LOCUS       sequence-323200-        8473 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expression of stdMCP-tdTomato in mammalian cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8473)
  AUTHORS   Xu H, Wang J, Liang Y, Fu Y, Li S, Huang J, Xu H, Zou W, Chen B
  TITLE     TriTag: an integrative tool to correlate chromatin dynamics and gene
            expression in living cells.
  JOURNAL   Nucleic Acids Res. 2020 Oct 26. pii: 5940501. doi: 
            10.1093/nar/gkaa906.
  PUBMED    33104788
REFERENCE   2  (bases 1 to 8473)
  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: "Nucleic 
            Acids Res. 2020 Oct 26. pii: 5940501. doi: 10.1093/nar/gkaa906."
COMMENT     Sequence Label: PHY23-phage-ubc-nls-ha-stdMCP-tdTomato
FEATURES             Location/Qualifiers
     source          1..8473
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             1..634
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    681..806
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1303..1536
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1721..1765
                     /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    2058..2175
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2218..2616
                     /label=UbC promoter
                     /note="human ubiquitin C promoter"
     CDS             2631..2651
                     /codon_start=1
                     /product="nuclear localization signal of SV40 (simian virus
                     40) large T antigen"
                     /label=SV40 NLS
                     /translation="PKKKRKV"
     CDS             2655..2681
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /note="This is a variant of the standard HA tag, which has 
                     sequence YPYDVPDYA. Some anti-HA antibodies may not 
                     recognize this variant."
                     /translation="YPYDVPDYA"
     CDS             2655..2681
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
     CDS             2682..2693
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     CDS             3408..4838
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     misc_feature    4863..5451
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4916..4936)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(5334..5345)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             5526..5759
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     primer_bind     complement(5878..5896)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5964..6068
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(6069..6137,6138..6929)
                     /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(6287..6306)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      7100..7688
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7589..7608
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7842..7859
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    8099..8120
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(8135..8140,8141..8158,8159..8165)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    8173..8189
                     /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     8178..8200
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     8197..8213
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     8197..8213
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     8263..8282
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
ORIGIN
        1 tggaagggct aattcactcc caaagaagac aagatatcct tgatctgtgg atctaccaca
       61 cacaaggcta cttccctgat tagcagaact acacaccagg gccaggggtc agatatccac
      121 tgacctttgg atggtgctac aagctagtac cagttgagcc agataaggta gaagaggcca
      181 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatgggatg gatgacccgg
      241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac gtggcccgag
      301 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg
      361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat
      421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga
      481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
      541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
      601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
      661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
      721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
      781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
      841 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
      901 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
      961 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     1021 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     1081 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     1141 aagcggccgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     1201 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     1261 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     1321 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     1381 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     1441 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     1501 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     1561 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     1621 gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt
     1681 aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt
     1741 ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta
     1801 tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt
     1861 actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct
     1921 cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga
     1981 cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgccgaa ttcacaaatg
     2041 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
     2101 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
     2161 aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg gactagtggc
     2221 ctccgcgccg ggttttggcg cctcccgcgg gcgcccccct cctcacggcg agcgctgcca
     2281 cgtcagacga agggcgcagc gagcgtcctg atccttccgc ccggacgctc aggacagcgg
     2341 cccgctgctc ataagactcg gccttagaac cccagtatca gcagaaggac attttaggac
     2401 gggacttggg tgactctagg gcactggttt tctttccaga gagcggaaca ggcgaggaaa
     2461 agtagtccct tctcggcgat tctgcggagg gatctccgtg gggcggtgaa cgccgatgat
     2521 tatataagga cgcgccgggt gtggcacagc tagttccgtc gcagccggga tttgggtcgc
     2581 ggttcttgtt tgtggatcgc tgtgatcgtc acttggcggc cgcaatgggc ccaaaaaaga
     2641 aaagaaaagt tggctacccc tacgacgtgc ccgactacgc catcgaaggc cgccatatgc
     2701 tagccgcttc taactttact cagttcgttc tcgtcgacaa tggcggaact ggcgacgtga
     2761 ctgtcgcccc aagcaacttc gctaacggga tcgctgaatg gatcagctct aactcgcgtt
     2821 cacaggctta caaagtaacc tgtagcgttc gtcagagctc tgcgcagaat cgcaaataca
     2881 ccatcaaagt cgaggtgcct aaaggcgcct ggcgttcgta cttaaatatg gaactaacca
     2941 ttccaatttt cgccacgaat tccgactgcg agcttattgt taaggcaatg caaggtctcc
     3001 taaaagatgg aaacccgatt ccctcagcaa tcgcagcaaa ctccggcatc tacgccatgg
     3061 ccagcaactt cacccagttc gtgctggtgg acaacggcgg caccggcgac gtgaccgtgg
     3121 cccccagcaa cttcgccaac ggcatcgccg agtggatcag cagcaacagc agaagccagg
     3181 cctacaaggt gacctgcagc gtgagacaga gcagcgccca gaacagaaag tacaccatca
     3241 aggtggaggt gcccaagggc gcctggagaa gctacctgaa catggagctg accatcccca
     3301 tcttcgccac caacagcgac tgcgagctga tcgtgaaggc catgcagggc ctgctgaagg
     3361 acggcaaccc catccccagc gccatcgccg ccaacagcga ttctagaatg gtgagcaagg
     3421 gcgaggaggt catcaaagag ttcatgcgct tcaaggtgcg catggagggc tccatgaacg
     3481 gccacgagtt cgagatcgag ggcgagggcg agggccgccc ctacgagggc acccagaccg
     3541 ccaagctgaa ggtgaccaag ggcggccccc tgcccttcgc ctgggacatc ctgtcccccc
     3601 agttcatgta cggctccaag gcgtacgtga agcaccccgc cgacatcccc gattacaaga
     3661 agctgtcctt ccccgagggc ttcaagtggg agcgcgtgat gaacttcgag gacggcggtc
     3721 tggtgaccgt gacccaggac tcctccctgc aggacggcac gctgatctac aaggtgaaga
     3781 tgcgcggcac caacttcccc cccgacggcc ccgtaatgca gaagaagacc atgggctggg
     3841 aggcctccac cgagcgcctg tacccccgcg acggcgtgct gaagggcgag atccaccagg
     3901 ccctgaagct gaaggacggc ggccactacc tggtggagtt caagaccatc tacatggcca
     3961 agaagcccgt gcaactgccc ggctactact acgtggacac caagctggac atcacctccc
     4021 acaacgagga ctacaccatc gtggaacagt acgagcgctc cgagggccgc caccacctgt
     4081 tcctggggca tggcaccggc agcaccggca gcggcagctc cggcaccgcc tcctccgagg
     4141 acaacaacat ggccgtcatc aaagagttca tgcgcttcaa ggtgcgcatg gagggctcca
     4201 tgaacggcca cgagttcgag atcgagggcg agggcgaggg ccgcccctac gagggcaccc
     4261 agaccgccaa gctgaaggtg accaagggcg gccccctgcc cttcgcctgg gacatcctgt
     4321 ccccccagtt catgtacggc tccaaggcgt acgtgaagca ccccgccgac atccccgatt
     4381 acaagaagct gtccttcccc gagggcttca agtgggagcg cgtgatgaac ttcgaggacg
     4441 gcggtctggt gaccgtgacc caggactcct ccctgcagga cggcacgctg atctacaagg
     4501 tgaagatgcg cggcaccaac ttcccccccg acggccccgt aatgcagaag aagaccatgg
     4561 gctgggaggc ctccaccgag cgcctgtacc cccgcgacgg cgtgctgaag ggcgagatcc
     4621 accaggccct gaagctgaag gacggcggcc actacctggt ggagttcaag accatctaca
     4681 tggccaagaa gcccgtgcaa ctgcccggct actactacgt ggacaccaag ctggacatca
     4741 cctcccacaa cgaggactac accatcgtgg aacagtacga gcgctccgag ggccgccacc
     4801 acctgttcct gtacggcatg gacgagctgt acaagtaatg tacaagtaaa tcgatagatc
     4861 ctaatcaacc tctggattac aaaatttgtg aaagattgac tggtattctt aactatgttg
     4921 ctccttttac gctatgtgga tacgctgctt taatgccttt gtatcatgct attgcttccc
     4981 gtatggcttt cattttctcc tccttgtata aatcctggtt gctgtctctt tatgaggagt
     5041 tgtggcccgt tgtcaggcaa cgtggcgtgg tgtgcactgt gtttgctgac gcaaccccca
     5101 ctggttgggg cattgccacc acctgtcagc tcctttccgg gactttcgct ttccccctcc
     5161 ctattgccac ggcggaactc atcgccgcct gccttgcccg ctgctggaca ggggctcggc
     5221 tgttgggcac tgacaattcc gtggtgttgt cggggaaatc atcgtccttt ccttggctgc
     5281 tcgcctgtgt tgccacctgg attctgcgcg ggacgtcctt ctgctacgtc ccttcggccc
     5341 tcaatccagc ggaccttcct tcccgcggcc tgctgccggc tctgcggcct cttccgcgtc
     5401 ttcgccttcg ccctcagacg agtcggatct ccctttgggc cgcctccccg cctgagatcc
     5461 tttaagacca atgacttaca aggcagctgt agatcttagc cactttttaa aagaaaaggg
     5521 gggactggaa gggctaattc actcccaacg aagacaagat ctgctttttg cttgtactgg
     5581 gtctctctgg ttagaccaga tctgagcctg ggagctctct ggctaactag ggaacccact
     5641 gcttaagcct caataaagct tgccttgagt gcttcaagta gtgtgtgccc gtctgttgtg
     5701 tgactctggt aactagagat ccctcagacc cttttagtca gtgtggaaaa tctctagcag
     5761 tagtagttca tgtcatctta ttattcagta tttataactt gcaaagaaat gaatatcaga
     5821 gagtgagagg cccgggttaa ttaaggaaag ggctagatca ttcttgaaga cgaaagggcc
     5881 tcgtgatacg cctattttta taggttaatg tcatgataat aatggtttct tagacgtcag
     5941 gtggcacttt tcggggaaat gtgcgcggaa cccctatttg tttatttttc taaatacatt
     6001 caaatatgta tccgctcatg agacaataac cctgataaat gcttcaataa tattgaaaaa
     6061 ggaagagtat gagtattcaa catttccgtg tcgcccttat tccctttttt gcggcatttt
     6121 gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt
     6181 tgggtgcacg agtgggttac atcgaactgg atctcaacag cggtaagatc cttgagagtt
     6241 ttcgccccga agaacgtttt ccaatgatga gcacttttaa agttctgcta tgtggcgcgg
     6301 tattatcccg tgttgacgcc gggcaagagc aactcggtcg ccgcatacac tattctcaga
     6361 atgacttggt tgagtactca ccagtcacag aaaagcatct tacggatggc atgacagtaa
     6421 gagaattatg cagtgctgcc ataaccatga gtgataacac tgcggccaac ttacttctga
     6481 caacgatcgg aggaccgaag gagctaaccg cttttttgca caacatgggg gatcatgtaa
     6541 ctcgccttga tcgttgggaa ccggagctga atgaagccat accaaacgac gagcgtgaca
     6601 ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact attaactggc gaactactta
     6661 ctctagcttc ccggcaacaa ttaatagact ggatggaggc ggataaagtt gcaggaccac
     6721 ttctgcgctc ggcccttccg gctggctggt ttattgctga taaatctgga gccggtgagc
     6781 gtgggtctcg cggtatcatt gcagcactgg ggccagatgg taagccctcc cgtatcgtag
     6841 ttatctacac gacggggagt caggcaacta tggatgaacg aaatagacag atcgctgaga
     6901 taggtgcctc actgattaag cattggtaac tgtcagacca agtttactca tatatacttt
     6961 agattgattt aaaacttcat ttttaattta aaaggatcta ggtgaagatc ctttttgata
     7021 atctcatgac caaaatccct taacgtgagt tttcgttcca ctgagcgtca gaccccgtag
     7081 aaaagatcaa aggatcttct tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa
     7141 caaaaaaacc accgctacca gcggtggttt gtttgccgga tcaagagcta ccaactcttt
     7201 ttccgaaggt aactggcttc agcagagcgc agataccaaa tactgttctt ctagtgtagc
     7261 cgtagttagg ccaccacttc aagaactctg tagcaccgcc tacatacctc gctctgctaa
     7321 tcctgttacc agtggctgct gccagtggcg ataagtcgtg tcttaccggg ttggactcaa
     7381 gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc
     7441 ccagcttgga gcgaacgacc tacaccgaac tgagatacct acagcgtgag ctatgagaaa
     7501 gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa
     7561 caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg
     7621 ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc
     7681 tatggaaaaa cgccagcaac gcggcctttt tacggttcct ggccttttgc tggccttttg
     7741 ctcacatgtt ctttcctgcg ttatcccctg attctgtgga taaccgtatt accgcctttg
     7801 agtgagctga taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg
     7861 aagcggaaga gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat
     7921 gcagcaagct catggctgac taattttttt tatttatgca gaggccgagg ccgcctcggc
     7981 ctctgagcta ttccagaagt agtgaggagg cttttttgga ggcctaggct tttgcaaaaa
     8041 gctccccgtg gcacgacagg tttcccgact ggaaagcggg cagtgagcgc aacgcaatta
     8101 atgtgagtta gctcactcat taggcacccc aggctttaca ctttatgctt ccggctcgta
     8161 tgttgtgtgg aattgtgagc ggataacaat ttcacacagg aaacagctat gacatgatta
     8221 cgaatttcac aaataaagca tttttttcac tgcattctag ttgtggtttg tccaaactca
     8281 tcaatgtatc ttatcatgtc tggatcaact ggataactca agctaaccaa aatcatccca
     8341 aacttcccac cccataccct attaccactg ccaattacct gtggtttcat ttactctaaa
     8401 cctgtgattc ctctgaatta ttttcatttt aaagaaattg tatttgttaa atatgtacta
     8461 caaacttagt agt
//
