LOCUS       sequence-383903-        6242 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses shRNA to knockdown mouse Syndecan-1.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6242)
  AUTHORS   Bray ER, Yungher BJ, Levay K, Ribeiro M, Dvoryanchikov G, Ayupe AC, 
            Thakor K, Marks V, Randolph M, Danzi MC, Schmidt TM, Chaudhari N, 
            Lemmon VP, Hattar S, Park KK
  TITLE     Thrombospondin-1 Mediates Axon Regeneration in Retinal Ganglion 
            Cells.
  JOURNAL   Neuron. 2019 Aug 21;103(4):642-657.e7. doi: 
            10.1016/j.neuron.2019.05.044. Epub 2019 Jun 26.
  PUBMED    31255486
REFERENCE   2  (bases 1 to 6242)
  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: 
            "10.1016/j.neuron.2019.05.044"; journalName: "Neuron"; date: 
            "2019-08-21- 21"; volume: "103"; issue: "4"; pages: "642-657.e7"
COMMENT     Sequence Label: pAAV.U6.shRNA-Sdc1-1376
FEATURES             Location/Qualifiers
     source          1..6242
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   1..130
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
     promoter        148..396
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     148..168
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     319..338
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     enhancer        529..832
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        833..1036
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     987..1007
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     1033..1057
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     intron          1185..1563
                     /label=chimeric intron
                     /note="fusion between human cytomegalovirus intron A and 
                     human beta-globin intron 2"
     regulatory      1643..1652
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(1649..1651,1652..1654,1655..2368)
                     /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(1649..1651,1652..1654,1655..2365)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(1694..1715)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(1955..1974)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2302..2323
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     misc_feature    2384..2972
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2437..2457)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2855..2866)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    2989..3465
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
     primer_bind     complement(3188..3207)
                     /label=hGH-PA-R
                     /note="Human growth hormone terminator, reverse primer"
     repeat_region   3505..3645
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   3505..3634
                     /label=AAV2 ITR
     rep_origin      3720..4175
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3807..3826)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4017..4038
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(4192..4211)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     4311..4333
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(4371..4389)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        4457..4561
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4562..4630,4631..5422)
                     /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(4780..4799)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5593..6181
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6082..6101
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 cctgcaggca gctgcgcgct cgctcgctca ctgaggccgc ccgggcgtcg ggcgaccttt
       61 ggtcgcccgg cctcagtgag cgagcgagcg cgcagagagg gagtggccaa ctccatcact
      121 aggggttcct gcggccgcac gcgtagagag ggcctatttc ccatgattcc ttcatatttg
      181 catatacgat acaaggctgt tagagagata attagaatta atttgactgt aaacacaaag
      241 atattagtac aaaatacgtg acgtagaaag taataatttc ttgggtagtt tgcagtttta
      301 aaattatgtt ttaaaatgga ctatcatatg cttaccgtaa cttgaaagta tttcgatttc
      361 ttggctttat atatcttgtg gaaaggacga ggtaccgggc ttgggtgcaa agggtttctc
      421 gaaagaaacc ctttgcaccc aagcttttta attctagatc tacgcgtcta gttattaata
      481 gtaatcaatt acggggtcat tagttcatag cccatatatg gagttccgcg ttacataact
      541 tacggtaaat ggcccgcctg gctgaccgcc caacgacccc cgcccattga cgtcaataat
      601 gacgtatgtt cccatagtaa cgccaatagg gactttccat tgacgtcaat gggtggagta
      661 tttacggtaa actgcccact tggcagtaca tcaagtgtat catatgccaa gtacgccccc
      721 tattgacgtc aatgacggta aatggcccgc ctggcattat gcccagtaca tgaccttatg
      781 ggactttcct acttggcagt acatctacgt attagtcatc gctattacca tggtgatgcg
      841 gttttggcag tacatcaatg ggcgtggata gcggtttgac tcacggggat ttccaagtct
      901 ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa aatcaacggg actttccaaa
      961 atgtcgtaac aactccgccc cattgacgca aatgggcggt aggcgtgtac ggtgggaggt
     1021 ctatataagc agagctcgtt tagtgaaccg tcagatcgcc tggagacgcc atccacgctg
     1081 ttttgacctc catagaagac accgggaccg atccagcctc cgcggattcg aatcccggcc
     1141 gggaacggtg cattggaacg cggattcccc gtgccaagag tgacgtaagt accgcctata
     1201 gagtctatag gcccacaaaa aatgctttct tcttttaata tacttttttg tttatcttat
     1261 ttctaatact ttccctaatc tctttctttc agggcaataa tgatacaatg tatcatgcct
     1321 ctttgcacca ttctaaagaa taacagtgat aatttctggg ttaaggcaat agcaatattt
     1381 ctgcatataa atatttctgc atataaattg taactgatgt aagaggtttc atattgctaa
     1441 tagcagctac aatccagcta ccattctgct tttattttat ggttgggata aggctggatt
     1501 attctgagtc caagctaggc ccttttgcta atcatgttca tacctcttat cttcctccca
     1561 cagctcctgg gcaacgtgct ggtctgtgtg ctggcccatc actttggcaa agaattggga
     1621 ttcgaacatc gattgaattg tcgccaccat ggtgagcaag ggcgaggagc tgttcaccgg
     1681 ggtggtgccc atcctggtcg agctggacgg cgacgtaaac ggccacaagt tcagcgtgtc
     1741 cggcgagggc gagggcgatg ccacctacgg caagctgacc ctgaagttca tctgcaccac
     1801 cggcaagctg cccgtgccct ggcccaccct cgtgaccacc ctgacctacg gcgtgcagtg
     1861 cttcagccgc taccccgacc acatgaagca gcacgacttc ttcaagtccg ccatgcccga
     1921 aggctacgtc caggagcgca ccatcttctt caaggacgac ggcaactaca agacccgcgc
     1981 cgaggtgaag ttcgagggcg acaccctggt gaaccgcatc gagctgaagg gcatcgactt
     2041 caaggaggac ggcaacatcc tggggcacaa gctggagtac aactacaaca gccacaacgt
     2101 ctatatcatg gccgacaagc agaagaacgg catcaaggtg aacttcaaga tccgccacaa
     2161 catcgaggac ggcagcgtgc agctcgccga ccactaccag cagaacaccc ccatcggcga
     2221 cggccccgtg ctgctgcccg acaaccacta cctgagcacc cagtccgccc tgagcaaaga
     2281 ccccaacgag aagcgcgatc acatggtcct gctggagttc gtgaccgccg ccgggatcac
     2341 tctcggcatg gacgagctgt acaagtaaag cggccgcgtc gacaatcaac ctctggatta
     2401 caaaatttgt gaaagattga ctggtattct taactatgtt gctcctttta cgctatgtgg
     2461 atacgctgct ttaatgcctt tgtatcatgc tattgcttcc cgtatggctt tcattttctc
     2521 ctccttgtat aaatcctggt tgctgtctct ttatgaggag ttgtggcccg ttgtcaggca
     2581 acgtggcgtg gtgtgcactg tgtttgctga cgcaaccccc actggttggg gcattgccac
     2641 cacctgtcag ctcctttccg ggactttcgc tttccccctc cctattgcca cggcggaact
     2701 catcgccgcc tgccttgccc gctgctggac aggggctcgg ctgttgggca ctgacaattc
     2761 cgtggtgttg tcggggaagc tgacgtcctt tccatggctg ctcgcctgtg ttgccacctg
     2821 gattctgcgc gggacgtcct tctgctacgt cccttcggcc ctcaatccag cggaccttcc
     2881 ttcccgcggc ctgctgccgg ctctgcggcc tcttccgcgt cttcgccttc gccctcagac
     2941 gagtcggatc tccctttggg ccgcctcccc gcctctcgag agatctacgg gtggcatccc
     3001 tgtgacccct ccccagtgcc tctcctggcc ctggaagttg ccactccagt gcccaccagc
     3061 cttgtcctaa taaaattaag ttgcatcatt ttgtctgact aggtgtcctt ctataatatt
     3121 atggggtgga ggggggtggt atggagcaag gggcaagttg ggaagacaac ctgtagggcc
     3181 tgcggggtct attgggaacc aagctggagt gcagtggcac aatcttggct cactgcaatc
     3241 tccgcctcct gggttcaagc gattctcctg cctcagcctc ccgagttgtt gggattccag
     3301 gcatgcatga ccaggctcag ctaatttttg tttttttggt agagacgggg tttcaccata
     3361 ttggccaggc tggtctccaa ctcctaatct caggtgatct acccaccttg gcctcccaaa
     3421 ttgctgggat tacaggcgtg aaccactgct cccttccctg tccttctgat tttgtaggta
     3481 accacgtgcg gaccgagcgg ccgcaggaac ccctagtgat ggagttggcc actccctctc
     3541 tgcgcgctcg ctcgctcact gaggccgggc gaccaaaggt cgcccgacgc ccgggctttg
     3601 cccgggcggc ctcagtgagc gagcgagcgc gcagctgcct gcaggggcgc ctgatgcggt
     3661 attttctcct tacgcatctg tgcggtattt cacaccgcat acgtcaaagc aaccatagta
     3721 cgcgccctgt agcggcgcat taagcgcggc gggtgtggtg gttacgcgca gcgtgaccgc
     3781 tacacttgcc agcgccttag cgcccgctcc tttcgctttc ttcccttcct ttctcgccac
     3841 gttcgccggc tttccccgtc aagctctaaa tcgggggctc cctttagggt tccgatttag
     3901 tgctttacgg cacctcgacc ccaaaaaact tgatttgggt gatggttcac gtagtgggcc
     3961 atcgccctga tagacggttt ttcgcccttt gacgttggag tccacgttct ttaatagtgg
     4021 actcttgttc caaactggaa caacactcaa ctctatctcg ggctattctt ttgatttata
     4081 agggattttg ccgatttcgg tctattggtt aaaaaatgag ctgatttaac aaaaatttaa
     4141 cgcgaatttt aacaaaatat taacgtttac aattttatgg tgcactctca gtacaatctg
     4201 ctctgatgcc gcatagttaa gccagccccg acacccgcca acacccgctg acgcgccctg
     4261 acgggcttgt ctgctcccgg catccgctta cagacaagct gtgaccgtct ccgggagctg
     4321 catgtgtcag aggttttcac cgtcatcacc gaaacgcgcg agacgaaagg gcctcgtgat
     4381 acgcctattt ttataggtta atgtcatgat aataatggtt tcttagacgt caggtggcac
     4441 ttttcgggga aatgtgcgcg gaacccctat ttgtttattt ttctaaatac attcaaatat
     4501 gtatccgctc atgagacaat aaccctgata aatgcttcaa taatattgaa aaaggaagag
     4561 tatgagtatt caacatttcc gtgtcgccct tattcccttt tttgcggcat tttgccttcc
     4621 tgtttttgct cacccagaaa cgctggtgaa agtaaaagat gctgaagatc agttgggtgc
     4681 acgagtgggt tacatcgaac tggatctcaa cagcggtaag atccttgaga gttttcgccc
     4741 cgaagaacgt tttccaatga tgagcacttt taaagttctg ctatgtggcg cggtattatc
     4801 ccgtattgac gccgggcaag agcaactcgg tcgccgcata cactattctc agaatgactt
     4861 ggttgagtac tcaccagtca cagaaaagca tcttacggat ggcatgacag taagagaatt
     4921 atgcagtgct gccataacca tgagtgataa cactgcggcc aacttacttc tgacaacgat
     4981 cggaggaccg aaggagctaa ccgctttttt gcacaacatg ggggatcatg taactcgcct
     5041 tgatcgttgg gaaccggagc tgaatgaagc cataccaaac gacgagcgtg acaccacgat
     5101 gcctgtagca atggcaacaa cgttgcgcaa actattaact ggcgaactac ttactctagc
     5161 ttcccggcaa caattaatag actggatgga ggcggataaa gttgcaggac cacttctgcg
     5221 ctcggccctt ccggctggct ggtttattgc tgataaatct ggagccggtg agcgtgggtc
     5281 tcgcggtatc attgcagcac tggggccaga tggtaagccc tcccgtatcg tagttatcta
     5341 cacgacgggg agtcaggcaa ctatggatga acgaaataga cagatcgctg agataggtgc
     5401 ctcactgatt aagcattggt aactgtcaga ccaagtttac tcatatatac tttagattga
     5461 tttaaaactt catttttaat ttaaaaggat ctaggtgaag atcctttttg ataatctcat
     5521 gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg tcagaccccg tagaaaagat
     5581 caaaggatct tcttgagatc ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa
     5641 accaccgcta ccagcggtgg tttgtttgcc ggatcaagag ctaccaactc tttttccgaa
     5701 ggtaactggc ttcagcagag cgcagatacc aaatactgtt cttctagtgt agccgtagtt
     5761 aggccaccac ttcaagaact ctgtagcacc gcctacatac ctcgctctgc taatcctgtt
     5821 accagtggct gctgccagtg gcgataagtc gtgtcttacc gggttggact caagacgata
     5881 gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt
     5941 ggagcgaacg acctacaccg aactgagata cctacagcgt gagctatgag aaagcgccac
     6001 gcttcccgaa gggagaaagg cggacaggta tccggtaagc ggcagggtcg gaacaggaga
     6061 gcgcacgagg gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg
     6121 ccacctctga cttgagcgtc gatttttgtg atgctcgtca ggggggcgga gcctatggaa
     6181 aaacgccagc aacgcggcct ttttacggtt cctggccttt tgctggcctt ttgctcacat
     6241 gt
//
