LOCUS       sequence-318475-        7877 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  timestamp Template A inserted into the 3' UTR of iRFP, in a second 
            generation lentiviral backbone with the Vivid promoter, with RNA 
            barcode CTG. AKA 149B3..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7877)
  AUTHORS   Rodriques SG, Chen LM, Liu S, Zhong ED, Scherrer JR, Boyden ES, Chen
            F
  TITLE     RNA timestamps identify the age of single molecules in RNA 
            sequencing.
  JOURNAL   Nat Biotechnol. 2020 Oct 19. pii: 10.1038/s41587-020-0704-z. doi: 
            10.1038/s41587-020-0704-z.
  PUBMED    33077959
REFERENCE   2  (bases 1 to 7877)
  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 
            Biotechnol. 2020 Oct 19. pii: 10.1038/s41587-020-0704-z. doi: 
            10.1038/s41587-020-0704-z."
COMMENT     Sequence Label: pLenti-5xUASG-iRFP-B3-timestamp-A
FEATURES             Location/Qualifiers
     source          1..7877
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     regulatory      1..10
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     misc_feature    1679..2267
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(1732..1752)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2150..2161)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             2342..2575
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     primer_bind     complement(2694..2712)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        2780..2884
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2885..2953,2954..3745)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(3103..3122)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3916..4504
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4405..4424
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4658..4675
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    4915..4936
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(4951..4956,4957..4974,4975..4981)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4989..5005
                     /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     4994..5016
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5013..5029
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5013..5029
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5079..5098
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     LTR             5290..5923
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    5970..6095
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6592..6825
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             7010..7054
                     /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    7347..7464
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
ORIGIN
        1 gccaccatgg tcgcaggaca cgcaagtgga agccccgact ttggaaccgc cgatccgagc
       61 gactgtgaga gagaagaaat ccatctggcc ggatccatcc agccacacgg aacactgctg
      121 gtggtctccg agcctgacca tagaatcatt caggcatctg ccaacgccgc tgaattcctg
      181 aatctgggaa gtgtgctggg agtccccctg gctgagatcg acggggatct gctgatcaag
      241 attctgcccc acctggaccc taccgcagaa ggaatgccag tggccgtcag gtgccgcatt
      301 ggaaacccct ccacagagta cgatggactg atgcatcgac cacctgaagg aggactgatc
      361 attgagctgg aacgggctgg gccacccatt gatctgagcg gaacactggc tcccgcactg
      421 gagcgaattc gaactgcagg atccctgagg gctctgtgcg acgatactgc actgctgttc
      481 cagcagtgta ccggctacga ccgagtgatg gtctatcggt tcgatgaaca ggggcacgga
      541 gaggtgtatt cagaaataca tgtgactgga ctggagagct actttggcaa caggtatcct
      601 agctccctcg tgccacagat ggcccggaga ctgtacgaaa gacagagggt gcgcgtcctg
      661 gtggatgtct cttatcagcc tgtgccactg gagccaagac tgagtcccct gactggcagg
      721 gacctggata tgtcagggtg ttttctgcgc tctatgagtc ctactcacct gcagttcctg
      781 aagaatatgg gcgtgcgggc aacactggtg gtcagcctgg tggtcggagg caaactgtgg
      841 gggctggtga tctgccacca ttatctgcca cgcttcatcc attttgagct gcgagcaatt
      901 tgtgagctgc tggccgaagc tatcgcaacc cgcattacag ccctgtaagc ggactgttac
      961 tgagctgcgt tttacaccct ttctttgaca aaacctaact tgcgcagaaa aaaaaaaaat
     1021 aagagacaac attggcatgg ctttgttttt ttaaattttt tttaaagttt tttttttttt
     1081 tttttttttt tttttaagtt tttttgtttt gttttggcgc ttttgactca ggatttaaaa
     1141 actggaacgg tgaaggcgac agcagttggt tggagcaaac atcccccaaa gttctacaaa
     1201 tgtggctgag gactttgtac attgttttgt tttttttttt ttttggtttt gtcttttttt
     1261 aatagtcatt ccaagtatcc atgaaataag tggttacagg aagtccctca ccctcccaaa
     1321 agccaccccc actcctaaga ggaggatggt cgcgtccatg ccctgagtcc accccgggga
     1381 aggtgacact ggcatgctta gattagatta gattagatta gattagatta gaaaaattaa
     1441 tatacgtaca ccatcagggt acgtcatata ttttttccaa tccaatccaa tccaatccaa
     1501 tccaatccaa tacgcgttag attagattag attagattag attagattag aaaaattaat
     1561 acgtacacca tcagggtacg tctcagacac catcagggtc tgtctggtac agcatcagcg
     1621 taccatatat tttttccaat ccaatccaat ccaatccaat ccaatccaaa tagatcctaa
     1681 tcaacctctg gattacaaaa tttgtgaaag attgactggt attcttaact atgttgctcc
     1741 ttttacgcta tgtggatacg ctgctttaat gcctttgtat catgctattg cttcccgtat
     1801 ggctttcatt ttctcctcct tgtataaatc ctggttgctg tctctttatg aggagttgtg
     1861 gcccgttgtc aggcaacgtg gcgtggtgtg cactgtgttt gctgacgcaa cccccactgg
     1921 ttggggcatt gccaccacct gtcagctcct ttccgggact ttcgctttcc ccctccctat
     1981 tgccacggcg gaactcatcg ccgcctgcct tgcccgctgc tggacagggg ctcggctgtt
     2041 gggcactgac aattccgtgg tgttgtcggg gaaatcatcg tcctttcctt ggctgctcgc
     2101 ctgtgttgcc acctggattc tgcgcgggac gtccttctgc tacgtccctt cggccctcaa
     2161 tccagcggac cttccttccc gcggcctgct gccggctctg cggcctcttc cgcgtcttcg
     2221 ccttcgccct cagacgagtc ggatctccct ttgggccgcc tccccgcctg agatccttta
     2281 agaccaatga cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga
     2341 ctggaagggc taattcactc ccaacgaaga caagatctgc tttttgcttg tactgggtct
     2401 ctctggttag accagatctg agcctgggag ctctctggct aactagggaa cccactgctt
     2461 aagcctcaat aaagcttgcc ttgagtgctt caagtagtgt gtgcccgtct gttgtgtgac
     2521 tctggtaact agagatccct cagacccttt tagtcagtgt ggaaaatctc tagcagtagt
     2581 agttcatgtc atcttattat tcagtattta taacttgcaa agaaatgaat atcagagagt
     2641 gagaggcccg ggttaattaa ggaaagggct agatcattct tgaagacgaa agggcctcgt
     2701 gatacgccta tttttatagg ttaatgtcat gataataatg gtttcttaga cgtcaggtgg
     2761 cacttttcgg ggaaatgtgc gcggaacccc tatttgttta tttttctaaa tacattcaaa
     2821 tatgtatccg ctcatgagac aataaccctg ataaatgctt caataatatt gaaaaaggaa
     2881 gagtatgagt attcaacatt tccgtgtcgc ccttattccc ttttttgcgg cattttgcct
     2941 tcctgttttt gctcacccag aaacgctggt gaaagtaaaa gatgctgaag atcagttggg
     3001 tgcacgagtg ggttacatcg aactggatct caacagcggt aagatccttg agagttttcg
     3061 ccccgaagaa cgttttccaa tgatgagcac ttttaaagtt ctgctatgtg gcgcggtatt
     3121 atcccgtgtt gacgccgggc aagagcaact cggtcgccgc atacactatt ctcagaatga
     3181 cttggttgag tactcaccag tcacagaaaa gcatcttacg gatggcatga cagtaagaga
     3241 attatgcagt gctgccataa ccatgagtga taacactgcg gccaacttac ttctgacaac
     3301 gatcggagga ccgaaggagc taaccgcttt tttgcacaac atgggggatc atgtaactcg
     3361 ccttgatcgt tgggaaccgg agctgaatga agccatacca aacgacgagc gtgacaccac
     3421 gatgcctgta gcaatggcaa caacgttgcg caaactatta actggcgaac tacttactct
     3481 agcttcccgg caacaattaa tagactggat ggaggcggat aaagttgcag gaccacttct
     3541 gcgctcggcc cttccggctg gctggtttat tgctgataaa tctggagccg gtgagcgtgg
     3601 gtctcgcggt atcattgcag cactggggcc agatggtaag ccctcccgta tcgtagttat
     3661 ctacacgacg gggagtcagg caactatgga tgaacgaaat agacagatcg ctgagatagg
     3721 tgcctcactg attaagcatt ggtaactgtc agaccaagtt tactcatata tactttagat
     3781 tgatttaaaa cttcattttt aatttaaaag gatctaggtg aagatccttt ttgataatct
     3841 catgaccaaa atcccttaac gtgagttttc gttccactga gcgtcagacc ccgtagaaaa
     3901 gatcaaagga tcttcttgag atcctttttt tctgcgcgta atctgctgct tgcaaacaaa
     3961 aaaaccaccg ctaccagcgg tggtttgttt gccggatcaa gagctaccaa ctctttttcc
     4021 gaaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta
     4081 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct
     4141 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg
     4201 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag
     4261 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc
     4321 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg
     4381 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt
     4441 tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg
     4501 gaaaaacgcc agcaacgcgg cctttttacg gttcctggcc ttttgctggc cttttgctca
     4561 catgttcttt cctgcgttat cccctgattc tgtggataac cgtattaccg cctttgagtg
     4621 agctgatacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc
     4681 ggaagagcgc ccaatacgca aaccgcctct ccccgcgcgt tggccgattc attaatgcag
     4741 caagctcatg gctgactaat tttttttatt tatgcagagg ccgaggccgc ctcggcctct
     4801 gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagctc
     4861 cccgtggcac gacaggtttc ccgactggaa agcgggcagt gagcgcaacg caattaatgt
     4921 gagttagctc actcattagg caccccaggc tttacacttt atgcttccgg ctcgtatgtt
     4981 gtgtggaatt gtgagcggat aacaatttca cacaggaaac agctatgaca tgattacgaa
     5041 tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa
     5101 tgtatcttat catgtctgga tcaactggat aactcaagct aaccaaaatc atcccaaact
     5161 tcccacccca taccctatta ccactgccaa ttacctgtgg tttcatttac tctaaacctg
     5221 tgattcctct gaattatttt cattttaaag aaattgtatt tgttaaatat gtactacaaa
     5281 cttagtagtt ggaagggcta attcactccc aaagaagaca agatatcctt gatctgtgga
     5341 tctaccacac acaaggctac ttccctgatt agcagaacta cacaccaggg ccaggggtca
     5401 gatatccact gacctttgga tggtgctaca agctagtacc agttgagcca gataaggtag
     5461 aagaggccaa taaaggagag aacaccagct tgttacaccc tgtgagcctg catgggatgg
     5521 atgacccgga gagagaagtg ttagagtgga ggtttgacag ccgcctagca tttcatcacg
     5581 tggcccgaga gctgcatccg gagtacttca agaactgctg atatcgagct tgctacaagg
     5641 gactttccgc tggggacttt ccagggaggc gtggcctggg cgggactggg gagtggcgag
     5701 ccctcagatc ctgcatataa gcagctgctt tttgcctgta ctgggtctct ctggttagac
     5761 cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa
     5821 agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag
     5881 agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagtggcgc ccgaacaggg
     5941 acttgaaagc gaaagggaaa ccagaggagc tctctcgacg caggactcgg cttgctgaag
     6001 cgcgcacggc aagaggcgag gggcggcgac tggtgagtac gccaaaaatt ttgactagcg
     6061 gaggctagaa ggagagagat gggtgcgaga gcgtcagtat taagcggggg agaattagat
     6121 cgcgatggga aaaaattcgg ttaaggccag ggggaaagaa aaaatataaa ttaaaacata
     6181 tagtatgggc aagcagggag ctagaacgat tcgcagttaa tcctggcctg ttagaaacat
     6241 cagaaggctg tagacaaata ctgggacagc tacaaccatc ccttcagaca ggatcagaag
     6301 aacttagatc attatataat acagtagcaa ccctctattg tgtgcatcaa aggatagaga
     6361 taaaagacac caaggaagct ttagacaaga tagaggaaga gcaaaacaaa agtaagacca
     6421 ccgcacagca agcggccggc cgctgatctt cagacctgga ggaggagata tgagggacaa
     6481 ttggagaagt gaattatata aatataaagt agtaaaaatt gaaccattag gagtagcacc
     6541 caccaaggca aagagaagag tggtgcagag agaaaaaaga gcagtgggaa taggagcttt
     6601 gttccttggg ttcttgggag cagcaggaag cactatgggc gcagcgtcaa tgacgctgac
     6661 ggtacaggcc agacaattat tgtctggtat agtgcagcag cagaacaatt tgctgagggc
     6721 tattgaggcg caacagcatc tgttgcaact cacagtctgg ggcatcaagc agctccaggc
     6781 aagaatcctg gctgtggaaa gatacctaaa ggatcaacag ctcctgggga tttggggttg
     6841 ctctggaaaa ctcatttgca ccactgctgt gccttggaat gctagttgga gtaataaatc
     6901 tctggaacag atttggaatc acacgacctg gatggagtgg gacagagaaa ttaacaatta
     6961 cacaagctta atacactcct taattgaaga atcgcaaaac cagcaagaaa agaatgaaca
     7021 agaattattg gaattagata aatgggcaag tttgtggaat tggtttaaca taacaaattg
     7081 gctgtggtat ataaaattat tcataatgat agtaggaggc ttggtaggtt taagaatagt
     7141 ttttgctgta ctttctatag tgaatagagt taggcaggga tattcaccat tatcgtttca
     7201 gacccacctc ccaaccccga ggggacccga caggcccgaa ggaatagaag aagaaggtgg
     7261 agagagagac agagacagat ccattcgatt agtgaacgga tctcgacggt atcgccgaat
     7321 tcacaaatgg cagtattcat ccacaatttt aaaagaaaag gggggattgg ggggtacagt
     7381 gcaggggaaa gaatagtaga cataatagca acagacatac aaactaaaga attacaaaaa
     7441 caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga tccagtttgg
     7501 actagtgagt ttctagacgg agtactgtcc tccgagcgga gtactgtcct ccgactcgag
     7561 cggagtactg tcctccgatc ggagtactgt cctccgcgaa ttccggagta ctgtcctccg
     7621 aagacgctag cggggggcta taaaaggggg tgggggcgtt cgtcctcact ctagatctgc
     7681 gatctaagtg cggccgctaa tacgactcac tatagaccta gtcaggccag ccggttaggc
     7741 tgccaccgaa ggttggtaga cggtgctgcc tgcgaccaac cccaggagga ctgggtatta
     7801 tagggtcaga tcggcgaaag tcgccacttc gccgaggagt gcaatctgtg aggccccagg
     7861 aggactgggt accggtc
//
