LOCUS       sequence-296567-        6506 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses a gRNA and mCherry in mammalian cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6506)
  AUTHORS   Schmid-Burgk JL, Gao L, Li D, Gardner Z, Strecker J, Lash B, Zhang F
  TITLE     Highly Parallel Profiling of Cas9 Variant Specificity.
  JOURNAL   Mol Cell. 2020 Mar 17. pii: S1097-2765(20)30143-X. doi: 
            10.1016/j.molcel.2020.02.023.
  PUBMED    32187529
REFERENCE   2  (bases 1 to 6506)
  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 Cell. 
            2020 Mar 17. pii: S1097-2765(20)30143-X. doi: 
            10.1016/j.molcel.2020.02.023."
COMMENT     Sequence Label: pmCherry-U6-EMX1
FEATURES             Location/Qualifiers
     source          1..6506
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        1..249
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     1..21
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     172..191
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_RNA        270..345
                     /label=gRNA scaffold
                     /note="guide RNA scaffold for the Streptococcus pyogenes 
                     CRISPR/Cas9 system"
     enhancer        426..805
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        806..1009
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     960..980
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     1054..1073
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        1054..1072
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     regulatory      1114..1123
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1120..1827
                     /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(1265..1283)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     1533..1552
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     CDS             1828..1854
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
     primer_bind     complement(1928..1945)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    1934..2158
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2204..2632
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2291..2310)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2501..2522
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2641..2661)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2646..2975
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2826..2961
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     2888..2907
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3042..3836
                     /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(3096..3115)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3706..3725
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4010..4131
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4047..4066)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4101..4120
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4180..4196)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4180..4196)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4193..4215)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4204..4220
                     /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(4228..4234,4235..4252,4253..4258))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4273..4294
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4411..4428)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4582..5170)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4662..4681)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5341..6132,6133..6201))
                     /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     5964..5983
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6202..6306)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6381..6400)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
       61 ataattggaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
      121 aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat ggactatcat
      181 atgcttaccg taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
      241 cgaaacaccg agtccgagca gaagaagaag ttttagagct agaaatagca agttaaaata
      301 aggctagtcc gttatcaact tgaaaaagtg gcaccgagtc ggtgcttttt tcaattgcat
      361 gaagaatctg cttagggtta ggcgttttgc gctgcttcgc gatgtacggg ccagatatac
      421 gcgttgacat tgattattga ctagttatta atagtaatca attacggggt cattagttca
      481 tagcccatat atggagttcc gcgttacata acttacggta aatggcccgc ctggctgacc
      541 gcccaacgac ccccgcccat tgacgtcaat aatgacgtat gttcccatag taacgccaat
      601 agggactttc cattgacgtc aatgggtgga gtatttacgg taaactgccc acttggcagt
      661 acatcaagtg tatcatatgc caagtacgcc ccctattgac gtcaatgacg gtaaatggcc
      721 cgcctggcat tatgcccagt acatgacctt atgggacttt cctacttggc agtacatcta
      781 cgtattagtc atcgctatta ccatggtgat gcggttttgg cagtacatca atgggcgtgg
      841 atagcggttt gactcacggg gatttccaag tctccacccc attgacgtca atgggagttt
      901 gttttggcac caaaatcaac gggactttcc aaaatgtcgt aacaactccg ccccattgac
      961 gcaaatgggc ggtaggcgtg tacggtggga ggtctatata agcagagctc tctggctaac
     1021 tagagaaccc actgcttact ggcttatcga aattaatacg actcactata gggagaccca
     1081 agctggctag cgtttaaact taagcttgcc ggtgccacca tggtgagcaa gggcgaggag
     1141 gataacatgg ccatcatcaa ggagttcatg cgcttcaagg tgcacatgga gggctccgtg
     1201 aacggccacg agttcgagat cgagggcgag ggcgagggcc gcccctacga gggcacccag
     1261 accgccaagc tgaaggtgac caagggtggc cccctgccct tcgcctggga catcctgtcc
     1321 cctcagttca tgtacggctc caaggcctac gtgaagcacc ccgccgacat ccccgactac
     1381 ttgaagctgt ccttccccga gggcttcaag tgggagcgcg tgatgaactt cgaggacggc
     1441 ggcgtggtga ccgtgaccca ggactcctcc ctgcaggacg gcgagttcat ctacaaggtg
     1501 aagctgcgcg gcaccaactt cccctccgac ggccccgtaa tgcagaagaa gaccatgggc
     1561 tgggaggcct cctccgagcg gatgtacccc gaggacggcg ccctgaaggg cgagatcaag
     1621 cagaggctga agctgaagga cggcggccac tacgacgctg aggtcaagac cacctacaag
     1681 gccaagaagc ccgtgcagct gcccggcgcc tacaacgtca acatcaagtt ggacatcacc
     1741 tcccacaacg aggactacac catcgtggaa cagtacgaac gcgccgaggg ccgccactcc
     1801 accggcggca tggacgagct gtacaagtac ccatacgatg ttccagatta cgcttaagaa
     1861 ttctgcagat atccagcaca gtggcggccg ctcgagtcta gagggcccgt ttaaacccgc
     1921 tgatcagcct cgactgtgcc ttctagttgc cagccatctg ttgtttgccc ctcccccgtg
     1981 ccttccttga ccctggaagg tgccactccc actgtccttt cctaataaaa tgaggaaatt
     2041 gcatcgcatt gtctgagtag gtgtcattct attctggggg gtggggtggg gcaggacagc
     2101 aagggggagg attgggaaga caatagcagg catgctgggg atgcggtggg ctctatggct
     2161 tctgaggcgg aaagaaccag ctggggctct agggggtatc cccacgcgcc ctgtagcggc
     2221 gcattaagcg cggcgggtgt ggtggttacg cgcagcgtga ccgctacact tgccagcgcc
     2281 ctagcgcccg ctcctttcgc tttcttccct tcctttctcg ccacgttcgc cggctttccc
     2341 cgtcaagctc taaatcgggg gctcccttta gggttccgat ttagtgcttt acggcacctc
     2401 gaccccaaaa aacttgatta gggtgatggt tcacgtagtg ggccatcgcc ctgatagacg
     2461 gtttttcgcc ctttgacgtt ggagtccacg ttctttaata gtggactctt gttccaaact
     2521 ggaacaacac tcaaccctat ctcggtctat tcttttgatt tataagggat tttgccgatt
     2581 tcggcctatt ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa ttaattctgt
     2641 ggaatgtgtg tcagttaggg tgtggaaagt ccccaggctc cccagcaggc agaagtatgc
     2701 aaagcatgca tctcaattag tcagcaacca ggtgtggaaa gtccccaggc tccccagcag
     2761 gcagaagtat gcaaagcatg catctcaatt agtcagcaac catagtcccg cccctaactc
     2821 cgcccatccc gcccctaact ccgcccagtt ccgcccattc tccgccccat ggctgactaa
     2881 ttttttttat ttatgcagag gccgaggccg cctctgcctc tgagctattc cagaagtagt
     2941 gaggaggctt ttttggaggc ctaggctttt gcaaaaagct cccgggagct tgtatatcca
     3001 ttttcggatc tgatcaagag acaggatgag gatcgtttcg catgattgaa caagatggat
     3061 tgcacgcagg ttctccggcc gcttgggtgg agaggctatt cggctatgac tgggcacaac
     3121 agacaatcgg ctgctctgat gccgccgtgt tccggctgtc agcgcagggg cgcccggttc
     3181 tttttgtcaa gaccgacctg tccggtgccc tgaatgaact gcaggacgag gcagcgcggc
     3241 tatcgtggct ggccacgacg ggcgttcctt gcgcagctgt gctcgacgtt gtcactgaag
     3301 cgggaaggga ctggctgcta ttgggcgaag tgccggggca ggatctcctg tcatctcacc
     3361 ttgctcctgc cgagaaagta tccatcatgg ctgatgcaat gcggcggctg catacgcttg
     3421 atccggctac ctgcccattc gaccaccaag cgaaacatcg catcgagcga gcacgtactc
     3481 ggatggaagc cggtcttgtc gatcaggatg atctggacga agagcatcag gggctcgcgc
     3541 cagccgaact gttcgccagg ctcaaggcgc gcatgcccga cggcgaggat ctcgtcgtga
     3601 cccatggcga tgcctgcttg ccgaatatca tggtggaaaa tggccgcttt tctggattca
     3661 tcgactgtgg ccggctgggt gtggcggacc gctatcagga catagcgttg gctacccgtg
     3721 atattgctga agagcttggc ggcgaatggg ctgaccgctt cctcgtgctt tacggtatcg
     3781 ccgctcccga ttcgcagcgc atcgccttct atcgccttct tgacgagttc ttctgagcgg
     3841 gactctgggg ttcgaaatga ccgaccaagc gacgcccaac ctgccatcac gagatttcga
     3901 ttccaccgcc gccttctatg aaaggttggg cttcggaatc gttttccggg acgccggctg
     3961 gatgatcctc cagcgcgggg atctcatgct ggagttcttc gcccacccca acttgtttat
     4021 tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa ataaagcatt
     4081 tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg
     4141 tataccgtcg acctctagct agagcttggc gtaatcatgg tcatagctgt ttcctgtgtg
     4201 aaattgttat ccgctcacaa ttccacacaa catacgagcc ggaagcataa agtgtaaagc
     4261 ctggggtgcc taatgagtga gctaactcac attaattgcg ttgcgctcac tgcccgcttt
     4321 ccagtcggga aacctgtcgt gccagctgca ttaatgaatc ggccaacgcg cggggagagg
     4381 cggtttgcgt attgggcgct cttccgcttc ctcgctcact gactcgctgc gctcggtcgt
     4441 tcggctgcgg cgagcggtat cagctcactc aaaggcggta atacggttat ccacagaatc
     4501 aggggataac gcaggaaaga acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa
     4561 aaaggccgcg ttgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa
     4621 tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc
     4681 ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc
     4741 cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcag
     4801 ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga
     4861 ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac acgacttatc
     4921 gccactggca gcagccactg gtaacaggat tagcagagcg aggtatgtag gcggtgctac
     4981 agagttcttg aagtggtggc ctaactacgg ctacactaga agaacagtat ttggtatctg
     5041 cgctctgctg aagccagtta ccttcggaaa aagagttggt agctcttgat ccggcaaaca
     5101 aaccaccgct ggtagcggtg gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa
     5161 aggatctcaa gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa
     5221 ctcacgttaa gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt
     5281 aaattaaaaa tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag
     5341 ttaccaatgc ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat
     5401 agttgcctga ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc
     5461 cagtgctgca atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa
     5521 ccagccagcc ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca
     5581 gtctattaat tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa
     5641 cgttgttgcc attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt
     5701 cagctccggt tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc
     5761 ggttagctcc ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact
     5821 catggttatg gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc
     5881 tgtgactggt gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg
     5941 ctcttgcccg gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct
     6001 catcattgga aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc
     6061 cagttcgatg taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag
     6121 cgtttctggg tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac
     6181 acggaaatgt tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg
     6241 ttattgtctc atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt
     6301 tccgcgcaca tttccccgaa aagtgccacc tgacgtcgac ggatcgggag atctcccgat
     6361 cccctatggt gcactctcag tacaatctgc tctgatgccg catagttaag ccagtatctg
     6421 ctccctgctt gtgtgttgga ggtcgctgag tagtgcgcga gcaaaattta agctacaaca
     6481 aggcaaggct tgaccgactt aattaa
//
