LOCUS       sequence-311758-        6276 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Tests for the impacts 4 uracils in a poly-uracil tract in 
            conjunctiuon with a hairpin 20 nts upstream 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(20)nts_Tornado-Corn
FEATURES             Location/Qualifiers
     source          1..6276
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    461..582
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     repeat_region   631..760
                     /label=AAV2 ITR
     rep_origin      complement(854..1309)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(991..1012)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     1203..1222
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     promoter        1336..1440
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1441..1509,1510..2301)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILDSFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(1659..1678)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      2472..3060
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     2961..2980
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     polyA_signal    3329..3463
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     CDS             complement(3888..3908)
                     /codon_start=1
                     /product="nuclear localization signal of SV40 (simian virus
                     40) large T antigen"
                     /label=SV40 NLS
                     /translation="PKKKRKV"
     intron          4038..4103
                     /label=small t intron
                     /note="SV40 (simian virus 40) small t antigen intron"
     CDS             complement(4523..5317)
                     /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(4634..4653)
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     5244..5263
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     promoter        complement(5674..6003)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      5688..5823
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     5988..6008
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6036..6276,1..8)
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     6036..6056
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     6207..6226
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
ORIGIN
        1 gaaacaccgt gctcgcttcg gcagcacatg gttgcggctt tctgctgcaa tctaactagc
       61 agccaactcc aattttcgac ggccatcagt cgccggtccc aagcccggat aaaatgggag
      121 ggggcgggaa accgcctaac catgccgact gatggcaggc ccggatagct cagtcggtag
      181 agcagcggcc gcgcgattcg aggaaggagg tctgaggagg tcactgaatc gcgcggccgc
      241 gggtccaggg ttcaagtccc tgttcgggcc taccatcagt cggcgtggac tgtagaacac
      301 tgccaatgcc ggtcccaagc ccggataaaa gtggagggta cagtccacgc tctagagcgg
      361 acttcggtcc gctttttact aggacctgca ggcatgcaag cttgacgtcg gttaccgata
      421 tccatatggc ggccgcatcg atctcgagcc gcggactagt aacttgttta ttgcagctta
      481 taatggttac aaataaagca atagcatcac aaatttcaca aataaagcat ttttttcact
      541 gcattctagt tgtggtttgt ccaaactcat caatgtatct tatcatgtct tacgtagata
      601 agtagcatgg cgggttaatc attaactaca aggaacccct agtgatggag ttggccactc
      661 cctctctgcg cgctcgctcg ctcactgagg ccgggcgacc aaaggtcgcc cgacgcccgg
      721 gctttgcccg ggcggcctca gtgagcgagc gagcgcgcag agagggacag atctgcagat
      781 ctgctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt tgcgcagcct
      841 gaatggcgaa tggaaattgt aagcgttaat attttgttaa aattcgcgtt aaatttttgt
      901 taaatcagct cattttttaa ccaataggcc gaaatcggca aaatccctta taaatcaaaa
      961 gaatagaccg agatagggtt gagtgttgtt ccagtttgga acaagagtcc actattaaag
     1021 aacgtggact ccaacgtcaa agggcgaaaa accgtctatc agggcgatgg cccactacgt
     1081 gaaccatcac cctaatcaag ttttttgggg tcgaggtgcc gtaaagcact aaatcggaac
     1141 cctaaaggga gcccccgatt tagagcttga cggggaaagc cggcgaacgt ggcgagaaag
     1201 gaagggaaga aagcgaaagg agcgggcgct agggcgctgg caagtgtagc ggtcacgctg
     1261 cgcgtaacca ccacacccgc cgcgcttaat gcgccgctac agggcgcgtc aggtggcact
     1321 tttcggggaa atgtgcgcgg aacccctatt tgtttatttt tctaaataca ttcaaatatg
     1381 tatccgctca tgagacaata accctgataa atgcttcaat aatattgaaa aaggaagagt
     1441 atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct
     1501 gtttttgctc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca
     1561 cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgatag ttttcgcccc
     1621 gaagaacgtt ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc
     1681 cgtattgacg ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg
     1741 gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta
     1801 tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc
     1861 ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt
     1921 gatcgttggg aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg
     1981 cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct
     2041 tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc
     2101 tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct
     2161 cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac
     2221 acgacgggga gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc
     2281 tcactgatta agcattggta actgtcagac caagtttact catatatact ttagattgat
     2341 ttaaaacttc atttttaatt taaaaggatc taggtgaaga tcctttttga taatctcatg
     2401 accaaaatcc cttaacgtga gttttcgttc cactgagcgt cagaccccgt agaaaagatc
     2461 aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcttgca aacaaaaaaa
     2521 ccaccgctac cagcggtggt ttgtttgccg gatcaagagc taccaactct ttttccgaag
     2581 gtaactggct tcagcagagc gcagatacca aatactgttc ttctagtgta gccgtagtta
     2641 ggccaccact tcaagaactc tgtagcaccg cctacatacc tcgctctgct aatcctgtta
     2701 ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg ggttggactc aagacgatag
     2761 ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg
     2821 gagcgaacga cctacaccga actgagatac ctacagcgtg agctatgaga aagcgccacg
     2881 cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag
     2941 cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc
     3001 cacctctgac ttgagcgtcg atttttgtga tgctcgtcag gggggcggag cctatggaaa
     3061 aacgccagca acgcggcctt tttacggttc ctggcctttt gctggccttt tgctcacatg
     3121 ttctttcctg cgttatcccc tgattctgtg gataaccgta ttaccgcctt tgagtgagct
     3181 gataccgctc gccgcagccg aacgaccgag cgcagcgagt cagtgagcga gcgcgcagag
     3241 agggagtggc caactccatc actaggggtt cctggagggg tggagtcgtg acgtgaatta
     3301 cgtcataggg ttagggaggt cctggatcga tccagacatg ataagataca ttgatgagtt
     3361 tggacaaacc acaactagaa tgcagtgaaa aaaatgcttt atttgtgaaa tttgtgatgc
     3421 tattgcttta tttgtaacca ttataagctg caataaacaa gttaacaaca acaattgcat
     3481 tcattttatg tttcaggttc agggggaggt gtgggaggtt ttttaaagca agtaaaacct
     3541 ctacaaatgt ggtatggctg attatgatct ctagtcaagg cactatacat caaatattcc
     3601 ttattaaccc ctttacaaat taaaaagcta aaggtacaca atttttgagc atagttatta
     3661 atagcagaca ctctatgcct gtgtggagta agaaaaaaca gtatgttatg attataactg
     3721 ttatgcctac ttataaaggt tacagaatat ttttccataa ttttcttgta tagcagtgca
     3781 gctttttcct ttgtggtgta aatagcaaag caagcaagag ttctattact aaacacagca
     3841 tgactcaaaa aacttagcaa ttctgaagga aagtccttgg ggtcttctac ctttctcttc
     3901 ttttttggag gagtagaatg ttgagagtca gcagtagcct catcatcact agatggcatt
     3961 tcttctgagc aaaacaggtt ttcctcatta aaggcattcc accactgctc ccattcatca
     4021 gttccatagg ttggaatcta aaatacacaa acaattagaa tcagtagttt aacacattat
     4081 acacttaaaa attttatatt taccttagag ctttaaatct ctgtaggtag tttgtccaat
     4141 tatgtcacac cacagaagta aggttccttc acaaagatcc ggaccaaagc ggccatcgtg
     4201 cctccccact cctgcagttc gggggcatgg atgcgcggat agccgctgct ggtttcctgg
     4261 atgccgacgg atttgcactg ccggtagaac tccgcgaggt cgtccagcct caggcagcag
     4321 ctgaaccaac tcgcgagggg atcgagcccg gggtgggcga agaactccag catgagatcc
     4381 ccgcgctgga ggatcatcca gccggcgtcc cggaaaacga ttccgaagcc caacctttca
     4441 tagaaggcgg cggtggaatc gaaatctcgt gatggcaggt tgggcgtcgc ttggtcggtc
     4501 atttcgaacc ccagagtccc gctcagaaga actcgtcaag aaggcgatag aaggcgatgc
     4561 gctgcgaatc gggagcggcg ataccgtaaa gcacgaggaa gcggtcagcc cattcgccgc
     4621 caagctcttc agcaatatca cgggtagcca acgctatgtc ctgatagcgg tccgccacac
     4681 ccagccggcc acagtcgatg aatccagaaa agcggccatt ttccaccatg atattcggca
     4741 agcaggcatc gccatgggtc acgacgagat cctcgccgtc gggcatgcgc gccttgagcc
     4801 tggcgaacag ttcggctggc gcgagcccct gatgctcttc gtccagatca tcctgatcga
     4861 caagaccggc ttccatccga gtacgtgctc gctcgatgcg atgtttcgct tggtggtcga
     4921 atgggcaggt agccggatca agcgtatgca gccgccgcat tgcatcagcc atgatggata
     4981 ctttctcggc aggagcaagg tgagatgaca ggagatcctg ccccggcact tcgcccaata
     5041 gcagccagtc ccttcccgct tcagtgacaa cgtcgagcac agctgcgcaa ggaacgcccg
     5101 tcgtggccag ccacgatagc cgcgctgcct cgtcctgcag ttcattcagg gcaccggaca
     5161 ggtcggtctt gacaaaaaga accgggcgcc cctgcgctga cagccggaac acggcggcat
     5221 cagagcagcc gattgtctgt tgtgcccagt catagccgaa tagcctctcc acccaagcgg
     5281 ccggagaacc tgcgtgcaat ccatcttgtt caatcatgcg aaacgatcct catcctgtct
     5341 cttgatcaga tcttgatccc ctgcgccatc agatccttgg cggcaagaaa gccatccagt
     5401 ttactttgca gggcttccca accttaccag agggcgcccc agctggcaat tccggttcgc
     5461 ttgctgtcca taaaaccgcc cagtctagct atcgccatgt aagcccactg caagctacct
     5521 gctttctctt tgcgcttgcg ttttcccttg tccagatagc ccagtagctg acattcatcc
     5581 ggggtcagca ccgtttctgc ggactggctt tctacgtgtt ccgcttcctt tagcagccct
     5641 tgcgccctga gtgcttgcgg cagcgtgaag ctttttgcaa aagcctaggc ctccaaaaaa
     5701 gcctcctcac tacttctgga atagctcaga ggccgaggcg gcctcggcct ctgcataaat
     5761 aaaaaaaatt agtcagccat ggggcggaga atgggcggaa ctgggcggag ttaggggcgg
     5821 gatgggcgga gttaggggcg ggactatggt tgctgactaa ttgagatgca tgctttgcat
     5881 acttctgcct gctggggagc ctggggactt tccacacctg gttgctgact aattgagatg
     5941 catgctttgc atacttctgc ctgctgggga gcctggggac tttccacacc ctaactgaca
     6001 cacattccac agccggatcc aaggtcgggc aggaagaggg cctatttccc atgattcctt
     6061 catatttgca tatacgatac aaggctgtta gagagataat tagaattaat ttgactgtaa
     6121 acacaaagat attagtacaa aatacgtgac gtagaaagta ataatttctt gggtagtttg
     6181 cagttttaaa attatgtttt aaaatggact atcatatgct taccgtaact tgaaagtatt
     6241 tcgatttctt ggctttatat atcttgtgga aaggac
//
