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Aliases for HIST1H3E Gene

Aliases for HIST1H3E Gene

  • Histone Cluster 1, H3e 2 3
  • H3FD 3 4 6
  • H3 Histone Family, Member D 2 3
  • Histone 1, H3e 2 3
  • Histone H3/D 3 4
  • H3.1 3 6
  • Histone H3.1 3
  • Histone H3/A 4
  • Histone H3/B 4
  • Histone H3/C 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/I 4
  • Histone H3/J 4
  • Histone H3/K 4
  • Histone H3/L 4
  • H3FC 4
  • H3FA 4
  • H3FB 4
  • H3FF 4
  • H3FH 4
  • H3FI 4
  • H3FJ 4
  • H3FK 4
  • H3FL 4
  • H3/D 3

External Ids for HIST1H3E Gene

Previous Symbols for HIST1H3E Gene

  • H3FD

Summaries for HIST1H3E Gene

Entrez Gene Summary for HIST1H3E 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 member of the histone H3 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, Jul 2008]

GeneCards Summary for HIST1H3E Gene

HIST1H3E (Histone Cluster 1, H3e) is a Protein Coding gene. Among its related pathways are Disease and ERK Signaling.

UniProtKB/Swiss-Prot for HIST1H3E 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 HIST1H3E Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3E Gene

Genomics for HIST1H3E Gene

Genomic Location for HIST1H3E Gene

26,225,155 bp from pter
26,225,616 bp from pter
462 bases
Plus strand

Genomic View for HIST1H3E Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H3E Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3E Gene

Regulatory Elements for HIST1H3E Gene

Proteins for HIST1H3E Gene

  • Protein details for HIST1H3E Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone H3.1
    Protein Accession:
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3E Gene

    136 amino acids
    Molecular mass:
    15404 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.
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2)

    Three dimensional structures from OCA and Proteopedia for HIST1H3E Gene

neXtProt entry for HIST1H3E Gene

Proteomics data for HIST1H3E Gene at MOPED

Post-translational modifications for HIST1H3E 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.
  • 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.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • 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.
  • 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 (PubMed:22483618).
  • 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.
  • Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). 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.
  • Phosphorylated at Thr-4 (H3T3ph) by GSG2/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 MLTK 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 Thr-12 (H3T11ph) by chromatin-associated CHEK1 regulates the transcription of cell cycle regulatory genes by modulating acetylation of Lys-10 (H3K9ac). Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys19, Lys24, Lys57, Lys65, Lys80, Lys116, and Lys123

Other Protein References for HIST1H3E Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3E Gene

Domains for HIST1H3E Gene

Gene Families for HIST1H3E Gene

  • HIST :Histones / Replication-dependent

Protein Domains for HIST1H3E Gene


  • Belongs to the histone H3 family.:
    • P68431
genes like me logo Genes that share domains with HIST1H3E: view

Function for HIST1H3E Gene

Molecular function for HIST1H3E 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

Gene Ontology (GO) - Molecular Function for HIST1H3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 10949293
GO:0042393 histone binding IPI 20498094
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H3E: view

Phenotypes for HIST1H3E Gene

GenomeRNAi human phenotypes for HIST1H3E:
genes like me logo Genes that share phenotypes with HIST1H3E: view

miRNA for HIST1H3E Gene

miRTarBase miRNAs that target HIST1H3E

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for HIST1H3E Gene

Localization for HIST1H3E Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H3E Gene

Nucleus. Chromosome.

Subcellular locations from

Jensen Localization Image for HIST1H3E Gene COMPARTMENTS Subcellular localization image for HIST1H3E gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2

Gene Ontology (GO) - Cellular Components for HIST1H3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000786 nucleosome IDA 21636898
GO:0000788 nuclear nucleosome IDA 20498094
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 21630459
genes like me logo Genes that share ontologies with HIST1H3E: view

Pathways for HIST1H3E Gene

genes like me logo Genes that share pathways with HIST1H3E: view

Gene Ontology (GO) - Biological Process for HIST1H3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
genes like me logo Genes that share ontologies with HIST1H3E: view

Transcripts for HIST1H3E Gene

mRNA/cDNA for HIST1H3E Gene

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

Unigene Clusters for HIST1H3E Gene

Histone cluster 1, H3e:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H3E Gene

No ASD Table

Relevant External Links for HIST1H3E Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIST1H3E Gene

mRNA expression in normal human tissues for HIST1H3E Gene

mRNA differential expression in normal tissues according to GTEx for HIST1H3E Gene

This gene is overexpressed in Heart - Left Ventricle (4.3).

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for HIST1H3E Gene

SOURCE GeneReport for Unigene cluster for HIST1H3E Gene Hs.443021

genes like me logo Genes that share expressions with HIST1H3E: view

Orthologs for HIST1H3E Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H3E Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC463171 36
  • 99.02 (n)
  • 100 (a)
(Bos Taurus)
Mammalia LOC523214 36
  • 87.5 (n)
  • 100 (a)
(Canis familiaris)
Mammalia LOC488306 36
  • 86.03 (n)
  • 100 (a)
(Mus musculus)
Mammalia Hist1h3e 16
Hist1h3h 36
  • 87.25 (n)
  • 100 (a)
(Rattus norvegicus)
Mammalia Hist1h2ail 36
  • 86.27 (n)
  • 100 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101732670 36
  • 82.6 (n)
  • 99.26 (a)
(Danio rerio)
Actinopterygii hist2h3c 36
  • 83.58 (n)
  • 99.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33836 36
  • 82.11 (n)
  • 99.26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G75600 36
  • 69.61 (n)
  • 92.65 (a)
(Oryza sativa)
Liliopsida Os03g0390600 36
  • 78.19 (n)
  • 96.32 (a)
Species with no ortholog for HIST1H3E:
  • 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIST1H3E Gene

Gene Tree for HIST1H3E (if available)
Gene Tree for HIST1H3E (if available)

Paralogs for HIST1H3E Gene

Selected SIMAP similar genes for HIST1H3E Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H3E: view

No data available for Paralogs for HIST1H3E Gene

Variants for HIST1H3E Gene

Sequence variations from dbSNP and Humsavar for HIST1H3E Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs811041 -- 26,225,804(+) TTTAG(C/G)TGGCT downstream-variant-500B
rs3823156 -- 26,225,187(+) AAATC(C/T)ACAGG reference, synonymous-codon
rs10214495 -- 26,223,380(+) CAAAC(C/G)GCCCA upstream-variant-2KB
rs34762445 -- 26,224,156(+) TTACA(-/G)GGGAA upstream-variant-2KB
rs55848726 -- 26,224,206(+) CATTC(C/T)TTAAG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3E Gene

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914
nsv883490 CNV Loss 21882294

Relevant External Links for HIST1H3E Gene

HapMap Linkage Disequilibrium report

Disorders for HIST1H3E Gene

Relevant External Links for HIST1H3E

Genetic Association Database (GAD)
genes like me logo Genes that share disorders with HIST1H3E: view

No data available for UniProtKB/Swiss-Prot for HIST1H3E Gene

Publications for HIST1H3E Gene

  1. 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
  2. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4
  3. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 3 4
  4. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W. … Doenecke D. (Hum. Genet. 1997) 3 4
  5. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. (PMID: 14718166) Tagami H. … Nakatani Y. (Cell 2004) 3 23

Products for HIST1H3E Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate HIST1H3E
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H3E
    • Block miRNA regulation of HIST1H3E using miScript Target Protectors

    Sources for HIST1H3E Gene

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