LOCUS       sequence-377400-        7362 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Lentiviral expression of SARS-CoV-2 5_ UTR SL1 alone.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7362)
  AUTHORS   Vora SM, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman J, 
            Gehrke L, Shi M, Wang L, Iwasaki A, Wu H
  TITLE     Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral 
            translation and Nsp1 evasion.
  JOURNAL   Proc Natl Acad Sci U S A. 2022 Mar 1;119(9). pii: 2117198119. doi: 
            10.1073/pnas.2117198119.
  PUBMED    35149555
REFERENCE   2  (bases 1 to 7362)
  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: "Proc Natl 
            Acad Sci U S A."; date: "2022-03-1"; volume: "119(9). pii: 
            2117198119. doi"; pages: " 10.1073/pnas.2117198119"
COMMENT     Sequence Label: pLV-mScarlet-SARS-CoV-2-SL1 alone
FEATURES             Location/Qualifiers
     source          1..7362
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             1..181
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    228..353
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    846..1079
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1264..1308
                     /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    1575..1691
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     enhancer        1714..2017
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        2018..2221
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     2172..2192
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     CDS             2274..2969
                     /codon_start=1
                     /product="bright monomeric red fluorescent protein evolved 
                     from a synthetic template (Bindels et al., 2016)"
                     /label=mScarlet
                     /translation="MVSKGEAVIKEFMRFKVHMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFSWDILSPQFMYGSRAFTKHPADIPDYYKQSFPEGFKWERVMNFEDGG
                     AVTVTQDTSLEDGTLIYKVKLRGTNFPPDGPVMQKKTMGWEASTERLYPEDGVLKGDIK
                     MALRLKDGGRYLADFKTTYKAKKPVQMPGAYNVDRKLDITSHNEDYTVVEQYERSEGRH
                     STGGMDELYK"
     primer_bind     complement(2407..2425)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     2675..2694
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     misc_feature    2979..3567
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3032..3052)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3450..3461)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             3654..3887
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    3959..4080
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3996..4015)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4050..4069
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      4120..4255
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(4275..4294)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4276..4294)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(4304..4321)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(4304..4320)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4313..4335)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      4462..4917
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4549..4568)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4759..4780
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        4943..5047
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5048..5116,5117..5908)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTVSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(5266..5285)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6079..6667
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6568..6587
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     6821..6838
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    6955..6976
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(6991..6996,6997..7014,7015..7021)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7029..7045
                     /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     7034..7056
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7053..7069
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7053..7069
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7088..7108
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        7090..7108
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        7136..7362
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
ORIGIN
        1 gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca
       61 ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg
      121 tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc
      181 agtggcgccc gaacagggac ttgaaagcga aagggaaacc agaggagctc tctcgacgca
      241 ggactcggct tgctgaagcg cgcacggcaa gaggcgaggg gcggcgactg gtgagtacgc
      301 caaaaatttt gactagcgga ggctagaagg agagagatgg gtgcgagagc gtcagtatta
      361 agcgggggag aattagatcg cgatgggaaa aaattcggtt aaggccaggg ggaaagaaaa
      421 aatataaatt aaaacatata gtatgggcaa gcagggagct agaacgattc gcagttaatc
      481 ctggcctgtt agaaacatca gaaggctgta gacaaatact gggacagcta caaccatccc
      541 ttcagacagg atcagaagaa cttagatcat tatataatac agtagcaacc ctctattgtg
      601 tgcatcaaag gatagagata aaagacacca aggaagcttt agacaagata gaggaagagc
      661 aaaacaaaag taagaccacc gcacagcaag cggccgctga tcttcagacc tggaggagga
      721 gatatgaggg acaattggag aagtgaatta tataaatata aagtagtaaa aattgaacca
      781 ttaggagtag cacccaccaa ggcaaagaga agagtggtgc agagagaaaa aagagcagtg
      841 ggaataggag ctttgttcct tgggttcttg ggagcagcag gaagcactat gggcgcagcg
      901 tcaatgacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca gcagcagaac
      961 aatttgctga gggctattga ggcgcaacag catctgttgc aactcacagt ctggggcatc
     1021 aagcagctcc aggcaagaat cctggctgtg gaaagatacc taaaggatca acagctcctg
     1081 gggatttggg gttgctctgg aaaactcatt tgcaccactg ctgtgccttg gaatgctagt
     1141 tggagtaata aatctctgga acagatttgg aatcacacga cctggatgga gtgggacaga
     1201 gaaattaaca attacacaag cttaatacac tccttaattg aagaatcgca aaaccagcaa
     1261 gaaaagaatg aacaagaatt attggaatta gataaatggg caagtttgtg gaattggttt
     1321 aacataacaa attggctgtg gtatataaaa ttattcataa tgatagtagg aggcttggta
     1381 ggtttaagaa tagtttttgc tgtactttct atagtgaata gagttaggca gggatattca
     1441 ccattatcgt ttcagaccca cctcccaacc ccgaggggac ccgacaggcc cgaaggaata
     1501 gaagaagaag gtggagagag agacagagac agatccattc gattagtgaa cggatctcga
     1561 cggtatcggt taacttttaa aagaaaaggg gggattgggg ggtatagtgc aggggaaaga
     1621 atagtagaca taatagcaac agacatacaa actaaagaat tacaaaaaca aattacaaaa
     1681 ttcaaaattt tatcgataag cttgggagtt ccgcgttaca taacttacgg taaatggccc
     1741 gcctggctga ccgcccaacg acccccgccc attgacgtca ataatgacgt atgttcccat
     1801 agtaacgcca atagggactt tccattgacg tcaatgggtg gagtatttac ggtaaactgc
     1861 ccacttggca gtacatcaag tgtatcatat gccaagtacg ccccctattg acgtcaatga
     1921 cggtaaatgg cccgcctggc attatgccca gtacatgacc ttatgggact ttcctacttg
     1981 gcagtacatc tacgtattag tcatcgctat taccatggtg atgcggtttt ggcagtacat
     2041 caatgggcgt ggatagcggt ttgactcacg gggatttcca agtctccacc ccattgacgt
     2101 caatgggagt ttgttttggc accaaaatca acgggacttt ccaaaatgtc gtaacaactc
     2161 cgccccattg acgcaaatgg gcggtaggcg tgtacggtgg gaggtctata taagcagagc
     2221 tcgtttagtg aaccattaaa ggtttatacc ttcccaggta acaaaccaac caaatggtga
     2281 gcaagggcga ggcagtgatc aaggagttca tgcggttcaa ggtgcacatg gagggctcca
     2341 tgaacggcca cgagttcgag atcgagggcg agggcgaggg ccgcccctac gagggcaccc
     2401 agaccgccaa gctgaaggtg accaagggtg gccccctgcc cttctcctgg gacatcctgt
     2461 cccctcagtt catgtacggc tccagggcct tcaccaagca ccccgccgac atccccgact
     2521 actataagca gtccttcccc gagggcttca agtgggagcg cgtgatgaac ttcgaggacg
     2581 gcggcgccgt gaccgtgacc caggacacct ccctggagga cggcaccctg atctacaagg
     2641 tgaagctccg cggcaccaac ttccctcctg acggccccgt aatgcagaag aagacaatgg
     2701 gctgggaagc gtccaccgag cggttgtacc ccgaggacgg cgtgctgaag ggcgacatta
     2761 agatggccct gcgcctgaag gacggcggcc gctacctggc ggacttcaag accacctaca
     2821 aggccaagaa gcccgtgcag atgcccggcg cctacaacgt cgaccgcaag ttggacatca
     2881 cctcccacaa cgaggactac accgtggtgg aacagtacga acgctccgag ggccgccact
     2941 ccaccggcgg catggacgag ctgtacaagt gagtcgacaa tcaacctctg gattacaaaa
     3001 tttgtgaaag attgactggt attcttaact atgttgctcc ttttacgcta tgtggatacg
     3061 ctgctttaat gcctttgtat catgctattg cttcccgtat ggctttcatt ttctcctcct
     3121 tgtataaatc ctggttgctg tctctttatg aggagttgtg gcccgttgtc aggcaacgtg
     3181 gcgtggtgtg cactgtgttt gctgacgcaa cccccactgg ttggggcatt gccaccacct
     3241 gtcagctcct ttccgggact ttcgctttcc ccctccctat tgccacggcg gaactcatcg
     3301 ccgcctgcct tgcccgctgc tggacagggg ctcggctgtt gggcactgac aattccgtgg
     3361 tgttgtcggg gaagctgacg tcctttccat ggctgctcgc ctgtgttgcc acctggattc
     3421 tgcgcgggac gtccttctgc tacgtccctt cggccctcaa tccagcggac cttccttccc
     3481 gcggcctgct gccggctctg cggcctcttc cgcgtcttcg ccttcgccct cagacgagtc
     3541 ggatctccct ttgggccgcc tccccgcctg gaattcgagc tcggtacctt taagaccaat
     3601 gacttacaag gcagctgtag atcttagcca ctttttaaaa gaaaaggggg gactggaagg
     3661 gctaattcac tcccaacgaa gacaagatct gctttttgct tgtactgggt ctctctggtt
     3721 agaccagatc tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca
     3781 ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa
     3841 ctagagatcc ctcagaccct tttagtcagt gtggaaaatc tctagcagta gtagttcatg
     3901 tcatcttatt attcagtatt tataacttgc aaagaaatga atatcagaga gtgagaggaa
     3961 cttgtttatt gcagcttata atggttacaa ataaagcaat agcatcacaa atttcacaaa
     4021 taaagcattt ttttcactgc attctagttg tggtttgtcc aaactcatca atgtatctta
     4081 tcatgtctgg ctctagctat cccgccccta actccgccca tcccgcccct aactccgccc
     4141 agttccgccc attctccgcc caatggctga ctaatttttt ttatttatgc agaggccgag
     4201 gccgcctcgg cctctgagct attccagaag tagtgaggag gcttttttgg aggcctaggg
     4261 acgtacccaa ttcgccctat agtgagtcgt attacgcgcg ctcactggcc gtcgttttac
     4321 aacgtcgtga ctgggaaaac cctggcgtta cccaacttaa tcgccttgca gcacatcccc
     4381 ctttcgccag ctggcgtaat agcgaagagg cccgcaccga tcgcccttcc caacagttgc
     4441 gcagcctgaa tggcgaatgg gacgcgccct gtagcggcgc attaagcgcg gcgggtgtgg
     4501 tggttacgcg cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt
     4561 tcttcccttc ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcgggggc
     4621 tccctttagg gttccgattt agtgctttac ggcacctcga ccccaaaaaa cttgattagg
     4681 gtgatggttc acgtagtggg ccatcgccct gatagacggt ttttcgccct ttgacgttgg
     4741 agtccacgtt ctttaatagt ggactcttgt tccaaactgg aacaacactc aaccctatct
     4801 cggtctattc ttttgattta taagggattt tgccgatttc ggcctattgg ttaaaaaatg
     4861 agctgattta acaaaaattt aacgcgaatt ttaacaaaat attaacgctt acaatttagg
     4921 tggcactttt cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc
     4981 aaatatgtat ccgatcatga gacaataacc ctgataaatg cttcaataat attgaaaaag
     5041 gaagagtatg agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg
     5101 ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt
     5161 gggtgcacga gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt
     5221 tcgccccgaa gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt
     5281 attatcccgt attgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa
     5341 tgacttggtt gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag
     5401 agaattatgc agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac
     5461 aacgatcgga ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac
     5521 tcgccttgat cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac
     5581 cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac
     5641 tctagcttcc cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact
     5701 tctgcgctcg gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg
     5761 tgggtctcgc ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt
     5821 tatctacacg acggtgagtc aggcaactat ggatgaacga aatagacaga tcgctgagat
     5881 aggtgcctca ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta
     5941 gattgattta aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa
     6001 tctcatgacc aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga
     6061 aaagatcaaa ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac
     6121 aaaaaaacca ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt
     6181 tccgaaggta actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc
     6241 gtagttaggc caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat
     6301 cctgttacca gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag
     6361 acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc
     6421 cagcttggag cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag
     6481 cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac
     6541 aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg
     6601 gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct
     6661 atggaaaaac gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc
     6721 tcacatgttc tttcctgcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga
     6781 gtgagctgat accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga
     6841 agcggaagag cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg
     6901 cagctggcac gacaggtttc ccgactggaa agcgggcagt gagcgcaacg caattaatgt
     6961 gagttagctc actcattagg caccccaggc tttccacttt atgcttccgg ctcgtatgtt
     7021 gtgtggaatt gtgagcggat aacaatttca cacaggaaac agctatgacc atgattacgc
     7081 caagcgcgca attaaccctc actaaaggga acaaaagctg gagctgcaag cttaatgtag
     7141 tcttatgcaa tactcttgta gtcttgcaac atggtaacga tgagttagca acatgcctta
     7201 caaggagaga aaaagcaccg tgcatgccga ttggtggaag taaggtggta cgatcgtgcc
     7261 ttattaggaa ggcaacagac gggtctgaca tggattggac gaaccactga attgccgcat
     7321 tgcagagata ttgtatttaa gtgcctagct cgatacataa ac
//
