LOCUS       sequence-432001-        7547 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Generate lentiviruses encoding for human SOX17E57Y (HMG box 
            numbering); for use in pluripotency reprogramming.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7547)
  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 7547)
  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-SOX17E57Y
FEATURES             Location/Qualifiers
     source          1..7547
                     /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"
     CDS             3639..3656
                     /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             3645..3662
                     /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    3955..4543
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4008..4028)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4426..4437)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     protein_bind    complement(4673..4706)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     LTR             4725..4905
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     primer_bind     complement(4952..4970)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5038..5142
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5143..5211,5212..6003)
                     /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(5361..5380)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6174..6762
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6916..6933
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    7173..7194
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(7209..7214,7215..7232,7233..7239)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7247..7263
                     /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     7252..7274
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7271..7287
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7271..7287
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7337..7356
                     /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 atgagcagcc
     2701 cggatgcggg atacgccagt gacgaccaga gccagaccca gagcgcgctg cccgcggtga
     2761 tggccgggct gggcccctgc ccctgggccg agtcgctgag ccccatcggg gacatgaagg
     2821 tgaagggcga ggcgccggcg aacagcggag caccggccgg ggccgcgggc cgagccaagg
     2881 gcgagtcccg tatccggcgg ccgatgaacg ctttcatggt gtgggctaag gacgagcgca
     2941 agcggctggc gcagcagaat ccagacctgc acaacgccga gttgagcaag atgctgggca
     3001 agtcgtggaa ggcgctgacg ctggcggaaa agcggccctt cgtggaggaa gcatatcggc
     3061 tgcgcgtgca gcacatgcag gaccacccca actacaagta ccggccgcgg cggcgcaagc
     3121 aggtgaagcg gctgaagcgg gtggagggcg gcttcctgca cggcctggct gagccgcagg
     3181 cggccgcgct gggccccgag ggcggccgcg tggccatgga cggcctgggc ctccagttcc
     3241 ccgagcaggg cttccccgcc ggcccgccgc tgctgcctcc gcacatgggc ggccactacc
     3301 gcgactgcca gagtctgggc gcgcctccgc tcgacggcta cccgttgccc acgcccgaca
     3361 cgtccccgct ggacggcgtg gaccccgacc cggctttctt cgccgccccg atgcccgggg
     3421 actgcccggc ggccggcacc tacagctacg cgcaggtctc ggactacgct ggccccccgg
     3481 agcctcccgc cggtcccatg cacccccgac tcggcccaga gcccgcgggt ccctcgattc
     3541 cgggcctcct ggcgccaccc agcgcccttc acgtgtacta cggcgcgatg ggctcgcccg
     3601 gggcgggcgg cgggcgcggc ttccagatgc agccgcaaca ccagcaccag caccagcacc
     3661 agcaccaccc cccgggcccc ggacagccgt cgccccctcc ggaggcactg ccctgccggg
     3721 acggcacgga ccccagtcag cccgccgagc tcctcgggga ggtggaccgc acggaatttg
     3781 aacagtatct gcacttcgtg tgcaagcctg agatgggcct cccctaccag gggcatgact
     3841 ccggtgtgaa tctccccgac agccacgggg ccatttcctc ggtggtgtcc gacgccagct
     3901 ccgcggtata ttactgcaac tatcctgacg tgtgagtcga catcgataga tcctaatcaa
     3961 cctctggatt acaaaatttg tgaaagattg actggtattc ttaactatgt tgctcctttt
     4021 acgctatgtg gatacgctgc tttaatgcct ttgtatcatg ctattgcttc ccgtatggct
     4081 ttcattttct cctccttgta taaatcctgg ttgctgtctc tttatgagga gttgtggccc
     4141 gttgtcaggc aacgtggcgt ggtgtgcact gtgtttgctg acgcaacccc cactggttgg
     4201 ggcattgcca ccacctgtca gctcctttcc gggactttcg ctttccccct ccctattgcc
     4261 acggcggaac tcatcgccgc ctgccttgcc cgctgctgga caggggctcg gctgttgggc
     4321 actgacaatt ccgtggtgtt gtcggggaaa tcatcgtcct ttccttggct gctcgcctgt
     4381 gttgccacct ggattctgcg cgggacgtcc ttctgctacg tcccttcggc cctcaatcca
     4441 gcggaccttc cttcccgcgg cctgctgccg gctctgcggc ctcttccgcg tcttcgcctt
     4501 cgccctcaga cgagtcggat ctccctttgg gccgcctccc cgcctggtac ctttaagacc
     4561 aatgacttac aaggcagctg tagatcttag ccacttttta aaagaaaagg ggggactgga
     4621 agggctaatt cactcccaac gaagacaaga tcacctgcag gacaggcgcg ccataacttc
     4681 gtatagcata cattatacga agttatctgc tttttgcttg tactgggtct ctctggttag
     4741 accagatctg agcctgggag ctctctggct aactagggaa cccactgctt aagcctcaat
     4801 aaagcttgcc ttgagtgctt caagtagtgt gtgcccgtct gttgtgtgac tctggtaact
     4861 agagatccct cagacccttt tagtcagtgt ggaaaatctc tagcacccgg gcgattaagg
     4921 aaagggctag atcattcttg aagacgaaag ggcctcgtga tacgcctatt tttataggtt
     4981 aatgtcatga taataatggt ttcttagacg tcaggtggca cttttcgggg aaatgtgcgc
     5041 ggaaccccta tttgtttatt tttctaaata cattcaaata tgtatccgct catgagacaa
     5101 taaccctgat aaatgcttca ataatattga aaaaggaaga gtatgagtat tcaacatttc
     5161 cgtgtcgccc ttattccctt ttttgcggca ttttgccttc ctgtttttgc tcacccagaa
     5221 acgctggtga aagtaaaaga tgctgaagat cagttgggtg cacgagtggg ttacatcgaa
     5281 ctggatctca acagcggtaa gatccttgag agttttcgcc ccgaagaacg ttttccaatg
     5341 atgagcactt ttaaagttct gctatgtggc gcggtattat cccgtgttga cgccgggcaa
     5401 gagcaactcg gtcgccgcat acactattct cagaatgact tggttgagta ctcaccagtc
     5461 acagaaaagc atcttacgga tggcatgaca gtaagagaat tatgcagtgc tgccataacc
     5521 atgagtgata acactgcggc caacttactt ctgacaacga tcggaggacc gaaggagcta
     5581 accgcttttt tgcacaacat gggggatcat gtaactcgcc ttgatcgttg ggaaccggag
     5641 ctgaatgaag ccataccaaa cgacgagcgt gacaccacga tgcctgtagc aatggcaaca
     5701 acgttgcgca aactattaac tggcgaacta cttactctag cttcccggca acaattaata
     5761 gactggatgg aggcggataa agttgcagga ccacttctgc gctcggccct tccggctggc
     5821 tggtttattg ctgataaatc tggagccggt gagcgtgggt ctcgcggtat cattgcagca
     5881 ctggggccag atggtaagcc ctcccgtatc gtagttatct acacgacggg gagtcaggca
     5941 actatggatg aacgaaatag acagatcgct gagataggtg cctcactgat taagcattgg
     6001 taactgtcag accaagttta ctcatatata ctttagattg atttaaaact tcatttttaa
     6061 tttaaaagga tctaggtgaa gatccttttt gataatctca tgaccaaaat cccttaacgt
     6121 gagttttcgt tccactgagc gtcagacccc gtagaaaaga tcaaaggatc ttcttgagat
     6181 cctttttttc tgcgcgtaat ctgctgcttg caaacaaaaa aaccaccgct accagcggtg
     6241 gtttgtttgc cggatcaaga gctaccaact ctttttccga aggtaactgg cttcagcaga
     6301 gcgcagatac caaatactgt tcttctagtg tagccgtagt taggccacca cttcaagaac
     6361 tctgtagcac cgcctacata cctcgctctg ctaatcctgt taccagtggc tgctgccagt
     6421 ggcgataagt cgtgtcttac cgggttggac tcaagacgat agttaccgga taaggcgcag
     6481 cggtcgggct gaacgggggg ttcgtgcaca cagcccagct tggagcgaac gacctacacc
     6541 gaactgagat acctacagcg tgagctatga gaaagcgcca cgcttcccga agggagaaag
     6601 gcggacaggt atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagcttcca
     6661 gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg acttgagcgt
     6721 cgatttttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccag caacgcggcc
     6781 tttttacggt tcctggcctt ttgctggcct tttgctcaca tgttctttcc tgcgttatcc
     6841 cctgattctg tggataaccg tattaccgcc tttgagtgag ctgataccgc tcgccgcagc
     6901 cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg aagagcgccc aatacgcaaa
     6961 ccgcctctcc ccgcgcgttg gccgattcat taatgcagca agctcatggc tgactaattt
     7021 tttttattta tgcagaggcc gaggccgcct cggcctctga gctattccag aagtagtgag
     7081 gaggcttttt tggaggccta ggcttttgca aaaagctccc cgtggcacga caggtttccc
     7141 gactggaaag cgggcagtga gcgcaacgca attaatgtga gttagctcac tcattaggca
     7201 ccccaggctt tacactttat gcttccggct cgtatgttgt gtggaattgt gagcggataa
     7261 caatttcaca caggaaacag ctatgacatg attacgaatt tcacaaataa agcatttttt
     7321 tcactgcatt ctagttgtgg tttgtccaaa ctcatcaatg tatcttatca tgtctggatc
     7381 aactggataa ctcaagctaa ccaaaatcat cccaaacttc ccaccccata ccctattacc
     7441 actgccaatt acctgtggtt tcatttactc taaacctgtg attcctctga attattttca
     7501 ttttaaagaa attgtatttg ttaaatatgt actacaaact tagtagt
//
