Histones are basic nuclear proteins responsible for 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 ... See more...

Aliases for H1-3 Gene

Aliases for H1-3 Gene

  • H1.3 Linker Histone, Cluster Member 2 3 5
  • Histone Cluster 1 H1 Family Member D 2 3
  • H1 Histone Family, Member 3 2 3
  • Histone Cluster 1, H1d 2 3
  • Histone 1, H1d 2 3
  • Histone H1s-2 3 4
  • Histone H1.3 3 4
  • Histone H1c 3 4
  • HIST1H1D 3 4
  • H1s-2 2 3
  • H1.3 2 3
  • H1F3 3 4
  • H1-3 5
  • H1D 3
  • H1d 2

External Ids for H1-3 Gene

Previous HGNC Symbols for H1-3 Gene

  • H1F3
  • HIST1H1D

Previous GeneCards Identifiers for H1-3 Gene

  • GC06M026827
  • GC06M027051
  • GC06M027296
  • GC06M027803

Summaries for H1-3 Gene

Entrez Gene Summary for H1-3 Gene

  • Histones are basic nuclear proteins responsible for 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 H1 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 H1-3 Gene

H1-3 (H1.3 Linker Histone, Cluster Member) is a Protein Coding gene. Diseases associated with H1-3 include Ovarian Cancer. Among its related pathways are Activation of DNA fragmentation factor and DNA Damage/Telomere Stress Induced Senescence. An important paralog of this gene is H1-4.

UniProtKB/Swiss-Prot Summary for H1-3 Gene

  • Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).

Gene Wiki entry for H1-3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H1-3 Gene

Genomics for H1-3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H1-3 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 H1-3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H1-3

Genomic Locations for H1-3 Gene

Latest Assembly
chr6:26,234,212-26,234,987
(GRCh38/hg38)
Size:
776 bases
Orientation:
Minus strand

Previous Assembly
chr6:26,234,440-26,235,215
(GRCh37/hg19 by Entrez Gene)
Size:
776 bases
Orientation:
Minus strand

chr6:26,234,440-26,235,216
(GRCh37/hg19 by Ensembl)
Size:
777 bases
Orientation:
Minus strand

Genomic View for H1-3 Gene

Genes around H1-3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H1-3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H1-3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H1-3 Gene

Proteins for H1-3 Gene

  • Protein details for H1-3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P16402-H13_HUMAN
    Recommended name:
    Histone H1.3
    Protein Accession:
    P16402
    Secondary Accessions:
    • B2R751
    • Q2M2I2

    Protein attributes for H1-3 Gene

    Size:
    221 amino acids
    Molecular mass:
    22350 Da
    Quaternary structure:
    No Data Available

neXtProt entry for H1-3 Gene

Post-translational modifications for H1-3 Gene

  • H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter.
  • Citrullination at Arg-55 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H1-3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H1-3 Gene

Domains & Families for H1-3 Gene

Gene Families for H1-3 Gene

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

Protein Domains for H1-3 Gene

InterPro:
Blocks:
  • Histone H1/H5

Suggested Antigen Peptide Sequences for H1-3 Gene

GenScript: Design optimal peptide antigens:
  • Histone H1c (H13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P16402

UniProtKB/Swiss-Prot:

H13_HUMAN :
  • The C-terminal domain is required for high-affinity binding to chromatin.
  • Belongs to the histone H1/H5 family.
Domain:
  • The C-terminal domain is required for high-affinity binding to chromatin.
Family:
  • Belongs to the histone H1/H5 family.
genes like me logo Genes that share domains with H1-3: view

Function for H1-3 Gene

Molecular function for H1-3 Gene

UniProtKB/Swiss-Prot Function:
Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).

Phenotypes From GWAS Catalog for H1-3 Gene

Gene Ontology (GO) - Molecular Function for H1-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IBA 21873635
GO:0003723 RNA binding HDA 22681889
GO:0031490 chromatin DNA binding IDA 15911621
GO:0031492 nucleosomal DNA binding IBA 21873635
genes like me logo Genes that share ontologies with H1-3: view
genes like me logo Genes that share phenotypes with H1-3: view

Animal Models for H1-3 Gene

MGI Knock Outs for H1-3:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H1-3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for H1-3 Gene

Localization for H1-3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H1-3 Gene

Nucleus. Chromosome. Note=According to PubMed:15911621 more commonly found in euchromatin. According to PubMed:10997781 is associated with inactive chromatin.

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 H1-3 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for H1-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 19882353
GO:0000786 nucleosome IEA --
GO:0000791 euchromatin IBA,IDA 15911621
GO:0005634 nucleus IBA 21873635
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H1-3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H1-3 Gene

Pathways & Interactions for H1-3 Gene

genes like me logo Genes that share pathways with H1-3: view

Pathways by source for H1-3 Gene

2 GeneGo (Thomson Reuters) pathways for H1-3 Gene
  • Cell cycle Start of DNA replication in early S phase
  • Cell cycle_Chromosome condensation in prometaphase
2 Qiagen pathways for H1-3 Gene
  • Granzyme-A Pathway
  • PKA Signaling

Gene Ontology (GO) - Biological Process for H1-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IEA --
GO:0016584 nucleosome positioning IBA 21873635
GO:0030261 chromosome condensation IBA 21873635
GO:0031936 negative regulation of chromatin silencing IBA 21873635
GO:0045910 negative regulation of DNA recombination IBA 21873635
genes like me logo Genes that share ontologies with H1-3: view

No data available for SIGNOR curated interactions for H1-3 Gene

Drugs & Compounds for H1-3 Gene

No Compound Related Data Available

Transcripts for H1-3 Gene

mRNA/cDNA for H1-3 Gene

1 REFSEQ mRNAs :
3 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 H1-3

Alternative Splicing Database (ASD) splice patterns (SP) for H1-3 Gene

No ASD Table

Relevant External Links for H1-3 Gene

GeneLoc Exon Structure for
H1-3

Expression for H1-3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H1-3

SOURCE GeneReport for Unigene cluster for H1-3 Gene:

Hs.136857

Evidence on tissue expression from TISSUES for H1-3 Gene

  • Spleen(4.6)
  • Nervous system(4.5)
  • Lung(2.7)
  • Intestine(2.5)
  • Skin(2.4)
  • Blood(2.1)
  • Kidney(2.1)
  • Heart(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 H1-3 Gene

Orthologs for H1-3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H1-3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HIST1H1D 30
  • 99 (a)
OneToOne
LOC472227 29
  • 98.49 (n)
Cow
(Bos Taurus)
Mammalia HIST1H1E 30
  • 82 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC611113 29
  • 81.86 (n)
-- 30
  • 73 (a)
OneToMany
-- 30
  • 67 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Hist1h1d 29 30
  • 80.84 (n)
OneToOne
H1f3 16
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 80 (a)
ManyToMany
-- 30
  • 73 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 33 (a)
OneToMany
Chicken
(Gallus gallus)
Aves HIST1H111L 30
  • 71 (a)
ManyToMany
HIST1H111R 30
  • 70 (a)
ManyToMany
-- 30
  • 64 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii CU457819.3 30
  • 67 (a)
ManyToMany
CABZ01086354.1 30
  • 67 (a)
ManyToMany
zgc:163061 30 30
  • 66 (a)
ManyToMany
si:ch211-113a14.12 30
  • 66 (a)
ManyToMany
zgc:110425 30
  • 66 (a)
ManyToMany
zgc:153405 30
  • 66 (a)
ManyToMany
FP325123.1 30
  • 66 (a)
ManyToMany
si:dkey-261m9.12 30
  • 65 (a)
ManyToMany
si:ch211-113a14.24 30
  • 65 (a)
ManyToMany
si:ch211-113a14.18 30
  • 65 (a)
ManyToMany
histh1l 30
  • 65 (a)
ManyToMany
si:dkey-108k21.10 30
  • 64 (a)
ManyToMany
si:dkey-108k21.14 30
  • 63 (a)
ManyToMany
si:dkey-108k21.21 30
  • 59 (a)
ManyToMany
Species where no ortholog for H1-3 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)
  • 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)
  • Lizard (Anolis carolinensis)
  • 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)
  • 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 H1-3 Gene

ENSEMBL:
Gene Tree for H1-3 (if available)
TreeFam:
Gene Tree for H1-3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H1-3: view image
Alliance of Genome Resources:
Additional Orthologs for H1-3

Paralogs for H1-3 Gene

Paralogs for H1-3 Gene

genes like me logo Genes that share paralogs with H1-3: view

Variants for H1-3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H1-3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
916277 Likely Benign: not provided 26,234,880(-) T/C
NM_005320.3(H1-3):c.54A>G (p.Thr18=)
SYNONYMOUS
rs2050949 -- p.Glu75Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H1-3 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 H1-3 Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
nsv1021294 CNV loss 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for H1-3 Gene

Residual Variation Intolerance Score: 51.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.50; 71.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H1-3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H1-3
Leiden Open Variation Database (LOVD)
H1-3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H1-3 Gene

Disorders for H1-3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for H1-3 Gene - From: LNC and COP

Disorder Aliases PubMed IDs
ovarian cancer
  • ovarian cancer, somatic
- elite association - COSMIC cancer census association via MalaCards
Search H1-3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H1-3

genes like me logo Genes that share disorders with H1-3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H1-3 Gene

Publications for H1-3 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W … Doenecke D (Genomics 1991) 2 3 4
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  4. H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain. (PMID: 15911621) Th'ng JP … Hendzel MJ (The Journal of biological chemistry 2005) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for H1-3 Gene

Sources for H1-3 Gene