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Aliases for HIST1H3B Gene

Aliases for HIST1H3B Gene

  • Histone Cluster 1, H3b 2 3 5
  • H3 Histone Family, Member L 2 3
  • Histone 1, H3b 2 3
  • Histone H3/L 3 4
  • H3FL 3 4
  • HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J 4
  • Histone H3/A 4
  • Histone H3/B 4
  • Histone H3/C 4
  • Histone H3/D 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/I 4
  • Histone H3/J 4
  • Histone H3/K 4
  • H3FA 4
  • H3FB 4
  • H3FC 4
  • H3FD 4
  • H3FF 4
  • H3FH 4
  • H3FI 4
  • H3FJ 4
  • H3FK 4
  • H3/L 3

External Ids for HIST1H3B Gene

Previous HGNC Symbols for HIST1H3B Gene

  • H3FL

Previous GeneCards Identifiers for HIST1H3B Gene

  • GC06M026089
  • GC06M026139
  • GC06M025974

Summaries for HIST1H3B Gene

Entrez Gene Summary for HIST1H3B 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 H3 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 HIST1H3B Gene

HIST1H3B (Histone Cluster 1, H3b) is a Protein Coding gene. Among its related pathways are Platelet activation, signaling and aggregation and Gene Expression. GO annotations related to this gene include protein heterodimerization activity and histone binding. An important paralog of this gene is HIST2H3D.

UniProtKB/Swiss-Prot for HIST1H3B 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 HIST1H3B Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3B Gene

Genomics for HIST1H3B Gene

Regulatory Elements for HIST1H3B Gene

Promoters for HIST1H3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HIST1H3B on UCSC Golden Path with GeneCards custom track

Genomic Location for HIST1H3B Gene

Chromosome:
6
Start:
26,031,589 bp from pter
End:
26,032,060 bp from pter
Size:
472 bases
Orientation:
Minus strand

Genomic View for HIST1H3B Gene

Genes around HIST1H3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3B Gene

Proteins for HIST1H3B Gene

  • Protein details for HIST1H3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P68431-H31_HUMAN
    Recommended name:
    Histone H3.1
    Protein Accession:
    P68431
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3B Gene

    Size:
    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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    Miscellaneous:
    • 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 HIST1H3B Gene

neXtProt entry for HIST1H3B Gene

Proteomics data for HIST1H3B Gene at MOPED

Post-translational modifications for HIST1H3B 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.
  • Ubiquitination at Lys 116
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H3B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3B Gene

Domains & Families for HIST1H3B Gene

Gene Families for HIST1H3B Gene

Protein Domains for HIST1H3B Gene

Graphical View of Domain Structure for InterPro Entry

P68431

UniProtKB/Swiss-Prot:

H31_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with HIST1H3B: view

No data available for Suggested Antigen Peptide Sequences for HIST1H3B Gene

Function for HIST1H3B Gene

Molecular function for HIST1H3B 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.
genes like me logo Genes that share phenotypes with HIST1H3B: view

Animal Model Products

miRNA for HIST1H3B Gene

miRNA Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H3B Gene

Localization for HIST1H3B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HIST1H3B Gene COMPARTMENTS Subcellular localization image for HIST1H3B gene
Compartment Confidence
extracellular 5
nucleus 5

Gene Ontology (GO) - Cellular Components for HIST1H3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
genes like me logo Genes that share ontologies with HIST1H3B: view

Pathways & Interactions for HIST1H3B Gene

SuperPathways for HIST1H3B Gene

Superpath Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence
3 Mitotic Prophase
4 Cell Cycle, Mitotic
.61
5 Chromatin organization
genes like me logo Genes that share pathways with HIST1H3B: view

Pathways by source for HIST1H3B Gene

Gene Ontology (GO) - Biological Process for HIST1H3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IMP 25615412
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
GO:0031047 gene silencing by RNA TAS --
GO:0044267 cellular protein metabolic process TAS --
GO:0045814 negative regulation of gene expression, epigenetic TAS --
genes like me logo Genes that share ontologies with HIST1H3B: view

No data available for SIGNOR curated interactions for HIST1H3B Gene

Drugs & Compounds for HIST1H3B Gene

No Compound Related Data Available

Transcripts for HIST1H3B Gene

mRNA/cDNA for HIST1H3B Gene

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

Unigene Clusters for HIST1H3B Gene

Histone cluster 1, H3b:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H3B Gene

No ASD Table

Relevant External Links for HIST1H3B Gene

GeneLoc Exon Structure for
HIST1H3B
ECgene alternative splicing isoforms for
HIST1H3B

Expression for HIST1H3B Gene

mRNA expression in normal human tissues for HIST1H3B Gene

mRNA differential expression in normal tissues according to GTEx for HIST1H3B Gene

This gene is overexpressed in Whole Blood (x10.7) and Testis (x6.2).

Protein differential expression in normal tissues from HIPED for HIST1H3B Gene

This gene is overexpressed in Heart (41.5), Urine (13.4), and Cervix (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for HIST1H3B Gene



SOURCE GeneReport for Unigene cluster for HIST1H3B Gene Hs.533292

genes like me logo Genes that share expression patterns with HIST1H3B: view

Protein tissue co-expression partners for HIST1H3B Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for HIST1H3B Gene

Orthologs for HIST1H3B Gene

This gene was present in the common ancestor of animals.

Orthologs for HIST1H3B Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Hist2h3b 35
  • 83.58 (n)
  • 99.26 (a)
Hist2h3b 16
chimpanzee
(Pan troglodytes)
Mammalia LOC101057734 35
  • 76.96 (n)
  • 93.38 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493036 35
  • 81.37 (n)
  • 99.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG31613 35
  • 79.41 (n)
  • 99.26 (a)
Species with no ortholog for HIST1H3B:
  • 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)
  • cow (Bos Taurus)
  • 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)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HIST1H3B Gene

ENSEMBL:
Gene Tree for HIST1H3B (if available)
TreeFam:
Gene Tree for HIST1H3B (if available)

Paralogs for HIST1H3B Gene

(9) SIMAP similar genes for HIST1H3B Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H3B: view

Variants for HIST1H3B Gene

Sequence variations from dbSNP and Humsavar for HIST1H3B Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs2213284 -- 26,031,640(-) AAAGT(C/T)ACTTT utr-variant-3-prime
rs2213285 -- 26,031,326(-) ATCTG(C/G/T)TAAGT downstream-variant-500B
rs3842707 -- 26,031,633(-) CTTTT(-/T)CATCA utr-variant-3-prime
rs10484434 -- 26,031,385(+) AGCTA(A/G)AGGCC downstream-variant-500B
rs10484435 -- 26,031,583(+) TTCGT(G/T)GGAAT downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3B Gene

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914
nsv509122 CNV Insertion 20534489

Variation tolerance for HIST1H3B Gene

Residual Variation Intolerance Score: 20.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.13; 2.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST1H3B Gene

HapMap Linkage Disequilibrium report
HIST1H3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H3B Gene

Disorders for HIST1H3B Gene

Relevant External Links for HIST1H3B

Genetic Association Database (GAD)
HIST1H3B
Human Genome Epidemiology (HuGE) Navigator
HIST1H3B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H3B

No disorders were found for HIST1H3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H3B Gene

Publications for HIST1H3B Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 67
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 3
  3. The primary structure and expression of four cloned human histone genes. (PMID: 6647026) Zhong R. … Heintz N. (Nucleic Acids Res. 1983) 2 3
  4. Human tNASP promotes in vitro nucleosome assembly with histone H3.3. (PMID: 25615412) Kato D. … Kurumizaka H. (Biochemistry 2015) 3
  5. Molecular analysis of diffuse intrinsic brainstem gliomas in adults. (PMID: 24242757) Reyes-Botero G. … Sanson M. (J. Neurooncol. 2014) 3

Products for HIST1H3B Gene

Sources for HIST1H3B Gene

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