LOCUS       sequence-243733-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  synthetic circular DNA
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7084)
  AUTHORS   Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, 
            Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G,
            Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, 
            Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, 
            Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna 
            JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Jr UR, Marie SK, Dahl
            O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer
            DG, Rustgi AK, Meyerson M
  TITLE     SOX2 is an amplified lineage-survival oncogene in lung and 
            esophageal squamous cell carcinomas.
  JOURNAL   Nat Genet. 2009 Nov . 41(11):1238-42.
  PUBMED    19801978
REFERENCE   2  (bases 1 to 7084)
  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: "Nat Genet. 
            2009 Nov . 41(11):1238-42."
COMMENT     Sequence Label: pLKO.1 Sox2 HM a
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     128..147
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     381..398
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    515..536
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(551..556,557..574,575..581)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    589..605
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     primer_bind     594..616
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     613..629
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     613..629
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     648..668
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        650..668
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        696..922
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             923..1103
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1150..1275
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1768..2001
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2186..2230
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     promoter        2528..2776
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     2528..2548
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     2699..2718
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    2873..2990
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        3039..3549
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     3468..3486
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             3571..4170
                     /codon_start=1
                     /gene="pac from Streptomyces alboniger"
                     /product="puromycin N-acetyltransferase"
                     /label=PuroR
                     /note="confers resistance to puromycin"
                     /translation="MTEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIER
                     VTELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLA
                     AQQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETS
                     APRNLPFYERLGFTVTADVEVPEGPRTWCMTRKPGA"
     primer_bind     complement(3571..3590)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     4067..4087
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             4298..4531
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    4603..4724
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4640..4659)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4694..4713
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      4764..4899
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(4919..4938)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4920..4938)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(4948..4965)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(4948..4964)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4957..4979)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      5106..5561
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5193..5212)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5403..5424
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5587..5691
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5692..5760,5761..6552)
                     /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(5910..5929)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      join(6723..7084,1..227)
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
ORIGIN
        1 acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
       61 gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc
      121 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg
      181 agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcaacg
      241 cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc tttcctgcgt
      301 tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat accgctcgcc
      361 gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag cgcccaatac
      421 gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagctggcac gacaggtttc
      481 ccgactggaa agcgggcagt gagcgcaacg caattaatgt gagttagctc actcattagg
      541 caccccaggc tttacacttt atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat
      601 aacaatttca cacaggaaac agctatgacc atgattacgc caagcgcgca attaaccctc
      661 actaaaggga acaaaagctg gagctgcaag cttaatgtag tcttatgcaa tactcttgta
      721 gtcttgcaac atggtaacga tgagttagca acatgcctta caaggagaga aaaagcaccg
      781 tgcatgccga ttggtggaag taaggtggta cgatcgtgcc ttattaggaa ggcaacagac
      841 gggtctgaca tggattggac gaaccactga attgccgcat tgcagagata ttgtatttaa
      901 gtgcctagct cgatacataa acgggtctct ctggttagac cagatctgag cctgggagct
      961 ctctggctaa ctagggaacc cactgcttaa gcctcaataa agcttgcctt gagtgcttca
     1021 agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag agatccctca gaccctttta
     1081 gtcagtgtgg aaaatctcta gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa
     1141 ccagaggagc tctctcgacg caggactcgg cttgctgaag cgcgcacggc aagaggcgag
     1201 gggcggcgac tggtgagtac gccaaaaatt ttgactagcg gaggctagaa ggagagagat
     1261 gggtgcgaga gcgtcagtat taagcggggg agaattagat cgcgatggga aaaaattcgg
     1321 ttaaggccag ggggaaagaa aaaatataaa ttaaaacata tagtatgggc aagcagggag
     1381 ctagaacgat tcgcagttaa tcctggcctg ttagaaacat cagaaggctg tagacaaata
     1441 ctgggacagc tacaaccatc ccttcagaca ggatcagaag aacttagatc attatataat
     1501 acagtagcaa ccctctattg tgtgcatcaa aggatagaga taaaagacac caaggaagct
     1561 ttagacaaga tagaggaaga gcaaaacaaa agtaagacca ccgcacagca agcggccgct
     1621 gatcttcaga cctggaggag gagatatgag ggacaattgg agaagtgaat tatataaata
     1681 taaagtagta aaaattgaac cattaggagt agcacccacc aaggcaaaga gaagagtggt
     1741 gcagagagaa aaaagagcag tgggaatagg agctttgttc cttgggttct tgggagcagc
     1801 aggaagcact atgggcgcag cgtcaatgac gctgacggta caggccagac aattattgtc
     1861 tggtatagtg cagcagcaga acaatttgct gagggctatt gaggcgcaac agcatctgtt
     1921 gcaactcaca gtctggggca tcaagcagct ccaggcaaga atcctggctg tggaaagata
     1981 cctaaaggat caacagctcc tggggatttg gggttgctct ggaaaactca tttgcaccac
     2041 tgctgtgcct tggaatgcta gttggagtaa taaatctctg gaacagattt ggaatcacac
     2101 gacctggatg gagtgggaca gagaaattaa caattacaca agcttaatac actccttaat
     2161 tgaagaatcg caaaaccagc aagaaaagaa tgaacaagaa ttattggaat tagataaatg
     2221 ggcaagtttg tggaattggt ttaacataac aaattggctg tggtatataa aattattcat
     2281 aatgatagta ggaggcttgg taggtttaag aatagttttt gctgtacttt ctatagtgaa
     2341 tagagttagg cagggatatt caccattatc gtttcagacc cacctcccaa ccccgagggg
     2401 acccgacagg cccgaaggaa tagaagaaga aggtggagag agagacagag acagatccat
     2461 tcgattagtg aacggatctc gacggtatcg atcacgagac tagcctcgag cggccgcccc
     2521 cttcaccgag ggcctatttc ccatgattcc ttcatatttg catatacgat acaaggctgt
     2581 tagagagata attggaatta atttgactgt aaacacaaag atattagtac aaaatacgtg
     2641 acgtagaaag taataatttc ttgggtagtt tgcagtttta aaattatgtt ttaaaatgga
     2701 ctatcatatg cttaccgtaa cttgaaagta tttcgatttc ttggctttat atatcttgtg
     2761 gaaaggacga aacaccggcg agataaacat ggcaatcaac tcgagttgat tgccatgttt
     2821 atctcgtttt tgaattctcg acctcgagac aaatggcagt attcatccac aattttaaaa
     2881 gaaaaggggg gattgggggg tacagtgcag gggaaagaat agtagacata atagcaacag
     2941 acatacaaac taaagaatta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt
     3001 acagggacag cagagatcca ctttggccgc ggctcgaggg ggttggggtt gcgccttttc
     3061 caaggcagcc ctgggtttgc gcagggacgc ggctgctctg ggcgtggttc cgggaaacgc
     3121 agcggcgccg accctgggtc tcgcacattc ttcacgtccg ttcgcagcgt cacccggatc
     3181 ttcgccgcta cccttgtggg ccccccggcg acgcttcctg ctccgcccct aagtcgggaa
     3241 ggttccttgc ggttcgcggc gtgccggacg tgacaaacgg aagccgcacg tctcactagt
     3301 accctcgcag acggacagcg ccagggagca atggcagcgc gccgaccgcg atgggctgtg
     3361 gccaatagcg gctgctcagc agggcgcgcc gagagcagcg gccgggaagg ggcggtgcgg
     3421 gaggcggggt gtggggcggt agtgtgggcc ctgttcctgc ccgcgcggtg ttccgcattc
     3481 tgcaagcctc cggagcgcac gtcggcagtc ggctccctcg ttgaccgaat caccgacctc
     3541 tctccccagg gggatccacc ggagcttacc atgaccgagt acaagcccac ggtgcgcctc
     3601 gccacccgcg acgacgtccc cagggccgta cgcaccctcg ccgccgcgtt cgccgactac
     3661 cccgccacgc gccacaccgt cgatccggac cgccacatcg agcgggtcac cgagctgcaa
     3721 gaactcttcc tcacgcgcgt cgggctcgac atcggcaagg tgtgggtcgc ggacgacggc
     3781 gccgcggtgg cggtctggac cacgccggag agcgtcgaag cgggggcggt gttcgccgag
     3841 atcggcccgc gcatggccga gttgagcggt tcccggctgg ccgcgcagca acagatggaa
     3901 ggcctcctgg cgccgcaccg gcccaaggag cccgcgtggt tcctggccac cgtcggcgtc
     3961 tcgcccgacc accagggcaa gggtctgggc agcgccgtcg tgctccccgg agtggaggcg
     4021 gccgagcgcg ccggggtgcc cgccttcctg gagacctccg cgccccgcaa cctccccttc
     4081 tacgagcggc tcggcttcac cgtcaccgcc gacgtcgagg tgcccgaagg accgcgcacc
     4141 tggtgcatga cccgcaagcc cggtgcctga cgcccgcccc acgacccgca gcgcccgacc
     4201 gaaaggagcg cacgacccca tgcatcggta cctttaagac caatgactta caaggcagct
     4261 gtagatctta gccacttttt aaaagaaaag gggggactgg aagggctaat tcactcccaa
     4321 cgaagacaag atctgctttt tgcttgtact gggtctctct ggttagacca gatctgagcc
     4381 tgggagctct ctggctaact agggaaccca ctgcttaagc ctcaataaag cttgccttga
     4441 gtgcttcaag tagtgtgtgc ccgtctgttg tgtgactctg gtaactagag atccctcaga
     4501 cccttttagt cagtgtggaa aatctctagc agtagtagtt catgtcatct tattattcag
     4561 tatttataac ttgcaaagaa atgaatatca gagagtgaga ggaacttgtt tattgcagct
     4621 tataatggtt acaaataaag caatagcatc acaaatttca caaataaagc atttttttca
     4681 ctgcattcta gttgtggttt gtccaaactc atcaatgtat cttatcatgt ctggctctag
     4741 ctatcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc gcccattctc
     4801 cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tcggcctctg
     4861 agctattcca gaagtagtga ggaggctttt ttggaggcct agggacgtac ccaattcgcc
     4921 ctatagtgag tcgtattacg cgcgctcact ggccgtcgtt ttacaacgtc gtgactggga
     4981 aaaccctggc gttacccaac ttaatcgcct tgcagcacat ccccctttcg ccagctggcg
     5041 taatagcgaa gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga
     5101 atgggacgcg ccctgtagcg gcgcattaag cgcggcgggt gtggtggtta cgcgcagcgt
     5161 gaccgctaca cttgccagcg ccctagcgcc cgctcctttc gctttcttcc cttcctttct
     5221 cgccacgttc gccggctttc cccgtcaagc tctaaatcgg gggctccctt tagggttccg
     5281 atttagtgct ttacggcacc tcgaccccaa aaaacttgat tagggtgatg gttcacgtag
     5341 tgggccatcg ccctgataga cggtttttcg ccctttgacg ttggagtcca cgttctttaa
     5401 tagtggactc ttgttccaaa ctggaacaac actcaaccct atctcggtct attcttttga
     5461 tttataaggg attttgccga tttcggccta ttggttaaaa aatgagctga tttaacaaaa
     5521 atttaacgcg aattttaaca aaatattaac gcttacaatt taggtggcac ttttcgggga
     5581 aatgtgcgcg gaacccctat ttgtttattt ttctaaatac attcaaatat gtatccgctc
     5641 atgagacaat aaccctgata aatgcttcaa taatattgaa aaaggaagag tatgagtatt
     5701 caacatttcc gtgtcgccct tattcccttt tttgcggcat tttgccttcc tgtttttgct
     5761 cacccagaaa cgctggtgaa agtaaaagat gctgaagatc agttgggtgc acgagtgggt
     5821 tacatcgaac tggatctcaa cagcggtaag atccttgaga gttttcgccc cgaagaacgt
     5881 tttccaatga tgagcacttt taaagttctg ctatgtggcg cggtattatc ccgtattgac
     5941 gccgggcaag agcaactcgg tcgccgcata cactattctc agaatgactt ggttgagtac
     6001 tcaccagtca cagaaaagca tcttacggat ggcatgacag taagagaatt atgcagtgct
     6061 gccataacca tgagtgataa cactgcggcc aacttacttc tgacaacgat cggaggaccg
     6121 aaggagctaa ccgctttttt gcacaacatg ggggatcatg taactcgcct tgatcgttgg
     6181 gaaccggagc tgaatgaagc cataccaaac gacgagcgtg acaccacgat gcctgtagca
     6241 atggcaacaa cgttgcgcaa actattaact ggcgaactac ttactctagc ttcccggcaa
     6301 caattaatag actggatgga ggcggataaa gttgcaggac cacttctgcg ctcggccctt
     6361 ccggctggct ggtttattgc tgataaatct ggagccggtg agcgtgggtc tcgcggtatc
     6421 attgcagcac tggggccaga tggtaagccc tcccgtatcg tagttatcta cacgacgggg
     6481 agtcaggcaa ctatggatga acgaaataga cagatcgctg agataggtgc ctcactgatt
     6541 aagcattggt aactgtcaga ccaagtttac tcatatatac tttagattga tttaaaactt
     6601 catttttaat ttaaaaggat ctaggtgaag atcctttttg ataatctcat gaccaaaatc
     6661 ccttaacgtg agttttcgtt ccactgagcg tcagaccccg tagaaaagat caaaggatct
     6721 tcttgagatc ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta
     6781 ccagcggtgg tttgtttgcc ggatcaagag ctaccaactc tttttccgaa ggtaactggc
     6841 ttcagcagag cgcagatacc aaatactgtt cttctagtgt agccgtagtt aggccaccac
     6901 ttcaagaact ctgtagcacc gcctacatac ctcgctctgc taatcctgtt accagtggct
     6961 gctgccagtg gcgataagtc gtgtcttacc gggttggact caagacgata gttaccggat
     7021 aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg
     7081 acct
//
