LOCUS       sequence-362944-        7083 bp    DNA     circular SYN 15-DEC-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 7083)
  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 7083)
  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"; doi: "10.1038/ng.3419"; 
            journalName: "Nat Genet"; date: "2015-11"; volume: "47"; issue: 
            "11"; pages: "1346-51"
COMMENT     Sequence Label: pLKO_FOXA1_#2
FEATURES             Location/Qualifiers
     source          1..7083
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    53..74
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(89..94,95..112,113..119)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    127..143
                     /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     132..154
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     151..167
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     151..167
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     186..206
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        188..206
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        234..460
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             461..641
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    688..813
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1306..1539
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1724..1768
                     /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        2066..2314
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     2066..2086
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     2237..2256
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    2410..2527
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2576..3086
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     3005..3023
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             3108..3707
                     /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(3108..3127)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     3604..3624
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             3835..4068
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    4140..4261
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4177..4196)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4231..4250
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      4301..4436
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(4456..4475)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4457..4475)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(4485..4502)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(4485..4501)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4494..4516)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      4643..5098
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4730..4749)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4940..4961
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5124..5228
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5229..5297,5298..6089)
                     /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(5447..5466)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6260..6848
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6749..6768
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7002..7019
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 gctggcacga caggtttccc gactggaaag cgggcagtga gcgcaacgca attaatgtga
       61 gttagctcac tcattaggca ccccaggctt tacactttat gcttccggct cgtatgttgt
      121 gtggaattgt gagcggataa caatttcaca caggaaacag ctatgaccat gattacgcca
      181 agcgcgcaat taaccctcac taaagggaac aaaagctgga gctgcaagct taatgtagtc
      241 ttatgcaata ctcttgtagt cttgcaacat ggtaacgatg agttagcaac atgccttaca
      301 aggagagaaa aagcaccgtg catgccgatt ggtggaagta aggtggtacg atcgtgcctt
      361 attaggaagg caacagacgg gtctgacatg gattggacga accactgaat tgccgcattg
      421 cagagatatt gtatttaagt gcctagctcg atacataaac gggtctctct ggttagacca
      481 gatctgagcc tgggagctct ctggctaact agggaaccca ctgcttaagc ctcaataaag
      541 cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg tgtgactctg gtaactagag
      601 atccctcaga cccttttagt cagtgtggaa aatctctagc agtggcgccc gaacagggac
      661 ttgaaagcga aagggaaacc agaggagctc tctcgacgca ggactcggct tgctgaagcg
      721 cgcacggcaa gaggcgaggg gcggcgactg gtgagtacgc caaaaatttt gactagcgga
      781 ggctagaagg agagagatgg gtgcgagagc gtcagtatta agcgggggag aattagatcg
      841 cgatgggaaa aaattcggtt aaggccaggg ggaaagaaaa aatataaatt aaaacatata
      901 gtatgggcaa gcagggagct agaacgattc gcagttaatc ctggcctgtt agaaacatca
      961 gaaggctgta gacaaatact gggacagcta caaccatccc ttcagacagg atcagaagaa
     1021 cttagatcat tatataatac agtagcaacc ctctattgtg tgcatcaaag gatagagata
     1081 aaagacacca aggaagcttt agacaagata gaggaagagc aaaacaaaag taagaccacc
     1141 gcacagcaag cggccgctga tcttcagacc tggaggagga gatatgaggg acaattggag
     1201 aagtgaatta tataaatata aagtagtaaa aattgaacca ttaggagtag cacccaccaa
     1261 ggcaaagaga agagtggtgc agagagaaaa aagagcagtg ggaataggag ctttgttcct
     1321 tgggttcttg ggagcagcag gaagcactat gggcgcagcg tcaatgacgc tgacggtaca
     1381 ggccagacaa ttattgtctg gtatagtgca gcagcagaac aatttgctga gggctattga
     1441 ggcgcaacag catctgttgc aactcacagt ctggggcatc aagcagctcc aggcaagaat
     1501 cctggctgtg gaaagatacc taaaggatca acagctcctg gggatttggg gttgctctgg
     1561 aaaactcatt tgcaccactg ctgtgccttg gaatgctagt tggagtaata aatctctgga
     1621 acagatttgg aatcacacga cctggatgga gtgggacaga gaaattaaca attacacaag
     1681 cttaatacac tccttaattg aagaatcgca aaaccagcaa gaaaagaatg aacaagaatt
     1741 attggaatta gataaatggg caagtttgtg gaattggttt aacataacaa attggctgtg
     1801 gtatataaaa ttattcataa tgatagtagg aggcttggta ggtttaagaa tagtttttgc
     1861 tgtactttct atagtgaata gagttaggca gggatattca ccattatcgt ttcagaccca
     1921 cctcccaacc ccgaggggac ccgacaggcc cgaaggaata gaagaagaag gtggagagag
     1981 agacagagac agatccattc gattagtgaa cggatctcga cggtatcgat cacgagacta
     2041 gcctcgagcg gccgccccct tcaccgaggg cctatttccc atgattcctt catatttgca
     2101 tatacgatac aaggctgtta gagagataat tggaattaat ttgactgtaa acacaaagat
     2161 attagtacaa aatacgtgac gtagaaagta ataatttctt gggtagtttg cagttttaaa
     2221 attatgtttt aaaatggact atcatatgct taccgtaact tgaaagtatt tcgatttctt
     2281 ggctttatat atcttgtgga aaggacgaaa caccgggcgt actaccaagg tgtgtatctc
     2341 gagatacaca ccttggtagt acgcttttta attctcgacc tcgagacaaa tggcagtatt
     2401 catccacaat tttaaaagaa aaggggggat tggggggtac agtgcagggg aaagaatagt
     2461 agacataata gcaacagaca tacaaactaa agaattacaa aaacaaatta caaaaattca
     2521 aaattttcgg gtttattaca gggacagcag agatccactt tggccgcggc tcgagggggt
     2581 tggggttgcg ccttttccaa ggcagccctg ggtttgcgca gggacgcggc tgctctgggc
     2641 gtggttccgg gaaacgcagc ggcgccgacc ctgggtctcg cacattcttc acgtccgttc
     2701 gcagcgtcac ccggatcttc gccgctaccc ttgtgggccc cccggcgacg cttcctgctc
     2761 cgcccctaag tcgggaaggt tccttgcggt tcgcggcgtg ccggacgtga caaacggaag
     2821 ccgcacgtct cactagtacc ctcgcagacg gacagcgcca gggagcaatg gcagcgcgcc
     2881 gaccgcgatg ggctgtggcc aatagcggct gctcagcagg gcgcgccgag agcagcggcc
     2941 gggaaggggc ggtgcgggag gcggggtgtg gggcggtagt gtgggccctg ttcctgcccg
     3001 cgcggtgttc cgcattctgc aagcctccgg agcgcacgtc ggcagtcggc tccctcgttg
     3061 accgaatcac cgacctctct ccccaggggg atccaccgga gcttaccatg accgagtaca
     3121 agcccacggt gcgcctcgcc acccgcgacg acgtccccag ggccgtacgc accctcgccg
     3181 ccgcgttcgc cgactacccc gccacgcgcc acaccgtcga tccggaccgc cacatcgagc
     3241 gggtcaccga gctgcaagaa ctcttcctca cgcgcgtcgg gctcgacatc ggcaaggtgt
     3301 gggtcgcgga cgacggcgcc gcggtggcgg tctggaccac gccggagagc gtcgaagcgg
     3361 gggcggtgtt cgccgagatc ggcccgcgca tggccgagtt gagcggttcc cggctggccg
     3421 cgcagcaaca gatggaaggc ctcctggcgc cgcaccggcc caaggagccc gcgtggttcc
     3481 tggccaccgt cggcgtctcg cccgaccacc agggcaaggg tctgggcagc gccgtcgtgc
     3541 tccccggagt ggaggcggcc gagcgcgccg gggtgcccgc cttcctggag acctccgcgc
     3601 cccgcaacct ccccttctac gagcggctcg gcttcaccgt caccgccgac gtcgaggtgc
     3661 ccgaaggacc gcgcacctgg tgcatgaccc gcaagcccgg tgcctgacgc ccgccccacg
     3721 acccgcagcg cccgaccgaa aggagcgcac gaccccatgc atcggtacct ttaagaccaa
     3781 tgacttacaa ggcagctgta gatcttagcc actttttaaa agaaaagggg ggactggaag
     3841 ggctaattca ctcccaacga agacaagatc tgctttttgc ttgtactggg tctctctggt
     3901 tagaccagat ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc
     3961 aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta
     4021 actagagatc cctcagaccc ttttagtcag tgtggaaaat ctctagcagt agtagttcat
     4081 gtcatcttat tattcagtat ttataacttg caaagaaatg aatatcagag agtgagagga
     4141 acttgtttat tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa
     4201 ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt
     4261 atcatgtctg gctctagcta tcccgcccct aactccgccc atcccgcccc taactccgcc
     4321 cagttccgcc cattctccgc cccatggctg actaattttt tttatttatg cagaggccga
     4381 ggccgcctcg gcctctgagc tattccagaa gtagtgagga ggcttttttg gaggcctagg
     4441 gacgtaccca attcgcccta tagtgagtcg tattacgcgc gctcactggc cgtcgtttta
     4501 caacgtcgtg actgggaaaa ccctggcgtt acccaactta atcgccttgc agcacatccc
     4561 cctttcgcca gctggcgtaa tagcgaagag gcccgcaccg atcgcccttc ccaacagttg
     4621 cgcagcctga atggcgaatg ggacgcgccc tgtagcggcg cattaagcgc ggcgggtgtg
     4681 gtggttacgc gcagcgtgac cgctacactt gccagcgccc tagcgcccgc tcctttcgct
     4741 ttcttccctt cctttctcgc cacgttcgcc ggctttcccc gtcaagctct aaatcggggg
     4801 ctccctttag ggttccgatt tagtgcttta cggcacctcg accccaaaaa acttgattag
     4861 ggtgatggtt cacgtagtgg gccatcgccc tgatagacgg tttttcgccc tttgacgttg
     4921 gagtccacgt tctttaatag tggactcttg ttccaaactg gaacaacact caaccctatc
     4981 tcggtctatt cttttgattt ataagggatt ttgccgattt cggcctattg gttaaaaaat
     5041 gagctgattt aacaaaaatt taacgcgaat tttaacaaaa tattaacgct tacaatttag
     5101 gtggcacttt tcggggaaat gtgcgcggaa cccctatttg tttatttttc taaatacatt
     5161 caaatatgta tccgctcatg agacaataac cctgataaat gcttcaataa tattgaaaaa
     5221 ggaagagtat gagtattcaa catttccgtg tcgcccttat tccctttttt gcggcatttt
     5281 gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt
     5341 tgggtgcacg agtgggttac atcgaactgg atctcaacag cggtaagatc cttgagagtt
     5401 ttcgccccga agaacgtttt ccaatgatga gcacttttaa agttctgcta tgtggcgcgg
     5461 tattatcccg tattgacgcc gggcaagagc aactcggtcg ccgcatacac tattctcaga
     5521 atgacttggt tgagtactca ccagtcacag aaaagcatct tacggatggc atgacagtaa
     5581 gagaattatg cagtgctgcc ataaccatga gtgataacac tgcggccaac ttacttctga
     5641 caacgatcgg aggaccgaag gagctaaccg cttttttgca caacatgggg gatcatgtaa
     5701 ctcgccttga tcgttgggaa ccggagctga atgaagccat accaaacgac gagcgtgaca
     5761 ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact attaactggc gaactactta
     5821 ctctagcttc ccggcaacaa ttaatagact ggatggaggc ggataaagtt gcaggaccac
     5881 ttctgcgctc ggcccttccg gctggctggt ttattgctga taaatctgga gccggtgagc
     5941 gtgggtctcg cggtatcatt gcagcactgg ggccagatgg taagccctcc cgtatcgtag
     6001 ttatctacac gacggggagt caggcaacta tggatgaacg aaatagacag atcgctgaga
     6061 taggtgcctc actgattaag cattggtaac tgtcagacca agtttactca tatatacttt
     6121 agattgattt aaaacttcat ttttaattta aaaggatcta ggtgaagatc ctttttgata
     6181 atctcatgac caaaatccct taacgtgagt tttcgttcca ctgagcgtca gaccccgtag
     6241 aaaagatcaa aggatcttct tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa
     6301 caaaaaaacc accgctacca gcggtggttt gtttgccgga tcaagagcta ccaactcttt
     6361 ttccgaaggt aactggcttc agcagagcgc agataccaaa tactgttctt ctagtgtagc
     6421 cgtagttagg ccaccacttc aagaactctg tagcaccgcc tacatacctc gctctgctaa
     6481 tcctgttacc agtggctgct gccagtggcg ataagtcgtg tcttaccggg ttggactcaa
     6541 gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc
     6601 ccagcttgga gcgaacgacc tacaccgaac tgagatacct acagcgtgag ctatgagaaa
     6661 gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa
     6721 caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg
     6781 ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc
     6841 tatggaaaaa cgccagcaac gcggcctttt tacggttcct ggccttttgc tggccttttg
     6901 ctcacatgtt ctttcctgcg ttatcccctg attctgtgga taaccgtatt accgcctttg
     6961 agtgagctga taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg
     7021 aagcggaaga gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat
     7081 gca
//
