LOCUS       sequence-194213-        9173 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 9173)
  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 9173)
  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..9173
                     /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"
     misc_feature    1410..1535
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    2032..2265
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2450..2494
                     /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    2792..2909
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        3046..3453
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     CDS             5409..5453
                     /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    6064..6652
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6117..6137)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6535..6546)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             7170..7350
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(7421..8009)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(7501..7520)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(8180..8971,8972..9040))
                     /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     8803..8822
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(9041..9145)
                     /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 gggtgcgaga gcgtcagtat taagcggggg agaattagat
     1561 cgcgatggga aaaaattcgg ttaaggccag ggggaaagaa aaaatataaa ttaaaacata
     1621 tagtatgggc aagcagggag ctagaacgat tcgcagttaa tcctggcctg ttagaaacat
     1681 cagaaggctg tagacaaata ctgggacagc tacaaccatc ccttcagaca ggatcagaag
     1741 aacttagatc attatataat acagtagcaa ccctctattg tgtgcatcaa aggatagaga
     1801 taaaagacac caaggaagct ttagacaaga tagaggaaga gcaaaacaaa agtaagacca
     1861 ccgcacagca agcggccggc cgctgatctt cagacctgga ggaggagata tgagggacaa
     1921 ttggagaagt gaattatata aatataaagt agtaaaaatt gaaccattag gagtagcacc
     1981 caccaaggca aagagaagag tggtgcagag agaaaaaaga gcagtgggaa taggagcttt
     2041 gttccttggg ttcttgggag cagcaggaag cactatgggc gcagcgtcaa tgacgctgac
     2101 ggtacaggcc agacaattat tgtctggtat agtgcagcag cagaacaatt tgctgagggc
     2161 tattgaggcg caacagcatc tgttgcaact cacagtctgg ggcatcaagc agctccaggc
     2221 aagaatcctg gctgtggaaa gatacctaaa ggatcaacag ctcctgggga tttggggttg
     2281 ctctggaaaa ctcatttgca ccactgctgt gccttggaat gctagttgga gtaataaatc
     2341 tctggaacag atttggaatc acacgacctg gatggagtgg gacagagaaa ttaacaatta
     2401 cacaagctta atacactcct taattgaaga atcgcaaaac cagcaagaaa agaatgaaca
     2461 agaattattg gaattagata aatgggcaag tttgtggaat tggtttaaca taacaaattg
     2521 gctgtggtat ataaaattat tcataatgat agtaggaggc ttggtaggtt taagaatagt
     2581 ttttgctgta ctttctatag tgaatagagt taggcaggga tattcaccat tatcgtttca
     2641 gacccacctc ccaaccccga ggggacccga caggcccgaa ggaatagaag aagaaggtgg
     2701 agagagagac agagacagat ccattcgatt agtgaacgga tcggcactgc gtgcgccaat
     2761 tctgcagaca aatggcagta ttcatccaca attttaaaag aaaagggggg attggggggt
     2821 acagtgcagg ggaaagaata gtagacataa tagcaacaga catacaaact aaagaattac
     2881 aaaaacaaat tacaaaaatt caaaattttc gggtttatta cagggacagc agagatccag
     2941 tttggttaat taactgcagc cccgataaaa taaaagattt tatttagtct ccagaaaaag
     3001 gggggaatga aagaccccac ctgtaggttt ggcaagctag ctgcagtaac gccattttgc
     3061 aaggcatgga aaaataccaa accaagaata gagaagttca gatcaagggc gggtacatga
     3121 aaatagctaa cgttgggcca aacaggatat ctgcggtgag cagtttcggc cccggcccgg
     3181 ggccaagaac agatggtcac cgcagtttcg gccccggccc gaggccaaga acagatggtc
     3241 cccagatatg gcccaaccct cagcagtttc ttaagaccca tcagatgttt ccaggctccc
     3301 ccaaggacct gaaatgaccc tgcgccttat ttgaattaac caatcagcct gcttctcgct
     3361 tctgttcgcg cgcttctgct tcccgagctc tataaaagag ctcacaaccc ctcactcggc
     3421 gcgccagtcc tccgacagac tgagtcgccc gggggtctag agccgccatg agagtgaaag
     3481 agaaatacca gcacctgtgg agatgggggt ggaaatgggg gactatgctg ctgggaatcc
     3541 tgatgatctg tagcgccaca gaaaagctgt gggtcaccgt ctactatggg gtacctgtct
     3601 ggaaagagac cacaactacc ctgttctgcg cttccgacgc taaggcatat gataccgagg
     3661 tgcacaacgt ctgggccacc catgcttgtg tgcctacaga cccaaatccc caggaggtgg
     3721 tcctggaaaa cgtgacagag gatttcaaca tgtggaagaa caacatggtg gaacagatgc
     3781 aggaggacgt catcaacctg tgggatcagt ctctgaagcc ttgcgtgaaa ctgaccccac
     3841 tgtgcgtcac actgaattgt aaggacgtga acgccactaa tacaactagc tcctctgaag
     3901 ggatgatgga gcgcggagaa atcaagaatt gcagtttcaa tatcaccaaa tcaattcggg
     3961 ataaggtgca gaaagagtac gctctgtttt ataaactgga cgtggtccct atcgataaca
     4021 agaacaatac caaataccgg ctgatctcat gcaatacaag cgtcattact caggcttgtc
     4081 ctaaggtgag cttcgagcct atcccaattc actattgcgc cccagctggc ttcgcaattc
     4141 ttaagtgtaa caacaagacc ttcaacggga agggccagtg caaaaatgtg agcaccgtcc
     4201 agtgcacaca tgggatcaga ccagtggtct ccactcagct gctgctgaac ggatctctgg
     4261 cagaggaaaa ggtggtcatt aggagtgaca acttcactga taatgccaag accatcattg
     4321 tgcagctgaa cgagtcagtc aaaatcaatt gtacaaggcc aagcaacaat acccgcaagt
     4381 ccatccacat tggacccggg cgcgcctttt acaccacagg agagatcatt ggcgacatcc
     4441 gccaggccca ttgtaacatt tcccgagctc agtggaacaa taccctgaag cagatcgtgg
     4501 aaaaactgcg ggagcagttc aacaataaga ctatcgtgtt tacccacagt tcaggcgggg
     4561 atccagaaat tgtgatgcat tctttcaact gcggaggcga gttcttttac tgtaattcta
     4621 cccagctgtt taacagtaca tggaatgaca ctgaaaaaag ctccgggaca gagggaaacg
     4681 atactatcat tctgccttgc agaatcaagc agattattaa tatgtggcag gaagtgggga
     4741 aggcaatgta tgccccccct atcaaaggac agattagatg ttctagtaac attaccggcc
     4801 tgctgctgac aagggacggg ggaaagaatg aaagcgagat cgaaattttt aggcccggcg
     4861 ggggagacat gcgcgacaat tggcgatccg aactttacaa gtataaagtg gtcaaaatcg
     4921 agccactggg agtggcacca accaaggcta aacggagagt ggtccagaga gagaagaggg
     4981 ctgtgggaat tggcgcactg ttcctgggct ttctgggggc tgcaggatca acaatgggcg
     5041 cagccagcat gacactgact gtgcaggcca gacagctgct gagcgggatc gtgcagcagc
     5101 agaacaatct gctgagggct attgaagcac agcagcacat gttgcagctg accgtgtggg
     5161 gcatcaagca gttgcaggca cgagtgctgg cagtcgagag atacctgaaa gaccagcagc
     5221 tgatgggcat ctgggggtgc agcggaaagc tgatttgtac taccgccgtg ccttggaaca
     5281 cctcatggag caacaagtcc ctggattcta tctggaacaa tatgacatgg atggagtggg
     5341 aaaaggagat cgaaaactac accaacacaa tctataccct gattgaggaa tctcagatcc
     5401 agcaggaaaa gaacgagcag gaattactcg agctggacaa atgggccagt ctgtggaatt
     5461 ggttcggcat tacaaagtgg ctgtggtaca tcaaaatttt tatcatgatc gtgggcgggc
     5521 tgatcggact gagaattgtg ttcagtgtcc tgtcaatcgt gaaccgagtc cggcagggct
     5581 atagccccct gtcctttcag actctgctgc ctgcaactcg gggacccgat agacctgaag
     5641 gcatcgagga agagggaggc gagagagaca gggatagatc cggacagctg gtcaatgggt
     5701 tcctggctct gatttgggtc gacctgcgct ccctgttcct gttttcttat catcgactgc
     5761 gggatctgct gctgactgtg acccgaatcg tcgaactgct gggaaggcga ggatgggaga
     5821 ttctgaaata ctggtggaac ctgttgcagt attggagcca ggagctgaag aactctgccg
     5881 tgagtctgct gaatgcaaca gcgatcgcag tggcagaagg cactgacaga atcattgagg
     5941 tggtccagag ggtgtacaga gccatcctgc acattcctac acgcattaga cagggactgg
     6001 agcgggcact gctgtgagaa ttcacgcgta tcgataccgg tggcccctgg ggccgcgatc
     6061 gctaatcaac ctctggatta caaaatttgt gaaagattga ctggtattct taactatgtt
     6121 gctcctttta cgctatgtgg atacgctgct ttaatgcctt tgtatcatgc tattgcttcc
     6181 cgtatggctt tcattttctc ctccttgtat aaatcctggt tgctgtctct ttatgaggag
     6241 ttgtggcccg ttgtcaggca acgtggcgtg gtgtgcactg tgtttgctga cgcaaccccc
     6301 actggttggg gcattgccac cacctgtcag ctcctttccg ggactttcgc tttccccctc
     6361 cctattgcca cggcggaact catcgccgcc tgccttgccc gctgctggac aggggctcgg
     6421 ctgttgggca ctgacaattc cgtggtgttg tcggggaagc tgacgtcctt tccatggctg
     6481 ctcgcctgtg ttgccacctg gattctgcgc gggacgtcct tctgctacgt cccttcggcc
     6541 ctcaatccag cggaccttcc ttcccgcggc ctgctgccgg ctctgcggcc tcttccgcgt
     6601 cttcgccttc gccctcagac gagtcggatc tccctttggg ccgcctcccc gcttaatcgc
     6661 gtcgagacct agaaaaacat ggagcaatca caagtagcaa tacagcagct accaatgctg
     6721 attgtgcctg gctagaagca caagaggagg aggaggtggg ttttccagtc acacctcagg
     6781 tacctttaag accaatgact tacaaggcag ctgtagatct tagccacttt ttaaaagaaa
     6841 aggggggact ggaagggcta attcactccc aacgaagaca agatatcctt gatctgtgga
     6901 tctaccacac acaaggctac ttccctgatt ggcagaacta cacaccaggg ccagggatca
     6961 gatatccact gacctttgga tggtgctaca agctagtacc agttgagcaa gagaaggtag
     7021 aagaagccaa tgaaggagag aacacccgct tgttacaccc tgtgagcctg catgggatgg
     7081 atgacccgga gagagaagta ttagagtgga ggtttgacag ccgcctagca tttcatcaca
     7141 tggcccgaga gctgcatccg gactgtactg ggtctctctg gttagaccag atctgagcct
     7201 gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc ttgccttgag
     7261 tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg taactagaga tccctcagac
     7321 ccttttagtc agtgtggaaa atctctagca gggcccgttt catgtgagca aaaggccagc
     7381 aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg ctccgccccc
     7441 ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat
     7501 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
     7561 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
     7621 cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
     7681 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
     7741 cggtaagaca cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga
     7801 ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc tacactagaa
     7861 gaacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta
     7921 gctcttgatc cggcaaacaa accaccgctg gtagcggtgg tttttttgtt tgcaagcagc
     7981 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg
     8041 acgctcagtg gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga
     8101 tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa agtatatatg
     8161 agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct
     8221 gtctatttcg ttcatccata gttgcctgac tccccgtcgt gtagataact acgatacggg
     8281 agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc
     8341 cagatttatc agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa
     8401 ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta agtagttcgc
     8461 cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt
     8521 cgtttggtat ggcttcattc agctccggtt cccaacgatc aaggcgagtt acatgatccc
     8581 ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt
     8641 tggccgcagt gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc
     8701 catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc tgagaatagt
     8761 gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata
     8821 gcagaacttt aaaagtgctc atcattggaa aacgttcttc ggggcgaaaa ctctcaagga
     8881 tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag
     8941 catcttttac tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa
     9001 aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt tttcaatatt
     9061 attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga
     9121 aaaataaaca aataggggtt ccgcgcacat ttccccgaaa agtgccacct gac
//
