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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

H3F3A Gene

protein-coding   GIFtS: 65
GCID: GC01P226249

H3 Histone, Family 3A


(Previous symbol: H3F3)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 4

Aliases
H3 Histone, Family 3A1 2
H3F31 2 3 5
H3.3A2 3
Histone H3.32
H3.3B3

External Ids:    HGNC: 47641   Entrez Gene: 30202   Ensembl: ENSG000001630417   OMIM: 6011285   UniProtKB: P842433   
ORGUL members:    fRNAdb10:FR174015      
H-InvDB12:HIT000101213    
NCBI13:D28384    
NONCODE14:n405475 n338541      
RNAdb15:HIV2288    

Export aliases for H3F3A gene to outside databases

Previous GC identifers: GC01P224732 GC01P222067 GC01P222656 GC01P223225 GC01P222557 GC01P224316 GC01P196767


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for H3F3A 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 contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded is a
replication-independent member of the histone H3 family. (provided by RefSeq, Jul 2008)

GeneCards Summary for H3F3A Gene: 
H3F3A (H3 histone, family 3A) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with H3F3A include retinoblastoma, and systemic lupus erythematosus, and among its related super-pathways are Signal transduction Activin A signaling regulation and Development NOTCH1-mediated pathway for NF-KB activity modulation. An important paralog of this gene is HIST2H3D.

UniProtKB/Swiss-Prot: H33_HUMAN, P84243
Function: Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes.
Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin
independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes,
suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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 H3F3A Gene

fRNAdb sequence ontology for H3F3A:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for H3F3A

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_167186.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the H3F3A gene promoter:
         AREB6   RP58   Sox5   AML1a   Nkx6-1   Sp1   Nkx2-5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidH3F3A promoter sequence
   Search SABiosciences Chromatin IP Primers for H3F3A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat H3F3A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q42.12   Ensembl cytogenetic band:  1q42.12   HGNC cytogenetic band: 1q42.12

H3F3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H3F3A gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P226249:  view genomic region     (about GC identifiers)

Start:
226,249,552 bp from pter      End:
226,259,703 bp from pter
Size:
10,152 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for H3F3A

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: H33_HUMAN, P84243 (See protein sequence)
Recommended Name: Histone H3.3  
Size: 136 amino acids; 15328 Da
Subunit: 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. Interacts with
HIRA, a chaperone required for its incorporation into nucleosomes
Subcellular location: Nucleus. Chromosome
Developmental stage: Expressed throughout the cell cycle independently of DNA synthesis
Sequence caution: Sequence=CAH73371.1; Type=Erroneous gene model prediction;
6/24 PDB 3D structures from and Proteopedia for H3F3A (see all 24):
2L43 (3D)        3ASK (3D)        3ASL (3D)        3AV2 (3D)        3JVK (3D)        3MUK (3D)    
Secondary accessions: P06351 P33155 Q5VV55 Q5VV56 Q66I33 Q9V3W4

Explore the universe of human proteins at neXtProt for H3F3A: NX_P84243

Explore proteomics data for H3F3A at MOPED 

Post-translational modifications:

  • UniProtKB: 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)
  • UniProtKB: Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription
  • UniProtKB: 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
  • UniProtKB: Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me),
    Lys-37 and Lys-80. 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), which are linked to gene repression, are underrepresented.
    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
  • UniProtKB: 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
    Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32
    (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes
  • UniProtKB: Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination
    (By similarity)
  • UniProtKB: 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)
  • UniProtKB: 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
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P84243

  • H3F3A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    H3F3A Protein Expression
    REFSEQ proteins: NP_002098.1  
    ENSEMBL proteins: 
     ENSP00000355781   ENSP00000355780   ENSP00000355779   ENSP00000355778  
    Reactome Protein details: P84243
    Human Recombinant Protein Products for H3F3A: 
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    Novus Biologicals H3F3A Proteins
    Novus Biologicals H3F3A Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for H3F3A 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000786nucleosome ----
    GO:0005576extracellular region ----
    GO:0005634nucleus ----
    GO:0005654nucleoplasm ----

    H3F3A for ontologies           About GeneDecksing



    H3F3A Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of H3F3A
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    Abcam antibodies for H3F3A
    Cloud-Clone Corp. Antibodies for H3F3A 
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    LSBio Antibodies in human, mouse, rat for H3F3A 

    Assay Products for H3F3A: 
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    R&D Systems ELISAs for H3F3A (Histone H3)         (see all)
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    Browse Enzo Life Sciences for kits & assays
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RIH: Histones / Replication-independent

    3 InterPro protein domains:
     IPR000164 Histone_H3
     IPR009072 Histone-fold
     IPR007125 Histone_core_D

    Graphical View of Domain Structure for InterPro Entry P84243

    ProtoNet protein and cluster: P84243

    UniProtKB/Swiss-Prot: H33_HUMAN, P84243
    Similarity: Belongs to the histone H3 family


    H3F3A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: H33_HUMAN, P84243
    Function: Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes.
    Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin
    independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes,
    suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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

         Genatlas biochemistry entry for H3F3A:
    histone family 3,replacement subtype,replication independent protein,species H3.3A

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0046982protein heterodimerization activity ----
         
    H3F3A for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for H3F3A:
     Decreased p24 protein expressi 

         5 MGI mutant phenotypes (inferred from 3 alleles(MGI details for H3f3a):
     behavior/neurological  growth/size  mortality/aging  normal  reproductive system 

    H3F3A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for H3F3A 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for H3F3A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for H3F3A 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for H3F3A 

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat H3F3A
    8/37 QIAGEN miScript miRNA Assays for microRNAs that regulate H3F3A (see all 37):
    hsa-miR-21* hsa-miR-549 hsa-miR-142-5p hsa-miR-548l hsa-miR-105 hsa-miR-155 hsa-miR-3148 hsa-miR-192*
    SwitchGear 3'UTR luciferase reporter plasmidH3F3A 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Gene Editing
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    Clone
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for H3F3A About   (see all 14)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Signal transduction Activin A signaling regulation
    Signal transduction Activin A signaling regulation0.31
    Histone modification0.31
    2Development NOTCH1-mediated pathway for NF-KB activity modulation
    Development NOTCH1-mediated pathway for NF-KB activity modulation0.88
    Transcription Sin3 and NuRD in transcription regulation0.35
    Development Notch Signaling Pathway0.54
    3UVA-Induced MAPK Signaling
    UVB-Induced MAPK Signaling0.38
    UVA-Induced MAPK Signaling0.38
    4Alcoholism
    Alcoholism0.34
    Systemic lupus erythematosus0.34
    5Rho Family GTPases
    ERK Signaling0.61

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5/6 EMD Millipore Pathways for H3F3A (see all 6)
        Development Notch Signaling Pathway
    Transcription Sin3 and NuRD in transcription regulation
    Histone modification
    Development NOTCH1-mediated pathway for NF-KB activity modulation
    Cell cycle Chromosome condensation in prometaphase

    1 R&D Systems Pathway for H3F3A
        Notch Signaling Pathways

    5/8 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for H3F3A (see all 8)
        Nuclear Receptor Activation by Vitamin-A
    PKA Signaling
    UVB-Induced MAPK Signaling
    Interferon Pathway
    Crosstalk Between CARM1 and ESRs

    5 GeneGo (Thomson Reuters) Pathways for H3F3A
        Cell cycle Chromosome condensation in prometaphase
    Signal transduction Activin A signaling regulation
    Development NOTCH1-mediated pathway for NF-KB activity modulation
    Transcription Sin3 and NuRD in transcription regulation
    Development Notch Signaling Pathway

    1 BioSystems Pathway for H3F3A
        Gastric cancer network 1

    5/6        Reactome Pathways for H3F3A (see all 6)
        Amyloids
    Hemostasis
    Factors involved in megakaryocyte development and platelet production
    Meiosis
    Meiotic Recombination


    3         Kegg Pathways  (Kegg details for H3F3A):
        Alcoholism
    Transcriptional misregulation in cancer
    Systemic lupus erythematosus


    H3F3A for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for H3F3A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/312 Interacting proteins for H3F3A (P842432, 3 ENSP000003557784) via UniProtKB, MINT, STRING, and/or I2D (see all 312)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4FP628053, ENSP000003669744I2D: score=23 STRING: ENSP00000366974
    HIST1H4AP628053, ENSP000003529804I2D: score=23 STRING: ENSP00000352980
    HIST1H4BP628053I2D: score=23 
    HIST1H4CP628053I2D: score=23 
    HIST1H4DP628053I2D: score=23 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006334nucleosome assembly ----
    GO:0007420brain development ----
    GO:0007596blood coagulation ----
    GO:0009725response to hormone stimulus ----

    H3F3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    EMD Millipore small molecules for H3F3A:
    Small Molecule - inhibitor
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for H3F3A (H33)

    Search CenterWatch for drugs/clinical trials and news about H3F3A / H33

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    1 fRNAdb Secondary structure:


    REFSEQ mRNAs for H3F3A gene: 
    NM_002107.4  

    Unigene Clusters for H3F3A:

    H3 histone, family 3A
    Hs.533624  [show with all ESTs], Hs.726012  [show with all ESTs]
    Unigene Representative Sequences: BM907805, BQ214023
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000366816 ENST00000366815(uc001hpw.3) ENST00000366814(uc010pvl.2)
    ENST00000366813(uc021pjv.1)
    miRNA
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    8/37 QIAGEN miScript miRNA Assays for microRNAs that regulate H3F3A (see all 37):
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    Additional mRNA sequence: AK293541.1 

    24/92 DOTS entries (see all 92):

    DT.95139642  DT.100695640  DT.100695654  DT.97864380  DT.100059951  DT.85101791  DT.100695644  DT.95223619 
    DT.120933375  DT.100046204  DT.120933330  DT.100862784  DT.87018230  DT.120933449  DT.121236364  DT.100034237 
    DT.100695647  DT.121461590  DT.120933504  DT.95378728  DT.100695645  DT.120782523  DT.91772344  DT.95212117 

    24/1292 AceView cDNA sequences (see all 1292):

    CD521299 NM_002107 H89123 BM272800 BM541395 AI492731 BU077579 AI540091 
    H88525 AA328608 AA327928 AA329127 CB136710 AA989136 CB129484 AI366878 
    BC029405 BI494120 BM770263 CA866060 CB135873 BM756666 BG163480 AW166433 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    H3F3A expression in normal human tissues (normalized intensities)      H3F3A embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTTTAATGT
    H3F3A Expression
    About this image


    H3F3A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/37 selected tissues (see all 37) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Uterus
             uterus, post-menopause ; glandular cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; peripheral nerve/ganglion   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex

    See H3F3A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for H3F3A

    SOURCE GeneReport for Unigene clusters: Hs.533624 Hs.726012
        SABiosciences Custom PCR Arrays for H3F3A
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H3F3A

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for H3F3A gene from 10/18 species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia H3f3a1 , 5 H3 histone, family 3A1, 5 96.08(n)1
    100(a)1
      1 (84.46 cM)5
    150781  NM_008210.41  NP_032236.11 
     1808008325 
    chicken
    (Gallus gallus)
    Aves H3F3C1 H3 histone, family 3C 87.5(n)
    99.26(a)
      427887  NM_001031482.1  NP_001026653.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Histone H3
    100(a)
    100(a)
    1 ↔ many
    1 ↔ many
    1(251560463-251571616)
    2(113659975-113666965)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.80342 Xenopus laevis cDNA clone MGC52829 IMAGE4884642, complete more 90.07(n)    BC042309.1 
    zebrafish
    (Danio rerio)
    Actinopterygii h3f3a1 H3 histone, family 3A 77.45(n)
    99.26(a)
      406269  NM_212996.1  NP_998161.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta His3.3B3 chromatin assembly/disassembly DNA
    binding
    100(a)
    (best of 2)
        --
    worm
    (Caenorhabditis elegans)
    Secernentea his-713
    his-741
    Histone H33
    Protein HIS-741
    99(a)
    (best of 4)3
    73.77(n)1
    93.38(a)1
      X(8016259-8017394)3
    1797341  NM_073763.31  NP_506164.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HHT16
    HHT26
    Histone H3, core histone protein required for chro...
    Histone H3, core histone protein required for chro...
    90(a)
    90(a)
    many ↔ many
    many ↔ many
    II(256331-256741)
    XIV(575640-576050)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G092001 histone H3 72.79(n)
    94.85(a)
      837440  NM_100790.2  NP_563838.1 
    rice
    (Oryza sativa)
    Liliopsida Os06g01595011 hypothetical protein 74.75(n)
    94.85(a)
      9269345  NM_001187682.1  NP_001174611.1 


    ENSEMBL Gene Tree for H3F3A (if available)
    TreeFam Gene Tree for H3F3A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for H3F3A gene
    H3F3B1 2  HIST2H3D2  HIST1H3D2  HIST2H3C2  H3F3C2  HIST1H3H2  HIST1H3A2  HIST3H32  
    HIST1H3F2  HIST1H3G2  HIST1H3I2  HIST1H3B2  HIST1H3C2  HIST1H3J2  HIST1H3E2  HIST2H3A2  
    18 SIMAP similar genes for H3F3A using alignment to 2 protein entries:     H33_HUMAN (see all proteins):
    HIST1H3A    HIST1H3B    HIST1H3C    HIST1H3D    HIST1H3E    HIST1H3F
    HIST1H3G    HIST1H3H    HIST1H3I    HIST1H3J    HIST2H3A    HIST2H3C
    HIST2H3D    HIST3H3    H3F3C    HIST2H3PS2    H3F3B    CENPA

    H3F3A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for H3F3A
    PGOHUM00000251091


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/200 SNPs in H3F3A are shown (see all 200)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs797169521,2
    F--226248593(+) CATAAT/CTACTC 1 -- us2k11Minor allele frequency- C:0.03WA 118
    rs759441341,2
    C,F--226248642(+) TAAAGC/GCAAGA 1 -- us2k12Minor allele frequency- G:0.06NA EA 240
    rs1405468901,2
    C--226248728(+) GCATT-/TAAC  
            
    TAATG
    1 -- us2k10--------
    rs1385435481,2
    --226248777(+) ATTTCA/GGTTTC 1 -- us2k10--------
    rs1159206451,2
    F--226248816(+) TAACTC/AATCTT 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1415071781,2
    --226249049(+) TATCTG/TATTTC 1 -- us2k10--------
    rs1508031631,2
    --226249102(+) GTGAGA/CTCTTC 1 -- us2k10--------
    rs1412787391,2
    C--226249215(+) TGAAG-/CCGTCA 1 -- us2k10--------
    rs1495121041,2
    --226249250(+) GTTCCA/CAAGCC 1 -- us2k10--------
    rs1162719131,2
    C,F--226249422(+) GACTAT/CCTATA 1 -- us2k11Minor allele frequency- C:0.03WA 118

    HapMap Linkage Disequilibrium report for H3F3A (226249552 - 226259703 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for H3F3A:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv873232CNV Gain21882294
    nsv832747CNV Gain17160897

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 601128OMIM information: 115665 116600 121800 155600 211420 600975 605225 605606 606788 606852 606928 607317 607671 608446 608543 608553 608995 601058    
    6 diseases for H3F3A:    About MalaCards
    retinoblastoma    systemic lupus erythematosus    lupus erythematosus    glioblastoma
    gastric cancer    alzheimer's disease

    2 diseases from the University of Copenhagen DISEASES database for H3F3A:
    Leukemia     Retinoblastoma

    H3F3A for disorders           About GeneDecksing

    Genetic Association Database (GAD): H3F3A
    Human Genome Epidemiology (HuGE) Navigator: H3F3A (1 document)

    Export disorders for H3F3A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for H3F3A gene, integrated from 9 sources (see all 117):
    (articles sorted by number of sources associating them with H3F3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family. (PubMed id 3031613)1, 2, 3 Wells D.... Kedes L. (1987)
    2. The human replacement histone H3.3B gene (H3F3B). (PubMed id 8586426)1, 2, 9 Albig W.... Doenecke D. (1995)
    3. Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. (PubMed id 17189264)1, 2 Morris S.A.... Strahl B.D. (2007)
    4. Organismal differences in post-translational modifications in histones H3 and H4. (PubMed id 17194708)1, 2 Garcia B.A.... Hunt D.F. (2007)
    5. Histone H3.3 deposition at E2F-regulated genes is linked to transcription. (PubMed id 16258499)1, 2 Daury L.... Trouche D. (2006)
    6. Coactivator-associated arginine methyltransferase-1 enhances nuclear factor-kappaB-mediated gene transcription through methylation of histone H3 at arginine 17. (PubMed id 16497732)1, 2 Miao F.... Natarajan R. (2006)
    7. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. (PubMed id 16267050)1, 2 Hake S.B.... Hunt D.F. (2006)
    8. Mass spectrometric characterization of human histone H3: a bird's eye view. (PubMed id 16457588)1, 2 Thomas C.E.... Mizzen C.A. (2006)
    9. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    10. Phosphorylation of Ser28 in histone H3 mediated by mixed lineage kinase-like mitogen-activated protein triple kinase alpha. (PubMed id 15684425)1, 2 Choi H.S.... Dong Z. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3020 HGNC: 4764 AceView: H3F3A Ensembl:ENSG00000163041 euGenes: HUgn3020
    ECgene: H3F3A Kegg: 3020 H-InvDB: H3F3A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for H3F3A Pharmacogenomics, SNPs, Pathways
    Wikipedia http://en.wikipedia.org/wiki/Histone_H3

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for H3F3A gene:
    Search GeneIP for patents involving H3F3A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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