LOCUS       sequence-491429-        7747 bp    DNA     circular SYN 03-NOV-2025
DEFINITION  Encodes PhiC31 recombinase downstream of a minimal promoter element.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7747)
  AUTHORS   Schick E, McCaffery SD, Keblish EE, Thakurdin C, Emerson MM
  TITLE     Lineage tracing analysis of cone photoreceptor associated 
            cis-regulatory elements in the developing chicken retina.
  JOURNAL   Sci Rep. 2019 Jun 27;9(1):9358. doi: 10.1038/s41598-019-45750-7.
  PUBMED    31249345
REFERENCE   2  (bases 1 to 7747)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Nov 3, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Sci Rep."; 
            date: "2019-06-27"; volume: "9(1):9358. doi"; pages: " 
            10.1038/s41598-019-45750-7"
COMMENT     Sequence Label: bp::PhiC31
FEATURES             Location/Qualifiers
     source          1..7747
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    47..95
                     /note="synthetic polyadenylation signal"
     misc_feature    109..200
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     149..168
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     CDS             312..2126
                     /codon_start=1
                     /product="integrase from phage phi-C31"
                     /label=phage phi-C31 integrase
                     /translation="MDTYAGAYDRQSRERENSSAASPATQRSANEDKAADLQREVERDG
                     GRFRFVGHFSEAPGTSAFGTAERPEFERILNECRAGRLNMIIVYDVSRFSRLKVMDAIP
                     IVSELLALGVTIVSTQEGVFRQGNVMDLIHLIMRLDASHKESSLKSAKILDTKNLQREL
                     GGYVGGKAPYGFELVSETKEITRNGRMVNVVINKLAHSTTPLTGPFEFEPDVIRWWWRE
                     IKTHKHLPFKPGSQAAIHPGSITGLCKRMDADAVPTRGETIGKKTASSAWDPATVMRIL
                     RDPRIAGFAAEVIYKKKPDGTPTTKIEGYRIQRDPITLRPVELDCGPIIEPAEWYELQA
                     WLDGRGRGKGLSRGQAILSAMDKLYCECGAVMTSKRGEESIKDSYRCRRRKVVDPSAPG
                     QHEGTCNVSMAALDKFVAERIFNKIRHAEGDEETLALLWEAARRFGKLTEAPEKSGERA
                     NLVAERADALNALEELYEDRAAGAYDGPVGRKHFRKQQAALTLRQQGAEERLAELEAAE
                     APKLPLDQWFPEDADADPTGPKSWWGRASVDDKRVFVGLFVDKIVVTKSTTGRGQGTPI
                     EKRASITWAKPPTDDDEDDAQDGTEDVAA"
     CDS             2127..2147
                     /codon_start=1
                     /product="nuclear localization signal of SV40 (simian virus
                     40) large T antigen"
                     /label=SV40 NLS
                     /translation="PKKKRKV"
     misc_feature    2188..2761
                     /label=IRES
                     /note="internal ribosome entry site (IRES) of the 
                     encephalomyocarditis virus (EMCV)"
     misc_feature    2211..2763
                     /label=IRES
                     /note="internal ribosome entry site (IRES) of the 
                     encephalomyocarditis virus (EMCV)"
     primer_bind     complement(2355..2372)
                     /label=IRES reverse
                     /note="IRES internal ribosome entry site, reverse primer. 
                     Also called pCDH-rev"
     primer_bind     2582..2601
                     /label=IRES-F
                     /note="IRES internal ribosome entry site, forward primer"
     CDS             2775..4274
                     /codon_start=1
                     /product="secreted alkaline phosphatase from human 
                     placenta"
                     /label=SEAP
                     /note="The natural enzyme has a C-terminal transmembrane 
                     sequence that is replaced by a GPI anchor."
                     /translation="LLLLLLLGLRLQLSLGIIPVEEENPDFWNREAAEALGAAKKLQPA
                     QTAAKNLIIFLGDGMGVSTVTAARILKGQKKDKLGPEIPLAMDRFPYVALSKTYNVDKH
                     VPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVISVMNRAKKAGKSVGVVT
                     TTRVQHASPAGTYAHTVNRNWYSDADVPASARQEGCQDIATQLISNMDIDVILGGGRKY
                     MFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAKRQGARYVWNRTELMQASLDPSVTHL
                     MGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRA
                     YRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSHVFSFGGYPLRGSSIFGLAPGKAR
                     DRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFAR
                     GPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPPAGTTD"
     primer_bind     complement(4769..4788)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    4834..4889
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(4888..4907)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(5250..5266)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5250..5266)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(5263..5285)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    5274..5290
                     /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(5298..5304,5305..5322,5323..5328))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5343..5364
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        5423..5618
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      5469..5604
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    5624..5758
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5661..5680)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     5715..5734
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(5826..5843)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5997..6585)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(6077..6096)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6756..7547,7548..7616))
                     /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     7379..7398
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7617..7721)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 ggtcgagaag taatattaag gtacgggagg tacttggagc ggccgcaata aaatatcttt
       61 attttcatta catctgtgtg ttggtttttt gtgtgaatcg atagtactaa catacgctct
      121 ccatcaaaac aaaacgaaac aaaacaaact agcaaaatag gctgtcccca gtgcaagtgc
      181 aggtgccaga acatttctct atcgatagtc gaccaattgc tcgaggaatt ctatataatg
      241 gaagcttgac cggagccgtt agttgcccgt cggacgcgat ttgcgaggcg ctttatgcgc
      301 gcaccgggac catggatacc tacgccggag cctacgacag acagagccgg gagagagaga
      361 acagcagcgc cgccagcccc gccacccaga gaagcgccaa cgaggataag gccgccgatc
      421 tgcagagaga ggtggagagg gacggcggca gattcagatt tgtgggccac ttcagcgagg
      481 cccctggcac cagcgccttc ggcaccgccg agagacccga gttcgagaga atcctgaacg
      541 agtgtagggc cggcaggctg aacatgatca tcgtgtacga cgtgtcccgg ttcagcaggc
      601 tgaaggtgat ggacgccatc cctatcgtgt ccgagctgct ggccctgggc gtgaccatcg
      661 tgtccaccca ggaaggcgtc tttagacagg gcaacgtgat ggacctgatc cacctgatca
      721 tgaggctgga cgccagccac aaggagagca gcctgaagag cgccaagatc ctggacacca
      781 agaacctgca gagggagctg ggcggctatg tgggcggcaa ggccccctac ggcttcgagc
      841 tggtgtccga gaccaaggag atcacccgga acggcaggat ggtgaacgtg gtgatcaaca
      901 agctggccca cagcaccacc cccctgaccg gccccttcga gtttgagccc gacgtgatca
      961 ggtggtggtg gcgggagatc aagacccaca agcacctgcc tttcaagccc ggcagccagg
     1021 ccgccatcca ccccggcagc atcaccggcc tgtgtaagag aatggacgcc gacgccgtgc
     1081 ccaccagagg cgagaccatc ggcaagaaaa ccgccagcag cgcctgggac cccgccaccg
     1141 tgatgagaat cctgagggac cctaggatcg ccggcttcgc cgccgaggtg atctacaaga
     1201 agaagcccga cggcaccccc accaccaaga tcgagggcta cagaatccag agagacccca
     1261 tcaccctgag acctgtggag ctggactgtg gccctatcat cgagcctgcc gagtggtacg
     1321 agctgcaggc ctggctggac ggcagaggca gaggcaaggg cctgagcaga ggccaggcca
     1381 tcctgagcgc catggacaag ctgtactgtg agtgtggcgc cgtgatgacc agcaagagag
     1441 gcgaggagag catcaaggac agctaccggt gccggagaag aaaggtggtg gaccccagcg
     1501 cccctggcca gcacgagggc acctgtaatg tgagcatggc cgccctggac aagttcgtgg
     1561 ccgagcggat cttcaacaag atccggcacg ccgagggcga cgaggagacc ctggccctgc
     1621 tgtgggaggc cgccagaaga ttcggcaagc tgaccgaggc ccccgagaag agcggcgaga
     1681 gggccaacct ggtggccgag agagccgacg ccctgaacgc cctggaggag ctgtacgagg
     1741 acagagccgc cggagcctat gacggccctg tgggcaggaa gcacttcaga aagcagcagg
     1801 ccgccctgac cctgagacag cagggcgccg aggaaagact ggccgagctg gaggccgccg
     1861 aggcccctaa gctgcccctg gatcagtggt tccccgagga tgccgacgcc gaccccaccg
     1921 gccccaagtc ctggtggggc agagccagcg tggacgacaa gagggtgttc gtgggcctgt
     1981 tcgtggataa gatcgtggtg accaagagca ccaccggcag gggccagggc acccccatcg
     2041 agaagagagc cagcatcacc tgggccaagc ctcccaccga cgacgacgag gatgacgccc
     2101 aggacggcac cgaggacgtg gccgccccta agaaaaagcg gaaagtgtga tgtacaagta
     2161 aagcggccaa ttccgccccc cccccccccc ctctccctcc ccccccccta acgttactgg
     2221 ccgaagccgc ttggaataag gccggtgtgc gtttgtctat atgttatttt ccaccatatt
     2281 gccgtctttt ggcaatgtga gggcccggaa acctggccct gtcttcttga cgagcattcc
     2341 taggggtctt tcccctctcg ccaaaggaat gcaaggtctg ttgaatgtcg tgaaggaagc
     2401 agttcctctg gaagcttctt gaagacaaac aacgtctgta gcgacccttt gcaggcagcg
     2461 gaacccccca cctggcgaca ggtgcctctg cggccaaaag ccacgtgtat aagatacacc
     2521 tgcaaaggcg gcacaacccc agtgccacgt tgtgagttgg atagttgtgg aaagagtcaa
     2581 atggctctcc tcaagcgtat tcaacaaggg gctgaaggat gcccagaagg taccccattg
     2641 tatgggatct gatctggggc ctcggtgcac atgctttaca tgtgtttagt cgaggttaaa
     2701 aaaacgtcta ggccccccga accacgggga cgtggttttc ctttgaaaaa cacgatgata
     2761 atatggggtc gaggctgctg ctgctgctgc tgctgggcct gaggctacag ctctccctgg
     2821 gcatcatccc agttgaggag gagaacccgg acttctggaa ccgcgaggca gccgaggccc
     2881 tgggtgccgc caagaagctg cagcctgcac agacagccgc caagaacctc atcatcttcc
     2941 tgggcgatgg gatgggggtg tctacggtga cagctgccag gatcctaaaa gggcagaaga
     3001 aggacaaact ggggcctgag atacccctgg ccatggaccg cttcccatat gtggctctgt
     3061 ccaagacata caatgtagac aaacatgtgc cagacagtgg agccacagcc acggcctacc
     3121 tgtgcggggt caagggcaac ttccagacca ttggcttgag tgcagccgcc cgctttaacc
     3181 agtgcaacac gacacgcggc aacgaggtca tctccgtgat gaatcgggcc aagaaagcag
     3241 ggaagtcagt gggagtggta accaccacac gagtgcagca cgcctcgcca gccggcacct
     3301 acgcccacac ggtgaaccgc aactggtact cggacgccga cgtgcctgcc tcggcccgcc
     3361 aggaggggtg ccaggacatc gctacgcagc tcatctccaa catggacatt gacgtgatcc
     3421 taggtggagg ccgaaagtac atgtttcgca tgggaacccc agaccctgag tacccagatg
     3481 actacagcca aggtgggacc aggctggacg ggaagaatct ggtgcaggaa tggctggcga
     3541 agcgccaggg tgcccggtat gtgtggaacc gcactgagct catgcaggct tccctggacc
     3601 cgtctgtgac ccatctcatg ggtctctttg agcctggaga catgaaatac gagatccacc
     3661 gagactccac actggacccc tccctgatgg agatgacaga ggctgccctg cgcctgctga
     3721 gcaggaaccc ccgcggcttc ttcctcttcg tggagggtgg tcgcatcgac catggtcatc
     3781 atgaaagcag ggcttaccgg gcactgactg agacgatcat gttcgacgac gccattgaga
     3841 gggcgggcca gctcaccagc gaggaggaca cgctgagcct cgtcactgcc gaccactccc
     3901 acgtcttctc cttcggaggc taccccctgc gagggagctc catcttcggg ctggcccctg
     3961 gcaaggcccg ggacaggaag gcctacacgg tcctcctata cggaaacggt ccaggctatg
     4021 tgctcaagga cggcgcccgg ccggatgtta ccgagagcga gagcgggagc cccgagtatc
     4081 ggcagcagtc agcagtgccc ctggacgaag agacccacgc aggcgaggac gtggcggtgt
     4141 tcgcgcgcgg cccgcaggcg cacctggttc acggcgtgca ggagcagacc ttcatagcgc
     4201 acgtcatggc cttcgccgcc tgcctggagc cctacaccgc ctgcgacctg gcgccccccg
     4261 ccggcaccac cgacgccgcg cacccggggc ggtccgtggt ccccgcgttg cttcctctgc
     4321 tggccgggac cctgctgctg ctggagacgg ccactgctcc ctgagtgtcc cgtccctggg
     4381 gctcctgctt ccccatcccg gagttctcct gctccccacc tcctgtcgtc ctgcctggcc
     4441 tccagcccga gtcgtcatcc ccggagtccc tatacagagg tcctgccatg gaaccttccc
     4501 ctccccgtgc gctctgggga ctgagcccat gacaccaaac ctgccccttg gctgctctcg
     4561 gactccctac cccaacccca gggactgcag gttgtgccct gtggctgcct gcaccccagg
     4621 aaaggagggg gctcaggcca tccagccacc acctacagcc cagtggggtc gaggatatcg
     4681 cggccggccg cactcctcag gtgcaggctg cctatcagaa ggtggtggct ggtgtggcca
     4741 atgccctggc tcacaaatac cactgagatc tttttccctc tgccaaaaat tatggggaca
     4801 tcatgaagcc ccttgagcat ctgacttctg gctaataaag gaaatttatt ttcattgcaa
     4861 tagtgtgttg gaattttttg tgtctctcac tcggaaggac atatgggagg gcaaatcatt
     4921 taaaacatca gaatgagtat ttggtttaga gtttggcaac atatgcccat atgctggctg
     4981 ccatgaacaa aggttggcta taaagaggtc atcagtatat gaaacagccc cctgctgtcc
     5041 attccttatt ccatagaaaa gccttgactt gaggttagat tttttttata ttttgttttg
     5101 tgttattttt ttctttaaca tccctaaaat tttccttaca tgttttacta gccagatttt
     5161 tcctcctctc ctgactactc ccagtcatag ctgtccctct tctcttatgg agatccctcg
     5221 acctgcagcc caagcttggc gtaatcatgg tcatagctgt ttcctgtgtg aaattgttat
     5281 ccgctcacaa ttccacacaa catacgagcc ggaagcataa agtgtaaagc ctggggtgcc
     5341 taatgagtga gctaactcac attaattgcg ttgcgctcac tgcccgcttt ccagtcggga
     5401 aacctgtcgt gccagcggat ccgcatctca attagtcagc aaccatagtc ccgcccctaa
     5461 ctccgcccat cccgccccta actccgccca gttccgccca ttctccgccc catggctgac
     5521 taattttttt tatttatgca gaggccgagg ccgcctcggc ctctgagcta ttccagaagt
     5581 agtgaggagg cttttttgga ggcctaggct tttgcaaaaa gctaacttgt ttattgcagc
     5641 ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc
     5701 actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg tctggatccg
     5761 ctgcattaat gaatcggcca acgcgcgggg agaggcggtt tgcgtattgg gcgctcttcc
     5821 gcttcctcgc tcactgactc gctgcgctcg gtcgttcggc tgcggcgagc ggtatcagct
     5881 cactcaaagg cggtaatacg gttatccaca gaatcagggg ataacgcagg aaagaacatg
     5941 tgagcaaaag gccagcaaaa ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc
     6001 cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca gaggtggcga
     6061 aacccgacag gactataaag ataccaggcg tttccccctg gaagctccct cgtgcgctct
     6121 cctgttccga ccctgccgct taccggatac ctgtccgcct ttctcccttc gggaagcgtg
     6181 gcgctttctc atagctcacg ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag
     6241 ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgccttatc cggtaactat
     6301 cgtcttgagt ccaacccggt aagacacgac ttatcgccac tggcagcagc cactggtaac
     6361 aggattagca gagcgaggta tgtaggcggt gctacagagt tcttgaagtg gtggcctaac
     6421 tacggctaca ctagaagaac agtatttggt atctgcgctc tgctgaagcc agttaccttc
     6481 ggaaaaagag ttggtagctc ttgatccggc aaacaaacca ccgctggtag cggtggtttt
     6541 tttgtttgca agcagcagat tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc
     6601 ttttctacgg ggtctgacgc tcagtggaac gaaaactcac gttaagggat tttggtcatg
     6661 agattatcaa aaaggatctt cacctagatc cttttaaatt aaaaatgaag ttttaaatca
     6721 atctaaagta tatatgagta aacttggtct gacagttacc aatgcttaat cagtgaggca
     6781 cctatctcag cgatctgtct atttcgttca tccatagttg cctgactccc cgtcgtgtag
     6841 ataactacga tacgggaggg cttaccatct ggccccagtg ctgcaatgat accgcgagac
     6901 ccacgctcac cggctccaga tttatcagca ataaaccagc cagccggaag ggccgagcgc
     6961 agaagtggtc ctgcaacttt atccgcctcc atccagtcta ttaattgttg ccgggaagct
     7021 agagtaagta gttcgccagt taatagtttg cgcaacgttg ttgccattgc tacaggcatc
     7081 gtggtgtcac gctcgtcgtt tggtatggct tcattcagct ccggttccca acgatcaagg
     7141 cgagttacat gatcccccat gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc
     7201 gttgtcagaa gtaagttggc cgcagtgtta tcactcatgg ttatggcagc actgcataat
     7261 tctcttactg tcatgccatc cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag
     7321 tcattctgag aatagtgtat gcggcgaccg agttgctctt gcccggcgtc aatacgggat
     7381 aataccgcgc cacatagcag aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg
     7441 cgaaaactct caaggatctt accgctgttg agatccagtt cgatgtaacc cactcgtgca
     7501 cccaactgat cttcagcatc ttttactttc accagcgttt ctgggtgagc aaaaacagga
     7561 aggcaaaatg ccgcaaaaaa gggaataagg gcgacacgga aatgttgaat actcatactc
     7621 ttcctttttc aatattattg aagcatttat cagggttatt gtctcatgag cggatacata
     7681 tttgaatgta tttagaaaaa taaacaaata ggggttccgc gcacatttcc ccgaaaagtg
     7741 ccacctg
//
