LOCUS       NM_004678               1206 bp    mRNA    linear   PRI 10-FEB-2024
DEFINITION  Homo sapiens basic charge Y-linked 2 (BPY2), mRNA.
ACCESSION   NM_004678
VERSION     NM_004678.3
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 1206)
  AUTHORS   Ahmadi Rastegar,D., Sharifi Tabar,M., Alikhani,M., Parsamatin,P.,
            Sahraneshin Samani,F., Sabbaghian,M., Sadighi Gilani,M.A., Mohammad
            Ahadi,A., Mohseni Meybodi,A., Piryaei,A., Ansari-Pour,N.,
            Gourabi,H., Baharvand,H. and Salekdeh,G.H.
  TITLE     Isoform-Level Gene Expression Profiles of Human Y Chromosome
            Azoospermia Factor Genes and Their X Chromosome Paralogs in the
            Testicular Tissue of Non-Obstructive Azoospermia Patients
  JOURNAL   J Proteome Res 14 (9), 3595-3605 (2015)
   PUBMED   26162009
REFERENCE   2  (bases 1 to 1206)
  AUTHORS   Lu,C., Jiang,J., Zhang,R., Wang,Y., Xu,M., Qin,Y., Lin,Y., Guo,X.,
            Ni,B., Zhao,Y., Diao,N., Chen,F., Shen,H., Sha,J., Xia,Y., Hu,Z.
            and Wang,X.
  TITLE     Gene copy number alterations in the azoospermia-associated AZFc
            region and their effect on spermatogenic impairment
  JOURNAL   Mol Hum Reprod 20 (9), 836-843 (2014)
   PUBMED   24935076
  REMARK    GeneRIF: genetic association study in Chinese population: Data
            suggest that combined patterns of copy number abnormality in BPY2
            (basic charge Y-linked protein 2) and/or DAZ1 (deleted in
            azoospermia 1) are associated with spermatogenic
            impairment/azoospermia.
REFERENCE   3  (bases 1 to 1206)
  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   4  (bases 1 to 1206)
  AUTHORS   Choi,J., Koh,E., Suzuki,H., Maeda,Y., Yoshida,A. and Namiki,M.
  TITLE     Alu sequence variants of the BPY2 gene in proven fertile and
            infertile men with Sertoli cell-only phenotype
  JOURNAL   Int J Urol 14 (5), 431-435 (2007)
   PUBMED   17511727
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   5  (bases 1 to 1206)
  AUTHORS   Wong,E.Y., Tse,J.Y., Yao,K.M., Lui,V.C., Tam,P.C. and Yeung,W.S.
  TITLE     Identification and characterization of human VCY2-interacting
            protein: VCY2IP-1, a microtubule-associated protein-like protein
  JOURNAL   Biol Reprod 70 (3), 775-784 (2004)
   PUBMED   14627543
REFERENCE   6  (bases 1 to 1206)
  AUTHORS   Tse,J.Y., Wong,E.Y., Cheung,A.N., O,W.S., Tam,P.C. and Yeung,W.S.
  TITLE     Specific expression of VCY2 in human male germ cells and its
            involvement in the pathogenesis of male infertility
  JOURNAL   Biol Reprod 69 (3), 746-751 (2003)
   PUBMED   12724276
  REMARK    GeneRIF: VCY2 was weakly expressed at the spermatogonia and
            immunonegative in spermatocytes and round spermatids in testicular
            biopsy specimens with maturation arrest or hypospermatogenesis.
REFERENCE   7  (bases 1 to 1206)
  AUTHORS   Skaletsky,H., Kuroda-Kawaguchi,T., Minx,P.J., Cordum,H.S.,
            Hillier,L., Brown,L.G., Repping,S., Pyntikova,T., Ali,J., Bieri,T.,
            Chinwalla,A., Delehaunty,A., Delehaunty,K., Du,H., Fewell,G.,
            Fulton,L., Fulton,R., Graves,T., Hou,S.F., Latrielle,P.,
            Leonard,S., Mardis,E., Maupin,R., McPherson,J., Miner,T., Nash,W.,
            Nguyen,C., Ozersky,P., Pepin,K., Rock,S., Rohlfing,T., Scott,K.,
            Schultz,B., Strong,C., Tin-Wollam,A., Yang,S.P., Waterston,R.H.,
            Wilson,R.K., Rozen,S. and Page,D.C.
  TITLE     The male-specific region of the human Y chromosome is a mosaic of
            discrete sequence classes
  JOURNAL   Nature 423 (6942), 825-837 (2003)
   PUBMED   12815422
REFERENCE   8  (bases 1 to 1206)
  AUTHORS   Wong,E.Y., Tse,J.Y., Yao,K.M., Tam,P.C. and Yeung,W.S.
  TITLE     VCY2 protein interacts with the HECT domain of ubiquitin-protein
            ligase E3A
  JOURNAL   Biochem Biophys Res Commun 296 (5), 1104-1111 (2002)
   PUBMED   12207887
  REMARK    GeneRIF: VCY2 protein interacts with the HECT domain of
            ubiquitin-protein ligase E3A
REFERENCE   9  (bases 1 to 1206)
  AUTHORS   Saut,N., Terriou,P., Navarro,A., Levy,N. and Mitchell,M.J.
  TITLE     The human Y chromosome genes BPY2, CDY1 and DAZ are not essential
            for sustained fertility
  JOURNAL   Mol Hum Reprod 6 (9), 789-793 (2000)
   PUBMED   10956550
REFERENCE   10 (bases 1 to 1206)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF000980.1 and AC006366.4.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_004678.2.
            
            Summary: This gene is located in the nonrecombining portion of the
            Y chromosome, and expressed specifically in testis. The encoded
            protein interacts with ubiquitin protein ligase E3A and may be
            involved in male germ cell development and male infertility. Three
            nearly identical copies of this gene exist on chromosome Y; two
            copies are part of a palindromic region. This record represents the
            copy outside of the palidromic region. [provided by RefSeq, Jul
            2008].
            
            CCDS Note: This CCDS ID represents the protein described in PMIDs:
            12724276 and 12207887. It should be noted this transcript is
            predicted to undergo nonsense-mediated mRNA decay (NMD). However,
            the protein is represented because it was detected endogenously in
            PMID: 12724276. Three identical copies of this gene exist on
            chromosome Y; two copies are part of a palindromic region. This
            record represents the copy outside of the palidromic region.
            
            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 :: AF000980.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148874
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000331070.8/ ENSP00000329106.3
            NMD candidate          :: PMID: 12207887, 12724276
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-633               AF000980.1         1-633
            634-634             AC006366.4         30804-30804         c
            635-925             AF000980.1         635-925
            926-926             AC006366.4         23176-23176         c
            927-1206            AF000980.1         927-1206
FEATURES             Location/Qualifiers
     source          1..1206
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="Y"
                     /map="Yq11.223"
     gene            1..1206
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /note="basic charge Y-linked 2"
                     /db_xref="GeneID:9083"
                     /db_xref="HGNC:HGNC:13508"
                     /db_xref="MIM:400013"
     exon            1..31
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            32..154
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            155..291
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            292..410
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     CDS             333..653
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /note="testis-specific basic protein on Y, 2; basic
                     protein on Y chromosome 2; variable charge, Y-linked, 2;
                     variably charged protein Y 2"
                     /codon_start=1
                     /product="testis-specific basic protein Y 2"
                     /protein_id="NP_004669.2"
                     /db_xref="CCDS:CCDS14800.1"
                     /db_xref="GeneID:9083"
                     /db_xref="HGNC:HGNC:13508"
                     /db_xref="MIM:400013"
                     /translation="MMTLVPRARTRAGQDHYSHPCPRFSQVLLTEGIMTYCLTKNLSD
                     VNILHRLLKNGNVRNTLLQSKVGLLTYYVKLYPGEVTLLTRPSIQMRLCCITGSVSRP
                     RSQK"
     exon            411..528
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            529..634
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            635..759
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            760..884
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
     exon            885..1206
                     /gene="BPY2"
                     /gene_synonym="BPY2A; VCY2; VCY2A"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 aatatctcag gacccaggac catgtgatat gggcccaaca cctggatgat gttactcttc
       61 tgcctaggtc atgcgtaaag agggaattag ggcatattgc ttggcccagt cccgtaatga
      121 tatgactctc ctgcttgtgc cagagccaca gaagtgtgct tggtgacata atctttgagg
      181 ctgtcacatc accaagatta tattgtatca ctggaccagc ataaagctga cacttctgac
      241 tatgcccagc cttcaaataa tactacactg tataattggc tcaacaccca ggtgatattg
      301 ttccatttac ctgagaccag ataaaaagcc taatgatgac gcttgtcccc agagccagga
      361 cacgtgcagg acaggatcat tactctcatc cctgccccag attttcacag gtgctgctta
      421 cagagggcat catgacatat tgcttgacaa agaacctaag tgatgttaat attctgcata
      481 ggttgctaaa aaatgggaat gtgagaaata ccttgcttca gtccaaagtg ggcttgctga
      541 catattatgt gaaactgtac ccgggtgaag tgactcttct gactaggccc agcatacaaa
      601 tgagattatg ctgtatcact ggctcagtgt cgaggcccag atcacagaag taattgtgcc
      661 atatgtggaa caagcagcta agcaatagat aacatccatc gtggctctgc cttcaaaggg
      721 aaattttaca tatgtcactg ggaccatcac ccagatgatg tcctgcccac taaaagaatt
      781 gtgacataac gctgactgca aaaactgggt aatgcaactc tcctctttat tctggagtct
      841 gccaaaacaa gggattatca catattgcgg agtccagcac ccaggtaaaa ttttgtcata
      901 tacccagctt cagataccat gcaataatac aactatcata cctggaccca aagaggagag
      961 atattttgat tctcattgcc attcttatgg ccacaagcaa agtaatggtt ctcatagtgg
     1021 tataaagttc acacagtatt atgacactcc cagcgtatca tagaaaatgt gagtagtaca
     1081 atgagtgtta taacagggaa cagcaaacca atgctattgt gattattgga ttcacaccca
     1141 gctgacgcga ctatcattct ctcacaagaa cagaacctgc aaataaagta ctaaatctca
     1201 ccaaaa
//
