LOCUS       sequence-129772-        4964 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  knock down expression of spliced Copia in Drosophila melanogaster.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4964)
  TITLE     Nilson lab plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4964)
  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: 
            "Unpublished"
COMMENT     Sequence Label: pCoHygro L16_shRNA of spliced Copia
FEATURES             Location/Qualifiers
     source          1..4964
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(29..51)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     151..170
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     364..386
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     378..395
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     379..395
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     promoter        complement(460..860)
                     /label=dU6-2 promoter
                     /note="RNA polymerase III promoter for Drosophila U6-2 
                     snRNA (Das et al., 1987)"
     promoter        939..1218
                     /label=copia promoter
                     /note="strong promoter from the Drosophila transposable 
                     element copia (Sinclair et al., 1986)"
     regulatory      1237..1246
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1243..2268
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MGKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCGDGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     polyA_signal    2581..2715
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2618..2637)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2672..2691
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(2743..2759)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2743..2759)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2756..2778)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2767..2783
                     /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(2791..2797,2798..2815,2816..2821))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    2836..2857
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(2974..2991)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3145..3733)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3225..3244)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3904..4695,4696..4764))
                     /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     4527..4546
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4765..4869)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     4937..4955
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
       61 cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
      121 ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc
      181 accatatgcg gtgtgaaata ccgcacagat gcgtaaggag aaaataccgc atcaggcgcc
      241 attcgccatt caggctgcgc aactgttggg aagggcgatc ggtgcgggcc tcttcgctat
      301 tacgccagct ggcgaaaggg ggatgtgctg caaggcgatt aagttgggta acgccagggt
      361 tttcccagtc acgacgttgt aaaacgacgg ccagtgccaa gcttaaaaag aaattcagag
      421 aatcaactgg tatttatccc aattaattct ctaaatttcg aagtattgag gaaaacatac
      481 ctatataaat gatcaacatc aggaaagagc agttgagaat tataagaatt ggcaaatggt
      541 cttaagaacc ctctgcttaa gattttcaaa atttccttta gaatcaaagt gtcctattgt
      601 tcgtttgttg aaaacacagt tcgatttatt gactataata aattgatagt tttaaatata
      661 gaggcacgac taagagagtt tggttttgtt ttggttaggg accaaaaaaa gtatacataa
      721 cgaataaaaa aggatttaag tgcaaatggt aaaaaagtgt cgagtttttc ttgagttgat
      781 tgtgctgtaa tgagactctg cattcggcat ttgactcggc ttttcctact cgtgccgtat
      841 ttcaggctgc aaagtcgaac tctagaggat ccggtgcgtg gtggtttcat gcttctggga
      901 acggcaaatg ggtttaggat tgggaacccc tcatcatctg ttggaatata ctattcaacc
      961 tacaaaagta acgttaaaca acactacttt atatttgata tgaatggcca caccttttat
     1021 gccataaaac atattgtaag agaataccac tctttttatt ccttctttcc ttcttgtacg
     1081 ttttttgctg taagtaggtc gtggtgctgg tgttgcagtt gaaataactt aaaatataaa
     1141 tcataaaact caaacataaa cttgactatt tatttattta ttaagaaagg aaatataaat
     1201 tataaattac aacaggttat ggggatcccc agcttggcca ccatgggaaa gcctgagctg
     1261 accgcgacgt ctgtcgagaa gtttctgatc gaaaagttcg acagcgtctc cgacctgatg
     1321 cagctctcgg agggcgaaga atctcgtgct ttcagcttcg atgtaggagg gcgtggatat
     1381 gtcctgcggg taaatagctg cggcgatggt ttctacaaag atcgttatgt ttatcggcac
     1441 tttgcatcgg ccgcgctccc gattccggaa gtgcttgaca ttggggaatt cagcgagagc
     1501 ctgacctatt gcatctcccg ccgtgcacag ggtgtcacgt tgcaagacct gcctgaaacc
     1561 gaactgcccg ctgttctgca gccggtcgcg gaggccatgg atgcgatcgc tgcggccgat
     1621 cttagccaga cgagcgggtt cggcccattc ggaccgcaag gaatcggtca atacactaca
     1681 tggcgtgatt tcatatgcgc gattgctgat ccccatgtgt atcactggca aactgtgatg
     1741 gacgacaccg tcagtgcgtc cgtcgcgcag gctctcgatg agctgatgct ttgggccgag
     1801 gactgccccg aagtccggca cctcgtgcac gcggatttcg gctccaacaa tgtcctgacg
     1861 gacaatggcc gcataacagc ggtcattgac tggagcgagg cgatgttcgg ggattcccaa
     1921 tacgaggtcg ccaacatctt cttctggagg ccgtggttgg cttgtatgga gcagcagacg
     1981 cgctacttcg agcggaggca tccggagctt gcaggatcgc cgcggctccg ggcgtatatg
     2041 ctccgcattg gtcttgacca actctatcag agcttggttg acggcaattt cgatgatgca
     2101 gcttgggcgc agggtcgatg cgacgcaatc gtccgatccg gagccgggac tgtcgggcgt
     2161 acacaaatcg cccgcagaag cgcggccgtc tggaccgatg gctgtgtaga agtactcgcc
     2221 gatagtggaa accgacgccc cagcactcgt ccgagggcaa aggaatagag tagatgccga
     2281 ccgaacaaga gctgatttcg agaacgcctc agccagcaac tcgcgcgagc ctagcaaggc
     2341 aaatgcgaga gaacggcctt acgcttggtg gcacagttct cgtccacagt tcgctaagct
     2401 cgctcggctg ggtcgcggga gggccggtcg cagtgattca ggcccttctg gattgtgttg
     2461 gtccccaggg cacgattgtc atgcccacgc actcgggtga tctgactgat cccgcagatt
     2521 ggagatcgcc gcccgtgcct gccgattggg tgcagatcag cctcgaggcc agctagcttg
     2581 aacttgttta ttgcagctta taatggttac aaataaagca atagcatcac aaatttcaca
     2641 aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct
     2701 tatcatgtct ggatcgggta ccgagctcga attcgtaatc atgtcatagc tgtttcctgt
     2761 gtgaaattgt tatccgctca caattccaca caacatacga gccggaagca taaagtgtaa
     2821 agcctggggt gcctaatgag tgagctaact cacattaatt gcgttgcgct cactgcccgc
     2881 tttccagtcg ggaaacctgt cgtgccagct gcattaatga atcggccaac gcgcggggag
     2941 aggcggtttg cgtattgggc gctcttccgc ttcctcgctc actgactcgc tgcgctcggt
     3001 cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg gtaatacggt tatccacaga
     3061 atcaggggat aacgcaggaa agaacatgtg agcaaaaggc cagcaaaagg ccaggaaccg
     3121 taaaaaggcc gcgttgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa
     3181 aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt
     3241 tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct
     3301 gtccgccttt ctcccttcgg gaagcgtggc gctttctcaa tgctcacgct gtaggtatct
     3361 cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc
     3421 cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa gacacgactt
     3481 atcgccactg gcagcagcca ctggtaacag gattagcaga gcgaggtatg taggcggtgc
     3541 tacagagttc ttgaagtggt ggcctaacta cggctacact agaaggacag tatttggtat
     3601 ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa
     3661 acaaaccacc gctggtagcg gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa
     3721 aaaaggatct caagaagatc ctttgatctt ttctacgggg tctgacgctc agtggaacga
     3781 aaactcacgt taagggattt tggtcatgag attatcaaaa aggatcttca cctagatcct
     3841 tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga
     3901 cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc
     3961 catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg
     4021 ccccagtgct gcaatgatac cgcgagaccc acgctcaccg gctccagatt tatcagcaat
     4081 aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat
     4141 ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg
     4201 caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc
     4261 attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa
     4321 agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc
     4381 actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt
     4441 ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag
     4501 ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa ctttaaaagt
     4561 gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag
     4621 atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac
     4681 cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc
     4741 gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca
     4801 gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg
     4861 ggttccgcgc acatttcccc gaaaagtgcc acctgacgtc taagaaacca ttattatcat
     4921 gacattaacc tataaaaata ggcgtatcac gaggcccttt cgtc
//
