LOCUS       sequence-343731-        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-ts1
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(54..74)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        59..388
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      239..374
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     301..320
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        400..779
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        781..979
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     934..954
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             997..1177
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1224..1349
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1846..2079
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2264..2308
                     /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    2606..2723
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2860..3267
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3982..3996
                     /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             4130..4310
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4381..4969)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4461..4480)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5140..5931,5932..6000))
                     /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     5763..5782
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6001..6105)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6180..6199)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 gggttaggcg ttttgcgctg cttcgcgatg tacgggccag atatacgcgc tgtggaatgt
       61 gtgtcagtta gggtgtggaa agtccccagg ctccccagca ggcagaagta tgcaaagcat
      121 gcatctcaat tagtcagcaa ccaggtgtgg aaagtcccca ggctccccag caggcagaag
      181 tatgcaaagc atgcatctca attagtcagc aaccatagtc ccgcccctaa ctccgcccat
      241 cccgccccta actccgccca gttccgccca ttctccgccc catggctgac taattttttt
      301 tatttatgca gaggccgagg ccgcctctgc ctctgagcta ttccagaagt agtgaggagg
      361 cttttttgga ggcctaggct tttgcaaaaa gctcgcgttg acattgatta ttgactagtt
      421 attaatagta atcaattacg gggtcattag ttcatagccc atatatggag ttccgcgtta
      481 cataacttac ggtaaatggc ccgcctggct gaccgcccaa cgacccccgc ccattgacgt
      541 caataatgac gtatgttccc atagtaacgc caatagggac tttccattga cgtcaatggg
      601 tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat atgccaagta
      661 cgccccctat tgacgtcaat gacggtaaat ggcccgcctg gcattatgcc cagtacatga
      721 ccttatggga ctttcctact tggcagtaca tctacgtatt agtcatcgct attaccatgg
      781 tgatgcggtt ttggcagtac atcaatgggc gtggatagcg gtttgactca cggggatttc
      841 caagtctcca ccccattgac gtcaatggga gtttgttttg gcaccaaaat caacgggact
      901 ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg cgtgtacggt
      961 gggaggtcta tataagcagc gcgttttgcc tgtactgggt ctctctggtt agaccagatc
     1021 tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg
     1081 ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgag actctggtaa ctagagatcc
     1141 ctcagaccct tttagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacttga
     1201 aagcgaaagg gaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca
     1261 cggcaagagg cgaggggcgg cgactggtga gtacgccaaa aattttgact agcggaggct
     1321 agaaggagag agatgggtgc gagagcgtca gtattaagcg ggggagaatt agatcgcgat
     1381 gggaaaaaat tcggttaagg ccagggggaa agaaaaaata taaattaaaa catatagtat
     1441 gggcaagcag ggagctagaa cgattcgcag ttaatcctgg cctgttagaa acatcagaag
     1501 gctgtagaca aatactggga cagctacaac catcccttca gacaggatca gaagaactta
     1561 gatcattata taatacagta gcaaccctct attgtgtgca tcaaaggata gagataaaag
     1621 acaccaagga agctttagac aagatagagg aagagcaaaa caaaagtaag accaccgcac
     1681 agcaagcggc cggccgctga tcttcagacc tggaggagga gatatgaggg acaattggag
     1741 aagtgaatta tataaatata aagtagtaaa aattgaacca ttaggagtag cacccaccaa
     1801 ggcaaagaga agagtggtgc agagagaaaa aagagcagtg ggaataggag ctttgttcct
     1861 tgggttcttg ggagcagcag gaagcactat gggcgcagcg tcaatgacgc tgacggtaca
     1921 ggccagacaa ttattgtctg gtatagtgca gcagcagaac aatttgctga gggctattga
     1981 ggcgcaacag catctgttgc aactcacagt ctggggcatc aagcagctcc aggcaagaat
     2041 cctggctgtg gaaagatacc taaaggatca acagctcctg gggatttggg gttgctctgg
     2101 aaaactcatt tgcaccactg ctgtgccttg gaatgctagt tggagtaata aatctctgga
     2161 acagatttgg aatcacacga cttggatgga gtgggacaga gaaattaaca attacacaag
     2221 cttaatacac tccttaattg aagaatcgca aaaccagcaa gaaaagaatg aacaagaatt
     2281 attggaatta gataaatggg caagtttgtg gaattggttt aacataacaa attggctgtg
     2341 gtatataaaa ttattcataa tgatagtagg aggcttggta ggtttaagaa tagtttttgc
     2401 tgtactttct atagtgaata gagttaggca gggatattca ccattatcgt ttcagaccca
     2461 cctcccaacc ccgaggggac ccgacaggcc cgaaggaata gaagaagaag gtggagagag
     2521 agacagagac agatccattc gattagtgaa cggatcggca ctgcgtgcgc caattctgca
     2581 gacaaatggc agtattcatc cacaatttta aaagaaaagg ggggattggg gggtacagtg
     2641 caggggaaag aatagtagac ataatagcaa cagacataca aactaaagaa ttacaaaaac
     2701 aaattacaaa aattcaaaat tttcgggttt attacaggga cagcagagat ccagtttggt
     2761 taattaactg cagccccgat aaaataaaag attttattta gtctccagaa aaagggggga
     2821 atgaaagacc ccacctgtag gtttggcaag ctagctgcag taacgccatt ttgcaaggca
     2881 tggaaaaata ccaaaccaag aatagagaag ttcagatcaa gggcgggtac atgaaaatag
     2941 ctaacgttgg gccaaacagg atatctgcgg tgagcagttt cggccccggc ccggggccaa
     3001 gaacagatgg tcaccgcagt ttcggccccg gcccgaggcc aagaacagat ggtccccaga
     3061 tatggcccaa ccctcagcag tttcttaaga cccatcagat gtttccaggc tcccccaagg
     3121 acctgaaatg accctgcgcc ttatttgaat taaccaatca gcctgcttct cgcttctgtt
     3181 cgcgcgcttc tgcttcccga gctctataaa agagctcaca acccctcact cggcgcgcca
     3241 gtcctccgac agactgagtc gcccgggggt ctagaacgcg tgccgccatg accgaataca
     3301 aacctaccgt gaggctggct acaagagatg atgtcccaag ggctgtgaga acactggccg
     3361 ccgcttttgc cgattaccct gccacacgcc acactgtgga cccagatcgg catatcgaga
     3421 gagtgactga gctgcaggaa ctgttcctga cccgagtggg cctggacatt gggaaggtct
     3481 gggtcgcaga cgatggagca gctgtggctg tctggaccac accagagagc gtggaagccg
     3541 gagctgtctt tgcagagatc ggccctagaa tggcagaact gagcggctcc aggctggcag
     3601 cacagcagca gatggaggga ctgctggccc cacacaggcc taaggaacca gcatggttcc
     3661 tggctaccgt gggggtctct cctgaccatc agggcaaagg actgggaagt gctgtggtcc
     3721 tgccaggagt ggaggctgca gaacgagctg gagtccctgc atttctggag acctctgctc
     3781 cacgaaacct gcccttctat gaacggctgg gctttactgt gaccgcagat gtggaggtcc
     3841 ccgaaggacc taggacctgg tgcatgacac gcaaacccgg cgcctgagcg atcgccgcgg
     3901 ccgccttctt aacccaacag aaggctcgag aaggtatatt gctgttgaca gtgagcgcac
     3961 gagaggaaca taaatattat agtgaagcca cagatgtata atatttatgt tcctctcgtt
     4021 tgcctactgc ctcggacttc aaggggctag aattcggcag ctgtagatct tagccacttt
     4081 ttaaaagaaa aggggggact ggaagggcta actgcatccg gactgtactg ggtctctctg
     4141 gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc
     4201 tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg
     4261 taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca gggcccgttt
     4321 catgtgagca aaaggccagc aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt
     4381 tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg
     4441 gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg
     4501 ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag
     4561 cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc
     4621 caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa
     4681 ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag cagccactgg
     4741 taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga agtggtggcc
     4801 taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga agccagttac
     4861 cttcggaaaa agagttggta gctcttgatc cggcaaacaa accaccgctg gtagcggtgg
     4921 tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt
     4981 gatcttttct acggggtctg acgctcagtg gaacgaaaac tcacgttaag ggattttggt
     5041 catgagatta tcaaaaagga tcttcaccta gatcctttta aattaaaaat gaagttttaa
     5101 atcaatctaa agtatatatg agtaaacttg gtctgacagt taccaatgct taatcagtga
     5161 ggcacctatc tcagcgatct gtctatttcg ttcatccata gttgcctgac tccccgtcgt
     5221 gtagataact acgatacggg agggcttacc atctggcccc agtgctgcaa tgataccgcg
     5281 agacccacgc tcaccggctc cagatttatc agcaataaac cagccagccg gaagggccga
     5341 gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag tctattaatt gttgccggga
     5401 agctagagta agtagttcgc cagttaatag tttgcgcaac gttgttgcca ttgctacagg
     5461 catcgtggtg tcacgctcgt cgtttggtat ggcttcattc agctccggtt cccaacgatc
     5521 aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc
     5581 gatcgttgtc agaagtaagt tggccgcagt gttatcactc atggttatgg cagcactgca
     5641 taattctctt actgtcatgc catccgtaag atgcttttct gtgactggtg agtactcaac
     5701 caagtcattc tgagaatagt gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg
     5761 ggataatacc gcgccacata gcagaacttt aaaagtgctc atcattggaa aacgttcttc
     5821 ggggcgaaaa ctctcaagga tcttaccgct gttgagatcc agttcgatgt aacccactcg
     5881 tgcacccaac tgatcttcag catcttttac tttcaccagc gtttctgggt gagcaaaaac
     5941 aggaaggcaa aatgccgcaa aaaagggaat aagggcgaca cggaaatgtt gaatactcat
     6001 actcttcctt tttcaatatt attgaagcat ttatcagggt tattgtctca tgagcggata
     6061 catatttgaa tgtatttaga aaaataaaca aataggggtt ccgcgcacat ttccccgaaa
     6121 agtgccacct gacgtcgacg gatcgggaga tctcccgatc ccctatggtg cactctcagt
     6181 acaatctgct ctgatgccgc atagttaagc cagtatctgc tccctgcttg tgtgttggag
     6241 gtcgctgagt agtgcgcgag caaaatttaa gctacaacaa ggcaaggctt gaccgacaat
     6301 tgcatgaaga atctgctta
//
