LOCUS       sequence-311047-        8039 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  This plasmid encodes an iRFP fused to H2A histone nuclear marker. It
            has CMV promoter driving the expression of iRFP fused to H2A. It has
            no selection markers.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8039)
  AUTHORS   Kaufman T, Nitzan E, Firestein N, Ginzberg MB, Iyengar S, Patel N, 
            Ben-Hamo R, Porat Z, Hunter J, Hilfinger A, Rotter V, Kafri R, 
            Straussman R
  TITLE     Visual barcodes for clonal-multiplexing of live microscopy-based 
            assays.
  JOURNAL   Nat Commun. 2022 May 18;13(1):2725. doi: 10.1038/s41467-022-30008-0.
  PUBMED    35585055
REFERENCE   2  (bases 1 to 8039)
  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: "2022-05-18"; volume: "13(1):2725. doi"; pages: " 
            10.1038/s41467-022-30008-0"
COMMENT     Sequence Label: iRFP-H2A
FEATURES             Location/Qualifiers
     source          1..8039
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        1..304
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        305..508
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     459..479
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     CDS             531..1463
                     /codon_start=1
                     /product="near-infrared fluorescent protein with an 
                     emission peak at 670 nm, engineered from a bacterial 
                     phytochrome (Shcherbakova and Verkhusha, 2013)"
                     /label=iRFP670
                     /note="derived from Rhodopseudomonas palustris RpBphP6"
                     /translation="MARKVDLTSCDREPIHIPGSIQPCGCLLACDAQAVRITRITENAG
                     AFFGRETPRVGELLADYFGETEAHALRNALAQSSDPKRPALIFGWRDGLTGRTFDISLH
                     RHDGTSIIEFEPAAAEQADNPLRLTRQIIARTKELKSLEEMAARVPRYLQAMLGYHRVM
                     LYRFADDGSGMVIGEAKRSDLESFLGQHFPASLVPQQARLLYLKNAIRVVSDSRGISSR
                     IVPEHDASGAALDLSFAHLRSISPCHLEFLRNMGVSASMSLSIIIDGTLWGLIICHHYE
                     PRAVPMAQRVAAEMFADFLSLHFTAAHHQR"
     misc_feature    1911..2499
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(1964..1984)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2382..2393)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             2571..2804
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2882..3003
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2919..2938)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2973..2992
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      3043..3178
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(3198..3217)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3199..3217)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3227..3244)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(3227..3243)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3236..3258)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3385..3840
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3472..3491)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3682..3703
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3866..3970
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3971..4039,4040..4831)
                     /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(4189..4208)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5002..5590
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5491..5510
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5744..5761
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5878..5899
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5914..5919,5920..5937,5938..5944)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5952..5968
                     /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     5957..5979
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5976..5992
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5976..5992
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     6011..6031
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        6013..6031
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        6059..6285
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             6286..6466
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6513..6638
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    7131..7364
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             7549..7593
                     /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    7806..7923
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
ORIGIN
        1 cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt
       61 gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca
      121 atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc
      181 aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta
      241 catgacctta tgggactttc ctacttggca gtacatctac gtattagtca tcgctattac
      301 catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg
      361 atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc aaaatcaacg
      421 ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt
      481 acggtgggag gtctatataa gcagagctct ctggctaact gtcgggatcc atggcgcgta
      541 aggtcgatct cacctcctgc gatcgcgagc cgatccacat ccccggcagc attcagccgt
      601 gcggctgcct gctagcctgc gacgcgcagg cggtgcggat cacgcgcatt acggaaaatg
      661 ccggcgcgtt ctttggacgc gaaactccgc gggtcggtga gctactcgcc gattacttcg
      721 gcgagaccga agcccatgcg ctgcgcaacg cactggcgca gtcctccgat ccaaagcgac
      781 cggcgctgat cttcggttgg cgcgacggcc tgaccggccg caccttcgac atctcactgc
      841 atcgccatga cggtacatcg atcatcgagt tcgagcctgc ggcggccgaa caggccgaca
      901 atccgctgcg gctgacgcgg cagatcatcg cgcgcaccaa agaactgaag tcgctcgaag
      961 agatggccgc acgggtgccg cgctatctgc aggcgatgct cggctatcac cgcgtgatgt
     1021 tgtaccgctt cgcggacgac ggctccggga tggtgatcgg cgaggcgaag cgcagcgacc
     1081 tcgagagctt tctcggtcag cactttccgg cgtcgctggt cccgcagcag gcgcggctac
     1141 tgtacttgaa gaacgcgatc cgcgtggtct cggattcgcg cggcatcagc agccggatcg
     1201 tgcccgagca cgacgcctcc ggcgccgcgc tcgatctgtc gttcgcgcac ctgcgcagca
     1261 tctcgccctg ccatctcgaa tttctgcgga acatgggcgt cagcgcctcg atgtcgctgt
     1321 cgatcatcat tgacggcacg ctatggggat tgatcatctg tcatcattac gagccgcgtg
     1381 ccgtgccgat ggcgcagcgc gtcgcggccg aaatgttcgc cgacttctta tcgctgcact
     1441 tcaccgccgc ccaccaccaa cggtacaagt actcagatct cgagctcaag cttcgaattc
     1501 tgatgtcggg acgcggcaag cagggaggca aagctcgcgc caaagccaag acccgctctt
     1561 ctcgtgccgg tctccagttc cccgtgggcc gagtgcaccg actgctccgc aagggcaact
     1621 atgctgagcg ggtcggggcc ggcgcgccgg tgtacctggc ggcggtgctg gagtacctga
     1681 ctgccgagat cctggagctg gcgggcaacg ccgcccgcga caacaagaag acccgcatta
     1741 tcccgcgcca cttgcagctg gccatccgca acgacgagga gctcaacaag ctgctgggca
     1801 aagtaaccat cgctcagggt ggtgtcctgc ccaacatcca ggctgtgcta ctgcccaaga
     1861 agaccgagag tcaccacaag gccaaaggca aataaacgcg ttaagtcgac aatcaacctc
     1921 tagattacaa aatttgtgaa agattgactg gtattcttaa ctatgttgct ccttttacgc
     1981 tatgtggata cgctgcttta atgcctttgt atcatgctat tgcttcccgt atggctttca
     2041 ttttctcctc cttgtataaa tcctggttgc tgtctcttta tgaggagttg tggcccgttg
     2101 tcaggcaacg tggcgtggtg tgcactgtgt ttgctgacgc aacccccact ggttggggca
     2161 ttgccaccac ctgtcagctc ctttccggga ctttcgcttt ccccctccct attgccacgg
     2221 cggaactcat cgccgcctgc cttgcccgct gctggacagg ggctcggctg ttgggcactg
     2281 acaattccgt ggtgttgtcg gggaaatcat cgtcctttcc ttggctgctc gcctgtgttg
     2341 ccacctggat tctgcgcggg acgtccttct gctacgtccc ttcggccctc aatccagcgg
     2401 accttccttc ccgcggcctg ctgccggctc tgcggcctct tccgcgtctt cgccttcgcc
     2461 ctcagacgag tcggatctcc ctttgggccg cctccccgcg tcgactttaa gaccaatgac
     2521 ttacaaggca gctgtagatc ttagccactt tttaaaagaa aaggggggac tggaagggct
     2581 aattcactcc caacgaagac aagatctgct ttttgcttgt actgggtctc tctggttaga
     2641 ccagatctga gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata
     2701 aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta
     2761 gagatccctc agaccctttt agtcagtgtg gaaaatctct agcagtacgt atagtagttc
     2821 atgtcatctt attattcagt atttataact tgcaaagaaa tgaatatcag agagtgagag
     2881 gaacttgttt attgcagctt ataatggtta caaataaagc aatagcatca caaatttcac
     2941 aaataaagca tttttttcac tgcattctag ttgtggtttg tccaaactca tcaatgtatc
     3001 ttatcatgtc tggctctagc tatcccgccc ctaactccgc ccatcccgcc cctaactccg
     3061 cccagttccg cccattctcc gccccatggc tgactaattt tttttattta tgcagaggcc
     3121 gaggccgcct cggcctctga gctattccag aagtagtgag gaggcttttt tggaggccta
     3181 gggacgtacc caattcgccc tatagtgagt cgtattacgc gcgctcactg gccgtcgttt
     3241 tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt gcagcacatc
     3301 cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt
     3361 tgcgcagcct gaatggcgaa tgggacgcgc cctgtagcgg cgcattaagc gcggcgggtg
     3421 tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc gctcctttcg
     3481 ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct ctaaatcggg
     3541 ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa aaacttgatt
     3601 agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc cctttgacgt
     3661 tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca ctcaacccta
     3721 tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat tggttaaaaa
     3781 atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg cttacaattt
     3841 aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt tctaaataca
     3901 ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat aatattgaaa
     3961 aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt
     4021 ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca
     4081 gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag
     4141 ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc tatgtggcgc
     4201 ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac actattctca
     4261 gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt
     4321 aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct
     4381 gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt
     4441 aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg acgagcgtga
     4501 caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact
     4561 tactctagct tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc
     4621 acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga
     4681 gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt
     4741 agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac agatcgctga
     4801 gataggtgcc tcactgatta agcattggta actgtcagac caagtttact catatatact
     4861 ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga tcctttttga
     4921 taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt cagaccccgt
     4981 agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcttgca
     5041 aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc taccaactct
     5101 ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc ttctagtgta
     5161 gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc tcgctctgct
     5221 aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg ggttggactc
     5281 aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca
     5341 gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg agctatgaga
     5401 aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg
     5461 aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt
     5521 cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag gggggcggag
     5581 cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt gctggccttt
     5641 tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta ttaccgcctt
     5701 tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt cagtgagcga
     5761 ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc cgattcatta
     5821 atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca acgcaattaa
     5881 tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc cggctcgtat
     5941 gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatg accatgatta
     6001 cgccaagcgc gcaattaacc ctcactaaag ggaacaaaag ctggagctgc aagcttaatg
     6061 tagtcttatg caatactctt gtagtcttgc aacatggtaa cgatgagtta gcaacatgcc
     6121 ttacaaggag agaaaaagca ccgtgcatgc cgattggtgg aagtaaggtg gtacgatcgt
     6181 gccttattag gaaggcaaca gacgggtctg acatggattg gacgaaccac tgaattgccg
     6241 cattgcagag atattgtatt taagtgccta gctcgataca taaacgggtc tctctggtta
     6301 gaccagatct gagcctggga gctctctggc taactaggga acccactgct taagcctcaa
     6361 taaagcttgc cttgagtgct tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac
     6421 tagagatccc tcagaccctt ttagtcagtg tggaaaatct ctagcagtgg cgcccgaaca
     6481 gggacttgaa agcgaaaggg aaaccagagg agctctctcg acgcaggact cggcttgctg
     6541 aagcgcgcac ggcaagaggc gaggggcggc gactggtgag tacgccaaaa attttgacta
     6601 gcggaggcta gaaggagaga gatgggtgcg agagcgtcag tattaagcgg gggagaatta
     6661 gatcgcgatg ggaaaaaatt cggttaaggc cagggggaaa gaaaaaatat aaattaaaac
     6721 atatagtatg ggcaagcagg gagctagaac gattcgcagt taatcctggc ctgttagaaa
     6781 catcagaagg ctgtagacaa atactgggac agctacaacc atcccttcag acaggatcag
     6841 aagaacttag atcattatat aatacagtag caaccctcta ttgtgtgcat caaaggatag
     6901 agataaaaga caccaaggaa gctttagaca agatagagga agagcaaaac aaaagtaaga
     6961 ccaccgcaca gcaagcggcc gctgatcttc agacctggag gaggagatat gagggacaat
     7021 tggagaagtg aattatataa atataaagta gtaaaaattg aaccattagg agtagcaccc
     7081 accaaggcaa agagaagagt ggtgcagaga gaaaaaagag cagtgggaat aggagctttg
     7141 ttccttgggt tcttgggagc agcaggaagc actatgggcg cagcgtcaat gacgctgacg
     7201 gtacaggcca gacaattatt gtctggtata gtgcagcagc agaacaattt gctgagggct
     7261 attgaggcgc aacagcatct gttgcaactc acagtctggg gcatcaagca gctccaggca
     7321 agaatcctgg ctgtggaaag atacctaaag gatcaacagc tcctggggat ttggggttgc
     7381 tctggaaaac tcatttgcac cactgctgtg ccttggaatg ctagttggag taataaatct
     7441 ctggaacaga tttggaatca cacgacctgg atggagtggg acagagaaat taacaattac
     7501 acaagcttaa tacactcctt aattgaagaa tcgcaaaacc agcaagaaaa gaatgaacaa
     7561 gaattattgg aattagataa atgggcaagt ttgtggaatt ggtttaacat aacaaattgg
     7621 ctgtggtata taaaattatt cataatgata gtaggaggct tggtaggttt aagaatagtt
     7681 tttgctgtac tttctatagt gaatagagtt aggcagggat attcaccatt atcgtttcag
     7741 acccacctcc caaccccgag gggacaattc tagatcttga gacaaatggc agtattcatc
     7801 cacaatttta aaagaaaagg ggggattggg gggtacagtg caggggaaag aatagtagac
     7861 ataatagcaa cagacataca aactaaagaa ttacaaaaac aaattacaaa aattcaaaat
     7921 tttcgggttt attacaggga cagcagagat ccactttggc gccggctcga gggggcccgg
     7981 ggttattaat agtaatcaat tacggggtca ttagttcata gcccatatat ggagttccg
//
