LOCUS       sequence-343447-        6319 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  IFIH1 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-IFIH1-ts1
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(125..145)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        130..459
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      310..445
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     372..391
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        471..850
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        852..1050
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1005..1025
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             1068..1248
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1295..1420
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1917..2150
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2335..2379
                     /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    2677..2794
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2931..3338
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           4053..4067
                     /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             4201..4381
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4452..5040)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4532..4551)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5211..6002,6003..6071))
                     /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     5834..5853
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6072..6176)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6251..6270)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 gtagtgcgcg agcaaaattt aagctacaac aaggcaaggc ttgaccgaca attgcatgaa
       61 gaatctgctt agggttaggc gttttgcgct gcttcgcgat gtacgggcca gatatacgcg
      121 ctgtggaatg tgtgtcagtt agggtgtgga aagtccccag gctccccagc aggcagaagt
      181 atgcaaagca tgcatctcaa ttagtcagca accaggtgtg gaaagtcccc aggctcccca
      241 gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccatagt cccgccccta
      301 actccgccca tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga
      361 ctaatttttt ttatttatgc agaggccgag gccgcctctg cctctgagct attccagaag
      421 tagtgaggag gcttttttgg aggcctaggc ttttgcaaaa agctcgcgtt gacattgatt
      481 attgactagt tattaatagt aatcaattac ggggtcatta gttcatagcc catatatgga
      541 gttccgcgtt acataactta cggtaaatgg cccgcctggc tgaccgccca acgacccccg
      601 cccattgacg tcaataatga cgtatgttcc catagtaacg ccaataggga ctttccattg
      661 acgtcaatgg gtggagtatt tacggtaaac tgcccacttg gcagtacatc aagtgtatca
      721 tatgccaagt acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct ggcattatgc
      781 ccagtacatg accttatggg actttcctac ttggcagtac atctacgtat tagtcatcgc
      841 tattaccatg gtgatgcggt tttggcagta catcaatggg cgtggatagc ggtttgactc
      901 acggggattt ccaagtctcc accccattga cgtcaatggg agtttgtttt ggcaccaaaa
      961 tcaacgggac tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa tgggcggtag
     1021 gcgtgtacgg tgggaggtct atataagcag cgcgttttgc ctgtactggg tctctctggt
     1081 tagaccagat ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc
     1141 aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta
     1201 actagagatc cctcagaccc ttttagtcag tgtggaaaat ctctagcagt ggcgcccgaa
     1261 cagggacttg aaagcgaaag ggaaaccaga ggagctctct cgacgcagga ctcggcttgc
     1321 tgaagcgcgc acggcaagag gcgaggggcg gcgactggtg agtacgccaa aaattttgac
     1381 tagcggaggc tagaaggaga gagatgggtg cgagagcgtc agtattaagc gggggagaat
     1441 tagatcgcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat ataaattaaa
     1501 acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg gcctgttaga
     1561 aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc agacaggatc
     1621 agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc atcaaaggat
     1681 agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa acaaaagtaa
     1741 gaccaccgca cagcaagcgg ccggccgctg atcttcagac ctggaggagg agatatgagg
     1801 gacaattgga gaagtgaatt atataaatat aaagtagtaa aaattgaacc attaggagta
     1861 gcacccacca aggcaaagag aagagtggtg cagagagaaa aaagagcagt gggaatagga
     1921 gctttgttcc ttgggttctt gggagcagca ggaagcacta tgggcgcagc gtcaatgacg
     1981 ctgacggtac aggccagaca attattgtct ggtatagtgc agcagcagaa caatttgctg
     2041 agggctattg aggcgcaaca gcatctgttg caactcacag tctggggcat caagcagctc
     2101 caggcaagaa tcctggctgt ggaaagatac ctaaaggatc aacagctcct ggggatttgg
     2161 ggttgctctg gaaaactcat ttgcaccact gctgtgcctt ggaatgctag ttggagtaat
     2221 aaatctctgg aacagatttg gaatcacacg acctggatgg agtgggacag agaaattaac
     2281 aattacacaa gcttaataca ctccttaatt gaagaatcgc aaaaccagca agaaaagaat
     2341 gaacaagaat tattggaatt agataaatgg gcaagtttgt ggaattggtt taacataaca
     2401 aattggctgt ggtatataaa attattcata atgatagtag gaggcttggt aggtttaaga
     2461 atagtttttg ctgtactttc tatagtgaat agagttaggc agggatattc accattatcg
     2521 tttcagaccc acctcccaac cccgagggga cccgacaggc ccgaaggaat agaagaagaa
     2581 ggtggagaga gagacagaga cagatccatt cgattagtga acggatcggc actgcgtgcg
     2641 ccaattctgc agacaaatgg cagtattcat ccacaatttt aaaagaaaag gggggattgg
     2701 ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac aaactaaaga
     2761 attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga
     2821 tccagtttgg ttaattaact gcagccccga taaaataaaa gattttattt agtctccaga
     2881 aaaagggggg aatgaaagac cccacctgta ggtttggcaa gctagctgca gtaacgccat
     2941 tttgcaaggc atggaaaaat accaaaccaa gaatagagaa gttcagatca agggcgggta
     3001 catgaaaata gctaacgttg ggccaaacag gatatctgcg gtgagcagtt tcggccccgg
     3061 cccggggcca agaacagatg gtcaccgcag tttcggcccc ggcccgaggc caagaacaga
     3121 tggtccccag atatggccca accctcagca gtttcttaag acccatcaga tgtttccagg
     3181 ctcccccaag gacctgaaat gaccctgcgc cttatttgaa ttaaccaatc agcctgcttc
     3241 tcgcttctgt tcgcgcgctt ctgcttcccg agctctataa aagagctcac aacccctcac
     3301 tcggcgcgcc agtcctccga cagactgagt cgcccggggg tctagaacgc gtgccgccat
     3361 gaccgaatac aaacctaccg tgaggctggc tacaagagat gatgtcccaa gggctgtgag
     3421 aacactggcc gccgcttttg ccgattaccc tgccacacgc cacactgtgg acccagatcg
     3481 gcatatcgag agagtgactg agctgcagga actgttcctg acccgagtgg gcctggacat
     3541 tgggaaggtc tgggtcgcag acgatggagc agctgtggct gtctggacca caccagagag
     3601 cgtggaagcc ggagctgtct ttgcagagat cggccctaga atggcagaac tgagcggctc
     3661 caggctggca gcacagcagc agatggaggg actgctggcc ccacacaggc ctaaggaacc
     3721 agcatggttc ctggctaccg tgggggtctc tcctgaccat cagggcaaag gactgggaag
     3781 tgctgtggtc ctgccaggag tggaggctgc agaacgagct ggagtccctg catttctgga
     3841 gacctctgct ccacgaaacc tgcccttcta tgaacggctg ggctttactg tgaccgcaga
     3901 tgtggaggtc cccgaaggac ctaggacctg gtgcatgaca cgcaaacccg gcgcctgagc
     3961 gatcgccgcg gccgccttct taacccaaca gaaggctcga gaaggtatat tgctgttgac
     4021 agtgagcgac cctacaaatt aatgacacaa tagtgaagcc acagatgtat tgtgtcatta
     4081 atttgtaggg ctgcctactg cctcggactt caaggggcta gaattcggca gctgtagatc
     4141 ttagccactt tttaaaagaa aaggggggac tggaagggct aactgcatcc ggactgtact
     4201 gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca
     4261 ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg
     4321 tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc
     4381 agggcccgtt tcatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg
     4441 ttgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca
     4501 agtcagaggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc
     4561 tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc
     4621 ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag
     4681 gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc
     4741 ttatccggta actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca
     4801 gcagccactg gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg
     4861 aagtggtggc ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg
     4921 aagccagtta ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct
     4981 ggtagcggtg gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa
     5041 gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa
     5101 gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa
     5161 tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc
     5221 ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga
     5281 ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca
     5341 atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc
     5401 ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat
     5461 tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc
     5521 attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt
     5581 tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc
     5641 ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg
     5701 gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt
     5761 gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg
     5821 gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga
     5881 aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg
     5941 taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg
     6001 tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt
     6061 tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc
     6121 atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca
     6181 tttccccgaa aagtgccacc tgacgtcgac ggatcgggag atctcccgat cccctatggt
     6241 gcactctcag tacaatctgc tctgatgccg catagttaag ccagtatctg ctccctgctt
     6301 gtgtgttgga ggtcgctga
//
