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H2AFB1 Gene

protein-coding   GIFtS: 41
GCID: GC0XP154113

H2A Histone Family, Member B1

  Search for H2AFB1
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 B11 2
H2A.Bbd2 3
H2A Barr Body-Deficient2 3
Histone H2A-Bbd Type 12

External Ids:    HGNC: 225161   Entrez Gene: 4743822   Ensembl: ENSG000001980827   UniProtKB: P0C5Y93   

Export aliases for H2AFB1 gene to outside databases

Previous GC identifers: GC00U917957 GC0XU900553 GC0XP153679 GC0XP153766 GC0XP142656


(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 H2AFB1 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 centromeric copy which is in intron 22 of the F8 gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for H2AFB1 Gene:
H2AFB1 (H2A histone family, member B1) is a protein-coding gene. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is H2AFY2.

UniProtKB/Swiss-Prot: H2AB1_HUMAN, P0C5Y9
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 Wiki entry for H2AFB1 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_000023.10  NC_018934.2  NT_011681.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the H2AFB1 gene promoter:
         Pax-5   Olf-1   AP-4   Nkx2-5   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidH2AFB1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat H2AFB1


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

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

H2AFB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H2AFB1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP154113:  view genomic region     (about GC identifiers)

Start:
154,113,317 bp from pter      End:
154,113,833 bp from pter
Size:
517 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: H2AB1_HUMAN, P0C5Y9 (See protein sequence)
Recommended Name: Histone H2A-Bbd type 1  
Size: 115 amino acids; 12697 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: A0PK90 P98176 Q5TZB2 Q6FG78 Q96PR7

Explore the universe of human proteins at neXtProt for H2AFB1: NX_P0C5Y9

Explore proteomics data for H2AFB1 at MOPED


See H2AFB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001017990.1  
ENSEMBL proteins: 
 ENSP00000346450  
Reactome Protein details: P0C5Y9

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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 P0C5Y9

ProtoNet protein and cluster: P0C5Y9

UniProtKB/Swiss-Prot: H2AB1_HUMAN, P0C5Y9
Domain: The docking domain is responsible for the weaker heterodimerization with H2B
Similarity: Belongs to the histone H2A family


Find genes that share domains with H2AFB1           About GenesLikeMe


(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:

     UniProtKB/Swiss-Prot Summary: H2AB1_HUMAN, P0C5Y9
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 IEA--
GO:0046982protein heterodimerization activity IEA--
     
Find genes that share ontologies with H2AFB1           About GenesLikeMe


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
H2AB1_HUMAN, P0C5Y9: 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 IDA--
GO:0005634nucleus ----
GO:0035327transcriptionally active chromatin IDA--

Find genes that share ontologies with H2AFB1           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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SuperPaths for H2AFB1 About   (see all 7)  
See pathways by source

SuperPathSelected contained pathways About (see all per SuperPath)
1RNA Polymerase I Promoter Opening
RNA Polymerase I Transcription0.78
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription0.73
RNA Polymerase I Chain Elongation0.78
Amyloids0.68
RNA Polymerase I Promoter Clearance0.78
Mitotic Prophase0.56
RNA Polymerase I Promoter Opening0.78
Systemic lupus erythematosus0.40
2Packaging Of Telomere Ends
Packaging Of Telomere Ends0.66
Chromosome Maintenance0.62
Meiotic Synapsis0.66
Nucleosome assembly0.59
DNA Damage/Telomere Stress Induced Senescence0.65
Deposition of New CENPA-containing Nucleosomes at the Centromere0.59
Telomere Maintenance0.64
3Cellular Senescence
Cellular Senescence0.81
Oxidative Stress Induced Senescence0.64
Cellular responses to stress0.81
Senescence-Associated Secretory Phenotype (SASP)0.57
4Cell Cycle, Mitotic
Cell Cycle, Mitotic0.90
M Phase0.62
Cell Cycle0.90
5Meiosis (REACTOME)
Meiosis0.74
Meiotic Recombination0.74


Find genes that share SuperPaths with H2AFB1           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways


Selected Reactome Pathways for H2AFB1 (see all 15)
    NoRC negatively regulates rRNA expression
Deposition of new CENPA-containing nucleosomes at the centromere
Meiotic recombination
formation of the beta-catenin:TCF transactivating complex
Oxidative Stress Induced Senescence


2 Kegg Pathways  (Kegg details for H2AFB1):
    Alcoholism
Systemic lupus erythematosus

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Interactions:

    Search GeneGlobe Interaction Network for H2AFB1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for H2AFB1 (ENSP000003464504) via UniProtKB, MINT, STRING, and/or I2D (see all 44)
InteractantInteraction Details
GeneCardExternal ID(s)
CBX1ENSP000002256034STRING: ENSP00000225603
CBX3ENSP000003366874STRING: ENSP00000336687
CFDP1ENSP000002838824STRING: ENSP00000283882
LEO1ENSP000002996014STRING: ENSP00000299601
BTAF1ENSP000002659904STRING: ENSP00000265990
About this table

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

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

Find genes that share ontologies with H2AFB1           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
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Browse Tocris compounds for H2AFB1 (H2AB1)



(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 H2AFB1 gene: 
NM_001017990.1  

Unigene Cluster for H2AFB1:

H2A histone family, member B1
Hs.592246  [show with all ESTs]
Unigene Representative Sequence: DB303349
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000354461(uc004fmu.3)
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  QuantiFast Probe-based Assays in human, mouse, rat H2AFB1

Additional mRNA sequence: 

BC128034.1 CR542230.1 

1 DOTS entry:

DT.99977757 

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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H2AFB1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
H2AFB1 Expression
About this image

H2AFB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

H2AFB1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.592246

UniProtKB/Swiss-Prot: H2AB1_HUMAN, P0C5Y9
Tissue specificity: Present in mature sperm

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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 H2AFB1 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia H2afb15
H2afb3-ps1
H2A histone family, member B15
H2A histone family, member B3, pseudogene1
64.52(n)1
59.14(a)1
  2 (12.81 cM)5
6249571  NM_001281531.11  NP_001268460.11 
 179964175 
chicken
(Gallus gallus)
Aves --
Histone H2A
22(a)
1 → many
4(81146282-81179179)
zebrafish
(Danio rerio)
Actinopterygii h2afy6
H2A histone family, member Y
12(a)
many ↔ many
21(44398183-44410214) ENSDARG00000053442
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 H2AFB1 (if available)
TreeFam Gene Tree for H2AFB1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for H2AFB1 gene
H2AFB21 2  H2AFB31 2  H2AFY22  H2AFY2  
Selected SIMAP similar genes for H2AFB1 using alignment to 1 protein entry:     H2AB1_HUMAN(see all similar genes):
H2AFB2    H2AFB3    H2AFX    HIST1H2AA    HIST1H2AB    HIST1H2AC
HIST1H2AD    HIST1H2AE    HIST1H2AG    HIST1H2AH    HIST1H2AI    HIST1H2AJ
HIST1H2AK    HIST1H2AL    HIST1H2AM    HIST1H2APS4    HIST2H2AA3    HIST2H2AA4

Find genes that share paralogs with H2AFB1           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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Structural Variations
     Database of Genomic Variants (DGV) 5 variations for H2AFB1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv508817CNV Insertion20534489
esv29972CNV Gain17803354
esv33784CNV Gain+Loss17666407
nsv499361OTHER Inversion21111241
nsv7470OTHER Inversion18451855

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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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  --

(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 H2AFB1 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with H2AFB1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Investigation of the factor VIII intron 22 repeated region (int22h) and the associated inversion junctions. (PubMed id 8528212)1, 2 Naylor J.A....Giannelli F. (Hum. Mol. Genet. 1995)
  3. 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)
  4. Analysis of the human HP1 interactome reveals novel binding partners. (PubMed id 21888893)1 Rosnoblet C....Angrand P.O. (Biochem. Biophys. Res. Commun. 2011)
  5. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. (PubMed id 20008104)2 Ishibashi T.... Ausio J. (Nucleic Acids Res. 2010)
  6. 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)
  7. 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)
  8. 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)
  9. Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. (PubMed id 16957777)2 Doyen C.M.... Dimitrov S. (EMBO J. 2006)
  10. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)

(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: 474382 HGNC: 22516 Ensembl:ENSG00000198082 euGenes: HUgn474382 ECgene: H2AFB1 Kegg: 474382
H-InvDB: H2AFB1

(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 H2AFB1 Pharmacogenomics, SNPs, Pathways
Wikipedia http://en.wikipedia.org/wiki/Histone_H2A

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for H2AFB1 gene:
Search GeneIP for patents involving H2AFB1

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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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