LOCUS       NM_004824               3503 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens chromodomain Y like (CDYL), transcript variant 1,
            mRNA.
ACCESSION   NM_004824 NM_170751
VERSION     NM_004824.4
KEYWORDS    RefSeq; MANE Select.
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 3503)
  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 3503)
  AUTHORS   Lan,K.C., Cheng,Y.H., Chang,Y.C., Wei,K.T., Weng,P.L. and Kang,H.Y.
  TITLE     Interaction between Chromodomain Y-like Protein and Androgen
            Receptor Signaling in Sertoli Cells Accounts for Spermatogenesis
  JOURNAL   Cells 13 (10), 851 (2024)
   PUBMED   38786072
  REMARK    GeneRIF: Interaction between Chromodomain Y-like Protein and
            Androgen Receptor Signaling in Sertoli Cells Accounts for
            Spermatogenesis.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3503)
  AUTHORS   Khalilian,S., Tabari,M.A.K., Omrani,M.A. and Ghafouri-Fard,S.
  TITLE     Emerging functions and significance of circCDYL in human disorders
  JOURNAL   Mol Biol Rep 51 (1), 7 (2023)
   PUBMED   38085365
  REMARK    GeneRIF: Emerging functions and significance of circCDYL in human
            disorders.
            Review article
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3503)
  AUTHORS   Kong,R., Wei,W., Man,Q., Chen,L., Jia,Y., Zhang,H., Liu,Z.,
            Cheng,K., Mao,C. and Liu,S.
  TITLE     Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex drives
            lung metastasis of cancer stem cells from hepatocellular carcinoma
  JOURNAL   Cancer Lett 578, 216442 (2023)
   PUBMED   37852428
  REMARK    GeneRIF: Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex
            drives lung metastasis of cancer stem cells from hepatocellular
            carcinoma.
REFERENCE   5  (bases 1 to 3503)
  AUTHORS   Wang,S., Liu,F., Ma,H., Cui,X., Yang,S. and Qin,R.
  TITLE     circCDYL Acts as a Tumor Suppressor in Triple Negative Breast
            Cancer by Sponging miR-190a-3p and Upregulating TP53INP1
  JOURNAL   Clin Breast Cancer 20 (5), 422-430 (2020)
   PUBMED   32741666
  REMARK    GeneRIF: circCDYL Acts as a Tumor Suppressor in Triple Negative
            Breast Cancer by Sponging miR-190a-3p and Upregulating TP53INP1.
REFERENCE   6  (bases 1 to 3503)
  AUTHORS   Caron,C., Pivot-Pajot,C., van Grunsven,L.A., Col,E., Lestrat,C.,
            Rousseaux,S. and Khochbin,S.
  TITLE     Cdyl: a new transcriptional co-repressor
  JOURNAL   EMBO Rep 4 (9), 877-882 (2003)
   PUBMED   12947414
REFERENCE   7  (bases 1 to 3503)
  AUTHORS   Shi,Y., Sawada,J., Sui,G., Affar el,B., Whetstine,J.R., Lan,F.,
            Ogawa,H., Luke,M.P., Nakatani,Y. and Shi,Y.
  TITLE     Coordinated histone modifications mediated by a CtBP co-repressor
            complex
  JOURNAL   Nature 422 (6933), 735-738 (2003)
   PUBMED   12700765
REFERENCE   8  (bases 1 to 3503)
  AUTHORS   Lahn,B.T., Tang,Z.L., Zhou,J., Barndt,R.J., Parvinen,M., Allis,C.D.
            and Page,D.C.
  TITLE     Previously uncharacterized histone acetyltransferases implicated in
            mammalian spermatogenesis
  JOURNAL   Proc Natl Acad Sci U S A 99 (13), 8707-8712 (2002)
   PUBMED   12072557
REFERENCE   9  (bases 1 to 3503)
  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   10 (bases 1 to 3503)
  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     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL022725.8, BC108725.1,
            BC043397.1 and BE874176.1.
            
            On Nov 23, 2018 this sequence version replaced NM_004824.3.
            
            Summary: Chromodomain Y is a primate-specific Y-chromosomal gene
            family expressed exclusively in the testis and implicated in
            infertility. Although the Y-linked genes are testis-specific, this
            autosomal gene is ubiquitously expressed. The Y-linked genes arose
            by retrotransposition of an mRNA from this gene, followed by
            amplification of the retroposed gene. Proteins encoded by this gene
            superfamily possess a chromodomain, a motif implicated in chromatin
            binding and gene suppression, and a catalytic domain believed to be
            involved in histone acetylation. Multiple proteins are encoded by
            transcript variants of this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript.
            
            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 :: BC108725.1, SRR1803614.141890.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000397588.8/ ENSP00000380718.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-42                AL022725.8         117664-117705       c
            43-2215             BC108725.1         12-2184
            2216-3469           BC043397.1         1947-3200
            3470-3503           BE874176.1         23-56
FEATURES             Location/Qualifiers
     source          1..3503
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p25.1"
     gene            1..3503
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /note="chromodomain Y like"
                     /db_xref="GeneID:9425"
                     /db_xref="HGNC:HGNC:1811"
                     /db_xref="MIM:603778"
     exon            1..404
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     CDS             381..2015
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /EC_number="2.3.1.48"
                     /note="isoform a is encoded by transcript variant 1;
                     CDY-like, autosomal; testis-specific chromodomain Y-like
                     protein; chromodomain protein, Y-like; crotonyl-CoA
                     hydratase"
                     /codon_start=1
                     /product="chromodomain Y-like protein isoform a"
                     /protein_id="NP_004815.3"
                     /db_xref="CCDS:CCDS4491.2"
                     /db_xref="GeneID:9425"
                     /db_xref="HGNC:HGNC:1811"
                     /db_xref="MIM:603778"
                     /translation="MASEELYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQH
                     LVNCEEYIHDFNRRHTEKQKESTLTRTNRTSPNNARKQISRSTNSNFSKTSPKALVIG
                     KDHESKNSQLFAASQKFRKNTAPSLSSRKNMDLAKSGIKILVPKSPVKSRTAVDGFQS
                     ESPEKLDPVEQGQEDTVAPEVAAEKPVGALLGPGAERARMGSRPRIHPLVPQVPGPVT
                     AAMATGLAVNGKGTSPFMDALTANGTTNIQTSVTGVTASKRKFIDDRRDQPFDKRLRF
                     SVRQTESAYRYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSK
                     LVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVN
                     GPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLL
                     SGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKME
                     LEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF"
     exon            405..1071
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     exon            1072..1328
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     exon            1329..1501
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     exon            1502..1712
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     exon            1713..1856
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     exon            1857..3503
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3479..3484
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /note="hexamer: AATAAA"
     polyA_site      3503
                     /gene="CDYL"
                     /gene_synonym="CDYL1"
                     /note="major polyA site"
ORIGIN      
        1 ggtcgcaagt aggaagcttt ctgcactaca ccggagaggg gagccgcgat ccggccgcgc
       61 cgcccgcacg ccgccgcgcc cgccccagcc cgcccggccc cgcggcgggg cgcgatgagc
      121 ccgagcgcga gccggcccgc cggggagtga gcgcggggcg cccagggcgc gttgcgtagc
      181 tgctcctgcg cacaaccccg ccgcgccgcc ggcccgcact ggccgcggag tgcaagaggc
      241 tcgtccgtgc ccagcgcccg gccggccgcg ggagcaggaa gcgcaggcca cgcaggaccc
      301 aactgaaaca aagtgtcggc cgcccggcgc cggcgcccgc cccgaccctg cccctcccgc
      361 ccgcaactcc gccgcccacc atggcttccg aggagctgta cgaggttgaa aggattgttg
      421 acaaaaggaa aaataaaaaa gggaagacag agtatttggt tcggtggaaa ggctatgaca
      481 gcgaggacga cacttgggag ccggaacagc acctcgtgaa ctgtgaggaa tacatccacg
      541 acttcaacag acgccacacg gagaagcaga aggagagcac attgaccaga acaaacagga
      601 cctctcccaa caatgctagg aaacaaatct ccagatccac caacagcaac ttttctaaga
      661 cctctcctaa ggcactcgtg attgggaaag accacgaatc caaaaacagc cagctgtttg
      721 ctgccagcca gaagttcagg aagaacacag ctccatctct ctccagccgg aagaacatgg
      781 acctagcgaa gtcaggtatc aagatcctcg tgcctaaaag ccccgttaag agcaggaccg
      841 cagtggacgg ctttcagagc gagagccctg agaaactgga ccccgtcgag cagggtcagg
      901 aggacacagt ggcacccgaa gtggcagcgg aaaagccggt cggagcttta ttgggccccg
      961 gtgccgagag ggccaggatg gggagcaggc ccaggataca cccactagtg cctcaggtgc
     1021 ccggccctgt gactgcagcc atggccacag gcttagctgt taacgggaaa ggtacatctc
     1081 cgttcatgga tgcattaaca gccaatggga caaccaacat acagacatct gttacaggag
     1141 tgactgccag caaaaggaaa tttattgacg acagaagaga ccagcctttt gacaagcgat
     1201 tgcgtttcag cgtgaggcaa acagaaagtg cctacagata cagagatatt gtggtcagga
     1261 agcaggatgg cttcacccac atcttgttat ccacaaagtc ctcagagaat aactcactaa
     1321 atccagaggt aatgagagaa gtccagagtg ctctgagcac ggccgctgcc gatgacagca
     1381 agctggtact gctcagcgcc gttggcagcg tcttctgttg tggacttgac tttatttatt
     1441 ttatacgacg tctgacagat gacaggaaaa gagaaagcac taaaatggca gaagctatca
     1501 gaaacttcgt gaatactttc attcaattta agaagcccat tattgtagca gtcaatggcc
     1561 cagccattgg tctaggagca tctatattgc ctctttgcga tgtggtttgg gctaatgaaa
     1621 aggcttggtt tcaaacaccc tataccacct tcggacagag tccagatggc tgttctaccg
     1681 ttatgtttcc caagataatg ggaggagcat ctgcaaacga gatgctgctc agtggacgga
     1741 agctgacagc gcaggaggcg tgtggcaagg gcctggtctc ccaggtgttt tggcccggga
     1801 cgttcactca ggaagtgatg gttcgcatta aggagcttgc ctcgtgcaat ccagttgtgc
     1861 ttgaggaatc caaagccctc gtgcgctgca acatgaagat ggagctggag caggccaacg
     1921 agagggagtg tgaggtgctg aagaaaatct ggggctcggc ccaggggatg gactccatgt
     1981 taaagtactt gcagaggaag atcgatgagt tctgagtgtc gggctgccca ctggtgacac
     2041 cgggatcggg ctgagcagga gaacatcacc ggctccagtt cccctgatcc attctcacag
     2101 cctgaaacaa gctcacccgt agcttacgct tggaagcagg actgggaaca tccacgctat
     2161 ttattatcga ggagttttaa agtactgtaa ctttaaaata aataactaca aagcttcttt
     2221 gtccaaacgt cattatttta tacttatata cacgcaggtg taaaagtata aaggtgagca
     2281 ctagactgct cttagaagct ctaatttttg ttttctttgg ctagtactgt ataaaaaaca
     2341 gaattgtgtt ttattggttt tggatgacag aaaagtctgg aataatgttt gttttcctca
     2401 tttcttcctt ctagaacaca gaatctaaag gggtattagc cagcctcgcc tccctgcccc
     2461 acgtagagac acagagtgat gtgaggcgtt ggctttttct ccaagaaggt acagatacct
     2521 cagattcggg aaactcaaaa tcaaaagact tagcttctag gataaatact tctgatgaaa
     2581 aatccgctga ggagcatacc ccaaaccaga catatgctta ggattcatgc tgagatatca
     2641 attggtttcc ccttcttttt aaaatacgtc cagttcttac ccagttaaca tgaagaaacc
     2701 actgtctcta gaagaaagct tgttttgcag tattagtgaa tcactgaata gcttaagtat
     2761 gactatctaa gttataagtt agtctttagt gggttttaaa tagtttttct gacccttctg
     2821 aaaaataact acataagtgc ttcttgttgc tgggtgagaa atactacttt atagacagtt
     2881 ttggttttct gtttgcagat atgattgatg tatttcacca aaataaaata tttttatgtt
     2941 tataaagtgt aatttttagg ttcacttaga atatatttta tttaataagt taaaattctt
     3001 ttggcacact attaaatgca aaaactcctt tcaaaacaaa aaagaactac cttatattca
     3061 acatttaatg ttcttggcct ctgcttttat gtctatacaa tatactgagt tcagtatggt
     3121 gtccaagagt gccctgtgtg gatagacatg tgcactcctt ccaggagtgg gtactgattc
     3181 cagactccag atgcctatta ttagttaggc ttctgagctt gcaatcatat tgaatgtatg
     3241 aagagcgaaa tcaaattctt atttttgtac agttttgaag tttatactta gaactgacca
     3301 cctccccggc cacgcggaga gctgtacagt gtgtaaatct gcctttatct tggattgatt
     3361 ggtacagtat ttttgcatct gtgggaccta ccttttcgtt cagtagtttg aactatatat
     3421 aaactgtaca atctgtaaag tttttataga ataaatattc agctgtgaaa actggttaaa
     3481 taaaactaat atttcttaac aca
//
