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H2AFB3 Gene

protein-coding   GIFtS: 42
GCID: GC0XM154689

H2A Histone Family, Member B3

(Previous names: H2A histone family, member B)
(Previous symbol: H2AFB)
  See 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
H2A Histone Family, Member B31 2     H2A Barr Body-Deficient2 3
H2AFB1 2 3 5     H2A Histone Family, Member B1
H2ABBD2 3 5     Histone H2A-Bbd Type 2/32
H2A.Bbd2 3     Histone Variant H2A, Barr-Body Deficient2

External Ids:    HGNC: 144551   Entrez Gene: 837402   Ensembl: ENSG000001859787   OMIM: 3004455   UniProtKB: P0C5Z03   

Export aliases for H2AFB3 gene to outside databases

Previous GC identifers: GC0XP154174 GC0XM154342 GC0XP143154


(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 H2AFB3 Gene:
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in
eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs
of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the
interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin
structures. This gene encodes a member of the histone H2A family. This gene is part of a region that is repeated
three times on chromosome X, once in intron 22 of the F8 gene and twice closer to the Xq telomere. This record
represents the most telomeric copy. (provided by RefSeq, Jul 2008)

GeneCards Summary for H2AFB3 Gene:
H2AFB3 (H2A histone family, member B3) is a protein-coding gene. Diseases associated with H2AFB3 include systemic lupus erythematosus, and hiv-1. An important paralog of this gene is H2AFB1.

UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
Function: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with
active transcription and mRNA processing. Nucleosomes wrap and compact DNA into chromatin, limiting DNA
accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role
in transcription regulation, DNA repair, DNA replication and chromosomal stability. Nucleosomes containing this
histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively
transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome
components and are required for mRNA splicing. May participate in spermatogenesis




(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:
NC_000023.11  NT_011681.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the H2AFB3 gene promoter:
         Pax-5   MyoD   Olf-1   AP-4   En-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for H2AFB3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat H2AFB3


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

Entrez Gene cytogenetic band: Xq28   Ensembl cytogenetic band:  Xq28   HGNC cytogenetic band: Xq28

H2AFB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H2AFB3 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM154689:  view genomic region     (about GC identifiers)

Start:
154,689,080 bp from pter      End:
154,689,596 bp from pter
Size:
517 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0 (See protein sequence)
Recommended Name: Histone H2A-Bbd type 2/3  
Size: 115 amino acids; 12713 Da
Subunit: The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one
H3-H4 heterotetramer and two H2A-H2B heterodimers. May be incorporated into a proportion of nucleosomes,
replacing one or more H2A molecules
Miscellaneous: In contrast to other H2A histones, it does not contain the conserved residues that are the target
of post-translational modifications
Secondary accessions: A1L4E4 P98176 Q5TZB2 Q6FG78 Q96PR7

Explore the universe of human proteins at neXtProt for H2AFB3: NX_P0C5Z0

Explore proteomics data for H2AFB3 at MOPED


See H2AFB3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_542451.1  
ENSEMBL proteins: 
 ENSP00000358452  

H2AFB3 Human Recombinant Protein Products:

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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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HGNC Gene Families:
RIH: Histones / Replication-independent

3 InterPro protein domains:
 IPR009072 Histone-fold
 IPR007125 Histone_core_D
 IPR002119 Histone_H2A

Graphical View of Domain Structure for InterPro Entry P0C5Z0

ProtoNet protein and cluster: P0C5Z0

UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
Domain: The docking domain is responsible for the weaker heterodimerization with H2B
Similarity: Belongs to the histone H2A family


H2AFB3 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: H2AB2_HUMAN, P0C5Z0
Function: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with
active transcription and mRNA processing. Nucleosomes wrap and compact DNA into chromatin, limiting DNA
accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role
in transcription regulation, DNA repair, DNA replication and chromosomal stability. Nucleosomes containing this
histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively
transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome
components and are required for mRNA splicing. May participate in spermatogenesis

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

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding ----
GO:0046982protein heterodimerization activity ----
     
H2AFB3 for ontologies           About GeneDecksing


Animal Models:
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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 UniProtKB/Swiss-Prot
H2AB2_HUMAN, P0C5Z0: Nucleus. Chromosome. Note=Associated with the active X chromosome and with autosomes, while
it is absent from the inactive X chromosome and excluded from Barr bodies
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
mitochondrion1

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000786nucleosome ----
GO:0000788nuclear nucleosome ----
GO:0005634nucleus ----
GO:0035327transcriptionally active chromatin ----

H2AFB3 for ontologies           About GeneDecksing


(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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SuperPaths for H2AFB3 About                                                                                                See pathways by source

SuperPathContained pathways About
1RNA Polymerase I Promoter Opening
Systemic lupus erythematosus0.40
Alcoholism0.34

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways




2 Kegg Pathways  (Kegg details for H2AFB3):
    Alcoholism
Systemic lupus erythematosus


H2AFB3 for pathways           About GeneDecksing

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for H2AFB3
Interactions:

    Search GeneGlobe Interaction Network for H2AFB3

STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

Selected Interacting proteins for H2AFB3 (ENSP000003584524) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
InteractantInteraction Details
GeneCardExternal ID(s)
CFDP1ENSP000002838824STRING: ENSP00000283882
LEO1ENSP000002996014STRING: ENSP00000299601
BTAF1ENSP000002659904STRING: ENSP00000265990
IPO9ENSP000003547424STRING: ENSP00000354742
KPNB1ENSP000002901584STRING: ENSP00000290158
About this table

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

GO IDQualified GO termEvidencePubMed IDs
GO:0006334nucleosome assembly ----
GO:0006397mRNA processing ----

H2AFB3 for ontologies           About GeneDecksing



(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 H2AFB3 (H2AB2)



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for H2AFB3 gene: 
NM_080720.1  

Unigene Cluster for H2AFB3:

H2A histone family, member B3
Hs.632841
Unigene Representative Sequence: BC130510
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000369444(uc004fnk.3)
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat H2AFB3

Additional mRNA sequence: 

AF254576.1 BC101415.1 BC101417.1 BC101418.1 BC130510.1 

2 DOTS entries:

DT.121303715  DT.410848 

16 AceView cDNA sequences:

AF254576 BM722299 AW183040 AI218259 BU740141 AA432232 AI018669 AA703660 
AA868831 AA993742 AA428596 AA879431 AA912999 AI205744 AI204297 AI218431 

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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H2AFB3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
H2AFB3 Expression
About this image

H2AFB3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

H2AFB3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.632841

UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
Tissue specificity: Present in mature sperm

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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 animals.

Orthologs for H2AFB3 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia H2afb3-ps1 H2A histone family, member B3, pseudogene 64.87(n)
60.22(a)
  624957  NM_001281531.1  NP_001268460.1 
chicken
(Gallus gallus)
Aves --
Histone H2A
22(a)
1 → many
4(81146282-81179179)
worm
(Caenorhabditis elegans)
Secernentea htas-16
Protein HTAS-1 (htas-1) mRNA, complete cds
26(a)
1 → many
IV(9682984-9683532) WBGene00014240


ENSEMBL Gene Tree for H2AFB3 (if available)
TreeFam Gene Tree for H2AFB3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for H2AFB3 gene
H2AFB21 2  H2AFB11 2  H2AFY22  H2AFY2  
Selected SIMAP similar genes for H2AFB3 using alignment to 1 protein entry:     H2AB2_HUMAN(see all similar genes):
H2AFB1    H2AFX    HIST1H2AA    HIST1H2AB    HIST1H2AC    HIST1H2AD
HIST1H2AE    HIST1H2AG    HIST1H2AH    HIST1H2AI    HIST1H2AJ    HIST1H2AK
HIST1H2AL    HIST1H2AM    HIST1H2APS4    HIST2H2AA3    HIST2H2AA4    HIST2H2AB

H2AFB3 for paralogs           About GeneDecksing



(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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2 SNPs for H2AFB3    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1879793331,2
--142657763(+) CAGTCC/TAGAAA 1 -- ds50010--------
rs2009509591,2
----142657744(+) CGGGGA/GGGGGG 1 -- ds50010--------

HapMap Linkage Disequilibrium report for H2AFB3 (154689080 - 154689596 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for H2AFB3:    About this table    
Variant IDTypeSubtypePubMed ID
nsv508817CNV Insertion20534489
esv29972CNV Gain17803354
esv33784CNV Gain+Loss17666407
nsv499361OTHER Inversion21111241
nsv7470OTHER Inversion18451855

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300445    OMIM disorders: --

3 diseases for H2AFB3:    About MalaCards
systemic lupus erythematosus    hiv-1    lupus erythematosus


H2AFB3 for disorders           About GeneDecksing


Export disorders for H2AFB3 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 H2AFB3 gene, integrated from 10 sources (see all 18):
(articles sorted by number of sources associating them with H2AFB3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  2. Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I. (PubMed id 16287874)1, 2 Okuwaki M.... Nagata K. (Mol. Cell. Biol. 2005)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. (PubMed id 15257289)1, 2 Bao Y.... Luger K. (EMBO J. 2004)
  5. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. (PubMed id 11266453)1, 2 Chadwick B.P. and Willard H.F. (J. Cell Biol. 2001)
  6. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (PubMed id 22795134)2 Tolstorukov M.Y....Park P.J. (Mol. Cell 2012)
  7. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. (PubMed id 20008104)2 Ishibashi T.... Ausio J. (Nucleic Acids Res. 2010)
  8. Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd. (PubMed id 18329190)2 Gonzalez-Romero R.... Eirin-Lopez J.M. (Gene 2008)
  9. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way. (PubMed id 17726088)2 Eirin-Lopez J.M.... Ausio J. (FASEB J. 2008)
  10. ATP-dependent chromatin remodeling is required for base excision repair in conventional but not in variant H2A.Bbd nucleosomes. (PubMed id 17591702)2 Menoni H.... Angelov D. (Mol. Cell. Biol. 2007)

(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: 83740 HGNC: 14455 AceView: H2AFB Ensembl:ENSG00000185978 euGenes: HUgn83740
ECgene: H2AFB3 Kegg: 83740 H-InvDB: H2AFB3

(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 H2AFB3 Pharmacogenomics, SNPs, Pathways
Wikipedia http://en.wikipedia.org/wiki/Histone_H2A

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Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for H2AFB3 gene:
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(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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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