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... See more...

Aliases for H2AC1 Gene

Aliases for H2AC1 Gene

  • H2A Clustered Histone 1 2 3 5
  • H2AFR 2 3 4
  • Histone Cluster 1 H2A Family Member A 2 3
  • H2A Histone Family, Member R 2 3
  • Histone Cluster 1, H2aa 2 3
  • Histone H2A Type 1-A 3 4
  • Histone 1, H2aa 2 3
  • Histone H2A/R 3 4
  • BA317E16.2 2 3
  • HIST1H2AA 3 4
  • H2A-Clustered Histone 1 4
  • H2AC1 5
  • H2AA 3
  • TH2A 3

External Ids for H2AC1 Gene

Previous HGNC Symbols for H2AC1 Gene

  • HIST1H2AA

Previous GeneCards Identifiers for H2AC1 Gene

  • GC06M025816
  • GC06M025827
  • GC06M025844
  • GC06M025854

Summaries for H2AC1 Gene

Entrez Gene Summary for H2AC1 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 H2AC1 Gene

H2AC1 (H2A Clustered Histone 1) is a Protein Coding gene. Diseases associated with H2AC1 include Amelogenesis Imperfecta, Type Iiia and Riddle Syndrome. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. An important paralog of this gene is H2AC6.

UniProtKB/Swiss-Prot Summary for H2AC1 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 H2AC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2AC1 Gene

Genomics for H2AC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2AC1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2AC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2AC1

Genomic Locations for H2AC1 Gene

Latest Assembly
chr6:25,726,063-25,726,562
(GRCh38/hg38)
Size:
500 bases
Orientation:
Minus strand

Previous Assembly
chr6:25,726,291-25,726,790
(GRCh37/hg19 by Entrez Gene)
Size:
500 bases
Orientation:
Minus strand

chr6:25,726,291-25,726,790
(GRCh37/hg19 by Ensembl)
Size:
500 bases
Orientation:
Minus strand

Genomic View for H2AC1 Gene

Genes around H2AC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2AC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2AC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AC1 Gene

Proteins for H2AC1 Gene

  • Protein details for H2AC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96QV6-H2A1A_HUMAN
    Recommended name:
    Histone H2A type 1-A
    Protein Accession:
    Q96QV6

    Protein attributes for H2AC1 Gene

    Size:
    131 amino acids
    Molecular mass:
    14234 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.

    Three dimensional structures from OCA and Proteopedia for H2AC1 Gene

neXtProt entry for H2AC1 Gene

Post-translational modifications for H2AC1 Gene

  • Deiminated on Arg-4 in granulocytes upon calcium entry.
  • Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM37 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 TRIM37 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 Lys14 and Lys16
  • Modification sites at PhosphoSitePlus

Other Protein References for H2AC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AC1 Gene

Domains & Families for H2AC1 Gene

Gene Families for H2AC1 Gene

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

Protein Domains for H2AC1 Gene

Suggested Antigen Peptide Sequences for H2AC1 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2A/r (H2A1A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96QV6

UniProtKB/Swiss-Prot:

H2A1A_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AC1: view

Function for H2AC1 Gene

Molecular function for H2AC1 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 H2AC1 Gene

Gene Ontology (GO) - Molecular Function for H2AC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA 21873635
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AC1: view
genes like me logo Genes that share phenotypes with H2AC1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2AC1 Gene

Localization for H2AC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AC1 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 H2AC1 gene
Compartment Confidence
nucleus 5
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for H2AC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region HDA 19135898
GO:0000785 chromatin IBA --
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IEA,HDA 21630459
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2AC1: view

Pathways & Interactions for H2AC1 Gene

genes like me logo Genes that share pathways with H2AC1: view

Pathways by source for H2AC1 Gene

Gene Ontology (GO) - Biological Process for H2AC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006342 chromatin silencing IBA 21873635
genes like me logo Genes that share ontologies with H2AC1: view

No data available for SIGNOR curated interactions for H2AC1 Gene

Drugs & Compounds for H2AC1 Gene

(1) Drugs for H2AC1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6959
genes like me logo Genes that share compounds with H2AC1: view

Transcripts for H2AC1 Gene

mRNA/cDNA for H2AC1 Gene

1 REFSEQ mRNAs :
1 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC1

Alternative Splicing Database (ASD) splice patterns (SP) for H2AC1 Gene

No ASD Table

Relevant External Links for H2AC1 Gene

GeneLoc Exon Structure for
H2AC1

Expression for H2AC1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2AC1

SOURCE GeneReport for Unigene cluster for H2AC1 Gene:

Hs.406739

Evidence on tissue expression from TISSUES for H2AC1 Gene

  • Nervous system(2)
No Expression Related Data Available

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2AC1 Gene

Orthologs for H2AC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H2AC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HIST1H2AA 30
  • 100 (a)
OneToOne
LOC462486 29
  • 98.47 (n)
Dog
(Canis familiaris)
Mammalia HIST1H2AA 29 30
  • 81.17 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hist1h2ak 29
  • 78.46 (n)
H2ac15 16
Cow
(Bos Taurus)
Mammalia HIST1H2AG 29
  • 77.69 (n)
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 85 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii zgc:163047 30
  • 91 (a)
ManyToMany
zgc:101846 30
  • 91 (a)
ManyToMany
si:ch211-113a14.19 30 30 30 30 30 30
  • 90 (a)
ManyToMany
zgc:195633 30 30 30
  • 90 (a)
ManyToMany
zgc:154164 30 30
  • 86 (a)
ManyToMany
Species where no ortholog for H2AC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)

Evolution for H2AC1 Gene

ENSEMBL:
Gene Tree for H2AC1 (if available)
TreeFam:
Gene Tree for H2AC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2AC1: view image
Alliance of Genome Resources:
Additional Orthologs for H2AC1

Paralogs for H2AC1 Gene

Pseudogenes.org Pseudogenes for H2AC1 Gene

genes like me logo Genes that share paralogs with H2AC1: view

Variants for H2AC1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2AC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for H2AC1 Gene

Variant ID Type Subtype PubMed ID
esv3570813 CNV loss 25503493

Variation tolerance for H2AC1 Gene

Residual Variation Intolerance Score: 15.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.34; 7.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2AC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2AC1
Leiden Open Variation Database (LOVD)
H2AC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H2AC1 Gene

Disorders for H2AC1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for H2AC1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
amelogenesis imperfecta, type iiia
  • ai3a
riddle syndrome
  • ridl
- elite association - COSMIC cancer census association via MalaCards
Search H2AC1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H2AC1

genes like me logo Genes that share disorders with H2AC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H2AC1 Gene

Publications for H2AC1 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S … Dantuma NP (Genes & development 2006) 3 4
  3. Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. (PMID: 15823041) Hagiwara T … Yamada M (Biochemistry 2005) 3 4
  4. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. (PMID: 16359901) Cao R … Zhang Y (Molecular cell 2005) 3 4
  5. Role of histone H2A ubiquitination in Polycomb silencing. (PMID: 15386022) Wang H … Zhang Y (Nature 2004) 3 4

Products for H2AC1 Gene

Sources for H2AC1 Gene