LOCUS       NM_001081387            3217 bp    mRNA    linear   ROD 10-FEB-2025
DEFINITION  Mus musculus CCCTC-binding factor like (Ctcfl), transcript variant
            2, mRNA.
ACCESSION   NM_001081387 XM_972768
VERSION     NM_001081387.2
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 3217)
  AUTHORS   Zuo,B.W., Yao,W.X., Fang,M.D., Ren,J., Tu,L.L., Fan,R.J. and
            Zhang,Y.M.
  TITLE     Boris knockout eliminates AOM/DSS-induced in situ colorectal cancer
            by suppressing DNA damage repair and inflammation
  JOURNAL   Cancer Sci 114 (5), 1972-1985 (2023)
   PUBMED   36692143
  REMARK    GeneRIF: Boris knockout eliminates AOM/DSS-induced in situ
            colorectal cancer by suppressing DNA damage repair and
            inflammation.
REFERENCE   2  (bases 1 to 3217)
  AUTHORS   Sati,L., Soygur,B., Goksu,E., Bassorgun,C.I. and McGrath,J.
  TITLE     CTCFL expression is associated with cerebral vascular abnormalities
  JOURNAL   Tissue Cell 72, 101528 (2021)
   PUBMED   33756271
  REMARK    GeneRIF: CTCFL expression is associated with cerebral vascular
            abnormalities.
REFERENCE   3  (bases 1 to 3217)
  AUTHORS   Rivero-Hinojosa,S., Pugacheva,E.M., Kang,S., Mendez-Catala,C.F.,
            Kovalchuk,A.L., Strunnikov,A.V., Loukinov,D., Lee,J.T. and
            Lobanenkov,V.V.
  TITLE     The combined action of CTCF and its testis-specific paralog BORIS
            is essential for spermatogenesis
  JOURNAL   Nat Commun 12 (1), 3846 (2021)
   PUBMED   34158481
  REMARK    GeneRIF: The combined action of CTCF and its testis-specific
            paralog BORIS is essential for spermatogenesis.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3217)
  AUTHORS   Nishana,M., Ha,C., Rodriguez-Hernaez,J., Ranjbaran,A., Chio,E.,
            Nora,E.P., Badri,S.B., Kloetgen,A., Bruneau,B.G., Tsirigos,A. and
            Skok,J.A.
  TITLE     Defining the relative and combined contribution of CTCF and CTCFL
            to genomic regulation
  JOURNAL   Genome Biol 21 (1), 108 (2020)
   PUBMED   32393311
  REMARK    GeneRIF: Defining the relative and combined contribution of CTCF
            and CTCFL to genomic regulation.
            Erratum:[Genome Biol. 2020 Jun 2;21(1):133. doi:
            10.1186/s13059-020-02056-6.. PMID: 32487268]
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3217)
  AUTHORS   Rivero-Hinojosa,S., Kang,S., Lobanenkov,V.V. and Zentner,G.E.
  TITLE     Testis-specific transcriptional regulators selectively occupy
            BORIS-bound CTCF target regions in mouse male germ cells
  JOURNAL   Sci Rep 7, 41279 (2017)
   PUBMED   28145452
  REMARK    GeneRIF: CTCF and BORIS cooperate with additional Testis-specific
            transcriptional regulators to regulate gene expression in
            developing male gametes.
            Erratum:[Sci Rep. 2017 Aug 04;7:46891. doi: 10.1038/srep46891..
            PMID: 28776597]
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3217)
  AUTHORS   Tamminga,J., Kathiria,P., Koturbash,I. and Kovalchuk,O.
  TITLE     DNA damage-induced upregulation of miR-709 in the germline
            downregulates BORIS to counteract aberrant DNA hypomethylation
  JOURNAL   Cell Cycle 7 (23), 3731-3736 (2008)
   PUBMED   19029807
  REMARK    GeneRIF: DNA damage-induced and ATR/Rfx1-mediated increase of
            miR-709 expression in exposed testes may be a protective mechanism
            that effectively decreases a cellular level of BORIS to prevent
            massive aberrant erasure of DNA methylation after radiation
            exposure.
REFERENCE   7  (bases 1 to 3217)
  AUTHORS   Nguyen,P., Bar-Sela,G., Sun,L., Bisht,K.S., Cui,H., Kohn,E.,
            Feinberg,A.P. and Gius,D.
  TITLE     BAT3 and SET1A form a complex with CTCFL/BORIS to modulate H3K4
            histone dimethylation and gene expression
  JOURNAL   Mol Cell Biol 28 (21), 6720-6729 (2008)
   PUBMED   18765639
REFERENCE   8  (bases 1 to 3217)
  AUTHORS   Nguyen,P., Cui,H., Bisht,K.S., Sun,L., Patel,K., Lee,R.S.,
            Kugoh,H., Oshimura,M., Feinberg,A.P. and Gius,D.
  TITLE     CTCFL/BORIS is a methylation-independent DNA-binding protein that
            preferentially binds to the paternal H19 differentially methylated
            region
  JOURNAL   Cancer Res 68 (14), 5546-5551 (2008)
   PUBMED   18632606
  REMARK    GeneRIF: CTCFL/BORIS is a methylation-independent DNA-binding
            protein that preferentially binds to the paternal H19
            differentially methylated region
REFERENCE   9  (bases 1 to 3217)
  AUTHORS   Jelinic,P., Stehle,J.C. and Shaw,P.
  TITLE     The testis-specific factor CTCFL cooperates with the protein
            methyltransferase PRMT7 in H19 imprinting control region
            methylation
  JOURNAL   PLoS Biol 4 (11), e355 (2006)
   PUBMED   17048991
  REMARK    GeneRIF: CTCFL and PRMT7 may play a role in male germline imprinted
            gene methylation.
REFERENCE   10 (bases 1 to 3217)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL837509.11 and AL928599.5.
            
            On May 24, 2007 this sequence version replaced NM_001081387.1.
            
            Transcript Variant: This variant (2) uses an alternate in-frame 3'
            splice junction compared to variant 1. The resulting isoform (2)
            has the same N- and C-termini but is shorter compared to isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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.
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-237               AL837509.11        26272-26508         c
            238-776             AL837509.11        25244-25782         c
            777-1002            AL837509.11        24161-24386         c
            1003-1173           AL837509.11        20526-20696         c
            1174-1307           AL837509.11        19227-19360         c
            1308-1428           AL837509.11        15166-15286         c
            1429-1578           AL837509.11        14692-14841         c
            1579-1739           AL837509.11        13015-13175         c
            1740-1922           AL837509.11        8865-9047           c
            1923-2043           AL837509.11        2312-2432           c
            2044-3217           AL928599.5         112356-113529       c
FEATURES             Location/Qualifiers
     source          1..3217
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 95.74 cM"
     gene            1..3217
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /note="CCCTC-binding factor like"
                     /db_xref="GeneID:664799"
                     /db_xref="MGI:MGI:3652571"
     exon            1..237
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            238..776
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     CDS             249..2159
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /note="isoform 2 is encoded by transcript variant 2; CTCF
                     paralog; CTCF-like protein; Transcriptional repressor
                     CTCFL; Brother of the regulator of imprinted sites; BORIS;
                     likely orthologue of H. sapiens CCCTC-binding factor-like
                     protein (CTCFL); CCCTC-binding factor (zinc finger
                     protein)-like"
                     /codon_start=1
                     /product="transcriptional repressor CTCFL isoform 2"
                     /protein_id="NP_001074856.1"
                     /db_xref="CCDS:CCDS38349.1"
                     /db_xref="GeneID:664799"
                     /db_xref="MGI:MGI:3652571"
                     /translation="MAAAEVPVPSGYFTQIKEQKLKPGDLEEEKEEDGVQRVEAQEGV
                     VKEVEAENSCLLLEARAPVESDRRILTLQTVHLESQDVHLQGLGWLSVPHSEELSGTV
                     PEAEGILQLPSVLWLDPEPQLSLQHCVTVSIPEELYPPEELQRIHFHLLRENVLMAEE
                     NPELTPDLDESTALKKPEEDEKDQLPPQGETDKREERLLLLEMKPKEGKDDEIVLTIS
                     HLSLEEQQDPPAANQTSVPGAKAAKPKRRRQTKGKPQSFQCDTCPFTSSKLSTFNRHI
                     KIHSNERPHLCHLCLKAFRTVTLLRNHVNTHTGTRPHKCRDCDMAFVTSGELVRHRRY
                     KHTYEKPFKCSLCKYASVEASKMKRHIRSHTGERPFQCCQCAYASRDSYKLKRHMRTH
                     SGEKPYECPTCHVRFTQSGTMKIHIAQKHGENVPKYECPHCATIIARKSDLRVHLRNL
                     HSQSPEEMKCRYCPAGFHERYALIQHQRTHKNEKKFKCKQCDYACKQERCLKAHMRMH
                     TGEKPFSCLACNKHFRQKQLLTVHLRKYHDPNFVPNLHLCLKCDKRFSRWSNLQRHRK
                     KCDPEHETLAPNKDRRPVTRTQASEGEAGHKEGEPQCPGEQALGHQGEAAGSQSPDHG
                     LTCEIIFNMMDK"
     exon            777..1002
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1003..1173
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1174..1307
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1308..1428
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1429..1578
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1579..1739
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1740..1922
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            1923..2043
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
     exon            2044..3217
                     /gene="Ctcfl"
                     /gene_synonym="Boris"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 tcttctctgt ccatcattcc cccgaggact ccagcgcccc cttggggtcc tgggaccctt
       61 actccattcc tccatctcca ccattttcct ctccttggct ccaccccttt cccgccagca
      121 cctgcgcagg gctctggtag agggaggtgg tggcagcggc tgctgcacga agagcaattt
      181 agcacgaggt ggcaaggtgg cggccacgcg gtcaacagtc caggccctgc ctctgtgggg
      241 tcgtcaccat ggctgccgct gaggtccctg tcccttctgg gtacttcacc cagatcaaag
      301 agcagaagtt gaagcctgga gacctagagg aggagaaaga ggaggacggg gtacaaagag
      361 tggaagccca ggagggagtt gtcaaggagg tggaggccga gaacagttgc ctgcttctgg
      421 aggccagggc cccggtggag agcgacaggc ggatcctgac cctgcaaacg gtgcacctgg
      481 agtcccagga tgtgcaccta caggggctgg gatggctgag cgtgccacac tctgaggagc
      541 tttcagggac ggtaccagag gcggaaggca tactgcagtt gccatccgtg ctgtggctcg
      601 acccagagcc ccagctcagc cttcagcatt gcgtgacggt cagcatcccg gaagagctgt
      661 acccaccaga ggagctgcag cggatacatt ttcacctgct gagagagaat gtgctaatgg
      721 ccgaggagaa cccagagtta acaccagact tggacgaaag cacagccctg aaaaagcccg
      781 aagaagatga aaaggaccag ctcccgcccc agggagagac agacaagaga gaagagaggt
      841 tgctccttct ggaaatgaaa ccaaaagagg gaaaagacga cgaaattgtc ctgaccattt
      901 cccatctaag cctcgaagaa cagcaagatc caccagcggc caatcagaca agtgtgccgg
      961 gagccaaagc cgcaaaacca aaacggcgga ggcagaccaa gggaaagcct cagagctttc
     1021 agtgtgacac ctgcccgttc acttcctcca agctctcaac tttcaatcgt cacatcaaaa
     1081 ttcacagcaa tgagaggcca cacctgtgtc acctgtgcct gaaggccttc cggactgtca
     1141 ctcttcttag gaaccatgtg aacacccaca caggaaccag gccccacaag tgcagggact
     1201 gcgacatggc gtttgtcacc agtggagaac tcgtccggca caggcgttac aaacacactt
     1261 atgagaagcc cttcaagtgc tccctgtgca agtacgccag cgtcgaggca agcaagatga
     1321 agcgtcacat ccgctcacac acgggtgagc gtcccttcca gtgttgccag tgtgcttacg
     1381 ccagcaggga ctcctacaag ctgaagcgcc acatgaggac acactcaggt gagaagccgt
     1441 atgaatgtcc cacctgtcac gtccggttca cccagagcgg gaccatgaaa atccatatag
     1501 cacagaagca cggagagaat gtgcccaaat acgagtgtcc ccactgtgcc accatcatcg
     1561 cgaggaagag cgacctgcgt gtccatctgc gtaacctgca cagccagagc ccggaggaga
     1621 tgaagtgccg atactgtccc gctggcttcc atgagcgcta tgccctcatt cagcaccaga
     1681 ggacccacaa gaacgagaag aagttcaagt gcaagcagtg cgattacgcg tgcaagcagg
     1741 agcgatgctt gaaggcgcac atgcgcatgc acacaggaga gaagcccttc tcctgcctgg
     1801 cctgcaacaa gcacttccga cagaagcagc tactgaccgt gcacctgagg aagtaccatg
     1861 acccgaactt cgtccccaat ctgcacctgt gcctcaagtg tgataaacgt ttctcccgct
     1921 ggagtaacct gcagagacac agaaagaagt gtgacccgga gcatgagacg ttagccccca
     1981 acaaggacag gagaccagtg acaaggacac aggcctcgga gggagaagca ggacacaagg
     2041 aaggggagcc tcagtgccct ggggagcagg ctctgggcca ccaaggagaa gcagcgggga
     2101 gccagagccc agaccacggc cttacctgcg agataatctt taacatgatg gataagtgat
     2161 ggataagtga gcagtcgtgc ctctccgtgc tgtggcctct gggggaagaa accagttaga
     2221 aataagttcc cagacacagc acagtgttct cagagtttga gatagtgtgt agaaatgttt
     2281 gagagaaggg gaaaaaaaac cctgcagcta tttccaaaga cttgagtcag agctcgaagt
     2341 gaaggtgcac atatctgggc cctagcaggt gcccagaatg agtcagggac agattctagg
     2401 tgatacttat gtccacgggg gctcagacca gttaacgcct tggtggtcag agcagaaaat
     2461 tttttgagtt gttgtaccca ccctcaatat ttcttttttt tttttttttt tttttttttt
     2521 tttttttttt tggtttttcg agacagggtt tctctgtgta gccctggctg tcctggaact
     2581 cactctgtag accaggctgg cctcgaactc agaaatccgc ctgcctctgc ctcccgagtg
     2641 ctgggattaa aggcgtgtgc caccacaccc ggctgatatt tctgatacta tgattttaag
     2701 cactaaaatg aattgtatat tttttttaaa tgccaatgaa ttttccatga catttaaagc
     2761 taccacgatg ctttcaatga attctaaagt caacctgaga atcttaatgc tgcggaaaga
     2821 tgaattggta gaaacaatgc tcatttaact agaaaaaaaa tatatatata tcatagctct
     2881 ttctttggca tagagcaagg ctcaccttta gtttttgccc ctcctccccc atcttgtagg
     2941 cctatgggtt aaacccaggg cttggcacaa tttagacaag tgccccacca ccaggccata
     3001 cccccagccc ccacacaact tccaaaaaaa attaaattat ccaggctgga tttgaactca
     3061 atttggagtc cagctgcact tcaaactgtc cattctcctg cctccgtctt gcaggaatga
     3121 cgagccttta ccaccaggcc gggcttgtct tctcttaatt gtagtcttcg cccgctatga
     3181 aattacactg gcattgttgc aagcattggc tttgttc
//
