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 ... See more...

Aliases for H2AC6 Gene

Aliases for H2AC6 Gene

  • H2A Clustered Histone 6 2 3
  • Histone Cluster 1 H2A Family Member C 2 3 5
  • H2A Histone Family, Member L 2 3
  • Histone Cluster 1, H2ac 2 3
  • Histone H2A Type 1-C 3 4
  • Histone 1, H2ac 2 3
  • Histone H2A/L 3 4
  • HIST1H2AC 3 5
  • H2AFL 3 4
  • Histone H2AC 3
  • DJ221C16.4 3
  • H2A/L 3

External Ids for H2AC6 Gene

Previous HGNC Symbols for H2AC6 Gene

  • H2AFL
  • HIST1H2AC

Summaries for H2AC6 Gene

Entrez Gene Summary for H2AC6 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 the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2AC6 Gene

H2AC6 (H2A Clustered Histone 6) is a Protein Coding gene. Among its related pathways are Cellular Senescence (REACTOME) and Meiosis. An important paralog of this gene is H2AW.

UniProtKB/Swiss-Prot Summary for H2AC6 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 H2AC6 Gene

Additional gene information for H2AC6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2AC6 Gene

Genomics for H2AC6 Gene

GeneHancer (GH) Regulatory Elements for H2AC6 Gene

Promoters and enhancers for H2AC6 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
GH06J026120 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 752.7 +0.2 199 8.5 PPP1R10 GTF3C2 SIN3A ZBTB40 SP1 SREBF1 ZBTB6 LCORL FOXA1 RBPJ H2AC6 H2BC4 piR-40096 piR-31751 piR-50446 ABT1 BTN2A3P HMGN4 BTN2A1 BTN2A2
GH06J026520 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas 1.3 +397.9 397856 4 GTF3C2 ZNF785 ZNF24 ZBTB40 CTCF ZBTB6 MLX SMARCE1 RBPJ POLR2A HCG11 LOC285819 TRL-CAG1-7 piR-39126-002 ZNF322 HMGN4 ABT1 BTN2A3P ENSG00000261584 ZNF391
GH06J026132 Enhancer 0.4 Ensembl 0.4 +8.7 8656 0.4 POLR2A SUPT5H SMAD5 BTN3A2 H1-6 H4C3 LARP1P1 ENSG00000218690 H2AC6 piR-40096 H1-4
GH06J026134 Enhancer 0.4 Ensembl 0.4 +11.6 11556 0.2 PRDM1 ZNF10 FOXA2 FOXA1 H1-6 H4C3 LARP1P1 ENSG00000218690 H2AC6 piR-40096 H1-4
GH06J026136 Enhancer 0.4 Ensembl 0.4 +12.5 12536 1.4 PRDM1 POLR2A PKNOX1 GATAD2A H1-6 H4C3 LARP1P1 ENSG00000218690 ENSG00000272462 H2AC6 piR-40096 H1-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2AC6 on UCSC Golden Path with GeneCards custom track

Genomic Locations for H2AC6 Gene

Genomic Locations for H2AC6 Gene
chr6:26,124,145-26,139,116
(GRCh38/hg38)
Size:
14,972 bases
Orientation:
Plus strand
chr6:26,124,373-26,139,344
(GRCh37/hg19)
Size:
14,972 bases
Orientation:
Plus strand

Genomic View for H2AC6 Gene

Genes around H2AC6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2AC6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2AC6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AC6 Gene

Proteins for H2AC6 Gene

  • Protein details for H2AC6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q93077-H2A1C_HUMAN
    Recommended name:
    Histone H2A type 1-C
    Protein Accession:
    Q93077
    Secondary Accessions:
    • B2R4F7
    • O00775
    • O00776
    • O00777
    • O00778
    • Q540R1

    Protein attributes for H2AC6 Gene

    Size:
    130 amino acids
    Molecular mass:
    14105 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 H2AC6 Gene

neXtProt entry for H2AC6 Gene

Post-translational modifications for H2AC6 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 Lys16
  • Modification sites at PhosphoSitePlus

Other Protein References for H2AC6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AC6 Gene

Domains & Families for H2AC6 Gene

Gene Families for H2AC6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for H2AC6 Gene

Suggested Antigen Peptide Sequences for H2AC6 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2A/l (H2A1C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q93077

UniProtKB/Swiss-Prot:

H2A1C_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AC6: view

Function for H2AC6 Gene

Molecular function for H2AC6 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 H2AC6 Gene

Gene Ontology (GO) - Molecular Function for H2AC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA 21873635
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AC6: view
genes like me logo Genes that share phenotypes with H2AC6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2AC6 Gene

Localization for H2AC6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AC6 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 H2AC6 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for H2AC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0000790 nuclear chromatin IBA 21873635
GO:0005634 nucleus IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2AC6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H2AC6 Gene

Pathways & Interactions for H2AC6 Gene

PathCards logo

SuperPathways for H2AC6 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 H2AC6: view

Gene Ontology (GO) - Biological Process for H2AC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IBA 21873635
GO:0008285 negative regulation of cell proliferation IMP 23956221
genes like me logo Genes that share ontologies with H2AC6: view

No data available for SIGNOR curated interactions for H2AC6 Gene

Drugs & Compounds for H2AC6 Gene

(1) Drugs for H2AC6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7773
genes like me logo Genes that share compounds with H2AC6: view

Transcripts for H2AC6 Gene

mRNA/cDNA for H2AC6 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AC6

Alternative Splicing Database (ASD) splice patterns (SP) for H2AC6 Gene

No ASD Table

Relevant External Links for H2AC6 Gene

GeneLoc Exon Structure for
H2AC6
ECgene alternative splicing isoforms for
H2AC6

Expression for H2AC6 Gene

NURSA nuclear receptor signaling pathways regulating expression of H2AC6 Gene:

H2AC6

SOURCE GeneReport for Unigene cluster for H2AC6 Gene:

Hs.484950

Evidence on tissue expression from TISSUES for H2AC6 Gene

  • Nervous system(3.3)
No Expression Related Data Available

Primer Products

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 H2AC6 Gene

Orthologs for H2AC6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H2AC6 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia HIST1H2AC 33
  • 100 (a)
OneToOne
LOC488268 32
  • 89.23 (n)
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2AC 33 32
  • 99.49 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Hist1h2al 33
  • 98 (a)
ManyToMany
Hist1h2ao 17 32
  • 87.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 95 (a)
ManyToMany
-- 33
  • 95 (a)
ManyToMany
-- 33
  • 95 (a)
ManyToMany
-- 33
  • 91 (a)
ManyToMany
-- 33
  • 91 (a)
ManyToMany
-- 33
  • 88 (a)
ManyToMany
-- 33
  • 88 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Hist3h2a 32
  • 86.15 (n)
cow
(Bos Taurus)
Mammalia HIST1H2AC 33 32
  • 85.64 (n)
OneToOne
chicken
(Gallus gallus)
Aves H2A-VII 33
  • 98 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 99 (a)
OneToMany
Species where no ortholog for H2AC6 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)
  • 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 H2AC6 Gene

ENSEMBL:
Gene Tree for H2AC6 (if available)
TreeFam:
Gene Tree for H2AC6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2AC6: view image

Paralogs for H2AC6 Gene

Variants for H2AC6 Gene

Sequence variations from dbSNP and Humsavar for H2AC6 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000511689 -- 26,123,136(+) G/A upstream_transcript_variant
rs1000779831 -- 26,124,984(+) A/G downstream_transcript_variant
rs1002014735 -- 26,123,329(+) C/T upstream_transcript_variant
rs1002069803 -- 26,124,684(+) C/T 3_prime_UTR_variant
rs1003687727 -- 26,124,041(+) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for H2AC6 Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
esv3608393 CNV gain 21293372
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914
nsv970082 CNV duplication 23825009

Variation tolerance for H2AC6 Gene

Residual Variation Intolerance Score: 22.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.16; 3.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2AC6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2AC6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H2AC6 Gene

Disorders for H2AC6 Gene

Additional Disease Information for H2AC6

No disorders were found for H2AC6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2AC6 Gene

Publications for H2AC6 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 56
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W … Doenecke D (Genomics 1997) 2 3 4 56
  3. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S … Dantuma NP (Genes & development 2006) 3 4 56
  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 56
  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 56

Products for H2AC6 Gene

Sources for H2AC6 Gene