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HIST2H2AA4 Gene(Protein Coding)

Histone Cluster 2 H2A Family Member A4

GCID:
GC01P149852
GIFtS:
39
Genes Participants
UDN Logo

Aliases for HIST2H2AA4 Gene

Aliases for HIST2H2AA4 Gene

  • Histone Cluster 2 H2A Family Member A4 2 3 5
  • Histone Cluster 2, H2aa4 2 3
  • Histone 2, H2aa4 2 3
  • HIST2H2AA3 HIST2H2AA4 4
  • Histone H2A Type 2-A 3
  • Histone H2A/R 3
  • Histone H2A.2 4
  • Histone H2A/O 4
  • HIST2H2AA 4
  • H2AFO 4
  • H2A/R 3

External Ids for HIST2H2AA4 Gene

Previous GeneCards Identifiers for HIST2H2AA4 Gene

  • GC01P148089
  • GC01P149822
  • GC01M121196

Summaries for HIST2H2AA4 Gene

Entrez Gene Summary for HIST2H2AA4 Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2A family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in a histone cluster on chromosome 1. This gene is one of four histone genes in the cluster that are duplicated; this record represents the telomeric copy. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST2H2AA4 Gene

HIST2H2AA4 (Histone Cluster 2 H2A Family Member A4) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Meiosis. GO annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST2H2AA3.

UniProtKB/Swiss-Prot for HIST2H2AA4 Gene

  • Core component of nucleosome. 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. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST2H2AA4 Gene

Genomics for HIST2H2AA4 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HIST2H2AA4 Gene

Enhancers for HIST2H2AA4 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
GH01G149851 0.2 dbSUPER 0.7 +1.2 1169 1.1 HIST2H2AA4 HIST2H3A
GH01G149852 0.2 dbSUPER 0.7 +1.2 1230 1.2 HIST2H2AA4 HIST2H3A
GH01G149859 0.2 dbSUPER 0.7 +1.2 1230 1.2 HIST2H3A HIST2H2AA4
GH01G149894 0.2 dbSUPER 0.7 +1.2 1212 1.2 HIST2H3A HIST2H2AA4
GH01G149901 0.2 dbSUPER 0.7 +1.2 1227 1.2 HIST2H2AA4 HIST2H3A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST2H2AA4 on UCSC Golden Path with GeneCards custom track

Promoters for HIST2H2AA4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000013438 539 4001 SIN3A POLR2A ZSCAN5C BCLAF1 SMAD5 L3MBTL2 BHLHE40 CHD1 JUND IKZF1

Transcription factor binding sites by QIAGEN in the HIST2H2AA4 gene promoter:

Genomic Location for HIST2H2AA4 Gene

Chromosome:
1
Start:
149,851,061 bp from pter
End:
149,851,624 bp from pter
Size:
564 bases
Orientation:
Plus strand

Genomic View for HIST2H2AA4 Gene

Genes around HIST2H2AA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST2H2AA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST2H2AA4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HIST2H2AA4 Gene

Proteins for HIST2H2AA4 Gene

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  2. Protein
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  • Protein details for HIST2H2AA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6FI13-H2A2A_HUMAN
    Recommended name:
    Histone H2A type 2-A
    Protein Accession:
    Q6FI13
    Secondary Accessions:
    • B2R5F0
    • P20670

    Protein attributes for HIST2H2AA4 Gene

    Size:
    130 amino acids
    Molecular mass:
    14095 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. The octamer wraps approximately 147 bp of DNA.
    • 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. The octamer wraps approximately 147 bp of DNA.

neXtProt entry for HIST2H2AA4 Gene

Protein Expression for HIST2H2AA4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HIST2H2AA4 Gene

  • Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
  • Deiminated on Arg-4 in granulocytes upon calcium entry.
  • Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239).
  • Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM27 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of Lys-27 of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Monoubiquitination of Lys-120 (H2AK119Ub) by TRIM27 may promote transformation of cells in a number of breast cancers (PubMed:25470042). Following DNA double-strand breaks (DSBs), it is ubiquitinated through Lys-63 linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and Lys-63-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend Lys-63-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced Lys-63-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events.
  • Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by VPRBP is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription.
  • Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • Ubiquitination at isoforms=14 and posLast=1616
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST2H2AA4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST2H2AA4 Gene

Domains & Families for HIST2H2AA4 Gene

Gene Families for HIST2H2AA4 Gene

HGNC:

Protein Domains for HIST2H2AA4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HIST2H2AA4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6FI13

UniProtKB/Swiss-Prot:

H2A2A_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with HIST2H2AA4: view

Function for HIST2H2AA4 Gene

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  2. CRISPR
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Molecular function for HIST2H2AA4 Gene

UniProtKB/Swiss-Prot Function:
Core component of nucleosome. 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. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Gene Ontology (GO) - Molecular Function for HIST2H2AA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST2H2AA4: view

Phenotypes for HIST2H2AA4 Gene

GenomeRNAi human phenotypes for HIST2H2AA4:
genes like me logo Genes that share phenotypes with HIST2H2AA4: view

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST2H2AA4 Gene

Localization for HIST2H2AA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST2H2AA4 Gene

Nucleus. Chromosome.

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 HIST2H2AA4 gene
Compartment Confidence
nucleus 3

Gene Ontology (GO) - Cellular Components for HIST2H2AA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0000790 nuclear chromatin IBA --
GO:0005634 nucleus IDA 16319397
GO:0005694 chromosome IEA --
GO:0070062 extracellular exosome IDA 19199708
genes like me logo Genes that share ontologies with HIST2H2AA4: view

Pathways & Interactions for HIST2H2AA4 Gene

SuperPathways for HIST2H2AA4 Gene

PathCards logo More details on SuperPathways for HIST2H2AA4
SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
DNA methylation
.88
RNA Polymerase I Promoter Opening
.88
B-WICH complex positively regulates rRNA expression
.86
Positive epigenetic regulation of rRNA expression
.86
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
.86
SIRT1 negatively regulates rRNA Expression
.84
NoRC negatively regulates rRNA expression
.83
RNA Polymerase I Chain Elongation
.83
PRC2 methylates histones and DNA
.83
RNA Polymerase I Transcription
.81
Negative epigenetic regulation of rRNA expression
.81
RNA Polymerase I Promoter Clearance
.81
Condensation of Prophase Chromosomes
.78
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
.76
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
.75
Epigenetic regulation of gene expression
.73
RHO GTPases activate PKNs
.72
Formation of the beta-catenin-TCF transactivating complex
.64
HDACs deacetylate histones
.60
Amyloid fiber formation
.55
Activation of anterior HOX genes in hindbrain development during early embryogenesis
.50
Activation of HOX genes during differentiation
.50
Systemic lupus erythematosus
.43
RMTs methylate histone arginines
.39
Alcoholism
.34
2 Cellular Senescence
Cellular Senescence
.64
Oxidative Stress Induced Senescence
.64
Senescence-Associated Secretory Phenotype (SASP)
.56
Cellular responses to stress
.44
3 Chromosome Maintenance
Chromosome Maintenance
.75
Telomere Maintenance
.75
Deposition of new CENPA-containing nucleosomes at the centromere
.66
Nucleosome assembly
.66
4 Cell Cycle, Mitotic
Cell Cycle
.83
Cell Cycle, Mitotic
.83
M Phase
.60
5 Chromatin organization
Chromatin modifying enzymes
.51
Chromatin organization
.51
HATs acetylate histones
.51
genes like me logo Genes that share pathways with HIST2H2AA4: view

Interacting Proteins for HIST2H2AA4 Gene

Selected Interacting proteins: Q6FI13-H2A2A_HUMAN for HIST2H2AA4 Gene via IID

Gene Ontology (GO) - Biological Process for HIST2H2AA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006342 chromatin silencing IBA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with HIST2H2AA4: view

No data available for SIGNOR curated interactions for HIST2H2AA4 Gene

Drugs & Compounds for HIST2H2AA4 Gene

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No Compound Related Data Available

Transcripts for HIST2H2AA4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
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mRNA/cDNA for HIST2H2AA4 Gene

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

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST2H2AA4 Gene

No ASD Table

Relevant External Links for HIST2H2AA4 Gene

GeneLoc Exon Structure for
HIST2H2AA4
ECgene alternative splicing isoforms for
HIST2H2AA4

Expression for HIST2H2AA4 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST2H2AA4 Gene

mRNA expression in normal human tissues for HIST2H2AA4 Gene
mRNA expression by BioGPS for HIST2H2AA4 Gene

mRNA differential expression in normal tissues according to GTEx for HIST2H2AA4 Gene

This gene is overexpressed in Whole Blood (x38.2).

Protein differential expression in normal tissues from HIPED for HIST2H2AA4 Gene

This gene is overexpressed in Tlymphocyte (48.9) and Urine (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HIST2H2AA4 Gene



Protein tissue co-expression partners for HIST2H2AA4 Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST2H2AA4 Gene:

HIST2H2AA4

SOURCE GeneReport for Unigene cluster for HIST2H2AA4 Gene:

Hs.745563
genes like me logo Genes that share expression patterns with HIST2H2AA4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST2H2AA4 Gene

Orthologs for HIST2H2AA4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for HIST2H2AA4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HIST2H2AA4 34
  • 99.74 (n)
cow
(Bos Taurus)
 Mammalia LOC788724 34
  • 91.54 (n)
mouse
(Mus musculus)
 Mammalia Hist2h2aa1 34
  • 89.49 (n)
Hist2h2aa2 16
rat
(Rattus norvegicus)
 Mammalia LOC690131 34
  • 89.49 (n)
Species where no ortholog for HIST2H2AA4 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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 HIST2H2AA4 Gene

ENSEMBL:
Gene Tree for HIST2H2AA4 (if available)
TreeFam:
Gene Tree for HIST2H2AA4 (if available)

Paralogs for HIST2H2AA4 Gene

Variants for HIST2H2AA4 Gene

Sequence variations from dbSNP and Humsavar for HIST2H2AA4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1009100588 -- 149,849,374(+) CACTG(C/T)TCCAG upstream-variant-2KB
rs1009565784 -- 149,849,706(+) GATTT(G/T)AGGGT downstream-variant-500B, upstream-variant-2KB
rs1013070338 -- 149,850,237(+) AGACG(C/T)GAAGC nc-transcript-variant, upstream-variant-2KB
rs1013085481 -- 149,850,002(+) ACTTA(C/T)CAAAA downstream-variant-500B, upstream-variant-2KB
rs1015153667 -- 149,849,708(+) TTTTA(C/G)GGTAT downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST2H2AA4 Gene

Variant ID Type Subtype PubMed ID
esv1007634 OTHER inversion 20482838
nsv46 OTHER inversion 15895083
nsv469694 CNV loss 16826518
nsv499132 OTHER inversion 21111241
nsv547843 CNV loss 21841781
nsv7182 OTHER inversion 18451855
nsv824564 CNV gain 20364138
nsv831503 CNV gain 17160897
nsv831525 CNV gain 17160897
nsv946379 CNV duplication 23825009
nsv946381 CNV duplication 23825009

Relevant External Links for HIST2H2AA4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST2H2AA4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for HIST2H2AA4 Gene

Disorders for HIST2H2AA4 Gene

Relevant External Links for HIST2H2AA4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST2H2AA4

No disorders were found for HIST2H2AA4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST2H2AA4 Gene

Publications for HIST2H2AA4 Gene

  1. Precise characterization of human histones in the H2A gene family by top down mass spectrometry. (PMID: 16457589) Boyne M.T. II … Kelleher N.L. (J. Proteome Res. 2006) 3 4 64
  2. Functional characterization of a human histone gene cluster duplication. (PMID: 15527963) Braastad C.D. … Stein G.S. (Gene 2004) 2 3 64
  3. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 3 4 64
  4. The relative expression of human histone H2A genes is similar in different types of proliferating cells. (PMID: 8179821) Mannironi C. … Bonner W. (DNA Cell Biol. 1994) 3 4 64
  5. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert J.P. … Gingras A.C. (J Proteomics 2015) 3 64

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