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Aliases for HIST3H2A Gene

Aliases for HIST3H2A Gene

  • Histone Cluster 3 H2A 2 3 5
  • Histone Cluster 3, H2a 2 3
  • Histone 3, H2a 2 3
  • Histone H2A Type 3 3

External Ids for HIST3H2A Gene

Previous GeneCards Identifiers for HIST3H2A Gene

  • GC01M224383
  • GC01M225030
  • GC01M225619
  • GC01M224951
  • GC01M226711
  • GC01M228645
  • GC01M199159

Summaries for HIST3H2A Gene

Entrez Gene Summary for HIST3H2A 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 is intronless and encodes a replication-dependent histone that is a member of the histone H2A family. Transcripts from this gene contain a palindromic termination element. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST3H2A Gene

HIST3H2A (Histone Cluster 3 H2A) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST1H2AC.

UniProtKB/Swiss-Prot for HIST3H2A 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 HIST3H2A Gene

Additional gene information for HIST3H2A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST3H2A Gene

Genomics for HIST3H2A Gene

GeneHancer (GH) Regulatory Elements for HIST3H2A Gene

Promoters and enhancers for HIST3H2A 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
GH01J228455 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 650.7 0.0 -28 4.2 CLOCK FEZF1 YY1 ZNF213 E2F8 ZNF143 SP3 ZFP41 ZNF610 GLIS1 GC01M228457 HIST3H2A HIST3H2BB CICP26 C1orf35 ENSG00000269890 ZNF678 PRSS38 HIST3H3 LOC100421842
GH01J228137 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10 +315.8 315808 8.8 DMAP1 YY1 E2F8 ZNF143 ZNF548 SP3 NFYC MEF2D GLIS1 NBN GUK1 OBSCN CICP26 ENSG00000269890 CDC42BPA ZNF678 OBSCN-AS1 C1orf35 FAM96AP2 MRPL55
GH01J228500 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 13.2 -43.0 -43028 1.8 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 ZNF766 ELK1 ZNF143 ATF7 RUNX3 HIST3H3 ZNF678 HIST3H2A HIST3H2BB RPL23AP15 CICP26 OBSCN-AS1 OBSCN C1orf35 RNF187
GH01J228212 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 10.8 +242.9 242890 4.8 ATF1 ZNF133 ARID4B SIN3A YBX1 GLI4 ZNF2 ZNF48 ETS1 ZNF280A OBSCN-AS1 PIR37830 OBSCN ZNF678 C1orf35 CICP26 RPL23AP15 HIST3H2BB HIST3H2A HIST3H3
GH01J228377 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.2 +79.2 79171 1.8 CLOCK SIN3A ZNF2 ZNF121 GLIS2 ZNF213 ZNF143 KLF7 SP3 REST PRSS38 LOC100421842 ENSG00000233920 ENSG00000231563 TRIM11 RPL23AP15 HIST3H2A HIST3H2BB OBSCN-AS1 OBSCN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HIST3H2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST3H2A gene promoter:
  • Nkx2-5
  • Max1
  • GCNF-2
  • GCNF-1
  • GCNF
  • E2F-1
  • E2F
  • FOXO4
  • FAC1
  • NF-Y

Genomic Locations for HIST3H2A Gene

Genomic Locations for HIST3H2A Gene
chr1:228,456,979-228,457,873
(GRCh38/hg38)
Size:
895 bases
Orientation:
Minus strand
chr1:228,645,065-228,645,560
(GRCh37/hg19)
Size:
496 bases
Orientation:
Minus strand

Genomic View for HIST3H2A Gene

Genes around HIST3H2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST3H2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST3H2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST3H2A Gene

Proteins for HIST3H2A Gene

  • Protein details for HIST3H2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7L7L0-H2A3_HUMAN
    Recommended name:
    Histone H2A type 3
    Protein Accession:
    Q7L7L0
    Secondary Accessions:
    • B2R4S4

    Protein attributes for HIST3H2A Gene

    Size:
    130 amino acids
    Molecular mass:
    14121 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.

neXtProt entry for HIST3H2A Gene

Post-translational modifications for HIST3H2A Gene

  • Deiminated on Arg-4 in granulocytes upon calcium entry.
  • 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.
  • 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).
  • Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • 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.
  • Ubiquitination at isoforms=16 and isoforms=14
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST3H2A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST3H2A Gene

Domains & Families for HIST3H2A Gene

Gene Families for HIST3H2A Gene

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

Protein Domains for HIST3H2A Gene

Suggested Antigen Peptide Sequences for HIST3H2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7L7L0

UniProtKB/Swiss-Prot:

H2A3_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with HIST3H2A: view

Function for HIST3H2A Gene

Molecular function for HIST3H2A 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.

Phenotypes From GWAS Catalog for HIST3H2A Gene

Gene Ontology (GO) - Molecular Function for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IDA 22334663
GO:0005515 protein binding IPI 20080676
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST3H2A: view
genes like me logo Genes that share phenotypes with HIST3H2A: view

Animal Model Products

CRISPR Products

miRNA for HIST3H2A Gene

miRTarBase miRNAs that target HIST3H2A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HIST3H2A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST3H2A Gene

Localization for HIST3H2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST3H2A 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 HIST3H2A gene
Compartment Confidence
extracellular 5
nucleus 5

Gene Ontology (GO) - Cellular Components for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000788 nuclear nucleosome IDA 22334663
GO:0000790 nuclear chromatin IBA --
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with HIST3H2A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HIST3H2A Gene

Pathways & Interactions for HIST3H2A Gene

genes like me logo Genes that share pathways with HIST3H2A: view

Pathways by source for HIST3H2A Gene

Gene Ontology (GO) - Biological Process for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IBA --
GO:0006337 nucleosome disassembly IMP 22334663
GO:0006342 chromatin silencing IBA --
GO:0070914 UV-damage excision repair IMP 22334663
genes like me logo Genes that share ontologies with HIST3H2A: view

No data available for SIGNOR curated interactions for HIST3H2A Gene

Drugs & Compounds for HIST3H2A Gene

(1) Drugs for HIST3H2A 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 HIST3H2A: view

Transcripts for HIST3H2A Gene

mRNA/cDNA for HIST3H2A Gene

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

Unigene Clusters for HIST3H2A Gene

Histone cluster 3, H2a:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HIST3H2A

Alternative Splicing Database (ASD) splice patterns (SP) for HIST3H2A Gene

No ASD Table

Relevant External Links for HIST3H2A Gene

GeneLoc Exon Structure for
HIST3H2A
ECgene alternative splicing isoforms for
HIST3H2A

Expression for HIST3H2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST3H2A Gene

mRNA differential expression in normal tissues according to GTEx for HIST3H2A Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.8) and Brain - Cerebellum (x4.8).

Protein differential expression in normal tissues from HIPED for HIST3H2A Gene

This gene is overexpressed in Saliva (40.6) and Heart (18.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HIST3H2A Gene



Protein tissue co-expression partners for HIST3H2A Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST3H2A Gene:

HIST3H2A

SOURCE GeneReport for Unigene cluster for HIST3H2A Gene:

Hs.26331

Evidence on tissue expression from TISSUES for HIST3H2A Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with HIST3H2A: view

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 HIST3H2A Gene

Orthologs for HIST3H2A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST3H2A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HIST3H2A 34 33
  • 99.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HIST3H2A 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia HIST3H2A 34
  • 98 (a)
OneToOne
LOC614881 33
  • 83.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
ManyToMany
-- 34
  • 94 (a)
ManyToMany
-- 34
  • 94 (a)
ManyToMany
-- 34
  • 91 (a)
ManyToMany
-- 34
  • 91 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hist3h2a 16 34 33
  • 86.67 (n)
rat
(Rattus norvegicus)
Mammalia Hist1h2aa 33
  • 84.36 (n)
chicken
(Gallus gallus)
Aves H2A-VII 34
  • 97 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 98 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.12821 33
barley
(Hordeum vulgare)
Liliopsida Hv.8481 33
Species where no ortholog for HIST3H2A 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)
  • 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)
  • 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 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 HIST3H2A Gene

ENSEMBL:
Gene Tree for HIST3H2A (if available)
TreeFam:
Gene Tree for HIST3H2A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HIST3H2A: view image

Paralogs for HIST3H2A Gene

Variants for HIST3H2A Gene

Sequence variations from dbSNP and Humsavar for HIST3H2A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000238442 -- 228,458,768(-) T/C upstream_transcript_variant
rs1001050817 -- 228,458,095(-) C/G/T upstream_transcript_variant
rs1002053230 -- 228,457,188(-) TGTTGTT/TGTT downstream_transcript_variant
rs1002084351 -- 228,457,042(-) G/T downstream_transcript_variant
rs1003133451 -- 228,457,383(-) C/A 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for HIST3H2A Gene

Variant ID Type Subtype PubMed ID
esv32853 CNV gain 17666407
nsv1013500 CNV gain 25217958
nsv517545 CNV loss 19592680
nsv523935 CNV loss 19592680
nsv549296 CNV gain 21841781
nsv826908 CNV gain 20364138
nsv827019 CNV loss 20364138
nsv945354 CNV duplication 23825009

Variation tolerance for HIST3H2A Gene

Residual Variation Intolerance Score: 37.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.24; 5.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIST3H2A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST3H2A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST3H2A Gene

Disorders for HIST3H2A Gene

Additional Disease Information for HIST3H2A

No disorders were found for HIST3H2A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST3H2A Gene

Publications for HIST3H2A Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 58
  2. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S … Dantuma NP (Genes & development 2006) 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. Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. (PMID: 15823041) Hagiwara T … Yamada M (Biochemistry 2005) 3 4 58
  5. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. (PMID: 16359901) Cao R … Zhang Y (Molecular cell 2005) 3 4 58

Products for HIST3H2A Gene

Sources for HIST3H2A Gene

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