LOCUS       sequence-386019-        7600 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  conditional knock down HDAC2.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7600)
  TITLE     Bordey Lab Plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7600)
  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: 
            "Unpublished"
COMMENT     Sequence Label: pSico-shHDAC2
FEATURES             Location/Qualifiers
     source          1..7600
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             337..381
                     /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    679..796
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     primer_bind     1086..1106
                     /label=mU6-F
                     /note="Mouse U6 promoter, forward primer"
     protein_bind    complement(1124..1157)
                     /label=loxP511
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATAC) (Shaw et al., 2021). loxP511 sites are 
                     compatible with each other, but incompatible with wild-type
                     loxP sites."
     enhancer        1257..1560
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        1561..1764
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     regulatory      1803..1812
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(1809..1811,1812..1814,1815..2528)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(1809..1811,1812..1814,1815..2525)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(1854..1875)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(2115..2134)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2462..2483
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     protein_bind    complement(2536..2569)
                     /label=loxP511
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATAC) (Shaw et al., 2021). loxP511 sites are 
                     compatible with each other, but incompatible with wild-type
                     loxP sites."
     primer_bind     2633..2649
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     misc_feature    2724..3312
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2777..2797)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3195..3206)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(3315..3331)
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     LTR             3841..4021
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4083..4671)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4163..4182)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4842..5633,5634..5702))
                     /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     5465..5484
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5703..5807)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5882..5901)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        6073..6452
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        6454..6652
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     LTR             6670..6850
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6897..7022
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    join(7519..7600,1..152)
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
ORIGIN
        1 caattattgt ctggtatagt gcagcagcag aacaatttgc tgagggctat tgaggcgcaa
       61 cagcatctgt tgcaactcac agtctggggc atcaagcagc tccaggcaag aatcctggct
      121 gtggaaagat acctaaagga tcaacagctc ctggggattt ggggttgctc tggaaaactc
      181 atttgcacca ctgctgtgcc ttggaatgct agttggagta ataaatctct ggaacagatt
      241 tggaatcaca cgacctggat ggagtgggac agagaaatta acaattacac aagcttaata
      301 cactccttaa ttgaagaatc gcaaaaccag caagaaaaga atgaacaaga attattggaa
      361 ttagataaat gggcaagttt gtggaattgg tttaacataa caaattggct gtggtatata
      421 aaattattca taatgatagt aggaggcttg gtaggtttaa gaatagtttt tgctgtactt
      481 tctatagtga atagagttag gcagggatat tcaccattat cgtttcagac ccacctccca
      541 accccgaggg gacccgacag gcccgaagga atagaagaag aaggtggaga gagagacaga
      601 gacagatcca ttcgattagt gaacggatcg gcactgcgtg cgccaattct gcagacaaat
      661 ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca gtgcagggga
      721 aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa aacaaattac
      781 aaaaattcaa aattttcggg tttattacag ggacagcaga gatccagttt ggttagtacc
      841 gggcccgctc tagagatccg acgcgccatc tctaggcccg cgccggcccc ctcgcacaga
      901 cttgtgggag aagctcggct actcccctgc cccggttaat ttgcatataa tatttcctag
      961 taactataga ggcttaatgt gcgataaaag acagataatc tgttcttttt aatactagct
     1021 acattttaca tgataggctt ggatttctat aagagataca aatactaaat tattatttta
     1081 aaaaacagca caaaaggaaa ctcaccctaa ctgtaaagta attataactt cgtatagtat
     1141 aaattatacg aagttataag ccttggtttt ttgaattccg tattaccgcc atgcattagt
     1201 tattaatagt aatcaattac ggggtcatta gttcatagcc catatatgga gttccgcgtt
     1261 acataactta cggtaaatgg cccgcctggc tgaccgccca acgacccccg cccattgacg
     1321 tcaataatga cgtatgttcc catagtaacg ccaataggga ctttccattg acgtcaatgg
     1381 gtggagtatt tacggtaaac tgcccacttg gcagtacatc aagtgtatca tatgccaagt
     1441 acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct ggcattatgc ccagtacatg
     1501 accttatggg actttcctac ttggcagtac atctacgtat tagtcatcgc tattaccatg
     1561 gtgatgcggt tttggcagta catcaatggg cgtggatagc ggtttgactc acggggattt
     1621 ccaagtctcc accccattga cgtcaatggg agtttgtttt ggcaccaaaa tcaacgggac
     1681 tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa tgggcggtag gcgtgtacgg
     1741 tgggaggtct atataagcag agctggttta gtgaaccgtc agatccgcta gcgctaccgg
     1801 tcgccaccat ggtgagcaag ggcgaggagc tgttcaccgg ggtggtgccc atcctggtcg
     1861 agctggacgg cgacgtaaac ggccacaagt tcagcgtgtc cggcgagggc gagggcgatg
     1921 ccacctacgg caagctgacc ctgaagttca tctgcaccac cggcaagctg cccgtgccct
     1981 ggcccaccct cgtgaccacc ctgacctacg gcgtgcagtg cttcagccgc taccccgacc
     2041 acatgaagca gcacgacttc ttcaagtccg ccatgcccga aggctacgtc caggagcgca
     2101 ccatcttctt caaggacgac ggcaactaca agacccgcgc cgaggtgaag ttcgagggcg
     2161 acaccctggt gaaccgcatc gagctgaagg gcatcgactt caaggaggac ggcaacatcc
     2221 tggggcacaa gctggagtac aactacaaca gccacaacgt ctatatcatg gccgacaagc
     2281 agaagaacgg catcaaggtg aacttcaaga tccgccacaa catcgaggac ggcagcgtgc
     2341 agctcgccga ccactaccag cagaacaccc ccatcggcga cggccccgtg ctgctgcccg
     2401 acaaccacta cctgagcacc cagtccgccc tgagcaaaga ccccaacgag aagcgcgatc
     2461 acatggtcct gctggagttc gtgaccgccg ccgggatcac tctcggcatg gacgagctgt
     2521 acaagtagcg gccgcataac ttcgtatagt ataaattata cgaagttata agccttgttt
     2581 gaccgtctca ttccataaac tcgagtttat ggaatgagac ggtctttttt ctcgaggtcg
     2641 acggtatcga taagctcgct tcacgagatc atgtttaagg gttccggttc cactaggtac
     2701 aattcgatat caagcttatc gataatcaac ctctggatta caaaatttgt gaaagattga
     2761 ctggtattct taactatgtt gctcctttta cgctatgtgg atacgctgct ttaatgcctt
     2821 tgtatcatgc tattgcttcc cgtatggctt tcattttctc ctccttgtat aaatcctggt
     2881 tgctgtctct ttatgaggag ttgtggcccg ttgtcaggca acgtggcgtg gtgtgcactg
     2941 tgtttgctga cgcaaccccc actggttggg gcattgccac cacctgtcag ctcctttccg
     3001 ggactttcgc tttccccctc cctattgcca cggcggaact catcgccgcc tgccttgccc
     3061 gctgctggac aggggctcgg ctgttgggca ctgacaattc cgtggtgttg tcggggaaat
     3121 catcgtcctt tccttggctg ctcgcctgtg ttgccacctg gattctgcgc gggacgtcct
     3181 tctgctacgt cccttcggcc ctcaatccag cggaccttcc ttcccgcggc ctgctgccgg
     3241 ctctgcggcc tcttccgcgt cttcgccttc gccctcagac gagtcggatc tccctttggg
     3301 ccgcctcccc gcatcgatac cgtcgacctc gatcgagacc tagaaaaaca tggagcaatc
     3361 acaagtagca atacagcagc taccaatgct gattgtgcct ggctagaagc acaagaggag
     3421 gaggaggtgg gttttccagt cacacctcag gtacctttaa gaccaatgac ttacaaggca
     3481 gctgtagatc ttagccactt tttaaaagaa aaggggggac tggaagggct aattcactcc
     3541 caacgaagac aagatatcct tgatctgtgg atctaccaca cacaaggcta cttccctgat
     3601 tggcagaact acacaccagg gccagggatc agatatccac tgacctttgg atggtgctac
     3661 aagctagtac cagttgagca agagaaggta gaagaagcca atgaaggaga gaacacccgc
     3721 ttgttacacc ctgtgagcct gcatgggatg gatgacccgg agagagaagt attagagtgg
     3781 aggtttgaca gccgcctagc atttcatcac atggcccgag agctgcatcc ggactgtact
     3841 gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca
     3901 ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg
     3961 tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc
     4021 agcatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg
     4081 tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg
     4141 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
     4201 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     4261 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc
     4321 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     4381 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact
     4441 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg
     4501 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt
     4561 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt
     4621 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct
     4681 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg
     4741 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt
     4801 aaatcaatct aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt
     4861 gaggcaccta tctcagcgat ctgtctattt cgttcatcca tagttgcctg actccccgtc
     4921 gtgtagataa ctacgatacg ggagggctta ccatctggcc ccagtgctgc aatgataccg
     4981 cgagacccac gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc
     5041 gagcgcagaa gtggtcctgc aactttatcc gcctccatcc agtctattaa ttgttgccgg
     5101 gaagctagag taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca
     5161 ggcatcgtgg tgtcacgctc gtcgtttggt atggcttcat tcagctccgg ttcccaacga
     5221 tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct
     5281 ccgatcgttg tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg
     5341 cataattctc ttactgtcat gccatccgta agatgctttt ctgtgactgg tgagtactca
     5401 accaagtcat tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata
     5461 cgggataata ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg aaaacgttct
     5521 tcggggcgaa aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact
     5581 cgtgcaccca actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa
     5641 acaggaaggc aaaatgccgc aaaaaaggga ataagggcga cacggaaatg ttgaatactc
     5701 atactcttcc tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga
     5761 tacatatttg aatgtattta gaaaaataaa caaatagggg ttccgcgcac atttccccga
     5821 aaagtgccac ctgacgtcga cggatcggga gatctcccga tcccctatgg tgcactctca
     5881 gtacaatctg ctctgatgcc gcatagttaa gccagtatct gctccctgct tgtgtgttgg
     5941 aggtcgctga gtagtgcgcg agcaaaattt aagctacaac aaggcaaggc ttgaccgaca
     6001 attgcatgaa gaatctgctt agggttaggc gttttgcgct gcttcgcgat gtacgggcca
     6061 gatatacgcg ttgacattga ttattgacta gttattaata gtaatcaatt acggggtcat
     6121 tagttcatag cccatatatg gagttccgcg ttacataact tacggtaaat ggcccgcctg
     6181 gctgaccgcc caacgacccc cgcccattga cgtcaataat gacgtatgtt cccatagtaa
     6241 cgccaatagg gactttccat tgacgtcaat gggtggagta tttacggtaa actgcccact
     6301 tggcagtaca tcaagtgtat catatgccaa gtacgccccc tattgacgtc aatgacggta
     6361 aatggcccgc ctggcattat gcccagtaca tgaccttatg ggactttcct acttggcagt
     6421 acatctacgt attagtcatc gctattacca tggtgatgcg gttttggcag tacatcaatg
     6481 ggcgtggata gcggtttgac tcacggggat ttccaagtct ccaccccatt gacgtcaatg
     6541 ggagtttgtt ttggcaccaa aatcaacggg actttccaaa atgtcgtaac aactccgccc
     6601 cattgacgca aatgggcggt aggcgtgtac ggtgggaggt ctatataagc agcgcgtttt
     6661 gcctgtactg ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta
     6721 gggaacccac tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc
     6781 cgtctgttgt gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa
     6841 atctctagca gtggcgcccg aacagggact tgaaagcgaa agggaaacca gaggagctct
     6901 ctcgacgcag gactcggctt gctgaagcgc gcacggcaag aggcgagggg cggcgactgg
     6961 tgagtacgcc aaaaattttg actagcggag gctagaagga gagagatggg tgcgagagcg
     7021 tcagtattaa gcgggggaga attagatcgc gatgggaaaa aattcggtta aggccagggg
     7081 gaaagaaaaa atataaatta aaacatatag tatgggcaag cagggagcta gaacgattcg
     7141 cagttaatcc tggcctgtta gaaacatcag aaggctgtag acaaatactg ggacagctac
     7201 aaccatccct tcagacagga tcagaagaac ttagatcatt atataataca gtagcaaccc
     7261 tctattgtgt gcatcaaagg atagagataa aagacaccaa ggaagcttta gacaagatag
     7321 aggaagagca aaacaaaagt aagaccaccg cacagcaagc ggccggccgc tgatcttcag
     7381 acctggagga ggagatatga gggacaattg gagaagtgaa ttatataaat ataaagtagt
     7441 aaaaattgaa ccattaggag tagcacccac caaggcaaag agaagagtgg tgcagagaga
     7501 aaaaagagca gtgggaatag gagctttgtt ccttgggttc ttgggagcag caggaagcac
     7561 tatgggcgca gcgtcaatga cgctgacggt acaggccaga
//
