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BPY2 Gene

protein-coding   GIFtS: 42
GCID: GC0YP025130

Basic Charge, Y-Linked, 2

(Previous names: variable charge, Y-linked, 2)
(Previous symbol: VCY2)
  See BPY2-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Basic Charge, Y-Linked, 21 2     Basic Protein On Y Chromosome 22
VCY21 2 3     Testis-Specific Basic Protein On Y, 22
Variable Charge, Y-Linked, 21 2     Testis-Specific Basic Protein Y 22
Variably Charged Protein Y 22 3     VCY2B3
BPY2A2 3     VCY2C3
VCY2A2 3     Basic Charge, Y-Linked 23

External Ids:    HGNC: 135081   Entrez Gene: 90832   Ensembl: ENSG000001837537   OMIM: 4000135   UniProtKB: O145993   

Export aliases for BPY2 gene to outside databases

Previous GC identifers: GC0YU900229 GC0YP023468 GC0YP023539


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for BPY2 Gene:
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)

GeneCards Summary for BPY2 Gene:
BPY2 (basic charge, Y-linked, 2) is a protein-coding gene. Diseases associated with BPY2 include y chromosome infertility, and male infertility. An important paralog of this gene is BPY2B.

Gene Wiki entry for BPY2 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000024.9  NT_011903.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for BPY2
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BPY2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11   Ensembl cytogenetic band:  Yq11.223   HGNC cytogenetic band: Yq11.223

BPY2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BPY2 gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP025130:  view genomic region     (about GC identifiers)

Start:
25,119,966 bp from pter      End:
25,151,612 bp from pter
Size:
31,647 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: VCY2_HUMAN, O14599 (See protein sequence)
Recommended Name: Testis-specific basic protein Y 2  
Size: 106 amino acids; 12063 Da
Subunit: Interacts with MAP1S. Interacts with UBE3A (via HECT domain)

Explore the universe of human proteins at neXtProt for BPY2: NX_O14599

Explore proteomics data for BPY2 at MOPED


See BPY2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_004669.2  
ENSEMBL proteins: 
 ENSP00000473270   ENSP00000329106   ENSP00000372028  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: O14599

UniProtKB/Swiss-Prot: VCY2_HUMAN, O14599
Similarity: Belongs to the VCX/VCY family


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:
     Genatlas biochemistry entry for BPY2:
basic protein on chromosome Y,2,testis specific,1,testis specific,in the AZFC deleted region

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0032399HECT domain binding ----
     
Find genes that share ontologies with BPY2           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus4
extracellular2
cytosol1
mitochondrion1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus ----

Find genes that share ontologies with BPY2           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for BPY2
Interactions:

    Search GeneGlobe Interaction Network for BPY2

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for BPY2 (O145991, 3 ENSP000003291064) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
MAP1SQ66K741, 3, ENSP000003253134EBI-2133713,EBI-2133734 I2D: score=4 STRING: ENSP00000325313
UBE3AQ050863, ENSP000003810454I2D: score=4 STRING: ENSP00000381045
About this table

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007283spermatogenesis ----
GO:0007338single fertilization ----

Find genes that share ontologies with BPY2           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for BPY2 (VCY2)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for BPY2 gene: 
NM_004678.2  

Unigene Cluster for BPY2:

Basic charge, Y-linked, 2
Hs.664724  [show with all ESTs]
Unigene Representative Sequence: NM_004678
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602732 ENST00000331070(uc011nbj.2) ENST00000602818 ENST00000382585(uc004fvj.3)

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Additional mRNA sequence: 

AF000980.1 BC171776.1 BC171778.1 BC171795.1 BC171796.1 

3 DOTS entries:

DT.120653943  DT.120654199  DT.40122102 

4 AceView cDNA sequences:

NM_001002760 NM_001002761 AF000980 NM_004678 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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BPY2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
BPY2 Expression
About this image

BPY2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

BPY2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.664724

UniProtKB/Swiss-Prot: VCY2_HUMAN, O14599
Tissue specificity: Expressed exclusively in testis. Expressed in ejaculated spermatozoa of germ cell. Expressed
in the nuclei of spermatogonia, spermatocytes, and round spermatids, except elongated spermatids (at protein
level)

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and chimp.

Orthologs for BPY2 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia BPY26
BPY26
Uncharacterized protein
98(a)
98(a)
many ↔ many
many ↔ many
Y(12587744-12593658)
Y(3959516-3965432)


ENSEMBL Gene Tree for BPY2 (if available)
TreeFam Gene Tree for BPY2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for BPY2 gene
BPY2B2  BPY2C2  

Find genes that share paralogs with BPY2           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for BPY2 (see all 12)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr Y posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs801865481,2
C--17920922(+) TTTTAC/TTCTTG 1 -- int10--------
rs559220331,2
C--25150751(+) ACGTGA/GCAATG 1 -- int10--------
rs3767251851,2
----17932959(+) AGGATA/GTCATA 1 -- int10--------
rs3769209631,2
----17920139(+) GATGTA/GAAATC 1 -- int10--------
rs3692337701,2
----17928892(+) CTCTTA/GGCTAG 1 -- int10--------
rs3678685281,2
----25142869(+) CTGGC-/CACAGG 1 -- int10--------

HapMap Linkage Disequilibrium report for BPY2 (25119966 - 25151612 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for BPY2 (see all 15):    About this table    
Variant IDTypeSubtypePubMed ID
nsv10034CNV Loss18304495
nsv442825CNV CNV18776908
nsv442826CNV CNV18776908
essv10843CNV CNV17122850
dgv2506e1CNV Complex17122850
dgv2505e1CNV Complex17122850
dgv2508e1CNV Complex17122850
dgv2504e1CNV Complex17122850
nsv515230CNV Complex21397061
dgv2510e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 400013    OMIM disorders: --

3 diseases for BPY2:    
About MalaCards
y chromosome infertility    male infertility    infertility


Find genes that share disorders with BPY2           About GenesLikeMe

Genetic Association Database (GAD): BPY2
Human Genome Epidemiology (HuGE) Navigator: BPY2 (2 documents)

Export disorders for BPY2 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for BPY2 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with BPY2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. VCY2 protein interacts with the HECT domain of ubiquitin-protein ligase E3A. (PubMed id 12207887)1, 2, 9 Wong E.Y.... Yeung W.S. (Biochem. Biophys. Res. Commun. 2002)
  2. Differential effect of specific gr/gr deletion subtypes on spermatogenesis in the Chinese Han population. (PubMed id 20039973)1, 4 Yang Y....Zhang S. (Int. J. Androl. 2010)
  3. Alu sequence variants of the BPY2 gene in proven fertile and infertile men with Sertoli cell-only phenotype. (PubMed id 17511727)1, 4 Choi J....Namiki M. (Int. J. Urol. 2007)
  4. Identification and characterization of a VCY2 interacting protein-1; VCY2IP-1, a MAP-like protein. (PubMed id 14627543)1, 2 Wong E.Y.... Yeung W.S. (Biol. Reprod. 2004)
  5. Specific expression of VCY2 in human male germ cells and its involvement in the pathogenesis of male infertility. (PubMed id 12724276)1, 2 Tse J.Y.... Yeung W.S. (Biol. Reprod. 2003)
  6. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2 Skaletsky H.... Page D.C. (Nature 2003)
  7. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2 Lahn B.T. and Page D.C. (Science 1997)
  8. A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region. (PubMed id 15177557)1 Repping S....Rozen S. (Genomics 2004)
  9. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)
  10. Y Chromosome Infertility (PubMed id 20301513)1 Pagon R.A....Stephens K. (1993)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 9083 HGNC: 13508 AceView: BPY2.1 Ensembl:ENSG00000183753 euGenes: HUgn9083
ECgene: BPY2 H-InvDB: BPY2

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for BPY2 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for BPY2 gene:
Search GeneIP for patents involving BPY2

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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