LOCUS       sequence-343173-        6319 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  DDX58 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-DDX58-ts3
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     37..56
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        136..515
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        517..715
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     670..690
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             733..913
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    960..1085
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1582..1815
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2000..2044
                     /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    2342..2459
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2596..3003
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3718..3732
                     /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             3866..4046
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4117..4705)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4197..4216)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4876..5667,5668..5736))
                     /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     5499..5518
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5737..5841)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5916..5935)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(6109..6129)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6114..6319,1..124)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(6294..6319,1..110)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
ORIGIN
        1 cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc
       61 ctctgcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg
      121 caaaaagctc gcgttgacat tgattattga ctagttatta atagtaatca attacggggt
      181 cattagttca tagcccatat atggagttcc gcgttacata acttacggta aatggcccgc
      241 ctggctgacc gcccaacgac ccccgcccat tgacgtcaat aatgacgtat gttcccatag
      301 taacgccaat agggactttc cattgacgtc aatgggtgga gtatttacgg taaactgccc
      361 acttggcagt acatcaagtg tatcatatgc caagtacgcc ccctattgac gtcaatgacg
      421 gtaaatggcc cgcctggcat tatgcccagt acatgacctt atgggacttt cctacttggc
      481 agtacatcta cgtattagtc atcgctatta ccatggtgat gcggttttgg cagtacatca
      541 atgggcgtgg atagcggttt gactcacggg gatttccaag tctccacccc attgacgtca
      601 atgggagttt gttttggcac caaaatcaac gggactttcc aaaatgtcgt aacaactccg
      661 ccccattgac gcaaatgggc ggtaggcgtg tacggtggga ggtctatata agcagcgcgt
      721 tttgcctgta ctgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa
      781 ctagggaacc cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt
      841 gcccgtctgt tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg
      901 aaaatctcta gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa ccagaggagc
      961 tctctcgacg caggactcgg cttgctgaag cgcgcacggc aagaggcgag gggcggcgac
     1021 tggtgagtac gccaaaaatt ttgactagcg gaggctagaa ggagagagat gggtgcgaga
     1081 gcgtcagtat taagcggggg agaattagat cgcgatggga aaaaattcgg ttaaggccag
     1141 ggggaaagaa aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat
     1201 tcgcagttaa tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc
     1261 tacaaccatc ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa
     1321 ccctctattg tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga
     1381 tagaggaaga gcaaaacaaa agtaagacca ccgcacagca agcggccggc cgctgatctt
     1441 cagacctgga ggaggagata tgagggacaa ttggagaagt gaattatata aatataaagt
     1501 agtaaaaatt gaaccattag gagtagcacc caccaaggca aagagaagag tggtgcagag
     1561 agaaaaaaga gcagtgggaa taggagcttt gttccttggg ttcttgggag cagcaggaag
     1621 cactatgggc gcagcgtcaa tgacgctgac ggtacaggcc agacaattat tgtctggtat
     1681 agtgcagcag cagaacaatt tgctgagggc tattgaggcg caacagcatc tgttgcaact
     1741 cacagtctgg ggcatcaagc agctccaggc aagaatcctg gctgtggaaa gatacctaaa
     1801 ggatcaacag ctcctgggga tttggggttg ctctggaaaa ctcatttgca ccactgctgt
     1861 gccttggaat gctagttgga gtaataaatc tctggaacag atttggaatc acacgacctg
     1921 gatggagtgg gacagagaaa ttaacaatta cacaagctta atacactcct taattgaaga
     1981 atcgcaaaac cagcaagaaa agaatgaaca agaattattg gaattagata aatgggcaag
     2041 tttgtggaat tggtttaaca taacaaattg gctgtggtat ataaaattat tcataatgat
     2101 agtaggaggc ttggtaggtt taagaatagt ttttgctgta ctttctatag tgaatagagt
     2161 taggcaggga tattcaccat tatcgtttca gacccacctc ccaaccccga ggggacccga
     2221 caggcccgaa ggaatagaag aagaaggtgg agagagagac agagacagat ccattcgatt
     2281 agtgaacgga tcggcactgc gtgcgccaat tctgcagaca aatggcagta ttcatccaca
     2341 attttaaaag aaaagggggg attggggggt acagtgcagg ggaaagaata gtagacataa
     2401 tagcaacaga catacaaact aaagaattac aaaaacaaat tacaaaaatt caaaattttc
     2461 gggtttatta cagggacagc agagatccag tttggttaat taactgcagc cccgataaaa
     2521 taaaagattt tatttagtct ccagaaaaag gggggaatga aagaccccac ctgtaggttt
     2581 ggcaagctag ctgcagtaac gccattttgc aaggcatgga aaaataccaa accaagaata
     2641 gagaagttca gatcaagggc gggtacatga aaatagctaa cgttgggcca aacaggatat
     2701 ctgcggtgag cagtttcggc cccggcccgg ggccaagaac agatggtcac cgcagtttcg
     2761 gccccggccc gaggccaaga acagatggtc cccagatatg gcccaaccct cagcagtttc
     2821 ttaagaccca tcagatgttt ccaggctccc ccaaggacct gaaatgaccc tgcgccttat
     2881 ttgaattaac caatcagcct gcttctcgct tctgttcgcg cgcttctgct tcccgagctc
     2941 tataaaagag ctcacaaccc ctcactcggc gcgccagtcc tccgacagac tgagtcgccc
     3001 gggggtctag aacgcgtgcc gccatgaccg aatacaaacc taccgtgagg ctggctacaa
     3061 gagatgatgt cccaagggct gtgagaacac tggccgccgc ttttgccgat taccctgcca
     3121 cacgccacac tgtggaccca gatcggcata tcgagagagt gactgagctg caggaactgt
     3181 tcctgacccg agtgggcctg gacattggga aggtctgggt cgcagacgat ggagcagctg
     3241 tggctgtctg gaccacacca gagagcgtgg aagccggagc tgtctttgca gagatcggcc
     3301 ctagaatggc agaactgagc ggctccaggc tggcagcaca gcagcagatg gagggactgc
     3361 tggccccaca caggcctaag gaaccagcat ggttcctggc taccgtgggg gtctctcctg
     3421 accatcaggg caaaggactg ggaagtgctg tggtcctgcc aggagtggag gctgcagaac
     3481 gagctggagt ccctgcattt ctggagacct ctgctccacg aaacctgccc ttctatgaac
     3541 ggctgggctt tactgtgacc gcagatgtgg aggtccccga aggacctagg acctggtgca
     3601 tgacacgcaa acccggcgcc tgagcgatcg ccgcggccgc cttcttaacc caacagaagg
     3661 ctcgagaagg tatattgctg ttgacagtga gcgctggatt gttacagttc agaaatagtg
     3721 aagccacaga tgtatttctg aactgtaaca atccattgcc tactgcctcg gacttcaagg
     3781 ggctagaatt cggcagctgt agatcttagc cactttttaa aagaaaaggg gggactggaa
     3841 gggctaactg catccggact gtactgggtc tctctggtta gaccagatct gagcctggga
     3901 gctctctggc taactaggga acccactgct taagcctcaa taaagcttgc cttgagtgct
     3961 tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccctt
     4021 ttagtcagtg tggaaaatct ctagcagggc ccgtttcatg tgagcaaaag gccagcaaaa
     4081 ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc cataggctcc gcccccctga
     4141 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     4201 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     4261 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     4321 ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     4381 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     4441 aagacacgac ttatcgccac tggcagcagc cactggtaac aggattagca gagcgaggta
     4501 tgtaggcggt gctacagagt tcttgaagtg gtggcctaac tacggctaca ctagaagaac
     4561 agtatttggt atctgcgctc tgctgaagcc agttaccttc ggaaaaagag ttggtagctc
     4621 ttgatccggc aaacaaacca ccgctggtag cggtggtttt tttgtttgca agcagcagat
     4681 tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc
     4741 tcagtggaac gaaaactcac gttaagggat tttggtcatg agattatcaa aaaggatctt
     4801 cacctagatc cttttaaatt aaaaatgaag ttttaaatca atctaaagta tatatgagta
     4861 aacttggtct gacagttacc aatgcttaat cagtgaggca cctatctcag cgatctgtct
     4921 atttcgttca tccatagttg cctgactccc cgtcgtgtag ataactacga tacgggaggg
     4981 cttaccatct ggccccagtg ctgcaatgat accgcgagac ccacgctcac cggctccaga
     5041 tttatcagca ataaaccagc cagccggaag ggccgagcgc agaagtggtc ctgcaacttt
     5101 atccgcctcc atccagtcta ttaattgttg ccgggaagct agagtaagta gttcgccagt
     5161 taatagtttg cgcaacgttg ttgccattgc tacaggcatc gtggtgtcac gctcgtcgtt
     5221 tggtatggct tcattcagct ccggttccca acgatcaagg cgagttacat gatcccccat
     5281 gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc gttgtcagaa gtaagttggc
     5341 cgcagtgtta tcactcatgg ttatggcagc actgcataat tctcttactg tcatgccatc
     5401 cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag tcattctgag aatagtgtat
     5461 gcggcgaccg agttgctctt gcccggcgtc aatacgggat aataccgcgc cacatagcag
     5521 aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg cgaaaactct caaggatctt
     5581 accgctgttg agatccagtt cgatgtaacc cactcgtgca cccaactgat cttcagcatc
     5641 ttttactttc accagcgttt ctgggtgagc aaaaacagga aggcaaaatg ccgcaaaaaa
     5701 gggaataagg gcgacacgga aatgttgaat actcatactc ttcctttttc aatattattg
     5761 aagcatttat cagggttatt gtctcatgag cggatacata tttgaatgta tttagaaaaa
     5821 taaacaaata ggggttccgc gcacatttcc ccgaaaagtg ccacctgacg tcgacggatc
     5881 gggagatctc ccgatcccct atggtgcact ctcagtacaa tctgctctga tgccgcatag
     5941 ttaagccagt atctgctccc tgcttgtgtg ttggaggtcg ctgagtagtg cgcgagcaaa
     6001 atttaagcta caacaaggca aggcttgacc gacaattgca tgaagaatct gcttagggtt
     6061 aggcgttttg cgctgcttcg cgatgtacgg gccagatata cgcgctgtgg aatgtgtgtc
     6121 agttagggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc
     6181 tcaattagtc agcaaccagg tgtggaaagt ccccaggctc cccagcaggc agaagtatgc
     6241 aaagcatgca tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc
     6301 ccctaactcc gcccagttc
//
