LOCUS       sequence-194231-        6480 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Repaired U3 allows LTR-based transcription by the provirus with GFP 
            as a marker for expression. WPRE was deleted..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6480)
  AUTHORS   McCauley SM, Kim K, Nowosielska A, Dauphin A, Yurkovetskiy L, Diehl 
            WE, Luban J
  TITLE     Intron-containing RNA from the HIV-1 provirus activates type I 
            interferon and inflammatory cytokines.
  JOURNAL   Nat Commun. 2018 Dec 13;9(1):5305. doi: 10.1038/s41467-018-07753-2.
  PUBMED    30546110
REFERENCE   2  (bases 1 to 6480)
  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: "2018-12-13"; volume: "9(1):5305. doi"; pages: " 
            10.1038/s41467-018-07753-2"
COMMENT     Sequence Label: pALPS_3'LTR GFP@gag start SFFV-
FEATURES             Location/Qualifiers
     source          1..6480
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(47..66)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(240..260)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        245..574
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      425..560
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     487..506
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        586..965
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        967..1165
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1120..1140
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             1183..1363
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     CDS             join(1519..1521,1522..1524,1525..2235)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     misc_feature    2398..2631
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2816..2860
                     /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    3158..3275
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        3412..3819
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     LTR             4027..4660
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4728..5316)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4808..4827)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5487..6278,6279..6347))
                     /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     6110..6129
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6348..6452)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 gtcgacggat cgggagatct cccgatcccc tatggtgcac tctcagtaca atctgctctg
       61 atgccgcata gttaagccag tatctgctcc ctgcttgtgt gttggaggtc gctgagtagt
      121 gcgcgagcaa aatttaagct acaacaaggc aaggcttgac cgacaattgc atgaagaatc
      181 tgcttagggt taggcgtttt gcgctgcttc gcgatgtacg ggccagatat acgcgctgtg
      241 gaatgtgtgt cagttagggt gtggaaagtc cccaggctcc ccagcaggca gaagtatgca
      301 aagcatgcat ctcaattagt cagcaaccag gtgtggaaag tccccaggct ccccagcagg
      361 cagaagtatg caaagcatgc atctcaatta gtcagcaacc atagtcccgc ccctaactcc
      421 gcccatcccg cccctaactc cgcccagttc cgcccattct ccgccccatg gctgactaat
      481 tttttttatt tatgcagagg ccgaggccgc ctctgcctct gagctattcc agaagtagtg
      541 aggaggcttt tttggaggcc taggcttttg caaaaagctc gcgttgacat tgattattga
      601 ctagttatta atagtaatca attacggggt cattagttca tagcccatat atggagttcc
      661 gcgttacata acttacggta aatggcccgc ctggctgacc gcccaacgac ccccgcccat
      721 tgacgtcaat aatgacgtat gttcccatag taacgccaat agggactttc cattgacgtc
      781 aatgggtgga gtatttacgg taaactgccc acttggcagt acatcaagtg tatcatatgc
      841 caagtacgcc ccctattgac gtcaatgacg gtaaatggcc cgcctggcat tatgcccagt
      901 acatgacctt atgggacttt cctacttggc agtacatcta cgtattagtc atcgctatta
      961 ccatggtgat gcggttttgg cagtacatca atgggcgtgg atagcggttt gactcacggg
     1021 gatttccaag tctccacccc attgacgtca atgggagttt gttttggcac caaaatcaac
     1081 gggactttcc aaaatgtcgt aacaactccg ccccattgac gcaaatgggc ggtaggcgtg
     1141 tacggtggga ggtctatata agcagcgcgt tttgcctgta ctgggtctct ctggttagac
     1201 cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa
     1261 agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag
     1321 agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagtggcgc ccgaacaggg
     1381 acttgaaagc gaaagggaaa ccagaggagc tctctcgacg caggactcgg cttgctgaag
     1441 cgcgcacggc aagaggcgag gggcggcgac tggtgagtac gccaaaaatt ttgactagcg
     1501 gaggctagaa ggagagagat ggtgtcaaaa ggagaagaac tgttcaccgg agtggtccca
     1561 atcctggtgg agctggacgg agatgtcaat ggccacaagt tcagcgtgag cggagaggga
     1621 gaaggagacg ctacatacgg caagctgact ctgaaattca tttgcaccac agggaagctg
     1681 cccgtgcctt ggccaaccct ggtcactacc ctgacatacg gcgtccagtg ttttagcaga
     1741 tatccagacc acatgaagca gcatgatttc tttaaatccg ccatgcccga gggctacgtg
     1801 caggaacgga caatcttctt taaggacgat ggaaactata aaactagagc tgaggtgaag
     1861 ttcgaaggag acaccctggt caacaggatc gagctgaagg gcattgactt taaagaagat
     1921 gggaatattc tgggacacaa gctggagtac aactacaact ctcataacgt gtatatcatg
     1981 gcagataagc agaaaaacgg cattaaggtc aatttcaaaa tccgccacaa tattgaagac
     2041 gggagcgtgc agctggccga tcattaccag cagaacacac ctatcggcga cggacccgtg
     2101 ctgctgcctg ataatcacta tctgtctact cagagtgccc tgtcaaagga cccaaacgag
     2161 aaacgagatc atatggtgct gctggagttt gtcaccgctg ctggaatcac actgggcatg
     2221 gatgagctgt acaagtaacg gccggccgct gatcttcaga cctggaggag gagatatgag
     2281 ggacaattgg agaagtgaat tatataaata taaagtagta aaaattgaac cattaggagt
     2341 agcacccacc aaggcaaaga gaagagtggt gcagagagaa aaaagagcag tgggaatagg
     2401 agctttgttc cttgggttct tgggagcagc aggaagcact atgggcgcag cgtcaatgac
     2461 gctgacggta caggccagac aattattgtc tggtatagtg cagcagcaga acaatttgct
     2521 gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca tcaagcagct
     2581 ccaggcaaga atcctggctg tggaaagata cctaaaggat caacagctcc tggggatttg
     2641 gggttgctct ggaaaactca tttgcaccac tgctgtgcct tggaatgcta gttggagtaa
     2701 taaatctctg gaacagattt ggaatcacac gacctggatg gagtgggaca gagaaattaa
     2761 caattacaca agcttaatac actccttaat tgaagaatcg caaaaccagc aagaaaagaa
     2821 tgaacaagaa ttattggaat tagataaatg ggcaagtttg tggaattggt ttaacataac
     2881 aaattggctg tggtatataa aattattcat aatgatagta ggaggcttgg taggtttaag
     2941 aatagttttt gctgtacttt ctatagtgaa tagagttagg cagggatatt caccattatc
     3001 gtttcagacc cacctcccaa ccccgagggg acccgacagg cccgaaggaa tagaagaaga
     3061 aggtggagag agagacagag acagatccat tcgattagtg aacggatcgg cactgcgtgc
     3121 gccaattctg cagacaaatg gcagtattca tccacaattt taaaagaaaa ggggggattg
     3181 gggggtacag tgcaggggaa agaatagtag acataatagc aacagacata caaactaaag
     3241 aattacaaaa acaaattaca aaaattcaaa attttcgggt ttattacagg gacagcagag
     3301 atccagtttg gttaattaac tgcagccccg ataaaataaa agattttatt tagtctccag
     3361 aaaaaggggg gaatgaaaga ccccacctgt aggtttggca agctagctgc agtaacgcca
     3421 ttttgcaagg catggaaaaa taccaaacca agaatagaga agttcagatc aagggcgggt
     3481 acatgaaaat agctaacgtt gggccaaaca ggatatctgc ggtgagcagt ttcggccccg
     3541 gcccggggcc aagaacagat ggtcaccgca gtttcggccc cggcccgagg ccaagaacag
     3601 atggtcccca gatatggccc aaccctcagc agtttcttaa gacccatcag atgtttccag
     3661 gctcccccaa ggacctgaaa tgaccctgcg ccttatttga attaaccaat cagcctgctt
     3721 ctcgcttctg ttcgcgcgct tctgcttccc gagctctata aaagagctca caacccctca
     3781 ctcggcgcgc cagtcctccg acagactgag tcgcccgggg gtctagaagc gctggatccg
     3841 tttaaacgcg gccgcccagc acagtggctc gagccgcggg ttaactggcc agaattcacg
     3901 cgtatcgata ccggtggccc ctggggccgc gatcgcagac ctgcaggtgg cctcaggtac
     3961 ctttaagacc aatgacttac aaggcagctg tagatcttag ccacttttta aaagaaaagg
     4021 ggggactgga agggctaatt cactcccaaa gaagacaaga tatccttgat ctgtggatct
     4081 accacacaca aggctacttc cctgattggc agaactacac accagggcca ggggtcagat
     4141 atccactgac ctttggatgg tgctacaagc tagtaccagt tgagccagat aaggtagaag
     4201 aggccaataa aggagagaac accagcttgt tacaccctgt gagcctgcat ggaatggatg
     4261 accctgagag agaagtgtta gagtggaggt ttgacagccg cctagcattt catcacgtgg
     4321 cccgagagct gcatccggag tacttcaaga actgctgaca tcgagcttgc tacaagggac
     4381 tttccgctgg ggactttcca gggaggcgtg gcctgggcgg gactggggag tggcgagccc
     4441 tcagatgctg catataagca gctgcttttt gcctgtactg ggtctctctg gttagaccag
     4501 atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc
     4561 ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg taactagaga
     4621 tccctcagac ccttttagtc agtgtggaaa atctctagca ggcgtttcat gtgagcaaaa
     4681 ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc
     4741 cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca
     4801 ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg
     4861 accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct
     4921 catagctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt
     4981 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag
     5041 tccaacccgg taagacacga cttatcgcca ctggcagcag ccactggtaa caggattagc
     5101 agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac
     5161 actagaagaa cagtatttgg tatctgcgct ctgctgaagc cagttacctt cggaaaaaga
     5221 gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc
     5281 aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctacg
     5341 gggtctgacg ctcagtggaa cgaaaactca cgttaaggga ttttggtcat gagattatca
     5401 aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt
     5461 atatatgagt aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca
     5521 gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg
     5581 atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca
     5641 ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt
     5701 cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt
     5761 agttcgccag ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca
     5821 cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca
     5881 tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga
     5941 agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact
     6001 gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga
     6061 gaatagtgta tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg
     6121 ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc
     6181 tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga
     6241 tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat
     6301 gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt
     6361 caatattatt gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt
     6421 atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctgac
//
