LOCUS Exported 8815 bp ds-DNA circular SYN 13-MAY-2021
DEFINITION Tet inducible scrambled shRNA..
ACCESSION .
VERSION .
KEYWORDS Tet-pLKO-puro-Scrambled
SOURCE synthetic DNA construct
ORGANISM synthetic DNA construct
REFERENCE 1 (bases 1 to 8815)
AUTHORS Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS,
Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt
D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S,
Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu
TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB,
Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD,
Brock MV, Seshagiri S
TITLE Comprehensive genomic analysis identifies SOX2 as a frequently
amplified gene in small-cell lung cancer.
JOURNAL Nat Genet. 2012 Oct;44(10):1111-6. doi: 10.1038/ng.2405. Epub 2012
Sep 2.
PUBMED 22941189
REFERENCE 2 (bases 1 to 8815)
AUTHORS .
TITLE Direct Submission
COMMENT SGRef: number: 1; type: "Journal Article"; doi: "10.1038/ng.2405";
journalName: "Nat Genet"; date: "2012-10"; volume: "44"; issue:
"10"; pages: "1111-6"
FEATURES Location/Qualifiers
source 1..8815
/organism="synthetic DNA construct"
/mol_type="other DNA"
primer_bind 258..278
/label=Puro-F
/note="Puromycin resistance gene, forward primer"
LTR 489..722
/label=3 LTR (Delta-U3)
/note="self-inactivating 3 long terminal repeat (LTR) from
HIV-1"
polyA_signal 794..915
/label=SV40 poly(A) signal
/note="SV40 polyadenylation signal"
primer_bind complement(831..850)
/label=SV40pA-R
/note="SV40 polyA, reverse primer"
primer_bind 885..904
/label=EBV-rev
/note="SV40 polyA terminator, reverse primer"
rep_origin 955..1090
/label=SV40 ori
/note="SV40 origin of replication"
primer_bind 1017..1036
/label=SV40pro-F
/note="SV40 promoter/origin, forward primer"
promoter complement(1111..1129)
/label=T7 promoter
/note="promoter for bacteriophage T7 RNA polymerase"
primer_bind complement(1139..1156)
/label=M13 Forward
/note="In lacZ gene. Also called M13-F20 or M13 (-21)
Forward"
primer_bind complement(1139..1155)
/label=M13 fwd
/note="common sequencing primer, one of multiple similar
variants"
primer_bind complement(1148..1170)
/label=M13/pUC Forward
/note="In lacZ gene"
rep_origin 1297..1752
/direction=RIGHT
/label=f1 ori
/note="f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis"
primer_bind complement(1384..1403)
/label=F1ori-R
/note="F1 origin, reverse primer"
primer_bind 1594..1615
/label=F1ori-F
/note="F1 origin, forward primer"
promoter 1778..1882
/gene="bla"
/label=AmpR promoter
CDS 1883..2743
/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(2101..2120)
/label=Amp-R
/note="Ampicillin resistance gene, reverse primer"
rep_origin 2914..3502
/direction=RIGHT
/label=ori
/note="high-copy-number ColE1/pMB1/pBR322/pUC origin of
replication"
primer_bind 3403..3422
/label=pBR322ori-F
/note="pBR322 origin, forward primer"
primer_bind 3656..3673
/label=L4440
/note="L4440 vector, forward primer"
protein_bind 3790..3811
/label=CAP binding site
/bound_moiety="E. coli catabolite activator protein"
/note="CAP binding activates transcription in the presence
of cAMP."
promoter 3826..3856
/label=lac promoter
/note="promoter for the E. coli lac operon"
protein_bind 3864..3880
/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 3869..3891
/label=M13/pUC Reverse
/note="In lacZ gene"
primer_bind 3888..3904
/label=M13 rev
/note="common sequencing primer, one of multiple similar
variants"
primer_bind 3888..3904
/label=M13 Reverse
/note="In lacZ gene. Also called M13-rev"
primer_bind 3923..3943
/label=T3
/note="T3 promoter, forward primer"
promoter 3925..3943
/label=T3 promoter
/note="promoter for bacteriophage T3 RNA polymerase"
promoter 3971..4197
/label=RSV promoter
/note="Rous sarcoma virus enhancer/promoter"
LTR 4198..4378
/label=5 LTR (truncated)
/note="truncated 5 long terminal repeat (LTR) from HIV-1"
misc_feature 4425..4550
/label=HIV-1 Psi
/note="packaging signal of human immunodeficiency virus
type 1"
misc_feature 5043..5276
/label=RRE
/note="The Rev response element (RRE) of HIV-1 allows for
Rev-dependent mRNA export from the nucleus to the
cytoplasm."
CDS 5461..5505
/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 5794..5888
/label=H1-2O2 promoter
/note="doxycycline-inducible variant of the human H1 RNA
promoter (Henriksen et al., 2007)"
primer_bind 5805..5824
/label=H1
/note="Human H1 promoter, forward primer"
protein_bind 5842..5860
/gene="tetO"
/label=tet operator
/bound_moiety="tetracycline repressor TetR"
/note="bacterial operator O2 for the tetR and tetA genes"
protein_bind 5870..5888
/gene="tetO"
/label=tet operator
/bound_moiety="tetracycline repressor TetR"
/note="bacterial operator O2 for the tetR and tetA genes"
misc_feature 5988..6105
/label=cPPT/CTS
/note="central polypurine tract and central termination
sequence of HIV-1"
promoter 6154..6664
/label=hPGK promoter
/note="human phosphoglycerate kinase 1 promoter"
primer_bind 6583..6601
/label=hPGK-F
/note="Human PGK promoter, forward primer"
intron 6673..7245
/label=beta-globin intron
/note="intron from rabbit beta-globin gene"
primer_bind 7253..7272
/label=pCAG-F
/note="Rabbit beta-globin intron, for pCAG plasmids,
forward primer"
promoter 7300..7318
/label=T7 promoter
/note="promoter for bacteriophage T7 RNA polymerase"
CDS 7329..7946
/codon_start=1
/gene="tetR from transposon Tn10"
/product="tetracycline repressor TetR"
/label=TetR
/note="TetR binds to the tetracycline operator tetO to
inhibit transcription. This inhibition can be relieved by
adding tetracycline or doxycycline."
/translation="MSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHV
KNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTR
PTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTT
DSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESG"
primer_bind complement(7402..7421)
/label=Tet-R
/note="Tetracycline resistance gene, reverse primer"
misc_feature 7984..8557
/label=IRES
/note="internal ribosome entry site (IRES) of the
encephalomyocarditis virus (EMCV)"
primer_bind complement(8151..8168)
/label=IRES reverse
/note="IRES internal ribosome entry site, reverse primer.
Also called pCDH-rev"
primer_bind 8378..8397
/label=IRES-F
/note="IRES internal ribosome entry site, forward primer"
CDS join(8577..8815,1..361)
/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(8577..8596)
/label=Puro-R
/note="Puromycin resistance gene, reverse primer. Also
called puro-variant-R"
