LOCUS       sequence-343344-        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-ts1
FEATURES             Location/Qualifiers
     source          1..6319
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(104..124)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        109..438
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      289..424
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     351..370
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     enhancer        450..829
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        831..1029
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     984..1004
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     LTR             1047..1227
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1274..1399
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1896..2129
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2314..2358
                     /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    2656..2773
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2910..3317
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     ncRNA           4032..4046
                     /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             4180..4360
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4431..5019)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4511..4530)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5190..5981,5982..6050))
                     /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     5813..5832
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6051..6155)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6230..6249)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 agctacaaca aggcaaggct tgaccgacaa ttgcatgaag aatctgctta gggttaggcg
       61 ttttgcgctg cttcgcgatg tacgggccag atatacgcgc tgtggaatgt gtgtcagtta
      121 gggtgtggaa agtccccagg ctccccagca ggcagaagta tgcaaagcat gcatctcaat
      181 tagtcagcaa ccaggtgtgg aaagtcccca ggctccccag caggcagaag tatgcaaagc
      241 atgcatctca attagtcagc aaccatagtc ccgcccctaa ctccgcccat cccgccccta
      301 actccgccca gttccgccca ttctccgccc catggctgac taattttttt tatttatgca
      361 gaggccgagg ccgcctctgc ctctgagcta ttccagaagt agtgaggagg cttttttgga
      421 ggcctaggct tttgcaaaaa gctcgcgttg acattgatta ttgactagtt attaatagta
      481 atcaattacg gggtcattag ttcatagccc atatatggag ttccgcgtta cataacttac
      541 ggtaaatggc ccgcctggct gaccgcccaa cgacccccgc ccattgacgt caataatgac
      601 gtatgttccc atagtaacgc caatagggac tttccattga cgtcaatggg tggagtattt
      661 acggtaaact gcccacttgg cagtacatca agtgtatcat atgccaagta cgccccctat
      721 tgacgtcaat gacggtaaat ggcccgcctg gcattatgcc cagtacatga ccttatggga
      781 ctttcctact tggcagtaca tctacgtatt agtcatcgct attaccatgg tgatgcggtt
      841 ttggcagtac atcaatgggc gtggatagcg gtttgactca cggggatttc caagtctcca
      901 ccccattgac gtcaatggga gtttgttttg gcaccaaaat caacgggact ttccaaaatg
      961 tcgtaacaac tccgccccat tgacgcaaat gggcggtagg cgtgtacggt gggaggtcta
     1021 tataagcagc gcgttttgcc tgtactgggt ctctctggtt agaccagatc tgagcctggg
     1081 agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc
     1141 ttcaagtagt gtgtgcccgt ctgttgtgag actctggtaa ctagagatcc ctcagaccct
     1201 tttagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacttga aagcgaaagg
     1261 gaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca cggcaagagg
     1321 cgaggggcgg cgactggtga gtacgccaaa aattttgact agcggaggct agaaggagag
     1381 agatgggtgc gagagcgtca gtattaagcg ggggagaatt agatcgcgat gggaaaaaat
     1441 tcggttaagg ccagggggaa agaaaaaata taaattaaaa catatagtat gggcaagcag
     1501 ggagctagaa cgattcgcag ttaatcctgg cctgttagaa acatcagaag gctgtagaca
     1561 aatactggga cagctacaac catcccttca gacaggatca gaagaactta gatcattata
     1621 taatacagta gcaaccctct attgtgtgca tcaaaggata gagataaaag acaccaagga
     1681 agctttagac aagatagagg aagagcaaaa caaaagtaag accaccgcac agcaagcggc
     1741 cggccgctga tcttcagacc tggaggagga gatatgaggg acaattggag aagtgaatta
     1801 tataaatata aagtagtaaa aattgaacca ttaggagtag cacccaccaa ggcaaagaga
     1861 agagtggtgc agagagaaaa aagagcagtg ggaataggag ctttgttcct tgggttcttg
     1921 ggagcagcag gaagcactat gggcgcagcg tcaatgacgc tgacggtaca ggccagacaa
     1981 ttattgtctg gtatagtgca gcagcagaac aatttgctga gggctattga ggcgcaacag
     2041 catctgttgc aactcacagt ctggggcatc aagcagctcc aggcaagaat cctggctgtg
     2101 gaaagatacc taaaggatca acagctcctg gggatttggg gttgctctgg aaaactcatt
     2161 tgcaccactg ctgtgccttg gaatgctagt tggagtaata aatctctgga acagatttgg
     2221 aatcacacga cttggatgga gtgggacaga gaaattaaca attacacaag cttaatacac
     2281 tccttaattg aagaatcgca aaaccagcaa gaaaagaatg aacaagaatt attggaatta
     2341 gataaatggg caagtttgtg gaattggttt aacataacaa attggctgtg gtatataaaa
     2401 ttattcataa tgatagtagg aggcttggta ggtttaagaa tagtttttgc tgtactttct
     2461 atagtgaata gagttaggca gggatattca ccattatcgt ttcagaccca cctcccaacc
     2521 ccgaggggac ccgacaggcc cgaaggaata gaagaagaag gtggagagag agacagagac
     2581 agatccattc gattagtgaa cggatcggca ctgcgtgcgc caattctgca gacaaatggc
     2641 agtattcatc cacaatttta aaagaaaagg ggggattggg gggtacagtg caggggaaag
     2701 aatagtagac ataatagcaa cagacataca aactaaagaa ttacaaaaac aaattacaaa
     2761 aattcaaaat tttcgggttt attacaggga cagcagagat ccagtttggt taattaactg
     2821 cagccccgat aaaataaaag attttattta gtctccagaa aaagggggga atgaaagacc
     2881 ccacctgtag gtttggcaag ctagctgcag taacgccatt ttgcaaggca tggaaaaata
     2941 ccaaaccaag aatagagaag ttcagatcaa gggcgggtac atgaaaatag ctaacgttgg
     3001 gccaaacagg atatctgcgg tgagcagttt cggccccggc ccggggccaa gaacagatgg
     3061 tcaccgcagt ttcggccccg gcccgaggcc aagaacagat ggtccccaga tatggcccaa
     3121 ccctcagcag tttcttaaga cccatcagat gtttccaggc tcccccaagg acctgaaatg
     3181 accctgcgcc ttatttgaat taaccaatca gcctgcttct cgcttctgtt cgcgcgcttc
     3241 tgcttcccga gctctataaa agagctcaca acccctcact cggcgcgcca gtcctccgac
     3301 agactgagtc gcccgggggt ctagaacgcg tgccgccatg accgaataca aacctaccgt
     3361 gaggctggct acaagagatg atgtcccaag ggctgtgaga acactggccg ccgcttttgc
     3421 cgattaccct gccacacgcc acactgtgga cccagatcgg catatcgaga gagtgactga
     3481 gctgcaggaa ctgttcctga cccgagtggg cctggacatt gggaaggtct gggtcgcaga
     3541 cgatggagca gctgtggctg tctggaccac accagagagc gtggaagccg gagctgtctt
     3601 tgcagagatc ggccctagaa tggcagaact gagcggctcc aggctggcag cacagcagca
     3661 gatggaggga ctgctggccc cacacaggcc taaggaacca gcatggttcc tggctaccgt
     3721 gggggtctct cctgaccatc agggcaaagg actgggaagt gctgtggtcc tgccaggagt
     3781 ggaggctgca gaacgagctg gagtccctgc atttctggag acctctgctc cacgaaacct
     3841 gcccttctat gaacggctgg gctttactgt gaccgcagat gtggaggtcc ccgaaggacc
     3901 taggacctgg tgcatgacac gcaaacccgg cgcctgagcg atcgccgcgg ccgccttctt
     3961 aacccaacag aaggctcgag aaggtatatt gctgttgaca gtgagcgaaa gactgagagt
     4021 tcaaccgaat agtgaagcca cagatgtatt cggttgaact ctcagtcttc tgcctactgc
     4081 ctcggacttc aaggggctag aattcggcag ctgtagatct tagccacttt ttaaaagaaa
     4141 aggggggact ggaagggcta actgcatccg gactgtactg ggtctctctg gttagaccag
     4201 atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc
     4261 ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg taactagaga
     4321 tccctcagac ccttttagtc agtgtggaaa atctctagca gggcccgttt catgtgagca
     4381 aaaggccagc aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg
     4441 ctccgccccc ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg
     4501 acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt
     4561 ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt
     4621 tctcatagct cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc caagctgggc
     4681 tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt
     4741 gagtccaacc cggtaagaca cgacttatcg ccactggcag cagccactgg taacaggatt
     4801 agcagagcga ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc
     4861 tacactagaa gaacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa
     4921 agagttggta gctcttgatc cggcaaacaa accaccgctg gtagcggtgg tttttttgtt
     4981 tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct
     5041 acggggtctg acgctcagtg gaacgaaaac tcacgttaag ggattttggt catgagatta
     5101 tcaaaaagga tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa
     5161 agtatatatg agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc
     5221 tcagcgatct gtctatttcg ttcatccata gttgcctgac tccccgtcgt gtagataact
     5281 acgatacggg agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc
     5341 tcaccggctc cagatttatc agcaataaac cagccagccg gaagggccga gcgcagaagt
     5401 ggtcctgcaa ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta
     5461 agtagttcgc cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg
     5521 tcacgctcgt cgtttggtat ggcttcattc agctccggtt cccaacgatc aaggcgagtt
     5581 acatgatccc ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc
     5641 agaagtaagt tggccgcagt gttatcactc atggttatgg cagcactgca taattctctt
     5701 actgtcatgc catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc
     5761 tgagaatagt gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc
     5821 gcgccacata gcagaacttt aaaagtgctc atcattggaa aacgttcttc ggggcgaaaa
     5881 ctctcaagga tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac
     5941 tgatcttcag catcttttac tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa
     6001 aatgccgcaa aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt
     6061 tttcaatatt attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa
     6121 tgtatttaga aaaataaaca aataggggtt ccgcgcacat ttccccgaaa agtgccacct
     6181 gacgtcgacg gatcgggaga tctcccgatc ccctatggtg cactctcagt acaatctgct
     6241 ctgatgccgc atagttaagc cagtatctgc tccctgcttg tgtgttggag gtcgctgagt
     6301 agtgcgcgag caaaattta
//
