LOCUS       sequence-311728-        6273 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Tests for the impacts 1 uracil in a poly-uracil tract in 
            conjunctiuon with a hairpin 10 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 6273)
  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 6273)
  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(1)_HairpinDistance(10)nts_Tornado-Corn
FEATURES             Location/Qualifiers
     source          1..6273
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        1..249
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     1..21
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     172..191
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     polyA_signal    699..820
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     repeat_region   869..998
                     /label=AAV2 ITR
     rep_origin      complement(1092..1547)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1229..1250)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     1441..1460
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     promoter        1574..1678
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1679..1747,1748..2539)
                     /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(1897..1916)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      2710..3298
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3199..3218
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     polyA_signal    3567..3701
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     CDS             complement(4126..4146)
                     /codon_start=1
                     /product="nuclear localization signal of SV40 (simian virus
                     40) large T antigen"
                     /label=SV40 NLS
                     /translation="PKKKRKV"
     intron          4276..4341
                     /label=small t intron
                     /note="SV40 (simian virus 40) small t antigen intron"
     CDS             complement(4761..5555)
                     /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(4872..4891)
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     5482..5501
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     promoter        complement(5912..6241)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      5926..6061
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     6226..6246
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
ORIGIN
        1 gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
       61 ataattagaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
      121 aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat ggactatcat
      181 atgcttaccg taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
      241 cgaaacaccg tgctcgcttc ggcagcacat atactagcag ggttgcggct ttctgctgca
      301 atcccaactc caatcgacgg ccatcagtcg ccggtcccaa gcccggataa aatgggaggg
      361 ggcgggaaac cgcctaacca tgccgactga tggcaggccc ggatagctca gtcggtagag
      421 cagcggccgc gcgattcgag gaaggaggtc tgaggaggtc actgaatcgc gcggccgcgg
      481 gtccagggtt caagtccctg ttcgggcctg ccatcagtcg gcgtggactg tagaacactg
      541 ccaatgccgg tcccaagccc ggataaaagt ggagggtaca gtccacgctc tagagcggac
      601 ttcggtccgc tttttactag gacctgcagg catgcaagct tgacgtcggt taccgatatc
      661 catatggcgg ccgcatcgat ctcgagccgc ggactagtaa cttgtttatt gcagcttata
      721 atggttacaa ataaagcaat agcatcacaa atttcacaaa taaagcattt ttttcactgc
      781 attctagttg tggtttgtcc aaactcatca atgtatctta tcatgtctta cgtagataag
      841 tagcatggcg ggttaatcat taactacaag gaacccctag tgatggagtt ggccactccc
      901 tctctgcgcg ctcgctcgct cactgaggcc gggcgaccaa aggtcgcccg acgcccgggc
      961 tttgcccggg cggcctcagt gagcgagcga gcgcgcagag agggacagat ctgcagatct
     1021 gctggcgtaa tagcgaagag gcccgcaccg atcgcccttc ccaacagttg cgcagcctga
     1081 atggcgaatg gaaattgtaa gcgttaatat tttgttaaaa ttcgcgttaa atttttgtta
     1141 aatcagctca ttttttaacc aataggccga aatcggcaaa atcccttata aatcaaaaga
     1201 atagaccgag atagggttga gtgttgttcc agtttggaac aagagtccac tattaaagaa
     1261 cgtggactcc aacgtcaaag ggcgaaaaac cgtctatcag ggcgatggcc cactacgtga
     1321 accatcaccc taatcaagtt ttttggggtc gaggtgccgt aaagcactaa atcggaaccc
     1381 taaagggagc ccccgattta gagcttgacg gggaaagccg gcgaacgtgg cgagaaagga
     1441 agggaagaaa gcgaaaggag cgggcgctag ggcgctggca agtgtagcgg tcacgctgcg
     1501 cgtaaccacc acacccgccg cgcttaatgc gccgctacag ggcgcgtcag gtggcacttt
     1561 tcggggaaat gtgcgcggaa cccctatttg tttatttttc taaatacatt caaatatgta
     1621 tccgctcatg agacaataac cctgataaat gcttcaataa tattgaaaaa ggaagagtat
     1681 gagtattcaa catttccgtg tcgcccttat tccctttttt gcggcatttt gccttcctgt
     1741 ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt tgggtgcacg
     1801 agtgggttac atcgaactgg atctcaacag cggtaagatc cttgagagtt ttcgccccga
     1861 agaacgtttt ccaatgatga gcacttttaa agttctgcta tgtggcgcgg tattatcccg
     1921 tattgacgcc gggcaagagc aactcggtcg ccgcatacac tattctcaga atgacttggt
     1981 tgagtactca ccagtcacag aaaagcatct tacggatggc atgacagtaa gagaattatg
     2041 cagtgctgcc ataaccatga gtgataacac tgcggccaac ttacttctga caacgatcgg
     2101 aggaccgaag gagctaaccg cttttttgca caacatgggg gatcatgtaa ctcgccttga
     2161 tcgttgggaa ccggagctga atgaagccat accaaacgac gagcgtgaca ccacgatgcc
     2221 tgtagcaatg gcaacaacgt tgcgcaaact attaactggc gaactactta ctctagcttc
     2281 ccggcaacaa ttaatagact ggatggaggc ggataaagtt gcaggaccac ttctgcgctc
     2341 ggcccttccg gctggctggt ttattgctga taaatctgga gccggtgagc gtgggtctcg
     2401 cggtatcatt gcagcactgg ggccagatgg taagccctcc cgtatcgtag ttatctacac
     2461 gacggggagt caggcaacta tggatgaacg aaatagacag atcgctgaga taggtgcctc
     2521 actgattaag cattggtaac tgtcagacca agtttactca tatatacttt agattgattt
     2581 aaaacttcat ttttaattta aaaggatcta ggtgaagatc ctttttgata atctcatgac
     2641 caaaatccct taacgtgagt tttcgttcca ctgagcgtca gaccccgtag aaaagatcaa
     2701 aggatcttct tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa caaaaaaacc
     2761 accgctacca gcggtggttt gtttgccgga tcaagagcta ccaactcttt ttccgaaggt
     2821 aactggcttc agcagagcgc agataccaaa tactgttctt ctagtgtagc cgtagttagg
     2881 ccaccacttc aagaactctg tagcaccgcc tacatacctc gctctgctaa tcctgttacc
     2941 agtggctgct gccagtggcg ataagtcgtg tcttaccggg ttggactcaa gacgatagtt
     3001 accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga
     3061 gcgaacgacc tacaccgaac tgagatacct acagcgtgag ctatgagaaa gcgccacgct
     3121 tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg
     3181 cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca
     3241 cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa
     3301 cgccagcaac gcggcctttt tacggttcct ggccttttgc tggccttttg ctcacatgtt
     3361 ctttcctgcg ttatcccctg attctgtgga taaccgtatt accgcctttg agtgagctga
     3421 taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagc gcgcagagag
     3481 ggagtggcca actccatcac taggggttcc tggaggggtg gagtcgtgac gtgaattacg
     3541 tcatagggtt agggaggtcc tggatcgatc cagacatgat aagatacatt gatgagtttg
     3601 gacaaaccac aactagaatg cagtgaaaaa aatgctttat ttgtgaaatt tgtgatgcta
     3661 ttgctttatt tgtaaccatt ataagctgca ataaacaagt taacaacaac aattgcattc
     3721 attttatgtt tcaggttcag ggggaggtgt gggaggtttt ttaaagcaag taaaacctct
     3781 acaaatgtgg tatggctgat tatgatctct agtcaaggca ctatacatca aatattcctt
     3841 attaacccct ttacaaatta aaaagctaaa ggtacacaat ttttgagcat agttattaat
     3901 agcagacact ctatgcctgt gtggagtaag aaaaaacagt atgttatgat tataactgtt
     3961 atgcctactt ataaaggtta cagaatattt ttccataatt ttcttgtata gcagtgcagc
     4021 tttttccttt gtggtgtaaa tagcaaagca agcaagagtt ctattactaa acacagcatg
     4081 actcaaaaaa cttagcaatt ctgaaggaaa gtccttgggg tcttctacct ttctcttctt
     4141 ttttggagga gtagaatgtt gagagtcagc agtagcctca tcatcactag atggcatttc
     4201 ttctgagcaa aacaggtttt cctcattaaa ggcattccac cactgctccc attcatcagt
     4261 tccataggtt ggaatctaaa atacacaaac aattagaatc agtagtttaa cacattatac
     4321 acttaaaaat tttatattta ccttagagct ttaaatctct gtaggtagtt tgtccaatta
     4381 tgtcacacca cagaagtaag gttccttcac aaagatccgg accaaagcgg ccatcgtgcc
     4441 tccccactcc tgcagttcgg gggcatggat gcgcggatag ccgctgctgg tttcctggat
     4501 gccgacggat ttgcactgcc ggtagaactc cgcgaggtcg tccagcctca ggcagcagct
     4561 gaaccaactc gcgaggggat cgagcccggg gtgggcgaag aactccagca tgagatcccc
     4621 gcgctggagg atcatccagc cggcgtcccg gaaaaagatt ccgaagccca acctttcata
     4681 gaaggcggcg gtggaatcga aatctcgtga tggcaggttg ggcgtcgctt ggtcggtcat
     4741 ttcgaacccc agagtcccgc tcagaagaac tcgtcaagaa ggcgatagaa ggcgatgcgc
     4801 tgcgaatcgg gagcggcgat accgtaaagc acgaggaagc ggtcagccca ttcgccgcca
     4861 agctcttcag caatatcacg ggtagccaac gctatgtcct gatagcggtc cgccacaccc
     4921 agccggccac agtcgatgaa tccagaaaag cggccatttt ccaccatgat attcggcaag
     4981 caggcatcgc catgggtcac gacgagatcc tcgccgtcgg gcatgcgcgc cttgagcctg
     5041 gcgaacagtt cggctggcgc gagcccctga tgctcttcgt ccagatcatc ctgatcgaca
     5101 agaccggctt ccatccgagt acgtgctcgc tcgatgcgat gtttcgcttg gtggtcgaat
     5161 gggcaggtag ccggatcaag cgtatgcagc cgccgcattg catcagccat gatggatact
     5221 ttctcggcag gagcaaggtg agatgacagg agatcctgcc ccggcacttc gcccaatagc
     5281 agccagtccc ttcccgcttc agtgacaacg tcgagcacag ctgcgcaagg aacgcccgtc
     5341 gtggccagcc acgatagccg cgctgcctcg tcctgcagtt cattcagggc accggacagg
     5401 tcggtcttga caaaaagaac cgggcgcccc tgcgctgaca gccggaacac ggcggcatca
     5461 gagcagccga ttgtctgttg tgcccagtca tagccgaata gcctctccac ccaagcggcc
     5521 ggagaacctg cgtgcaatcc atcttgttca atcatgcgaa acgatcctca tcctgtctct
     5581 tgatcagatc ttgatcccct gcgccatcag atccttggcg gcaagaaagc catccagttt
     5641 actttgcagg gcttcccaac cttaccagag ggcgccccag ctggcaattc cggttcgctt
     5701 gctgtccata aaaccgccca gtctagctat cgccatgtaa gcccactgca agctacctgc
     5761 tttctctttg cgcttgcgtt ttcccttgtc cagatagccc agtagctgac attcatccgg
     5821 ggtcagcacc gtttctgcgg actggctttc tacgtgttcc gcttccttta gcagcccttg
     5881 cgccctgagt gcttgcggca gcgtgaagct ttttgcaaaa gcctaggcct ccaaaaaagc
     5941 ctcctcacta cttctggaat agctcagagg ccgaggcggc ctcggcctct gcataaataa
     6001 aaaaaattag tcagccatgg ggcggagaat gggcggaact gggcggagtt aggggcggga
     6061 tgggcggagt taggggcggg actatggttg ctgactaatt gagatgcatg ctttgcatac
     6121 ttctgcctgc tggggagcct ggggactttc cacacctggt tgctgactaa ttgagatgca
     6181 tgctttgcat acttctgcct gctggggagc ctggggactt tccacaccct aactgacaca
     6241 cattccacag ccggatccaa ggtcgggcag gaa
//
