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 H3C13 Gene

Aliases for H3C13 Gene

  • H3 Clustered Histone 13 2 3 5
  • Histone Cluster 2 H3 Family Member D 2 3
  • H3-Clustered Histone 14 3 4
  • H3-Clustered Histone 15 3 4
  • Histone Cluster 2, H3d 2 3
  • Histone 2, H3d 2 3
  • Histone H3.2 3 4
  • HIST2H3D 3 4
  • H3-Clustered Histone 13 4
  • Histone H3/M 4
  • Histone H3/O 4
  • HIST2H3A 4
  • HIST2H3C 4
  • H3C14 3
  • H3C15 3
  • H3C13 5
  • H3F2 4
  • H3FM 4

External Ids for H3C13 Gene

Previous HGNC Symbols for H3C13 Gene

  • HIST2H3D

Previous GeneCards Identifiers for H3C13 Gene

  • GC01M149875
  • GC01M149915

Summaries for H3C13 Gene

Entrez Gene Summary for H3C13 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 H3 family. [provided by RefSeq, Aug 2015]

GeneCards Summary for H3C13 Gene

H3C13 (H3 Clustered Histone 13) is a Protein Coding gene. Diseases associated with H3C13 include Childhood Brain Stem Glioma. Among its related pathways are Chromatin organization and Transcriptional misregulation in cancer. An important paralog of this gene is H3C14.

UniProtKB/Swiss-Prot Summary for H3C13 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.

Additional gene information for H3C13 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H3C13 Gene

Genomics for H3C13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H3C13 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
GH01J149810 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +1.6 1592 4.6 ARHGAP35 SP1 CREB1 PRDM10 ZNF629 RFX1 ZNF692 POLR2A BACH1 LARP7 H2BC18 H3C13 lnc-HIST2H3D-2 piR-30912-003 PRPF3 SF3B4 H2BC19P SV2A H2BC20P UBE2D3P3
GH01J149826 Enhancer 0.2 Ensembl 0.4 -13.5 -13507 2.4 RF00017-323 piR-57664-001 H4C14 H3C13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H3C13 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H3C13

Genomic Locations for H3C13 Gene

Genomic Locations for H3C13 Gene
chr1:149,813,225-149,813,693
(GRCh38/hg38)
Size:
469 bases
Orientation:
Minus strand
chr1:149,784,780-149,785,236
(GRCh37/hg19)
Size:
457 bases
Orientation:
Minus strand

Genomic View for H3C13 Gene

Genes around H3C13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3C13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3C13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3C13 Gene

Proteins for H3C13 Gene

  • Protein details for H3C13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q71DI3-H32_HUMAN
    Recommended name:
    Histone H3.2
    Protein Accession:
    Q71DI3
    Secondary Accessions:
    • A2BDF6
    • A6NFS4
    • Q6B053

    Protein attributes for H3C13 Gene

    Size:
    136 amino acids
    Molecular mass:
    15388 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. During nucleosome assembly the chaperone ASF1A interacts with the histone H3-H4 heterodimer.

    Three dimensional structures from OCA and Proteopedia for H3C13 Gene

neXtProt entry for H3C13 Gene

Post-translational modifications for H3C13 Gene

  • Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters.
  • Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication.
  • Phosphorylated at Thr-4 (H3T3ph) by HASPIN during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MAP3K20 isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination. Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins.
  • Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression.
  • 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.
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Succinylation at Lys-80 (H3K79succ) by KAT2A takes place with a maximum frequency around the transcription start sites of genes (PubMed:29211711). It gives a specific tag for epigenetic transcription activation (PubMed:29211711). Desuccinylation at Lys-123 (H3K122succ) by SIRT7 in response to DNA damage promotes chromatin condensation and double-strand breaks (DSBs) repair (PubMed:27436229).
  • Serine ADP-ribosylation constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (PubMed:29480802). Serine ADP-ribosylation at Ser-11 (H3S10ADPr) is mutually exclusive with phosphorylation at Ser-11 (H3S10ph) and impairs acetylation at Lys-10 (H3K9ac) (PubMed:30257210).
  • Ubiquitination at Lys116
  • Modification sites at PhosphoSitePlus

Other Protein References for H3C13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H3C13 Gene

Domains & Families for H3C13 Gene

Gene Families for H3C13 Gene

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

Protein Domains for H3C13 Gene

InterPro:
Blocks:
  • Histone H3
ProtoNet:

Suggested Antigen Peptide Sequences for H3C13 Gene

GenScript: Design optimal peptide antigens:
  • Histone H3/o (H32_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q71DI3

UniProtKB/Swiss-Prot:

H32_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3C13: view

Function for H3C13 Gene

Molecular function for H3C13 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 H3C13 Gene

Gene Ontology (GO) - Molecular Function for H3C13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 20580717
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H3C13: view

Phenotypes for H3C13 Gene

genes like me logo Genes that share phenotypes with H3C13: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H3C13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H3C13 Gene

Localization for H3C13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3C13 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 H3C13 gene
Compartment Confidence
nucleus 5
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for H3C13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IDA 21636898
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IBA,IDA 21636898
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H3C13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H3C13 Gene

Pathways & Interactions for H3C13 Gene

PathCards logo

SuperPathways for H3C13 Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence (REACTOME)
3 Cell Cycle, Mitotic
.60
4 Chromatin organization
5 Mitotic Prophase
genes like me logo Genes that share pathways with H3C13: view

Gene Ontology (GO) - Biological Process for H3C13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IDA 21636898
GO:0007596 blood coagulation TAS --
GO:0038111 interleukin-7-mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with H3C13: view

No data available for SIGNOR curated interactions for H3C13 Gene

Drugs & Compounds for H3C13 Gene

No Compound Related Data Available

Transcripts for H3C13 Gene

mRNA/cDNA for H3C13 Gene

1 REFSEQ mRNAs :
1 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 H3C13

Alternative Splicing Database (ASD) splice patterns (SP) for H3C13 Gene

No ASD Table

Relevant External Links for H3C13 Gene

GeneLoc Exon Structure for
H3C13

Expression for H3C13 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H3C13

SOURCE GeneReport for Unigene cluster for H3C13 Gene:

Hs.712062

Evidence on tissue expression from TISSUES for H3C13 Gene

  • Spleen(4)
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 H3C13 Gene

Orthologs for H3C13 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for H3C13 Gene

Organism Taxonomy Gene Similarity Type Details
Mouse
(Mus musculus)
Mammalia Hist1h3f 31
  • 100 (a)
ManyToMany
Hist1h3c 30
  • 90.2 (n)
H3c3 17
Cow
(Bos Taurus)
Mammalia -- 31
  • 99 (a)
ManyToMany
LOC531990 30
  • 91.67 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 98 (a)
ManyToMany
Chimpanzee
(Pan troglodytes)
Mammalia LOC746430 30
  • 97.06 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia HIST2H3D 31
  • 95 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC684762 30
  • 88.73 (n)
Chicken
(Gallus gallus)
Aves LOC770022 30
  • 92.16 (n)
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 100 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100495338 30
  • 83.82 (n)
Zebrafish
(Danio rerio)
Actinopterygii HIST2H3D 31
  • 100 (a)
OneToOne
LOC564732 30
  • 83.33 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta His3:CG31613 31
  • 100 (a)
OneToOne
His3:CG33851 30
  • 81.62 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CSE4 33
Species where no ortholog for H3C13 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)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for H3C13 Gene

ENSEMBL:
Gene Tree for H3C13 (if available)
TreeFam:
Gene Tree for H3C13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H3C13: view image

Paralogs for H3C13 Gene

Pseudogenes.org Pseudogenes for H3C13 Gene

genes like me logo Genes that share paralogs with H3C13: view

Variants for H3C13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H3C13 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
719341 Benign: not provided 149,813,508(-) A/G SYNONYMOUS_VARIANT
791809 Benign: not provided 149,813,484(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for H3C13 Gene

Structural Variations from Database of Genomic Variants (DGV) for H3C13 Gene

Variant ID Type Subtype PubMed ID
esv1007634 OTHER inversion 20482838
nsv469694 CNV loss 16826518
nsv7182 OTHER inversion 18451855
nsv824564 CNV gain 20364138
nsv831503 CNV gain 17160897
nsv831525 CNV gain 17160897
nsv952802 CNV duplication 24416366

Variation tolerance for H3C13 Gene

Residual Variation Intolerance Score: 68% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.24; 5.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H3C13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H3C13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H3C13 Gene

Disorders for H3C13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for H3C13 Gene - From: DISEASES

Disorder Aliases PubMed IDs
childhood brain stem glioma
  • pediatric glioma of the brainstem
- elite association - COSMIC cancer census association via MalaCards
Search H3C13 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with H3C13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H3C13 Gene

Publications for H3C13 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 3 4
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics. (PMID: 31542297) Bao X … Li XD (Molecular cell 2019) 4
  4. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. (PMID: 30575818) Tiemann K … Kani K (Oncogene 2019) 3
  5. Serine is the major residue for ADP-ribosylation upon DNA damage. (PMID: 29480802) Palazzo L … Ahel I (eLife 2018) 4

Products for H3C13 Gene

Sources for H3C13 Gene