LOCUS       sequence-496414-        6191 bp    DNA     circular SYN 07-JAN-2026
DEFINITION  Vector for transient expression of CRY2hiclu-mCherry in mammalian 
            cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6191)
  AUTHORS   Stortz M, Keikhosravi A, Pegoraro G, Misteli T
  TITLE     OptoLoop: An optogenetic tool to probe the functional role of genome
            organization
  JOURNAL   bioRxiv 2025.11.06.686574
REFERENCE   2  (bases 1 to 6191)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Jan 7, 2026 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "bioRxiv 
            2025.11.06.686574"
COMMENT     Sequence Label: pCMV-CRY2hiclu-mCherry
FEATURES             Location/Qualifiers
     source          1..6191
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        59..362
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        363..566
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     517..537
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     CDS             623..2116
                     /codon_start=1
                     /product="N-terminal photolyase homology region of 
                     Arabidopsis thaliana cryptochrome 2"
                     /label=CRY2PHR
                     /note="binds to CIB1 upon exposure to blue light (Kennedy 
                     et al., 2010)"
                     /translation="MKMDKKTIVWFRRDLRIEDNPALAAAAHEGSVFPVFIWCPEEEGQ
                     FYPGRASRWWMKQSLAHLSQSLKALGSDLTLIKTHNTISAILDCIRVTGATKVVFNHLY
                     DPVSLVRDHTVKEKLVERGISVQSYNGDLLYEPWEIYCEKGKPFTSFNSYWKKCLDMSI
                     ESVMLPPPWRLMPITAAAEAIWACSIEELGLENEAEKPSNALLTRAWSPGWSNADKLLN
                     EFIEKQLIDYAKNSKKVVGNSTSLLSPYLHFGEISVRHVFQCARMKQIIWARDKNSEGE
                     ESADLFLRGIGLREYSRYICFNFPFTHEQSLLSHLRFFPWDADVDKFKAWRQGRTGYPL
                     VDAGMRELWATGWMHNRIRVIVSSFAVKFLLLPWKWGMKYFWDTLLDADLECDILGWQY
                     ISGSIPDGHELDRLDNPALQGAKYDPEGEYIRQWLPELARLPTEWIHHPWDAPLTVLKA
                     SGVELGTNYAKPIVDIDTARELLAKAISRTRRAQIMIGAA"
     CDS             2144..2854
                     /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(2289..2307)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     2557..2576
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     polyA_signal    2977..3098
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3014..3033)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3068..3087
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      complement(3105..3560)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3242..3263)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     3454..3473
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     promoter        3587..3691
                     /gene="bla"
                     /label=AmpR promoter
     promoter        3693..4050
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     enhancer        3693..3884
                     /label=SV40 enhancer
                     /note="enhancer for the SV40 early promoter (Herr, 1993)"
     primer_bind     complement(3716..3736)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      3901..4036
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     CDS             4085..4879
                     /codon_start=1
                     /product="aminoglycoside phosphotransferase"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     CDS             4085..4879
                     /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
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(4139..4158)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     4749..4768
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     complement(5067..5086)
                     /label=TK-pA-R
                     /note="Thymidine kinase polyA, reverse primer"
     polyA_signal    5111..5158
                     /label=HSV TK poly(A) signal
                     /note="herpes simplex virus thymidine kinase 
                     polyadenylation signal (Cole and Stacy, 1985)"
     rep_origin      5487..6075
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5976..5995
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 gttattaata gtaatcaatt acggggtcat tagttcatag cccatatatg gagttccgcg
       61 ttacataact tacggtaaat ggcccgcctg gctgaccgcc caacgacccc cgcccattga
      121 cgtcaataat gacgtatgtt cccatagtaa cgccaatagg gactttccat tgacgtcaat
      181 gggtggagta tttacggtaa actgcccact tggcagtaca tcaagtgtat catatgccaa
      241 gtacgccccc tattgacgtc aatgacggta aatggcccgc ctggcattat gcccagtaca
      301 tgaccttatg ggactttcct acttggcagt acatctacgt attagtcatc gctattacca
      361 tggtgatgcg gttttggcag tacatcaatg ggcgtggata gcggtttgac tcacggggat
      421 ttccaagtct ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa aatcaacggg
      481 actttccaaa atgtcgtaac aactccgccc cattgacgca aatgggcggt aggcgtgtac
      541 ggtgggaggt ctatataagc agagctggtt tagtgaaccg tcagatccgc tagcgctacc
      601 ggactcagat ctcgaggcca ccatgaagat ggacaaaaag actatagttt ggtttagaag
      661 agacctaagg attgaggata atcctgcatt agcagcagct gctcacgaag gatctgtttt
      721 tcctgtcttc atttggtgtc ctgaagaaga aggacagttt tatcctggaa gagcttcaag
      781 atggtggatg aaacaatcac ttgctcactt atctcaatcc ttgaaggctc ttggatctga
      841 cctcacttta atcaaaaccc acaacacgat ttcagcgatc ttggattgta tccgcgttac
      901 cggtgctaca aaagtcgtct ttaaccacct ctatgatcct gtttcgttag ttcgggacca
      961 taccgtaaag gagaagctgg tggaacgtgg gatctctgtg caaagctaca atggagatct
     1021 attgtatgaa ccgtgggaga tatactgcga aaagggcaaa ccttttacga gtttcaattc
     1081 ttactggaag aaatgcttag atatgtcgat tgaatccgtt atgcttcctc ctccttggcg
     1141 gttgatgcca ataactgcag cggctgaagc gatttgggcg tgttcgattg aagaactagg
     1201 gctggagaat gaggccgaga aaccgagcaa tgcgttgtta actagagctt ggtctccagg
     1261 atggagcaat gctgataagt tactaaatga gttcatcgag aagcagttga tagattatgc
     1321 aaagaacagc aagaaagttg ttgggaattc tacttcacta ctttctccgt atctccattt
     1381 cggggaaata agcgtcagac acgttttcca gtgtgcccgg atgaaacaaa ttatatgggc
     1441 aagagataag aacagtgaag gagaagaaag tgcagatctt tttcttaggg gaatcggttt
     1501 aagagagtat tctcggtata tatgtttcaa cttcccgttt actcacgagc aatcgttgtt
     1561 gagtcatctt cggtttttcc cttgggatgc tgatgttgat aagttcaagg cctggagaca
     1621 aggcaggacc ggttatccgt tggtggatgc cggaatgaga gagctttggg ctaccggatg
     1681 gatgcataac agaataagag tgattgtttc aagctttgct gtgaagtttc ttctccttcc
     1741 atggaaatgg ggaatgaagt atttctggga tacacttttg gatgctgatt tggaatgtga
     1801 catccttggc tggcagtata tctctgggag tatccccgat ggccacgagc ttgatcgctt
     1861 ggacaatccc gcgttacaag gcgccaaata tgacccagaa ggtgagtaca taaggcaatg
     1921 gcttcccgag cttgcgagat tgccaactga atggatccat catccatggg acgctccttt
     1981 aaccgtactc aaagcttctg gtgtggaact cggaacaaac tatgcgaaac ccattgtaga
     2041 catcgacaca gctcgtgagc tactagctaa agctatttca agaacccgta gagcacagat
     2101 catgatcgga gcagcagccc gggatccacc ggacctcgac aacatggtga gcaagggcga
     2161 ggaggataac atggccatca tcaaggagtt catgcgcttc aaggtgcaca tggagggctc
     2221 cgtgaacggc cacgagttcg agatcgaggg cgagggcgag ggccgcccct acgagggcac
     2281 ccagaccgcc aagctgaagg tgaccaaggg tggccccctg cccttcgcct gggacatcct
     2341 gtcccctcag ttcatgtacg gctccaaggc ctacgtgaag caccccgccg acatccccga
     2401 ctacttgaag ctgtccttcc ccgagggctt caagtgggag cgcgtgatga acttcgagga
     2461 cggcggcgtg gtgaccgtga cccaggactc ctccctgcag gacggcgagt tcatctacaa
     2521 ggtgaagctg cgcggcacca acttcccctc cgacggcccc gtaatgcaga agaagaccat
     2581 gggctgggag gcctcctccg agcggatgta ccccgaggac ggcgccctga agggcgagat
     2641 caagcagagg ctgaagctga aggacggcgg ccactacgac gctgaggtca agaccaccta
     2701 caaggccaag aagcccgtgc agctgcccgg cgcctacaac gtcaacatca agttggacat
     2761 cacctcccac aacgaggact acaccatcgt ggaacagtac gaacgcgccg agggccgcca
     2821 ctccaccggc ggcatggacg agctgtacaa gtaaagcggc cgcgactcta gatcataatc
     2881 agccatacca catttgtaga ggttttactt gctttaaaaa acctcccaca cctccccctg
     2941 aacctgaaac ataaaatgaa tgcaattgtt gttgttaact tgtttattgc agcttataat
     3001 ggttacaaat aaagcaatag catcacaaat ttcacaaata aagcattttt ttcactgcat
     3061 tctagttgtg gtttgtccaa actcatcaat gtatcttaag gcgtaaattg taagcgttaa
     3121 tattttgtta aaattcgcgt taaatttttg ttaaatcagc tcatttttta accaataggc
     3181 cgaaatcggc aaaatccctt ataaatcaaa agaatagacc gagatagggt tgagtgttgt
     3241 tccagtttgg aacaagagtc cactattaaa gaacgtggac tccaacgtca aagggcgaaa
     3301 aaccgtctat cagggcgatg gcccactacg tgaaccatca ccctaatcaa gttttttggg
     3361 gtcgaggtgc cgtaaagcac taaatcggaa ccctaaaggg agcccccgat ttagagcttg
     3421 acggggaaag ccggcgaacg tggcgagaaa ggaagggaag aaagcgaaag gagcgggcgc
     3481 tagggcgctg gcaagtgtag cggtcacgct gcgcgtaacc accacacccg ccgcgcttaa
     3541 tgcgccgcta cagggcgcgt caggtggcac ttttcgggga aatgtgcgcg gaacccctat
     3601 ttgtttattt ttctaaatac attcaaatat gtatccgctc atgagacaat aaccctgata
     3661 aatgcttcaa taatattgaa aaaggaagag tcctgaggcg gaaagaacca gctgtggaat
     3721 gtgtgtcagt tagggtgtgg aaagtcccca ggctccccag caggcagaag tatgcaaagc
     3781 atgcatctca attagtcagc aaccaggtgt ggaaagtccc caggctcccc agcaggcaga
     3841 agtatgcaaa gcatgcatct caattagtca gcaaccatag tcccgcccct aactccgccc
     3901 atcccgcccc taactccgcc cagttccgcc cattctccgc cccatggctg actaattttt
     3961 tttatttatg cagaggccga ggccgcctcg gcctctgagc tattccagaa gtagtgagga
     4021 ggcttttttg gaggcctagg cttttgcaaa gatcgatcaa gagacaggat gaggatcgtt
     4081 tcgcatgatt gaacaagatg gattgcacgc aggttctccg gccgcttggg tggagaggct
     4141 attcggctat gactgggcac aacagacaat cggctgctct gatgccgccg tgttccggct
     4201 gtcagcgcag gggcgcccgg ttctttttgt caagaccgac ctgtccggtg ccctgaatga
     4261 actgcaagac gaggcagcgc ggctatcgtg gctggccacg acgggcgttc cttgcgcagc
     4321 tgtgctcgac gttgtcactg aagcgggaag ggactggctg ctattgggcg aagtgccggg
     4381 gcaggatctc ctgtcatctc accttgctcc tgccgagaaa gtatccatca tggctgatgc
     4441 aatgcggcgg ctgcatacgc ttgatccggc tacctgccca ttcgaccacc aagcgaaaca
     4501 tcgcatcgag cgagcacgta ctcggatgga agccggtctt gtcgatcagg atgatctgga
     4561 cgaagagcat caggggctcg cgccagccga actgttcgcc aggctcaagg cgagcatgcc
     4621 cgacggcgag gatctcgtcg tgacccatgg cgatgcctgc ttgccgaata tcatggtgga
     4681 aaatggccgc ttttctggat tcatcgactg tggccggctg ggtgtggcgg accgctatca
     4741 ggacatagcg ttggctaccc gtgatattgc tgaagagctt ggcggcgaat gggctgaccg
     4801 cttcctcgtg ctttacggta tcgccgctcc cgattcgcag cgcatcgcct tctatcgcct
     4861 tcttgacgag ttcttctgag cgggactctg gggttcgaaa tgaccgacca agcgacgccc
     4921 aacctgccat cacgagattt cgattccacc gccgccttct atgaaaggtt gggcttcgga
     4981 atcgttttcc gggacgccgg ctggatgatc ctccagcgcg gggatctcat gctggagttc
     5041 ttcgcccacc ctagggggag gctaactgaa acacggaagg agacaatacc ggaaggaacc
     5101 cgcgctatga cggcaataaa aagacagaat aaaacgcacg gtgttgggtc gtttgttcat
     5161 aaacgcgggg ttcggtccca gggctggcac tctgtcgata ccccaccgag accccattgg
     5221 ggccaatacg cccgcgtttc ttccttttcc ccaccccacc ccccaagttc gggtgaaggc
     5281 ccagggctcg cagccaacgt cggggcggca ggccctgcca tagcctcagg ttactcatat
     5341 atactttaga ttgatttaaa acttcatttt taatttaaaa ggatctaggt gaagatcctt
     5401 tttgataatc tcatgaccaa aatcccttaa cgtgagtttt cgttccactg agcgtcagac
     5461 cccgtagaaa agatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc
     5521 ttgcaaacaa aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca
     5581 actctttttc cgaaggtaac tggcttcagc agagcgcaga taccaaatac tgttcttcta
     5641 gtgtagccgt agttaggcca ccacttcaag aactctgtag caccgcctac atacctcgct
     5701 ctgctaatcc tgttaccagt ggctgctgcc agtggcgata agtcgtgtct taccgggttg
     5761 gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc
     5821 acacagccca gcttggagcg aacgacctac accgaactga gatacctaca gcgtgagcta
     5881 tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg
     5941 gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt
     6001 cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg
     6061 cggagcctat ggaaaaacgc cagcaacgcg gcctttttac ggttcctggc cttttgctgg
     6121 ccttttgctc acatgttctt tcctgcgtta tcccctgatt ctgtggataa ccgtattacc
     6181 gccatgcatt a
//
