LOCUS       sequence-191105-        9169 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Encodes codon optimized JR-CSF env.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9169)
  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 9169)
  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 env
FEATURES             Location/Qualifiers
     source          1..9169
                     /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        582..961
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        963..1161
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1116..1136
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             1179..1359
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1406..1531
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    2028..2261
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2446..2490
                     /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    2788..2905
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        3042..3449
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     CDS             5405..5449
                     /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    6060..6648
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6113..6133)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6531..6542)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             7166..7346
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(7417..8005)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(7497..7516)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(8176..8967,8968..9036))
                     /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     8799..8818
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(9037..9141)
                     /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 caaaaagctt tgacattgat tattgactag
      601 ttattaatag taatcaatta cggggtcatt agttcatagc ccatatatgg agttccgcgt
      661 tacataactt acggtaaatg gcccgcctgg ctgaccgccc aacgaccccc gcccattgac
      721 gtcaataatg acgtatgttc ccatagtaac gccaataggg actttccatt gacgtcaatg
      781 ggtggagtat ttacggtaaa ctgcccactt ggcagtacat caagtgtatc atatgccaag
      841 tacgccccct attgacgtca atgacggtaa atggcccgcc tggcattatg cccagtacat
      901 gaccttatgg gactttccta cttggcagta catctacgta ttagtcatcg ctattaccat
      961 ggtgatgcgg ttttggcagt acatcaatgg gcgtggatag cggtttgact cacggggatt
     1021 tccaagtctc caccccattg acgtcaatgg gagtttgttt tggcaccaaa atcaacggga
     1081 ctttccaaaa tgtcgtaaca actccgcccc attgacgcaa atgggcggta ggcgtgtacg
     1141 gtgggaggtc tatataagca gcgcgttttg cctgtactgg gtctctctgg ttagaccaga
     1201 tctgagcctg ggagctctct ggctaactag ggaacccact gcttaagcct caataaagct
     1261 tgccttgagt gcttcaagta gtgtgtgccc gtctgttgtg tgactctggt aactagagat
     1321 ccctcagacc cttttagtca gtgtggaaaa tctctagcag tggcgcccga acagggactt
     1381 gaaagcgaaa gggaaaccag aggagctctc tcgacgcagg actcggcttg ctgaagcgcg
     1441 cacggcaaga ggcgaggggc ggcgactggt gagtacgcca aaaattttga ctagcggagg
     1501 ctagaaggag agagatgggt gcgagagcgt cagtattaag cgggggagaa ttagatcgcg
     1561 atgggaaaaa attcggttaa ggccaggggg aaagaaaaaa tataaattaa aacatatagt
     1621 atgggcaagc agggagctag aacgattcgc agttaatcct ggcctgttag aaacatcaga
     1681 aggctgtaga caaatactgg gacagctaca accatccctt cagacaggat cagaagaact
     1741 tagatcatta tataatacag tagcaaccct ctattgtgtg catcaaagga tagagataaa
     1801 agacaccaag gaagctttag acaagataga ggaagagcaa aacaaaagta agaccaccgc
     1861 acagcaagcg gccggccgct gatcttcaga cctggaggag gagatatgag ggacaattgg
     1921 agaagtgaat tatataaata taaagtagta aaaattgaac cattaggagt agcacccacc
     1981 aaggcaaaga gaagagtggt gcagagagaa aaaagagcag tgggaatagg agctttgttc
     2041 cttgggttct tgggagcagc aggaagcact atgggcgcag cgtcaatgac gctgacggta
     2101 caggccagac aattattgtc tggtatagtg cagcagcaga acaatttgct gagggctatt
     2161 gaggcgcaac agcatctgtt gcaactcaca gtctggggca tcaagcagct ccaggcaaga
     2221 atcctggctg tggaaagata cctaaaggat caacagctcc tggggatttg gggttgctct
     2281 ggaaaactca tttgcaccac tgctgtgcct tggaatgcta gttggagtaa taaatctctg
     2341 gaacagattt ggaatcacac gacctggatg gagtgggaca gagaaattaa caattacaca
     2401 agcttaatac actccttaat tgaagaatcg caaaaccagc aagaaaagaa tgaacaagaa
     2461 ttattggaat tagataaatg ggcaagtttg tggaattggt ttaacataac aaattggctg
     2521 tggtatataa aattattcat aatgatagta ggaggcttgg taggtttaag aatagttttt
     2581 gctgtacttt ctatagtgaa tagagttagg cagggatatt caccattatc gtttcagacc
     2641 cacctcccaa ccccgagggg acccgacagg cccgaaggaa tagaagaaga aggtggagag
     2701 agagacagag acagatccat tcgattagtg aacggatcgg cactgcgtgc gccaattctg
     2761 cagacaaatg gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag
     2821 tgcaggggaa agaatagtag acataatagc aacagacata caaactaaag aattacaaaa
     2881 acaaattaca aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg
     2941 gttaattaac tgcagccccg ataaaataaa agattttatt tagtctccag aaaaaggggg
     3001 gaatgaaaga ccccacctgt aggtttggca agctagctgc agtaacgcca ttttgcaagg
     3061 catggaaaaa taccaaacca agaatagaga agttcagatc aagggcgggt acatgaaaat
     3121 agctaacgtt gggccaaaca ggatatctgc ggtgagcagt ttcggccccg gcccggggcc
     3181 aagaacagat ggtcaccgca gtttcggccc cggcccgagg ccaagaacag atggtcccca
     3241 gatatggccc aaccctcagc agtttcttaa gacccatcag atgtttccag gctcccccaa
     3301 ggacctgaaa tgaccctgcg ccttatttga attaaccaat cagcctgctt ctcgcttctg
     3361 ttcgcgcgct tctgcttccc gagctctata aaagagctca caacccctca ctcggcgcgc
     3421 cagtcctccg acagactgag tcgcccgggg gtctagagcc gccatgagag tgaaagagaa
     3481 ataccagcac ctgtggagat gggggtggaa atgggggact atgctgctgg gaatcctgat
     3541 gatctgtagc gccacagaaa agctgtgggt caccgtctac tatggggtac ctgtctggaa
     3601 agagaccaca actaccctgt tctgcgcttc cgacgctaag gcatatgata ccgaggtgca
     3661 caacgtctgg gccacccatg cttgtgtgcc tacagaccca aatccccagg aggtggtcct
     3721 ggaaaacgtg acagaggatt tcaacatgtg gaagaacaac atggtggaac agatgcagga
     3781 ggacgtcatc aacctgtggg atcagtctct gaagccttgc gtgaaactga ccccactgtg
     3841 cgtcacactg aattgtaagg acgtgaacgc cactaataca actagctcct ctgaagggat
     3901 gatggagcgc ggagaaatca agaattgcag tttcaatatc accaaatcaa ttcgggataa
     3961 ggtgcagaaa gagtacgctc tgttttataa actggacgtg gtccctatcg ataacaagaa
     4021 caataccaaa taccggctga tctcatgcaa tacaagcgtc attactcagg cttgtcctaa
     4081 ggtgagcttc gagcctatcc caattcacta ttgcgcccca gctggcttcg caattcttaa
     4141 gtgtaacaac aagaccttca acgggaaggg ccagtgcaaa aatgtgagca ccgtccagtg
     4201 cacacatggg atcagaccag tggtctccac tcagctgctg ctgaacggat ctctggcaga
     4261 ggaaaaggtg gtcattagga gtgacaactt cactgataat gccaagacca tcattgtgca
     4321 gctgaacgag tcagtcaaaa tcaattgtac aaggccaagc aacaataccc gcaagtccat
     4381 ccacattgga cccgggcgcg ccttttacac cacaggagag atcattggcg acatccgcca
     4441 ggcccattgt aacatttccc gagctcagtg gaacaatacc ctgaagcaga tcgtggaaaa
     4501 actgcgggag cagttcaaca ataagactat cgtgtttacc cacagttcag gcggggatcc
     4561 agaaattgtg atgcattctt tcaactgcgg aggcgagttc ttttactgta attctaccca
     4621 gctgtttaac agtacatgga atgacactga aaaaagctcc gggacagagg gaaacgatac
     4681 tatcattctg ccttgcagaa tcaagcagat tattaatatg tggcaggaag tggggaaggc
     4741 aatgtatgcc ccccctatca aaggacagat tagatgttct agtaacatta ccggcctgct
     4801 gctgacaagg gacgggggaa agaatgaaag cgagatcgaa atttttaggc ccggcggggg
     4861 agacatgcgc gacaattggc gatccgaact ttacaagtat aaagtggtca aaatcgagcc
     4921 actgggagtg gcaccaacca aggctaaacg gagagtggtc cagagagaga agagggctgt
     4981 gggaattggc gcactgttcc tgggctttct gggggctgca ggatcaacaa tgggcgcagc
     5041 cagcatgaca ctgactgtgc aggccagaca gctgctgagc gggatcgtgc agcagcagaa
     5101 caatctgctg agggctattg aagcacagca gcacatgttg cagctgaccg tgtggggcat
     5161 caagcagttg caggcacgag tgctggcagt cgagagatac ctgaaagacc agcagctgat
     5221 gggcatctgg gggtgcagcg gaaagctgat ttgtactacc gccgtgcctt ggaacacctc
     5281 atggagcaac aagtccctgg attctatctg gaacaatatg acatggatgg agtgggaaaa
     5341 ggagatcgaa aactacacca acacaatcta taccctgatt gaggaatctc agatccagca
     5401 ggaaaagaac gagcaggaat tactcgagct ggacaaatgg gccagtctgt ggaattggtt
     5461 cggcattaca aagtggctgt ggtacatcaa aatttttatc atgatcgtgg gcgggctgat
     5521 cggactgaga attgtgttca gtgtcctgtc aatcgtgaac cgagtccggc agggctatag
     5581 ccccctgtcc tttcagactc tgctgcctgc aactcgggga cccgatagac ctgaaggcat
     5641 cgaggaagag ggaggcgaga gagacaggga tagatccgga cagctggtca atgggttcct
     5701 ggctctgatt tgggtcgacc tgcgctccct gttcctgttt tcttatcatc gactgcggga
     5761 tctgctgctg actgtgaccc gaatcgtcga actgctggga aggcgaggat gggagattct
     5821 gaaatactgg tggaacctgt tgcagtattg gagccaggag ctgaagaact ctgccgtgag
     5881 tctgctgaat gcaacagcga tcgcagtggc agaaggcact gacagaatca ttgaggtggt
     5941 ccagagggtg tacagagcca tcctgcacat tcctacacgc attagacagg gactggagcg
     6001 ggcactgctg tgagaattca cgcgtatcga taccggtggc ccctggggcc gcgatcgcta
     6061 atcaacctct ggattacaaa atttgtgaaa gattgactgg tattcttaac tatgttgctc
     6121 cttttacgct atgtggatac gctgctttaa tgcctttgta tcatgctatt gcttcccgta
     6181 tggctttcat tttctcctcc ttgtataaat cctggttgct gtctctttat gaggagttgt
     6241 ggcccgttgt caggcaacgt ggcgtggtgt gcactgtgtt tgctgacgca acccccactg
     6301 gttggggcat tgccaccacc tgtcagctcc tttccgggac tttcgctttc cccctcccta
     6361 ttgccacggc ggaactcatc gccgcctgcc ttgcccgctg ctggacaggg gctcggctgt
     6421 tgggcactga caattccgtg gtgttgtcgg ggaagctgac gtcctttcca tggctgctcg
     6481 cctgtgttgc cacctggatt ctgcgcggga cgtccttctg ctacgtccct tcggccctca
     6541 atccagcgga ccttccttcc cgcggcctgc tgccggctct gcggcctctt ccgcgtcttc
     6601 gccttcgccc tcagacgagt cggatctccc tttgggccgc ctccccgctt aatcgcgtcg
     6661 agacctagaa aaacatggag caatcacaag tagcaataca gcagctacca atgctgattg
     6721 tgcctggcta gaagcacaag aggaggagga ggtgggtttt ccagtcacac ctcaggtacc
     6781 tttaagacca atgacttaca aggcagctgt agatcttagc cactttttaa aagaaaaggg
     6841 gggactggaa gggctaattc actcccaacg aagacaagat atccttgatc tgtggatcta
     6901 ccacacacaa ggctacttcc ctgattggca gaactacaca ccagggccag ggatcagata
     6961 tccactgacc tttggatggt gctacaagct agtaccagtt gagcaagaga aggtagaaga
     7021 agccaatgaa ggagagaaca cccgcttgtt acaccctgtg agcctgcatg ggatggatga
     7081 cccggagaga gaagtattag agtggaggtt tgacagccgc ctagcatttc atcacatggc
     7141 ccgagagctg catccggact gtactgggtc tctctggtta gaccagatct gagcctggga
     7201 gctctctggc taactaggga acccactgct taagcctcaa taaagcttgc cttgagtgct
     7261 tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccctt
     7321 ttagtcagtg tggaaaatct ctagcagggc ccgtttcatg tgagcaaaag gccagcaaaa
     7381 ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc cataggctcc gcccccctga
     7441 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     7501 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     7561 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     7621 ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     7681 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     7741 aagacacgac ttatcgccac tggcagcagc cactggtaac aggattagca gagcgaggta
     7801 tgtaggcggt gctacagagt tcttgaagtg gtggcctaac tacggctaca ctagaagaac
     7861 agtatttggt atctgcgctc tgctgaagcc agttaccttc ggaaaaagag ttggtagctc
     7921 ttgatccggc aaacaaacca ccgctggtag cggtggtttt tttgtttgca agcagcagat
     7981 tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc
     8041 tcagtggaac gaaaactcac gttaagggat tttggtcatg agattatcaa aaaggatctt
     8101 cacctagatc cttttaaatt aaaaatgaag ttttaaatca atctaaagta tatatgagta
     8161 aacttggtct gacagttacc aatgcttaat cagtgaggca cctatctcag cgatctgtct
     8221 atttcgttca tccatagttg cctgactccc cgtcgtgtag ataactacga tacgggaggg
     8281 cttaccatct ggccccagtg ctgcaatgat accgcgagac ccacgctcac cggctccaga
     8341 tttatcagca ataaaccagc cagccggaag ggccgagcgc agaagtggtc ctgcaacttt
     8401 atccgcctcc atccagtcta ttaattgttg ccgggaagct agagtaagta gttcgccagt
     8461 taatagtttg cgcaacgttg ttgccattgc tacaggcatc gtggtgtcac gctcgtcgtt
     8521 tggtatggct tcattcagct ccggttccca acgatcaagg cgagttacat gatcccccat
     8581 gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc gttgtcagaa gtaagttggc
     8641 cgcagtgtta tcactcatgg ttatggcagc actgcataat tctcttactg tcatgccatc
     8701 cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag tcattctgag aatagtgtat
     8761 gcggcgaccg agttgctctt gcccggcgtc aatacgggat aataccgcgc cacatagcag
     8821 aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg cgaaaactct caaggatctt
     8881 accgctgttg agatccagtt cgatgtaacc cactcgtgca cccaactgat cttcagcatc
     8941 ttttactttc accagcgttt ctgggtgagc aaaaacagga aggcaaaatg ccgcaaaaaa
     9001 gggaataagg gcgacacgga aatgttgaat actcatactc ttcctttttc aatattattg
     9061 aagcatttat cagggttatt gtctcatgag cggatacata tttgaatgta tttagaaaaa
     9121 taaacaaata ggggttccgc gcacatttcc ccgaaaagtg ccacctgac
//
