LOCUS       NM_004680               2366 bp    mRNA    linear   PRI 13-OCT-2024
DEFINITION  Homo sapiens chromodomain Y-linked 1 (CDY1), transcript variant 2,
            mRNA.
ACCESSION   NM_004680
VERSION     NM_004680.3
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 2366)
  AUTHORS   Ghorbel,M., Baklouti-Gargouri,S., Keskes,R., Sellami,A.,
            McElreavy,K. and Ammar-Keskes,L.
  TITLE     Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in
            Tunisian infertile male
  JOURNAL   Hum Fertil (Camb) 26 (5), 1238-1247 (2023)
   PUBMED   36591797
  REMARK    GeneRIF: Y-chromosome haplogroups and Azoospermia Factor (AZF)
            analysis in Tunisian infertile male.
REFERENCE   2  (bases 1 to 2366)
  AUTHORS   Ghorbel,M., Baklouti-Gargouri,S., Keskes,R., Chakroun,N.,
            Sellami,A., Fakhfakh,F. and Ammar-Keskes,L.
  TITLE     Deletion of CDY1b copy of Y chromosome CDY1 gene is a risk factor
            of male infertility in Tunisian men
  JOURNAL   Gene 548 (2), 251-255 (2014)
   PUBMED   25042452
  REMARK    GeneRIF: Findings showed that deletion of CDY1b copy gene is a
            significant risk factor for male infertility independent of sperm
            concentration, whereas deletion of CDY1a gene seems to have no
            effect on fertility in the Tunisian population.
REFERENCE   3  (bases 1 to 2366)
  AUTHORS   Kleiman,S.E., Lehavi,O., Hauser,R., Botchan,A., Paz,G., Yavetz,H.
            and Yogev,L.
  TITLE     CDY1 and BOULE transcripts assessed in the same biopsy as
            predictive markers for successful testicular sperm retrieval
  JOURNAL   Fertil Steril 95 (7), 2297-2302 (2011)
   PUBMED   21474125
  REMARK    GeneRIF: Assessing the expression of both CDY1 and BOULE by
            qualitative RT-PCR is a sensitive and feasible test for predicting
            the presence of sperm cells in testicular tissue biopsies.
REFERENCE   4  (bases 1 to 2366)
  AUTHORS   Yang,Y., Ma,M., Li,L., Su,D., Chen,P., Ma,Y., Liu,Y., Tao,D.,
            Lin,L. and Zhang,S.
  TITLE     Differential effect of specific gr/gr deletion subtypes on
            spermatogenesis in the Chinese Han population
  JOURNAL   Int J Androl 33 (5), 745-754 (2010)
   PUBMED   20039973
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   5  (bases 1 to 2366)
  AUTHORS   Sin,H.S., Koh,E., Shigehara,K., Sugimoto,K., Maeda,Y., Yoshida,A.,
            Kyono,K. and Namiki,M.
  TITLE     Features of constitutive gr/gr deletion in a Japanese population
  JOURNAL   Hum Reprod 25 (9), 2396-2403 (2010)
   PUBMED   20663794
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   6  (bases 1 to 2366)
  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   7  (bases 1 to 2366)
  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]
REFERENCE   8  (bases 1 to 2366)
  AUTHORS   Yen,P.H.
  TITLE     A long-range restriction map of deletion interval 6 of the human Y
            chromosome: a region frequently deleted in azoospermic males
  JOURNAL   Genomics 54 (1), 5-12 (1998)
   PUBMED   9806824
REFERENCE   9  (bases 1 to 2366)
  AUTHORS   Lahn,B.T. and Page,D.C.
  TITLE     Functional coherence of the human Y chromosome
  JOURNAL   Science 278 (5338), 675-680 (1997)
   PUBMED   9381176
REFERENCE   10 (bases 1 to 2366)
  AUTHORS   Fan,Y. and Silber,S.J.
  TITLE     Y Chromosome Infertility
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301513
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC007562.4.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Aug 14, 2020 this sequence version replaced NM_004680.2.
            
            Summary: This gene encodes a protein containing a chromodomain and
            a histone acetyltransferase catalytic domain. Chromodomain proteins
            are components of heterochromatin-like complexes and can act as
            gene repressors. This protein is localized to the nucleus of late
            spermatids where histone hyperacetylation takes place. Histone
            hyperacetylation is thought to facilitate the transition in which
            protamines replace histones as the major DNA-packaging protein. The
            human chromosome Y has two identical copies of this gene within a
            palindromic region; this record represents the more telomeric copy.
            Chromosome Y also contains a pair of closely related genes in
            another more telomeric palindrome as well as several related
            pseudogenes. Two protein isoforms are encoded by transcript
            variants of this gene. Additional transcript variants have been
            described, but their full-length nature has not been determined.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2), also called the minor
            variant, lacks a segment in the 3' end of the coding sequence,
            compared to variant 1. Variant 2 encodes isoform b which has a
            longer and distinct C-terminus, compared to isoform a.
            
            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##
            RNAseq introns :: single sample supports all introns SAMEA1968968,
                              SAMEA2148874 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000306609.5/ ENSP00000302968.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1918              AC007562.4         111311-113228
            1919-2366           AC007562.4         113649-114096
FEATURES             Location/Qualifiers
     source          1..2366
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="Y"
                     /map="Yq11.23"
     gene            1..2366
                     /gene="CDY1"
                     /gene_synonym="CDY; CDY1A"
                     /note="chromodomain Y-linked 1"
                     /db_xref="GeneID:9085"
                     /db_xref="HGNC:HGNC:1809"
                     /db_xref="MIM:400016"
     exon            1..1918
                     /gene="CDY1"
                     /gene_synonym="CDY; CDY1A"
                     /inference="alignment:Splign:2.1.0"
     CDS             327..1991
                     /gene="CDY1"
                     /gene_synonym="CDY; CDY1A"
                     /EC_number="2.3.1.48"
                     /note="isoform b is encoded by transcript variant 2;
                     chromodomain protein, Y chromosome, 1; testis-specific
                     chromodomain protein on Y; testis-specific chromodomain
                     protein Y 1; chromodomain protein, Y-linked, 1"
                     /codon_start=1
                     /product="testis-specific chromodomain protein Y 1 isoform
                     b"
                     /protein_id="NP_004671.1"
                     /db_xref="CCDS:CCDS14801.1"
                     /db_xref="GeneID:9085"
                     /db_xref="HGNC:HGNC:1809"
                     /db_xref="MIM:400016"
                     /translation="MASQEFEVEAIVDKRQDKNGNTQYLVRWKGYDKQDDTWEPEQHL
                     MNCEKCVHDFNRRQTEKQKKLTWTTTSRIFSNNARRRTSRSTKANYSKNSPKTPVTDK
                     HHRSKNRKLFAASKNVRRKAASILSDTKNMEIINSTIETLAPDSPFDHKTVSGFQKLE
                     KLDPIAADQQDTVVFKVTEGKLLRDPLSRPGAEQTGIQNKTQIHPLMSQMSGSVTASM
                     ATGSATRKGIVVLIDPLAANGTTDMHTSVPRVKGGQRNITDDSRDQPFIKKMHFTIRL
                     TESASTYRDIVVKKEDGFTQIVLSTRSTEKNALNTEVIKEIVNALNSAAADDSKLVLF
                     SAAGSVFCCGLDFGYFVKHLRNNRNTASLEMVDTIKNFVNTFIQFKKPIVVSVNGPAI
                     GLGASILPLCDLVWANEKAWFQTPYTTFGQSPDGCSSITFPKMMGKASANEMLIAGRK
                     LTAREACAKGLVSQVFLTGTFTQEVMIQIKELASYNPIVLEECKALVRCNIKLELEQA
                     NERECEVLRKIWSSAQGIESMLKIPLLGYKAAFPPRKTQNDQRWCP"
     exon            1919..2366
                     /gene="CDY1"
                     /gene_synonym="CDY; CDY1A"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 aacaggcagg aagaaagctt tctgtactac accagagggt tggggctgtg gatttagcta
       61 ctctcacctg aggctactga gcaagttgtc atgcaccatg agacaaagcc caagctgtcc
      121 caccaggcag taagtatgga gaggttcagg cacatggcat agctgctatt tcgcacaatt
      181 ttcactacac cagtggtgac aaaatagaag aggttcatcc atacacagaa cctggtgaag
      241 agctggaggc agaaagaagt gtctatgtgg agacgcaact gaaacaaagg tggcacagca
      301 actgttccaa tcccgtgtct ttcctcatgg cttcccagga gtttgaggtt gaagctattg
      361 ttgacaaaag acaggataaa aatgggaata cacagtattt ggttcggtgg aaaggttatg
      421 acaaacagga tgacacttgg gaaccagagc agcacctcat gaactgtgaa aaatgtgtac
      481 atgattttaa tagacgacag actgaaaaac agaaaaaact gacatggact acaaccagta
      541 gaattttttc aaacaatgcc agaagaagaa cttccagatc tacaaaagca aactattcta
      601 agaactctcc taaaacgcca gtgactgata aacaccacag gtccaaaaac cgcaagttat
      661 ttgctgccag caagaacgtt aggagaaagg cagcttcaat tctctccgac acaaagaata
      721 tggagataat aaattcaact attgagaccc ttgcacctga cagccccttt gaccacaaaa
      781 ctgtgagtgg ctttcagaaa cttgagaaac tggaccctat tgcagcagat cagcaggaca
      841 cggtggtctt caaggtgaca gaagggaaac tcctccggga ccctttgtca cgtcctggtg
      901 cagaacagac tggaatacag aacaagactc agatacaccc actaatgtcg cagatgtctg
      961 gctcagttac tgcttctatg gccacaggtt cagctacccg aaagggtata gtggtattaa
     1021 tagacccatt agcagccaat gggacaacag acatgcatac ctcagttcca agagtgaaag
     1081 gtgggcaaag aaatattact gatgacagca gagaccagcc ttttatcaag aagatgcact
     1141 tcaccataag gctaacagaa agtgccagca catacagaga cattgtagtg aagaaagagg
     1201 atggattcac ccagatagtg ctatcaacta gatcgacaga aaaaaatgca ctgaatacag
     1261 aagtaattaa agaaatagtt aatgctctga atagcgctgc tgcagatgac agcaagctcg
     1321 tgctgttcag tgcagctgga agtgtctttt gctgcggtct tgattttggg tactttgtga
     1381 agcacttaag gaataacaga aacacagcaa gccttgaaat ggtggacacc atcaagaact
     1441 ttgtgaatac ttttattcaa tttaaaaagc ctattgttgt atcagtcaat ggccctgcga
     1501 ttggactagg tgcatccatc ctgcctcttt gtgatctcgt gtgggctaat gaaaaggctt
     1561 ggttccaaac cccttatacg acctttggac agagtccaga tggctgttct tctattacat
     1621 tccccaaaat gatgggtaaa gcatctgcca atgaaatgtt aattgctggg cgaaagctga
     1681 cagcaaggga ggcatgcgcc aaaggcctgg tctctcaggt atttttgact ggaactttca
     1741 cccaagaggt tatgattcaa attaaggagc ttgcctcata caatccaatt gtactggaag
     1801 aatgtaaggc cctcgttcgc tgtaatatta agttggagtt ggaacaggcc aatgagagag
     1861 agtgtgaggt gctgaggaag atctggagct cagcccaagg gatagaatcc atgttaaaaa
     1921 tacctctgtt gggatataaa gcagccttcc ctcccagaaa gacacagaat gatcagagat
     1981 ggtgcccttg actttatagt ggcacaaacg cttcagagac acacaattat aagagactta
     2041 tcttttagca taaatactta tggctcaaaa tccactgacg atcattctcc taaactgaac
     2101 acatgactag aattggtggt gagatatcgc ttgattttct tttcctttat aaatgtctag
     2161 ttcttaccca gttaacaaaa gaaaacttta tcgctctaaa gtaaaacttg ttacaccaca
     2221 ttagtgaatt atggaatgat tttggtggaa atatccaggt tctaatgtgt ggaatgtgca
     2281 gatttaggtt actttagtgt atgttctagt taataagtta aaattctgga cacattatta
     2341 aaggcagaaa cttctttcaa agcaaa
//
