LOCUS       sequence-345048-        6233 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Negative control guide, Cre-inducible plasmid expressing nuclear 
            RFP..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6233)
  AUTHORS   Jonsson ME, Garza R, Sharma Y, Petri R, Sodersten E, Johansson JG, 
            Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan
            R, Holmberg J, Larsson J, Jern P, Jakobsson J
  TITLE     Activation of endogenous retroviruses during brain development 
            causes an inflammatory response.
  JOURNAL   EMBO J. 2021 Mar 1:e106423. doi: 10.15252/embj.2020106423.
  PUBMED    33644903
REFERENCE   2  (bases 1 to 6233)
  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: "EMBO J. 
            2021 Mar 1:e106423. doi: 10.15252/embj.2020106423."
COMMENT     Sequence Label: pAAV.U6gLacZ.hSyn.flex.H2B.RFP
FEATURES             Location/Qualifiers
     source          1..6233
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     258..277
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_RNA        357..432
                     /label=gRNA scaffold
                     /note="guide RNA scaffold for the Streptococcus pyogenes 
                     CRISPR/Cas9 system"
     protein_bind    complement(1029..1062)
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     protein_bind    complement(1113..1146)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(1163..1873)
                     /codon_start=1
                     /product="monomeric derivative of DsRed fluorescent protein
                     (Shaner et al., 2004)"
                     /label=mCherry
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEG
                     TQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNF
                     EDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALK
                     GEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERA
                     EGRHSTGGMDELYK"
     primer_bind     complement(1441..1460)
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     primer_bind     1710..1728
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     regulatory      1870..1879
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             complement(1892..2269)
                     /codon_start=1
                     /gene="HIST1H2BB"
                     /product="human histone H2B"
                     /label=H2B
                     /translation="MPEPSKSAPAPKKGSKKAITKAQKKDGKKRKRSRKESYSIYVYKV
                     LKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLP
                     GELAKHAVSEGTKAVTKYTSSK"
     protein_bind    2299..2332
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     protein_bind    2383..2416
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    2441..3029
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2494..2514)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2912..2923)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    3077..3211
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3114..3133)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3168..3187
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      complement(3646..4234)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3726..3745)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4405..5196,5197..5265))
                     /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     5028..5047
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5266..5370)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     5438..5456
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     primer_bind     complement(5494..5516)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     5616..5635
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     rep_origin      complement(5702..6157)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5839..5860)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     6051..6070
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
ORIGIN
        1 cggcctcagt gagcgagcga gcgcgcagag agggagtggc caactccatc actaggggtt
       61 cctcagatcg ggctgcagga attggccgct ctagatttcc catgattcct tcatatttgc
      121 atatacgata caaggctgtt agagagataa ttagaattaa tttgactgta aacacaaaga
      181 tattagtaca aaatacgtga cgtagaaagt aataatttct tgggtagttt gcagttttaa
      241 aattatgttt taaaatggac tatcatatgc ttaccgtaac ttgaaagtat ttcgatttct
      301 tggctttata tatcttgtgg aaaggacgaa acaccgtgcg aatacgccca cgcgatgttt
      361 tagagctaga aatagcaagt taaaataagg ctagtccgtt atcaacttga aaaagtggca
      421 ccgagtcggt gctttttttc tagactctag ctgcagaggg acctgcgtat gagtgcaagt
      481 gggttttagg accaggatga ggcggggtgg gggtgcctac ctgacgaccg accccgaccc
      541 actggacaag cacccaaccc ccattcccca aattgcgcat cccctatcag agagggggag
      601 gggaaacagg atgcggcgag gcgcgtgcgc actgccagct tcagcaccgc ggacagtgcc
      661 ttcgcccccg cctggcggcg cgcgccaccg ccgcctcagc actgaaggcg cgctgacgtc
      721 actcgccggt cccccgcaaa ctccccttcc cggccacctt ggtcgcgtcc gcgccgccgc
      781 cggcccagcc ggaccgcacc acgcgaggcg cgagataggg gggcacgggc gcgaccatct
      841 gcgctgcggc gccggcccag ccggaccgca ccacgcgagg cgcgagatag gggggcacgg
      901 gcgcgaccat ctgcgctgcg gcgccggcga ctcagcgctg cctcagtctg cggtgggcag
      961 cggaggagtc gtgtcgtgcc tgagagcgca gtcgagaagg taccggatcc tctagagtcg
     1021 actccggaat aacttcgtat aggatacttt atacgaagtt atgcagaatg gtagctggat
     1081 tgtagctgct attagcaata tgaaacctct taataacttc gtatagcata cattatacga
     1141 agttatggcg cgccatacta gtttacttgt acagctcgtc catgccgccg gtggagtggc
     1201 ggccctcggc gcgttcgtac tgttccacga tggtgtagtc ctcgttgtgg gaggtgatgt
     1261 ccaacttgat gttgacgttg taggcgccgg gcagctgcac gggcttcttg gccttgtagg
     1321 tggtcttgac ctcagcgtcg tagtggccgc cgtccttcag cttcagcctc tgcttgatct
     1381 cgcccttcag ggcgccgtcc tcggggtaca tccgctcgga ggaggcctcc cagcccatgg
     1441 tcttcttctg cattacgggg ccgtcggagg ggaagttggt gccgcgcagc ttcaccttgt
     1501 agatgaactc gccgtcctgc agggaggagt cctgggtcac ggtcaccacg ccgccgtcct
     1561 cgaagttcat cacgcgctcc cacttgaagc cctcggggaa ggacagcttc aagtagtcgg
     1621 ggatgtcggc ggggtgcttc acgtaggcct tggagccgta catgaactga ggggacagga
     1681 tgtcccaggc gaagggcagg gggccaccct tggtcacctt cagcttggcg gtctgggtgc
     1741 cctcgtaggg gcggccctcg ccctcgccct cgatctcgaa ctcgtggccg ttcacggagc
     1801 cctccatgtg caccttgaag cgcatgaact ccttgatgat ggccatgtta tcctcctcgc
     1861 ccttgctcac catggtggcg accggtggat ccttagagct agtgtacttg gtaactgcct
     1921 tagtgccctc ggacacagca tgcttagcca gctccccagg cagcagcagg cgcacagccg
     1981 tctgaatctc cctggaggtg atggtcgagc gcttattgta gtgagccagg cgagaagcct
     2041 cgcccgcgat gcgctcgaag atgtcgttga cgaaggagtt catgatcccc atggccttgg
     2101 atgagatgcc ggtgtcgggg tggacctgct tcagaacctt gtacacatag atagaatagc
     2161 tctccttgcg gctgcgctta cgcttcttac catccttctt ctgcgcctta gtgatagcct
     2221 tcttagaacc ctttttaggg gctggagcag acttagaggg ttcaggcatg gtggcggtac
     2281 cggtggatcc ttgctagcat aacttcgtat aaagtatcct atacgaagtt atttgcctta
     2341 acccagaaat tatcactgtt attctttaga atggtgcaaa gaataacttc gtataatgta
     2401 tgctatacga agttatgaat tcgatatcaa gcttatcgat aatcaacctc tggattacaa
     2461 aatttgtgaa agattgactg gtattcttaa ctatgttgct ccttttacgc tatgtggata
     2521 cgctgcttta atgcctttgt atcatgctat tgcttcccgt atggctttca ttttctcctc
     2581 cttgtataaa tcctggttgc tgtctcttta tgaggagttg tggcccgttg tcaggcaacg
     2641 tggcgtggtg tgcactgtgt ttgctgacgc aacccccact ggttggggca ttgccaccac
     2701 ctgtcagctc ctttccggga ctttcgcttt ccccctccct attgccacgg cggaactcat
     2761 cgccgcctgc cttgcccgct gctggacagg ggctcggctg ttgggcactg acaattccgt
     2821 ggtgttgtcg gggaaatcat cgtcctttcc ttggctgctc gcctatgttg ccacctggat
     2881 tctgcgcggg acgtccttct gctacgtccc ttcggccctc aatccagcgg accttccttc
     2941 ccgcggcctg ctgccggctc tgcggcctct tccgcgtctt cgccttcgcc ctcagacgag
     3001 tcggatctcc ctttgggccg cctccccgcc tggaattcga gctcggtaca gcttatcgat
     3061 accgtcgact tcgagcaact tgtttattgc agcttataat ggttacaaat aaagcaatag
     3121 catcacaaat ttcacaaata aagcattttt ttcactgcat tctagttgtg gtttgtccaa
     3181 actcatcaat gtatcttatc atgtctggat cgtctagcat cgaagatccc ccgatctgag
     3241 gaacccctag tgatggagtt ggccactccc tctctgcdss cyssmwywmt rrwtsdgsyn
     3301 nykskcsrrr mkmrkcrrtk trycttwtsr tgtctggatc gtctagcatc gaagatcccc
     3361 cgatctgagg aacccctagt gatggagttg gccactcccy cyctgcagcc tgcattaatg
     3421 aatcggccaa cgcgcgggga gaggcggttt gcgtattggg cgctcttccg cttcctcgct
     3481 cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg gtatcagctc actcaaaggc
     3541 ggtaatacgg ttatccacag aatcagggga taacgcagga aagaacatgt gagcaaaagg
     3601 ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg gcgtttttcc ataggctccg
     3661 cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg
     3721 actataaaga taccaggcgt ttccccctgg aagctccctc gtgcgctctc ctgttccgac
     3781 cctgccgctt accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca
     3841 tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt
     3901 gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc
     3961 caacccggta agacacgact tatcgccact ggcagcagcc actggtaaca ggattagcag
     4021 agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg tggcctaact acggctacac
     4081 tagaagaaca gtatttggta tctgcgctct gctgaagcca gttaccttcg gaaaaagagt
     4141 tggtagctct tgatccggca aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa
     4201 gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat cctttgatct tttctacggg
     4261 gtctgacgct cagtggaacg aaaactcacg ttaagggatt ttggtcatga gattatcaaa
     4321 aaggatcttc acctagatcc ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat
     4381 atatgagtaa acttggtctg acagttacca atgcttaatc agtgaggcac ctatctcagc
     4441 gatctgtcta tttcgttcat ccatagttgc ctgactcccc gtcgtgtaga taactacgat
     4501 acgggagggc ttaccatctg gccccagtgc tgcaatgata ccgcgagacc cacgctcacc
     4561 ggctccagat ttatcagcaa taaaccagcc agccggaagg gccgagcgca gaagtggtcc
     4621 tgcaacttta tccgcctcca tccagtctat taattgttgc cgggaagcta gagtaagtag
     4681 ttcgccagtt aatagtttgc gcaacgttgt tgccattgct acaggcatcg tggtgtcacg
     4741 ctcgtcgttt ggtatggctt cattcagctc cggttcccaa cgatcaaggc gagttacatg
     4801 atcccccatg ttgtgcaaaa aagcggttag ctccttcggt cctccgatcg ttgtcagaag
     4861 taagttggcc gcagtgttat cactcatggt tatggcagca ctgcataatt ctcttactgt
     4921 catgccatcc gtaagatgct tttctgtgac tggtgagtac tcaaccaagt cattctgaga
     4981 atagtgtatg cggcgaccga gttgctcttg cccggcgtca atacgggata ataccgcgcc
     5041 acatagcaga actttaaaag tgctcatcat tggaaaacgt tcttcggggc gaaaactctc
     5101 aaggatctta ccgctgttga gatccagttc gatgtaaccc actcgtgcac ccaactgatc
     5161 ttcagcatct tttactttca ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc
     5221 cgcaaaaaag ggaataaggg cgacacggaa atgttgaata ctcatactct tcctttttca
     5281 atattattga agcatttatc agggttattg tctcatgagc ggatacatat ttgaatgtat
     5341 ttagaaaaat aaacaaatag gggttccgcg cacatttccc cgaaaagtgc cacctgacgt
     5401 ctaagaaacc attattatca tgacattaac ctataaaaat aggcgtatca cgaggccctt
     5461 tcgtctcgcg cgtttcggtg atgacggtga aaacctctga cacatgcagc tcccggagac
     5521 ggtcacagct tgtctgtaag cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagc
     5581 gggtgttggc gggtgtcggg gctggcttaa ctatgcggca tcagagcaga ttgtactgag
     5641 agtgcaccat atgcggtgtg aaataccgca cagatgcgta aggagaaaat accgcatcag
     5701 gaaattgtaa gcgttaatat tttgttaaaa ttcgcgttaa atttttgtta aatcagctca
     5761 ttttttaacc aataggccga aatcggcaaa atcccttata aatcaaaaga atagaccgag
     5821 atagggttga gtgttgttcc agtttggaac aagagtccac tattaaagaa cgtggactcc
     5881 aacgtcaaag ggcgaaaaac cgtctatcag ggcgatggcc cactacgtga accatcaccc
     5941 taatcaagtt ttttggggtc gaggtgccgt aaagcactaa atcggaaccc taaagggagc
     6001 ccccgattta gagcttgacg gggaaagccg gcgaacgtgg cgagaaagga agggaagaaa
     6061 gcgaaaggag cgggcgctag ggcgctggca agtgtagcgg tcacgctgcg cgtaaccacc
     6121 acacccgccg cgcttaatgc gccgctacag ggcgcgtcca ttcgccattc aggctgcgca
     6181 actgttggga agggcgatcg gtgcgggcct cttcgctatt acgccaggct gca
//
