LOCUS       sequence-288726-        4654 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Bacterial Expression of DrUPF1.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4654)
  AUTHORS   Wittkopp N, Huntzinger E, Weiler C, Sauliere J, Schmidt S, Sonawane 
            M, Izaurralde E
  TITLE     Nonsense-mediated mRNA decay effectors are essential for zebrafish 
            embryonic development and survival.
  JOURNAL   Mol Cell Biol. 2009 Jul . 29(13):3517-28.
  PUBMED    19414594
REFERENCE   2  (bases 1 to 4654)
  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: "Mol Cell 
            Biol. 2009 Jul . 29(13):3517-28."
COMMENT     Sequence Label: pCRII-TOPO-DrUPF1_F
FEATURES             Location/Qualifiers
     source          1..4654
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    107..128
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(143..148,149..166,167..173)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    181..197
                     /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     186..208
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     205..221
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     205..221
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     promoter        239..257
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     239..256
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     RBS             697..705
                     /label=Shine-Dalgarno sequence
                     /note="full consensus sequence for ribosome-binding sites 
                     upstream of start codons in E. coli; complementary to a 
                     region in the 3' end of the 16S rRNA (Chen et al., 1994)"
     primer_bind     complement(1087..1106)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(1088..1106)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(1113..1130)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1113..1129)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1122..1144)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      1270..1698
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1357..1376)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1567..1588
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     CDS             2042..2836
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(2096..2115)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2706..2725
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     CDS             join(2854..2922,2923..3714)
                     /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(3072..3091)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3885..4473
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4374..4393
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4627..4644
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 agcgcccaat acgcaaaccg cctctccccg cgcgttggcc gattcattaa tgcagctggc
       61 acgacaggtt tcccgactgg aaagcgggca gtgagcgcaa cgcaattaat gtgagttagc
      121 tcactcatta ggcaccccag gctttacact ttatgcttcc ggctcgtatg ttgtgtggaa
      181 ttgtgagcgg ataacaattt cacacaggaa acagctatga ccatgattac gccaagctat
      241 ttaggtgaca ctatagaata ctcaagctat gcatcaagct tggtaccgag ctcggatcca
      301 ctagtaacgg ccgccagtgt gctggaattc gccctttcct catctactcc aggcttctcc
      361 aaatcttcca gcgtcgctgt tgggttttcc ttccagagct cctccagttt gttaatctgc
      421 tgcgccgtga tctgccgggc cctcagctgc tcctgctcag acgggatctt caccagccag
      481 gagagaaagc atcggtcctg gatgaggggc tgccattgag agctgtccca gttaatgtcc
      541 ttcagactgc tctgactggc acacggctgc ctgcacagaa gcaccaccac agagtctgct
      601 ttcgcaggga tgaagccgag caggaagacg ttacggcagc cacagttgta gcactccaga
      661 acagtctctc ccagcggccc gtccttatgc agcgtcacct ccttacattt ggcccccacc
      721 aggtggttca caatatgact gccagaggtg ttgccgcggc cgttgcaaaa ccacttcttg
      781 ctggtgttgc agtaaaccac acatgcggga tcatggattc cacagtagct gcaggcgtgc
      841 accggcaggt ctttagtgta gtaagtgtct tcctcgtcct cctcaaagtt cagctcggcc
      901 agaagttggc tggttttccc cactgcatct tctccattgg gcagaactcc atcaggcccg
      961 ttcgcctggt tgtcgagctg actctgtgtc tggccttgcg tctgggtctg gctgggcaag
     1021 ggcgaattct gcagatatcc atcacactgg cggccgctcg agcatgcatc tagagggccc
     1081 aattcgccct atagtgagtc gtattacaat tcactggccg tcgttttaca acgtcgtgac
     1141 tgggaaaacc ctggcgttac ccaacttaat cgccttgcag cacatccccc tttcgccagc
     1201 tggcgtaata gcgaagaggc ccgcaccgat cgcccttccc aacagttgcg cagcctgaat
     1261 ggcgaatgga cgcgccctgt agcggcgcat taagcgcggc gggtgtggtg gttacgcgca
     1321 gcgtgaccgc tacacttgcc agcgccctag cgcccgctcc tttcgctttc ttcccttcct
     1381 ttctcgccac gttcgccggc tttccccgtc aagctctaaa tcgggggctc cctttagggt
     1441 tccgatttag tgctttacgg cacctcgacc ccaaaaaact tgattagggt gatggttcac
     1501 gtagtgggcc atcgccctga tagacggttt ttcgcccttt gacgttggag tccacgttct
     1561 ttaatagtgg actcttgttc caaactggaa caacactcaa ccctatctcg gtctattctt
     1621 ttgatttata agggattttg ccgatttcgg cctattggtt aaaaaatgag ctgatttaac
     1681 aaaaatttaa cgcgaatttt aacaaaattc agggcgcaag ggctgctaaa ggaagcggaa
     1741 cacgtagaaa gccagtccgc agaaacggtg ctgaccccgg atgaatgtca gctactgggc
     1801 tatctggaca agggaaaacg caagcgcaaa gagaaagcag gtagcttgca gtgggcttac
     1861 atggcgatag ctagactggg cggttttatg gacagcaagc gaaccggaat tgccagctgg
     1921 ggcgccctct ggtaaggttg ggaagccctg caaagtaaac tggatggctt tcttgccgcc
     1981 aaggatctga tggcgcaggg gatcaagatc tgatcaagag acaggatgag gatcgtttcg
     2041 catgattgaa caagatggat tgcacgcagg ttctccggcc gcttgggtgg agaggctatt
     2101 cggctatgac tgggcacaac agacaatcgg ctgctctgat gccgccgtgt tccggctgtc
     2161 agcgcagggg cgcccggttc tttttgtcaa gaccgacctg tccggtgccc tgaatgaact
     2221 gcaggacgag gcagcgcggc tatcgtggct ggccacgacg ggcgttcctt gcgcagctgt
     2281 gctcgacgtt gtcactgaag cgggaaggga ctggctgcta ttgggcgaag tgccggggca
     2341 ggatctcctg tcatcccacc ttgctcctgc cgagaaagta tccatcatgg ctgatgcaat
     2401 gcggcggctg catacgcttg atccggctac ctgcccattc gaccaccaag cgaaacatcg
     2461 catcgagcga gcacgtactc ggatggaagc cggtcttgtc gatcaggatg atctggacga
     2521 agagcatcag gggctcgcgc cagccgaact gttcgccagg ctcaaggcgc gcatgcccga
     2581 cggcgaggat ctcgtcgtga cccatggcga tgcctgcttg ccgaatatca tggtggaaaa
     2641 tggccgcttt tctggattca tcgactgtgg ccggctgggt gtggcggacc gctatcagga
     2701 catagcgttg gctacccgtg atattgctga agagcttggc ggcgaatggg ctgaccgctt
     2761 cctcgtgctt tacggtatcg ccgctcccga ttcgcagcgc atcgccttct atcgccttct
     2821 tgacgagttc ttctgaattg aaaaaggaag agtatgagta ttcaacattt ccgtgtcgcc
     2881 cttattccct tttttgcggc attttgcctt cctgtttttg ctcacccaga aacgctggtg
     2941 aaagtaaaag atgctgaaga tcagttgggt gcacgagtgg gttacatcga actggatctc
     3001 aacagcggta agatccttga gagttttcgc cccgaagaac gttttccaat gatgagcact
     3061 tttaaagttc tgctatgtgg cgcggtatta tcccgtattg acgccgggca agagcaactc
     3121 ggtcgccgca tacactattc tcagaatgac ttggttgagt actcaccagt cacagaaaag
     3181 catcttacgg atggcatgac agtaagagaa ttatgcagtg ctgccataac catgagtgat
     3241 aacactgcgg ccaacttact tctgacaacg atcggaggac cgaaggagct aaccgctttt
     3301 ttgcacaaca tgggggatca tgtaactcgc cttgatcgtt gggaaccgga gctgaatgaa
     3361 gccataccaa acgacgagcg tgacaccacg atgcctgtag caatggcaac aacgttgcgc
     3421 aaactattaa ctggcgaact acttactcta gcttcccggc aacaattaat agactggatg
     3481 gaggcggata aagttgcagg accacttctg cgctcggccc ttccggctgg ctggtttatt
     3541 gctgataaat ctggagccgg tgagcgtggg tctcgcggta tcattgcagc actggggcca
     3601 gatggtaagc cctcccgtat cgtagttatc tacacgacgg ggagtcaggc aactatggat
     3661 gaacgaaata gacagatcgc tgagataggt gcctcactga ttaagcattg gtaactgtca
     3721 gaccaagttt actcatatat actttagatt gatttaaaac ttcattttta atttaaaagg
     3781 atctaggtga agatcctttt tgataatctc atgaccaaaa tcccttaacg tgagttttcg
     3841 ttccactgag cgtcagaccc cgtagaaaag atcaaaggat cttcttgaga tccttttttt
     3901 ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc taccagcggt ggtttgtttg
     3961 ccggatcaag agctaccaac tctttttccg aaggtaactg gcttcagcag agcgcagata
     4021 ccaaatactg ttcttctagt gtagccgtag ttaggccacc acttcaagaa ctctgtagca
     4081 ccgcctacat acctcgctct gctaatcctg ttaccagtgg ctgctgccag tggcgataag
     4141 tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc
     4201 tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga
     4261 tacctacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg
     4321 tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc agggggaaac
     4381 gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg tcgatttttg
     4441 tgatgctcgt caggggggcg gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg
     4501 ttcctggcct tttgctggcc ttttgctcac atgttctttc ctgcgttatc ccctgattct
     4561 gtggataacc gtattaccgc ctttgagtga gctgataccg ctcgccgcag ccgaacgacc
     4621 gagcgcagcg agtcagtgag cgaggaagcg gaag
//
