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Aliases for HIST2H2AA3 Gene

Aliases for HIST2H2AA3 Gene

  • Histone Cluster 2 H2A Family Member A3 2 3 5
  • H2A Histone Family, Member O 2 3
  • Histone Cluster 2, H2aa3 2 3
  • Histone 2, H2aa3 2 3
  • HIST2H2AA 3 4
  • H2AFO 3 4
  • HIST2H2AA3 HIST2H2AA4 4
  • Histone H2A Type 2-A 3
  • Histone 2, H2aa 2
  • Histone H2A.2 4
  • Histone H2A/O 4
  • H2a-615 3
  • H2A.2 3
  • H2A/O 3
  • H2A/Q 3
  • H2A 3

External Ids for HIST2H2AA3 Gene

Previous HGNC Symbols for HIST2H2AA3 Gene

  • H2AFO
  • HIST2H2AA

Previous GeneCards Identifiers for HIST2H2AA3 Gene

  • GC01M148080
  • GC01M149813
  • GC01P121205

Summaries for HIST2H2AA3 Gene

Entrez Gene Summary for HIST2H2AA3 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 centromeric copy. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST2H2AA3 Gene

HIST2H2AA3 (Histone Cluster 2 H2A Family Member A3) is a Protein Coding gene. Diseases associated with HIST2H2AA3 include Riddle Syndrome and Retinitis Pigmentosa 20. Among its related pathways are Mitotic Prophase and Meiosis. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST2H2AA4.

UniProtKB/Swiss-Prot for HIST2H2AA3 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.

Gene Wiki entry for HIST2H2AA3 Gene

Additional gene information for HIST2H2AA3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST2H2AA3 Gene

Genomics for HIST2H2AA3 Gene

GeneHancer (GH) Regulatory Elements for HIST2H2AA3 Gene

Promoters and enhancers for HIST2H2AA3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I149840 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 555.4 -0.5 -546 6.2 HDAC1 INSM2 SIN3A ELK1 ZSCAN5C RCOR1 FOS SMAD5 CEBPB ZNF623 HIST2H2AA3 GC01P149843 HIST2H2BD HIST2H3C SV2A HIST2H2AC HIST2H2BE BOLA1 MTMR11 ENSG00000261716
GH01I149846 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 4.8 -7.5 -7508 6.7 CLOCK FOXA2 SIN3A ZNF335 E2F8 ZSCAN5C SMAD5 SP1 ATF4 GLIS1 ENSG00000261716 GC01M149850 HIST2H2AA4 HIST2H2BC HIST2H3A BOLA1 HIST2H2AC HIST2H2BE MTMR11 HIST2H2AA3
GH01I150061 Enhancer 0.8 Ensembl ENCODE 10.3 -219.1 -219082 0.9 MEIS2 PKNOX1 CEBPB CEBPG TSHZ1 ARHGAP35 ZNF316 JUND FOS MAFK HIST2H2AC OTUD7B MTMR11 PLEKHO1 HIST2H2AA3 HIST2H2BD SF3B4 HIST2H3C HIST2H2BE BOLA1
GH01I150015 Enhancer 1.1 Ensembl ENCODE dbSUPER 4.8 -174.2 -174156 2.3 NCOA3 PKNOX1 ESRRA USF1 SIN3A NFXL1 ZFHX2 CTBP1 GATA3 EGR1 SV2A MTMR11 ENSG00000261716 HIST2H2AA3 HIST2H2AB OTUD7B GC01P150029
GH01I150000 Enhancer 0.8 dbSUPER 4.4 -159.8 -159821 4 HDAC1 TCF12 ZNF121 ZNF766 ZNF213 SIRT6 ZBTB11 ZC3H11A ZNF623 ZNF518A SV2A PRPF3 HIST2H2AB SF3B4 SETDB1 RPRD2 UBE2D3P3 VPS45 ARNT MTMR11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HIST2H2AA3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST2H2AA3 gene promoter:

Genomic Locations for HIST2H2AA3 Gene

Genomic Locations for HIST2H2AA3 Gene
chr1:149,842,188-149,842,751
(GRCh38/hg38)
Size:
564 bases
Orientation:
Minus strand
chr1:149,813,505-149,814,478
(GRCh37/hg19)

Genomic View for HIST2H2AA3 Gene

Genes around HIST2H2AA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST2H2AA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST2H2AA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST2H2AA3 Gene

Proteins for HIST2H2AA3 Gene

  • Protein details for HIST2H2AA3 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 HIST2H2AA3 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 HIST2H2AA3 Gene

Post-translational modifications for HIST2H2AA3 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. Deubiquitinated by USP51 at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) after damaged DNA is repaired (PubMed:27083998). 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 DCAF1 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 isoforms=16

Other Protein References for HIST2H2AA3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST2H2AA3 Gene

Domains & Families for HIST2H2AA3 Gene

Gene Families for HIST2H2AA3 Gene

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

Protein Domains for HIST2H2AA3 Gene

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 HIST2H2AA3: view

No data available for Suggested Antigen Peptide Sequences for HIST2H2AA3 Gene

Function for HIST2H2AA3 Gene

Molecular function for HIST2H2AA3 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 HIST2H2AA3 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 HIST2H2AA3: view
genes like me logo Genes that share phenotypes with HIST2H2AA3: view

miRNA for HIST2H2AA3 Gene

miRTarBase miRNAs that target HIST2H2AA3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST2H2AA3 Gene

Localization for HIST2H2AA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST2H2AA3 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 HIST2H2AA3 gene
Compartment Confidence
extracellular 5
nucleus 5
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HIST2H2AA3 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 HDA,IDA 19199708
genes like me logo Genes that share ontologies with HIST2H2AA3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HIST2H2AA3 Gene

Pathways & Interactions for HIST2H2AA3 Gene

SuperPathways for HIST2H2AA3 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 Chromatin organization
genes like me logo Genes that share pathways with HIST2H2AA3: view

Gene Ontology (GO) - Biological Process for HIST2H2AA3 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 HIST2H2AA3: view

No data available for SIGNOR curated interactions for HIST2H2AA3 Gene

Drugs & Compounds for HIST2H2AA3 Gene

(1) Drugs for HIST2H2AA3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with HIST2H2AA3: view

Transcripts for HIST2H2AA3 Gene

mRNA/cDNA for HIST2H2AA3 Gene

(1) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(128) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HIST2H2AA3 Gene

Histone cluster 2, H2aa3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST2H2AA3 Gene

No ASD Table

Relevant External Links for HIST2H2AA3 Gene

GeneLoc Exon Structure for
HIST2H2AA3
ECgene alternative splicing isoforms for
HIST2H2AA3

Expression for HIST2H2AA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST2H2AA3 Gene

mRNA differential expression in normal tissues according to GTEx for HIST2H2AA3 Gene

This gene is overexpressed in Whole Blood (x16.1).

Protein differential expression in normal tissues from HIPED for HIST2H2AA3 Gene

This gene is overexpressed in Saliva (23.3), Tlymphocyte (21.2), Heart (9.5), and Urine (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HIST2H2AA3 Gene



Protein tissue co-expression partners for HIST2H2AA3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST2H2AA3 Gene:

HIST2H2AA3

SOURCE GeneReport for Unigene cluster for HIST2H2AA3 Gene:

Hs.530461

Evidence on tissue expression from TISSUES for HIST2H2AA3 Gene

  • Blood(2.7)
  • Liver(2.2)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with HIST2H2AA3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST2H2AA3 Gene

Orthologs for HIST2H2AA3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST2H2AA3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HIST2H2AC 34 34
  • 100 (a)
ManyToMany
LOC788724 33
  • 91.54 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Hist2h2aa1 34
  • 100 (a)
OneToMany
Hist2h2aa2 33
  • 89.49 (n)
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 100 (a)
OneToMany
HIST2H2AA4 33
  • 99.74 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia LOC690131 33
  • 89.49 (n)
chicken
(Gallus gallus)
Aves H2A-VII 34
  • 98 (a)
ManyToMany
Species where no ortholog for HIST2H2AA3 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)
  • 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)
  • 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 HIST2H2AA3 Gene

ENSEMBL:
Gene Tree for HIST2H2AA3 (if available)
TreeFam:
Gene Tree for HIST2H2AA3 (if available)

Paralogs for HIST2H2AA3 Gene

Variants for HIST2H2AA3 Gene

Sequence variations from dbSNP and Humsavar for HIST2H2AA3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1007920943 -- 149,844,530(-) A/G upstream_transcript_variant
rs1008923766 -- 149,843,539(-) T/A upstream_transcript_variant
rs1011724730 -- 149,844,454(-) T/G upstream_transcript_variant
rs1013129127 -- 149,843,932(-) A/G upstream_transcript_variant
rs1014933455 -- 149,843,543(-) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HIST2H2AA3 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

Additional Variant Information for HIST2H2AA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST2H2AA3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for HIST2H2AA3 Gene

Disorders for HIST2H2AA3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HIST2H2AA3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
riddle syndrome
  • radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties
retinitis pigmentosa 20
  • rp20
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HIST2H2AA3

genes like me logo Genes that share disorders with HIST2H2AA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HIST2H2AA3 Gene

Publications for HIST2H2AA3 Gene

  1. The relative expression of human histone H2A genes is similar in different types of proliferating cells. (PMID: 8179821) Mannironi C … Bonner W (DNA and cell biology 1994) 2 3 4 58
  2. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. (PMID: 22980979) Mattiroli F … Sixma TK (Cell 2012) 3 4 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Precise characterization of human histones in the H2A gene family by top down mass spectrometry. (PMID: 16457589) Boyne MT … Kelleher NL (Journal of proteome research 2006) 3 4 58
  5. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S … Dantuma NP (Genes & development 2006) 3 4 58

Products for HIST2H2AA3 Gene

Sources for HIST2H2AA3 Gene

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