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H3F3A Gene

protein-coding   GIFtS: 65
GCID: GC01P226249

H3 Histone, Family 3A


(Previous symbol: H3F3)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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   

Export aliases for H3F3A gene to outside databases

Previous GC identifers: GC01P224732 GC01P222067 GC01P222656 GC01P223225 GC01P222557 GC01P224316 GC01P196767


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. Diseases associated with H3F3A include primitive neuroectodermal tumor, and acute leukemia. An important paralog of this gene is HIST2H3C.

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


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_167186.2  
Regulatory elements:
   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 Chromatin IP Primers for H3F3A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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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
Developmental stage: Expressed throughout the cell cycle independently of DNA synthesis
Sequence caution: Sequence=CAH73371.1; Type=Erroneous gene model prediction;
Selected PDB 3D structures from and Proteopedia for H3F3A (see all 25):
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: 

  • 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 instability1
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription1
  • 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 promoters1
  • 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 replication1
  • 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 chromosomes1
  • Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination
    (By similarity)1
  • 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)1
  • 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 autosomes1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See H3F3A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002098.1  
    ENSEMBL proteins: 
     ENSP00000355781   ENSP00000355780   ENSP00000355779   ENSP00000355778  
    Reactome Protein details: P84243

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    Cloud-Clone Corp. CLIAs for H3F3A


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0005515protein 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/body  mortality/aging  normal  reproductive system 

    H3F3A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for H3F3A
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models 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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    hsa-mir-34a-5p (MIRT025401), hsa-mir-100-5p (MIRT048417)

    Block miRNA regulation of human, mouse, rat H3F3A using miScript Target Protectors
    Selected qRT-PCR 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
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    H33_HUMAN, P84243: Nucleus. Chromosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    extracellular4
    cytoskeleton2
    mitochondrion1

    Gene Ontology (GO): 4 cellular component terms:    About this table

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

    H3F3A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for H3F3A About   (see all 21)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1RNA Polymerase I Promoter Opening
    RNA Polymerase I Transcription0.78
    RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription0.73
    RNA Polymerase I Chain Elongation0.78
    Amyloids0.68
    RNA Polymerase I Promoter Clearance0.78
    Mitotic Prophase0.56
    RNA Polymerase I Promoter Opening0.78
    Systemic lupus erythematosus0.40
    2Packaging Of Telomere Ends
    Signal transduction Activin A signaling regulation0.40
    Histone modification0.31
    3Cellular Senescence
    Cellular Senescence0.81
    Oxidative Stress Induced Senescence0.64
    Cellular responses to stress0.81
    Senescence-Associated Secretory Phenotype (SASP)0.57
    4Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    M Phase0.62
    Cell Cycle0.90
    5Development NOTCH1 mediated pathway for NF KB activity modulation
    Development NOTCH1 mediated pathway for NF KB activity modulation0.50
    Transcription Sin3 and NuRD in transcription regulation0.35
    Development Notch Signaling Pathway0.50

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for H3F3A
        Notch Signaling Pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe 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


    Selected Reactome Pathways for H3F3A (see all 12)
        NoRC negatively regulates rRNA expression
    Meiotic recombination
    formation of the beta-catenin:TCF transactivating complex
    Amyloids
    Oxidative Stress Induced Senescence


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


    H3F3A for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for H3F3A
    Interactions:

        Search GeneGlobe Interaction Network for H3F3A

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

    Selected Interacting proteins for H3F3A (P842431, 2, 3 ENSP000003557784) via UniProtKB, MINT, STRING, and/or I2D (see all 475)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST4H4P628051, 3, ENSP000003507674EBI-120658,EBI-302023 I2D: score=23 STRING: ENSP00000350767
    HIST1H4BP628051, 3EBI-120658,EBI-302023 I2D: score=23 
    HIST1H4CP628051, 3EBI-120658,EBI-302023 I2D: score=23 
    HIST1H4DP628051, 3EBI-120658,EBI-302023 I2D: score=23 
    HIST1H4EP628051, 3EBI-120658,EBI-302023 I2D: score=23 
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

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

    H3F3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for H3F3A gene: 
    NM_002107.4  

    Unigene Cluster for H3F3A:

    H3 histone, family 3A
    Hs.533624  [show with all ESTs]
    Unigene Representative Sequence: BM907805
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000366816 ENST00000366815(uc001hpw.3) ENST00000366814(uc010pvl.2)
    ENST00000366813(uc021pjv.1)

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    Additional mRNA sequence: 

    AK291102.1 AK311905.1 BC013857.1 BC029405.1 BC038989.1 BC066901.1 BC067757.1 BC081560.1 
    BC081561.1 BC095447.1 M11354.1 NR_002315.1 

    Selected DOTS entries (see all 80):

    DT.95139642  DT.100695640  DT.100695654  DT.97864380  DT.100059951  DT.85101791  DT.95223619  DT.100695644 
    DT.120933375  DT.100046204  DT.100862784  DT.120933330  DT.120933449  DT.100695647  DT.100695645  DT.120933504 
    DT.121236364  DT.121461590  DT.100034237  DT.87018230  DT.95212117  DT.95378728  DT.100695642  DT.100695661 

    Selected AceView cDNA sequences (see all 1292):

    BP372328 H89230 CB306947 BU661508 CR594694 AW510960 CB215330 AI114639 
    BM044822 BI497423 CB135873 BM756666 BG163480 AW166433 AA961103 CB218921 
    AA075161 AI669540 D56631 BM468053 BM874552 CB129472 CB106860 CB106917 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    H3F3A expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 23) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Telencephalon
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    H3F3A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    H3F3A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.533624
        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)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for H3F3A gene from Selected species (see all 15)    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 LOC1008596291 histone H3.3-like 79.17(n)
    100(a)
      100859629  XM_003643474.2  XP_003643522.1 
    lizard
    (Anolis carolinensis)
    Reptilia H3F3A6
    H3 histone, family 3A
    100(a)
    1 ↔ 1
    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 LOC5650281 histone H3.2-like 79.66(n)
    97.06(a)
      565028  XM_688339.4  XP_693431.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta His3.3B3
    His3:CG338571
    chromatin assembly/disassembly DNA
    binding3
    His3:CG338571
    100(a)
    (best of 2)3
    79.17(n)1
    97.06(a)1
      37722311  NM_001032202.11  NP_001027373.11 
    worm
    (Caenorhabditis elegans)
    Secernentea his-713 Histone H3 99(a)
    (best of 4)
      X(8016259-8017394)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HHT26
    HHT16
    Histone H3, core histone protein required for chro...
    Histone H3, core histone protein required for chro...
    90(a)
    90(a)
    many ↔ many
    many ↔ many
    XIV(575640-576050) YNL031C
    II(256331-256741) YBR010W


    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)
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    Paralogs for H3F3A gene
    H3F3B1 2  HIST2H3C2  H3F3C2  HIST1H3A2  HIST2H3PS22  HIST1H3B2  HIST1H3J2  HIST1H3E2  
    HIST2H3D2  HIST1H3D2  HIST1H3H2  HIST3H32  HIST1H3F2  HIST1H3I2  HIST1H3G2  HIST1H3C2  
    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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for H3F3A (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing H3F3A
    DNA2.0 Custom Variant and Variant Library Synthesis for H3F3A

    (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

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    OMIM gene information: 601128    OMIM disorders: --

    17 diseases for H3F3A:    
    About MalaCards
    primitive neuroectodermal tumor    acute leukemia    retinoblastoma    non-hodgkin lymphoma
    hiv-1    systemic lupus erythematosus    astrocytoma    lupus erythematosus
    tonsillitis    hodgkin's lymphoma    alzheimer's disease    thyroiditis
    leukemia    malaria    cerebritis    prostatitis
    endotheliitis

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

    H3F3A for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    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)
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    PubMed articles for H3F3A gene, integrated from 10 sources (see all 122):
    (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. (Nucleic Acids Res. 1987)
    2. The human replacement histone H3.3B gene (H3F3B). (PubMed id 8586426)1, 2, 9 Albig W.... Doenecke D. (Genomics 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. (J. Biol. Chem. 2007)
    4. Organismal differences in post-translational modifications in histones H3 and H4. (PubMed id 17194708)1, 2 Garcia B.A.... Hunt D.F. (J. Biol. Chem. 2007)
    5. Histone H3.3 deposition at E2F-regulated genes is linked to transcription. (PubMed id 16258499)1, 2 Daury L.... Trouche D. (EMBO Rep. 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. (Mol. Endocrinol. 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. (J. Biol. Chem. 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. (J. Proteome Res. 2006)
    9. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 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. (J. Biol. Chem. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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

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    Entrez Gene: 3020 HGNC: 4764 AceView: H3F3A Ensembl:ENSG00000163041 euGenes: HUgn3020
    ECgene: H3F3A Kegg: 3020 H-InvDB: H3F3A

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    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

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    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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