LOCUS       NM_001269041            3868 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens CCCTC-binding factor like (CTCFL), transcript variant
            3, mRNA.
ACCESSION   NM_001269041
VERSION     NM_001269041.2
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 3868)
  AUTHORS   Wei,L., Liu,Z., Qin,L., Xian,L., Chen,K., Zhou,S., Hu,L., Xiong,Y.,
            Li,B. and Qin,Y.
  TITLE     BORIS variant SF2(C2/A4) promotes the malignant development of
            liver cancer by activating epithelial-mesenchymal transition and
            hepatic stellate cells
  JOURNAL   Mol Carcinog 62 (6), 731-742 (2023)
   PUBMED   36929051
  REMARK    GeneRIF: BORIS variant SF2(C2/A4) promotes the malignant
            development of liver cancer by activating epithelial-mesenchymal
            transition and hepatic stellate cells.
REFERENCE   2  (bases 1 to 3868)
  AUTHORS   Akhtar,M.S., Akhter,N., Talat,A., Alharbi,R.A., Sindi,A.A.A.,
            Klufah,F., Alyahyawi,H.E., Alruwetei,A., Ahmad,A., Zamzami,M.A.,
            Deo,S., Husain,S.A., Badi,O.A. and Khan,M.J.
  TITLE     Association of mutation and expression of the brother of the
            regulator of imprinted sites (BORIS) gene with breast cancer
            progression
  JOURNAL   Oncotarget 14, 528-541 (2023)
   PUBMED   37235839
  REMARK    GeneRIF: Association of mutation and expression of the brother of
            the regulator of imprinted sites (BORIS) gene with breast cancer
            progression.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3868)
  AUTHORS   Moscona,R., Janssen,S.M., Elchebly,M., Papadakis,A.I., Rubin,E. and
            Spatz,A.
  TITLE     BORIS/CTCFL-mediated chromatin accessibility alterations promote a
            pro-invasive transcriptional signature in melanoma cells
  JOURNAL   Pigment Cell Melanoma Res 36 (3-4), 299-313 (2023)
   PUBMED   37082838
  REMARK    GeneRIF: BORIS/CTCFL-mediated chromatin accessibility alterations
            promote a pro-invasive transcriptional signature in melanoma cells.
REFERENCE   4  (bases 1 to 3868)
  AUTHORS   Rao,G.K., Makani,V.K.K., Mendonza,J.J., Edathara,P.M., Patel,N.,
            Ramakrishna,M., Cilamkoti,P., Chiring Phukon,J., Jose,J., Bhadra,U.
            and Bhadra,M.P.
  TITLE     Downregulation of BORIS/CTCFL leads to ROS-dependent cellular
            senescence and drug sensitivity in MYCN-amplified neuroblastoma
  JOURNAL   FEBS J 289 (10), 2915-2934 (2022)
   PUBMED   34854238
  REMARK    GeneRIF: Downregulation of BORIS/CTCFL leads to ROS-dependent
            cellular senescence and drug sensitivity in MYCN-amplified
            neuroblastoma.
REFERENCE   5  (bases 1 to 3868)
  AUTHORS   Salgado-Albarran,M., Spath,J., Gonzalez-Barrios,R., Baumbach,J. and
            Soto-Reyes,E.
  TITLE     CTCFL regulates the PI3K-Akt pathway and it is a target for
            personalized ovarian cancer therapy
  JOURNAL   NPJ Syst Biol Appl 8 (1), 5 (2022)
   PUBMED   35132075
  REMARK    GeneRIF: CTCFL regulates the PI3K-Akt pathway and it is a target
            for personalized ovarian cancer therapy.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3868)
  AUTHORS   Hoffmann,M.J., Muller,M., Engers,R. and Schulz,W.A.
  TITLE     Epigenetic control of CTCFL/BORIS and OCT4 expression in urogenital
            malignancies
  JOURNAL   Biochem Pharmacol 72 (11), 1577-1588 (2006)
   PUBMED   16854382
  REMARK    GeneRIF: The lack of hypomethylation in the CFCFL promoter
            reinforces evidence that 'genome-wide' hypomethylation is not
            random.
REFERENCE   7  (bases 1 to 3868)
  AUTHORS   Hong,J.A., Kang,Y., Abdullaev,Z., Flanagan,P.T., Pack,S.D.,
            Fischette,M.R., Adnani,M.T., Loukinov,D.I., Vatolin,S.,
            Risinger,J.I., Custer,M., Chen,G.A., Zhao,M., Nguyen,D.M.,
            Barrett,J.C., Lobanenkov,V.V. and Schrump,D.S.
  TITLE     Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter
            coincides with derepression of this cancer-testis gene in lung
            cancer cells
  JOURNAL   Cancer Res 65 (17), 7763-7774 (2005)
   PUBMED   16140944
  REMARK    GeneRIF: Data indicate that reciprocal binding of CTCF and BORIS to
            the NY-ESO-1 promoter mediates epigenetic regulation of this CT
            gene in lung cancer cells.
REFERENCE   8  (bases 1 to 3868)
  AUTHORS   Klenova,E.M., Morse,H.C. 3rd, Ohlsson,R. and Lobanenkov,V.V.
  TITLE     The novel BORIS + CTCF gene family is uniquely involved in the
            epigenetics of normal biology and cancer
  JOURNAL   Semin Cancer Biol 12 (5), 399-414 (2002)
   PUBMED   12191639
  REMARK    Review article
REFERENCE   9  (bases 1 to 3868)
  AUTHORS   Loukinov,D.I., Pugacheva,E., Vatolin,S., Pack,S.D., Moon,H.,
            Chernukhin,I., Mannan,P., Larsson,E., Kanduri,C., Vostrov,A.A.,
            Cui,H., Niemitz,E.L., Rasko,J.E., Docquier,F.M., Kistler,M.,
            Breen,J.J., Zhuang,Z., Quitschke,W.W., Renkawitz,R., Klenova,E.M.,
            Feinberg,A.P., Ohlsson,R., Morse,H.C. 3rd and Lobanenkov,V.V.
  TITLE     BORIS, a novel male germ-line-specific protein associated with
            epigenetic reprogramming events, shares the same 11-zinc-finger
            domain with CTCF, the insulator protein involved in reading
            imprinting marks in the soma
  JOURNAL   Proc Natl Acad Sci U S A 99 (10), 6806-6811 (2002)
   PUBMED   12011441
REFERENCE   10 (bases 1 to 3868)
  AUTHORS   Deloukas,P., Matthews,L.H., Ashurst,J., Burton,J., Gilbert,J.G.,
            Jones,M., Stavrides,G., Almeida,J.P., Babbage,A.K., Bagguley,C.L.,
            Bailey,J., Barlow,K.F., Bates,K.N., Beard,L.M., Beare,D.M.,
            Beasley,O.P., Bird,C.P., Blakey,S.E., Bridgeman,A.M., Brown,A.J.,
            Buck,D., Burrill,W., Butler,A.P., Carder,C., Carter,N.P.,
            Chapman,J.C., Clamp,M., Clark,G., Clark,L.N., Clark,S.Y.,
            Clee,C.M., Clegg,S., Cobley,V.E., Collier,R.E., Connor,R.,
            Corby,N.R., Coulson,A., Coville,G.J., Deadman,R., Dhami,P.,
            Dunn,M., Ellington,A.G., Frankland,J.A., Fraser,A., French,L.,
            Garner,P., Grafham,D.V., Griffiths,C., Griffiths,M.N., Gwilliam,R.,
            Hall,R.E., Hammond,S., Harley,J.L., Heath,P.D., Ho,S., Holden,J.L.,
            Howden,P.J., Huckle,E., Hunt,A.R., Hunt,S.E., Jekosch,K.,
            Johnson,C.M., Johnson,D., Kay,M.P., Kimberley,A.M., King,A.,
            Knights,A., Laird,G.K., Lawlor,S., Lehvaslaiho,M.H., Leversha,M.,
            Lloyd,C., Lloyd,D.M., Lovell,J.D., Marsh,V.L., Martin,S.L.,
            McConnachie,L.J., McLay,K., McMurray,A.A., Milne,S., Mistry,D.,
            Moore,M.J., Mullikin,J.C., Nickerson,T., Oliver,K., Parker,A.,
            Patel,R., Pearce,T.A., Peck,A.I., Phillimore,B.J.,
            Prathalingam,S.R., Plumb,R.W., Ramsay,H., Rice,C.M., Ross,M.T.,
            Scott,C.E., Sehra,H.K., Shownkeen,R., Sims,S., Skuce,C.D.,
            Smith,M.L., Soderlund,C., Steward,C.A., Sulston,J.E., Swann,M.,
            Sycamore,N., Taylor,R., Tee,L., Thomas,D.W., Thorpe,A., Tracey,A.,
            Tromans,A.C., Vaudin,M., Wall,M., Wallis,J.M., Whitehead,S.L.,
            Whittaker,P., Willey,D.L., Williams,L., Williams,S.A., Wilming,L.,
            Wray,P.W., Hubbard,T., Durbin,R.M., Bentley,D.R., Beck,S. and
            Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 20
  JOURNAL   Nature 414 (6866), 865-871 (2001)
   PUBMED   11780052
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL035541.15 and AL160176.3.
            
            On Sep 18, 2020 this sequence version replaced NM_001269041.1.
            
            Summary: CCCTC-binding factor (CTCF), an 11-zinc-finger factor
            involved in gene regulation, utilizes different zinc fingers to
            bind varying DNA target sites. CTCF forms methylation-sensitive
            insulators that regulate X-chromosome inactivation. This gene is a
            paralog of CTCF and appears to be expressed primarily in the
            cytoplasm of spermatocytes, unlike CTCF which is expressed
            primarily in the nucleus of somatic cells. CTCF and the protein
            encoded by this gene are normally expressed in a mutually exclusive
            pattern that correlates with resetting of methylation marks during
            male germ cell differentiation. Multiple alternatively spliced
            transcript variants encoding different isoforms have been found for
            this gene. [provided by RefSeq, Jun 2012].
            
            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 :: DQ778110.1, SRR14038195.237972.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1968540 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-440               AL035541.15        101-540             c
            441-1035            AL160176.3         56318-56912         c
            1036-1246           AL160176.3         55723-55933         c
            1247-1417           AL160176.3         51862-52032         c
            1418-1551           AL160176.3         51413-51546         c
            1552-1672           AL160176.3         48369-48489         c
            1673-1822           AL160176.3         47247-47396         c
            1823-1983           AL160176.3         45247-45407         c
            1984-2166           AL160176.3         41261-41443         c
            2167-2332           AL160176.3         36091-36256         c
            2333-3868           AL160176.3         29821-31356         c
FEATURES             Location/Qualifiers
     source          1..3868
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20q13.31"
     gene            1..3868
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /note="CCCTC-binding factor like"
                     /db_xref="GeneID:140690"
                     /db_xref="HGNC:HGNC:16234"
                     /db_xref="MIM:607022"
     exon            1..1035
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     CDS             493..2484
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /note="isoform 1 is encoded by transcript variant 3;
                     cancer/testis antigen 27; brother of the regulator of
                     imprinted sites; BORIS-like protein"
                     /codon_start=1
                     /product="transcriptional repressor CTCFL isoform 1"
                     /protein_id="NP_001255970.1"
                     /db_xref="CCDS:CCDS13459.1"
                     /db_xref="GeneID:140690"
                     /db_xref="HGNC:HGNC:16234"
                     /db_xref="MIM:607022"
                     /translation="MAATEISVLSEQFTKIKELELMPEKGLKEEEKDGVCREKDHRSP
                     SELEAERTSGAFQDSVLEEEVELVLAPSEESEKYILTLQTVHFTSEAVELQDMSLLSI
                     QQQEGVQVVVQQPGPGLLWLEEGPRQSLQQCVAISIQQELYSPQEMEVLQFHALEENV
                     MVASEDSKLAVSLAETTGLIKLEEEQEKNQLLAERTKEQLFFVETMSGDERSDEIVLT
                     VSNSNVEEQEDQPTAGQADAEKAKSTKNQRKTKGAKGTFHCDVCMFTSSRMSSFNRHM
                     KTHTSEKPHLCHLCLKTFRTVTLLRNHVNTHTGTRPYKCNDCNMAFVTSGELVRHRRY
                     KHTHEKPFKCSMCKYASVEASKLKRHVRSHTGERPFQCCQCSYASRDTYKLKRHMRTH
                     SGEKPYECHICHTRFTQSGTMKIHILQKHGENVPKYQCPHCATIIARKSDLRVHMRNL
                     HAYSAAELKCRYCSAVFHERYALIQHQKTHKNEKRFKCKHCSYACKQERHMTAHIRTH
                     TGEKPFTCLSCNKCFRQKQLLNAHFRKYHDANFIPTVYKCSKCGKGFSRWINLHRHSE
                     KCGSGEAKSAASGKGRRTRKRKQTILKEATKGQKEAAKGWKEAANGDEAAAEEASTTK
                     GEQFPGEMFPVACRETTARVKEEVDEGVTCEMLLNTMDK"
     exon            1036..1246
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1247..1417
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1418..1551
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1552..1672
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1673..1822
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1823..1983
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            1984..2166
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            2167..2332
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     exon            2333..3868
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3846..3851
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /note="hexamer: AATGAA"
     polyA_site      3868
                     /gene="CTCFL"
                     /gene_synonym="BORIS; CT27; CTCF-T; dJ579F20.2; HMGB1L1"
                     /note="major polyA site"
ORIGIN      
        1 ctcgctgggc gccgggtgtg cactggcccg gggcctgctt ggacctgaaa cttgctaggc
       61 ccaggatatg cactggccga gagcctgctg ggcccaaacc ttactaggcc caggatgttc
      121 actgactgaa ccggctcagg cctaaccttg ctaggcccag gatatgcact gggccagagt
      181 gtgctcaggc ggaaccttgc caggcgcagg atgtgtgctg gccctaagcc tgctgaggcc
      241 caaacctgtt cgttctaggg ttttgtacaa aatcctgctt tagcctaaat cctgcttagc
      301 cttgaccccc tcctagaccc aagccagatc agcattgttc tgaccctact aagtccaaaa
      361 ccttttgagg ccagaccttg tttcaactcc aaagcctgct aggttccagc accccccgca
      421 tccctcctca taccaccccc ttctcccccc tatggaaacc gcttgcttat ttttcaaaca
      481 ggccaagtca ttatggcagc cactgagatc tctgtccttt ctgagcaatt caccaagatc
      541 aaagaactcg agttgatgcc ggaaaaaggc ctgaaggagg aggaaaaaga cggagtgtgc
      601 agagagaaag accatcggag ccctagtgag ttggaggccg agcgtacctc tggggccttc
      661 caggacagcg tcctggagga agaagtggag ctggtgctgg ccccctcgga ggagagcgag
      721 aagtacatcc tgaccctgca gacggtgcac ttcacttctg aagctgtgga gttgcaggat
      781 atgagcttgc tgagcataca gcagcaagaa ggggtgcagg tggtggtgca acagcctggc
      841 cctgggttgc tgtggcttga ggaagggccc cggcagagcc tgcagcagtg tgtggccatt
      901 agtatccagc aagagctgta ctccccgcaa gagatggagg tgttgcagtt ccacgctcta
      961 gaggagaatg tgatggtggc cagtgaagac agtaagttag cggtgagcct ggctgaaact
     1021 actggactga tcaagctcga ggaagagcag gagaagaacc agttattggc tgaaagaaca
     1081 aaggagcagc tcttttttgt ggaaacaatg tcaggagatg aaagaagtga cgaaattgtt
     1141 ctcacagttt caaattcaaa tgtggaagaa caagaggatc aacctacagc tggtcaagca
     1201 gatgctgaaa aggccaaatc tacaaaaaat caaagaaaga caaagggagc aaaaggaacc
     1261 ttccactgtg atgtctgcat gttcacctct tctagaatgt caagttttaa tcgtcatatg
     1321 aaaactcaca ccagtgagaa gcctcacctg tgtcacctct gcctgaaaac cttccgtacg
     1381 gtcactctgc tgcggaacca tgttaacacc cacacaggaa ccaggcccta caagtgtaac
     1441 gactgcaaca tggcatttgt caccagtgga gaactcgtcc gacacaggcg ctataaacat
     1501 actcatgaga aaccctttaa atgttccatg tgcaagtatg ccagtgtgga ggcaagtaaa
     1561 ttgaagcgcc atgtccgatc ccacactggg gagcgcccct ttcagtgttg ccagtgcagc
     1621 tatgccagca gagataccta caagctgaaa cgccacatga gaacgcactc aggtgagaag
     1681 ccttacgaat gccacatctg ccacacccgc ttcacccaga gcgggaccat gaaaatacat
     1741 attctgcaga aacacggcga aaatgtcccc aaataccagt gtccccattg tgccaccatc
     1801 attgcacgga aaagcgacct acgtgtgcat atgcgcaact tgcatgctta cagcgctgca
     1861 gagctgaaat gccgctactg ttctgctgtc ttccatgaac gctatgccct cattcagcac
     1921 cagaaaactc ataagaatga gaagaggttc aagtgcaaac actgcagtta tgcctgcaag
     1981 caggaacgtc atatgaccgc tcacattcgt acccacactg gagagaaacc attcacctgc
     2041 ctttcttgca ataaatgttt ccgacagaag caacttctaa acgctcactt caggaaatac
     2101 cacgatgcaa atttcatccc gactgtttac aaatgctcca agtgtggcaa aggcttttcc
     2161 cgctggatta acctgcacag acattcggag aagtgtggat caggggaagc aaagtcggct
     2221 gcttcaggaa agggaagaag aacaagaaag aggaagcaga ccatcctgaa ggaagccaca
     2281 aagggtcaga aggaagctgc gaagggatgg aaggaagccg cgaacggaga cgaagctgct
     2341 gctgaggagg cttccaccac gaagggagaa cagttcccag gagagatgtt tcctgtcgcc
     2401 tgcagagaaa ccacagccag agtcaaagag gaagtggatg aaggcgtgac ctgtgaaatg
     2461 ctcctcaaca cgatggataa gtgagaggga ttcgggttgc gtgttcactg cccccaattc
     2521 ctaaagcaag ttagaagttt ttagcattta aggtgtgaaa tgctcctcaa cacgatggat
     2581 aagtgagaga gagtcaggtt gcatgttcac tgcccctaat tcctaaagca agttagaaat
     2641 ttttagcatt ttctttgaaa caattaagtt catgacaatg gatgacacaa gtttgaggta
     2701 gtgtctagaa ttgttctcct gtttgtagct ggatatttca aagaaacatt gcaggtattt
     2761 tataaaagtt ttaaaccttg aatgagaggg taacacctca aacctatgga ttcattcact
     2821 tgatattggc aaggtggccc acaatgagtg agtagtgatt tttggatatt tcaaaatagt
     2881 ctagaccagc tagtgcttcc acagtcaaag ctggacattt ttatgttgca ttatatacac
     2941 ccatgatatt tctaataata tatggtttta aacattaaag acaaatgttt ttatacaaat
     3001 gaattttcta caaaatttaa agctaccata atgcttttaa ttagttctaa attcaaccaa
     3061 aaaatgtttt actcttataa aaaggaaaac tgagtaggaa atgaaatact agattagact
     3121 agaaaataag gaataaatcg attttacttt ggtataggag caaggttcac ctttagattt
     3181 ttgtattctc ttttaattat gctccttggc aggtatgaaa ttgccctggt tacattccat
     3241 tattgcttat tagtatttca ctccataacc cttttttctg ctaaaactac tctttttata
     3301 tttgtaaaat aattggcaga gtgagaagaa acataaaatc agataaggca aatgtgtacc
     3361 tgtaaggaat ttgtactttt tcataatgcc cagtgattag tgagtatttc ccttttgcca
     3421 gttgacaaga tttttccacc ctcgagcagc gtgagagatg cctctttaac acttgaaatt
     3481 catttctatc tggatacaga ggcagatttt tcttcattgc ttagttgagc agtttgtttt
     3541 gctgccaacc tgtctccacc cctgtatttc aagatcattg ataagcccta aattcaaatt
     3601 cttaagatat ggacctttta ttgaaaatat cacaagttca gaatccctat acaatgtgaa
     3661 tatgtggaaa taatttccca gcaggaagag cattatattc tctttgtacc agcaaattaa
     3721 tttaactcaa ctcacatgag atttaaattc tgtgggctgt agtatgccat cattgtgact
     3781 gaatttgtgc aatggtttct taattttttt actgttattt aaagatgttt tacataattc
     3841 aataaaatga aatgacttaa aattgcta
//
