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    H3-3A H3.3 histone A [ Homo sapiens (human) ]

    Gene ID: 3020, updated on 7-Jul-2024

    Summary

    Official Symbol
    H3-3Aprovided by HGNC
    Official Full Name
    H3.3 histone Aprovided by HGNC
    Primary source
    HGNC:HGNC:4764
    See related
    Ensembl:ENSG00000163041 MIM:601128; AllianceGenome:HGNC:4764
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    H3F3; H3-3B; H3.3A; H3F3A; BRYLIB1
    Summary
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 595.8), appendix (RPKM 347.4) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See H3-3A in Genome Data Viewer
    Location:
    1q42.12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (226061831..226072019)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225249743..225259926)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (226249532..226259720)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2643 Neighboring gene SDE2 telomere maintenance homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2644 Neighboring gene H3-3A divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226249972-226250137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226270255-226271122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1872 Neighboring gene long intergenic non-protein coding RNA 1703 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226295966-226296160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226299196-226299703 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:226302781-226303585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2646 Neighboring gene Sharpr-MPRA regulatory region 5028 Neighboring gene NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 8-like

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of H3 histone, family 3A (H3F3A) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Tat stimulates NF-kappaB-inducing kinase IKKalpha translocation from the cytoplasm to the nucleus in monocytes, which leads to IKKalpha and CBP/p300 recruitment to the IL-10 promoter and histone H3 phosphorylation (Ser 10) and acetylation (Lys 14) PubMed
    tat HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC87782, MGC87783

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryo implantation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nucleosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleus organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in oocyte maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pericentric heterochromatin formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of centromere complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in single fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in subtelomeric heterochromatin formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in telomere organization TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Barr body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    part_of inner kinetochore IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    part_of nucleosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone H3.3
    Names
    H3 histone family member 3A
    H3 histone, family 3A

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_065173.1 RefSeqGene

      Range
      5010..14313
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1410

    mRNA and Protein(s)

    1. NM_001379043.1NP_001365972.1  histone H3.3

      Status: REVIEWED

      Source sequence(s)
      AL512343
      Consensus CDS
      CCDS1550.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Related
      ENSP00000355781.1, ENST00000366816.5
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional
    2. NM_001379045.1NP_001365974.1  histone H3.3

      Status: REVIEWED

      Source sequence(s)
      AL512343
      Consensus CDS
      CCDS1550.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional
    3. NM_001379046.1NP_001365975.1  histone H3.3

      Status: REVIEWED

      Source sequence(s)
      AL512343
      Consensus CDS
      CCDS1550.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional
    4. NM_001379047.1NP_001365976.1  histone H3.3

      Status: REVIEWED

      Source sequence(s)
      AL512343
      Consensus CDS
      CCDS1550.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional
    5. NM_002107.7NP_002098.1  histone H3.3

      See identical proteins and their annotated locations for NP_002098.1

      Status: REVIEWED

      Source sequence(s)
      AL512343
      Consensus CDS
      CCDS1550.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Related
      ENSP00000355780.3, ENST00000366815.10
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      226061831..226072019
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      225249743..225259926
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)