LOCUS       sequence-330872-        7544 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  For producing fluorescently labeled HIV-1; expresses HIV-1 integrase
            fused to Vpr for packaging into HIV-1 and the fluorophore mRuby3.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7544)
  AUTHORS   Zhong Z, Ning J, Boggs EA, Jang S, Wallace C, Telmer C, Bruchez MP, 
            Ahn J, Engelman AN, Zhang P, Watkins SC, Ambrose Z
  TITLE     Cytoplasmic CPSF6 Regulates HIV-1 Capsid Trafficking and Infection 
            in a Cyclophilin A-Dependent Manner.
  JOURNAL   mBio. 2021 Mar 23;12(2). pii: mBio.03142-20. doi: 
            10.1128/mBio.03142-20.
  PUBMED    33758083
REFERENCE   2  (bases 1 to 7544)
  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: "mBio."; 
            date: "2021-03-23"; volume: "12(2). pii: mBio.03142-20. doi"; pages:
            " 10.1128/mBio.03142-20"
COMMENT     Sequence Label: pcDNA5-TO-Vpr-mRuby3-IN
FEATURES             Location/Qualifiers
     source          1..7544
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(103..123)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        108..437
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      288..423
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     350..369
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             486..1511
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     CDS             486..1511
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     polyA_signal    1641..1762
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1678..1697)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1732..1751
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(1811..1827)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1811..1827)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1824..1846)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1835..1851
                     /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)."
     promoter        complement(join(1859..1865,1866..1883,1884..1889))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1904..1925
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(2042..2059)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2213..2801)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2293..2312)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2972..3763,3764..3832))
                     /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     3595..3614
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3833..3937)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(4012..4031)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        4203..4582
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        4583..4786
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     4737..4757
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     protein_bind    4788..4806
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    4809..4827
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     primer_bind     4837..4861
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     CDS             5290..6000
                     /codon_start=1
                     /product="monomeric red fluorescent protein derived from 
                     mRuby2, with improved brightness and photostability (Bajar 
                     et al., 2016)"
                     /label=mRuby3
                     /translation="MVSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGRPYEGTQTM
                     RIKVIEGGPLPFAFDILATSFMYGSRTFIKYPADIPDFFKQSFPEGFTWERVTRYEDGG
                     VVTVTQDTSLEDGELVYNVKVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTD
                     IALKVDGGGHLHCNFVTTYRSKKTVGNIKMPGVHAVDHRLERIEESDNETYVVQREVAV
                     AKYSNLGGGMDELYK"
     misc_feature    6588..6705
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     primer_bind     complement(6934..6951)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    6940..7164
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      join(7210..7544,1..94)
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(7297..7316)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     7507..7528
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
ORIGIN
        1 atctcggtct attcttttga tttataaggg attttgccga tttcggccta ttggttaaaa
       61 aatgagctga tttaacaaaa atttaacgcg aattaattct gtggaatgtg tgtcagttag
      121 ggtgtggaaa gtccccaggc tccccagcag gcagaagtat gcaaagcatg catctcaatt
      181 agtcagcaac caggtgtgga aagtccccag gctccccagc aggcagaagt atgcaaagca
      241 tgcatctcaa ttagtcagca accatagtcc cgcccctaac tccgcccatc ccgcccctaa
      301 ctccgcccag ttccgcccat tctccgcccc atggctgact aatttttttt atttatgcag
      361 aggccgaggc cgcctctgcc tctgagctat tccagaagta gtgaggaggc ttttttggag
      421 gcctaggctt ttgcaaaaag ctcccgggag cttgtatatc cattttcgga tctgatcagc
      481 acgtgatgaa aaagcctgaa ctcaccgcga cgtctgtcga gaagtttctg atcgaaaagt
      541 tcgacagcgt ctccgacctg atgcagctct cggagggcga agaatctcgt gctttcagct
      601 tcgatgtagg agggcgtgga tatgtcctgc gggtaaatag ctgcgccgat ggtttctaca
      661 aagatcgtta tgtttatcgg cactttgcat cggccgcgct cccgattccg gaagtgcttg
      721 acattgggga attcagcgag agcctgacct attgcatctc ccgccgtgca cagggtgtca
      781 cgttgcaaga cctgcctgaa accgaactgc ccgctgttct gcagccggtc gcggaggcca
      841 tggatgcgat cgctgcggcc gatcttagcc agacgagcgg gttcggccca ttcggaccgc
      901 aaggaatcgg tcaatacact acatggcgtg atttcatatg cgcgattgct gatccccatg
      961 tgtatcactg gcaaactgtg atggacgaca ccgtcagtgc gtccgtcgcg caggctctcg
     1021 atgagctgat gctttgggcc gaggactgcc ccgaagtccg gcacctcgtg cacgcggatt
     1081 tcggctccaa caatgtcctg acggacaatg gccgcataac agcggtcatt gactggagcg
     1141 aggcgatgtt cggggattcc caatacgagg tcgccaacat cttcttctgg aggccgtggt
     1201 tggcttgtat ggagcagcag acgcgctact tcgagcggag gcatccggag cttgcaggat
     1261 cgccgcggct ccgggcgtat atgctccgca ttggtcttga ccaactctat cagagcttgg
     1321 ttgacggcaa tttcgatgat gcagcttggg cgcagggtcg atgcgacgca atcgtccgat
     1381 ccggagccgg gactgtcggg cgtacacaaa tcgcccgcag aagcgcggcc gtctggaccg
     1441 atggctgtgt agaagtactc gccgatagtg gaaaccgacg ccccagcact cgtccgaggg
     1501 caaaggaata gcacgtgcta cgagatttcg attccaccgc cgccttctat gaaaggttgg
     1561 gcttcggaat cgttttccgg gacgccggct ggatgatcct ccagcgcggg gatctcatgc
     1621 tggagttctt cgcccacccc aacttgttta ttgcagctta taatggttac aaataaagca
     1681 atagcatcac aaatttcaca aataaagcat ttttttcact gcattctagt tgtggtttgt
     1741 ccaaactcat caatgtatct tatcatgtct gtataccgtc gacctctagc tagagcttgg
     1801 cgtaatcatg gtcatagctg tttcctgtgt gaaattgtta tccgctcaca attccacaca
     1861 acatacgagc cggaagcata aagtgtaaag cctggggtgc ctaatgagtg agctaactca
     1921 cattaattgc gttgcgctca ctgcccgctt tccagtcggg aaacctgtcg tgccagctgc
     1981 attaatgaat cggccaacgc gcggggagag gcggtttgcg tattgggcgc tcttccgctt
     2041 cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta tcagctcact
     2101 caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag aacatgtgag
     2161 caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg tttttccata
     2221 ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc
     2281 cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg cgctctcctg
     2341 ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga agcgtggcgc
     2401 tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc tccaagctgg
     2461 gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt aactatcgtc
     2521 ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga
     2581 ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg
     2641 gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt accttcggaa
     2701 aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg
     2761 tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct ttgatctttt
     2821 ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgagat
     2881 tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt aaatcaatct
     2941 aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta
     3001 tctcagcgat ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa
     3061 ctacgatacg ggagggctta ccatctggcc ccagtgctgc aatgataccg cgagacccac
     3121 gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa
     3181 gtggtcctgc aactttatcc gcctccatcc agtctattaa ttgttgccgg gaagctagag
     3241 taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg
     3301 tgtcacgctc gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag
     3361 ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg
     3421 tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc
     3481 ttactgtcat gccatccgta agatgctttt ctgtgactgg tgagtactca accaagtcat
     3541 tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata
     3601 ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa
     3661 aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact cgtgcaccca
     3721 actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc
     3781 aaaatgccgc aaaaaaggga ataagggcga cacggaaatg ttgaatactc atactcttcc
     3841 tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg
     3901 aatgtattta gaaaaataaa caaatagggg ttccgcgcac atttccccga aaagtgccac
     3961 ctgacgtcga cggatcggga gatctcccga tcccctatgg tgcactctca gtacaatctg
     4021 ctctgatgcc gcatagttaa gccagtatct gctccctgct tgtgtgttgg aggtcgctga
     4081 gtagtgcgcg agcaaaattt aagctacaac aaggcaaggc ttgaccgaca attgcatgaa
     4141 gaatctgctt agggttaggc gttttgcgct gcttcgcgat gtacgggcca gatatacgcg
     4201 ttgacattga ttattgacta gttattaata gtaatcaatt acggggtcat tagttcatag
     4261 cccatatatg gagttccgcg ttacataact tacggtaaat ggcccgcctg gctgaccgcc
     4321 caacgacccc cgcccattga cgtcaataat gacgtatgtt cccatagtaa cgccaatagg
     4381 gactttccat tgacgtcaat gggtggagta tttacggtaa actgcccact tggcagtaca
     4441 tcaagtgtat catatgccaa gtacgccccc tattgacgtc aatgacggta aatggcccgc
     4501 ctggcattat gcccagtaca tgaccttatg ggactttcct acttggcagt acatctacgt
     4561 attagtcatc gctattacca tggtgatgcg gttttggcag tacatcaatg ggcgtggata
     4621 gcggtttgac tcacggggat ttccaagtct ccaccccatt gacgtcaatg ggagtttgtt
     4681 ttggcaccaa aatcaacggg actttccaaa atgtcgtaac aactccgccc cattgacgca
     4741 aatgggcggt aggcgtgtac ggtgggaggt ctatataagc agagctctcc ctatcagtga
     4801 tagagatctc cctatcagtg atagagatcg tcgacgagct cgtttagtga accgtcagat
     4861 cgcctggaga cgccatccac gctgttttga cctccataga agacaccggg accgatccag
     4921 cctccggact ctagcgctac catggaacaa gccccagaag accaagggcc acagagggag
     4981 ccgcacaatg aatggacact agagctttta gaggagctta agagagaagc tgttagacat
     5041 tttcctaggc catggctaca tggcttagga caacatatct atgaaactta tggagatact
     5101 tgggcaggag tggaagccat aataagaatt ctgcaacaac tgctgtttat tcatttcaga
     5161 attgggtgtc aacatagcag aataggcatt attcaacaga ggagagcaag aaatggagcc
     5221 agtagatcag atctagtaga taaattaggt gctggtatcc gtaaagtact atttttagat
     5281 ggaatagata tggtgtctaa gggcgaagag ctgatcaagg aaaatatgcg tatgaaggtg
     5341 gtcatggaag gttcggtcaa cggccaccaa ttcaaatgca caggtgaagg agaaggcaga
     5401 ccgtacgagg gaactcaaac catgaggatc aaagtcatcg agggaggacc cctgccattt
     5461 gcctttgaca ttcttgccac gtcgttcatg tatggcagcc gtacttttat caagtacccg
     5521 gccgacatcc ctgatttctt taaacagtcc tttcctgagg gttttacttg ggaaagagtt
     5581 acgagatacg aagatggtgg agtcgtcacc gtcacgcagg acaccagcct tgaggatggc
     5641 gagctcgtct acaacgtcaa ggtcagaggg gtaaactttc cctccaatgg tcccgtgatg
     5701 cagaagaaga ccaagggttg ggagcctaat acagagatga tgtatccagc agatggtggt
     5761 ctgagaggat acactgacat cgcactgaaa gttgatggtg gtggccatct gcactgcaac
     5821 ttcgtgacaa cttacaggtc aaaaaagacc gtcgggaaca tcaagatgcc cggtgtccat
     5881 gccgttgatc accgcctgga aaggatcgag gagagtgaca atgaaaccta cgtagtgcaa
     5941 cgcgaagtgg cagttgccaa atacagcaac cttggtggtg gcatggacga gctgtacaag
     6001 ggatccgctg gctccgctgc tggttctggc gaattctttt tagatggaat agataaggcc
     6061 caagaagaac atgagaaata tcacagtaat tggagagcca tggctagtga ttttaactta
     6121 ccacctgtag tagcaaaaga aatagtagcc agctgtgata aatgtcagct aaaaggagaa
     6181 gccatgcatg gacaagtaga ctgtagtcca ggaatatggc aactagattg cacacatcta
     6241 gaaggaaaaa ttatcctggt ggcggttcat gtagccagtg gatatataga agcagaagtt
     6301 attccagcag agacagggca ggaaacagca tactttctct taaaattagc aggaagatgg
     6361 ccagtaaaaa caatacatac agacaatggc agcaatttca ccagtaccac ggttaaggcc
     6421 gcctgttggt gggcagggat caagcaggaa tttggcattc cctacaatcc ccaaagtcaa
     6481 ggagtagtag aatctatgaa taaagaatta aagaaaatta taggacaggt aagagatcag
     6541 gctgaacatc ttaaaacagc agtacaaatg gcagtattta tccacaattt taaaagaaaa
     6601 ggggggattg gggggtacag tgcaggggaa agaatagtag acataatagc aacagacata
     6661 caaactaaag aactacaaaa acaaattaca aaaattcaaa attttcgggt ttattacagg
     6721 gacaacaaag atccactttg gaaaggacca gcaaagcttc tctggaaagg tgaaggggca
     6781 gtagtaatac aagataatag tgacataaaa gtagtgccaa gaagaaaagc aaagatcatt
     6841 agagattatg gaaaacagat ggcaggtgat gattgtgtgg caagtagaca ggatgaggat
     6901 tgaaccgcgg gcccgtttaa acccgctgat cagcctcgac tgtgccttct agttgccagc
     6961 catctgttgt ttgcccctcc cccgtgcctt ccttgaccct ggaaggtgcc actcccactg
     7021 tcctttccta ataaaatgag gaaattgcat cgcattgtct gagtaggtgt cattctattc
     7081 tggggggtgg ggtggggcag gacagcaagg gggaggattg ggaagacaat agcaggcatg
     7141 ctggggatgc ggtgggctct atggcttctg aggcggaaag aaccagctgg ggctctaggg
     7201 ggtatcccca cgcgccctgt agcggcgcat taagcgcggc gggtgtggtg gttacgcgca
     7261 gcgtgaccgc tacacttgcc agcgccctag cgcccgctcc tttcgctttc ttcccttcct
     7321 ttctcgccac gttcgccggc tttccccgtc aagctctaaa tcgggggctc cctttagggt
     7381 tccgatttag tgctttacgg cacctcgacc ccaaaaaact tgattagggt gatggttcac
     7441 gtagtgggcc atcgccctga tagacggttt ttcgcccttt gacgttggag tccacgttct
     7501 ttaatagtgg actcttgttc caaactggaa caacactcaa ccct
//
