LOCUS       NM_001403724            4271 bp    mRNA    linear   ROD 25-FEB-2025
DEFINITION  Mus musculus CCCTC-binding factor (Ctcf), transcript variant 4,
            mRNA.
ACCESSION   NM_001403724 XM_006530648
VERSION     NM_001403724.1
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 4271)
  AUTHORS   Clemot-Dupont,S., Lourenco Fernandes,J.A., Larrigan,S., Sun,X.,
            Medisetti,S., Stanley,R., El Hankouri,Z., Joshi,S.V.,
            Picketts,D.J., Shekhar,K. and Mattar,P.
  TITLE     The chromatin remodeler ADNP regulates neurodevelopmental disorder
            risk genes and neocortical neurogenesis
  JOURNAL   Proc Natl Acad Sci U S A 122 (3), e2405981122 (2025)
   PUBMED   39808658
REFERENCE   2  (bases 1 to 4271)
  AUTHORS   Zhang,J., Hu,G., Lu,Y., Ren,H., Huang,Y., Wen,Y., Ji,B., Wang,D.,
            Wang,H., Liu,H., Ma,N., Zhang,L., Pan,G., Qu,Y., Wang,H., Zhang,W.,
            Miao,Z. and Yao,H.
  TITLE     CTCF mutation at R567 causes developmental disorders via 3D genome
            rearrangement and abnormal neurodevelopment
  JOURNAL   Nat Commun 15 (1), 5524 (2024)
   PUBMED   38951485
  REMARK    GeneRIF: CTCF mutation at R567 causes developmental disorders via
            3D genome rearrangement and abnormal neurodevelopment.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 4271)
  AUTHORS   Iurlaro,M., Masoni,F., Flyamer,I.M., Wirbelauer,C., Iskar,M.,
            Burger,L., Giorgetti,L. and Schubeler,D.
  TITLE     Systematic assessment of ISWI subunits shows that NURF creates
            local accessibility for CTCF
  JOURNAL   Nat Genet 56 (6), 1203-1212 (2024)
   PUBMED   38816647
  REMARK    GeneRIF: Systematic assessment of ISWI subunits shows that NURF
            creates local accessibility for CTCF.
            Erratum:[Nat Genet. 2024 Nov;56(11):2574-2575. doi:
            10.1038/s41588-024-01985-3. PMID: 39487354]
REFERENCE   4  (bases 1 to 4271)
  AUTHORS   Liu,C., Nagashima,H., Fernando,N., Bass,V., Gopalakrishnan,J.,
            Signorella,S., Montgomery,W., Lim,A.I., Harrison,O., Reich,L.,
            Yao,C., Sun,H.W., Brooks,S.R., Jiang,K., Nagarajan,V., Zhao,Y.,
            Jung,S., Phillips,R., Mikami,Y., Lareau,C.A., Kanno,Y.,
            Jankovic,D., Aryee,M.J., Pekowska,A., Belkaid,Y., O'Shea,J. and
            Shih,H.Y.
  TITLE     A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine
            expression profiles and plays a critical role in early Th1 cell
            fate specification
  JOURNAL   Immunity 57 (5), 1005-1018 (2024)
   PUBMED   38697116
  REMARK    GeneRIF: A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes
            cytokine expression profiles and plays a critical role in early Th1
            cell fate specification.
REFERENCE   5  (bases 1 to 4271)
  AUTHORS   Wang,W., Gao,R., Yang,D., Ma,M., Zang,R., Wang,X., Chen,C., Kou,X.,
            Zhao,Y., Chen,J., Liu,X., Lu,J., Xu,B., Liu,J., Huang,Y., Chen,C.,
            Wang,H., Gao,S., Zhang,Y. and Gao,Y.
  TITLE     ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst
            formation in mice
  JOURNAL   Genes Dev 38 (3-4), 168-188 (2024)
   PUBMED   38479840
  REMARK    GeneRIF: ADNP modulates SINE B2-derived CTCF-binding sites during
            blastocyst formation in mice.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4271)
  AUTHORS   Farrell,C.M., West,A.G. and Felsenfeld,G.
  TITLE     Conserved CTCF insulator elements flank the mouse and human
            beta-globin loci
  JOURNAL   Mol Cell Biol 22 (11), 3820-3831 (2002)
   PUBMED   11997516
  REMARK    GeneRIF: Conserved CTCF insulator elements flank the mouse and
            human beta-globin loci.
REFERENCE   7  (bases 1 to 4271)
  AUTHORS   Burke,L.J., Hollemann,T., Pieler,T. and Renkawitz,R.
  TITLE     Molecular cloning and expression of the chromatin insulator protein
            CTCF in Xenopus laevis
  JOURNAL   Mech Dev 113 (1), 95-98 (2002)
   PUBMED   11900981
REFERENCE   8  (bases 1 to 4271)
  AUTHORS   Chao,W., Huynh,K.D., Spencer,R.J., Davidow,L.S. and Lee,J.T.
  TITLE     CTCF, a candidate trans-acting factor for X-inactivation choice
  JOURNAL   Science 295 (5553), 345-347 (2002)
   PUBMED   11743158
  REMARK    GeneRIF: It's proposed that Tsix and CTCF together establish a
            regulatable epigenetic switch for X-inactivation.
REFERENCE   9  (bases 1 to 4271)
  AUTHORS   Lutz,M., Burke,L.J., Barreto,G., Goeman,F., Greb,H., Arnold,R.,
            Schultheiss,H., Brehm,A., Kouzarides,T., Lobanenkov,V. and
            Renkawitz,R.
  TITLE     Transcriptional repression by the insulator protein CTCF involves
            histone deacetylases
  JOURNAL   Nucleic Acids Res 28 (8), 1707-1713 (2000)
   PUBMED   10734189
REFERENCE   10 (bases 1 to 4271)
  AUTHORS   Filippova,G.N., Fagerlie,S., Klenova,E.M., Myers,C., Dehner,Y.,
            Goodwin,G., Neiman,P.E., Collins,S.J. and Lobanenkov,V.V.
  TITLE     An exceptionally conserved transcriptional repressor, CTCF, employs
            different combinations of zinc fingers to bind diverged promoter
            sequences of avian and mammalian c-myc oncogenes
  JOURNAL   Mol Cell Biol 16 (6), 2802-2813 (1996)
   PUBMED   8649389
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC127419.3 and AC152826.2.
            
            On Apr 4, 2022 this sequence version replaced XM_006530648.2.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13948564.4200465.1,
                                           SRR13422600.150052.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849380, SAMN00849381
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-631               AC127419.3         128038-128668
            632-748             AC127419.3         134605-134721
            749-1538            AC127419.3         154843-155632
            1539-1709           AC127419.3         155945-156115
            1710-1843           AC127419.3         157748-157881
            1844-1964           AC127419.3         161320-161440
            1965-2114           AC127419.3         162380-162529
            2115-2275           AC127419.3         165958-166118
            2276-2290           AC127419.3         167085-167099
            2291-2458           AC152826.2         157916-158083       c
            2459-2594           AC152826.2         156744-156879       c
            2595-2783           AC152826.2         153835-154023       c
            2784-4271           AC152826.2         151172-152659       c
FEATURES             Location/Qualifiers
     source          1..4271
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="8"
                     /map="8 53.04 cM"
     gene            1..4271
                     /gene="Ctcf"
                     /note="CCCTC-binding factor"
                     /db_xref="GeneID:13018"
                     /db_xref="MGI:MGI:109447"
     exon            1..631
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            632..748
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            749..1538
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     CDS             758..2968
                     /gene="Ctcf"
                     /note="isoform 1 is encoded by transcript variant 4;
                     transcriptional repressor CTCF; CTCFL paralog; 11-zinc
                     finger protein"
                     /codon_start=1
                     /product="transcriptional repressor CTCF isoform 1"
                     /protein_id="NP_001390653.1"
                     /db_xref="GeneID:13018"
                     /db_xref="MGI:MGI:109447"
                     /translation="MEGEAVEAIVEESETFIKGKERKTYQRRREGGQEEDACHLPQNQ
                     TDGGEVVQDVNSSVQMVMMEQLDPTLLQMKTEVMEGTVAPEAEAAVDDTQIITLQVVN
                     MEEQPINIGELQLVQVPVPVTVPVATTSVEELQGAYENEVSKEGLAESEPMICHTLPL
                     PEGFQVVKVGANGEVETLEQGELPPQEDSSWQKDPDYQPPAKKTKKTKKSKLRYTEEG
                     KDVDVSVYDFEEEQQEGLLSEVNAEKVVGNMKPPKPTKIKKKGVKKTFQCELCSYTCP
                     RRSNLDRHMKSHTDERPHKCHLCGRAFRTVTLLRNHLNTHTGTRPHKCPDCDMAFVTS
                     GELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTY
                     KLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKS
                     DLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYACRQER
                     HMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTR
                     RNTMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKKEDSSDSEENAEPDLDDNE
                     EEEEPAVEIEPEPEPQPQPPPPPQPVAPAPPPAKKRRGRPPGRTNQPKQNQPTAIIQV
                     EDQNTGAIENIIVEVKKEPDAEPAEGEEEEAQAATTDAPNGDLTPEMILSMMDR"
     exon            1539..1709
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            1710..1843
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            1844..1964
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            1965..2114
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            2115..2275
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            2276..2458
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            2459..2594
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            2595..2783
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     exon            2784..4271
                     /gene="Ctcf"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4246..4251
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ctcf"
                     /note="hexamer: AATAAA"
     polyA_site      4271
                     /gene="Ctcf"
                     /note="major polyA site"
ORIGIN      
        1 ccctcctccc aacatggtag gcctctggcg gcggtggcga cagaggcctg cgcgctcggc
       61 gactccattt tccttccttt gtctctaccc tcgaggccgg cttttggccc ggctgatctt
      121 cgggccacgg cccgccctct gcccctcccg cgacggatac cccttaccga gtctggaccc
      181 tctgaggctc ggttgccgcc gcttgcttcg cctaggggtt ctgaaccctc ggccggccgc
      241 ttagccaggt cccggaaccg tgtgggtgtc gggtcccgac cgacgcgcct cagactcccc
      301 atcttcaagt ccagccggtc ccggaaccta cccgatctcc ctgcgttgct tctccagcag
      361 ctggggtgct ctctagtctc tcgtagtccg atcgtccccg ctgccggtct ccgtcgccgc
      421 cgagtgtcgc aggcggcgct gctgtggctg cgagcagagg ggacccctga gctgccgaga
      481 gctccctctg caaggctggc tgagctgctc gcgcctcgac gccgcccgag cgggcggggg
      541 aacgcgcgct cgccgccccc gccgggcccc gctgcgcccc caaactcacg ccagggcatc
      601 gcgcgggacc cgaccggtgc ggcccccaat gaatgaccac aaatctagaa ccaaagaaca
      661 cgatgcacta gcagacagac tcgaagctag agactggaga tctgggttct tttgtccttc
      721 ctcaaactga ttttgcagcc acggagagga aggggagatg gaaggtgagg cggttgaagc
      781 cattgtggag gagtctgaaa ctttcattaa aggaaaagaa agaaagactt accagagacg
      841 ccgggaaggg ggccaggaag aagatgcttg ccacctgccc cagaaccaga cagatggggg
      901 tgaggtggtc caggatgtca acagcagtgt acagatggta atgatggaac agctggatcc
      961 tacccttctc cagatgaaga ctgaagtcat ggagggtaca gtggctccgg aagcagaggc
     1021 tgcagtggac gatacccaga tcataacctt gcaggttgta aatatggagg aacagcccat
     1081 taacatagga gagcttcagc ttgtccaagt acctgttcct gtgacggtac ctgttgctac
     1141 tacttcagta gaagaacttc agggggctta tgagaatgaa gtgtctaaag agggccttgc
     1201 agaaagtgaa ccgatgatat gtcacacctt acctttgcct gaaggatttc aggtggtgaa
     1261 agtgggggcc aatggagaag tggagacact agagcagggc gagcttcctc ctcaggaaga
     1321 ctctagctgg caaaaagacc cagactatca gccaccagcc aaaaaaacaa agaaaaccaa
     1381 aaagagcaaa cttcgttaca cagaagaggg caaagacgtg gatgtgtctg tgtatgattt
     1441 tgaggaagaa cagcaggaag gactgctgtc tgaggttaat gcagagaaag tagttggtaa
     1501 tatgaagcct ccgaagccaa caaaaattaa aaaaaaaggt gtaaagaaaa cattccagtg
     1561 tgagctttgc agttacacat gtccccggcg ttcaaatttg gatcgtcaca tgaaaagcca
     1621 cactgatgag agaccacaca aatgccatct gtgtggcaga gcattcagaa cagtgaccct
     1681 cctgaggaat catctgaaca cacacacagg tactcgtcct cacaagtgcc cagactgcga
     1741 tatggccttt gtgaccagtg gagaattggt gcggcatcgt cgttataaac acactcatga
     1801 gaaaccattt aagtgttcca tgtgtgatta tgccagtgta gaagtcagca aattaaaacg
     1861 acacattcgc tctcatactg gagagcgccc gttccagtgc agtttgtgca gttatgccag
     1921 cagggacaca tacaagctga aaaggcatat gagaacccat tcaggggaaa aaccttatga
     1981 atgttatatt tgtcacgctc ggtttaccca gagtggtacc atgaagatgc acattttaca
     2041 gaagcacaca gaaaatgtgg ccaaatttca ttgtccccat tgtgacactg tcatagcccg
     2101 aaaaagtgat ttgggtgtcc acttgcgaaa gcagcattcc tatattgaac agggcaaaaa
     2161 atgtcgctac tgtgatgctg tgtttcatga gcgatatgct ctcatccagc atcaaaaatc
     2221 acacaaaaat gagaagcgct tcaagtgtga ccagtgtgat tatgcttgta gacaggagcg
     2281 gcacatgatc atgcacaagc gcactcacac gggggagaag ccttatgcct gcagccactg
     2341 cgacaagacc ttccgccaga aacagctcct cgacatgcat ttcaagcgct atcatgatcc
     2401 caactttgtc cctgctgcct ttgtctgttc caagtgtggg aaaacattca cccgccggaa
     2461 cacaatggca agacatgcag ataactgtgc tggtccagat ggcgtagagg gggaaaatgg
     2521 aggggagaca aagaagagca aacgaggaag aaaaagaaag atgcgatcta aaaaagaaga
     2581 ctcctctgac agtgaagaaa atgctgagcc ggatctcgat gacaatgagg aggaggagga
     2641 gcctgctgta gaaattgaac ctgagccaga gcctcagccc cagcctccgc ctccacctca
     2701 gcctgtggcc ccggcccccc cacctgccaa gaagagaagg gggcgacctc ctggaagaac
     2761 caaccagccc aaacagaacc agccaacagc catcattcag gtcgaagatc agaatacagg
     2821 tgcaattgag aacattatag ttgaagtcaa aaaggagcca gatgccgagc ctgcggaggg
     2881 ggaagaagag gaggctcagg cagccaccac agacgccccc aacggagacc tcacgcctga
     2941 gatgatcctc agcatgatgg accggtgatg ctggggcctt gctcggcacc aggactattg
     3001 ggctgtgttt aaacggccca aatcttaatt tttctctttt ttttctttgg ctttgggaac
     3061 ggcataattt tacaccattt taccaaacat actgagaacg aaaacttcaa ggatgatgtt
     3121 agaaaaatgt gatttaacta gaacttgttt gatgttagca aatcatggaa tgttctaagt
     3181 ctctgagggt ttactgtgaa gtgttgagga cagtgttgat gcctaactag ttttcttaga
     3241 tggaaacaga gacattgagc cctctctctt gatcgtaaac cactccagaa cggccacggg
     3301 tttcccagag ttctatggtc ttcccaagag aatttttaat tgtaaatgca gacttgggaa
     3361 ggacttggac ttttaacctg gttttgcttt tgcttttcct gactcccttt gctcagagtc
     3421 agttgcacac cagtaggatg gcatgctacg atcagtttct gtcctgaaag ctttgcctct
     3481 ttcttggcaa agtttctggt atggtcaagc ttgtaaataa ccttttttac attttaatct
     3541 tttccattaa ttaagaggtt gaaaagaagt acagtgtaag aaaacccagc attttaatta
     3601 tttgcaaatt aaggtgccac agacacagac ttagtggtat gtaaatgttg actcggatca
     3661 caatcatgta gcagagggca ctgggcctgt tgcctgccag tcatggacac ccatgtgaaa
     3721 aatcctgatt tccagctcat ggagccagcg tttgaacctt gaacaaataa atttcattta
     3781 tgattttctc atcaacattt tctttgctct gtttgtagct gaatgttaca tttttttaaa
     3841 aatctctgtt caagccagaa gagttgatta tgagtggcca cagcaaccct ggcaagctgg
     3901 gccaaaaaat ttcagtaggt cagtaattta aacttcacat ctggaaaaaa aattattaat
     3961 aatgtgaaac aaaccaactt aaaaagtgat tcttgcacat gaattgtcac atattatatg
     4021 tgttttttaa agagcctcag tctgactgat ttcaaacact ttttttctcc tgtgtattgc
     4081 ttttaagaga gccatcagtt agctatcaga atctaggttg atgcattttt gtacttagct
     4141 gtactgtgtg atatttttca ttattttagg atgccaacat gagacctgta ataaaatatg
     4201 taatggggtt gaaggctggg gaggaggatc tactgctgta cagctaataa atcataacgg
     4261 attaacaggc a
//
