LOCUS       sequence-343474-        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-ts2
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     misc_feature    513..746
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             931..975
                     /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    1273..1390
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1527..1934
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           2649..2663
                     /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             2797..2977
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(3048..3636)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3128..3147)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3807..4598,4599..4667))
                     /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     4430..4449
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4668..4772)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(4847..4866)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(5040..5060)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        5045..5374
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      5225..5360
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     5287..5306
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        5386..5765
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        5767..5965
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     5920..5940
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             5983..6163
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    join(6210..6319,1..16)
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
ORIGIN
        1 tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg aaaaaattcg
       61 gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg caagcaggga
      121 gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct gtagacaaat
      181 actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat cattatataa
      241 tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca ccaaggaagc
      301 tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc aagcggccgg
      361 ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag tgaattatat
      421 aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc aaagagaaga
      481 gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg gttcttggga
      541 gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc cagacaatta
      601 ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc gcaacagcat
      661 ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct ggctgtggaa
      721 agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa actcatttgc
      781 accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca gatttggaat
      841 cacacgactt ggatggagtg ggacagagaa attaacaatt acacaagctt aatacactcc
      901 ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt ggaattagat
      961 aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta tataaaatta
     1021 ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt actttctata
     1081 gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct cccaaccccg
     1141 aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga cagagacaga
     1201 tccattcgat tagtgaacgg atcggcactg cgtgcgccaa ttctgcagac aaatggcagt
     1261 attcatccac aattttaaaa gaaaaggggg gattgggggg tacagtgcag gggaaagaat
     1321 agtagacata atagcaacag acatacaaac taaagaatta caaaaacaaa ttacaaaaat
     1381 tcaaaatttt cgggtttatt acagggacag cagagatcca gtttggttaa ttaactgcag
     1441 ccccgataaa ataaaagatt ttatttagtc tccagaaaaa ggggggaatg aaagacccca
     1501 cctgtaggtt tggcaagcta gctgcagtaa cgccattttg caaggcatgg aaaaatacca
     1561 aaccaagaat agagaagttc agatcaaggg cgggtacatg aaaatagcta acgttgggcc
     1621 aaacaggata tctgcggtga gcagtttcgg ccccggcccg gggccaagaa cagatggtca
     1681 ccgcagtttc ggccccggcc cgaggccaag aacagatggt ccccagatat ggcccaaccc
     1741 tcagcagttt cttaagaccc atcagatgtt tccaggctcc cccaaggacc tgaaatgacc
     1801 ctgcgcctta tttgaattaa ccaatcagcc tgcttctcgc ttctgttcgc gcgcttctgc
     1861 ttcccgagct ctataaaaga gctcacaacc cctcactcgg cgcgccagtc ctccgacaga
     1921 ctgagtcgcc cgggggtcta gaacgcgtgc cgccatgacc gaatacaaac ctaccgtgag
     1981 gctggctaca agagatgatg tcccaagggc tgtgagaaca ctggccgccg cttttgccga
     2041 ttaccctgcc acacgccaca ctgtggaccc agatcggcat atcgagagag tgactgagct
     2101 gcaggaactg ttcctgaccc gagtgggcct ggacattggg aaggtctggg tcgcagacga
     2161 tggagcagct gtggctgtct ggaccacacc agagagcgtg gaagccggag ctgtctttgc
     2221 agagatcggc cctagaatgg cagaactgag cggctccagg ctggcagcac agcagcagat
     2281 ggagggactg ctggccccac acaggcctaa ggaaccagca tggttcctgg ctaccgtggg
     2341 ggtctctcct gaccatcagg gcaaaggact gggaagtgct gtggtcctgc caggagtgga
     2401 ggctgcagaa cgagctggag tccctgcatt tctggagacc tctgctccac gaaacctgcc
     2461 cttctatgaa cggctgggct ttactgtgac cgcagatgtg gaggtccccg aaggacctag
     2521 gacctggtgc atgacacgca aacccggcgc ctgagcgatc gccgcggccg ccttcttaac
     2581 ccaacagaag gctcgagaag gtatattgct gttgacagtg agcgccacaa acaaagtttc
     2641 tccccatagt gaagccacag atgtatgggg agaaactttg tttgtgttgc ctactgcctc
     2701 ggacttcaag gggctagaat tcggcagctg tagatcttag ccacttttta aaagaaaagg
     2761 ggggactgga agggctaact gcatccggac tgtactgggt ctctctggtt agaccagatc
     2821 tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg
     2881 ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc
     2941 ctcagaccct tttagtcagt gtggaaaatc tctagcaggg cccgtttcat gtgagcaaaa
     3001 ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc
     3061 cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca
     3121 ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg
     3181 accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct
     3241 catagctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt
     3301 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag
     3361 tccaacccgg taagacacga cttatcgcca ctggcagcag ccactggtaa caggattagc
     3421 agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac
     3481 actagaagaa cagtatttgg tatctgcgct ctgctgaagc cagttacctt cggaaaaaga
     3541 gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc
     3601 aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctacg
     3661 gggtctgacg ctcagtggaa cgaaaactca cgttaaggga ttttggtcat gagattatca
     3721 aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt
     3781 atatatgagt aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca
     3841 gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg
     3901 atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca
     3961 ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt
     4021 cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt
     4081 agttcgccag ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca
     4141 cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca
     4201 tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga
     4261 agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact
     4321 gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga
     4381 gaatagtgta tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg
     4441 ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc
     4501 tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga
     4561 tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat
     4621 gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt
     4681 caatattatt gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt
     4741 atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctgac
     4801 gtcgacggat cgggagatct cccgatcccc tatggtgcac tctcagtaca atctgctctg
     4861 atgccgcata gttaagccag tatctgctcc ctgcttgtgt gttggaggtc gctgagtagt
     4921 gcgcgagcaa aatttaagct acaacaaggc aaggcttgac cgacaattgc atgaagaatc
     4981 tgcttagggt taggcgtttt gcgctgcttc gcgatgtacg ggccagatat acgcgctgtg
     5041 gaatgtgtgt cagttagggt gtggaaagtc cccaggctcc ccagcaggca gaagtatgca
     5101 aagcatgcat ctcaattagt cagcaaccag gtgtggaaag tccccaggct ccccagcagg
     5161 cagaagtatg caaagcatgc atctcaatta gtcagcaacc atagtcccgc ccctaactcc
     5221 gcccatcccg cccctaactc cgcccagttc cgcccattct ccgccccatg gctgactaat
     5281 tttttttatt tatgcagagg ccgaggccgc ctctgcctct gagctattcc agaagtagtg
     5341 aggaggcttt tttggaggcc taggcttttg caaaaagctc gcgttgacat tgattattga
     5401 ctagttatta atagtaatca attacggggt cattagttca tagcccatat atggagttcc
     5461 gcgttacata acttacggta aatggcccgc ctggctgacc gcccaacgac ccccgcccat
     5521 tgacgtcaat aatgacgtat gttcccatag taacgccaat agggactttc cattgacgtc
     5581 aatgggtgga gtatttacgg taaactgccc acttggcagt acatcaagtg tatcatatgc
     5641 caagtacgcc ccctattgac gtcaatgacg gtaaatggcc cgcctggcat tatgcccagt
     5701 acatgacctt atgggacttt cctacttggc agtacatcta cgtattagtc atcgctatta
     5761 ccatggtgat gcggttttgg cagtacatca atgggcgtgg atagcggttt gactcacggg
     5821 gatttccaag tctccacccc attgacgtca atgggagttt gttttggcac caaaatcaac
     5881 gggactttcc aaaatgtcgt aacaactccg ccccattgac gcaaatgggc ggtaggcgtg
     5941 tacggtggga ggtctatata agcagcgcgt tttgcctgta ctgggtctct ctggttagac
     6001 cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa
     6061 agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgagactc tggtaactag
     6121 agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagtggcgc ccgaacaggg
     6181 acttgaaagc gaaagggaaa ccagaggagc tctctcgacg caggactcgg cttgctgaag
     6241 cgcgcacggc aagaggcgag gggcggcgac tggtgagtac gccaaaaatt ttgactagcg
     6301 gaggctagaa ggagagaga
//
