatcgacaa gaccggcttc catccgagta
     4141 cgtgctcgct cgatgcgatg tttcgcttgg tggtcgaatg ggcaggtagc cggatcaagc
     4201 gtatgcagcc gccgcattgc atcagccatg atggatactt tctcggcagg agcaaggtga
     4261 gatgacagga gatcctgccc cggcacttcg cccaatagca gccagtccct tcccgcttca
     4321 gtgacaacgt cgagcacagc tgcgcaagga acgcccgtcg tggccagcca cgatagccgc
     4381 gctgcctcgt cctgcagttc attcagggca ccggacaggt cggtcttgac aaaaagaacc
     4441 gggcgcccct gcgctgacag ccggaacacg gcggcatcag agcagccgat tgtctgttgt
     4501 gcccagtcat agccgaatag cctctccacc caagcggccg gagaacctgc gtgcaatcca
     4561 tcttgttcaa tcatgcgaaa cgatcctcat cctgtctctt gatcagatct tgatcccctg
     4621 cgccatcaga tccttggcgg caagaaagcc atccagttta ctttgcaggg cttcccaacc
     4681 ttaccagagg gcgccccagc tggcaattcc ggttcgcttg ctgtccataa aaccgcccag
     4741 tctagctatc gccatgtaag cccactgcaa gctacctgct ttctctttgc gcttgcgttt
     4801 tcccttgtcc agatagccca gtagctgaca ttcatccggg gtcagcaccg tttctgcgga
     4861 ctggctttct acgtgttccg cttcctttag cagcccttgc gccctgagtg cttgcggcag
     4921 cgtgaagctt tttgcaaaag cctaggcctc caaaaaagcc tcctcactac ttctggaata
     4981 gctcagaggc cgaggcggcc tcggcctctg cataaataaa aaaaattagt cagccatggg
     5041 gcggagaatg ggcggaactg ggcggagtta ggggcgggat gggcggagtt aggggcggga
     5101 ctatggttgc tgactaattg agatgcatgc tttgcatact tctgcctgct ggggagcctg
     5161 gggactttcc acacctggtt gctgactaat tgagatgcat gctttgcata cttctgcctg
     5221 ctggggagcc tggggacttt ccacacccta actgacacac attccacagc cggatccaag
     5281 gtcgggcagg aagagggcct atttcccatg attccttcat atttgcatat acgatacaag
     5341 gctgttagag agataattag aattaatttg actgtaaaca caaagatatt agtacaaaat
     5401 acgtgacgta gaaagtaata atttcttggg tagtttgcag ttttaaaatt atgttttaaa
     5461 atggactatc atatgcttac cgtaacttga aagtatttcg atttcttggc tttatatatc
     5521 ttgtggaaag gacgaaacac cgtgctcgct tcggcagcac atatactagc agccaactcc
     5581 aaggttgcgg ctttctgctg caatcttttc gacggccatc agtcgccggt cccaagcccg
     5641 gataaaatgg gagggggcgg gaaaccgcct aaccatgccg actgatggca ggcccggata
     5701 gctcagtcgg tagagcagcg gccgcgcgat tcgaggaagg aggtctgagg aggtcactga
     5761 atcgcgcggc cgcgggtcca gggttcaagt ccctgttcgg gcctgccatc agtcggcgtg
     5821 gactgtagaa cactgccaat gccggtccca agcccggata aaagtggagg gtacagtcca
     5881 cgctctagag cggacttcgg tccgcttttt actaggacct gcaggcatgc aagcttgacg
     5941 tcggttaccg atatccatat ggcggccgca tcgatctcga gccgcggact agtaacttgt
     6001 ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag
     6061 catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg
     6121 tcttacgtag ataagtagca tggcgggtta atcattaact acaaggaacc cctagtgatg
     6181 gagttggcca ctccctctct gcgcgctcgc tcgctcactg aggccgggcg accaaaggtc
     6241 gcccgacgcc cgggctttgc ccgggcggcc tcagtg
//
