LOCUS       sequence-343473-        6319 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  DDX3X 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-DDX3X-ts2
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(65..85)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        70..399
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      250..385
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     312..331
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        411..790
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        792..990
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     945..965
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             1008..1188
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1235..1360
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1857..2090
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2275..2319
                     /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    2617..2734
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2871..3278
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3993..4007
                     /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             4141..4321
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4392..4980)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4472..4491)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5151..5942,5943..6011))
                     /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     5774..5793
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6012..6116)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6191..6210)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 gaatctgctt agggttaggc gttttgcgct gcttcgcgat gtacgggcca gatatacgcg
       61 ctgtggaatg tgtgtcagtt agggtgtgga aagtccccag gctccccagc aggcagaagt
      121 atgcaaagca tgcatctcaa ttagtcagca accaggtgtg gaaagtcccc aggctcccca
      181 gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccatagt cccgccccta
      241 actccgccca tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga
      301 ctaatttttt ttatttatgc agaggccgag gccgcctctg cctctgagct attccagaag
      361 tagtgaggag gcttttttgg aggcctaggc ttttgcaaaa agctcgcgtt gacattgatt
      421 attgactagt tattaatagt aatcaattac ggggtcatta gttcatagcc catatatgga
      481 gttccgcgtt acataactta cggtaaatgg cccgcctggc tgaccgccca acgacccccg
      541 cccattgacg tcaataatga cgtatgttcc catagtaacg ccaataggga ctttccattg
      601 acgtcaatgg gtggagtatt tacggtaaac tgcccacttg gcagtacatc aagtgtatca
      661 tatgccaagt acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct ggcattatgc
      721 ccagtacatg accttatggg actttcctac ttggcagtac atctacgtat tagtcatcgc
      781 tattaccatg gtgatgcggt tttggcagta catcaatggg cgtggatagc ggtttgactc
      841 acggggattt ccaagtctcc accccattga cgtcaatggg agtttgtttt ggcaccaaaa
      901 tcaacgggac tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa tgggcggtag
      961 gcgtgtacgg tgggaggtct atataagcag cgcgttttgc ctgtactggg tctctctggt
     1021 tagaccagat ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc
     1081 aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtga gactctggta
     1141 actagagatc cctcagaccc ttttagtcag tgtggaaaat ctctagcagt ggcgcccgaa
     1201 cagggacttg aaagcgaaag ggaaaccaga ggagctctct cgacgcagga ctcggcttgc
     1261 tgaagcgcgc acggcaagag gcgaggggcg gcgactggtg agtacgccaa aaattttgac
     1321 tagcggaggc tagaaggaga gagatgggtg cgagagcgtc agtattaagc gggggagaat
     1381 tagatcgcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat ataaattaaa
     1441 acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg gcctgttaga
     1501 aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc agacaggatc
     1561 agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc atcaaaggat
     1621 agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa acaaaagtaa
     1681 gaccaccgca cagcaagcgg ccggccgctg atcttcagac ctggaggagg agatatgagg
     1741 gacaattgga gaagtgaatt atataaatat aaagtagtaa aaattgaacc attaggagta
     1801 gcacccacca aggcaaagag aagagtggtg cagagagaaa aaagagcagt gggaatagga
     1861 gctttgttcc ttgggttctt gggagcagca ggaagcacta tgggcgcagc gtcaatgacg
     1921 ctgacggtac aggccagaca attattgtct ggtatagtgc agcagcagaa caatttgctg
     1981 agggctattg aggcgcaaca gcatctgttg caactcacag tctggggcat caagcagctc
     2041 caggcaagaa tcctggctgt ggaaagatac ctaaaggatc aacagctcct ggggatttgg
     2101 ggttgctctg gaaaactcat ttgcaccact gctgtgcctt ggaatgctag ttggagtaat
     2161 aaatctctgg aacagatttg gaatcacacg acttggatgg agtgggacag agaaattaac
     2221 aattacacaa gcttaataca ctccttaatt gaagaatcgc aaaaccagca agaaaagaat
     2281 gaacaagaat tattggaatt agataaatgg gcaagtttgt ggaattggtt taacataaca
     2341 aattggctgt ggtatataaa attattcata atgatagtag gaggcttggt aggtttaaga
     2401 atagtttttg ctgtactttc tatagtgaat agagttaggc agggatattc accattatcg
     2461 tttcagaccc acctcccaac cccgagggga cccgacaggc ccgaaggaat agaagaagaa
     2521 ggtggagaga gagacagaga cagatccatt cgattagtga acggatcggc actgcgtgcg
     2581 ccaattctgc agacaaatgg cagtattcat ccacaatttt aaaagaaaag gggggattgg
     2641 ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac aaactaaaga
     2701 attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga
     2761 tccagtttgg ttaattaact gcagccccga taaaataaaa gattttattt agtctccaga
     2821 aaaagggggg aatgaaagac cccacctgta ggtttggcaa gctagctgca gtaacgccat
     2881 tttgcaaggc atggaaaaat accaaaccaa gaatagagaa gttcagatca agggcgggta
     2941 catgaaaata gctaacgttg ggccaaacag gatatctgcg gtgagcagtt tcggccccgg
     3001 cccggggcca agaacagatg gtcaccgcag tttcggcccc ggcccgaggc caagaacaga
     3061 tggtccccag atatggccca accctcagca gtttcttaag acccatcaga tgtttccagg
     3121 ctcccccaag gacctgaaat gaccctgcgc cttatttgaa ttaaccaatc agcctgcttc
     3181 tcgcttctgt tcgcgcgctt ctgcttcccg agctctataa aagagctcac aacccctcac
     3241 tcggcgcgcc agtcctccga cagactgagt cgcccggggg tctagaacgc gtgccgccat
     3301 gaccgaatac aaacctaccg tgaggctggc tacaagagat gatgtcccaa gggctgtgag
     3361 aacactggcc gccgcttttg ccgattaccc tgccacacgc cacactgtgg acccagatcg
     3421 gcatatcgag agagtgactg agctgcagga actgttcctg acccgagtgg gcctggacat
     3481 tgggaaggtc tgggtcgcag acgatggagc agctgtggct gtctggacca caccagagag
     3541 cgtggaagcc ggagctgtct ttgcagagat cggccctaga atggcagaac tgagcggctc
     3601 caggctggca gcacagcagc agatggaggg actgctggcc ccacacaggc ctaaggaacc
     3661 agcatggttc ctggctaccg tgggggtctc tcctgaccat cagggcaaag gactgggaag
     3721 tgctgtggtc ctgccaggag tggaggctgc agaacgagct ggagtccctg catttctgga
     3781 gacctctgct ccacgaaacc tgcccttcta tgaacggctg ggctttactg tgaccgcaga
     3841 tgtggaggtc cccgaaggac ctaggacctg gtgcatgaca cgcaaacccg gcgcctgagc
     3901 gatcgccgcg gccgccttct taacccaaca gaaggctcga gaaggtatat tgctgttgac
     3961 agtgagcgcc cagtgcaaaa gcatgctata tagtgaagcc acagatgtat atagcatgct
     4021 tttgcactgg atgcctactg cctcggactt caaggggcta gaattcggca gctgtagatc
     4081 ttagccactt tttaaaagaa aaggggggac tggaagggct aactgcatcc ggactgtact
     4141 gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca
     4201 ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg
     4261 tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc
     4321 agggcccgtt tcatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg
     4381 ttgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca
     4441 agtcagaggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc
     4501 tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc
     4561 ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag
     4621 gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc
     4681 ttatccggta actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca
     4741 gcagccactg gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg
     4801 aagtggtggc ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg
     4861 aagccagtta ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct
     4921 ggtagcggtg gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa
     4981 gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa
     5041 gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa
     5101 tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc
     5161 ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga
     5221 ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca
     5281 atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc
     5341 ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat
     5401 tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc
     5461 attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt
     5521 tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc
     5581 ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg
     5641 gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt
     5701 gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg
     5761 gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga
     5821 aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg
     5881 taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg
     5941 tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt
     6001 tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc
     6061 atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca
     6121 tttccccgaa aagtgccacc tgacgtcgac ggatcgggag atctcccgat cccctatggt
     6181 gcactctcag tacaatctgc tctgatgccg catagttaag ccagtatctg ctccctgctt
     6241 gtgtgttgga ggtcgctgag tagtgcgcga gcaaaattta agctacaaca aggcaaggct
     6301 tgaccgacaa ttgcatgaa
//
