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BPY2B Gene

protein-coding   GIFtS: 31
GCID: GC0YP026764

Basic Charge, Y-Linked, 2B

  See BPY2B-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, 2B1 2     Variable Charge, Y-Linked, 22
Basic Charge, Y-Linked 22 3     BPY2A3
Variably Charged Protein Y 22 3     VCY23
VCY2B2 3     VCY2A3
Basic Protein On Y Chromosome 22     VCY2C3
Testis-Specific Basic Protein Y 22     

External Ids:    HGNC: 254491   Entrez Gene: 4428672   Ensembl: ENSG000001837957   UniProtKB: O145993   

Export aliases for BPY2B gene to outside databases

Previous GC identifers: GC0YP023476 GC0YU900266 GC0YP025173 GC0YP017912


(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 BPY2B 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 more centromeric copy within the palindrome. (provided by RefSeq,
Jul 2008)

GeneCards Summary for BPY2B Gene:
BPY2B (basic charge, Y-linked, 2B) is a protein-coding gene. Diseases associated with BPY2B include male infertility, and infertility. An important paralog of this gene is BPY2C.




(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 BPY2B
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBPY2B promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BPY2B


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

Entrez Gene cytogenetic band: Yq11.223   Ensembl cytogenetic band:  Yq11.23   HGNC cytogenetic band: Yq11.223

BPY2B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BPY2B gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP026764:  view genomic region     (about GC identifiers)

Start:
26,753,707 bp from pter      End:
26,785,354 bp from pter
Size:
31,648 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,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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 BPY2B: NX_O14599

Explore proteomics data for BPY2B at MOPED


See BPY2B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001002760.1  
ENSEMBL proteins: 
 ENSP00000473491   ENSP00000371829  

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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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     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 BPY2B           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 BPY2B           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 BPY2B
Interactions:

    Search GeneGlobe Interaction Network for BPY2B

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

2 Interacting proteins for BPY2B (O145991, 3 ENSP000003718294) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
MAP1SQ66K741, 3EBI-2133713,EBI-2133734 I2D: score=4 
UBE3AQ050863, ENSP000003810454I2D: score=4 STRING: ENSP00000381045
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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 BPY2B           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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for BPY2B (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 BPY2B gene: 
NM_001002760.1  

Unigene Cluster for BPY2B:

Basic charge, Y-linked, 2B
Hs.632848
Unigene Representative Sequence: NM_001002760
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602770 ENST00000382392(uc004fwi.3 uc011nbs.2) ENST00000602549

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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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BPY2B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
BPY2B Expression
About this image

BPY2B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

BPY2B Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.632848

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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(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 BPY2B 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(3959516-3965432)
Y(12587744-12593658)


ENSEMBL Gene Tree for BPY2B (if available)
TreeFam Gene Tree for BPY2B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for BPY2B gene
BPY2C2  BPY22  

Find genes that share paralogs with BPY2B           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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4 SNPs for BPY2B    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr Y posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs3707100601,2
----26780953(+) AAGGAA/GGATTT 1 -- int10--------
rs3760961821,2
----26777158(+) TGTGAC/TTCTCA 1 -- int10--------

HapMap Linkage Disequilibrium report for BPY2B (26753707 - 26785354 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for BPY2B (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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2 diseases for BPY2B:    
About MalaCards
male infertility    infertility


Find genes that share disorders with BPY2B           About GenesLikeMe


Export disorders for BPY2B 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 BPY2B gene integrated from 10 sources:
(articles sorted by number of sources associating them with BPY2B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. 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)
  3. 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)
  4. VCY2 protein interacts with the HECT domain of ubiquitin-protein ligase E3A. (PubMed id 12207887)1, 2 Wong E.Y.... Yeung W.S. (Biochem. Biophys. Res. Commun. 2002)
  5. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2 Lahn B.T. and Page D.C. (Science 1997)
  6. 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)
  7. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)

(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: 442867 HGNC: 25449 Ensembl:ENSG00000183795 euGenes: HUgn442867 ECgene: BPY2B
H-InvDB: BPY2B

(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 BPY2B 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 BPY2B gene:
Search GeneIP for patents involving BPY2B

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
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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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