LOCUS       sequence-343340-        6319 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  MATR3 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-MATR3-ts2
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        43..422
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        424..622
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     577..597
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             640..820
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    867..992
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1489..1722
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1907..1951
                     /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    2249..2366
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2503..2910
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           3625..3639
                     /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             3773..3953
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4024..4612)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4104..4123)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4783..5574,5575..5643))
                     /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     5406..5425
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5644..5748)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5823..5842)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     complement(6016..6036)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        join(6021..6319,1..31)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(6201..6319,1..17)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     6263..6282
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
ORIGIN
        1 aggctttttt ggaggcctag gcttttgcaa aaagctcgcg ttgacattga ttattgacta
       61 gttattaata gtaatcaatt acggggtcat tagttcatag cccatatatg gagttccgcg
      121 ttacataact tacggtaaat ggcccgcctg gctgaccgcc caacgacccc cgcccattga
      181 cgtcaataat gacgtatgtt cccatagtaa cgccaatagg gactttccat tgacgtcaat
      241 gggtggagta tttacggtaa actgcccact tggcagtaca tcaagtgtat catatgccaa
      301 gtacgccccc tattgacgtc aatgacggta aatggcccgc ctggcattat gcccagtaca
      361 tgaccttatg ggactttcct acttggcagt acatctacgt attagtcatc gctattacca
      421 tggtgatgcg gttttggcag tacatcaatg ggcgtggata gcggtttgac tcacggggat
      481 ttccaagtct ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa aatcaacggg
      541 actttccaaa atgtcgtaac aactccgccc cattgacgca aatgggcggt aggcgtgtac
      601 ggtgggaggt ctatataagc agcgcgtttt gcctgtactg ggtctctctg gttagaccag
      661 atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc
      721 ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gagactctgg taactagaga
      781 tccctcagac ccttttagtc agtgtggaaa atctctagca gtggcgcccg aacagggact
      841 tgaaagcgaa agggaaacca gaggagctct ctcgacgcag gactcggctt gctgaagcgc
      901 gcacggcaag aggcgagggg cggcgactgg tgagtacgcc aaaaattttg actagcggag
      961 gctagaagga gagagatggg tgcgagagcg tcagtattaa gcgggggaga attagatcgc
     1021 gatgggaaaa aattcggtta aggccagggg gaaagaaaaa atataaatta aaacatatag
     1081 tatgggcaag cagggagcta gaacgattcg cagttaatcc tggcctgtta gaaacatcag
     1141 aaggctgtag acaaatactg ggacagctac aaccatccct tcagacagga tcagaagaac
     1201 ttagatcatt atataataca gtagcaaccc tctattgtgt gcatcaaagg atagagataa
     1261 aagacaccaa ggaagcttta gacaagatag aggaagagca aaacaaaagt aagaccaccg
     1321 cacagcaagc ggccggccgc tgatcttcag acctggagga ggagatatga gggacaattg
     1381 gagaagtgaa ttatataaat ataaagtagt aaaaattgaa ccattaggag tagcacccac
     1441 caaggcaaag agaagagtgg tgcagagaga aaaaagagca gtgggaatag gagctttgtt
     1501 ccttgggttc ttgggagcag caggaagcac tatgggcgca gcgtcaatga cgctgacggt
     1561 acaggccaga caattattgt ctggtatagt gcagcagcag aacaatttgc tgagggctat
     1621 tgaggcgcaa cagcatctgt tgcaactcac agtctggggc atcaagcagc tccaggcaag
     1681 aatcctggct gtggaaagat acctaaagga tcaacagctc ctggggattt ggggttgctc
     1741 tggaaaactc atttgcacca ctgctgtgcc ttggaatgct agttggagta ataaatctct
     1801 ggaacagatt tggaatcaca cgacttggat ggagtgggac agagaaatta acaattacac
     1861 aagcttaata cactccttaa ttgaagaatc gcaaaaccag caagaaaaga atgaacaaga
     1921 attattggaa ttagataaat gggcaagttt gtggaattgg tttaacataa caaattggct
     1981 gtggtatata aaattattca taatgatagt aggaggcttg gtaggtttaa gaatagtttt
     2041 tgctgtactt tctatagtga atagagttag gcagggatat tcaccattat cgtttcagac
     2101 ccacctccca accccgaggg gacccgacag gcccgaagga atagaagaag aaggtggaga
     2161 gagagacaga gacagatcca ttcgattagt gaacggatcg gcactgcgtg cgccaattct
     2221 gcagacaaat ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca
     2281 gtgcagggga aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa
     2341 aacaaattac aaaaattcaa aattttcggg tttattacag ggacagcaga gatccagttt
     2401 ggttaattaa ctgcagcccc gataaaataa aagattttat ttagtctcca gaaaaagggg
     2461 ggaatgaaag accccacctg taggtttggc aagctagctg cagtaacgcc attttgcaag
     2521 gcatggaaaa ataccaaacc aagaatagag aagttcagat caagggcggg tacatgaaaa
     2581 tagctaacgt tgggccaaac aggatatctg cggtgagcag tttcggcccc ggcccggggc
     2641 caagaacaga tggtcaccgc agtttcggcc ccggcccgag gccaagaaca gatggtcccc
     2701 agatatggcc caaccctcag cagtttctta agacccatca gatgtttcca ggctccccca
     2761 aggacctgaa atgaccctgc gccttatttg aattaaccaa tcagcctgct tctcgcttct
     2821 gttcgcgcgc ttctgcttcc cgagctctat aaaagagctc acaacccctc actcggcgcg
     2881 ccagtcctcc gacagactga gtcgcccggg ggtctagaac gcgtgccgcc atgaccgaat
     2941 acaaacctac cgtgaggctg gctacaagag atgatgtccc aagggctgtg agaacactgg
     3001 ccgccgcttt tgccgattac cctgccacac gccacactgt ggacccagat cggcatatcg
     3061 agagagtgac tgagctgcag gaactgttcc tgacccgagt gggcctggac attgggaagg
     3121 tctgggtcgc agacgatgga gcagctgtgg ctgtctggac cacaccagag agcgtggaag
     3181 ccggagctgt ctttgcagag atcggcccta gaatggcaga actgagcggc tccaggctgg
     3241 cagcacaaca gcagatggag ggactgctgg ccccacacag gcctaaggaa ccagcatggt
     3301 tcctggctac cgtgggggtc tctcctgacc atcagggcaa aggactggga agtgctgtgg
     3361 tcctgccagg agtggaggct gcagaacgag ctggagtccc tgcatttctg gagacctctg
     3421 ctccacgaaa cctgcccttc tatgaacggc tgggctttac tgtgaccgca gatgtggagg
     3481 tccccgaagg acctaggacc tggtgcatga cacgcaaacc cggcgcctga gcgatcgccg
     3541 cggccgcctt cttaacccaa cagaaggctc gagaaggtat attgctgttg acagtgagcg
     3601 ccgagaccga tcttgctaat tatagtgaag ccacagatgt ataattagca agatcggtct
     3661 cgttgcctac tgcctcggac ttcaaggggc tagaattcgg cagctgtaga tcttagccac
     3721 tttttaaaag aaaagggggg actggaaggg ctaactgcat ccggactgta ctgggtctct
     3781 ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa
     3841 gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc
     3901 tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagggcccg
     3961 tttcatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg cgttgctggc
     4021 gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag
     4081 gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa gctccctcgt
     4141 gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg
     4201 aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt aggtcgttcg
     4261 ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg ccttatccgg
     4321 taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg cagcagccac
     4381 tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct tgaagtggtg
     4441 gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc tgaagccagt
     4501 taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg ctggtagcgg
     4561 tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc aagaagatcc
     4621 tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt aagggatttt
     4681 ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa aatgaagttt
     4741 taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat gcttaatcag
     4801 tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct gactccccgt
     4861 cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg caatgatacc
     4921 gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag ccggaagggc
     4981 cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta attgttgccg
     5041 ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg ccattgctac
     5101 aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg gttcccaacg
     5161 atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct ccttcggtcc
     5221 tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta tggcagcact
     5281 gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg gtgagtactc
     5341 aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc cggcgtcaat
     5401 acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg gaaaacgttc
     5461 ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga tgtaacccac
     5521 tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg ggtgagcaaa
     5581 aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat gttgaatact
     5641 catactcttc ctttttcaat attattgaag catttatcag ggttattgtc tcatgagcgg
     5701 atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca catttccccg
     5761 aaaagtgcca cctgacgtcg acggatcggg agatctcccg atcccctatg gtgcactctc
     5821 agtacaatct gctctgatgc cgcatagtta agccagtatc tgctccctgc ttgtgtgttg
     5881 gaggtcgctg agtagtgcgc gagcaaaatt taagctacaa caaggcaagg cttgaccgac
     5941 aattgcatga agaatctgct tagggttagg cgttttgcgc tgcttcgcga tgtacgggcc
     6001 agatatacgc gctgtggaat gtgtgtcagt tagggtgtgg aaagtcccca ggctccccag
     6061 caggcagaag tatgcaaagc atgcatctca attagtcagc aaccaggtgt ggaaagtccc
     6121 caggctcccc agcaggcaga agtatgcaaa gcatgcatct caattagtca gcaaccatag
     6181 tcccgcccct aactccgccc atcccgcccc taactccgcc cagttccgcc cattctccgc
     6241 cccatggctg actaattttt tttatttatg cagaggccga ggccgcctct gcctctgagc
     6301 tattccagaa gtagtgagg
//
