LOCUS       NM_004679                510 bp    mRNA    linear   PRI 12-JUN-2024
DEFINITION  Homo sapiens variable charge Y-linked (VCY), mRNA.
ACCESSION   NM_004679
VERSION     NM_004679.4
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 510)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   2  (bases 1 to 510)
  AUTHORS   Taguchi,A., Taylor,A.D., Rodriguez,J., Celiktas,M., Liu,H., Ma,X.,
            Zhang,Q., Wong,C.H., Chin,A., Girard,L., Behrens,C., Lam,W.L.,
            Lam,S., Minna,J.D., Wistuba,I.I., Gazdar,A.F. and Hanash,S.M.
  TITLE     A search for novel cancer/testis antigens in lung cancer identifies
            VCX/Y genes, expanding the repertoire of potential
            immunotherapeutic targets
  JOURNAL   Cancer Res 74 (17), 4694-4705 (2014)
   PUBMED   24970476
  REMARK    GeneRIF: Identified members of the VCX/Y gene family as novel CT
            antigens.
REFERENCE   3  (bases 1 to 510)
  AUTHORS   Hansen,M.A., Nielsen,J.E., Retelska,D., Larsen,N. and Leffers,H.
  TITLE     A shared promoter region suggests a common ancestor for the human
            VCX/Y, SPANX, and CSAG gene families and the murine CYPT family
  JOURNAL   Mol Reprod Dev 75 (2), 219-229 (2008)
   PUBMED   17342728
  REMARK    GeneRIF: Human VCX/Y, SPANX, and CSAG2 gene families together with
            the murine SPANX gene and the CYPT family may share a common
            ancestor.
REFERENCE   4  (bases 1 to 510)
  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   5  (bases 1 to 510)
  AUTHORS   Lahn,B.T. and Page,D.C.
  TITLE     A human sex-chromosomal gene family expressed in male germ cells
            and encoding variably charged proteins
  JOURNAL   Hum Mol Genet 9 (2), 311-319 (2000)
   PUBMED   10607842
REFERENCE   6  (bases 1 to 510)
  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 AF000979.1 and AI149997.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 20, 2020 this sequence version replaced NM_004679.3.
            
            Summary: The protein encoded by this gene is a member of a family
            of human VCX/Y genes. This gene family has multiple members on both
            X and Y chromosomes, and all are expressed exclusively in male germ
            cells. Members of the VCX/Y family share a high degree of sequence
            identity, with the exception that a 30-bp unit is tandemly repeated
            in X-linked members but occurs only once in Y-linked members. VCX/Y
            genes encode small and highly charged proteins of unknown function.
            This gene encodes a small, positively charged protein. The presence
            of a putative bipartite nuclear localization signal suggests that
            this gene encodes a nuclear protein. The genome has two identical
            copies of this gene within a palindromic region; this record
            represents the more centromeric copy. [provided by RefSeq, Jul
            2008].
            
            ##Evidence-Data-START##
            Transcript exon combination :: HY250623.1, AI149997.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2158188, SAMEA2161674
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000250825.5/ ENSP00000250825.4
            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
            1-506               AF000979.1         40-545
            507-510             AI149997.1         3-6                 c
FEATURES             Location/Qualifiers
     source          1..510
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="Y"
                     /map="Yq11.221"
     gene            1..510
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /note="variable charge Y-linked"
                     /db_xref="GeneID:9084"
                     /db_xref="HGNC:HGNC:12668"
                     /db_xref="MIM:400012"
     exon            1..135
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /inference="alignment:Splign:2.1.0"
     CDS             34..411
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /note="variable charge, Y chromosome; basic protein on Y
                     chromosome, 1; testis-specific basic protein on Y, 1;
                     basic charge, Y-linked 1; variably charged protein Y"
                     /codon_start=1
                     /product="testis-specific basic protein Y 1"
                     /protein_id="NP_004670.1"
                     /db_xref="CCDS:CCDS56617.1"
                     /db_xref="GeneID:9084"
                     /db_xref="HGNC:HGNC:12668"
                     /db_xref="MIM:400012"
                     /translation="MSPKPRASGPPAKAKETGKRKSSSQPSPSGPKKKTTKVAEKGEA
                     VRGGRRGKKGAATKMAAVTAPEAESGPAAPGPSDQPSQELPQHELPPEEPVSEGTQHD
                     PLSQESELEEPLSKGRPSTPLSP"
     exon            136..510
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      490..495
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /note="hexamer: AATGAA"
     polyA_site      510
                     /gene="VCY"
                     /gene_synonym="BPY1; VCY1; VCY1A"
                     /note="major polyA site"
ORIGIN      
        1 agtcgaccgt tgcgagacgt tgagctgcgg cagatgagtc caaagccgag agcctcggga
       61 cctccggcca aggccaagga gacaggaaag aggaagtcct cctctcagcc gagccccagt
      121 ggcccgaaga agaagactac caaggtggcc gagaagggag aagcagttcg tggagggaga
      181 cgcgggaaga aaggggctgc gacaaagatg gcggccgtga cggcacctga ggcggagagc
      241 gggccagcgg cacccggccc cagcgaccag cccagccagg agctccctca gcacgagctg
      301 ccgccggagg agccagtgag cgaggggacc cagcacgacc ccctgagtca ggagagcgag
      361 ctggaggaac cactgagtaa ggggcgccca tctactcccc tatctccctg agcagcaact
      421 aagtttaggc ccagctgcca gacctcagag atctcaccag cagggtgctt cccatgttga
      481 tgacaataaa atgaatgtgt tgcaaaccga
//
