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Aliases for HIST1H2AD Gene

Aliases for HIST1H2AD Gene

  • Histone Cluster 1 H2A Family Member D 2 3 5
  • H2A Histone Family, Member G 2 3
  • Histone Cluster 1, H2ad 2 3
  • Histone 1, H2ad 2 3
  • Histone H2A.3 3 4
  • Histone H2A/G 3 4
  • H2AFG 3 4
  • Histone H2A Type 1-D 3
  • Histone H2AD 3
  • H2A.3 3
  • H2A/G 3

External Ids for HIST1H2AD Gene

Previous HGNC Symbols for HIST1H2AD Gene

  • H2AFG

Previous GeneCards Identifiers for HIST1H2AD Gene

  • GC06M026256
  • GC06M026309
  • GC06M026311
  • GC06M026313
  • GC06M026315
  • GC06M026199
  • GC06M026142

Summaries for HIST1H2AD Gene

Entrez Gene Summary for HIST1H2AD Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an 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 lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST1H2AD Gene

HIST1H2AD (Histone Cluster 1 H2A Family Member D) is a Protein Coding gene. 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 ENSG00000282988.

UniProtKB/Swiss-Prot for HIST1H2AD 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 HIST1H2AD Gene

Additional gene information for HIST1H2AD Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H2AD Gene

Genomics for HIST1H2AD Gene

GeneHancer (GH) Regulatory Elements for HIST1H2AD Gene

Promoters and enhancers for HIST1H2AD 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
GH06I026193 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 550.8 -1.5 -1499 14.6 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ENSG00000282988 HIST1H2AD HIST1H2BF HIST1H3D HIST1H4E RPS10P1 ABT1 HMGN4 BTN2A3P BTN2A1
GH06I026309 Enhancer 1.5 Ensembl ENCODE dbSUPER 10.5 -112.5 -112548 4.9 MLX YBX1 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 NFYC MEF2D GC06M026658 TRQ-TTG3-1 TRQ-TTG3-2 TRS-TGA3-1 TRX-CAT1-3 ABT1 ZNF322 BTN2A2 BTN2A1 BTN3A2
GH06I026162 Enhancer 0.6 Ensembl 11.2 +37.8 37792 0.2 BCOR ARNT MNT DPF2 FOSL1 POLR2B PRDM6 POLR2A IKZF1 ZSCAN5C HIST1H4D HIST1H1PS1 HIST1H3D HIST1H2AD HIST1H3E HIST1H2APS3 HIST1H2BF RPS10P1 HIST1H4C HIST1H4F
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HIST1H2AD on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST1H2AD gene promoter:

Genomic Locations for HIST1H2AD Gene

Genomic Locations for HIST1H2AD Gene
chr6:26,198,784-26,199,293
(GRCh38/hg38)
Size:
510 bases
Orientation:
Minus strand
chr6:26,199,012-26,199,471
(GRCh37/hg19)

Genomic View for HIST1H2AD Gene

Genes around HIST1H2AD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H2AD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H2AD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H2AD Gene

Proteins for HIST1H2AD Gene

  • Protein details for HIST1H2AD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P20671-H2A1D_HUMAN
    Recommended name:
    Histone H2A type 1-D
    Protein Accession:
    P20671
    Secondary Accessions:
    • A0PK91
    • P57754
    • Q6FGY6

    Protein attributes for HIST1H2AD Gene

    Size:
    130 amino acids
    Molecular mass:
    14107 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 HIST1H2AD Gene

neXtProt entry for HIST1H2AD Gene

Post-translational modifications for HIST1H2AD 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 posLast=1414 and isoforms=16

Other Protein References for HIST1H2AD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H2AD Gene

Domains & Families for HIST1H2AD Gene

Gene Families for HIST1H2AD Gene

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

Protein Domains for HIST1H2AD Gene

Suggested Antigen Peptide Sequences for HIST1H2AD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P20671

UniProtKB/Swiss-Prot:

H2A1D_HUMAN :
  • Belongs to the histone H2A family.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with HIST1H2AD: view

Function for HIST1H2AD Gene

Molecular function for HIST1H2AD 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 HIST1H2AD Gene

Gene Ontology (GO) - Molecular Function for HIST1H2AD 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 HIST1H2AD: view
genes like me logo Genes that share phenotypes with HIST1H2AD: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H2AD Gene

Localization for HIST1H2AD Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H2AD 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 HIST1H2AD gene
Compartment Confidence
extracellular 5
nucleus 5

Gene Ontology (GO) - Cellular Components for HIST1H2AD 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 20458337
genes like me logo Genes that share ontologies with HIST1H2AD: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HIST1H2AD Gene

Pathways & Interactions for HIST1H2AD Gene

SuperPathways for HIST1H2AD 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 HIST1H2AD: view

Gene Ontology (GO) - Biological Process for HIST1H2AD 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 HIST1H2AD: view

No data available for SIGNOR curated interactions for HIST1H2AD Gene

Drugs & Compounds for HIST1H2AD Gene

(1) Drugs for HIST1H2AD 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 HIST1H2AD: view

Transcripts for HIST1H2AD Gene

mRNA/cDNA for HIST1H2AD Gene

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

Unigene Clusters for HIST1H2AD Gene

Histone cluster 1, H2ad:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H2AD Gene

No ASD Table

Relevant External Links for HIST1H2AD Gene

GeneLoc Exon Structure for
HIST1H2AD
ECgene alternative splicing isoforms for
HIST1H2AD

Expression for HIST1H2AD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST1H2AD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HIST1H2AD Gene

This gene is overexpressed in Blymphocyte (27.2), Tlymphocyte (16.0), Liver, secretome (8.0), and Monocytes (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HIST1H2AD Gene



Protein tissue co-expression partners for HIST1H2AD Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST1H2AD Gene:

HIST1H2AD

SOURCE GeneReport for Unigene cluster for HIST1H2AD Gene:

Hs.626666

Evidence on tissue expression from TISSUES for HIST1H2AD Gene

  • Lung(4.2)
genes like me logo Genes that share expression patterns with HIST1H2AD: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H2AD Gene

Orthologs for HIST1H2AD Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST1H2AD Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HIST1H2AD 34
  • 100 (a)
OneToOne
LOC100848734 33
  • 88.46 (n)
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2AD 34
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hist1h2ad 34
  • 99 (a)
ManyToMany
Hist1h2ab 33 16
  • 87.44 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 98 (a)
ManyToMany
-- 34
  • 93 (a)
ManyToMany
LOC100856200 33
  • 88.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
OneToMany
-- 34
  • 91 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 93 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia LOC100360754 33
  • 85.64 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 98 (a)
ManyToMany
-- 34
  • 98 (a)
ManyToMany
Species where no ortholog for HIST1H2AD 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)
  • 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)
  • 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 HIST1H2AD Gene

ENSEMBL:
Gene Tree for HIST1H2AD (if available)
TreeFam:
Gene Tree for HIST1H2AD (if available)

Paralogs for HIST1H2AD Gene

Variants for HIST1H2AD Gene

Sequence variations from dbSNP and Humsavar for HIST1H2AD Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1001285373 -- 26,200,351(-) A/C upstream_transcript_variant
rs1001612008 -- 26,200,208(-) T/A upstream_transcript_variant
rs1003050974 -- 26,198,736(-) G/A downstream_transcript_variant
rs1005162636 -- 26,198,723(-) A/G downstream_transcript_variant
rs1006103571 -- 26,199,335(-) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H2AD Gene

Variant ID Type Subtype PubMed ID
dgv375n21 CNV loss 19592680
dgv5926n100 CNV gain 25217958
esv3608397 CNV loss 21293372
esv3608398 CNV loss 21293372
esv3608399 CNV gain 21293372
nsv1021294 CNV loss 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for HIST1H2AD Gene

Residual Variation Intolerance Score: 23.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.26; 5.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIST1H2AD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H2AD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H2AD Gene

Disorders for HIST1H2AD Gene

Additional Disease Information for HIST1H2AD

No disorders were found for HIST1H2AD Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H2AD Gene

Publications for HIST1H2AD Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 58
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W … Doenecke D (Genomics 1997) 2 3 4 58
  3. 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
  4. Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. (PMID: 27105115) Xie Z … Zhao Y (Molecular cell 2016) 4 58
  5. USP51 deubiquitylates H2AK13,15ub and regulates DNA damage response. (PMID: 27083998) Wang Z … Zhang Z (Genes & development 2016) 4 58

Products for HIST1H2AD Gene

Sources for HIST1H2AD Gene

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