LOCUS       sequence-349209-        6357 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expression Recording Islands (XRIs) for recording cellular 
            physiological histories along intracellular protein self-assembly. 
            Contains XRI subunit with FLAG tag, under UBC promoter with a FLEX 
            switch..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6357)
  AUTHORS   Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C,
            Park D, Park WM, Ramirez S, Boyden ES
  TITLE     Recording of cellular physiological histories along optically 
            readable self-assembling protein chains.
  JOURNAL   Nat Biotechnol. 2023 Jan 2. doi: 10.1038/s41587-022-01586-7.
  PUBMED    36593405
REFERENCE   2  (bases 1 to 6357)
  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. 2023 Jan 2. doi: 10.1038/s41587-022-01586-7."
COMMENT     Sequence Label: pAAV-UBC-FLEX-XRI-FLAG
FEATURES             Location/Qualifiers
     source          1..6357
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(182..770)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(262..281)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(941..1732,1733..1801))
                     /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     1564..1583
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1802..1906)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1932..2387)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2069..2090)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2281..2300
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   2459..2588
                     /label=AAV2 ITR
     promoter        2661..3059
                     /label=UbC promoter
                     /note="human ubiquitin C promoter"
     protein_bind    3069..3102
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     protein_bind    3165..3198
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(4320..4343)
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     protein_bind    complement(5611..5644)
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     protein_bind    complement(5715..5748)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     polyA_signal    5796..6003
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     repeat_region   6173..6302
                     /label=AAV2 ITR
ORIGIN
        1 cttccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat
       61 cagctcactc aaaggcggta atacggttat ccacagaatc aggggataac gcaggaaaga
      121 acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg ttgctggcgt
      181 ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca agtcagaggt
      241 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc
      301 gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa
      361 gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag gtcgttcgct
      421 ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta
      481 actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca gcagccactg
      541 gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg aagtggtggc
      601 ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg aagccagtta
      661 ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct ggtagcggtg
      721 gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa gaagatcctt
      781 tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa gggattttgg
      841 tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa tgaagtttta
      901 aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc ttaatcagtg
      961 aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga ctccccgtcg
     1021 tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca atgataccgc
     1081 gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc ggaagggccg
     1141 agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat tgttgccggg
     1201 aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc attgctacag
     1261 gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt tcccaacgat
     1321 caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc ttcggtcctc
     1381 cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg gcagcactgc
     1441 ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt gagtactcaa
     1501 ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg gcgtcaatac
     1561 gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga aaacgttctt
     1621 cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg taacccactc
     1681 gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg tgagcaaaaa
     1741 caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt tgaatactca
     1801 tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc atgagcggat
     1861 acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca tttccccgaa
     1921 aagtgccacc taaattgtaa gcgttaatat tttgttaaaa ttcgcgttaa atttttgtta
     1981 aatcagctca ttttttaacc aataggccga aatcggcaaa atcccttata aatcaaaaga
     2041 atagaccgag atagggttga gtgttgttcc agtttggaac aagagtccac tattaaagaa
     2101 cgtggactcc aacgtcaaag ggcgaaaaac cgtctatcag ggcgatggcc cactacgtga
     2161 accatcaccc taatcaagtt ttttggggtc gaggtgccgt aaagcactaa atcggaaccc
     2221 taaagggagc ccccgattta gagcttgacg gggaaagccg gcgaacgtgg cgagaaagga
     2281 agggaagaaa gcgaaaggag cgggcgctag ggcgctggca agtgtagcgg tcacgctgcg
     2341 cgtaaccacc acacccgccg cgcttaatgc gccgctacag ggcgcgtccc attcgccatt
     2401 caggctgcgc aactgttggg aagggcgatc ggtgcgggcc tcttcgctat tacgccagct
     2461 gcgcgctcgc tcgctcactg aggccgcccg ggcaaagccc gggcgtcggg cgacctttgg
     2521 tcgcccggcc tcagtgagcg agcgagcgcg cagagaggga gtggccaact ccatcactag
     2581 gggttccttg tagttaatga ttaacccgcc atgctactta tctacgtagc catgctctag
     2641 gaagatcgta ggttaattaa ggcctccgcg ccgggttttg gcgcctcccg cgggcgcccc
     2701 cctcctcacg gcgagcgctg ccacgtcaga cgaagggcgc agcgagcgtc ctgatccttc
     2761 cgcccggacg ctcaggacag cggcccgctg ctcataagac tcggccttag aaccccagta
     2821 tcagcagaag gacattttag gacgggactt gggtgactct agggcactgg ttttctttcc
     2881 agagagcgga acaggcgagg aaaagtagtc ccttctcggc gattctgcgg agggatctcc
     2941 gtggggcggt gaacgccgat gattatataa ggacgcgccg ggtgtggcac agctagttcc
     3001 gtcgcagccg ggatttgggt cgcggttctt gtttgtggat cgctgtgatc gtcacttggc
     3061 gaattcccat aacttcgtat aaagtatcct atacgaagtt atatcaaaat aggaagacca
     3121 atgcttcacc atcgacccga attgccaagc atcaccatcg acccataact tcgtataatg
     3181 tatgctatac gaagttatac tagctagcct taggtctgtg cgtctttcag ggcttcatcc
     3241 acggtctgtc tgccagaagc tgcgttgata acagcggtcc tcacggcata ccagaatgcg
     3301 ctcatctgtg ggatgtttgg catgatctca cccttctgtg cgttctccat tgtagcagcg
     3361 atgcgagggt ccttggccag ttcttcttcg tagctcttca gagccacggc acccagtggc
     3421 ttgtccttgt tcactgcctc cagaccttcg tctgtcagca ggtagttctc cagaaactcc
     3481 ttagccagct ctttgttagg agaggcagcg ttgatacctg cgctcagcac gccaacgaaa
     3541 ggtttgcttg gctgaccctt gaaggttggc agaacggtga caccgtagtt gactttgcta
     3601 gtgtcgatgt tagaccatgc ccaaggacca ttgatagtca ttgcggtttc gcctttgttg
     3661 aaagcagcct ctgcgataga atagtcagtg tctgcattca tgtgcttgtt cttgatcaga
     3721 tccaccagga aagtcagacc agctttggca ccagcattgt ccacacccac atctttgatg
     3781 tcgtacttac cattctcgta cttgaaagcg taaccaccgt cggcagcaat cagtggccag
     3841 gtaaagtaag gctcctgcag gttgaacatc agtgcggact tgcctttggc cttcagttcc
     3901 ttgtccagtg cagggatttc ttcccatgtc ttaggaggat taggcagcag gtccttgttg
     3961 tagatcaggc tcagagcttc cacagcaata gggtatgcga tcagcttgcc attgtatctc
     4021 acagcatccc aggtgaatgg atacagcttg tcctggaaag ccttatcagg agtaatctca
     4081 gccagcaggc cagattgggc atagccaccg aacctatcgt gtgcccagaa gatgatgtct
     4141 ggaccgtcgc cagttgctgc gacctgaggg aacttctcct ccagcttatc tgggtgttcc
     4201 acagtaactt tgatgcctgt atctttctcg aacttcttac cgacctctgc caggccattg
     4261 tagcccttat cgccattgat ccagataacc agtttgccct cttcaatctt accggatcct
     4321 ttgtcatcat cgtccttgta gtcaccggta cctccagaac cgccagtacc tccagagcct
     4381 ccagtccctc cagaccctcc ggtgcctcca gagccaccag cagtctcgaa tgtgcccttg
     4441 acacaagcct ttccgtcctt aaccatcagc tttcctcttg catagacctg ctcaatgcgc
     4501 agttcgggtg tcatcaccag cagatcagcg tcattaccag ggaggatttc gcctttacca
     4561 gtcaggttca ggaagccagc gacgctagag gtgagtggtc tgagagcgtc agaaatgctg
     4621 aagtcgtagt ccttaaccag aacctgaact gtttccagga gagtttcaaa tccagccacg
     4681 ccaatgtgag tcagatttcc ttcatcatcg aagaatggct gggagccgtt gccatcagag
     4741 ctgagtgtca cccttgccag tgggatacct gcttggacag cccttgcgat tccctcagct
     4801 ggagcgacgg gttcatcaat gctagaggtg atgtcgatgg tgccaccctt tcttgcgaac
     4861 tccagagctt ggtagaagag aggcacgttc ctgttgacgt gggtaggcag cagcttggag
     4921 attgggacgt cacagttctc cagcaggtca tagatgggtt gcagtgcctt cttagagtca
     4981 cccatgtgga acacggtaac tcctggcttg ccaccgagca gaccaccgac tctgctctcg
     5041 gctgccatgt tggccaggtg atagacgtcg ggagcagcgc tcctgtggtc ggagatagcg
     5101 cacttaacac cgatcactct gtcgatgatt gcaacgtcct tctccacgct gccagtaatg
     5161 gtgcgagatg ggacgtgata agcaccagtc agcatccaag cggagatacc ctcctcattg
     5221 agggctctgg tctttgccag cagagactca gggtgcctag agatgctatc agtacccagg
     5281 agtcccacga cggaggtaac gcctgcctct gtgaggcgag acagtgcgac ttcgggagtt
     5341 ctagtagtag gaccagcttc gcctcctcct ccaatgaggt gcacgtgctg atcaatgaat
     5401 cctggacaga ggatctgtcc gctcagatcg acaacggtgc agtttggaac gatgtcgcta
     5461 ggaatgttgg aggccacagc gatgatctta ccgttggcaa ccagcacatc gcagatacct
     5521 ctgtcttcag gagcgtacag atgtgcacct tggaggaggg tgaaaccagc agcagtatag
     5581 tcaatcatgg tggcactagt ggtacctagt ataacttcgt ataggatact ttatacgaag
     5641 ttatcattgg gattcttcct attttgatcc aagcatcacc atcgaccctc tagtccagat
     5701 ctcaccatcg acccataact tcgtatagca tacattatac gaagttatgt ccctcgaaga
     5761 ggttcgcgaa gcttgcggcc gctcataaag ctcgactgtg ccttctagtt gccagccatc
     5821 tgttgtttgc ccctcccccg tgccttcctt gaccctggaa ggtgccactc ccactgtcct
     5881 ttcctaataa aatgaggaaa ttgcatcgca ttgtctgagt aggtgtcatt ctattctggg
     5941 gggtggggtg gggcaggaca gcaaggggga ggattgggaa gacaatagca ggcatgctgg
     6001 ggatgcggtc cggactgtac aattgcattc attttatgtt tcaggttcag ggggagatgt
     6061 gggaggtttt ttaaagcaag taaaacctct acaaatgtgg taaaatcgat aaggatcttc
     6121 ctagagcatg gctacgtaga taagtagcat ggcgggttaa tcattaacta caaggaaccc
     6181 ctagtgatgg agttggccac tccctctctg cgcgctcgct cgctcactga ggccgggcga
     6241 ccaaaggtcg cccgacgccc gggctttgcc cgggcggcct cagtgagcga gcgagcgcgc
     6301 agctgcatta atgaatcggc caacgcgcgg ggagaggcgg tttgcgtatt gggcgct
//
