LOCUS       sequence-465424-        7262 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses reconstructed Ancestral SoxB in mammalian cells, for 
            lentivirus generation.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7262)
  AUTHORS   Gao Y, Tan DS, Girbig M, Hu H, Zhou X, Xie Q, Yeung SW, Lee KS, Ho 
            SY, Cojocaru V, Yan J, Hochberg GKA, de Mendoza A, Jauch R
  TITLE     The emergence of Sox and POU transcription factors predates the 
            origins of animal stem cells.
  JOURNAL   Nat Commun. 2024 Nov 14;15(1):9868. doi: 10.1038/s41467-024-54152-x.
  PUBMED    39543096
REFERENCE   2  (bases 1 to 7262)
  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 
            Commun."; date: "2024-11-14"; volume: "15(1):9868. doi"; pages: " 
            10.1038/s41467-024-54152-x"
COMMENT     Sequence Label: pHAGE2-TetO-AncSoxB
FEATURES             Location/Qualifiers
     source          1..7262
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             1..634
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    681..806
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1303..1536
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1721..1765
                     /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"
     misc_feature    2058..2175
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     protein_bind    join(2251..2269,2270..2292,2293..2311,2312..2334,2335..2353,
                     2354..2376,2377..2395,2396..2418,2419..2437,2438..2460,
                     2461..2479,2480..2502,2503..2521)
                     /label=tetracycline response element
                     /bound_moiety="tetracycline repressor TetR"
                     /note="contains seven copies of the tetracycline operator 
                     tetO"
     primer_bind     2589..2613
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     misc_feature    3670..4258
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3723..3743)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4141..4152)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     protein_bind    complement(4388..4421)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     LTR             4440..4620
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     primer_bind     complement(4667..4685)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        4753..4857
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4858..4926,4927..5718)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(5076..5095)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5889..6477
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6631..6648
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    6888..6909
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(6924..6929,6930..6947,6948..6954)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6962..6978
                     /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     6967..6989
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     6986..7002
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     6986..7002
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7052..7071
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
ORIGIN
        1 tggaagggct aattcactcc caaagaagac aagatatcct tgatctgtgg atctaccaca
       61 cacaaggcta cttccctgat tagcagaact acacaccagg gccaggggtc agatatccac
      121 tgacctttgg atggtgctac aagctagtac cagttgagcc agataaggta gaagaggcca
      181 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatgggatg gatgacccgg
      241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac gtggcccgag
      301 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg
      361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat
      421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga
      481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
      541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
      601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
      661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
      721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
      781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
      841 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
      901 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
      961 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     1021 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     1081 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     1141 aagcggccgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     1201 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     1261 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     1321 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     1381 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     1441 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     1501 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     1561 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     1621 gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt
     1681 aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt
     1741 ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta
     1801 tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt
     1861 actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct
     1921 cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga
     1981 cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgccgaa ttcacaaatg
     2041 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
     2101 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
     2161 aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg gactagtcca
     2221 caccctaact gacacactcg agtttaccac tccctatcag tgatagagaa aagtgaaagt
     2281 cgagtttacc actccctatc agtgatagag aaaagtgaaa gtcgagttta ccactcccta
     2341 tcagtgatag agaaaagtga aagtcgagtt taccactccc tatcagtgat agagaaaagt
     2401 gaaagtcgag tttaccactc cctatcagtg atagagaaaa gtgaaagtcg agtttaccac
     2461 tccctatcag tgatagagaa aagtgaaagt cgagtttacc actccctatc agtgatagag
     2521 aaaagtgaaa gtcgagctcg gtacccgggt cgaggtaggc atgtacggtg ggaggcctat
     2581 ataagcagag ctcgtttagt gaaccgtcag atcgcctgga gacgccatcc acgctgtttt
     2641 gacctccata gaagacaccg ggaccgatcc agcctgcggc caccaccggt atgtacaaca
     2701 tgatggagac cgagctgaag ccccccggcc ctcagcaagc tagcggcgga ggcggaggag
     2761 gcggaaacgc taccgccgct gccaccggcg gcaatcagaa gaacagccct gaccacatca
     2821 agaggcctat gaacgccttc atggtgtgga gcaaggagca gaggaggaag atcgcccaag
     2881 agaaccctaa gatgcacaac agcgagatca gcaagaggct gggcgccgag tggaagatgc
     2941 tgagcgacga ggagaagagg cctttcgtgg aggaggccaa gaggctgagg gctcagcaca
     3001 tgaaggagca ccctgactac aagtataggc ctaggaggaa gaaaaagacc ctgatgaaga
     3061 aggataaata caccctgccc ggcggcctgc tggctcctgg cggcaactcc atggctagcg
     3121 gcgtcggcgt cggcgccgga ctgggcgccg gcgtgaatca gaggatggac agctacgccc
     3181 acatgaacgg ctggagcaac ggcagctaca gcatgatgca agagcagctg ggctaccctc
     3241 agcaccctgg cctgaacgcc cacggcgccg ctcagatgca gcctatgcat aggtacgacg
     3301 tgagcgccct gcagtacaac agcatgacaa gcagccaaac ctacatgaac ggcagcccta
     3361 cctacagcat gagctacagc caacaaggca cccctggcat ggccctgggc agcatgggca
     3421 gcgtggtgaa gagcgaggct agcagcagcc ctcctgtggt gacaagcagc agccacagca
     3481 gagccccttg ccaagccggc gacctgaggg acatgatcag catgtacctg cctggcgccg
     3541 aggtgcctga gcctgccgcc cctagcagac tgcacatggc tcagcactat cagagcggcc
     3601 ctgtgcctgg caccgccatc aacggcaccc tgcctctgag ccacatgtga gtcgacatcg
     3661 atagatccta atcaacctct ggattacaaa atttgtgaaa gattgactgg tattcttaac
     3721 tatgttgctc cttttacgct atgtggatac gctgctttaa tgcctttgta tcatgctatt
     3781 gcttcccgta tggctttcat tttctcctcc ttgtataaat cctggttgct gtctctttat
     3841 gaggagttgt ggcccgttgt caggcaacgt ggcgtggtgt gcactgtgtt tgctgacgca
     3901 acccccactg gttggggcat tgccaccacc tgtcagctcc tttccgggac tttcgctttc
     3961 cccctcccta ttgccacggc ggaactcatc gccgcctgcc ttgcccgctg ctggacaggg
     4021 gctcggctgt tgggcactga caattccgtg gtgttgtcgg ggaaatcatc gtcctttcct
     4081 tggctgctcg cctgtgttgc cacctggatt ctgcgcggga cgtccttctg ctacgtccct
     4141 tcggccctca atccagcgga ccttccttcc cgcggcctgc tgccggctct gcggcctctt
     4201 ccgcgtcttc gccttcgccc tcagacgagt cggatctccc tttgggccgc ctccccgcct
     4261 ggtaccttta agaccaatga cttacaaggc agctgtagat cttagccact ttttaaaaga
     4321 aaagggggga ctggaagggc taattcactc ccaacgaaga caagatcacc tgcaggacag
     4381 gcgcgccata acttcgtata gcatacatta tacgaagtta tctgcttttt gcttgtactg
     4441 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac
     4501 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt
     4561 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca
     4621 cccgggcgat taaggaaagg gctagatcat tcttgaagac gaaagggcct cgtgatacgc
     4681 ctatttttat aggttaatgt catgataata atggtttctt agacgtcagg tggcactttt
     4741 cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat
     4801 ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag gaagagtatg
     4861 agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt
     4921 tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt gggtgcacga
     4981 gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa
     5041 gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt
     5101 gttgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa tgacttggtt
     5161 gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc
     5221 agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac aacgatcgga
     5281 ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat
     5341 cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct
     5401 gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac tctagcttcc
     5461 cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg
     5521 gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg tgggtctcgc
     5581 ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg
     5641 acggggagtc aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca
     5701 ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta gattgattta
     5761 aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc
     5821 aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga aaagatcaaa
     5881 ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca
     5941 ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta
     6001 actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc gtagttaggc
     6061 caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca
     6121 gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta
     6181 ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag
     6241 cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt
     6301 cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc
     6361 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
     6421 ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
     6481 gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc
     6541 tttcctgcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat
     6601 accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag
     6661 cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagcaagctc
     6721 atggctgact aatttttttt atttatgcag aggccgaggc cgcctcggcc tctgagctat
     6781 tccagaagta gtgaggaggc ttttttggag gcctaggctt ttgcaaaaag ctccccgtgg
     6841 cacgacaggt ttcccgactg gaaagcgggc agtgagcgca acgcaattaa tgtgagttag
     6901 ctcactcatt aggcacccca ggctttacac tttatgcttc cggctcgtat gttgtgtgga
     6961 attgtgagcg gataacaatt tcacacagga aacagctatg acatgattac gaatttcaca
     7021 aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct
     7081 tatcatgtct ggatcaactg gataactcaa gctaaccaaa atcatcccaa acttcccacc
     7141 ccatacccta ttaccactgc caattacctg tggtttcatt tactctaaac ctgtgattcc
     7201 tctgaattat tttcatttta aagaaattgt atttgttaaa tatgtactac aaacttagta
     7261 gt
//
