LOCUS       sequence-343172-        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-ts1
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     15..34
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        114..493
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        495..693
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     648..668
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             711..891
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    938..1063
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1560..1793
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1978..2022
                     /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    2320..2437
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2574..2981
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3696..3710
                     /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             3844..4024
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4095..4683)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4175..4194)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4854..5645,5646..5714))
                     /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     5477..5496
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5715..5819)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5894..5913)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(6087..6107)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6092..6319,1..102)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(6272..6319,1..88)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
ORIGIN
        1 tgactaattt tttttattta tgcagaggcc gaggccgcct ctgcctctga gctattccag
       61 aagtagtgag gaggcttttt tggaggccta ggcttttgca aaaagctcgc gttgacattg
      121 attattgact agttattaat agtaatcaat tacggggtca ttagttcata gcccatatat
      181 ggagttccgc gttacataac ttacggtaaa tggcccgcct ggctgaccgc ccaacgaccc
      241 ccgcccattg acgtcaataa tgacgtatgt tcccatagta acgccaatag ggactttcca
      301 ttgacgtcaa tgggtggagt atttacggta aactgcccac ttggcagtac atcaagtgta
      361 tcatatgcca agtacgcccc ctattgacgt caatgacggt aaatggcccg cctggcatta
      421 tgcccagtac atgaccttat gggactttcc tacttggcag tacatctacg tattagtcat
      481 cgctattacc atggtgatgc ggttttggca gtacatcaat gggcgtggat agcggtttga
      541 ctcacgggga tttccaagtc tccaccccat tgacgtcaat gggagtttgt tttggcacca
      601 aaatcaacgg gactttccaa aatgtcgtaa caactccgcc ccattgacgc aaatgggcgg
      661 taggcgtgta cggtgggagg tctatataag cagcgcgttt tgcctgtact gggtctctct
      721 ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca ctgcttaagc
      781 ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg tgtgactctg
      841 gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc agtggcgccc
      901 gaacagggac ttgaaagcga aagggaaacc agaggagctc tctcgacgca ggactcggct
      961 tgctgaagcg cgcacggcaa gaggcgaggg gcggcgactg gtgagtacgc caaaaatttt
     1021 gactagcgga ggctagaagg agagagatgg gtgcgagagc gtcagtatta agcgggggag
     1081 aattagatcg cgatgggaaa aaattcggtt aaggccaggg ggaaagaaaa aatataaatt
     1141 aaaacatata gtatgggcaa gcagggagct agaacgattc gcagttaatc ctggcctgtt
     1201 agaaacatca gaaggctgta gacaaatact gggacagcta caaccatccc ttcagacagg
     1261 atcagaagaa cttagatcat tatataatac agtagcaacc ctctattgtg tgcatcaaag
     1321 gatagagata aaagacacca aggaagcttt agacaagata gaggaagagc aaaacaaaag
     1381 taagaccacc gcacagcaag cggccggccg ctgatcttca gacctggagg aggagatatg
     1441 agggacaatt ggagaagtga attatataaa tataaagtag taaaaattga accattagga
     1501 gtagcaccca ccaaggcaaa gagaagagtg gtgcagagag aaaaaagagc agtgggaata
     1561 ggagctttgt tccttgggtt cttgggagca gcaggaagca ctatgggcgc agcgtcaatg
     1621 acgctgacgg tacaggccag acaattattg tctggtatag tgcagcagca gaacaatttg
     1681 ctgagggcta ttgaggcgca acagcatctg ttgcaactca cagtctgggg catcaagcag
     1741 ctccaggcaa gaatcctggc tgtggaaaga tacctaaagg atcaacagct cctggggatt
     1801 tggggttgct ctggaaaact catttgcacc actgctgtgc cttggaatgc tagttggagt
     1861 aataaatctc tggaacagat ttggaatcac acgacctgga tggagtggga cagagaaatt
     1921 aacaattaca caagcttaat acactcctta attgaagaat cgcaaaacca gcaagaaaag
     1981 aatgaacaag aattattgga attagataaa tgggcaagtt tgtggaattg gtttaacata
     2041 acaaattggc tgtggtatat aaaattattc ataatgatag taggaggctt ggtaggttta
     2101 agaatagttt ttgctgtact ttctatagtg aatagagtta ggcagggata ttcaccatta
     2161 tcgtttcaga cccacctccc aaccccgagg ggacccgaca ggcccgaagg aatagaagaa
     2221 gaaggtggag agagagacag agacagatcc attcgattag tgaacggatc ggcactgcgt
     2281 gcgccaattc tgcagacaaa tggcagtatt catccacaat tttaaaagaa aaggggggat
     2341 tggggggtac agtgcagggg aaagaatagt agacataata gcaacagaca tacaaactaa
     2401 agaattacaa aaacaaatta caaaaattca aaattttcgg gtttattaca gggacagcag
     2461 agatccagtt tggttaatta actgcagccc cgataaaata aaagatttta tttagtctcc
     2521 agaaaaaggg gggaatgaaa gaccccacct gtaggtttgg caagctagct gcagtaacgc
     2581 cattttgcaa ggcatggaaa aataccaaac caagaataga gaagttcaga tcaagggcgg
     2641 gtacatgaaa atagctaacg ttgggccaaa caggatatct gcggtgagca gtttcggccc
     2701 cggcccgggg ccaagaacag atggtcaccg cagtttcggc cccggcccga ggccaagaac
     2761 agatggtccc cagatatggc ccaaccctca gcagtttctt aagacccatc agatgtttcc
     2821 aggctccccc aaggacctga aatgaccctg cgccttattt gaattaacca atcagcctgc
     2881 ttctcgcttc tgttcgcgcg cttctgcttc ccgagctcta taaaagagct cacaacccct
     2941 cactcggcgc gccagtcctc cgacagactg agtcgcccgg gggtctagaa cgcgtgccgc
     3001 catgaccgaa tacaaaccta ccgtgaggct ggctacaaga gatgatgtcc caagggctgt
     3061 gagaacactg gccgccgctt ttgccgatta ccctgccaca cgccacactg tggacccaga
     3121 tcggcatatc gagagagtga ctgagctgca ggaactgttc ctgacccgag tgggcctgga
     3181 cattgggaag gtctgggtcg cagacgatgg agcagctgtg gctgtctgga ccacaccaga
     3241 gagcgtggaa gccggagctg tctttgcaga gatcggccct agaatggcag aactgagcgg
     3301 ctccaggctg gcagcacagc agcagatgga gggactgctg gccccacaca ggcctaagga
     3361 accagcatgg ttcctggcta ccgtgggggt ctctcctgac catcagggca aaggactggg
     3421 aagtgctgtg gtcctgccag gagtggaggc tgcagaacga gctggagtcc ctgcatttct
     3481 ggagacctct gctccacgaa acctgccctt ctatgaacgg ctgggcttta ctgtgaccgc
     3541 agatgtggag gtccccgaag gacctaggac ctggtgcatg acacgcaaac ccggcgcctg
     3601 agcgatcgcc gcggccgcct tcttaaccca acagaaggct cgagaaggta tattgctgtt
     3661 gacagtgagc gcgcaggtta ttctggactt tattagtgaa gccacagatg taataaagtc
     3721 cagaataacc tgcatgccta ctgcctcgga cttcaagggg ctagaattcg gcagctgtag
     3781 atcttagcca ctttttaaaa gaaaaggggg gactggaagg gctaactgca tccggactgt
     3841 actgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta actagggaac
     3901 ccactgctta agcctcaata aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg
     3961 ttgtgtgact ctggtaacta gagatccctc agaccctttt agtcagtgtg gaaaatctct
     4021 agcagggccc gtttcatgtg agcaaaaggc cagcaaaagg ccaggaaccg taaaaaggcc
     4081 gcgttgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatcgacgc
     4141 tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctgga
     4201 agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct gtccgccttt
     4261 ctcccttcgg gaagcgtggc gctttctcat agctcacgct gtaggtatct cagttcggtg
     4321 taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc
     4381 gccttatccg gtaactatcg tcttgagtcc aacccggtaa gacacgactt atcgccactg
     4441 gcagcagcca ctggtaacag gattagcaga gcgaggtatg taggcggtgc tacagagttc
     4501 ttgaagtggt ggcctaacta cggctacact agaagaacag tatttggtat ctgcgctctg
     4561 ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa acaaaccacc
     4621 gctggtagcg gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa aaaaggatct
     4681 caagaagatc ctttgatctt ttctacgggg tctgacgctc agtggaacga aaactcacgt
     4741 taagggattt tggtcatgag attatcaaaa aggatcttca cctagatcct tttaaattaa
     4801 aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga cagttaccaa
     4861 tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc catagttgcc
     4921 tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg ccccagtgct
     4981 gcaatgatac cgcgagaccc acgctcaccg gctccagatt tatcagcaat aaaccagcca
     5041 gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat ccagtctatt
     5101 aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg caacgttgtt
     5161 gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc attcagctcc
     5221 ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa agcggttagc
     5281 tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc actcatggtt
     5341 atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt ttctgtgact
     5401 ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag ttgctcttgc
     5461 ccggcgtcaa tacgggataa taccgcgcca catagcagaa ctttaaaagt gctcatcatt
     5521 ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag atccagttcg
     5581 atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac cagcgtttct
     5641 gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc gacacggaaa
     5701 tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca gggttattgt
     5761 ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg ggttccgcgc
     5821 acatttcccc gaaaagtgcc acctgacgtc gacggatcgg gagatctccc gatcccctat
     5881 ggtgcactct cagtacaatc tgctctgatg ccgcatagtt aagccagtat ctgctccctg
     5941 cttgtgtgtt ggaggtcgct gagtagtgcg cgagcaaaat ttaagctaca acaaggcaag
     6001 gcttgaccga caattgcatg aagaatctgc ttagggttag gcgttttgcg ctgcttcgcg
     6061 atgtacgggc cagatatacg cgctgtggaa tgtgtgtcag ttagggtgtg gaaagtcccc
     6121 aggctcccca gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccaggtg
     6181 tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc
     6241 agcaaccata gtcccgcccc taactccgcc catcccgccc ctaactccgc ccagttccgc
     6301 ccattctccg ccccatggc
//
