LOCUS       sequence-288729-        5020 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Bacterial Expression of DrUPF3b.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5020)
  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 5020)
  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-DrUPF3b_F
FEATURES             Location/Qualifiers
     source          1..5020
                     /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"
     primer_bind     complement(1453..1472)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(1454..1472)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(1479..1496)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1479..1495)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1488..1510)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      1636..2064
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1723..1742)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1933..1954
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     CDS             2408..3202
                     /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(2462..2481)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3072..3091
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     CDS             join(3220..3288,3289..4080)
                     /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(3438..3457)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4251..4839
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4740..4759
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4993..5010
                     /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 gccctttcag gaaaagcgtg tgaagtaaaa
      361 caagtttggc tgtgtaccaa aagtaaggtc acttcgattt accatggtcg ctttggcttc
      421 tctcatggtt atgccccgtt tctcagatct aaccgtcggt taggacttgc cttgctcatg
      481 aacagaaaca ctgcagggct cattcaggca ctggagggca acaggtatgt gctctcatgt
      541 catggacaga gagtgtgttt gttttataag tggggggatt ttaatggcag caccatgttt
      601 gtcctgatta gaacagagcc cctctccgct tgcgagacat cctttcatgc gacacaaagc
      661 tgctttctca ctcggctgct ttttcttgat ttttcttggc ctcccgctca gctctctttt
      721 ctgctgctgg tccatctcct cctgttcctc ctccacctcc tcctcctcga gtacgattcc
      781 tagacccggg ctggtacagc tgaattgcag gtcgatcctt atttctcaga cggtcctttc
      841 tggcactttc ctcttttttg ctgtcccttg atgacttttc aggacgagca ctgccagagg
      901 actctccggt gtgttcattc ttccttttct cccaaacgcg ctccttatct ttcttccctt
      961 cctcctctct ttttctgtag gtgttttctc catcctggtg ttcccttctc ctcctccgtt
     1021 cctcatcctg tcttctgatg cgctctttct ccttctgtct tcgctctctc tctctgtccc
     1081 ggtctcgctc tctttctcca tcacgatctc ggtactcttt atgtccaaca tcctcgggtt
     1141 ttcccccttt ctcctctctg tgttcaccat tctgccgctt tttcaggtct cctccagaag
     1201 gtcgatcttc cttctgtctc tctctgtctt gtttcttggg cttgtctttt ggcttttcag
     1261 tttcaccatc atctgctttc tctggttttc tcaagagctt gatttttggc tgctcatctt
     1321 tatgttggtc cttatccttc tcaaatgcct tttccacttt tttcagtttc tcagcctctt
     1381 ttctagggcg aattctgcag atatccatca cactggcggc cgctcgagca tgcatctaga
     1441 gggcccaatt cgccctatag tgagtcgtat tacaattcac tggccgtcgt tttacaacgt
     1501 cgtgactggg aaaaccctgg cgttacccaa cttaatcgcc ttgcagcaca tccccctttc
     1561 gccagctggc gtaatagcga agaggcccgc accgatcgcc cttcccaaca gttgcgcagc
     1621 ctgaatggcg aatggacgcg ccctgtagcg gcgcattaag cgcggcgggt gtggtggtta
     1681 cgcgcagcgt gaccgctaca cttgccagcg ccctagcgcc cgctcctttc gctttcttcc
     1741 cttcctttct cgccacgttc gccggctttc cccgtcaagc tctaaatcgg gggctccctt
     1801 tagggttccg atttagtgct ttacggcacc tcgaccccaa aaaacttgat tagggtgatg
     1861 gttcacgtag tgggccatcg ccctgataga cggtttttcg ccctttgacg ttggagtcca
     1921 cgttctttaa tagtggactc ttgttccaaa ctggaacaac actcaaccct atctcggtct
     1981 attcttttga tttataaggg attttgccga tttcggccta ttggttaaaa aatgagctga
     2041 tttaacaaaa atttaacgcg aattttaaca aaattcaggg cgcaagggct gctaaaggaa
     2101 gcggaacacg tagaaagcca gtccgcagaa acggtgctga ccccggatga atgtcagcta
     2161 ctgggctatc tggacaaggg aaaacgcaag cgcaaagaga aagcaggtag cttgcagtgg
     2221 gcttacatgg cgatagctag actgggcggt tttatggaca gcaagcgaac cggaattgcc
     2281 agctggggcg ccctctggta aggttgggaa gccctgcaaa gtaaactgga tggctttctt
     2341 gccgccaagg atctgatggc gcaggggatc aagatctgat caagagacag gatgaggatc
     2401 gtttcgcatg attgaacaag atggattgca cgcaggttct ccggccgctt gggtggagag
     2461 gctattcggc tatgactggg cacaacagac aatcggctgc tctgatgccg ccgtgttccg
     2521 gctgtcagcg caggggcgcc cggttctttt tgtcaagacc gacctgtccg gtgccctgaa
     2581 tgaactgcag gacgaggcag cgcggctatc gtggctggcc acgacgggcg ttccttgcgc
     2641 agctgtgctc gacgttgtca ctgaagcggg aagggactgg ctgctattgg gcgaagtgcc
     2701 ggggcaggat ctcctgtcat cccaccttgc tcctgccgag aaagtatcca tcatggctga
     2761 tgcaatgcgg cggctgcata cgcttgatcc ggctacctgc ccattcgacc accaagcgaa
     2821 acatcgcatc gagcgagcac gtactcggat ggaagccggt cttgtcgatc aggatgatct
     2881 ggacgaagag catcaggggc tcgcgccagc cgaactgttc gccaggctca aggcgcgcat
     2941 gcccgacggc gaggatctcg tcgtgaccca tggcgatgcc tgcttgccga atatcatggt
     3001 ggaaaatggc cgcttttctg gattcatcga ctgtggccgg ctgggtgtgg cggaccgcta
     3061 tcaggacata gcgttggcta cccgtgatat tgctgaagag cttggcggcg aatgggctga
     3121 ccgcttcctc gtgctttacg gtatcgccgc tcccgattcg cagcgcatcg ccttctatcg
     3181 ccttcttgac gagttcttct gaattgaaaa aggaagagta tgagtattca acatttccgt
     3241 gtcgccctta ttcccttttt tgcggcattt tgccttcctg tttttgctca cccagaaacg
     3301 ctggtgaaag taaaagatgc tgaagatcag ttgggtgcac gagtgggtta catcgaactg
     3361 gatctcaaca gcggtaagat ccttgagagt tttcgccccg aagaacgttt tccaatgatg
     3421 agcactttta aagttctgct atgtggcgcg gtattatccc gtattgacgc cgggcaagag
     3481 caactcggtc gccgcataca ctattctcag aatgacttgg ttgagtactc accagtcaca
     3541 gaaaagcatc ttacggatgg catgacagta agagaattat gcagtgctgc cataaccatg
     3601 agtgataaca ctgcggccaa cttacttctg acaacgatcg gaggaccgaa ggagctaacc
     3661 gcttttttgc acaacatggg ggatcatgta actcgccttg atcgttggga accggagctg
     3721 aatgaagcca taccaaacga cgagcgtgac accacgatgc ctgtagcaat ggcaacaacg
     3781 ttgcgcaaac tattaactgg cgaactactt actctagctt cccggcaaca attaatagac
     3841 tggatggagg cggataaagt tgcaggacca cttctgcgct cggcccttcc ggctggctgg
     3901 tttattgctg ataaatctgg agccggtgag cgtgggtctc gcggtatcat tgcagcactg
     3961 gggccagatg gtaagccctc ccgtatcgta gttatctaca cgacggggag tcaggcaact
     4021 atggatgaac gaaatagaca gatcgctgag ataggtgcct cactgattaa gcattggtaa
     4081 ctgtcagacc aagtttactc atatatactt tagattgatt taaaacttca tttttaattt
     4141 aaaaggatct aggtgaagat cctttttgat aatctcatga ccaaaatccc ttaacgtgag
     4201 ttttcgttcc actgagcgtc agaccccgta gaaaagatca aaggatcttc ttgagatcct
     4261 ttttttctgc gcgtaatctg ctgcttgcaa acaaaaaaac caccgctacc agcggtggtt
     4321 tgtttgccgg atcaagagct accaactctt tttccgaagg taactggctt cagcagagcg
     4381 cagataccaa atactgttct tctagtgtag ccgtagttag gccaccactt caagaactct
     4441 gtagcaccgc ctacatacct cgctctgcta atcctgttac cagtggctgc tgccagtggc
     4501 gataagtcgt gtcttaccgg gttggactca agacgatagt taccggataa ggcgcagcgg
     4561 tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaacgac ctacaccgaa
     4621 ctgagatacc tacagcgtga gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg
     4681 gacaggtatc cggtaagcgg cagggtcgga acaggagagc gcacgaggga gcttccaggg
     4741 ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc acctctgact tgagcgtcga
     4801 tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccagcaa cgcggccttt
     4861 ttacggttcc tggccttttg ctggcctttt gctcacatgt tctttcctgc gttatcccct
     4921 gattctgtgg ataaccgtat taccgccttt gagtgagctg ataccgctcg ccgcagccga
     4981 acgaccgagc gcagcgagtc agtgagcgag gaagcggaag
//
