LOCUS       sequence-365050-        7956 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cre Dependent ubiquitous expression of constitutively active 
            Retinoic Acid Receptor alpha.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7956)
  AUTHORS   Amamoto R, Wallick GK, Cepko CL
  TITLE     Retinoic acid signaling mediates peripheral cone photoreceptor 
            survival in a mouse model of retina degeneration.
  JOURNAL   Elife. 2022 Mar 22;11. pii: 76389. doi: 10.7554/eLife.76389.
  PUBMED    35315776
REFERENCE   2  (bases 1 to 7956)
  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: "Elife."; 
            date: "2022-03-22"; volume: "11. pii: 76389. doi"; pages: " 
            10.7554/eLife.76389"
COMMENT     Sequence Label: CALNL-RARa-VP16
FEATURES             Location/Qualifiers
     source          1..7956
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        80..383
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     intron          663..1679
                     /label=chimeric intron
                     /note="chimera between introns from chicken beta-actin and 
                     rabbit beta-globin"
     primer_bind     1603..1625
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     1687..1706
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     protein_bind    complement(1754..1787)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             1837..2631
                     /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(1891..1910)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2501..2520
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    2811..2945
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     protein_bind    complement(2959..2992)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     regulatory      3060..3069
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             4602..4835
                     /codon_start=1
                     /gene="UL48"
                     /product="transcriptional activation domain of herpes 
                     simplex virus protein VP16 (Triezenberg et al., 1988; 
                     Cousens et al., 1989)"
                     /label=VP16 AD
                     /translation="APPTDVSLGDELHLDGEDVAMAHADALDDFDLDMLGDGDSPGPGF
                     TPHDSAPYGALDMADFEFEQMFTDALGIDEYGG"
     primer_bind     complement(4946..4965)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    5011..5066
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(5065..5084)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(5427..5443)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5427..5443)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(5440..5462)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    5451..5467
                     /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(5475..5481,5482..5499,5500..5505))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5520..5541
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     rep_origin      5626..5760
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    5780..5914
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5982..5999)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(6153..6741)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(6233..6252)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6912..7703,7704..7772))
                     /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     7535..7554
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7773..7877)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 rkykncatwg myyatwkayk rrktwyyrmk wkwmatmamt tacggggtca ttagttcata
       61 gcccatatat ggagttccgc gttacataac ttacggtaaa tggcccgcct ggctgaccgc
      121 ccaacgaccc ccgcccattg acgtcaataa tgacgtatgt tcccatagta acgccaatag
      181 ggactttcca ttgacgtcaa tgggtggagt atttacggta aactgcccac ttggcagtac
      241 atcaagtgta tcatatgcca agtacgcccc ctattgacgt caatgacggt aaatggcccg
      301 cctggcatta tgcccagtac atgaccttat gggactttcc tacttggcag tacatctacg
      361 tattagtcat cgctattacc atggtcgagg tgagccccac gttctgcttc actctcccca
      421 tctccccccc ctccccaccc ccaattttgt atttatttat tttttaatta ttttgtgcag
      481 cgatgggggc gggggggggg ggggggsgcg cgccrggsgg ggsggggsgg ggsgrggggs
      541 ggggsggggs grggsggrgr ggkgsggsgg crgccaatca gagcggcgcg ctccgaaagt
      601 ttccttttat ggcgaggcgg cggcggcggc ggccctataa aaagcgaagc gcgcggcggg
      661 cgggagtcgc tgcgcgctgc cttcgccccg tgccccgctc cgccgccgcc tcgcgccgcc
      721 cgccccggct ctgactgacc gcgttactcc cacaggtgag cgggcgggac ggcccttctc
      781 ctccgggctg taattagcgc ttggtttaat gacggcttgt ttcttttctg tggctgcgtg
      841 aaagccttga ggggctccgg gagggccctt tgtgcggggg gagcggctcg gggggtgcgt
      901 gcgtgtgtgt gtgcgtgggg agcgccgcgt gcggctccgc gctgcccggc ggctgtgagc
      961 gctgcgggcg cggcgcgggg ctttgtgcgc tccgcagtgt gcgcgagggg agcgcggccg
     1021 ggggcggtgc cccgcggtgc ggggggggct gcgaggggaa caaaggctgc gtgcggggtg
     1081 tgtgcgtggg ggggtgagca gggggtgtgg gcgcgtcggt cgggctgcaa ccccccctgc
     1141 acccccctcc ccgagttgct gagcacggcc cggcttcggg tgcggggctc cgtacggggc
     1201 gtggcgcggg gctcgccgtg ccgggcgggg ggtggcggca ggkgggggtg ccgggcgggg
     1261 cggggccgcc ycgggccggg grgggckcgg gggrggggcg cggcggcccc cggagcgccg
     1321 gcggctgtcg aggcgcggcg agccgcagcc attgcctttt atggtaatcg tgcgagaggg
     1381 cgcagggact tcctttgtcc caaatctgtg cggagccgaa atctgggagg cgccgccgca
     1441 ccccctctag cgggcgcggg gcgaagcggt gcggcgccgg caggaaggaa atgggcgggg
     1501 agggccttcg tgcgtcgccg cgccgccgtc cccttctccc tctccagcct cggggctgtc
     1561 cgcgggggga cggctgcctt cgggggggac ggggcagggc ggggttcggc ttctggcgtg
     1621 tgaccggcgg ctctagagcc tctgctaacc atgttcatgc cttcttcttt ttcctacagc
     1681 tcctgggcaa cgtgctggtt attgtgctgt ctcatcattt tggcaaagaa ttgattaatt
     1741 cgagcgaacg cgtataactt cgtatagcat acattatacg aagttatctc gagtcggatt
     1801 tgatctgatc aagagacagg atgaggatcg tttcgcatga ttgaacaaga tggattgcac
     1861 gcaggttctc cggccgcttg ggtggagagg ctattcggct atgactgggc acaacagaca
     1921 atcggctgct ctgatgccgc cgtgttccgg ctgtcagcgc aggggcgccc ggttcttttt
     1981 gtcaagaccg acctgtccgg tgccctgaat gaactgcagg acgaggcagc gcggctatcg
     2041 tggctggcca cgacgggcgt tccttgcgca gctgtgctcg acgttgtcac tgaagcggga
     2101 agggactggc tgctattggg cgaagtgccg gggcaggatc tcctgtcatc tcaccttgct
     2161 cctgccgaga aagtatccat catggctgat gcaatgcggc ggctgcatac gcttgatccg
     2221 gctacctgcc cattcgacca ccaagcgaaa catcgcatcg agcgagcacg tactcggatg
     2281 gaagccggtc ttgtcgatca ggatgatctg gacgaagagc atcaggggct cgcgccagcc
     2341 gaactgttcg ccaggctcaa ggcgcgcatg cccgacggcg aggatctcgt cgtgacccat
     2401 ggcgatgcct gcttgccgaa tatcatggtg gaaaatggcc gcttttctgg attcatcgac
     2461 tgtggccggc tgggtgtggc ggaccgctat caggacatag cgttggctac ccgtgatatt
     2521 gctgaagagc ttggcggcga atgggctgac cgcttcctcg tgctttacgg tatcgccgct
     2581 cccgattcgc agcgcatcgc cttctatcgc cttcttgacg agttcttctg agcgggactc
     2641 tggggttcga aatgaccgac caagcgacgc ccaacctgcc atcacgagat ttcgattcca
     2701 ccgccgcctt ctatgaaagg ttgggcttcg gaatcgtttt ccgggacgcc ggctggatga
     2761 tcctccagcg cggggatctc atgctggagt tcttcgccca ccccatcgat aacttgttta
     2821 ttgcagctta taatggttac aaataaagca atagcatcac aaatttcaca aataaagcat
     2881 ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct tatcatgtct
     2941 ggatcaatcc gaacgcgtat aacttcgtat agcatacatt atacgaagtt atctcgagtc
     3001 gctcggtacg atttaaattg aattctgcag tcgacggtac cgcgggcccg ggatccaccg
     3061 ccaccatggc cagcaatagc agttcctgcc caacacctgg gggcgggcac ctcaatgggt
     3121 acccagtacc cccctacgcc ttcttctttc cccctatgct gggtggactc tccccacccg
     3181 gcgctctcac cagcctccag caccagcttc cagtcagtgg ttacagcaca ccgtccccag
     3241 ccaccatcga gacccagagc agcagttccg aagagatagt acccagccct ccctcaccac
     3301 cgcccctgcc ccgcatctac aagccttgct ttgtttgtca agacaaatca tccggctacc
     3361 actatggggt cagtgcctgt gagggctgta agggcttctt ccgacgaagc atccagaaga
     3421 acatggtgta tacgtgtcac cgggacaaga actgcatcat caacaaggtg acccggaacc
     3481 gctgccagta ctgccggctg cagaaatgtt tcgacgtggg catgtcccag gagtcggtgc
     3541 gaaacgatcg aaacaaaaag aagaaagagg cacccaagcc cgagtgctca gagagctaca
     3601 cgctgacgcc tgaggtgggc gagctcattg agaaggttcg caaagcgcac caggagacct
     3661 tcccggccct ctgccagctg ggcaagtaca ctacgaacaa cagctcagaa caacgagtct
     3721 ccctggacat tgacctctgg gacaagttca gtgaactctc caccaagtgc atcattaaga
     3781 ctgtggagtt cgccaagcag cttcccggct tcaccaccct caccatcgcc gaccagatca
     3841 ccctcctcaa ggctgcctgc ctggatatcc tgattctgcg aatctgcacg cggtacacgc
     3901 ctgagcaaga cacaatgacc ttctcagatg gactgaccct gaaccggact cagatgcaca
     3961 acgctggctt tggccccctc accgacttgg tctttgcctt cgccaaccag ctgctgcccc
     4021 tggagatgga cgatgctgag actggactgc tcagtgccat ctgcctcatc tgtggagacc
     4081 gacaggacct ggagcagcca gacaaggtgg acatgctgca agagccgctg ctggaagcac
     4141 tgaaagtcta cgtccggaaa cggaggccca gccgacccca catgttcccc aagatgctga
     4201 tgaagatcac agaccttcgg agcatcagcg ccaagggagc tgaacgggtg atcacattga
     4261 agatggagat cccaggctcc atgccaccgc tgatccagga aatgctggag aactctgagg
     4321 gcttggacac tctaagcgga cagtcggggg gcggaacacg agatgggggt ggcctggccc
     4381 cccctccggg tagctgtagc cccagcctca gtcccagctc ccacagaagc agcccagcca
     4441 cccaatcccc aggaccggtc cgcgcgcgta cgaaaaacaa ttacgggtct accatcgagg
     4501 gcctgctcga tctcccggac gacgacgccc ccgaagaggc ggggctggcg gctccgcgcc
     4561 tgtcctttct ccccgcggga cacacgcgca gactgtcgac ggcccccccg accgatgtca
     4621 gcctggggga cgagctccac ttagacggcg aggacgtggc gatggcgcat gccgacgcgc
     4681 tagacgattt cgatctggac atgttggggg acggggattc cccgggtccg ggatttaccc
     4741 cccacgactc cgccccctac ggcgctctgg atatggccga cttcgagttt gagcagatgt
     4801 ttaccgatgc ccttggaatt gacgagtacg gtgggtaggc ggccgctctc ctcacgtgca
     4861 ggctgtgcac tcctcaggtg caggctgcct atcagaaggt ggtggctggt gtggccaatg
     4921 ccctggctca caaataccac tgagatcttt ttccctctgc caaaaattat ggggacatca
     4981 tgaagcccct tgagcatctg acttctggct aataaaggaa atttattttc attgcaatag
     5041 tgtgttggaa ttttttgtgt ctctcactcg gaaggacata tgggagggca aatcatttaa
     5101 aacatcagaa tgagtatttg gtttagagtt tggcaacata tgcccatatg ctggctgcca
     5161 tgaacaaagg ttggctataa agaggtcatc agtatatgaa acagccccct gctgtccatt
     5221 ccttattcca tagaaaagcc ttgacttgag gttagatttt ttttatattt tgttttgtgt
     5281 tatttttttc tttaacatcc ctaaaatttt ccttacatgt tttactagcc agatttttcc
     5341 tcctctcctg actactccca gtcatagctg tccctcttct cttatggaga tccctcgacc
     5401 tgcagcccaa gcttggcgta atcatggtca tagctgtttc ctgtgtgaaa ttgttatccg
     5461 ctcacaattc cacacaacat acgagccgga agcataaagt gtaaagcctg gggtgcctaa
     5521 tgagtgagct aactcacatt aattgcgttg cgctcactgc ccgctttcca gtcgggaaac
     5581 ctgtcgtgcc agcggatccg catctcaatt agtcagcaac catagtcccg cccctaactc
     5641 cgcccagttc cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg
     5701 ccgaggccgc ctcggcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc
     5761 taggcttttg caaaaagcta acttgtttat tgcagcttat aatggttaca aataaagcaa
     5821 tagcatcaca aatttcacaa ataaagcatt tttttcactg cattctagtt gtggtttgtc
     5881 caaactcatc aatgtatctt atcatgtctg gatccgctgc attaatgaat cggccaacgc
     5941 gcggggagag gcggtttgcg tattgggcgc tcttccgctt cctcgctcac tgactcgctg
     6001 cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaaggcggt aatacggtta
     6061 tccacagaat caggggataa cgcaggaaag aacatgtgag caaaaggcca gcaaaaggcc
     6121 aggaaccgta aaaaggccgc gttgctggcg tttttccata ggctccgccc ccctgacgag
     6181 catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac
     6241 caggcgtttc cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc
     6301 ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag ctcacgctgt
     6361 aggtatctca gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc
     6421 gttcagcccg accgctgcgc cttatccggt aactatcgtc ttgagtccaa cccggtaaga
     6481 cacgacttat cgccactggc agcagccact ggtaacagga ttagcagagc gaggtatgta
     6541 ggcggtgcta cagagttctt gaagtggtgg cctaactacg gctacactag aagaacagta
     6601 tttggtatct gcgctctgct gaagccagtt accttcggaa aaagagttgg tagctcttga
     6661 tccggcaaac aaaccaccgc tggtagcggt ggtttttttg tttgcaagca gcagattacg
     6721 cgcagaaaaa aaggatctca agaagatcct ttgatctttt ctacggggtc tgacgctcag
     6781 tggaacgaaa actcacgtta agggattttg gtcatgagat tatcaaaaag gatcttcacc
     6841 tagatccttt taaattaaaa atgaagtttt aaatcaatct aaagtatata tgagtaaact
     6901 tggtctgaca gttaccaatg cttaatcagt gaggcaccta tctcagcgat ctgtctattt
     6961 cgttcatcca tagttgcctg actccccgtc gtgtagataa ctacgatacg ggagggctta
     7021 ccatctggcc ccagtgctgc aatgataccg cgagacccac gctcaccggc tccagattta
     7081 tcagcaataa accagccagc cggaagggcc gagcgcagaa gtggtcctgc aactttatcc
     7141 gcctccatcc agtctattaa ttgttgccgg gaagctagag taagtagttc gccagttaat
     7201 agtttgcgca acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc gtcgtttggt
     7261 atggcttcat tcagctccgg ttcccaacga tcaaggcgag ttacatgatc ccccatgttg
     7321 tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg tcagaagtaa gttggccgca
     7381 gtgttatcac tcatggttat ggcagcactg cataattctc ttactgtcat gccatccgta
     7441 agatgctttt ctgtgactgg tgagtactca accaagtcat tctgagaata gtgtatgcgg
     7501 cgaccgagtt gctcttgccc ggcgtcaata cgggataata ccgcgccaca tagcagaact
     7561 ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa aactctcaag gatcttaccg
     7621 ctgttgagat ccagttcgat gtaacccact cgtgcaccca actgatcttc agcatctttt
     7681 actttcacca gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc aaaaaaggga
     7741 ataagggcga cacggaaatg ttgaatactc atactcttcc tttttcaata ttattgaagc
     7801 atttatcagg gttattgtct catgagcgga tacatatttg aatgtattta gaaaaataaa
     7861 caaatagggg ttccgcgcac atttccccga aaagtgccac ctgggtcgac attgattatt
     7921 gactagttat taatagtmmy saawwrygss rycwkk
//
