LOCUS       NM_009881               3444 bp    mRNA    linear   ROD 12-NOV-2024
DEFINITION  Mus musculus chromodomain protein, Y chromosome-like (Cdyl),
            transcript variant 1, mRNA.
ACCESSION   NM_009881
VERSION     NM_009881.3
KEYWORDS    RefSeq; RefSeq Select.
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 3444)
  AUTHORS   Yang,Y., Chen,B.R., Ye,X.C., Ni,L.Y., Zhang,X.Y., Liu,Y.Z.,
            Lyu,T.J., Tian,Y., Fu,Y.J. and Wang,Y.
  TITLE     The chromodomain protein CDYL confers forebrain identity to human
            cortical organoids by inhibiting neuronatin
  JOURNAL   Cell Rep 43 (10), 114814 (2024)
   PUBMED   39378153
  REMARK    GeneRIF: The chromodomain protein CDYL confers forebrain identity
            to human cortical organoids by inhibiting neuronatin.
REFERENCE   2  (bases 1 to 3444)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   3  (bases 1 to 3444)
  AUTHORS   Okashita,N., Maeda,R. and Tachibana,M.
  TITLE     CDYL reinforces male gonadal sex determination through
            epigenetically repressing Wnt4 transcription in mice
  JOURNAL   Proc Natl Acad Sci U S A 120 (20), e2221499120 (2023)
   PUBMED   37155872
  REMARK    GeneRIF: CDYL reinforces male gonadal sex determination through
            epigenetically repressing Wnt4 transcription in mice.
REFERENCE   4  (bases 1 to 3444)
  AUTHORS   Wan,L., Hu,X., Xia,T., Li,F., Chi,Q., Ma,H., Yan,S., Li,W. and
            Huang,W.
  TITLE     Disruption of Cdyl gene impairs mouse lung epithelium
            differentiation and maturation
  JOURNAL   Gene 853, 147088 (2023)
   PUBMED   36464171
  REMARK    GeneRIF: Disruption of Cdyl gene impairs mouse lung epithelium
            differentiation and maturation.
REFERENCE   5  (bases 1 to 3444)
  AUTHORS   Li,J., Cheng,C., Xu,J., Zhang,T., Tokat,B., Dolios,G.,
            Ramakrishnan,A., Shen,L., Wang,R. and Xu,P.X.
  TITLE     The transcriptional coactivator Eya1 exerts transcriptional
            repressive activity by interacting with REST corepressors and
            REST-binding sequences to maintain nephron progenitor identity
  JOURNAL   Nucleic Acids Res 50 (18), 10343-10359 (2022)
   PUBMED   36130284
REFERENCE   6  (bases 1 to 3444)
  AUTHORS   Dorus,S., Gilbert,S.L., Forster,M.L., Barndt,R.J. and Lahn,B.T.
  TITLE     The CDY-related gene family: coordinated evolution in copy number,
            expression profile and protein sequence
  JOURNAL   Hum Mol Genet 12 (14), 1643-1650 (2003)
   PUBMED   12837688
REFERENCE   7  (bases 1 to 3444)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   8  (bases 1 to 3444)
  AUTHORS   Jones,D.O., Cowell,I.G. and Singh,P.B.
  TITLE     Mammalian chromodomain proteins: their role in genome organisation
            and expression
  JOURNAL   Bioessays 22 (2), 124-137 (2000)
   PUBMED   10655032
  REMARK    Review article
REFERENCE   9  (bases 1 to 3444)
  AUTHORS   Araki,K., Imaizumi,T., Sekimoto,T., Yoshinobu,K., Yoshimuta,J.,
            Akizuki,M., Miura,K., Araki,M. and Yamamura,K.
  TITLE     Exchangeable gene trap using the Cre/mutated lox system
  JOURNAL   Cell Mol Biol (Noisy-le-grand) 45 (5), 737-750 (1999)
   PUBMED   10512203
REFERENCE   10 (bases 1 to 3444)
  AUTHORS   Lahn,B.T. and Page,D.C.
  TITLE     Retroposition of autosomal mRNA yielded testis-specific gene family
            on human Y chromosome
  JOURNAL   Nat Genet 21 (4), 429-433 (1999)
   PUBMED   10192397
  REMARK    Erratum:[Nat Genet 1999 Jun;22(2):209]
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY090531.1, BC055103.1, AK028162.1 and BG229669.1.
            
            On Apr 17, 2008 this sequence version replaced NM_009881.2.
            
            Transcript Variant: This variant (1) encodes the longer 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 :: AF081261.1, AF081260.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849384 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-51                BY090531.1         2-52
            52-2193             BC055103.1         1-2142
            2194-3439           AK028162.1         1940-3185
            3440-3444           BG229669.1         1-5                 c
FEATURES             Location/Qualifiers
     source          1..3444
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="13"
                     /map="13 14.39 cM"
     gene            1..3444
                     /gene="Cdyl"
                     /note="chromodomain protein, Y chromosome-like"
                     /db_xref="GeneID:12593"
                     /db_xref="MGI:MGI:1339956"
     exon            1..132
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            133..269
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     CDS             267..2048
                     /gene="Cdyl"
                     /EC_number="2.3.1.48"
                     /note="isoform 1 is encoded by transcript variant 1;
                     chromodomain Y-like protein; CDY-like; crotonyl-CoA
                     hydratase; putative histone acetyltransferase Cdyl"
                     /codon_start=1
                     /product="chromodomain Y-like protein isoform 1"
                     /protein_id="NP_034011.1"
                     /db_xref="CCDS:CCDS49235.1"
                     /db_xref="GeneID:12593"
                     /db_xref="MGI:MGI:1339956"
                     /translation="MGIGNSQPNSQEAQLCTLPEKAEQPTDDNTCQQNNVVPATVSEP
                     DQASPAIQDAETQVESIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIH
                     DFNRRHNERQKEGSLARASRASPSNARKQISRSTHSTLSKTNSKALVVGKDHESKSSQ
                     LLAASQKFRKNPAPSLANRKNMDLAKSGIKILVPKSPVKGRTSVDGFQGESPEKLDPV
                     DQGAEDTVAPEVTAEKPTGALLGPGAERARMGSRPRIHPLVPQVSGPVTAAMATGLAV
                     NGKGTSPFMDALAANGTVTIQTSVTGVTAGKRKFIDDRRDQPFDKRLRFSVRQTESAY
                     RYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMKEVQSALSTAAADDSKLVLLSAVGS
                     VFCCGLDFIYFIRRLTDDRKRESTKMADAIRNFVNTFIQFKKPIIVAVNGPAIGLGAS
                     ILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLFSGRKLTAQE
                     ACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANEREC
                     EVLKKIWGSAQGMDSMLKYLQRKIDEF"
     exon            270..362
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            363..437
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            438..1104
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            1105..1361
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            1362..1534
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            1535..1745
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            1746..1889
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     exon            1890..3442
                     /gene="Cdyl"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2194
                     /gene="Cdyl"
     regulatory      3418..3423
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Cdyl"
                     /note="hexamer: AATAAA"
     polyA_site      3442
                     /gene="Cdyl"
                     /note="major polyA site"
ORIGIN      
        1 atgatggagg cgatcttgct ttgaggtggt ttagcatccc acttgttcct tgaggacatc
       61 tgttcctacc taagagcact cacctgagat gctcaaaggt ccagaagaaa cacttctcgg
      121 gtgacaaagc aggtggtgac cagagaacag aggcccccca aaaattttat ggcattcaag
      181 gcaaagcaca gccaacccgg agggaaagca agagtccagc ctggaaatac atagcccaac
      241 ccgaaggtta tctctgaagg aaaacaatgg gcataggcaa tagccagcct aattcacagg
      301 aagcccagct ctgcacactt ccagagaaag ctgaacaacc tactgatgat aacacctgcc
      361 agcaaaataa tgtggttcct gcaacagtct cagaacccga tcaagcgtcc cctgcaattc
      421 aagacgcgga gactcaggtg gaaagtatcg ttgacaaaag gaaaaacaag aaagggaaga
      481 cagaatatct ggtgcggtgg aaaggctatg acagtgagga tgacacgtgg gagcctgagc
      541 agcacctggt gaactgtgag gaatacatcc atgacttcaa ccggcgccac aacgagaggc
      601 aaaaggaagg tagcctggct cgtgccagca gagcctcccc cagcaacgcc cggaagcaga
      661 tttccaggtc cacccacagc actctctcca agaccaactc caaagcactt gtggtaggca
      721 aagatcatga gtccaaaagc agccagctgt tggctgccag ccagaagttc aggaaaaacc
      781 cagccccatc tcttgcaaac cgcaagaaca tggacctcgc caagtcaggg atcaaaattc
      841 tcgtgcctaa gagccccgtt aagggcagga cctcggttga tggctttcag ggggagagcc
      901 ccgagaagct ggaccctgtg gatcagggtg ccgaggacac tgtagcccca gaggtgactg
      961 cagagaagcc cactggggct ttgctgggcc ctggtgcgga gcgagccagg atggggagca
     1021 ggccccgaat acatccacta gtgcctcagg tttctggccc cgtgactgct gccatggcca
     1081 caggcttagc tgttaatgga aaaggtacat ctccattcat ggatgcgcta gcagccaacg
     1141 gaacagtcac catacagaca tccgtaacag gagtgacagc cgggaaaagg aaatttattg
     1201 acgacagaag agaccaacct tttgacaagc ggttgcgttt cagtgtgagg cagacagaga
     1261 gtgcctacag atacagagat attgtcgtca ggaagcaaga tggcttcacc cacatcttgt
     1321 tatccacaaa atcgtcagag aataactcac taaacccaga ggtgatgaaa gaagtgcaga
     1381 gcgccctgag cacagctgca gccgacgaca gcaagctggt tctgctcagc gccgtgggca
     1441 gcgtcttctg ctgtggtctg gactttattt attttattcg gcgcctcaca gatgaccgaa
     1501 agagagaaag cactaaaatg gcagacgcta tcagaaactt cgtgaatact ttcattcagt
     1561 ttaagaagcc tattattgta gctgttaatg gcccagccat tggactagga gcatccatat
     1621 tgcctctttg tgatgtggtt tgggctaacg aaaaggcttg gtttcaaaca ccctatacca
     1681 ccttcggaca gagtccagat ggctgctcta ccgttatgtt tcccaagatt atgggaggag
     1741 catctgcgaa tgaaatgctg ttcagtgggc ggaagttgac ggcacaggag gcctgtggca
     1801 agggtctggt ctcccaggtg ttttggccag gaaccttcac acaggaagtc atggttcgaa
     1861 tcaaggagct ggcttcatgt aacccagttg tcctggagga atccaaagcc ctggtgcgct
     1921 gcaatatgaa gatggagcta gagcaggcca atgagagaga atgtgaagtg ctgaagaaga
     1981 tctggggctc cgcccagggc atggactcca tgttaaagta cttacagagg aaaatcgatg
     2041 agttctgatg ggcaggctga gcaggacatc ggtggctccc acttgctacg tcgtcctgca
     2101 gtggctcgtg cttggaggca gaactggaaa catccgagct atttattgcc gcggagtttt
     2161 taagtactgt aactttaaaa taactacaaa gcttctttgt ctaagcgtct ttattttata
     2221 ctcatgtata cacaagtata aaaatgtaat tgagcactag gctgctcttg gaagctctaa
     2281 ttttcttgta agctagttgt ggatttttgt tttgtttttg tttttaaaag gaattatgtt
     2341 ttcattttgg gtgacagaag agtttgaaat aatgtttgtt ttactctttt tttttttcct
     2401 taaatctaga tcacagaccc tcaagaatac tagccagcct tctccccctc cctctactga
     2461 aacatgtaga aatacttaaa catgttcctg cctctagggg ggagggggag gtgtgagtac
     2521 ctcaatgctg aaaacagttc tgatcaaact taagaccaac ctggtagaaa aagcatcact
     2581 gatggaaaat cccacccacg ggggcgtggg tttctgctga aatgcccgcc gctctacctt
     2641 tcttactgtc ccattcttac ccagccaccg tgaagagccc agtgtctgga ggaaagcagg
     2701 tggtccagtg tctgtgagtc actccgtagc tcgagtgtta cttgctaagt tatgaattag
     2761 cattagtggg tttaaatagt ttttctgacc ctttttgaaa aataactaca taagtactcc
     2821 ttgtggctgg gtgagaaata ctactttgca tagttttgtt tgtctatctg cagatatgat
     2881 tgctgtatta caccaaaagt attttttatg tttataaagt gtaattttta ggttcactta
     2941 gaatatattt tatttaattt aaaattctct tggcacacta ttaaatacgt aaactccttt
     3001 cagaacagaa aagaactacc ttatatttga catttattat ccagtctctg ctcttatgtc
     3061 tgccatatat tgcgcacggt ttcgtgttca cgagtacccc atggtgtggg gactaacttc
     3121 agatgcctat tatgactaag gcttctaggt ttgcaatcat attgaatgta tgaagactga
     3181 aataaaataa aaaaccttat ttttgtacag ttttgaagtt tatactcaga actgacgcct
     3241 ccccggccat gtggagcgct gtgcagtgtg tacatctgtc tttaccttgg atggattggt
     3301 acagtatttt tgcatctgtg ggaccttctc tttggttcag tagtttgaac tatatatata
     3361 aactgtacac tctgtaaagt ttttatagaa taaatattca gctgtgaaaa ctggttaaat
     3421 aaaactaata tttcttaaca caaa
//
