LOCUS       sequence-431995-        7589 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Generate lentiviruses encoding for human SOX17E57W(HMG box 
            numbering); for use in pluripotency reprogramming.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7589)
  AUTHORS   Ho SY, Hu H, Ho DHH, Renom APS, Yeung SW, Boerner F, Weng M, 
            Hutchins AP, Jauch R
  TITLE     An acidic residue within the OCT4 dimerization interface of SOX17 is
            necessary and sufficient to overcome its pluripotency-inducing 
            activity.
  JOURNAL   Stem Cell Reports. 2025 Mar 11;20(3):102398. doi: 
            10.1016/j.stemcr.2025.102398. Epub 2025 Feb 6.
  PUBMED    39919754
REFERENCE   2  (bases 1 to 7589)
  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: "Stem Cell 
            Reports."; date: "2025-03-11"; volume: "20(3):102398. doi"; pages: "
            10.1016/j.stemcr.2025.102398. Epub 2025 Feb 6"
COMMENT     Sequence Label: pHAGE2-TetO-SOX17E57W
FEATURES             Location/Qualifiers
     source          1..7589
                     /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"
     protein_bind    join(2293..2311,2312..2334,2335..2353,2354..2376,2377..2395,
                     2396..2418,2419..2437,2438..2460,2461..2479,2480..2502,
                     2503..2521,2522..2544,2545..2563)
                     /label=tetracycline response element
                     /bound_moiety="tetracycline repressor TetR"
                     /note="contains seven copies of the tetracycline operator 
                     tetO"
     primer_bind     2631..2655
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     CDS             3681..3698
                     /codon_start=1
                     /product="HQHQHQ metal affinity tag"
                     /label=HQ tag
                     /note="The HQ tag binds to nickel and other metal ions much
                     like the 6xHis tag, but may allow elution at lower 
                     concentrations of imidazole (Godat et al., 2008)."
                     /translation="HQHQHQ"
     CDS             3687..3704
                     /codon_start=1
                     /product="HQHQHQ metal affinity tag"
                     /label=HQ tag
                     /note="The HQ tag binds to nickel and other metal ions much
                     like the 6xHis tag, but may allow elution at lower 
                     concentrations of imidazole (Godat et al., 2008)."
                     /translation="HQHQHQ"
     misc_feature    3997..4585
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4050..4070)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4468..4479)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     protein_bind    complement(4715..4748)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     LTR             4767..4947
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     primer_bind     complement(4994..5012)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5080..5184
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5185..5253,5254..6045)
                     /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(5403..5422)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6216..6804
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6958..6975
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    7215..7236
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(7251..7256,7257..7274,7275..7281)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7289..7305
                     /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     7294..7316
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7313..7329
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7313..7329
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7379..7398
                     /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 gtcgagttta ccactcccta tcagtgatag agaaaagtga aagtcgagct
     2581 cggtacccgg gtcgaggtag gcatgtacgg tgggaggcct atataagcag agctcgttta
     2641 gtgaaccgtc agatcgcctg gagacgccat ccacgctgtt ttgacctcca tagaagacac
     2701 cgggaccgat ccagcctgcg gccaccaccg gtatgagcag cccggatgcg ggatacgcca
     2761 gtgacgacca gagccagacc cagagcgcgc tgcccgcggt gatggccggg ctgggcccct
     2821 gcccctgggc cgagtcgctg agccccatcg gggacatgaa ggtgaagggc gaggcgccgg
     2881 cgaacagcgg agcaccggcc ggggccgcgg gccgagccaa gggcgagtcc cgtatccggc
     2941 ggccgatgaa cgctttcatg gtgtgggcta aggacgagcg caagcggctg gcgcagcaga
     3001 atccagacct gcacaacgcc gagttgagca agatgctggg caagtcgtgg aaggcgctga
     3061 cgctggcgga aaagcggccc ttcgtggagg aagcatggcg gctgcgcgtg cagcacatgc
     3121 aggaccaccc caactacaag taccggccgc ggcggcgcaa gcaggtgaag cggctgaagc
     3181 gggtggaggg cggcttcctg cacggcctgg ctgagccgca ggcggccgcg ctgggccccg
     3241 agggcggccg cgtggccatg gacggcctgg gcctccagtt ccccgagcag ggcttccccg
     3301 ccggcccgcc gctgctgcct ccgcacatgg gcggccacta ccgcgactgc cagagtctgg
     3361 gcgcgcctcc gctcgacggc tacccgttgc ccacgcccga cacgtccccg ctggacggcg
     3421 tggaccccga cccggctttc ttcgccgccc cgatgcccgg ggactgcccg gcggccggca
     3481 cctacagcta cgcgcaggtc tcggactacg ctggcccccc ggagcctccc gccggtccca
     3541 tgcacccccg actcggccca gagcccgcgg gtccctcgat tccgggcctc ctggcgccac
     3601 ccagcgccct tcacgtgtac tacggcgcga tgggctcgcc cggggcgggc ggcgggcgcg
     3661 gcttccagat gcagccgcaa caccagcacc agcaccagca ccagcaccac cccccgggcc
     3721 ccggacagcc gtcgccccct ccggaggcac tgccctgccg ggacggcacg gaccccagtc
     3781 agcccgccga gctcctcggg gaggtggacc gcacggaatt tgaacagtat ctgcacttcg
     3841 tgtgcaagcc tgagatgggc ctcccctacc aggggcatga ctccggtgtg aatctccccg
     3901 acagccacgg ggccatttcc tcggtggtgt ccgacgccag ctccgcggta tattactgca
     3961 actatcctga cgtgtgagtc gacatcgata gatcctaatc aacctctgga ttacaaaatt
     4021 tgtgaaagat tgactggtat tcttaactat gttgctcctt ttacgctatg tggatacgct
     4081 gctttaatgc ctttgtatca tgctattgct tcccgtatgg ctttcatttt ctcctccttg
     4141 tataaatcct ggttgctgtc tctttatgag gagttgtggc ccgttgtcag gcaacgtggc
     4201 gtggtgtgca ctgtgtttgc tgacgcaacc cccactggtt ggggcattgc caccacctgt
     4261 cagctccttt ccgggacttt cgctttcccc ctccctattg ccacggcgga actcatcgcc
     4321 gcctgccttg cccgctgctg gacaggggct cggctgttgg gcactgacaa ttccgtggtg
     4381 ttgtcgggga aatcatcgtc ctttccttgg ctgctcgcct gtgttgccac ctggattctg
     4441 cgcgggacgt ccttctgcta cgtcccttcg gccctcaatc cagcggacct tccttcccgc
     4501 ggcctgctgc cggctctgcg gcctcttccg cgtcttcgcc ttcgccctca gacgagtcgg
     4561 atctcccttt gggccgcctc cccgcctggt acctttaaga ccaatgactt acaaggcagc
     4621 tgtagatctt agccactttt taaaagaaaa ggggggactg gaagggctaa ttcactccca
     4681 acgaagacaa gatcacctgc aggacaggcg cgccataact tcgtatagca tacattatac
     4741 gaagttatct gctttttgct tgtactgggt ctctctggtt agaccagatc tgagcctggg
     4801 agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc
     4861 ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct
     4921 tttagtcagt gtggaaaatc tctagcaccc gggcgattaa ggaaagggct agatcattct
     4981 tgaagacgaa agggcctcgt gatacgccta tttttatagg ttaatgtcat gataataatg
     5041 gtttcttaga cgtcaggtgg cacttttcgg ggaaatgtgc gcggaacccc tatttgttta
     5101 tttttctaaa tacattcaaa tatgtatccg ctcatgagac aataaccctg ataaatgctt
     5161 caataatatt gaaaaaggaa gagtatgagt attcaacatt tccgtgtcgc ccttattccc
     5221 ttttttgcgg cattttgcct tcctgttttt gctcacccag aaacgctggt gaaagtaaaa
     5281 gatgctgaag atcagttggg tgcacgagtg ggttacatcg aactggatct caacagcggt
     5341 aagatccttg agagttttcg ccccgaagaa cgttttccaa tgatgagcac ttttaaagtt
     5401 ctgctatgtg gcgcggtatt atcccgtgtt gacgccgggc aagagcaact cggtcgccgc
     5461 atacactatt ctcagaatga cttggttgag tactcaccag tcacagaaaa gcatcttacg
     5521 gatggcatga cagtaagaga attatgcagt gctgccataa ccatgagtga taacactgcg
     5581 gccaacttac ttctgacaac gatcggagga ccgaaggagc taaccgcttt tttgcacaac
     5641 atgggggatc atgtaactcg ccttgatcgt tgggaaccgg agctgaatga agccatacca
     5701 aacgacgagc gtgacaccac gatgcctgta gcaatggcaa caacgttgcg caaactatta
     5761 actggcgaac tacttactct agcttcccgg caacaattaa tagactggat ggaggcggat
     5821 aaagttgcag gaccacttct gcgctcggcc cttccggctg gctggtttat tgctgataaa
     5881 tctggagccg gtgagcgtgg gtctcgcggt atcattgcag cactggggcc agatggtaag
     5941 ccctcccgta tcgtagttat ctacacgacg gggagtcagg caactatgga tgaacgaaat
     6001 agacagatcg ctgagatagg tgcctcactg attaagcatt ggtaactgtc agaccaagtt
     6061 tactcatata tactttagat tgatttaaaa cttcattttt aatttaaaag gatctaggtg
     6121 aagatccttt ttgataatct catgaccaaa atcccttaac gtgagttttc gttccactga
     6181 gcgtcagacc ccgtagaaaa gatcaaagga tcttcttgag atcctttttt tctgcgcgta
     6241 atctgctgct tgcaaacaaa aaaaccaccg ctaccagcgg tggtttgttt gccggatcaa
     6301 gagctaccaa ctctttttcc gaaggtaact ggcttcagca gagcgcagat accaaatact
     6361 gttcttctag tgtagccgta gttaggccac cacttcaaga actctgtagc accgcctaca
     6421 tacctcgctc tgctaatcct gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt
     6481 accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg
     6541 ggttcgtgca cacagcccag cttggagcga acgacctaca ccgaactgag atacctacag
     6601 cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta
     6661 agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat
     6721 ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg
     6781 tcaggggggc ggagcctatg gaaaaacgcc agcaacgcgg cctttttacg gttcctggcc
     6841 ttttgctggc cttttgctca catgttcttt cctgcgttat cccctgattc tgtggataac
     6901 cgtattaccg cctttgagtg agctgatacc gctcgccgca gccgaacgac cgagcgcagc
     6961 gagtcagtga gcgaggaagc ggaagagcgc ccaatacgca aaccgcctct ccccgcgcgt
     7021 tggccgattc attaatgcag caagctcatg gctgactaat tttttttatt tatgcagagg
     7081 ccgaggccgc ctcggcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc
     7141 taggcttttg caaaaagctc cccgtggcac gacaggtttc ccgactggaa agcgggcagt
     7201 gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc tttacacttt
     7261 atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca cacaggaaac
     7321 agctatgaca tgattacgaa tttcacaaat aaagcatttt tttcactgca ttctagttgt
     7381 ggtttgtcca aactcatcaa tgtatcttat catgtctgga tcaactggat aactcaagct
     7441 aaccaaaatc atcccaaact tcccacccca taccctatta ccactgccaa ttacctgtgg
     7501 tttcatttac tctaaacctg tgattcctct gaattatttt cattttaaag aaattgtatt
     7561 tgttaaatat gtactacaaa cttagtagt
//
