LOCUS       sequence-199096-        7132 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 7132)
  AUTHORS   Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi 
            D, Firth A, Singer O, Trono D, Pfaff SL
  TITLE     Embryonic stem cell potency fluctuates with endogenous retrovirus 
            activity.
  JOURNAL   Nature. 2012 Jul 5;487(7405):57-63.
  PUBMED    22722858
REFERENCE   2  (bases 1 to 7132)
  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: "Nature."; 
            date: "2012-07-5"; volume: "487(7405)"; pages: "57-63"
COMMENT     Sequence Label: 2C::tdTomato Reporter
FEATURES             Location/Qualifiers
     source          1..7132
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(75..94)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     CDS             1067..2497
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEDVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     primer_bind     complement(2585..2602)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2591..2815
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2861..3289
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2948..2967)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3158..3179
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(3298..3318)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        3303..3632
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      3483..3618
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3545..3564
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3681..4706
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     CDS             3681..4706
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     polyA_signal    4836..4957
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4873..4892)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4927..4946
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(5006..5022)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5006..5022)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(5019..5041)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    5030..5046
                     /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)."
     promoter        complement(join(5054..5060,5061..5078,5079..5084))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5099..5120
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(5237..5254)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5408..5996)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5488..5507)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6167..6958,6959..7027))
                     /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     6790..6809
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7028..7132)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 cacatttccc cgaaaagtgc cacctgacgt cgacggatcg ggagatctcc cgatccccta
       61 tggtgcactc tcagtacaat ctgctctgat gccgcatagt taagccagta tctgctccct
      121 gcttgtgtgt tggaggtcgc tgagtagtgc gcgagcaaaa tttaagctac aacaaggcaa
      181 ggcttgaccg acaattgcat gaagaatctg cttagggtta ggcgttttgc gctgcttcgc
      241 gatgtacggg ccagatatac gcgtgctagc tgtagtggtt attcctggtt gtcaacttga
      301 caatatttgg aatgaactac agtccggaat tggaaggctc accagtgacc cttatctgga
      361 ggcttggaga tccttatctg gatcttggtt tgaagatctt gagccatagt ggctatggat
      421 tccagaagat tgaatctccg agtttaagga acacaccttt aatctgggct acgcctttca
      481 tctgggatta aaggtgtggt ggaacacacc tttaatctgg gctacacctt ctgctggaga
      541 caatataagg acattggaag aagggagtct agctcttgct cctgctcctt cgcctgcttg
      601 ctgcgtgaga ctgagtaact gctagatcct tggacttcca ttcacagctg tgactgaacg
      661 attgttggga attgagctgc cgactgtaag tcatcaataa attcctttat tatctagaga
      721 ctatccataa gttctgtgac tctagagaac cctgactaat acagaagttg gtaccaggag
      781 tggttctaga gtaacagaag tacaaggatg aatcttttaa aattctggaa ttggcttgtt
      841 gatccaccag cactttcaac tattgaaacc tctccagatt ctctccctcc tgggagctca
      901 gagaattttg aagacccatg gttgaaacta tattccgaac ttaaagaagc taatgccctt
      961 gattttctta atgaattagg tgattcagtg cacaaagctt ggtaccgagc tcggatccac
     1021 tagtaacggc cgccagtgtg ctggaattcg cccttgtctg tctagaatgg tgagcaaggg
     1081 cgaggacgtc atcaaagagt tcatgcgctt caaggtgcgc atggagggct ccatgaacgg
     1141 ccacgagttc gagatcgagg gcgagggcga gggccgcccc tacgagggca cccagaccgc
     1201 caagctgaag gtgaccaagg gcggccccct gcccttcgcc tgggacatcc tgtcccccca
     1261 gttcatgtac ggctccaagg cgtacgtgaa gcaccccgcc gacatccccg attacaagaa
     1321 gctgtccttc cccgagggct tcaagtggga gcgcgtgatg aacttcgagg acggcggtct
     1381 ggtgaccgtg acccaggact cctccctgca ggacggcacg ctgatctaca aggtgaagat
     1441 gcgcggcacc aacttccccc ccgacggccc cgtaatgcag aagaagacca tgggctggga
     1501 ggcctccacc gagcgcctgt acccccgcga cggcgtgctg aagggcgaga tccaccaggc
     1561 cctgaagctg aaggacggcg gccactacct ggtggagttc aagaccatct acatggccaa
     1621 gaagcccgtg caactgcccg gctactacta cgtggacacc aagctggaca tcacctccca
     1681 caacgaggac tacaccatcg tggaacagta cgagcgctcc gagggccgcc accacctgtt
     1741 cctggggcat ggcaccggca gcaccggcag cggcagctcc ggcaccgcct cctccgagga
     1801 caacaacatg gccgtcatca aagagttcat gcgcttcaag gtgcgcatgg agggctccat
     1861 gaacggccac gagttcgaga tcgagggcga gggcgagggc cgcccctacg agggcaccca
     1921 gaccgccaag ctgaaggtga ccaagggcgg ccccctgccc ttcgcctggg acatcctgtc
     1981 cccccagttc atgtacggct ccaaggcgta cgtgaagcac cccgccgaca tccccgatta
     2041 caagaagctg tccttccccg agggcttcaa gtgggagcgc gtgatgaact tcgaggacgg
     2101 cggtctggtg accgtgaccc aggactcctc cctgcaggac ggcacgctga tctacaaggt
     2161 gaagatgcgc ggcaccaact tcccccccga cggccccgta atgcagaaga agaccatggg
     2221 ctgggaggcc tccaccgagc gcctgtaccc ccgcgacggc gtgctgaagg gcgagatcca
     2281 ccaggccctg aagctgaagg acggcggcca ctacctggtg gagttcaaga ccatctacat
     2341 ggccaagaag cccgtgcaac tgcccggcta ctactacgtg gacaccaagc tggacatcac
     2401 ctcccacaac gaggactaca ccatcgtgga acagtacgag cgctccgagg gccgccacca
     2461 cctgttcctg tacggcatgg acgagctgta caagtaatct agacccccaa gggcgaattc
     2521 tgcagatatc catcacactg gcggccgctc gagtctagag ggcccgttta aacccgctga
     2581 tcagcctcga ctgtgccttc tagttgccag ccatctgttg tttgcccctc ccccgtgcct
     2641 tccttgaccc tggaaggtgc cactcccact gtcctttcct aataaaatga ggaaattgca
     2701 tcgcattgtc tgagtaggtg tcattctatt ctggggggtg gggtggggca ggacagcaag
     2761 ggggaggatt gggaagacaa tagcaggcat gctggggatg cggtgggctc tatggcttct
     2821 gaggcggaaa gaaccagctg gggctctagg gggtatcccc acgcgccctg tagcggcgca
     2881 ttaagcgcgg cgggtgtggt ggttacgcgc agcgtgaccg ctacacttgc cagcgcccta
     2941 gcgcccgctc ctttcgcttt cttcccttcc tttctcgcca cgttcgccgg ctttccccgt
     3001 caagctctaa atcgggggct ccctttaggg ttccgattta gtgctttacg gcacctcgac
     3061 cccaaaaaac ttgattaggg tgatggttca cgtagtgggc catcgccctg atagacggtt
     3121 tttcgccctt tgacgttgga gtccacgttc tttaatagtg gactcttgtt ccaaactgga
     3181 acaacactca accctatctc ggtctattct tttgatttat aagggatttt gccgatttcg
     3241 gcctattggt taaaaaatga gctgatttaa caaaaattta acgcgaatta attctgtgga
     3301 atgtgtgtca gttagggtgt ggaaagtccc caggctcccc agcaggcaga agtatgcaaa
     3361 gcatgcatct caattagtca gcaaccaggt gtggaaagtc cccaggctcc ccagcaggca
     3421 gaagtatgca aagcatgcat ctcaattagt cagcaaccat agtcccgccc ctaactccgc
     3481 ccatcccgcc cctaactccg cccagttccg cccattctcc gccccatggc tgactaattt
     3541 tttttattta tgcagaggcc gaggccgcct ctgcctctga gctattccag aagtagtgag
     3601 gaggcttttt tggaggccta ggcttttgca aaaagctccc gggagcttgt atatccattt
     3661 tcggatctga tcagcacgtg atgaaaaagc ctgaactcac cgcgacgtct gtcgagaagt
     3721 ttctgatcga aaagttcgac agcgtctccg acctgatgca gctctcggag ggcgaagaat
     3781 ctcgtgcttt cagcttcgat gtaggagggc gtggatatgt cctgcgggta aatagctgcg
     3841 ccgatggttt ctacaaagat cgttatgttt atcggcactt tgcatcggcc gcgctcccga
     3901 ttccggaagt gcttgacatt ggggaattca gcgagagcct gacctattgc atctcccgcc
     3961 gtgcacaggg tgtcacgttg caagacctgc ctgaaaccga actgcccgct gttctgcagc
     4021 cggtcgcgga ggccatggat gcgatcgctg cggccgatct tagccagacg agcgggttcg
     4081 gcccattcgg accgcaagga atcggtcaat acactacatg gcgtgatttc atatgcgcga
     4141 ttgctgatcc ccatgtgtat cactggcaaa ctgtgatgga cgacaccgtc agtgcgtccg
     4201 tcgcgcaggc tctcgatgag ctgatgcttt gggccgagga ctgccccgaa gtccggcacc
     4261 tcgtgcacgc ggatttcggc tccaacaatg tcctgacgga caatggccgc ataacagcgg
     4321 tcattgactg gagcgaggcg atgttcgggg attcccaata cgaggtcgcc aacatcttct
     4381 tctggaggcc gtggttggct tgtatggagc agcagacgcg ctacttcgag cggaggcatc
     4441 cggagcttgc aggatcgccg cggctccggg cgtatatgct ccgcattggt cttgaccaac
     4501 tctatcagag cttggttgac ggcaatttcg atgatgcagc ttgggcgcag ggtcgatgcg
     4561 acgcaatcgt ccgatccgga gccgggactg tcgggcgtac acaaatcgcc cgcagaagcg
     4621 cggccgtctg gaccgatggc tgtgtagaag tactcgccga tagtggaaac cgacgcccca
     4681 gcactcgtcc gagggcaaag gaatagcacg tgctacgaga tttcgattcc accgccgcct
     4741 tctatgaaag gttgggcttc ggaatcgttt tccgggacgc cggctggatg atcctccagc
     4801 gcggggatct catgctggag ttcttcgccc accccaactt gtttattgca gcttataatg
     4861 gttacaaata aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt
     4921 ctagttgtgg tttgtccaaa ctcatcaatg tatcttatca tgtctgtata ccgtcgacct
     4981 ctagctagag cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc
     5041 tcacaattcc acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat
     5101 gagtgagcta actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc
     5161 tgtcgtgcca gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg
     5221 ggcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag
     5281 cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag
     5341 gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc
     5401 tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc
     5461 agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc
     5521 tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt
     5581 cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg
     5641 ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
     5701 ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag
     5761 ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt
     5821 ggtggcctaa ctacggctac actagaagaa cagtatttgg tatctgcgct ctgctgaagc
     5881 cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta
     5941 gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag
     6001 atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga
     6061 ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa
     6121 gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa
     6181 tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc
     6241 ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga
     6301 taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa
     6361 gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt
     6421 gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg
     6481 ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc
     6541 aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg
     6601 gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag
     6661 cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt
     6721 actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt
     6781 caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac
     6841 gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac
     6901 ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag
     6961 caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa
     7021 tactcatact cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga
     7081 gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cg
//
