Free for academic non-profit institutions. Other users need a Commercial license

Aliases for H2AFB1 Gene

Aliases for H2AFB1 Gene

  • H2A Histone Family Member B1 2 3 5
  • H2A Barr Body-Deficient 3 4
  • H2A.Bbd 3 4
  • H2A.B 3 4
  • H2A Histone Family, Member B1 2
  • Histone H2A-Bbd Type 1 3

External Ids for H2AFB1 Gene

Previous GeneCards Identifiers for H2AFB1 Gene

  • GC00U917957
  • GC0XU900553
  • GC0XP153679
  • GC0XP153766
  • GC0XP154113
  • GC0XP142656

Summaries for H2AFB1 Gene

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 replication-independent histone that is 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, Oct 2015]

GeneCards Summary for H2AFB1 Gene

H2AFB1 (H2A Histone Family Member B1) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Cell Cycle, Mitotic. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is H2AFB2.

UniProtKB/Swiss-Prot for H2AFB1 Gene

  • Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with active transcription and mRNA processing (PubMed:22795134). 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 (PubMed:15257289, PubMed:16287874, PubMed:16957777, PubMed:17591702, PubMed:17726088, PubMed:18329190, PubMed:22795134). Nucleosomes containing this histone are less rigid and organize less DNA than canonical nucleosomes in vivo (PubMed:15257289, PubMed:16957777, PubMed:17591702, PubMed:24336483). They are enriched in actively transcribed genes and associate with the elongating form of RNA polymerase (PubMed:17591702, PubMed:24753410). They associate with spliceosome components and are required for mRNA splicing (PubMed:22795134).

Gene Wiki entry for H2AFB1 Gene

Additional gene information for H2AFB1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H2AFB1 Gene

Genomics for H2AFB1 Gene

Regulatory Elements for H2AFB1 Gene

Enhancers for H2AFB1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH154488 1 ENCODE 8.1 -394.7 -394690 2 PKNOX1 ATF1 ARID4B SIN3A YY1 GLIS2 ELK1 ATF7 SP3 ZHX2 FAM3A H2AFB1 TMEM187 SLC10A3 PIR45081
GH0XH154883 0.2 Ensembl 0.7 -0.4 -372 1 H2AFB1 SMIM9
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around H2AFB1 on UCSC Golden Path with GeneCards custom track

Promoters for H2AFB1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000249717 1628 1601

Genomic Location for H2AFB1 Gene

Chromosome:
X
Start:
154,884,972 bp from pter
End:
154,885,558 bp from pter
Size:
587 bases
Orientation:
Plus strand

Genomic View for H2AFB1 Gene

Genes around H2AFB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2AFB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2AFB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AFB1 Gene

Proteins for H2AFB1 Gene

  • Protein details for H2AFB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0C5Y9-H2AB1_HUMAN
    Recommended name:
    Histone H2A-Bbd type 1
    Protein Accession:
    P0C5Y9
    Secondary Accessions:
    • A0PK90
    • P98176
    • Q5TZB2
    • Q6FG78
    • Q96PR7

    Protein attributes for H2AFB1 Gene

    Size:
    115 amino acids
    Molecular mass:
    12697 Da
    Quaternary structure:
    • 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.

neXtProt entry for H2AFB1 Gene

Post-translational modifications for H2AFB1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H2AFB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AFB1 Gene

Domains & Families for H2AFB1 Gene

Gene Families for H2AFB1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for H2AFB1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for H2AFB1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P0C5Y9

UniProtKB/Swiss-Prot:

H2AB1_HUMAN :
  • The docking domain is responsible for the weaker heterodimerization with H2B.
  • Belongs to the histone H2A family.
Domain:
  • The docking domain is responsible for the weaker heterodimerization with H2B.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AFB1: view

Function for H2AFB1 Gene

Molecular function for H2AFB1 Gene

UniProtKB/Swiss-Prot Function:
Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with active transcription and mRNA processing (PubMed:22795134). 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 (PubMed:15257289, PubMed:16287874, PubMed:16957777, PubMed:17591702, PubMed:17726088, PubMed:18329190, PubMed:22795134). Nucleosomes containing this histone are less rigid and organize less DNA than canonical nucleosomes in vivo (PubMed:15257289, PubMed:16957777, PubMed:17591702, PubMed:24336483). They are enriched in actively transcribed genes and associate with the elongating form of RNA polymerase (PubMed:17591702, PubMed:24753410). They associate with spliceosome components and are required for mRNA splicing (PubMed:22795134).

Gene Ontology (GO) - Molecular Function for H2AFB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AFB1: view
genes like me logo Genes that share phenotypes with H2AFB1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for H2AFB1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for H2AFB1 Gene

Localization for H2AFB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AFB1 Gene

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. {ECO:0000269 PubMed:20008104}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for H2AFB1 gene
Compartment Confidence
nucleus 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for H2AFB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000788 nuclear nucleosome IDA 22795134
GO:0005634 nucleus IDA 21630459
GO:0005694 chromosome IEA --
GO:0035327 transcriptionally active chromatin IDA 22795134
genes like me logo Genes that share ontologies with H2AFB1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H2AFB1 Gene

Pathways & Interactions for H2AFB1 Gene

SuperPathways for H2AFB1 Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence (REACTOME)
3 Chromosome Maintenance
4 Cell Cycle, Mitotic
.60
5 Mitotic Prophase
genes like me logo Genes that share pathways with H2AFB1: view

Interacting Proteins for H2AFB1 Gene

Selected Interacting proteins: P0C5Y9-H2AB1_HUMAN for H2AFB1 Gene via IID

Gene Ontology (GO) - Biological Process for H2AFB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IDA 22795134
GO:0006342 chromatin silencing IBA --
GO:0006397 mRNA processing IMP 22795134
genes like me logo Genes that share ontologies with H2AFB1: view

No data available for SIGNOR curated interactions for H2AFB1 Gene

Drugs & Compounds for H2AFB1 Gene

No Compound Related Data Available

Transcripts for H2AFB1 Gene

mRNA/cDNA for H2AFB1 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for H2AFB1 Gene

H2A histone family, member B1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for H2AFB1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for H2AFB1 Gene

No ASD Table

Relevant External Links for H2AFB1 Gene

GeneLoc Exon Structure for
H2AFB1
ECgene alternative splicing isoforms for
H2AFB1

Expression for H2AFB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for H2AFB1 Gene

mRNA differential expression in normal tissues according to GTEx for H2AFB1 Gene

This gene is overexpressed in Testis (x24.7) and Whole Blood (x4.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for H2AFB1 Gene



NURSA nuclear receptor signaling pathways regulating expression of H2AFB1 Gene:

H2AFB1

SOURCE GeneReport for Unigene cluster for H2AFB1 Gene:

Hs.592246

mRNA Expression by UniProt/SwissProt for H2AFB1 Gene:

P0C5Y9-H2AB1_HUMAN
Tissue specificity: Present in mature sperm.
genes like me logo Genes that share expression patterns with H2AFB1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2AFB1 Gene

Orthologs for H2AFB1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2AFB1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC528006 33
  • 72.9 (n)
dog
(Canis familiaris)
Mammalia LOC102152481 33
  • 69.57 (n)
mouse
(Mus musculus)
Mammalia H2afb3-ps 33
  • 64.52 (n)
rat
(Rattus norvegicus)
Mammalia H2afb3 33
  • 63.44 (n)
Species where no ortholog for H2AFB1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for H2AFB1 Gene

ENSEMBL:
Gene Tree for H2AFB1 (if available)
TreeFam:
Gene Tree for H2AFB1 (if available)

Paralogs for H2AFB1 Gene

Variants for H2AFB1 Gene

Sequence variations from dbSNP and Humsavar for H2AFB1 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs113683431 -- 154,886,026(+) GTTTC(C/G)TTTGG intron-variant, downstream-variant-500B, upstream-variant-2KB
rs187979333 -- 154,885,988(+) CAGTC(C/T)AGAAA intron-variant, downstream-variant-500B, upstream-variant-2KB
rs200950959 -- 154,885,969(+) CGGGG(A/G)GGGGG intron-variant, downstream-variant-500B, upstream-variant-2KB
rs201105445 -- 154,885,331(+) CACAA(C/T)GACAG intron-variant, upstream-variant-2KB, reference, synonymous-codon
rs202076232 -- 154,885,372(+) CATCT(C/G)TCAAG intron-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for H2AFB1 Gene

Variant ID Type Subtype PubMed ID
dgv2549e212 CNV gain 25503493
esv29972 CNV gain 17803354
esv33784 CNV gain+loss 17666407
esv3577568 CNV gain 25503493
esv3577574 CNV gain 25503493
nsv1076287 CNV deletion 25765185
nsv499361 OTHER inversion 21111241
nsv508817 CNV insertion 20534489
nsv7470 OTHER inversion 18451855

Relevant External Links for H2AFB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2AFB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for H2AFB1 Gene

Disorders for H2AFB1 Gene

Relevant External Links for H2AFB1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
H2AFB1

No disorders were found for H2AFB1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2AFB1 Gene

Publications for H2AFB1 Gene

  1. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (PMID: 22795134) Tolstorukov MY … Park PJ (Molecular cell 2012) 3 4 60
  2. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. (PMID: 15257289) Bao Y … Luger K (The EMBO journal 2004) 3 4 60
  3. Investigation of the factor VIII intron 22 repeated region (int22h) and the associated inversion junctions. (PMID: 8528212) Naylor JA … Giannelli F (Human molecular genetics 1995) 3 4 60
  4. Corrigendum: Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin. (PMID: 26166249) Arimura Y … Kurumizaka H (Scientific reports 2015) 4 60
  5. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. (PMID: 25731851) Shaytan AK … Panchenko AR (Current opinion in structural biology 2015) 3 60

Products for H2AFB1 Gene

Sources for H2AFB1 Gene

Content
Loading form....