LOCUS       sequence-343733-        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-ts3
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        57..436
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        438..636
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     591..611
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             654..834
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    881..1006
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1503..1736
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1921..1965
                     /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    2263..2380
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2517..2924
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3639..3653
                     /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             3787..3967
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4038..4626)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4118..4137)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4797..5588,5589..5657))
                     /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     5420..5439
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5658..5762)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5837..5856)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(6030..6050)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6035..6319,1..45)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(6215..6319,1..31)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     6277..6296
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
ORIGIN
        1 cagaagtagt gaggaggctt ttttggaggc ctaggctttt gcaaaaagct cgcgttgaca
       61 ttgattattg actagttatt aatagtaatc aattacgggg tcattagttc atagcccata
      121 tatggagttc cgcgttacat aacttacggt aaatggcccg cctggctgac cgcccaacga
      181 cccccgccca ttgacgtcaa taatgacgta tgttcccata gtaacgccaa tagggacttt
      241 ccattgacgt caatgggtgg agtatttacg gtaaactgcc cacttggcag tacatcaagt
      301 gtatcatatg ccaagtacgc cccctattga cgtcaatgac ggtaaatggc ccgcctggca
      361 ttatgcccag tacatgacct tatgggactt tcctacttgg cagtacatct acgtattagt
      421 catcgctatt accatggtga tgcggttttg gcagtacatc aatgggcgtg gatagcggtt
      481 tgactcacgg ggatttccaa gtctccaccc cattgacgtc aatgggagtt tgttttggca
      541 ccaaaatcaa cgggactttc caaaatgtcg taacaactcc gccccattga cgcaaatggg
      601 cggtaggcgt gtacggtggg aggtctatat aagcagcgcg ttttgcctgt actgggtctc
      661 tctggttaga ccagatctga gcctgggagc tctctggcta actagggaac ccactgctta
      721 agcctcaata aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg ttgtgagact
      781 ctggtaacta gagatccctc agaccctttt agtcagtgtg gaaaatctct agcagtggcg
      841 cccgaacagg gacttgaaag cgaaagggaa accagaggag ctctctcgac gcaggactcg
      901 gcttgctgaa gcgcgcacgg caagaggcga ggggcggcga ctggtgagta cgccaaaaat
      961 tttgactagc ggaggctaga aggagagaga tgggtgcgag agcgtcagta ttaagcgggg
     1021 gagaattaga tcgcgatggg aaaaaattcg gttaaggcca gggggaaaga aaaaatataa
     1081 attaaaacat atagtatggg caagcaggga gctagaacga ttcgcagtta atcctggcct
     1141 gttagaaaca tcagaaggct gtagacaaat actgggacag ctacaaccat cccttcagac
     1201 aggatcagaa gaacttagat cattatataa tacagtagca accctctatt gtgtgcatca
     1261 aaggatagag ataaaagaca ccaaggaagc tttagacaag atagaggaag agcaaaacaa
     1321 aagtaagacc accgcacagc aagcggccgg ccgctgatct tcagacctgg aggaggagat
     1381 atgagggaca attggagaag tgaattatat aaatataaag tagtaaaaat tgaaccatta
     1441 ggagtagcac ccaccaaggc aaagagaaga gtggtgcaga gagaaaaaag agcagtggga
     1501 ataggagctt tgttccttgg gttcttggga gcagcaggaa gcactatggg cgcagcgtca
     1561 atgacgctga cggtacaggc cagacaatta ttgtctggta tagtgcagca gcagaacaat
     1621 ttgctgaggg ctattgaggc gcaacagcat ctgttgcaac tcacagtctg gggcatcaag
     1681 cagctccagg caagaatcct ggctgtggaa agatacctaa aggatcaaca gctcctgggg
     1741 atttggggtt gctctggaaa actcatttgc accactgctg tgccttggaa tgctagttgg
     1801 agtaataaat ctctggaaca gatttggaat cacacgactt ggatggagtg ggacagagaa
     1861 attaacaatt acacaagctt aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa
     1921 aagaatgaac aagaattatt ggaattagat aaatgggcaa gtttgtggaa ttggtttaac
     1981 ataacaaatt ggctgtggta tataaaatta ttcataatga tagtaggagg cttggtaggt
     2041 ttaagaatag tttttgctgt actttctata gtgaatagag ttaggcaggg atattcacca
     2101 ttatcgtttc agacccacct cccaaccccg aggggacccg acaggcccga aggaatagaa
     2161 gaagaaggtg gagagagaga cagagacaga tccattcgat tagtgaacgg atcggcactg
     2221 cgtgcgccaa ttctgcagac aaatggcagt attcatccac aattttaaaa gaaaaggggg
     2281 gattgggggg tacagtgcag gggaaagaat agtagacata atagcaacag acatacaaac
     2341 taaagaatta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag
     2401 cagagatcca gtttggttaa ttaactgcag ccccgataaa ataaaagatt ttatttagtc
     2461 tccagaaaaa ggggggaatg aaagacccca cctgtaggtt tggcaagcta gctgcagtaa
     2521 cgccattttg caaggcatgg aaaaatacca aaccaagaat agagaagttc agatcaaggg
     2581 cgggtacatg aaaatagcta acgttgggcc aaacaggata tctgcggtga gcagtttcgg
     2641 ccccggcccg gggccaagaa cagatggtca ccgcagtttc ggccccggcc cgaggccaag
     2701 aacagatggt ccccagatat ggcccaaccc tcagcagttt cttaagaccc atcagatgtt
     2761 tccaggctcc cccaaggacc tgaaatgacc ctgcgcctta tttgaattaa ccaatcagcc
     2821 tgcttctcgc ttctgttcgc gcgcttctgc ttcccgagct ctataaaaga gctcacaacc
     2881 cctcactcgg cgcgccagtc ctccgacaga ctgagtcgcc cgggggtcta gaacgcgtgc
     2941 cgccatgacc gaatacaaac ctaccgtgag gctggctaca agagatgatg tcccaagggc
     3001 tgtgagaaca ctggccgccg cttttgccga ttaccctgcc acacgccaca ctgtggaccc
     3061 agatcggcat atcgagagag tgactgagct gcaggaactg ttcctgaccc gagtgggcct
     3121 ggacattggg aaggtctggg tcgcagacga tggagcagct gtggctgtct ggaccacacc
     3181 agagagcgtg gaagccggag ctgtctttgc agagatcggc cctagaatgg cagaactgag
     3241 cggctccagg ctggcagcac agcagcagat ggagggactg ctggccccac acaggcctaa
     3301 ggaaccagca tggttcctgg ctaccgtggg ggtctctcct gaccatcagg gcaaaggact
     3361 gggaagtgct gtggtcctgc caggagtgga ggctgcagaa cgagctggag tccctgcatt
     3421 tctggagacc tctgctccac gaaacctgcc cttctatgaa cggctgggct ttactgtgac
     3481 cgcagatgtg gaggtccccg aaggacctag gacctggtgc atgacacgca aacccggcgc
     3541 ctgagcgatc gccgcggccg ccttcttaac ccaacagaag gctcgagaag gtatattgct
     3601 gttgacagtg agcgcggcac ctactgttca agagtatagt gaagccacag atgtatactc
     3661 ttgaacagta ggtgccatgc ctactgcctc ggacttcaag gggctagaat tcggcagctg
     3721 tagatcttag ccacttttta aaagaaaagg ggggactgga agggctaact gcatccggac
     3781 tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactaggg
     3841 aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt
     3901 ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt gtggaaaatc
     3961 tctagcaggg cccgtttcat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag
     4021 gccgcgttgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga
     4081 cgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct
     4141 ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc
     4201 tttctccctt cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg
     4261 gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc
     4321 tgcgccttat ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca
     4381 ctggcagcag ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag
     4441 ttcttgaagt ggtggcctaa ctacggctac actagaagaa cagtatttgg tatctgcgct
     4501 ctgctgaagc cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc
     4561 accgctggta gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga
     4621 tctcaagaag atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca
     4681 cgttaaggga ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat
     4741 taaaaatgaa gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac
     4801 caatgcttaa tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt
     4861 gcctgactcc ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt
     4921 gctgcaatga taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag
     4981 ccagccggaa gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct
     5041 attaattgtt gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt
     5101 gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc
     5161 tccggttccc aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt
     5221 agctccttcg gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg
     5281 gttatggcag cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg
     5341 actggtgagt actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct
     5401 tgcccggcgt caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc
     5461 attggaaaac gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt
     5521 tcgatgtaac ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt
     5581 tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg
     5641 aaatgttgaa tactcatact cttccttttt caatattatt gaagcattta tcagggttat
     5701 tgtctcatga gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg
     5761 cgcacatttc cccgaaaagt gccacctgac gtcgacggat cgggagatct cccgatcccc
     5821 tatggtgcac tctcagtaca atctgctctg atgccgcata gttaagccag tatctgctcc
     5881 ctgcttgtgt gttggaggtc gctgagtagt gcgcgagcaa aatttaagct acaacaaggc
     5941 aaggcttgac cgacaattgc atgaagaatc tgcttagggt taggcgtttt gcgctgcttc
     6001 gcgatgtacg ggccagatat acgcgctgtg gaatgtgtgt cagttagggt gtggaaagtc
     6061 cccaggctcc ccagcaggca gaagtatgca aagcatgcat ctcaattagt cagcaaccag
     6121 gtgtggaaag tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta
     6181 gtcagcaacc atagtcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc
     6241 cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc
     6301 ctctgcctct gagctattc
//
