LOCUS       sequence-377399-        7555 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Lentiviral expression of SARS-CoV-2 5' UTR Delta-SL1.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7555)
  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 7555)
  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-2-5'UTR-Delta-SL1
FEATURES             Location/Qualifiers
     source          1..7555
                     /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             2467..3162
                     /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(2600..2618)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     2868..2887
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     misc_feature    3172..3760
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3225..3245)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3643..3654)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             3847..4080
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    4152..4273
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4189..4208)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4243..4262
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      4313..4448
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(4468..4487)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4469..4487)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(4497..4514)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(4497..4513)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4506..4528)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      4655..5110
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4742..4761)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4952..4973
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5136..5240
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5241..5309,5310..6101)
                     /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     complement(5459..5478)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6272..6860
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6761..6780
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7014..7031
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    7148..7169
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(7184..7189,7190..7207,7208..7214)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7222..7238
                     /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     7227..7249
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7246..7262
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7246..7262
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     7281..7301
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        7283..7301
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        7329..7555
                     /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 aaccaaccaa ctttcgatct cttgtagatc tgttctctaa acgaacttta
     2281 aaatctgtgt ggctgtcact cggctgcatg cttagtgcac tcacgcagta taattaataa
     2341 ctaattactg tcgttgacag gacacgagta actcgtctat cttctgcagg ctgcttacgg
     2401 tttcgtccgt gttgcagccg atcatcagca catctaggtt tcgtccgggt gtgaccgaaa
     2461 ggtaagatgg tgagcaaggg cgaggcagtg atcaaggagt tcatgcggtt caaggtgcac
     2521 atggagggct ccatgaacgg ccacgagttc gagatcgagg gcgagggcga gggccgcccc
     2581 tacgagggca cccagaccgc caagctgaag gtgaccaagg gtggccccct gcccttctcc
     2641 tgggacatcc tgtcccctca gttcatgtac ggctccaggg ccttcaccaa gcaccccgcc
     2701 gacatccccg actactataa gcagtccttc cccgagggct tcaagtggga gcgcgtgatg
     2761 aacttcgagg acggcggcgc cgtgaccgtg acccaggaca cctccctgga ggacggcacc
     2821 ctgatctaca aggtgaagct ccgcggcacc aacttccctc ctgacggccc cgtaatgcag
     2881 aagaagacaa tgggctggga agcgtccacc gagcggttgt accccgagga cggcgtgctg
     2941 aagggcgaca ttaagatggc cctgcgcctg aaggacggcg gccgctacct ggcggacttc
     3001 aagaccacct acaaggccaa gaagcccgtg cagatgcccg gcgcctacaa cgtcgaccgc
     3061 aagttggaca tcacctccca caacgaggac tacaccgtgg tggaacagta cgaacgctcc
     3121 gagggccgcc actccaccgg cggcatggac gagctgtaca agtgagtcga caatcaacct
     3181 ctggattaca aaatttgtga aagattgact ggtattctta actatgttgc tccttttacg
     3241 ctatgtggat acgctgcttt aatgcctttg tatcatgcta ttgcttcccg tatggctttc
     3301 attttctcct ccttgtataa atcctggttg ctgtctcttt atgaggagtt gtggcccgtt
     3361 gtcaggcaac gtggcgtggt gtgcactgtg tttgctgacg caacccccac tggttggggc
     3421 attgccacca cctgtcagct cctttccggg actttcgctt tccccctccc tattgccacg
     3481 gcggaactca tcgccgcctg ccttgcccgc tgctggacag gggctcggct gttgggcact
     3541 gacaattccg tggtgttgtc ggggaagctg acgtcctttc catggctgct cgcctgtgtt
     3601 gccacctgga ttctgcgcgg gacgtccttc tgctacgtcc cttcggccct caatccagcg
     3661 gaccttcctt cccgcggcct gctgccggct ctgcggcctc ttccgcgtct tcgccttcgc
     3721 cctcagacga gtcggatctc cctttgggcc gcctccccgc ctggaattcg agctcggtac
     3781 ctttaagacc aatgacttac aaggcagctg tagatcttag ccacttttta aaagaaaagg
     3841 ggggactgga agggctaatt cactcccaac gaagacaaga tctgcttttt gcttgtactg
     3901 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac
     3961 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt
     4021 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca
     4081 gtagtagttc atgtcatctt attattcagt atttataact tgcaaagaaa tgaatatcag
     4141 agagtgagag gaacttgttt attgcagctt ataatggtta caaataaagc aatagcatca
     4201 caaatttcac aaataaagca tttttttcac tgcattctag ttgtggtttg tccaaactca
     4261 tcaatgtatc ttatcatgtc tggctctagc tatcccgccc ctaactccgc ccatcccgcc
     4321 cctaactccg cccagttccg cccattctcc gccccatggc tgactaattt tttttattta
     4381 tgcagaggcc gaggccgcct cggcctctga gctattccag aagtagtgag gaggcttttt
     4441 tggaggccta gggacgtacc caattcgccc tatagtgagt cgtattacgc gcgctcactg
     4501 gccgtcgttt tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt
     4561 gcagcacatc cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct
     4621 tcccaacagt tgcgcagcct gaatggcgaa tgggacgcgc cctgtagcgg cgcattaagc
     4681 gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc
     4741 gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct
     4801 ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa
     4861 aaacttgatt agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc
     4921 cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca
     4981 ctcaacccta tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat
     5041 tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg
     5101 cttacaattt aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt
     5161 tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat
     5221 aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt
     5281 ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg
     5341 ctgaagatca gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga
     5401 tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc
     5461 tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac
     5521 actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg
     5581 gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca
     5641 acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg
     5701 gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg
     5761 acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg
     5821 gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag
     5881 ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg
     5941 gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct
     6001 cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac
     6061 agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact
     6121 catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga
     6181 tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt
     6241 cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct
     6301 gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc
     6361 taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc
     6421 ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc
     6481 tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg
     6541 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt
     6601 cgtgcacaca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg
     6661 agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg
     6721 gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt
     6781 atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag
     6841 gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt
     6901 gctggccttt tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta
     6961 ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt
     7021 cagtgagcga ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc
     7081 cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca
     7141 acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttccac tttatgcttc
     7201 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatg
     7261 accatgatta cgccaagcgc gcaattaacc ctcactaaag ggaacaaaag ctggagctgc
     7321 aagcttaatg tagtcttatg caatactctt gtagtcttgc aacatggtaa cgatgagtta
     7381 gcaacatgcc ttacaaggag agaaaaagca ccgtgcatgc cgattggtgg aagtaaggtg
     7441 gtacgatcgt gccttattag gaaggcaaca gacgggtctg acatggattg gacgaaccac
     7501 tgaattgccg cattgcagag atattgtatt taagtgccta gctcgataca taaac
//
