LOCUS       NM_001191022            2853 bp    mRNA    linear   PRI 05-OCT-2024
DEFINITION  Homo sapiens CCCTC-binding factor (CTCF), transcript variant 2,
            mRNA.
ACCESSION   NM_001191022
VERSION     NM_001191022.2
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2853)
  AUTHORS   Ma,D.B., Zhang,H., Wang,X.L. and Wu,Q.G.
  TITLE     METTL3 aggravates cell damage induced by Streptococcus pneumoniae
            via the NEAT1/CTCF/MUC19 axis
  JOURNAL   Kaohsiung J Med Sci 40 (8), 722-731 (2024)
   PUBMED   38757482
  REMARK    GeneRIF: METTL3 aggravates cell damage induced by Streptococcus
            pneumoniae via the NEAT1/CTCF/MUC19 axis.
REFERENCE   2  (bases 1 to 2853)
  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 2853)
  AUTHORS   Pandey,A., Kakani,P. and Shukla,S.
  TITLE     CTCF and BORIS-mediated autophagy regulation via alternative
            splicing of BNIP3L in breast cancer
  JOURNAL   J Biol Chem 300 (7), 107416 (2024)
   PUBMED   38810696
  REMARK    GeneRIF: CTCF and BORIS-mediated autophagy regulation via
            alternative splicing of BNIP3L in breast cancer.
REFERENCE   4  (bases 1 to 2853)
  AUTHORS   Huber,J., Tanasie,N.L., Zernia,S. and Stigler,J.
  TITLE     Single-molecule imaging reveals a direct role of CTCF's zinc
            fingers in SA interaction and cluster-dependent RNA recruitment
  JOURNAL   Nucleic Acids Res 52 (11), 6490-6506 (2024)
   PUBMED   38742641
  REMARK    GeneRIF: Single-molecule imaging reveals a direct role of CTCF's
            zinc fingers in SA interaction and cluster-dependent RNA
            recruitment.
REFERENCE   5  (bases 1 to 2853)
  AUTHORS   He,T., You,M., Zhu,H., Chen,P. and Fang,S.
  TITLE     CCCTC-binding factor suppresses alpha-2-macroglobulin transcription
            to improve vascular endothelial cell functions in lower extremity
            arteriosclerosis obliterans
  JOURNAL   Gen Physiol Biophys 43 (3), 231-242 (2024)
   PUBMED   38774923
  REMARK    GeneRIF: CCCTC-binding factor suppresses alpha-2-macroglobulin
            transcription to improve vascular endothelial cell functions in
            lower extremity arteriosclerosis obliterans.
REFERENCE   6  (bases 1 to 2853)
  AUTHORS   Bell,A.C., West,A.G. and Felsenfeld,G.
  TITLE     The protein CTCF is required for the enhancer blocking activity of
            vertebrate insulators
  JOURNAL   Cell 98 (3), 387-396 (1999)
   PUBMED   10458613
REFERENCE   7  (bases 1 to 2853)
  AUTHORS   Filippova,G.N., Lindblom,A., Meincke,L.J., Klenova,E.M.,
            Neiman,P.E., Collins,S.J., Doggett,N.A. and Lobanenkov,V.V.
  TITLE     A widely expressed transcription factor with multiple DNA sequence
            specificity, CTCF, is localized at chromosome segment 16q22.1
            within one of the smallest regions of overlap for common deletions
            in breast and prostate cancers
  JOURNAL   Genes Chromosomes Cancer 22 (1), 26-36 (1998)
   PUBMED   9591631
REFERENCE   8  (bases 1 to 2853)
  AUTHORS   Vostrov,A.A. and Quitschke,W.W.
  TITLE     The zinc finger protein CTCF binds to the APBbeta domain of the
            amyloid beta-protein precursor promoter. Evidence for a role in
            transcriptional activation
  JOURNAL   J Biol Chem 272 (52), 33353-33359 (1997)
   PUBMED   9407128
REFERENCE   9  (bases 1 to 2853)
  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
REFERENCE   10 (bases 1 to 2853)
  AUTHORS   Valverde de Morales,H.G., Wang,H.L., Garber,K., Corces,V. and Li,H.
  TITLE     CTCF-Related Disorder
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   38662876
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB229066.1, AB209793.1 and
            AA814313.1.
            
            On May 31, 2019 this sequence version replaced NM_001191022.1.
            
            Summary: This gene is a member of the BORIS + CTCF gene family and
            encodes a transcriptional regulator protein with 11 highly
            conserved zinc finger (ZF) domains. This nuclear protein is able to
            use different combinations of the ZF domains to bind different DNA
            target sequences and proteins. Depending upon the context of the
            site, the protein can bind a histone acetyltransferase
            (HAT)-containing complex and function as a transcriptional
            activator or bind a histone deacetylase (HDAC)-containing complex
            and function as a transcriptional repressor. If the protein is
            bound to a transcriptional insulator element, it can block
            communication between enhancers and upstream promoters, thereby
            regulating imprinted expression. Mutations in this gene have been
            associated with invasive breast cancers, prostate cancers, and
            Wilms' tumors. Alternatively spliced transcript variants encoding
            different isoforms have been found for this gene. [provided by
            RefSeq, Jul 2010].
            
            Transcript Variant: This variant (2) lacks internal two consecutive
            exons, resulting in a downstream AUG start codon, as compared to
            variant 1. The resulting isoform (2) has a shorter N-terminus, as
            compared to isoform 1.
            
            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 :: AB209793.1, SRR1803612.158608.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA2142348
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-47                DB229066.1         120-166
            48-2844             AB209793.1         1-2797
            2845-2853           AA814313.1         14-22               c
FEATURES             Location/Qualifiers
     source          1..2853
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q22.1"
     gene            1..2853
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /note="CCCTC-binding factor"
                     /db_xref="GeneID:10664"
                     /db_xref="HGNC:HGNC:13723"
                     /db_xref="MIM:604167"
     exon            1..199
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            200..316
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            317..450
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     CDS             349..1548
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /note="isoform 2 is encoded by transcript variant 2;
                     transcriptional repressor CTCF; CTCFL paralog; 11-zinc
                     finger protein; 11 zinc finger transcriptional repressor;
                     CCCTC-binding factor (zinc finger protein)"
                     /codon_start=1
                     /product="transcriptional repressor CTCF isoform 2"
                     /protein_id="NP_001177951.1"
                     /db_xref="CCDS:CCDS54029.1"
                     /db_xref="GeneID:10664"
                     /db_xref="HGNC:HGNC:13723"
                     /db_xref="MIM:604167"
                     /translation="MAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRS
                     HTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKH
                     TENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKS
                     HKNEKRFKCDQCDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYH
                     DPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRS
                     KKEDSSDSENAEPDLDDNEDEEEPAVEIEPEPEPQPVTPAPPPAKKRRGRPPGRTNQP
                     KQNQPTAIIQVEDQNTGAIENIIVEVKKEPDAEPAEGEEEEAQPAATDAPNGDLTPEM
                     ILSMMDR"
     exon            451..571
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            572..721
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            722..882
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            883..1065
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            1066..1201
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            1202..1363
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     exon            1364..2853
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2827..2832
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /note="hexamer: AATAAA"
     polyA_site      2853
                     /gene="CTCF"
                     /gene_synonym="CFAP108; FAP108; MRD21"
                     /note="major polyA site"
ORIGIN      
        1 gacgcaggcg cactgcaccg cgccgccgcc attttgtgtc tgagcctgtg gagcgattaa
       61 accgtgcgcg gagctgcttc tttggcggca gcggcggcgg cggtggccgg tgcggacgcg
      121 cggagctcgc cggagacgcc gggtggccgg agccgtggag cggcggcgga gcgggcgccg
      181 cggggggtgt ggcgcggaga atgattacgg acctgaagcc aaagaacaag atgcgctagt
      241 ggacagattg ctgaccaggg gcttgagagc tgggttctat tttccctcct caaactgact
      301 ttgcagccac ggagaggtac tcgtcctcac aagtgcccag actgcgacat ggcctttgtg
      361 accagtggag aattggttcg gcatcgtcgt tacaaacaca cccacgagaa gccattcaag
      421 tgttccatgt gcgattacgc cagtgtagaa gtcagcaaat taaaacgtca cattcgctct
      481 catactggag agcgtccgtt tcagtgcagt ttgtgcagtt atgccagcag ggacacatac
      541 aagctgaaaa ggcacatgag aacccattca ggggaaaagc cttatgaatg ttatatttgt
      601 catgctcggt ttacccaaag tggtaccatg aagatgcaca ttttacagaa gcacacagaa
      661 aatgtggcca aatttcactg tccccactgt gacacagtca tagcccgaaa aagtgatttg
      721 ggtgtccact tgcgaaagca gcattcctat attgagcaag gcaagaaatg ccgttactgt
      781 gatgctgtgt ttcatgagcg ctatgccctc atccagcatc agaagtcaca caagaatgag
      841 aagcgcttta agtgtgacca gtgtgattac gcttgtagac aggagaggca catgatcatg
      901 cacaagcgca cccacaccgg ggagaagcct tacgcctgca gccactgcga taagaccttc
      961 cgccagaagc agcttctcga catgcacttc aagcgctatc acgaccccaa cttcgtccct
     1021 gcggcttttg tctgttctaa gtgtgggaaa acatttacac gtcggaatac catggcaaga
     1081 catgctgata attgtgctgg cccagatggc gtagaggggg aaaatggagg agaaacgaag
     1141 aagagtaaac gtggaagaaa aagaaagatg cgctctaaga aagaagattc ctctgacagt
     1201 gaaaatgctg aaccagatct ggacgacaat gaggatgagg aggagcctgc cgtagaaatt
     1261 gaacctgagc cagagcctca gcctgtgacc ccagccccac cacccgccaa gaagcggaga
     1321 ggacgacccc ctggcagaac caaccagccc aaacagaacc agccaacagc tatcattcag
     1381 gttgaagacc agaatacagg tgcaattgag aacattatag ttgaagtaaa aaaagagcca
     1441 gatgctgagc ccgcagaggg agaggaagag gaggcccagc cagctgccac agatgccccc
     1501 aacggagacc tcacgcccga gatgatcctc agcatgatgg accggtgatg gcggagcctt
     1561 gtgcgtcgcc aggacttctc tgggctgtgt ttaaacggcc cgcatcttaa tttttctccc
     1621 ttctttcttt ttttggcttt gggaaaagca tcattttacc aaacataccg agaacgaaaa
     1681 cttcaaggat gatgttagaa aaaaatgtga tttaactaga acttgctgtc tgatgttagc
     1741 aaatcatgga atgttctgag tccctgaggg tttactgtga agtgctgagg acagtgttga
     1801 caactaactc gttttcctag atggaaacgg agacattgac ccctccctcc atgtggtaaa
     1861 ccactccaga atggccacca ggcttcccag agttctatgg tcttcttccc aagagagttt
     1921 ttaattgtaa atgcatactt gggaaggact tagagtttta aactgttttt tgcttttgct
     1981 tttccctgac tccctttgct tggagtcagc tgcacaccag tagtatggca tgctacgatc
     2041 aggttctgtc ctgaaagctt tgcctctttc ttggcaaagt ttctggtatg gtcaagcttg
     2101 taaataactt tttttacatt ttaatctttt ccattaatta agaggttgaa aagaagtgca
     2161 gtgtaagaaa acccagcatt ttaattactt gcaaattaag ttaccacaga ctctgtagtg
     2221 tgtaaatgtt gacaaggaat tggatcacaa tcatgtagca gaatggcacc cagaccactg
     2281 cccaccagtg acggacatgc acgtggcaga tcatgatttc cagcccacgg agccagcatt
     2341 tgaaccttgt ataattaact ttcagttatg atttcccatc gacattttct ttgccctgtt
     2401 tgtagctgat tgttgtgttt tataaatctt ctgttaaggc agaagggtga ttatgagtgg
     2461 ttcacagcag cccttataag ctgggccaga aaatttcact aggtcagtaa tttaaacctt
     2521 ggatcttcaa aaaataaaat aatgtgaagc aaaaccaact aaaaagtgat tcttgcacat
     2581 gaactgtcac atgtttaaaa atgtgttttt tagagagcct cagtcttact gatttcaaac
     2641 acttttttct tctgtgtatt gcttttaaga gagccatcag ttagctatca gactctaggt
     2701 tgatgcattt tgtacttagc tgtactgtgt gatatttttc attattttag gacgccaaca
     2761 tgagacctgt aataaaatat gtaatggggt tgaaagctgg ggaggaggat ctactgctgt
     2821 acagctaata aatcataacg gattaacaag tgc
//
