LOCUS       sequence-307447-        7518 bp    DNA     circular SYN 14-APR-2025
DEFINITION  Expression of shRNA to human FOXA1, puromycin selection.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7518)
  AUTHORS   Pomerantz MM, Li F, Takeda DY, Lenci R, Chonkar A, Chabot M, Cejas 
            P, Vazquez F, Cook J, Shivdasani RA, Bowden M, Lis R, Hahn WC, 
            Kantoff PW, Brown M, Loda M, Long HW, Freedman ML
  TITLE     The androgen receptor cistrome is extensively reprogrammed in human 
            prostate tumorigenesis.
  JOURNAL   Nat Genet. 2015 Nov;47(11):1346-51. doi: 10.1038/ng.3419. Epub 2015 
            Oct 12.
  PUBMED    26457646
REFERENCE   2  (bases 1 to 7518)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Apr 14, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; doi: "10.1038/ng.3419"; 
            journalName: "Nat Genet"; date: "2015-11"; volume: "47"; issue: 
            "11"; pages: "1346-51"
COMMENT     Sequence Label: pLKO_FOXA1_#1
FEATURES             Location/Qualifiers
     source          1..7518
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     misc_feature    21..254
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             439..483
                     /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"
     promoter        661..909
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     661..681
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     832..851
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    1006..1123
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1172..1682
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1601..1619
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1704..2303
                     /codon_start=1
                     /gene="pac from Streptomyces alboniger"
                     /product="puromycin N-acetyltransferase"
                     /label=PuroR
                     /note="confers resistance to puromycin"
                     /translation="MTEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIER
                     VTELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLA
                     AQQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETS
                     APRNLPFYERLGFTVTADVEVPEGPRTWCMTRKPGA"
     primer_bind     complement(1704..1723)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     2200..2220
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     misc_feature    2319..2907
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2372..2392)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2790..2801)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             2979..3212
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    3290..3411
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3327..3346)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3381..3400
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      3451..3586
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(3606..3625)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3607..3625)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3635..3652)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(3635..3651)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3644..3666)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3793..4248
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3880..3899)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4090..4111
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        4274..4378
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4379..4447,4448..5239)
                     /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     complement(4597..4616)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5410..5998
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5899..5918
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     6152..6169
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    6286..6307
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(6322..6327,6328..6345,6346..6352)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6360..6376
                     /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)."
     primer_bind     6365..6387
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     6384..6400
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     6384..6400
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     6419..6439
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        6421..6439
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        6467..6693
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             6694..6874
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6921..7046
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
ORIGIN
        1 gaaaaaagag cagtgggaat aggagctttg ttccttgggt tcttgggagc agcaggaagc
       61 actatgggcg cagcgtcaat gacgctgacg gtacaggcca gacaattatt gtctggtata
      121 gtgcagcagc agaacaattt gctgagggct attgaggcgc aacagcatct gttgcaactc
      181 acagtctggg gcatcaagca gctccaggca agaatcctgg ctgtggaaag atacctaaag
      241 gatcaacagc tcctggggat ttggggttgc tctggaaaac tcatttgcac cactgctgtg
      301 ccttggaatg ctagttggag taataaatct ctggaacaga tttggaatca cacgacctgg
      361 atggagtggg acagagaaat taacaattac acaagcttaa tacactcctt aattgaagaa
      421 tcgcaaaacc agcaagaaaa gaatgaacaa gaattattgg aattagataa atgggcaagt
      481 ttgtggaatt ggtttaacat aacaaattgg ctgtggtata taaaattatt cataatgata
      541 gtaggaggct tggtaggttt aagaatagtt tttgctgtac tttctatagt gaatagagtt
      601 aggcagggat attcaccatt atcgtttcag acccacctcc caaccccgag gggacccaga
      661 gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
      721 ataattagaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
      781 aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat ggactatcat
      841 atgcttaccg taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
      901 cgaggtaccg gtctagtttg tggagggtta ttctcgagaa taaccctcca caaactagat
      961 ttttgaattc tagatcttga gacaaatggc agtattcatc cacaatttta aaagaaaagg
     1021 ggggattggg gggtacagtg caggggaaag aatagtagac ataatagcaa cagacataca
     1081 aactaaagaa ttacaaaaac aaattacaaa aattcaaaat tttcgggttt attacaggga
     1141 cagcagagat ccactttggc gccggctcga gggggcccgg gttgcgcctt ttccaaggca
     1201 gccctgggtt tgcgcaggga cgcggctgct ctgggcgtgg ttccgggaaa cgcagcggcg
     1261 ccgaccctgg gtctcgcaca ttcttcacgt ccgttcgcag cgtcacccgg atcttcgccg
     1321 ctacccttgt gggccccccg gcgacgcttc ctgctccgcc cctaagtcgg gaaggttcct
     1381 tgcggttcgc ggcgtgccgg acgtgacaaa cggaagccgc acgtctcact agtaccctcg
     1441 cagacggaca gcgccaggga gcaatggcag cgcgccgacc gcgatgggct gtggccaata
     1501 gcggctgctc agcagggcgc gccgagagca gcggccggga aggggcggtg cgggaggcgg
     1561 ggtgtggggc ggtagtgtgg gccctgttcc tgcccgcgcg gtgttccgca ttctgcaagc
     1621 ctccggagcg cacgtcggca gtcggctccc tcgttgaccg aatcaccgac ctctctcccc
     1681 agggggatcc accggagctt accatgaccg agtacaagcc cacggtgcgc ctcgccaccc
     1741 gcgacgacgt ccccagggcc gtacgcaccc tcgccgccgc gttcgccgac taccccgcca
     1801 cgcgccacac cgtcgatccg gaccgccaca tcgagcgggt caccgagctg caagaactct
     1861 tcctcacgcg cgtcgggctc gacatcggca aggtgtgggt cgcggacgac ggcgccgccg
     1921 tggcggtctg gaccacgccg gagagcgtcg aagcgggggc ggtgttcgcc gagatcggcc
     1981 cgcgcatggc cgagttgagc ggttcccggc tggccgcgca gcaacagatg gaaggcctcc
     2041 tggcgccgca ccggcccaag gagcccgcgt ggttcctggc caccgtcggc gtctcgcccg
     2101 accaccaggg caagggtctg ggcagcgccg tcgtgctccc cggagtggag gcggccgagc
     2161 gcgccggggt gcccgccttc ctggagacct ccgcgccccg caacctcccc ttctacgagc
     2221 ggctcggctt caccgtcacc gccgacgtcg aggtgcccga aggaccgcgc acctggtgca
     2281 tgacccgcaa gcccggtgcc tgaacgcgtt aagtcgacaa tcaacctctg gattacaaaa
     2341 tttgtgaaag attgactggt attcttaact atgttgctcc ttttacgcta tgtggatacg
     2401 ctgctttaat gcctttgtat catgctattg cttcccgtat ggctttcatt ttctcctcct
     2461 tgtataaatc ctggttgctg tctctttatg aggagttgtg gcccgttgtc aggcaacgtg
     2521 gcgtggtgtg cactgtgttt gctgacgcaa cccccactgg ttggggcatt gccaccacct
     2581 gtcagctcct ttccgggact ttcgctttcc ccctccctat tgccacggcg gaactcatcg
     2641 ccgcctgcct tgcccgctgc tggacagggg ctcggctgtt gggcactgac aattccgtgg
     2701 tgttgtcggg gaaatcatcg tcctttcctt ggctgctcgc ctgtgttgcc acctggattc
     2761 tgcgcgggac gtccttctgc tacgtccctt cggccctcaa tccagcggac cttccttccc
     2821 gcggcctgct gccggctctg cggcctcttc cgcgtcttcg ccttcgccct cagacgagtc
     2881 ggatctccct ttgggccgcc tccccgcgtc gactttaaga ccaatgactt acaaggcagc
     2941 tgtagatctt agccactttt taaaagaaaa ggggggactg gaagggctaa ttcactccca
     3001 acgaagacaa gatctgcttt ttgcttgtac tgggtctctc tggttagacc agatctgagc
     3061 ctgggagctc tctggctaac tagggaaccc actgcttaag cctcaataaa gcttgccttg
     3121 agtgcttcaa gtagtgtgtg cccgtctgtt gtgtgactct ggtaactaga gatccctcag
     3181 acccttttag tcagtgtgga aaatctctag cagtacgtat agtagttcat gtcatcttat
     3241 tattcagtat ttataacttg caaagaaatg aatatcagag agtgagagga acttgtttat
     3301 tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa ataaagcatt
     3361 tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg
     3421 gctctagcta tcccgcccct aactccgccc atcccgcccc taactccgcc cagttccgcc
     3481 cattctccgc cccatggctg actaattttt tttatttatg cagaggccga ggccgcctcg
     3541 gcctctgagc tattccagaa gtagtgagga ggcttttttg gaggcctagg gacgtaccca
     3601 attcgcccta tagtgagtcg tattacgcgc gctcactggc cgtcgtttta caacgtcgtg
     3661 actgggaaaa ccctggcgtt acccaactta atcgccttgc agcacatccc cctttcgcca
     3721 gctggcgtaa tagcgaagag gcccgcaccg atcgcccttc ccaacagttg cgcagcctga
     3781 atggcgaatg ggacgcgccc tgtagcggcg cattaagcgc ggcgggtgtg gtggttacgc
     3841 gcagcgtgac cgctacactt gccagcgccc tagcgcccgc tcctttcgct ttcttccctt
     3901 cctttctcgc cacgttcgcc ggctttcccc gtcaagctct aaatcggggg ctccctttag
     3961 ggttccgatt tagtgcttta cggcacctcg accccaaaaa acttgattag ggtgatggtt
     4021 cacgtagtgg gccatcgccc tgatagacgg tttttcgccc tttgacgttg gagtccacgt
     4081 tctttaatag tggactcttg ttccaaactg gaacaacact caaccctatc tcggtctatt
     4141 cttttgattt ataagggatt ttgccgattt cggcctattg gttaaaaaat gagctgattt
     4201 aacaaaaatt taacgcgaat tttaacaaaa tattaacgct tacaatttag gtggcacttt
     4261 tcggggaaat gtgcgcggaa cccctatttg tttatttttc taaatacatt caaatatgta
     4321 tccgctcatg agacaataac cctgataaat gcttcaataa tattgaaaaa ggaagagtat
     4381 gagtattcaa catttccgtg tcgcccttat tccctttttt gcggcatttt gccttcctgt
     4441 ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt tgggtgcacg
     4501 agtgggttac atcgaactgg atctcaacag cggtaagatc cttgagagtt ttcgccccga
     4561 agaacgtttt ccaatgatga gcacttttaa agttctgcta tgtggcgcgg tattatcccg
     4621 tattgacgcc gggcaagagc aactcggtcg ccgcatacac tattctcaga atgacttggt
     4681 tgagtactca ccagtcacag aaaagcatct tacggatggc atgacagtaa gagaattatg
     4741 cagtgctgcc ataaccatga gtgataacac tgcggccaac ttacttctga caacgatcgg
     4801 aggaccgaag gagctaaccg cttttttgca caacatgggg gatcatgtaa ctcgccttga
     4861 tcgttgggaa ccggagctga atgaagccat accaaacgac gagcgtgaca ccacgatgcc
     4921 tgtagcaatg gcaacaacgt tgcgcaaact attaactggc gaactactta ctctagcttc
     4981 ccggcaacaa ttaatagact ggatggaggc ggataaagtt gcaggaccac ttctgcgctc
     5041 ggcccttccg gctggctggt ttattgctga taaatctgga gccggtgagc gtgggtctcg
     5101 cggtatcatt gcagcactgg ggccagatgg taagccctcc cgtatcgtag ttatctacac
     5161 gacggggagt caggcaacta tggatgaacg aaatagacag atcgctgaga taggtgcctc
     5221 actgattaag cattggtaac tgtcagacca agtttactca tatatacttt agattgattt
     5281 aaaacttcat ttttaattta aaaggatcta ggtgaagatc ctttttgata atctcatgac
     5341 caaaatccct taacgtgagt tttcgttcca ctgagcgtca gaccccgtag aaaagatcaa
     5401 aggatcttct tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa caaaaaaacc
     5461 accgctacca gcggtggttt gtttgccgga tcaagagcta ccaactcttt ttccgaaggt
     5521 aactggcttc agcagagcgc agataccaaa tactgttctt ctagtgtagc cgtagttagg
     5581 ccaccacttc aagaactctg tagcaccgcc tacatacctc gctctgctaa tcctgttacc
     5641 agtggctgct gccagtggcg ataagtcgtg tcttaccggg ttggactcaa gacgatagtt
     5701 accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga
     5761 gcgaacgacc tacaccgaac tgagatacct acagcgtgag ctatgagaaa gcgccacgct
     5821 tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg
     5881 cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca
     5941 cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa
     6001 cgccagcaac gcggcctttt tacggttcct ggccttttgc tggccttttg ctcacatgtt
     6061 ctttcctgcg ttatcccctg attctgtgga taaccgtatt accgcctttg agtgagctga
     6121 taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga
     6181 gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca
     6241 cgacaggttt cccgactgga aagcgggcag tgagcgcaac gcaattaatg tgagttagct
     6301 cactcattag gcaccccagg ctttacactt tatgcttccg gctcgtatgt tgtgtggaat
     6361 tgtgagcgga taacaatttc acacaggaaa cagctatgac catgattacg ccaagcgcgc
     6421 aattaaccct cactaaaggg aacaaaagct ggagctgcaa gcttaatgta gtcttatgca
     6481 atactcttgt agtcttgcaa catggtaacg atgagttagc aacatgcctt acaaggagag
     6541 aaaaagcacc gtgcatgccg attggtggaa gtaaggtggt acgatcgtgc cttattagga
     6601 aggcaacaga cgggtctgac atggattgga cgaaccactg aattgccgca ttgcagagat
     6661 attgtattta agtgcctagc tcgatacata aacgggtctc tctggttaga ccagatctga
     6721 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
     6781 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
     6841 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
     6901 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
     6961 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
     7021 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
     7081 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
     7141 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
     7201 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     7261 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     7321 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     7381 aagcggccgc tgatcttcag acctggagga ggagatatga gggacaattg gagaagtgaa
     7441 ttatataaat ataaagtagt aaaaattgaa ccattaggag tagcacccac caaggcaaag
     7501 agaagagtgg tgcagaga
//
