LOCUS       sequence-386020-        7604 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  conditional knock down TSG101.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7604)
  TITLE     Bordey Lab Plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7604)
  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            "Unpublished"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: pSico-shTsg101
FEATURES             Location/Qualifiers
     source          1..7604
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             337..381
                     /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"
     misc_feature    679..796
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     primer_bind     1086..1106
                     /label=mU6-F
                     /note="Mouse U6 promoter, forward primer"
     protein_bind    complement(1124..1157)
                     /label=loxP511
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATAC) (Shaw et al., 2021). loxP511 sites are 
                     compatible with each other, but incompatible with wild-type
                     loxP sites."
     enhancer        1257..1560
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        1561..1764
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     regulatory      1803..1812
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(1809..1811,1812..1814,1815..2528)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(1809..1811,1812..1814,1815..2525)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(1854..1875)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(2115..2134)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2462..2483
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     protein_bind    complement(2536..2569)
                     /label=loxP511
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATAC) (Shaw et al., 2021). loxP511 sites are 
                     compatible with each other, but incompatible with wild-type
                     loxP sites."
     primer_bind     2637..2653
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     misc_feature    2728..3316
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2781..2801)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3199..3210)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(3319..3335)
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     LTR             3845..4025
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(4087..4675)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4167..4186)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4846..5637,5638..5706))
                     /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     5469..5488
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5707..5811)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(5886..5905)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        6077..6456
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        6458..6656
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     LTR             6674..6854
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6901..7026
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    join(7523..7604,1..152)
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
ORIGIN
        1 caattattgt ctggtatagt gcagcagcag aacaatttgc tgagggctat tgaggcgcaa
       61 cagcatctgt tgcaactcac agtctggggc atcaagcagc tccaggcaag aatcctggct
      121 gtggaaagat acctaaagga tcaacagctc ctggggattt ggggttgctc tggaaaactc
      181 atttgcacca ctgctgtgcc ttggaatgct agttggagta ataaatctct ggaacagatt
      241 tggaatcaca cgacctggat ggagtgggac agagaaatta acaattacac aagcttaata
      301 cactccttaa ttgaagaatc gcaaaaccag caagaaaaga atgaacaaga attattggaa
      361 ttagataaat gggcaagttt gtggaattgg tttaacataa caaattggct gtggtatata
      421 aaattattca taatgatagt aggaggcttg gtaggtttaa gaatagtttt tgctgtactt
      481 tctatagtga atagagttag gcagggatat tcaccattat cgtttcagac ccacctccca
      541 accccgaggg gacccgacag gcccgaagga atagaagaag aaggtggaga gagagacaga
      601 gacagatcca ttcgattagt gaacggatcg gcactgcgtg cgccaattct gcagacaaat
      661 ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca gtgcagggga
      721 aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa aacaaattac
      781 aaaaattcaa aattttcggg tttattacag ggacagcaga gatccagttt ggttagtacc
      841 gggcccgctc tagagatccg acgcgccatc tctaggcccg cgccggcccc ctcgcacaga
      901 cttgtgggag aagctcggct actcccctgc cccggttaat ttgcatataa tatttcctag
      961 taactataga ggcttaatgt gcgataaaag acagataatc tgttcttttt aatactagct
     1021 acattttaca tgataggctt ggatttctat aagagataca aatactaaat tattatttta
     1081 aaaaacagca caaaaggaaa ctcaccctaa ctgtaaagta attataactt cgtatagtat
     1141 aaattatacg aagttataag ccttggtttt ttgaattccg tattaccgcc atgcattagt
     1201 tattaatagt aatcaattac ggggtcatta gttcatagcc catatatgga gttccgcgtt
     1261 acataactta cggtaaatgg cccgcctggc tgaccgccca acgacccccg cccattgacg
     1321 tcaataatga cgtatgttcc catagtaacg ccaataggga ctttccattg acgtcaatgg
     1381 gtggagtatt tacggtaaac tgcccacttg gcagtacatc aagtgtatca tatgccaagt
     1441 acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct ggcattatgc ccagtacatg
     1501 accttatggg actttcctac ttggcagtac atctacgtat tagtcatcgc tattaccatg
     1561 gtgatgcggt tttggcagta catcaatggg cgtggatagc ggtttgactc acggggattt
     1621 ccaagtctcc accccattga cgtcaatggg agtttgtttt ggcaccaaaa tcaacgggac
     1681 tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa tgggcggtag gcgtgtacgg
     1741 tgggaggtct atataagcag agctggttta gtgaaccgtc agatccgcta gcgctaccgg
     1801 tcgccaccat ggtgagcaag ggcgaggagc tgttcaccgg ggtggtgccc atcctggtcg
     1861 agctggacgg cgacgtaaac ggccacaagt tcagcgtgtc cggcgagggc gagggcgatg
     1921 ccacctacgg caagctgacc ctgaagttca tctgcaccac cggcaagctg cccgtgccct
     1981 ggcccaccct cgtgaccacc ctgacctacg gcgtgcagtg cttcagccgc taccccgacc
     2041 acatgaagca gcacgacttc ttcaagtccg ccatgcccga aggctacgtc caggagcgca
     2101 ccatcttctt caaggacgac ggcaactaca agacccgcgc cgaggtgaag ttcgagggcg
     2161 acaccctggt gaaccgcatc gagctgaagg gcatcgactt caaggaggac ggcaacatcc
     2221 tggggcacaa gctggagtac aactacaaca gccacaacgt ctatatcatg gccgacaagc
     2281 agaagaacgg catcaaggtg aacttcaaga tccgccacaa catcgaggac ggcagcgtgc
     2341 agctcgccga ccactaccag cagaacaccc ccatcggcga cggccccgtg ctgctgcccg
     2401 acaaccacta cctgagcacc cagtccgccc tgagcaaaga ccccaacgag aagcgcgatc
     2461 acatggtcct gctggagttc gtgaccgccg ccgggatcac tctcggcatg gacgagctgt
     2521 acaagtagcg gccgcataac ttcgtatagt ataaattata cgaagttata agccttgttt
     2581 gctattgaag acactatctt tctcgagaaa gatagtgtct tcaatagctt ttttctcgag
     2641 gtcgacggta tcgataagct cgcttcacga gatcatgttt aagggttccg gttccactag
     2701 gtacaattcg atatcaagct tatcgataat caacctctgg attacaaaat ttgtgaaaga
     2761 ttgactggta ttcttaacta tgttgctcct tttacgctat gtggatacgc tgctttaatg
     2821 cctttgtatc atgctattgc ttcccgtatg gctttcattt tctcctcctt gtataaatcc
     2881 tggttgctgt ctctttatga ggagttgtgg cccgttgtca ggcaacgtgg cgtggtgtgc
     2941 actgtgtttg ctgacgcaac ccccactggt tggggcattg ccaccacctg tcagctcctt
     3001 tccgggactt tcgctttccc cctccctatt gccacggcgg aactcatcgc cgcctgcctt
     3061 gcccgctgct ggacaggggc tcggctgttg ggcactgaca attccgtggt gttgtcgggg
     3121 aaatcatcgt cctttccttg gctgctcgcc tgtgttgcca cctggattct gcgcgggacg
     3181 tccttctgct acgtcccttc ggccctcaat ccagcggacc ttccttcccg cggcctgctg
     3241 ccggctctgc ggcctcttcc gcgtcttcgc cttcgccctc agacgagtcg gatctccctt
     3301 tgggccgcct ccccgcatcg ataccgtcga cctcgatcga gacctagaaa aacatggagc
     3361 aatcacaagt agcaatacag cagctaccaa tgctgattgt gcctggctag aagcacaaga
     3421 ggaggaggag gtgggttttc cagtcacacc tcaggtacct ttaagaccaa tgacttacaa
     3481 ggcagctgta gatcttagcc actttttaaa agaaaagggg ggactggaag ggctaattca
     3541 ctcccaacga agacaagata tccttgatct gtggatctac cacacacaag gctacttccc
     3601 tgattggcag aactacacac cagggccagg gatcagatat ccactgacct ttggatggtg
     3661 ctacaagcta gtaccagttg agcaagagaa ggtagaagaa gccaatgaag gagagaacac
     3721 ccgcttgtta caccctgtga gcctgcatgg gatggatgac ccggagagag aagtattaga
     3781 gtggaggttt gacagccgcc tagcatttca tcacatggcc cgagagctgc atccggactg
     3841 tactgggtct ctctggttag accagatctg agcctgggag ctctctggct aactagggaa
     3901 cccactgctt aagcctcaat aaagcttgcc ttgagtgctt caagtagtgt gtgcccgtct
     3961 gttgtgtgac tctggtaact agagatccct cagacccttt tagtcagtgt ggaaaatctc
     4021 tagcagcatg tgagcaaaag gccagcaaaa ggccaggaac cgtaaaaagg ccgcgttgct
     4081 ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca
     4141 gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg gaagctccct
     4201 cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct ttctcccttc
     4261 gggaagcgtg gcgctttctc atagctcacg ctgtaggtat ctcagttcgg tgtaggtcgt
     4321 tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgccttatc
     4381 cggtaactat cgtcttgagt ccaacccggt aagacacgac ttatcgccac tggcagcagc
     4441 cactggtaac aggattagca gagcgaggta tgtaggcggt gctacagagt tcttgaagtg
     4501 gtggcctaac tacggctaca ctagaagaac agtatttggt atctgcgctc tgctgaagcc
     4561 agttaccttc ggaaaaagag ttggtagctc ttgatccggc aaacaaacca ccgctggtag
     4621 cggtggtttt tttgtttgca agcagcagat tacgcgcaga aaaaaaggat ctcaagaaga
     4681 tcctttgatc ttttctacgg ggtctgacgc tcagtggaac gaaaactcac gttaagggat
     4741 tttggtcatg agattatcaa aaaggatctt cacctagatc cttttaaatt aaaaatgaag
     4801 ttttaaatca atctaaagta tatatgagta aacttggtct gacagttacc aatgcttaat
     4861 cagtgaggca cctatctcag cgatctgtct atttcgttca tccatagttg cctgactccc
     4921 cgtcgtgtag ataactacga tacgggaggg cttaccatct ggccccagtg ctgcaatgat
     4981 accgcgagac ccacgctcac cggctccaga tttatcagca ataaaccagc cagccggaag
     5041 ggccgagcgc agaagtggtc ctgcaacttt atccgcctcc atccagtcta ttaattgttg
     5101 ccgggaagct agagtaagta gttcgccagt taatagtttg cgcaacgttg ttgccattgc
     5161 tacaggcatc gtggtgtcac gctcgtcgtt tggtatggct tcattcagct ccggttccca
     5221 acgatcaagg cgagttacat gatcccccat gttgtgcaaa aaagcggtta gctccttcgg
     5281 tcctccgatc gttgtcagaa gtaagttggc cgcagtgtta tcactcatgg ttatggcagc
     5341 actgcataat tctcttactg tcatgccatc cgtaagatgc ttttctgtga ctggtgagta
     5401 ctcaaccaag tcattctgag aatagtgtat gcggcgaccg agttgctctt gcccggcgtc
     5461 aatacgggat aataccgcgc cacatagcag aactttaaaa gtgctcatca ttggaaaacg
     5521 ttcttcgggg cgaaaactct caaggatctt accgctgttg agatccagtt cgatgtaacc
     5581 cactcgtgca cccaactgat cttcagcatc ttttactttc accagcgttt ctgggtgagc
     5641 aaaaacagga aggcaaaatg ccgcaaaaaa gggaataagg gcgacacgga aatgttgaat
     5701 actcatactc ttcctttttc aatattattg aagcatttat cagggttatt gtctcatgag
     5761 cggatacata tttgaatgta tttagaaaaa taaacaaata ggggttccgc gcacatttcc
     5821 ccgaaaagtg ccacctgacg tcgacggatc gggagatctc ccgatcccct atggtgcact
     5881 ctcagtacaa tctgctctga tgccgcatag ttaagccagt atctgctccc tgcttgtgtg
     5941 ttggaggtcg ctgagtagtg cgcgagcaaa atttaagcta caacaaggca aggcttgacc
     6001 gacaattgca tgaagaatct gcttagggtt aggcgttttg cgctgcttcg cgatgtacgg
     6061 gccagatata cgcgttgaca ttgattattg actagttatt aatagtaatc aattacgggg
     6121 tcattagttc atagcccata tatggagttc cgcgttacat aacttacggt aaatggcccg
     6181 cctggctgac cgcccaacga cccccgccca ttgacgtcaa taatgacgta tgttcccata
     6241 gtaacgccaa tagggacttt ccattgacgt caatgggtgg agtatttacg gtaaactgcc
     6301 cacttggcag tacatcaagt gtatcatatg ccaagtacgc cccctattga cgtcaatgac
     6361 ggtaaatggc ccgcctggca ttatgcccag tacatgacct tatgggactt tcctacttgg
     6421 cagtacatct acgtattagt catcgctatt accatggtga tgcggttttg gcagtacatc
     6481 aatgggcgtg gatagcggtt tgactcacgg ggatttccaa gtctccaccc cattgacgtc
     6541 aatgggagtt tgttttggca ccaaaatcaa cgggactttc caaaatgtcg taacaactcc
     6601 gccccattga cgcaaatggg cggtaggcgt gtacggtggg aggtctatat aagcagcgcg
     6661 ttttgcctgt actgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta
     6721 actagggaac ccactgctta agcctcaata aagcttgcct tgagtgcttc aagtagtgtg
     6781 tgcccgtctg ttgtgtgact ctggtaacta gagatccctc agaccctttt agtcagtgtg
     6841 gaaaatctct agcagtggcg cccgaacagg gacttgaaag cgaaagggaa accagaggag
     6901 ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg caagaggcga ggggcggcga
     6961 ctggtgagta cgccaaaaat tttgactagc ggaggctaga aggagagaga tgggtgcgag
     7021 agcgtcagta ttaagcgggg gagaattaga tcgcgatggg aaaaaattcg gttaaggcca
     7081 gggggaaaga aaaaatataa attaaaacat atagtatggg caagcaggga gctagaacga
     7141 ttcgcagtta atcctggcct gttagaaaca tcagaaggct gtagacaaat actgggacag
     7201 ctacaaccat cccttcagac aggatcagaa gaacttagat cattatataa tacagtagca
     7261 accctctatt gtgtgcatca aaggatagag ataaaagaca ccaaggaagc tttagacaag
     7321 atagaggaag agcaaaacaa aagtaagacc accgcacagc aagcggccgg ccgctgatct
     7381 tcagacctgg aggaggagat atgagggaca attggagaag tgaattatat aaatataaag
     7441 tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc aaagagaaga gtggtgcaga
     7501 gagaaaaaag agcagtggga ataggagctt tgttccttgg gttcttggga gcagcaggaa
     7561 gcactatggg cgcagcgtca atgacgctga cggtacaggc caga
//
