LOCUS       sequence-343339-        6319 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  DDX1 knockdown.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6319)
  AUTHORS   Guney MH, Nagalekshmi K, McCauley SM, Carbone C, Aydemir O, Luban J
  TITLE     IFIH1 (MDA5) is required for innate immune detection of 
            intron-containing RNA expressed from the HIV-1 provirus.
  JOURNAL   Proc Natl Acad Sci U S A. 2024 Jul 16;121(29):e2404349121. doi: 
            10.1073/pnas.2404349121. Epub 2024 Jul 10.
  PUBMED    38985764
REFERENCE   2  (bases 1 to 6319)
  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: "Proc Natl 
            Acad Sci U S A."; date: "2024-07-16"; volume: "121(29):e2404349121. 
            doi"; pages: " 10.1073/pnas.2404349121. Epub 2024 Jul 10"
COMMENT     Sequence Label: pAPM-miR30-DDX1-ts1
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     49..68
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        148..527
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        529..727
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     682..702
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             745..925
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    972..1097
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1594..1827
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2012..2056
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     misc_feature    2354..2471
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2608..3015
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3730..3744
                     /label=miR-30a loop
                     /note="loop from the the 71-nt precursor of the human 
                     miR-30a microRNA (Zeng et al., 2002)"
                     /ncRNA_class="miRNA"
     LTR             3878..4058
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4129..4717)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4209..4228)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4888..5679,5680..5748))
                     /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     5511..5530
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5749..5853)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5928..5947)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(6121..6141)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6126..6319,1..136)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(6306..6319,1..122)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
ORIGIN
        1 tccgcccagt tccgcccatt ctccgcccca tggctgacta atttttttta tttatgcaga
       61 ggccgaggcc gcctctgcct ctgagctatt ccagaagtag tgaggaggct tttttggagg
      121 cctaggcttt tgcaaaaagc tcgcgttgac attgattatt gactagttat taatagtaat
      181 caattacggg gtcattagtt catagcccat atatggagtt ccgcgttaca taacttacgg
      241 taaatggccc gcctggctga ccgcccaacg acccccgccc attgacgtca ataatgacgt
      301 atgttcccat agtaacgcca atagggactt tccattgacg tcaatgggtg gagtatttac
      361 ggtaaactgc ccacttggca gtacatcaag tgtatcatat gccaagtacg ccccctattg
      421 acgtcaatga cggtaaatgg cccgcctggc attatgccca gtacatgacc ttatgggact
      481 ttcctacttg gcagtacatc tacgtattag tcatcgctat taccatggtg atgcggtttt
      541 ggcagtacat caatgggcgt ggatagcggt ttgactcacg gggatttcca agtctccacc
      601 ccattgacgt caatgggagt ttgttttggc accaaaatca acgggacttt ccaaaatgtc
      661 gtaacaactc cgccccattg acgcaaatgg gcggtaggcg tgtacggtgg gaggtctata
      721 taagcagcgc gttttgcctg tactgggtct ctctggttag accagatctg agcctgggag
      781 ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt
      841 caagtagtgt gtgcccgtct gttgtgagac tctggtaact agagatccct cagacccttt
      901 tagtcagtgt ggaaaatctc tagcagtggc gcccgaacag ggacttgaaa gcgaaaggga
      961 aaccagagga gctctctcga cgcaggactc ggcttgctga agcgcgcacg gcaagaggcg
     1021 aggggcggcg actggtgagt acgccaaaaa ttttgactag cggaggctag aaggagagag
     1081 atgggtgcga gagcgtcagt attaagcggg ggagaattag atcgcgatgg gaaaaaattc
     1141 ggttaaggcc agggggaaag aaaaaatata aattaaaaca tatagtatgg gcaagcaggg
     1201 agctagaacg attcgcagtt aatcctggcc tgttagaaac atcagaaggc tgtagacaaa
     1261 tactgggaca gctacaacca tcccttcaga caggatcaga agaacttaga tcattatata
     1321 atacagtagc aaccctctat tgtgtgcatc aaaggataga gataaaagac accaaggaag
     1381 ctttagacaa gatagaggaa gagcaaaaca aaagtaagac caccgcacag caagcggccg
     1441 gccgctgatc ttcagacctg gaggaggaga tatgagggac aattggagaa gtgaattata
     1501 taaatataaa gtagtaaaaa ttgaaccatt aggagtagca cccaccaagg caaagagaag
     1561 agtggtgcag agagaaaaaa gagcagtggg aataggagct ttgttccttg ggttcttggg
     1621 agcagcagga agcactatgg gcgcagcgtc aatgacgctg acggtacagg ccagacaatt
     1681 attgtctggt atagtgcagc agcagaacaa tttgctgagg gctattgagg cgcaacagca
     1741 tctgttgcaa ctcacagtct ggggcatcaa gcagctccag gcaagaatcc tggctgtgga
     1801 aagataccta aaggatcaac agctcctggg gatttggggt tgctctggaa aactcatttg
     1861 caccactgct gtgccttgga atgctagttg gagtaataaa tctctggaac agatttggaa
     1921 tcacacgact tggatggagt gggacagaga aattaacaat tacacaagct taatacactc
     1981 cttaattgaa gaatcgcaaa accagcaaga aaagaatgaa caagaattat tggaattaga
     2041 taaatgggca agtttgtgga attggtttaa cataacaaat tggctgtggt atataaaatt
     2101 attcataatg atagtaggag gcttggtagg tttaagaata gtttttgctg tactttctat
     2161 agtgaataga gttaggcagg gatattcacc attatcgttt cagacccacc tcccaacccc
     2221 gaggggaccc gacaggcccg aaggaataga agaagaaggt ggagagagag acagagacag
     2281 atccattcga ttagtgaacg gatcggcact gcgtgcgcca attctgcaga caaatggcag
     2341 tattcatcca caattttaaa agaaaagggg ggattggggg gtacagtgca ggggaaagaa
     2401 tagtagacat aatagcaaca gacatacaaa ctaaagaatt acaaaaacaa attacaaaaa
     2461 ttcaaaattt tcgggtttat tacagggaca gcagagatcc agtttggtta attaactgca
     2521 gccccgataa aataaaagat tttatttagt ctccagaaaa aggggggaat gaaagacccc
     2581 acctgtaggt ttggcaagct agctgcagta acgccatttt gcaaggcatg gaaaaatacc
     2641 aaaccaagaa tagagaagtt cagatcaagg gcgggtacat gaaaatagct aacgttgggc
     2701 caaacaggat atctgcggtg agcagtttcg gccccggccc ggggccaaga acagatggtc
     2761 accgcagttt cggccccggc ccgaggccaa gaacagatgg tccccagata tggcccaacc
     2821 ctcagcagtt tcttaagacc catcagatgt ttccaggctc ccccaaggac ctgaaatgac
     2881 cctgcgcctt atttgaatta accaatcagc ctgcttctcg cttctgttcg cgcgcttctg
     2941 cttcccgagc tctataaaag agctcacaac ccctcactcg gcgcgccagt cctccgacag
     3001 actgagtcgc ccgggggtct agaacgcgtg ccgccatgac cgaatacaaa cctaccgtga
     3061 ggctggctac aagagatgat gtcccaaggg ctgtgagaac actggccgcc gcttttgccg
     3121 attaccctgc cacacgccac actgtggacc cagatcggca tatcgagaga gtgactgagc
     3181 tgcaggaact gttcctgacc cgagtgggcc tggacattgg gaaggtctgg gtcgcagacg
     3241 atggagcagc tgtggctgtc tggaccacac cagagagcgt ggaagccgga gctgtctttg
     3301 cagagatcgg ccctagaatg gcagaactga gcggctccag gctggcagca cagcagcaga
     3361 tggagggact gctggcccca cacaggccta aggaaccagc atggttcctg gctaccgtgg
     3421 gggtctctcc tgaccatcag ggcaaaggac tgggaagtgc tgtggtcctg ccaggagtgg
     3481 aggctgcaga acgagctgga gtccctgcat ttctggagac ctctgctcca cgaaacctgc
     3541 ccttctatga acggctgggc tttactgtga ccgcagatgt ggaggtcccc gaaggaccta
     3601 ggacctggtg catgacacgc aaacccggcg cctgagcgat cgccgcggcc gccttcttaa
     3661 cccaacagaa ggctcgagaa ggtatattgc tgttgacagt gagcgagaca ccagttctca
     3721 tgtgttatag tgaagccaca gatgtataac acatgagaac tggtgtcctg cctactgcct
     3781 cggacttcaa ggggctagaa ttcggcagct gtagatctta gccacttttt aaaagaaaag
     3841 gggggactgg aagggctaac tgcatccgga ctgtactggg tctctctggt tagaccagat
     3901 ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc aataaagctt
     3961 gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc
     4021 cctcagaccc ttttagtcag tgtggaaaat ctctagcagg gcccgtttca tgtgagcaaa
     4081 aggccagcaa aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccataggct
     4141 ccgcccccct gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac
     4201 aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc
     4261 gaccctgccg cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc
     4321 tcatagctca cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg
     4381 tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga
     4441 gtccaacccg gtaagacacg acttatcgcc actggcagca gccactggta acaggattag
     4501 cagagcgagg tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta
     4561 cactagaaga acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag
     4621 agttggtagc tcttgatccg gcaaacaaac caccgctggt agcggtggtt tttttgtttg
     4681 caagcagcag attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac
     4741 ggggtctgac gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc
     4801 aaaaaggatc ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag
     4861 tatatatgag taaacttggt ctgacagtta ccaatgctta atcagtgagg cacctatctc
     4921 agcgatctgt ctatttcgtt catccatagt tgcctgactc cccgtcgtgt agataactac
     4981 gatacgggag ggcttaccat ctggccccag tgctgcaatg ataccgcgag acccacgctc
     5041 accggctcca gatttatcag caataaacca gccagccgga agggccgagc gcagaagtgg
     5101 tcctgcaact ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag
     5161 tagttcgcca gttaatagtt tgcgcaacgt tgttgccatt gctacaggca tcgtggtgtc
     5221 acgctcgtcg tttggtatgg cttcattcag ctccggttcc caacgatcaa ggcgagttac
     5281 atgatccccc atgttgtgca aaaaagcggt tagctccttc ggtcctccga tcgttgtcag
     5341 aagtaagttg gccgcagtgt tatcactcat ggttatggca gcactgcata attctcttac
     5401 tgtcatgcca tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg
     5461 agaatagtgt atgcggcgac cgagttgctc ttgcccggcg tcaatacggg ataataccgc
     5521 gccacatagc agaactttaa aagtgctcat cattggaaaa cgttcttcgg ggcgaaaact
     5581 ctcaaggatc ttaccgctgt tgagatccag ttcgatgtaa cccactcgtg cacccaactg
     5641 atcttcagca tcttttactt tcaccagcgt ttctgggtga gcaaaaacag gaaggcaaaa
     5701 tgccgcaaaa aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt
     5761 tcaatattat tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg
     5821 tatttagaaa aataaacaaa taggggttcc gcgcacattt ccccgaaaag tgccacctga
     5881 cgtcgacgga tcgggagatc tcccgatccc ctatggtgca ctctcagtac aatctgctct
     5941 gatgccgcat agttaagcca gtatctgctc cctgcttgtg tgttggaggt cgctgagtag
     6001 tgcgcgagca aaatttaagc tacaacaagg caaggcttga ccgacaattg catgaagaat
     6061 ctgcttaggg ttaggcgttt tgcgctgctt cgcgatgtac gggccagata tacgcgctgt
     6121 ggaatgtgtg tcagttaggg tgtggaaagt ccccaggctc cccagcaggc agaagtatgc
     6181 aaagcatgca tctcaattag tcagcaacca ggtgtggaaa gtccccaggc tccccagcag
     6241 gcagaagtat gcaaagcatg catctcaatt agtcagcaac catagtcccg cccctaactc
     6301 cgcccatccc gcccctaac
//
