LOCUS       sequence-213637-        6431 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  shRNA negative control.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6431)
  TITLE     Di Giovanni Lab neuroscience plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6431)
  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            "Unpublished"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: pRNATU6.1 HDAC3 shRNA4neg
FEATURES             Location/Qualifiers
     source          1..6431
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     151..170
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        151..169
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        300..548
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     300..320
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     471..490
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     primer_bind     complement(639..656)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     enhancer        709..1012
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        1013..1216
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1167..1187
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     CDS             1261..1977
                     /codon_start=1
                     /product="Aequorea coerulescens GFP"
                     /label=AcGFP1
                     /note="mammalian codon-optimized"
                     /translation="MSKGAELFTGIVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLSYGVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFEDDG
                     NYKSRAEVKFEGDTLVNRIELTGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMIYFG
                     FVTAAAITHGMDELYK"
     polyA_signal    1992..2113
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     rep_origin      2214..2642
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2301..2320)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2511..2532
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2651..2671)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2656..2985
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2836..2971
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     2898..2917
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3052..3846
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(3106..3125)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3716..3735
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4020..4141
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4190..4206)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4190..4206)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4203..4225)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4214..4230
                     /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(4238..4244,4245..4262,4263..4268))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4283..4304
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4421..4438)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4592..5180)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4672..4691)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5351..6142,6143..6211))
                     /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     5974..5993
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6212..6316)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6391..6410)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 tccctgcttg tgtgttggag gtcgctgagt agtgcgcgag caaaatttaa gctacaacaa
       61 ggcaaggctt gaccgacaat tgcatgaaga atctgcttag ggttaggcgt tttgcgctgc
      121 ttcgcgatgt acgggccaga tatacgcgtt taatacgact cactataggg agagagagag
      181 aattaccctc actaaaggga ggagaagcat gaattcccca gtggaaagac gcgcaggcaa
      241 aacgcaccac gtgacggagc gtgaccgcgc gccgagcgcg cgccaaggtc gggcaggaag
      301 agggcctatt tcccatgatt ccttcatatt tgcatatacg atacaaggct gttagagaga
      361 taattagaat taatttgact gtaaacacaa agatattagt acaaaatacg tgacgtagaa
      421 agtaataatt tcttgggtag tttgcagttt taaaattatg ttttaaaatg gactatcata
      481 tgcttaccgt aacttgaaag tatttcgatt tcttgggttt atatatcttg tggaaaggac
      541 gcgggatccc atagttgtac tcgcgtacgg tttgatatcc gaccgtacgc gagtacaact
      601 atttttttcc aaaagcttaa gtttaaaccg ctgatcagcc tcgactgtgc cttctaaata
      661 gtaatcaatt acggggtcat tagttcatag cccatatatg gagttccgcg ttacataact
      721 tacggtaaat ggcccgcctg gctgaccgcc caacgacccc cgcccattga cgtcaataat
      781 gacgtatgtt cccatagtaa cgccaatagg gactttccat tgacgtcaat gggtggagta
      841 tttacggtaa actgcccact tggcagtaca tcaagtgtat catatgccaa gtacgccccc
      901 tattgacgtc aatgacggta aatggcccgc ctggcattat gcccagtaca tgaccttatg
      961 ggactttcct acttggcagt acatctacgt attagtcatc gctattacca tggtgatgcg
     1021 gttttggcag tacatcaatg ggcgtggata gcggtttgac tcacggggat ttccaagtct
     1081 ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa aatcaacggg actttccaaa
     1141 atgtcgtaac aactccgccc cattgacgca aatgggcggt aggcgtgtac ggtgggaggt
     1201 ctatataagc agagctggtt tagtgaaccg tcagatccgc tagcgctacc ggtcgccacc
     1261 atgagcaagg gcgccgagct gttcaccggc atcgtgccca tcctgatcga gctgaatggc
     1321 gatgtgaatg gccacaagtt cagcgtgagc ggcgagggcg agggcgatgc cacctacggc
     1381 aagctgaccc tgaagttcat ctgcaccacc ggcaagctgc ctgtgccctg gcccaccctg
     1441 gtgaccaccc tgagctacgg cgtgcagtgc ttctcacgct accccgatca catgaagcag
     1501 cacgacttct tcaagagcgc catgcctgag ggctacatcc aggagcgcac catcttcttc
     1561 gaggatgacg gcaactacaa gtcgcgcgcc gaggtgaagt tcgagggcga taccctggtg
     1621 aatcgcatcg agctgaccgg caccgatttc aaggaggatg gcaacatcct gggcaataag
     1681 atggagtaca actacaacgc ccacaatgtg tacatcatga ccgacaaggc caagaatggc
     1741 atcaaggtga acttcaagat ccgccacaac atcgaggatg gcagcgtgca gctggccgac
     1801 cactaccagc agaatacccc catcggcgat ggccctgtgc tgctgcccga taaccactac
     1861 ctgtccaccc agagcgccct gtccaaggac cccaacgaga agcgcgatca catgatctac
     1921 ttcggcttcg tgaccgccgc cgccatcacc cacggcatgg atgagctgta caagtgagga
     1981 ctagataact gaacttgttt attgcagctt ataatggtta caaataaagc aatagcatca
     2041 caaatttcac aaataaagca tttttttcac tgcattctag ttgtggtttg tccaaactca
     2101 tcaatgtatc ttatcatgtc tgtgggaaga caatagcagg catgctgggg atgcggtggg
     2161 ctctatggct tctgaggcgg aaagaaccag ctggggctct agggggtatc cccacgcgcc
     2221 ctgtagcggc gcattaagcg cggcgggtgt ggtggttacg cgcagcgtga ccgctacact
     2281 tgccagcgcc ctagcgcccg ctcctttcgc tttcttccct tcctttctcg ccacgttcgc
     2341 cggctttccc cgtcaagctc taaatcgggg gctcccttta gggttccgat ttagtgcttt
     2401 acggcacctc gaccccaaaa aacttgatta gggtgatggt tcacgtagtg ggccatcgcc
     2461 ctgatagacg gtttttcgcc ctttgacgtt ggagtccacg ttctttaata gtggactctt
     2521 gttccaaact ggaacaacac tcaaccctat ctcggtctat tcttttgatt tataagggat
     2581 tttgccgatt tcggcctatt ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa
     2641 ttaattctgt ggaatgtgtg tcagttaggg tgtggaaagt ccccaggctc cccagcaggc
     2701 agaagtatgc aaagcatgca tctcaattag tcagcaacca ggtgtggaaa gtccccaggc
     2761 tccccagcag gcagaagtat gcaaagcatg catctcaatt agtcagcaac catagtcccg
     2821 cccctaactc cgcccatccc gcccctaact ccgcccagtt ccgcccattc tccgccccat
     2881 ggctgactaa ttttttttat ttatgcagag gccgaggccg cctctgcctc tgagctattc
     2941 cagaagtagt gaggaggctt ttttggaggc ctaggctttt gcaaaaagct cccgggagct
     3001 tgtatatcca ttttcggatc tgatcaagag acaggatgag gatcgtttcg catgattgaa
     3061 caagatggat tgcacgcagg ttctccggcc gcttgggtgg agaggctatt cggctatgac
     3121 tgggcacaac agacaatcgg ctgctctgat gccgccgtgt tccggctgtc agcgcagggg
     3181 cgcccggttc tttttgtcaa gaccgacctg tccggtgccc tgaatgaact gcaggacgag
     3241 gcagcgcggc tatcgtggct ggccacgacg ggcgttcctt gcgcagctgt gctcgacgtt
     3301 gtcactgaag cgggaaggga ctggctgcta ttgggcgaag tgccggggca ggatctcctg
     3361 tcatctcacc ttgctcctgc cgagaaagta tccatcatgg ctgatgcaat gcggcggctg
     3421 catacgcttg atccggctac ctgcccattc gaccaccaag cgaaacatcg catcgagcga
     3481 gcacgtactc ggatggaagc cggtcttgtc gatcaggatg atctggacga agagcatcag
     3541 gggctcgcgc cagccgaact gttcgccagg ctcaaggcgc gcatgcccga cggcgaggat
     3601 ctcgtcgtga cccatggcga tgcctgcttg ccgaatatca tggtggaaaa tggccgcttt
     3661 tctggattca tcgactgtgg ccggctgggt gtggcggacc gctatcagga catagcgttg
     3721 gctacccgtg atattgctga agagcttggc ggcgaatggg ctgaccgctt cctcgtgctt
     3781 tacggtatcg ccgctcccga ttcgcagcgc atcgccttct atcgccttct tgacgagttc
     3841 ttctgagcgg gactctgggg ttcgaaatga ccgaccaagc gacgcccaac ctgccatcac
     3901 gagatttcga ttccaccgcc gccttctatg aaaggttggg cttcggaatc gttttccggg
     3961 acgccggctg gatgatcctc cagcgcgggg atctcatgct ggagttcttc gcccacccca
     4021 acttgtttat tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa
     4081 ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt
     4141 atcatgtctg tataccgtcg acctctagct agagcttggc gtaatcatgg tcatagctgt
     4201 ttcctgtgtg aaattgttat ccgctcacaa ttccacacaa catacgagcc ggaagcataa
     4261 agtgtaaagc ctggggtgcc taatgagtga gctaactcac attaattgcg ttgcgctcac
     4321 tgcccgcttt ccagtcggga aacctgtcgt gccagctgca ttaatgaatc ggccaacgcg
     4381 cggggagagg cggtttgcgt attgggcgct cttccgcttc ctcgctcact gactcgctgc
     4441 gctcggtcgt tcggctgcgg cgagcggtat cagctcactc aaaggcggta atacggttat
     4501 ccacagaatc aggggataac gcaggaaaga acatgtgagc aaaaggccag caaaaggcca
     4561 ggaaccgtaa aaaggccgcg ttgctggcgt ttttccatag gctccgcccc cctgacgagc
     4621 atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc
     4681 aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg
     4741 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta
     4801 ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
     4861 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac
     4921 acgacttatc gccactggca gcagccactg gtaacaggat tagcagagcg aggtatgtag
     4981 gcggtgctac agagttcttg aagtggtggc ctaactacgg ctacactaga agaacagtat
     5041 ttggtatctg cgctctgctg aagccagtta ccttcggaaa aagagttggt agctcttgat
     5101 ccggcaaaca aaccaccgct ggtagcggtg gtttttttgt ttgcaagcag cagattacgc
     5161 gcagaaaaaa aggatctcaa gaagatcctt tgatcttttc tacggggtct gacgctcagt
     5221 ggaacgaaaa ctcacgttaa gggattttgg tcatgagatt atcaaaaagg atcttcacct
     5281 agatcctttt aaattaaaaa tgaagtttta aatcaatcta aagtatatat gagtaaactt
     5341 ggtctgacag ttaccaatgc ttaatcagtg aggcacctat ctcagcgatc tgtctatttc
     5401 gttcatccat agttgcctga ctccccgtcg tgtagataac tacgatacgg gagggcttac
     5461 catctggccc cagtgctgca atgataccgc gagacccacg ctcaccggct ccagatttat
     5521 cagcaataaa ccagccagcc ggaagggccg agcgcagaag tggtcctgca actttatccg
     5581 cctccatcca gtctattaat tgttgccggg aagctagagt aagtagttcg ccagttaata
     5641 gtttgcgcaa cgttgttgcc attgctacag gcatcgtggt gtcacgctcg tcgtttggta
     5701 tggcttcatt cagctccggt tcccaacgat caaggcgagt tacatgatcc cccatgttgt
     5761 gcaaaaaagc ggttagctcc ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag
     5821 tgttatcact catggttatg gcagcactgc ataattctct tactgtcatg ccatccgtaa
     5881 gatgcttttc tgtgactggt gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc
     5941 gaccgagttg ctcttgcccg gcgtcaatac gggataatac cgcgccacat agcagaactt
     6001 taaaagtgct catcattgga aaacgttctt cggggcgaaa actctcaagg atcttaccgc
     6061 tgttgagatc cagttcgatg taacccactc gtgcacccaa ctgatcttca gcatctttta
     6121 ctttcaccag cgtttctggg tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa
     6181 taagggcgac acggaaatgt tgaatactca tactcttcct ttttcaatat tattgaagca
     6241 tttatcaggg ttattgtctc atgagcggat acatatttga atgtatttag aaaaataaac
     6301 aaataggggt tccgcgcaca tttccccgaa aagtgccacc tgacgtcgac ggatcgggag
     6361 atctcccgat cccctatggt gcactctcag tacaatctgc tctgatgccg catagttaag
     6421 ccagtatctg c
//
