LOCUS       sequence-439163-        7453 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Retroviral expression vector for an shScramble.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7453)
  AUTHORS   Sweatt AJ, Griffiths CD, Groves SM, Paudel BB, Wang L, Kashatus DF, 
            Janes KA
  TITLE     Proteome-wide copy-number estimation from transcriptomics.
  JOURNAL   Mol Syst Biol. 2024 Sep 27. doi: 10.1038/s44320-024-00064-3.
  PUBMED    39333715
REFERENCE   2  (bases 1 to 7453)
  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: "Mol Syst 
            Biol. 2024 Sep 27. doi: 10.1038/s44320-024-00064-3."
COMMENT     Sequence Label: pSuperior.retro.neo GFP shScramble
FEATURES             Location/Qualifiers
     source          1..7453
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     misc_feature    579..920
                     /label=MESV Psi
                     /note="packaging signal of murine embryonic stem cell 
                     virus"
     CDS             987..1403
                     /label=gag (truncated)
                     /note="truncated Moloney murine leukemia virus (MMLV) gag 
                     gene lacking the start codon"
     primer_bind     1333..1355
                     /label=pLXSN 5'
                     /note="Murine stem cell virus, forward primer. Also called 
                     MSCV"
     primer_bind     1371..1387
                     /label=pBABE 5'
                     /note="Psi packaging signal, forward primer for pBABE 
                     vectors"
     primer_bind     1421..1437
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     primer_bind     1422..1438
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    1508..1526
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     primer_bind     complement(1572..1591)
                     /label=H1
                     /note="Human H1 promoter, forward primer"
     promoter        1737..2240
                     /label=PGK promoter
                     /note="mouse phosphoglycerate kinase 1 promoter"
     primer_bind     complement(1772..1795)
                     /label=MSCV-rev
                     /note="Murine stem cell virus, reverse primer"
     primer_bind     2173..2192
                     /label=mPGK-F
                     /note="Mouse PGK promoter, forward primer"
     regulatory      2269..2278
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(2275..2277,2278..2280,2281..2991)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(2275..2277,2278..2280,2281..2991)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(2320..2341)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(2581..2600)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2928..2949
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     CDS             3055..3849
                     /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(3109..3128)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3719..3738
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    3913..3961
                     /note="synthetic polyadenylation signal"
     protein_bind    4522..4538
                     /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(4546..4552,4553..4570,4571..4576))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4591..4612
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4729..4746)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4900..5488)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4980..4999)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5659..6450,6451..6519))
                     /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     6282..6301
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6520..6624)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     6692..6710
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     primer_bind     complement(6748..6770)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     6870..6889
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     7083..7105
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     7233..7252
                     /label=pBRrevBam
                     /note="pBR322 vectors, tet region, downstream of BamHI, 
                     reverse primer"
     LTR             join(7452..7453,1..515)
                     /label=5' LTR
                     /note="5' long terminal repeat from murine embryonic stem 
                     cell virus"
ORIGIN
        1 tgaaagaccc cacctgtagg tttggcaagc tagcttaagt aacgccattt tgcaaggcat
       61 ggaaaataca taactgagaa tagagaagtt cagatcaagg ttaggaacag agagacagca
      121 gaatatgggc caaacaggat atctgtggta agcagttcct gccccggctc agggccaaga
      181 acagatggtc cccagatgcg gtcccgccct cagcagtttc tagagaacca tcagatgttt
      241 ccagggtgcc ccaaggacct gaaatgaccc tgtgccttat ttgaactaac caatcagttc
      301 gcttctcgct tctgttcgcg cgcttctgct ccccgagctc aataaaagag cccacaaccc
      361 ctcactcggc gcgccagtcc tccgatagac tgcgtcgccc gggtacccgt attcccaata
      421 aagcctcttg ctgtttgcat ccgaatcgtg gactcgctga tccttgggag ggtctcctca
      481 gattgattga ctgcccacct cgggggtctt tcatttggag gttccaccga gatttggaga
      541 cccctgccca gggaccaccg acccccccgc cgggaggtaa gctggccagc ggtcgtttcg
      601 tgtctgtctc tgtctttgtg cgtgtttgtg ccggcatcta atgtttgcgc ctgcgtctgt
      661 actagttagc taactagctc tgtatctggc ggacccgtgg tggaactgac gagttctgaa
      721 cacccggccg caaccctggg agacgtccca gggactttgg gggccgtttt tgtggcccga
      781 cctgaggaag ggagtcgatg tggaatccga ccccgtcagg atatgtggtt ctggtaggag
      841 acgagaacct aaaacagttc ccgcctccgt ctgaattttt gctttcggtt tggaaccgaa
      901 gccgcgcgtc ttgtctgctg cagcgctgca gcatcgttct gtgttgtctc tgtctgactg
      961 tgtttctgta tttgtctgaa aattagggcc agactgttac cactccctta agtttgacct
     1021 taggtcactg gaaagatgtc gagcggatcg ctcacaacca gtcggtagat gtcaagaaga
     1081 gacgttgggt taccttctgc tctgcagaat ggccaacctt taacgtcgga tggccgcgag
     1141 acggcacctt taaccgagac ctcatcaccc aggttaagat caaggtcttt tcacctggcc
     1201 cgcatggaca cccagaccag gtcccctaca tcgtgacctg ggaagccttg gcttttgacc
     1261 cccctccctg ggtcaagccc tttgtacacc ctaagcctcc gcctcctctt cctccatccg
     1321 ccccgtctct cccccttgaa cctcctcgtt cgaccccgcc tcgatcctcc ctttatccag
     1381 ccctcactcc ttctctaggc gccggaatta gatcgatctc tcgaggtcga cggtatcgat
     1441 aagcttaaaa agaaccggat tatactacag gttctcttga aacctgtagt ataatccggt
     1501 tcggggatct ctatcactga tagggaactt ataagattcc caaatccaaa gacatttcac
     1561 gtttatggtg atttcccaga acacatagcg acatgcaaat attgcagggc gccactcccc
     1621 tgtccctcac agccatcttc ctgccagggc gcacgcgcgc tgggtgttcc cgcctagtga
     1681 cactgggccc gcgattcctt ggagcgggtt gatgacgtca gcgttcgaat tctaccgggt
     1741 aggggaggcg cttttcccaa ggcagtctgg agcatgcgct ttagcagccc cgctgggcac
     1801 ttggcgctac acaagtggcc tctggcctcg cacacattcc acatccaccg gccggtaggc
     1861 gccaaccggc tccgttcttt ggtggcccct tcgcgccacc ttctactcct cccctagtca
     1921 ggaagttccc ccccgccccg cagctcgcgt cgtgcaggac gtgacaaatg gaagtagcac
     1981 gtctcactag tctcgtgcag atggacagca ccgctgagca atggaagcgg gtaggccttt
     2041 ggggcagcgg ccaatagcag ctttgctcct tcgctttctg ggctcagagg ctgggaaggg
     2101 gtgggtccgg gggcgggctc aggggcgggc tcaggggcgg ggcgggcgcc cgaaggtcct
     2161 ccggaggccc ggcattctgc acgcttcaaa agcgcacgtc tgccgcgctg ttctcctctt
     2221 cctcatctcc gggcctttcg acctgcagcc caagctagct taccggtcgc caccatggtg
     2281 agcaagggcg aggagctgtt caccggggtg gtgcccatcc tggtcgagct ggacggcgac
     2341 gtaaacggcc acaagttcag cgtgtccggc gagggcgagg gcgatgccac ctacggcaag
     2401 ctgaccctga agttcatctg caccaccggc aagctgcccg tgccctggcc caccctcgtg
     2461 accaccctga cctacggcgt gcagtgcttc agccgctacc ccgaccacat gaagcagcac
     2521 gacttcttca agtccgccat gcccgaaggc tacgtccagg agcgcaccat cttcttcaag
     2581 gacgacggca actacaagac ccgcgccgag gtgaagttcg agggcgacac cctggtgaac
     2641 cgcatcgagc tgaagggcat cgacttcaag gaggacggca acatcctggg gcacaagctg
     2701 gagtacaact acaacagcca caacgtctat atcatggccg acaagcagaa gaacggcatc
     2761 aaggtgaact tcaagatccg ccacaacatc gaggacggca gcgtgcagct cgccgaccac
     2821 taccagcaga acacccccat cggcgacggc cccgtgctgc tgcccgacaa ccactacctg
     2881 agcacccagt ccgccctgag caaagacccc aacgagaagc gcgatcacat ggtcctgctg
     2941 gagttcgtga ccgccgccgg gatcactctc ggcatggacg agctgtacaa gtccggactc
     3001 agatcagctt gattcttctg acacaacagt ctcgaactta aggctagagc caccatgatt
     3061 gaacaagatg gattgcacgc aggttctccg gccgcttggg tggagaggct attcggctat
     3121 gactgggcac aacagacaat cggctgctct gatgccgccg tgttccggct gtcagcgcag
     3181 gggcgcccgg ttctttttgt caagaccgac ctgtccggtg ccctgaatga actgcaggac
     3241 gaggcagcgc ggctatcgtg gctggccacg acgggcgttc cttgcgcagc tgtgctcgac
     3301 gttgtcactg aagcgggaag ggactggctg ctattgggcg aagtgccggg gcaggatctc
     3361 ctgtcatctc accttgctcc tgccgagaaa gtatccatca tggctgatgc aatgcggcgg
     3421 ctgcatacgc ttgatccggc tacctgccca ttcgaccacc aagcgaaaca tcgcatcgag
     3481 cgagcacgta ctcggatgga agccggtctt gtcgatcagg atgatctgga cgaagagcat
     3541 caggggctcg cgccagccga actgttcgcc aggctcaagg cgcgcatgcc cgacggcgag
     3601 gatctcgtcg tgacccatgg cgatgcctgc ttgccgaata tcatggtgga aaatggccgc
     3661 ttttctggat tcatcgactg tggccggctg ggtgtggcgg accgctatca ggacatagcg
     3721 ttggctaccc gtgatattgc tgaagagctt ggcggcgaat gggctgaccg cttcctcgtg
     3781 ctttacggta tcgccgctcc cgattcgcag cgcatcgcct tctatcgcct tcttgacgag
     3841 ttcttctgag cgggactctg gggttcgaaa tgaccgacca agcgacgccc aacctgccat
     3901 cacgatggcc gcaataaaat atctttattt tcattacatc tgtgtgttgg ttttttgtgt
     3961 gaatcgatag cgataaggat cggggatgca tcgataaaat aaaagatttt atttagtctc
     4021 cagaaaaagg ggggaatgaa agaccccacc tgtaggtttg gcaagctaga gaaccatcag
     4081 atgtttccag ggtgccccaa ggacctgaaa tgaccctgtg ccttatttga actaaccaat
     4141 cagttcgctt ctcgcttctg ttcgcgcgct tctgctcccc gagctcaata aaagagccca
     4201 caacccctca ctcggcgcgc cagtcctccg atagactgcg tcgcccgggt acccgtgtat
     4261 ccaataaacc ctcttgcagt tgcatccgac ttgtggtctc gctgttcctt gggagggtct
     4321 cctctgagtg attgactacc cgtcagcggg ggtctttcat gggtaacagt ttcttgaagt
     4381 tggagaacaa cattctgagg gtaggagtcg aatattaagt aatcctgact caattagcca
     4441 ctgttttgaa tccacatact ccaatactcc tgaaatagtt cattatggac agcgcagaaa
     4501 gagctgggga gaattgtgaa attgttatcc gctcacaatt ccacacaaca tacgagccgg
     4561 aagcataaag tgtaaagcct ggggtgccta atgagtgagc taactcacat taattgcgtt
     4621 gcgctcactg cccgctttcc agtcgggaaa cctgtcgtgc cagctgcatt aatgaatcgg
     4681 ccaacgcgcg gggagaggcg gtttgcgtat tgggcgctct tccgcttcct cgctcactga
     4741 ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca gctcactcaa aggcggtaat
     4801 acggttatcc acagaatcag gggataacgc aggaaagaac atgtgagcaa aaggccagca
     4861 aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc
     4921 tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata
     4981 aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc
     5041 gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
     5101 acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga
     5161 accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc
     5221 ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag
     5281 gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag
     5341 aacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag
     5401 ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca
     5461 gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga
     5521 cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat
     5581 cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga
     5641 gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg
     5701 tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga
     5761 gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc
     5821 agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac
     5881 tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc
     5941 agttaatagt ttgcgcaacg ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc
     6001 gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc
     6061 catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt
     6121 ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc
     6181 atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg
     6241 tatgcggcga ccgagttgct cttgcccggc gtcaatacgg gataataccg cgccacatag
     6301 cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat
     6361 cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc
     6421 atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa
     6481 aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta
     6541 ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa
     6601 aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtctaaga
     6661 aaccattatt atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct
     6721 cgcgcgtttc ggtgatgacg gtgaaaacct ctgacacatg cagctcccgg agacggtcac
     6781 agcttgtctg taagcggatg ccgggagcag acaagcccgt cagggcgcgt cagcgggtgt
     6841 tggcgggtgt cggggctggc ttaactatgc ggcatcagag cagattgtac tgagagtgca
     6901 ccatatgcgg tgtgaaatac cgcacagatg cgtaaggaga aaataccgca tcaggcgcca
     6961 ttcgccattc aggctgcgca actgttggga agggcgatcg gtgcgggcct cttcgctatt
     7021 acgccagctg gcgaaagggg gatgtgctgc aaggcgatta agttgggtaa cgccagggtt
     7081 ttcccagtca cgacgttgta aaacgacggc gcaaggaatg gtgcatgcaa ggagatggcg
     7141 cccaacagtc ccccggccac ggggcctgcc accataccca cgccgaaaca agcgctcatg
     7201 agcccgaagt ggcgagcccg atcttcccca tcggtgatgt cggcgatata ggcgccagca
     7261 accgcacctg tggcgccggt gatgccggcc acgatgcgtc cggcgtagag gcgattagtc
     7321 caatttgtta aagacaggat atcagtggtc caggctctag ttttgactca acaatatcac
     7381 cagctgaagc ctatagagta cgagccatag ataaaataaa agattttatt tagtctccag
     7441 aaaaaggggg gaa
//
