LOCUS       sequence-431939-        7552 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Generate lentiviruses encoding for human SOX17E57R (HMG box 
            numbering); for use in pluripotency reprogramming.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7552)
  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 7552)
  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-SOX17E57R
FEATURES             Location/Qualifiers
     source          1..7552
                     /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    2251..2269
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2293..2311
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2335..2353
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2382..2400
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2424..2442
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2466..2484
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2508..2526
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     primer_bind     2594..2618
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     CDS             3644..3661
                     /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             3650..3667
                     /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    3960..4548
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4013..4033)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4431..4442)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     protein_bind    complement(4678..4711)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     LTR             4730..4910
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     primer_bind     complement(4957..4975)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5043..5147
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5148..5216,5217..6008)
                     /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(5366..5385)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6179..6767
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6921..6938
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    7178..7199
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(7214..7219,7220..7237,7238..7244)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7252..7268
                     /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     7257..7279
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7276..7292
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7276..7292
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7342..7361
                     /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 aagtcgagtc gagtttacca ctccctatca gtgatagaga
     2401 aaagtgaaag tcgagtttac cactccctat cagtgataga gaaaagtgaa agtcgagttt
     2461 accactccct atcagtgata gagaaaagtg aaagtcgagt ttaccactcc ctatcagtga
     2521 tagagaaaag tgaaagtcga gctcggtacc cgggtcgagg taggcatgta cggtgggagg
     2581 cctatataag cagagctcgt ttagtgaacc gtcagatcgc ctggagacgc catccacgct
     2641 gttttgacct ccatagaaga caccgggacc gatccagcct gcggccacca ccggtatgag
     2701 cagcccggat gcgggatacg ccagtgacga ccagagccag acccagagcg cgctgcccgc
     2761 ggtgatggcc gggctgggcc cctgcccctg ggccgagtcg ctgagcccca tcggggacat
     2821 gaaggtgaag ggcgaggcgc cggcgaacag cggagcaccg gccggggccg cgggccgagc
     2881 caagggcgag tcccgtatcc ggcggccgat gaacgctttc atggtgtggg ctaaggacga
     2941 gcgcaagcgg ctggcgcagc agaatccaga cctgcacaac gccgagttga gcaagatgct
     3001 gggcaagtcg tggaaggcgc tgacgctggc ggaaaagcgg cccttcgtgg aggaagcaag
     3061 gcggctgcgc gtgcagcaca tgcaggacca ccccaactac aagtaccggc cgcggcggcg
     3121 caagcaggtg aagcggctga agcgggtgga gggcggcttc ctgcacggcc tggctgagcc
     3181 gcaggcggcc gcgctgggcc ccgagggcgg ccgcgtggcc atggacggcc tgggcctcca
     3241 gttccccgag cagggcttcc ccgccggccc gccgctgctg cctccgcaca tgggcggcca
     3301 ctaccgcgac tgccagagtc tgggcgcgcc tccgctcgac ggctacccgt tgcccacgcc
     3361 cgacacgtcc ccgctggacg gcgtggaccc cgacccggct ttcttcgccg ccccgatgcc
     3421 cggggactgc ccggcggccg gcacctacag ctacgcgcag gtctcggact acgctggccc
     3481 cccggagcct cccgccggtc ccatgcaccc ccgactcggc ccagagcccg cgggtccctc
     3541 gattccgggc ctcctggcgc cacccagcgc ccttcacgtg tactacggcg cgatgggctc
     3601 gcccggggcg ggcggcgggc gcggcttcca gatgcagccg caacaccagc accagcacca
     3661 gcaccagcac caccccccgg gccccggaca gccgtcgccc cctccggagg cactgccctg
     3721 ccgggacggc acggacccca gtcagcccgc cgagctcctc ggggaggtgg accgcacgga
     3781 atttgaacag tatctgcact tcgtgtgcaa gcctgagatg ggcctcccct accaggggca
     3841 tgactccggt gtgaatctcc ccgacagcca cggggccatt tcctcggtgg tgtccgacgc
     3901 cagctccgcg gtatattact gcaactatcc tgacgtgtga gtcgacatcg atagatccta
     3961 atcaacctct ggattacaaa atttgtgaaa gattgactgg tattcttaac tatgttgctc
     4021 cttttacgct atgtggatac gctgctttaa tgcctttgta tcatgctatt gcttcccgta
     4081 tggctttcat tttctcctcc ttgtataaat cctggttgct gtctctttat gaggagttgt
     4141 ggcccgttgt caggcaacgt ggcgtggtgt gcactgtgtt tgctgacgca acccccactg
     4201 gttggggcat tgccaccacc tgtcagctcc tttccgggac tttcgctttc cccctcccta
     4261 ttgccacggc ggaactcatc gccgcctgcc ttgcccgctg ctggacaggg gctcggctgt
     4321 tgggcactga caattccgtg gtgttgtcgg ggaaatcatc gtcctttcct tggctgctcg
     4381 cctgtgttgc cacctggatt ctgcgcggga cgtccttctg ctacgtccct tcggccctca
     4441 atccagcgga ccttccttcc cgcggcctgc tgccggctct gcggcctctt ccgcgtcttc
     4501 gccttcgccc tcagacgagt cggatctccc tttgggccgc ctccccgcct ggtaccttta
     4561 agaccaatga cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga
     4621 ctggaagggc taattcactc ccaacgaaga caagatcacc tgcaggacag gcgcgccata
     4681 acttcgtata gcatacatta tacgaagtta tctgcttttt gcttgtactg ggtctctctg
     4741 gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc
     4801 tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg
     4861 taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca cccgggcgat
     4921 taaggaaagg gctagatcat tcttgaagac gaaagggcct cgtgatacgc ctatttttat
     4981 aggttaatgt catgataata atggtttctt agacgtcagg tggcactttt cggggaaatg
     5041 tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat ccgctcatga
     5101 gacaataacc ctgataaatg cttcaataat attgaaaaag gaagagtatg agtattcaac
     5161 atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt tttgctcacc
     5221 cagaaacgct ggtgaaagta aaagatgctg aagatcagtt gggtgcacga gtgggttaca
     5281 tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc
     5341 caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt gttgacgccg
     5401 ggcaagagca actcggtcgc cgcatacact attctcagaa tgacttggtt gagtactcac
     5461 cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc agtgctgcca
     5521 taaccatgag tgataacact gcggccaact tacttctgac aacgatcgga ggaccgaagg
     5581 agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat cgttgggaac
     5641 cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg
     5701 caacaacgtt gcgcaaacta ttaactggcg aactacttac tctagcttcc cggcaacaat
     5761 taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg gcccttccgg
     5821 ctggctggtt tattgctgat aaatctggag ccggtgagcg tgggtctcgc ggtatcattg
     5881 cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg acggggagtc
     5941 aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca ctgattaagc
     6001 attggtaact gtcagaccaa gtttactcat atatacttta gattgattta aaacttcatt
     6061 tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc aaaatccctt
     6121 aacgtgagtt ttcgttccac tgagcgtcag accccgtaga aaagatcaaa ggatcttctt
     6181 gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag
     6241 cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta actggcttca
     6301 gcagagcgca gataccaaat actgttcttc tagtgtagcc gtagttaggc caccacttca
     6361 agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca gtggctgctg
     6421 ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     6481 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     6541 acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     6601 gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc
     6661 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg
     6721 agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcaacg
     6781 cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc tttcctgcgt
     6841 tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat accgctcgcc
     6901 gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag cgcccaatac
     6961 gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagcaagctc atggctgact
     7021 aatttttttt atttatgcag aggccgaggc cgcctcggcc tctgagctat tccagaagta
     7081 gtgaggaggc ttttttggag gcctaggctt ttgcaaaaag ctccccgtgg cacgacaggt
     7141 ttcccgactg gaaagcgggc agtgagcgca acgcaattaa tgtgagttag ctcactcatt
     7201 aggcacccca ggctttacac tttatgcttc cggctcgtat gttgtgtgga attgtgagcg
     7261 gataacaatt tcacacagga aacagctatg acatgattac gaatttcaca aataaagcat
     7321 ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct tatcatgtct
     7381 ggatcaactg gataactcaa gctaaccaaa atcatcccaa acttcccacc ccatacccta
     7441 ttaccactgc caattacctg tggtttcatt tactctaaac ctgtgattcc tctgaattat
     7501 tttcatttta aagaaattgt atttgttaaa tatgtactac aaacttagta gt
//
