LOCUS       sequence-237010-        6601 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses shRNA targeting ATRX. Construct has inverted repeats to be
            used in Sleeping beauty system..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6601)
  AUTHORS   Nunez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, 
            Garcia-Fabiani MB, Haase S, Koschmann C, Calinescu AA, Kamran N, 
            Saxena M, Patel R, Carney S, Guo MZ, Edwards M, Ljungman M, Qin T, 
            Sartor MA, Tagett R, Venneti S, Brosnan-Cashman J, Meeker A, 
            Gorbunova V, Zhao L, Kremer DM, Zhang L, Lyssiotis CA, Jones L, 
            Herting CJ, Ross JL, Hambardzumyan D, Hervey-Jumper S, Figueroa ME, 
            Lowenstein PR, Castro MG
  TITLE     IDH1-R132H acts as a tumor suppressor in glioma via epigenetic 
            up-regulation of the DNA damage response.
  JOURNAL   Sci Transl Med. 2019 Feb 13;11(479). pii: 11/479/eaaq1427. doi: 
            10.1126/scitranslmed.aaq1427.
  PUBMED    30760578
REFERENCE   2  (bases 1 to 6601)
  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: "Sci Transl 
            Med."; date: "2019-02-13"; volume: "11(479). pii: 11/479/eaaq1427. 
            doi"; pages: " 10.1126/scitranslmed.aaq1427"
COMMENT     Sequence Label: pT2-shATRX
FEATURES             Location/Qualifiers
     source          1..6601
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     85..107
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     99..116
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     100..116
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     126..145
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        126..144
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     LTR             531..1047
                     /label=5' LTR
                     /note="5' long terminal repeat from murine embryonic stem 
                     cell virus"
     misc_feature    1111..1452
                     /label=MESV Psi
                     /note="packaging signal of murine embryonic stem cell 
                     virus"
     CDS             1519..1935
                     /label=gag (truncated)
                     /note="truncated Moloney murine leukemia virus (MMLV) gag 
                     gene lacking the start codon"
     primer_bind     1865..1887
                     /label=pLXSN 5'
                     /note="Murine stem cell virus, forward primer. Also called 
                     MSCV"
     primer_bind     1903..1919
                     /label=pBABE 5'
                     /note="Psi packaging signal, forward primer for pBABE 
                     vectors"
     ncRNA           1975..2096
                     /label=5' miR-30a
                     /note="sequence upstream of the 71-nt precursor of the 
                     human miR-30a microRNA (Zeng et al., 2002)"
                     /ncRNA_class="miRNA"
     ncRNA           2124..2138
                     /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"
     ncRNA           2166..2292
                     /label=3' miR-30a
                     /note="sequence downstream of the 71-nt precursor of the 
                     human miR-30a microRNA (Zeng et al., 2002)"
                     /ncRNA_class="miRNA"
     primer_bind     complement(2325..2345)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2343..2640
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2510..2644
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     LTR             2688..3202
                     /label=3' LTR
                     /note="3' long terminal repeat from murine embryonic stem 
                     cell virus"
     protein_bind    3364..3380
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(3388..3394,3395..3412,3413..3418))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3433..3454
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        complement(3913..3931)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(3952..3968)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3952..3968)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     protein_bind    3976..3992
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(4000..4006,4007..4024,4025..4030))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4045..4066
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4183..4200)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4354..4942)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4434..4453)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5113..5904,5905..5973))
                     /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     5736..5755
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5974..6078)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      6105..6560
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6192..6211)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     6402..6423
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
ORIGIN
        1 cggtgcgggc ctcttcgcta ttacgccagc tggcgaaagg gggatgtgct gcaaggcgat
       61 taagttgggt aacgccaggg ttttcccagt cacgacgttg taaaacgacg gccagtgagc
      121 gcgcgtaata cgactcacta tagggcgaat tggagctcgg atccctatac agttgaagtc
      181 ggaagtttac atacacttaa gttggagtca ttaaaactcg tttttcaact actccacaaa
      241 tttcttgtta acaaacaata gttttggcaa gtcagttagg acatctactt tgtgcatgac
      301 acaagtcatt tttccaacaa ttgtttacag acagattatt tcacttataa ttcactgtat
      361 cacaattcca gtgggtcaga agtttacata cactaagttg actgtgcctt taaacagctt
      421 ggaaaattcc agaaaatgat gtcatggctt tagaagcttg atctgaagcc tatagagtac
      481 gagccataga taaaataaaa gattttattt agtctccaga aaaagggggg aatgaaagac
      541 cccacctgta ggtttggcaa gctagcttaa gtaacgccat tttgcaaggc atggaaaata
      601 cataactgag aatagagaag ttcagatcaa ggttaggaac agagagacag cagaatatgg
      661 gccaaacagg atatctgtgg taagcagttc ctgccccggc tcagggccaa gaacagatgg
      721 tccccagatg cggtcccgcc ctcagcagtt tctagagaac catcagatgt ttccagggtg
      781 ccccaaggac ctgaaatgac cctgtgcctt atttgaacta accaatcagt tcgcttctcg
      841 cttctgttcg cgcgcttctg ctccccgagc tcaataaaag agcccacaac ccctcactcg
      901 gcgcgccagt cctccgatag actgcgtcgc ccgggtaccc gtattcccaa taaagcctct
      961 tgctgtttgc atccgaatcg tggactcgct gatccttggg agggtctcct cagattgatt
     1021 gactgcccac ctcgggggtc tttcatttgg aggttccacc gagatttgga gacccctgcc
     1081 cagggaccac cgaccccccc gccgggaggt aagctggcca gcggtcgttt cgtgtctgtc
     1141 tctgtctttg tgcgtgtttg tgccggcatc taatgtttgc gcctgcgtct gtactagtta
     1201 gctaactagc tctgtatctg gcggacccgt ggtggaactg acgagttctg aacacccggc
     1261 cgcaaccctg ggagacgtcc cagggacttt gggggccgtt tttgtggccc gacctgagga
     1321 agggagtcga tgtggaatcc gaccccgtca ggatatgtgg ttctggtagg agacgagaac
     1381 ctaaaacagt tcccgcctcc gtctgaattt ttgctttcgg tttggaaccg aagccgcgcg
     1441 tcttgtctgc tgcagcgctg cagcatcgtt ctgtgttgtc tctgtctgac tgtgtttctg
     1501 tatttgtctg aaaattaggg ccagactgtt accactccct taagtttgac cttaggtcac
     1561 tggaaagatg tcgagcggat cgctcacaac cagtcggtag atgtcaagaa gagacgttgg
     1621 gttaccttct gctctgcaga atggccaacc tttaacgtcg gatggccgcg agacggcacc
     1681 tttaaccgag acctcatcac ccaggttaag atcaaggtct tttcacctgg cccgcatgga
     1741 cacccagacc aggtccccta catcgtgacc tgggaagcct tggcttttga cccccctccc
     1801 tgggtcaagc cctttgtaca ccctaagcct ccgcctcctc ttcctccatc cgccccgtct
     1861 ctcccccttg aacctcctcg ttcgaccccg cctcgatcct ccctttatcc agccctcact
     1921 ccttctctag gcgccggaat tagatctctc gactagggat aacagggtaa ttgtttgaat
     1981 gaggcttcag tactttacag aatcgttgcc tgcacatctt ggaaacactt gctgggatta
     2041 cttcttcagg ttaacccaac agaaggctcg agaaggtata ttgctgttga cagtgagcgc
     2101 ccgcttggat ggttctacta atagtgaagc cacagatgta ttagtagaac catccaagcg
     2161 gttgcctact gcctcggaat tcaaggggct actttaggag caattatctt gtttactaaa
     2221 actgaatacc ttgctatctc tttgatacat ttttacaaag ctgaattaaa atggtataaa
     2281 ttaaatcact tttttcaatt cgccagcaca gtggtcgacc ctgtggaatg tgtgtcagtt
     2341 agggtgtgga aagtccccag gctccccagc aggcagaagt atgcaaagca tgcatctcaa
     2401 ttagtcagca accaggtgtg gaaagtcccc aggctcccca gcaggcagaa gtatgcaaag
     2461 catgcatctc aattagtcag caaccatagt cccgccccta actccgccca tcccgcccct
     2521 aactccgccc agttccgccc attctccgcc ccatggctga ctaatttttt ttatttatgc
     2581 agaggccgag gccgcctcgg cctctgagct attccagaag tagtgaggag gcttttttgg
     2641 aggcgataaa ataaaagatt ttatttagtc tccagaaaaa ggggggaatg aaagacccca
     2701 cctgtaggtt tggcaagcta gcttaagtaa cgccattttg caaggcatgg aaaatacata
     2761 actgagaata gagaagttca gatcaaggtt aggaacagag agacagcaga atatgggcca
     2821 aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac agatggtccc
     2881 cagatgcggt cccgccctca gcagtttcta gagaaccatc agatgtttcc agggtgcccc
     2941 aaggacctga aatgaccctg tgccttattt gaactaacca atcagttcgc ttctcgcttc
     3001 tgttcgcgcg cttctgctcc ccgagctcaa taaaagagcc cacaacccct cactcggcgc
     3061 gccagtcctc cgatagactg cgtcgcccgg gtacccgtgt atccaataaa ccctcttgca
     3121 gttgcatccg acttgtggtc tcgctgttcc ttgggagggt ctcctctgag tgattgacta
     3181 cccgtcagcg ggggtctttc atgggtaaca gtttcttgaa gttggagaac aacattctga
     3241 gggtaggagt cgaatattaa gtaatcctga ctcaattagc cactgttttg aatccacata
     3301 ctccaatact cctgaaatag ttcattatgg acagcgcaga aagagctggg gagaattgtg
     3361 aaattgttat ccgctcacaa ttccacacaa catacgagcc ggaagcataa agtgtaaagc
     3421 ctggggtgcc taatgagtga gctaactcac attaattgcg ttgcgctcac tgcccgcttt
     3481 ccagtcggga aacctgtcgt gccagatcca tggaattcac tagtgcgcgc ggccgctcta
     3541 gatggccaga tctagcttgt ggaaggctac tcgaaatgtt tgacccaagt taaacaattt
     3601 aaaggcaatg ctaccaaata ctaattgagt gtatgtaaac ttctgaccca ctgggaatgt
     3661 gatgaaagaa ataaaagctg aaatgaatca ttctctctac tattattctg atatttcaca
     3721 ttcttaaaat aaagtggtga tcctaactga cctaagacag ggaattttta ctaggattaa
     3781 atgtcaggaa ttgtgaaaaa gtgagtttaa atgtatttgg ctaaggtgta tgtaaacttc
     3841 cgacttcaac tgtataggga tcctctagct agagtcgacc tcgagggggg gcccggtacc
     3901 cagcttttgt tccctttagt gagggttaat ttcgagcttg gcgtaatcat ggtcatagct
     3961 gtttcctgtg tgaaattgtt atccgctcac aattccacac aacatacgag ccggaagcat
     4021 aaagtgtaaa gcctggggtg cctaatgagt gagctaactc acattaattg cgttgcgctc
     4081 actgcccgct ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg
     4141 cgcggggaga ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct
     4201 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
     4261 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
     4321 caggaaccgt aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga
     4381 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
     4441 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
     4501 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
     4561 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
     4621 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
     4681 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
     4741 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaaggacagt
     4801 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
     4861 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
     4921 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
     4981 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
     5041 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
     5101 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
     5161 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
     5221 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
     5281 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
     5341 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
     5401 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
     5461 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
     5521 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
     5581 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
     5641 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
     5701 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
     5761 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
     5821 gctgttgaga tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt
     5881 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
     5941 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
     6001 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
     6061 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgcgc cctgtagcgg
     6121 cgcattaagc gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc
     6181 cctagcgccc gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc
     6241 ccgtcaagct ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct
     6301 cgaccccaaa aaacttgatt agggtgatgg ttcacgtagt gggccatcgc cctgatagac
     6361 ggtttttcgc cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac
     6421 tggaacaaca ctcaacccta tctcggtcta ttcttttgat ttataaggga ttttgccgat
     6481 ttcggcctat tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attttaacaa
     6541 aatattaacg cttacaattt ccattcgcca ttcaggctgc gcaactgttg ggaagggcga
     6601 t
//
