LOCUS       sequence-194063-        8865 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Deletion from the start of gag until 229 bases before the cPPT.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8865)
  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 8865)
  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: pBS NL4-3 envFS eGFP Delta-gag/pol
FEATURES             Location/Qualifiers
     source          1..8865
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      7..435
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(94..113)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     304..325
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     LTR             833..1090
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1477..1594
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     misc_feature    4457..4690
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             4875..4919
                     /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"
     CDS             5213..5239
                     /codon_start=1
                     /product="nuclear export signal from the HIV Rev protein 
                     (Fischer et al., 1995)"
                     /label=NES
                     /translation="LPPLERLTL"
     CDS             join(5506..5508,5509..6222)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="VSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG
                     NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLE
                     FVTAAGITLGMDELYK"
     CDS             join(5506..5508,5509..6219)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="VSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG
                     NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLE
                     FVTAAGITLGMDELYK"
     primer_bind     complement(5548..5569)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(5809..5828)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     6156..6177
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     LTR             6412..7045
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(7121..7709)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(7201..7220)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(7880..8671,8672..8740))
                     /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     8503..8522
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(8741..8845)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 cacctgacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg
       61 tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc ccttcctttc
      121 tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct ttagggttcc
      181 gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat ggttcacgta
      241 gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc acgttcttta
      301 atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc tattcttttg
      361 atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg atttaacaaa
      421 aatttaacgc gaattttaac aaaatatttt aattaatgga agggctaatt tggtcccaaa
      481 aaagacaaga gatccttgat ctgtggatct accacacaca aggctacttc cctgattggc
      541 agaactacac accagggcca gggatcagat atccactgac ctttggatgg tgcttcaagt
      601 tagtaccagt tgaaccagag caagtagaag aggccaatga aggagagaac aacagcttgt
      661 tacaccctat gagccagcat gggatggagg acccggaggg agaagtatta gtgtggaagt
      721 ttgacagcct cctagcattt cgtcacatgg cccgagagct gcatccggag tactacaaag
      781 actgctgaca tcgagctttc tacaagggac tttccgctgg ggactttcca gggaggtgtg
      841 gcctgggcgg gactggggag tggcgagccc tcagatgcta catataagca gctgcttttt
      901 gcctgtactg ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta
      961 gggaacccac tgcttaagcc tcaataaagc ttgccttgag tgctcaaagt agtgtgtgcc
     1021 cgtctgttgt gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa
     1081 atctctagca gtggcgcccg aacagggact tgaaagcgaa agtaaagcca gaggagatct
     1141 ctcgacgcag gactcggctt gctgaagcgc gcacggcaag aggcgagggg cggcgactgg
     1201 tgagtacgcc aaaaattttg actagcggag gctagaagga gagagatggc cagtaaaaac
     1261 agtacataca gacaatggca gcaatttcac cagtactaca gttaaggccg cctgttggtg
     1321 ggcggggatc aagcaggaat ttggcattcc ctacaatccc caaagtcaag gagtaataga
     1381 atctatgaat aaagaattaa agaaaattat aggacaggta agagatcagg ctgaacatct
     1441 taagacagca gtacaaatgg cagtattcat ccacaatttt aaaagaaaag gggggattgg
     1501 ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac aaactaaaga
     1561 attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga
     1621 tccagtttgg aaaggaccag caaagctcct ctggaaaggt gaaggggcag tagtaataca
     1681 agataatagt gacataaaag tagtgccaag aagaaaagca aagatcatca gggattatgg
     1741 aaaacagatg gcaggtgatg attgtgtggc aagtagacag gatgaggatt aacacatgga
     1801 aaagattagt aaaacaccat atgtatattt caaggaaagc taaggactgg ttttatagac
     1861 atcactatga aagtactaat ccaaaaataa gttcagaagt acacatccca ctaggggatg
     1921 ctaaattagt aataacaaca tattggggtc tgcatacagg agaaagagac tggcatttgg
     1981 gtcagggagt ctccatagaa tggaggaaaa agagatatag cacacaagta gaccctgacc
     2041 tagcagacca actaattcat ctgcactatt ttgattgttt ttcagaatct gctataagaa
     2101 ataccatatt aggacgtata gttagtccta ggtgtgaata tcaagcagga cataacaagg
     2161 taggatctct acagtacttg gcactagcag cattaataaa accaaaacag ataaagccac
     2221 ctttgcctag tgttaggaaa ctgacagagg acagatggaa caagccccag aagaccaagg
     2281 gccacagagg gagccataca atgaatggac actagagctt ttagaggaac ttaagagtga
     2341 agctgttaga cattttccta ggatatggct ccataactta ggacaacata tctatgaaac
     2401 ttacggggat acttgggcag gagtggaagc cataataaga attctgcaac aactgctgtt
     2461 tatccatttc agaattgggt gtcgacatag cagaataggc gttactcgac agaggagagc
     2521 aagaaatgga gccagtagat cctagactag agccctggaa gcatccagga agtcagccta
     2581 aaactgcttg taccaattgc tattgtaaaa agtgttgctt tcattgccaa gtttgtttca
     2641 tgacaaaagc cttaggcatc tcctatggca ggaagaagcg gagacagcga cgaagagctc
     2701 atcagaacag tcagactcat caagcttctc tatcaaagca gtaagtagta catgtaatgc
     2761 aacctataat agtagcaata gtagcattag tagtagcaat aataatagca atagttgtgt
     2821 ggtccatagt aatcatagaa tataggaaaa tattaagaca aagaaaaata gacaggttaa
     2881 ttgatagact aatagaaaga gcagaagaca gtggcaatga gagtgaagga gaagtatcag
     2941 cacttgtgga gatgggggtg gaaatggggc accatgctcc ttgggatatt gatgatctgt
     3001 agtgctacag aaaaattgtg ggtcaccgtc tattatgggg tacctgtgtg gaaggaagca
     3061 accaccactc tattttgtgc atcagatgct aaagcatata tgatacagag gtacataatg
     3121 tttgggccac acatgcctgt gtacccacag accccaaccc acaagaagta gtattggtaa
     3181 atgtgacaga aaattttaac atgtggaaaa atgacatggt agaacagatg catgaggata
     3241 taatcagttt atgggatcaa agcctaaagc catgtgtaaa attaacccca ctctgtgtta
     3301 gtttaaagtg cactgatttg aagaatgata ctaataccaa tagtagtagc gggagaatga
     3361 taatggagaa aggagagata aaaaactgct ctttcaatat cagcacaagc ataagagata
     3421 aggtgcagaa agaatatgca ttcttttata aacttgatat agtaccaata gataatacca
     3481 gctataggtt gataagttgt aacacctcag tcattacaca ggcctgtcca aaggtatcct
     3541 ttgagccaat tcccatacat tattgtgccc cggctggttt tgcgattcta aaatgtaata
     3601 ataagacgtt caatggaaca ggaccatgta caaatgtcag cacagtacaa tgtacacatg
     3661 gaatcaggcc agtagtatca actcaactgc tgttaaatgg cagtctagca gaagaagatg
     3721 tagtaattag atctgccaat ttcacagaca atgctaaaac cataatagta cagctgaaca
     3781 catctgtaga aattaattgt acaagaccca acaacaatac aagaaaaagt atccgtatcc
     3841 agaggggacc agggagagca tttgttacaa taggaaaaat aggaaatatg agacaagcac
     3901 attgtaacat tagtagagca aaatggaatg ccactttaaa acagatagct agcaaattaa
     3961 gagaacaatt tggaaataat aaaacaataa tctttaagca atcctcagga ggggacccag
     4021 aaattgtaac gcacagtttt aattgtggag gggaattttt ctactgtaat tcaacacaac
     4081 tgtttaatag tacttggttt aatagtactt ggagtactga agggtcaaat aacactgaag
     4141 gaagtgacac aatcacactc ccatgcagaa taaaacaatt tataaacatg tggcaggaag
     4201 taggaaaagc aatgtatgcc cctcccatca gtggacaaat tagatgttca tcaaatatta
     4261 ctgggctgct attaacaaga gatggtggta ataacaacaa tgggtccgag atcttcagac
     4321 ctggaggagg cgatatgagg gacaattgga gaagtgaatt atataaatat aaagtagtaa
     4381 aaattgaacc attaggagta gcacccacca aggcaaagag aagagtggtg cagagagaaa
     4441 aaagagcagt gggaatagga gctttgttcc ttgggttctt gggagcagca ggaagcacta
     4501 tgggcgcagc gtcaatgacg ctgacggtac aggccagaca attattgtct gatatagtgc
     4561 agcagcagaa caatttgctg agggctattg aggcgcaaca gcatctgttg caactcacag
     4621 tctggggcat caaacagctc caggcaagaa tcctggctgt ggaaagatac ctaaaggatc
     4681 aacagctcct ggggatttgg ggttgctctg gaaaactcat ttgcaccact gctgtgcctt
     4741 ggaatgctag ttggagtaat aaatctctgg aacagatttg gaataacatg acctggatgg
     4801 agtgggacag agaaattaac aattacacaa gcttaataca ctccttaatt gaagaatcgc
     4861 aaaaccagca agaaaagaat gaacaagaat tattggaatt agataaatgg gcaagtttgt
     4921 ggaattggtt taacataaca aattggctgt ggtatataaa attattcata atgatagtag
     4981 gaggcttggt aggtttaaga atagtttttg ctgtactttc tatagtgaat agagttaggc
     5041 agggatattc accattatcg tttcagaccc acctcccaat cccgagggga cccgacaggc
     5101 ccgaaggaat agaagaagaa ggtggagaga gagacagaga cagatccatt cgattagtga
     5161 acggatcctt agcacttatc tgggacgatc tgcggagcct gtgcctcttc agctaccacc
     5221 gcttgagaga cttactcttg attgtaacga ggattgtgga acttctggga cgcagggggt
     5281 gggaagccct caaatattgg tggaatctcc tacaatattg gagtcaggag ctaaagaata
     5341 gtgctgttag cttgctcaat gccacagcca tagcagtagc tgaggggaca gatagggtta
     5401 tagaagtagt acaaggagct tgtagagcta ttcgccacat acctagaaga ataagacagg
     5461 gcttggaaag gattttgcta taagatgggt ggcgcggccg ctctggtgag caagggcgag
     5521 gagctgttca ccggggtggt gcccatcctg gtcgagctgg acggcgacgt aaacggccac
     5581 aagttcagcg tgtccggcga gggcgagggc gatgccacct acggcaagct gaccctgaag
     5641 ttcatctgca ccaccggcaa gctgcccgtg ccctggccca ccctcgtgac caccctgacc
     5701 tacggcgtgc agtgcttcag ccgctacccc gaccacatga agcagcacga cttcttcaag
     5761 tccgccatgc ccgaaggcta cgtccaggag cgcaccatct tcttcaagga cgacggcaac
     5821 tacaagaccc gcgccgaggt gaagttcgag ggcgacaccc tggtgaaccg catcgagctg
     5881 aagggcatcg acttcaagga ggacggcaac atcctggggc acaagctgga gtacaactac
     5941 aacagccaca acgtctatat catggccgac aagcagaaga acggcatcaa ggtgaacttc
     6001 aagatccgcc acaacatcga ggacggcagc gtgcagctcg ccgaccacta ccagcagaac
     6061 acccccatcg gcgacggccc cgtgctgctg cccgacaacc actacctgag cacccagtcc
     6121 gccctgagca aagaccccaa cgagaagcgc gatcacatgg tcctgctgga gttcgtgacc
     6181 gccgccggga tcactctcgg catggacgag ctgtacaagt aactcgagac ctagaaaaac
     6241 atggagcaat cacaagtagc aatacagcag ctaacaatgc tgcttgtgcc tggctagaag
     6301 cacaagagga ggaagaggtg ggttttccag tcacacctca ggtaccttta agaccaatga
     6361 cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc
     6421 taattcactc ccaaagaaga caagatatcc ttgatctgtg gatctaccac acacaaggct
     6481 acttccctga ttggcagaac tacacaccag ggccaggggt cagatatcca ctgacctttg
     6541 gatggtgcta caagctagta ccagttgagc cagataaggt agaagaggcc aataaaggag
     6601 agaacaccag cttgttacac cctgtgagcc tgcatggaat ggatgaccct gagagagaag
     6661 tgttagagtg gaggtttgac agccgcctag catttcatca cgtggcccga gagctgcatc
     6721 cggagtactt caagaactgc tgacatcgag cttgctacaa gggactttcc gctggggact
     6781 ttccagggag gcgtggcctg ggcgggactg gggagtggcg agccctcaga tgctgcatat
     6841 aagcagctgc tttttgcctg tactgggtct ctctggttag accagatctg agcctgggag
     6901 ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt
     6961 caagtagtgt gtgcccgtct gttgtgtgac tctggtaact agagatccct cagacccttt
     7021 tagtcagtgt ggaaaatctc tagcaggccg gcccaattga catgtgagca aaaggccagc
     7081 aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg ctccgccccc
     7141 ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat
     7201 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
     7261 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
     7321 cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
     7381 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
     7441 cggtaagaca cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga
     7501 ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc tacactagaa
     7561 gaacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta
     7621 gctcttgatc cggcaaacaa accaccgctg gtagcggtgg tttttttgtt tgcaagcagc
     7681 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg
     7741 acgctcagtg gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga
     7801 tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa agtatatatg
     7861 agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct
     7921 gtctatttcg ttcatccata gttgcctgac tccccgtcgt gtagataact acgatacggg
     7981 agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc
     8041 cagatttatc agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa
     8101 ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta agtagttcgc
     8161 cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt
     8221 cgtttggtat ggcttcattc agctccggtt cccaacgatc aaggcgagtt acatgatccc
     8281 ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt
     8341 tggccgcagt gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc
     8401 catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc tgagaatagt
     8461 gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata
     8521 gcagaacttt aaaagtgctc atcattggaa aacgttcttc ggggcgaaaa ctctcaagga
     8581 tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag
     8641 catcttttac tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa
     8701 aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt tttcaatatt
     8761 attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga
     8821 aaaataaaca aataggggtt ccgcgcacat ttccccgaaa agtgc
//
