LOCUS       sequence-182485-        7566 bp    DNA     linear   UNA 15-DEC-2025
DEFINITION  For lncRNA CAG promoter homologue recombination mediated knockin.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      natural DNA sequence
  ORGANISM  unspecified
REFERENCE   1  (bases 1 to 7566)
  AUTHORS   Yin Y, Yan P, Lu J, Song G, Zhu Y, Li Z, Zhao Y, Shen B, Huang X, 
            Zhu H, Orkin SH, Shen X
  TITLE     Opposing Roles for the lncRNA Haunt and Its Genomic Locus in 
            Regulating HOXA Gene Activation during Embryonic Stem Cell 
            Differentiation.
  JOURNAL   Cell Stem Cell. 2015 May 7;16(5):504-16. doi: 
            10.1016/j.stem.2015.03.007. Epub 2015 Apr 16.
  PUBMED    25891907
REFERENCE   2  (bases 1 to 7566)
  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.stem.2015.03.007"; journalName: "Cell Stem Cell"; date: 
            "2015-05-7- 7"; volume: "16"; issue: "5"; pages: "504-16"
COMMENT     Sequence Label: PB-CAG-HRKI(Haunt P-Inr2-cDNA KI)
FEATURES             Location/Qualifiers
     source          1..7566
                     /mol_type="genomic DNA"
                     /organism="unspecified"
     primer_bind     325..347
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     409..428
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     polyA_signal    1050..1171
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1087..1106)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1141..1160
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     protein_bind    1201..1234
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     promoter        complement(1459..1477)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(1484..1501)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1484..1500)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1493..1515)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      1642..2097
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1729..1748)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1939..1960
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        2123..2227
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2228..2296,2297..3088)
                     /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(2446..2465)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3259..3847
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3748..3767
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4001..4018
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    4135..4156
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(4171..4176,4177..4194,4195..4201)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4209..4225
                     /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)."
     primer_bind     4214..4236
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     4233..4249
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     4233..4249
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     CDS             complement(5284..6309)
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     CDS             complement(5284..6309)
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRG
                     YVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLP
                     ETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQ
                     TVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMF
                     GDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDG
                     NFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAK
                     E"
     promoter        complement(6328..6827)
                     /label=PGK promoter
                     /note="mouse phosphoglycerate kinase 1 promoter"
     primer_bind     complement(6376..6395)
                     /label=mPGK-F
                     /note="Mouse PGK promoter, forward primer"
     primer_bind     6769..6792
                     /label=MSCV-rev
                     /note="Murine stem cell virus, reverse primer"
     protein_bind    6850..6883
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     enhancer        6899..7278
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        7280..7555
                     /label=chicken beta-actin promoter
ORIGIN
        1 gggagggctc gggggagggg cgcggcggcc cccggagcgc cggcggctgt cgaggcgcgg
       61 cgagccgcag ccattgcctt ttatggtaat cgtgcgagag ggcgcaggga cttcctttgt
      121 cccaaatctg tgcggagccg aaatctggga ggcgccgccg caccccctct agcgggcgcg
      181 gggcgaagcg gtgcggcgcc ggcaggaagg aaatgggcgg ggagggcctt cgtgcgtcgc
      241 cgcgccgccg tccccttctc cctctccagc ctcggggctg tccgcggggg gacggctgcc
      301 ttcggggggg acggggcagg gcggggttcg gcttctggcg tgtgaccggc ggctctagag
      361 cctctgctaa ccatgttcat gccttcttct ttttcctaca gctcctgggc aacgtgctgg
      421 ttattgtgct gtctcatcat tttggcaaag aattcctcga cggtatcgat aagctatcac
      481 aagtttgtac attcgaactc tcagctggga gaccgtgggc ggaggtgata caacctgact
      541 gatgatggct gacaaaagaa gaagaaagta gctgagaacc agcagctgaa gaaagcaaga
      601 aaatatgagt gaagtcacaa atgtcaccaa ggaaaggaag aacagaaaaa taacttgaat
      661 attcaagatg ggcagcctag ttcaacgaca catcaagcct tgtgaaaagg tgactccgag
      721 acatggaggc acatgcctgt agcctcacca cacaggcagg tggtggtgaa ttctacacta
      781 accttggcta cacagtgaca cactgcccca aaacagaaac aaaaagcaaa aagtttctca
      841 gtgaacctca gaaaaggttc ctaaggtaac aaaagaatca aaatatgccc tagctcaccc
      901 caaatgccaa gagccttgct atgtttagta agcacctcca taaaatgctg ttttcccgga
      961 agagagctga ggccagagaa gttgccaagt gtcaatccta ccacatcacg ttcctacgtc
     1021 tgccctgtcc tccactcggc accagcgtta acttgtttat tgcagcttat aatggttaca
     1081 aataaagcaa tagcatcaca aatttcacaa ataaagcatt tttttcactg cattctagtt
     1141 gtggtttgtc caaactcatc aatgtatctt aggtacaagt aggcggccgg ccgcgtcgag
     1201 ataacttcgt ataatgtatg ctatacgaag ttatgttttg ttactttata gaagaaattt
     1261 tgagtttttg ttttttttta ataaataaat aaacataaat aaattgtttg ttgaatttat
     1321 tattagtatg taagtgtaaa tataataaaa cttaatatct attcaaatta ataaataaac
     1381 ctcgatatac agactctact ccctgatgct taaagcagct caatgtatcc cactgaagtt
     1441 ctcaggtacc caattcgccc tatagtgagt cgtattacaa ttcactggcc gtcgttttac
     1501 aacgtcgtga ctgggaaaac cctggcgtta cccaacttaa tcgccttgca gcacatcccc
     1561 ctttcgccag ctggcgtaat agcgaagagg cccgcaccga tcgcccttcc caacagttgc
     1621 gcagcctgaa tggcgaatgg gacgcgccct gtagcggcgc attaagcgcg gcgggtgtgg
     1681 tggttacgcg cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt
     1741 tcttcccttc ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcgggggc
     1801 tccctttagg gttccgattt agtgctttac ggcacctcga ccccaaaaaa cttgattagg
     1861 gtgatggttc acgtagtggg ccatcgccct gatagacggt ttttcgccct ttgacgttgg
     1921 agtccacgtt ctttaatagt ggactcttgt tccaaactgg aacaacactc aaccctatct
     1981 cggtctattc ttttgattta taagggattt tgccgatttc ggcctattgg ttaaaaaatg
     2041 agctgattta acaaaaattt aacgcgaatt ttaacaaaat attaacgctt acaatttagg
     2101 tggcactttt cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc
     2161 aaatatgtat ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag
     2221 gaagagtatg agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg
     2281 ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt
     2341 gggtgcacga gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt
     2401 tcgccccgaa gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt
     2461 attatcccgt attgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa
     2521 tgacttggtt gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag
     2581 agaattatgc agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac
     2641 aacgatcgga ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac
     2701 tcgccttgat cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac
     2761 cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac
     2821 tctagcttcc cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact
     2881 tctgcgctcg gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg
     2941 tgggtctcgc ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt
     3001 tatctacacg acggggagtc aggcaactat ggatgaacga aatagacaga tcgctgagat
     3061 aggtgcctca ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta
     3121 gattgattta aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa
     3181 tcttatgacc aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga
     3241 aaagatcaaa ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac
     3301 aaaaaaacca ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt
     3361 tccgaaggta actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc
     3421 gtagttaggc caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat
     3481 cctgttacca gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag
     3541 acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc
     3601 cagcttggag cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag
     3661 cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac
     3721 aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg
     3781 gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct
     3841 atggaaaaac gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc
     3901 tcacatgttc tttcctgcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga
     3961 gtgagctgat accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga
     4021 agcggaagag cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg
     4081 cagctggcac gacaggtttc ccgactggaa agcgggcagt gagcgcaacg caattaatgt
     4141 gagttagctc actcattagg caccccaggc tttacacttt atgcttccgg ctcgtatgtt
     4201 gtgtggaatt gtgagcggat aacaatttca cacaggaaac agctatgacc atgattacgc
     4261 caagctcgaa attaacactc actatagggc gaattgggta cctgagaact tcagtgggat
     4321 acattgagct gctttaagca tcagggagta gaacctgtgt gcactgccat agtgcttcat
     4381 ttatttagac ctaatagaat cagatcagtg tctctccatt tacctttgcc atgctttcaa
     4441 gacattagaa acaagctctt ttgacttcag agacacaaca attagatata aaacactagc
     4501 cttgagtgga tcttggactg tttgaaagcg tcctgacagg taagtgattt ttctatatgc
     4561 ttgaaagttt tcaaaataaa aactttgaag gaagggctct tttccttgtc cttcacttag
     4621 ccgtgctaca gggtgtccgg acaggataat gtatgaggac tgatgtaccc ttttgacctg
     4681 gtggtgtgct ttttcaggca ggttgcttac tgcccaaggg ctccataact ggggaggaca
     4741 caatgagaaa tcaaaccctc acaaacatat cgaggagggt tatcaacacc tcagccaaca
     4801 tgcattcttg aaatattgct ctctctttct aaatagcgcg aatccgtcgc tgtgcattta
     4861 ggacatctca gtcgccgctt ggagctcccg tgaggcgtgc ttgtcaatgc ggtaagtgtc
     4921 actgattttg aactataacg accgcgtgag tcaaaatgac gcatgattat cttttacgtg
     4981 acttttaaga tttaactcat acgataatta tattgttatt tcatgttcta cttacgtgat
     5041 aacttattat atatatattt tcttgttata gatatccaac tatgaaacat tatcataaag
     5101 caatagtaaa gagccttcag taaagagcag gcatttatct aatcccaccc cacccccacc
     5161 cccgtagctc caatccttcc attcaaaatg taggtactct gttctcaccc ttcttaacaa
     5221 agtatgacag gaaaaacttc catgtggaca tctttattgt ttaatagatc atcaatttct
     5281 cgactattcc tttgccctcg gacgagtgct ggggcgtcgg tttccactat cggcgagtac
     5341 ttctacacag ccatcggtcc agacggccgc gcttctgcgg gcgatttgtg tacgcccgac
     5401 agtcccggct ccggatcgga cgattgcgtc gcatcgaccc tgcgcccaag ctgcatcatc
     5461 gaaattgccg tcaaccaagc tctgatagag ttggtcaaga ccaatgcgga gcatatacgc
     5521 ccggagccgc ggcgatcctg caagctccgg atgcctccgc tcgaagtagc gcgtctgctg
     5581 ctccatacaa gccaaccacg gcctccagaa gaagatgttg gcgacctcgt attgggaatc
     5641 cccgaacatc gcctcgctcc agtcaatgac cgctgttatg cggccattgt ccgtcaggac
     5701 attgttggag ccgaaatccg cgtgcacgag gtgccggact tcggggcagt cctcggccca
     5761 aagcatcagc tcatcgagag cctgcgcgac ggacgcactg acggtgtcgt ccatcacagt
     5821 ttgccagtga tacacatggg gatcagcaat cgcgcatatg aaatcacgcc atgtagtgta
     5881 ttgaccgatt ccttgcggtc cgaatgggcc gaacccgctc gtctggctaa gatcggccgc
     5941 agcgatcgca tccatggcct ccgcgaccgg ctgcagaaca gcgggcagtt cggtttcagg
     6001 caggtcttgc aacgtgacac cctgtgcacg gcgggagatg caataggtca ggctctcgct
     6061 gaattcccca atgtcaagca cttccggaat cgggagcgcg gccgatgcaa agtgccgata
     6121 aacataacga tctttgtaga aaccatcggc gcagctattt acccgcagga catatccacg
     6181 ccctcctaca tcgaagctga aagcacgaga ttcttcgccc tccgagagct gcatcaggtc
     6241 ggagacgctg tcgaactttt cgatcagaaa cttctcgaca gacgtcgcgg tgagttcagg
     6301 ctttttcatg gtggcggctg gatcggtcga aaggcccgga gatgaggaag aggagaacag
     6361 cgcggcagac gtgcgctttt gaagcgtgca gaatgccggg cctccggagg accttcgggc
     6421 gcccgccccg cccctgagcc cgcccctgag cccgcccccg gacccacccc ttcccagcct
     6481 ctgagcccag aaagcgaagg agcaaagctg ctattggccg ctgccccaaa ggcctacccg
     6541 cttccattgc tcagcggtgc tgtccatctg cacgagacta gtgagacgtg ctacttccat
     6601 ttgtcacgtc ctgcacgacg cgagctgcgg ggcggggggg aacttcctga ctaggggagg
     6661 agtagaaggt ggcgcgaagg ggccaccaaa gaacggagcc ggttggcgcc taccggtgga
     6721 tgtggaatgt gtgcgaggcc agaggccact tgtgtagcgc caagtgccca gcggggctgc
     6781 taaagcgcat gctccagact gccttgggaa aagcgcctcc cctacccggt agaattcatc
     6841 gatgatatca taacttcgta taatgtatgc tatacgaagt tatgcggccc tcgaggtcga
     6901 cattgattat tgactagtta ttaatagtaa tcaattacgg ggtcattagt tcatagccca
     6961 tatatggagt tccgcgttac ataacttacg gtaaatggcc cgcctggctg accgcccaac
     7021 gacccccgcc cattgacgtc aataatgacg tatgttccca tagtaacgcc aatagggact
     7081 ttccattgac gtcaatgggt ggagtattta cggtaaactg cccacttggc agtacatcaa
     7141 gtgtatcata tgccaagtac gccccctatt gacgtcaatg acggtaaatg gcccgcctgg
     7201 cattatgccc agtacatgac cttatgggac tttcctactt ggcagtacat ctacgtatta
     7261 gtcatcgcta ttaccatggt cgaggtgagc cccacgttct gcttcactct ccccatctcc
     7321 cccccctccc cacccccaat tttgtattta tttatttttt aattattttg tgcagcgatg
     7381 ggggcggggg gggggggggc gcgcgccagg cggggcgggg cggggcgagg ggcggggccg
     7441 ggcgaggcgg agaggtgcgg cggcagccaa tcagagcggc gcgctccgaa agtttccttt
     7501 tatggcgagg cggcggcggc ggcggcccta taaaaagcga agcgcgcggc gggcgggagt
     7561 cgctgc
//
