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

    Gene ID: 3021, updated on 10-Dec-2024

    Summary

    Official Symbol
    H3-3Bprovided by HGNC
    Official Full Name
    H3.3 histone Bprovided by HGNC
    Primary source
    HGNC:HGNC:4765
    See related
    Ensembl:ENSG00000132475 MIM:601058; AllianceGenome:HGNC:4765
    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
    H3-3A; H3.3B; H3F3B; BRYLIB2
    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 by this gene is a replication-independent histone that is a member of the histone H3 family. Pseudogenes of this gene have been identified on the X chromosome, and on chromosomes 5, 13 and 17. [provided by RefSeq, Oct 2015]
    Expression
    Broad expression in bone marrow (RPKM 868.3), ovary (RPKM 358.6) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See H3-3B in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75776434..75779779, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76669660..76678707, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73772515..73775860, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SAP30 binding protein Neighboring gene SAP30BP antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684215-73684716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684717-73685216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73693087-73693798 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:73695788-73696987 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73702471-73703670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717282-73717820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717821-73718359 Neighboring gene ITGB4 intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73724533-73725033 Neighboring gene integrin subunit beta 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73749848-73750621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754136-73754662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754663-73755189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8980 Neighboring gene galactokinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73769871-73770371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12776 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73774948-73775552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12777 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73780981-73781559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73781560-73782137 Neighboring gene microRNA 4738 Neighboring gene unk zinc finger Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73810697-73811198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73811199-73811698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73812483-73812984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73812985-73813484

    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

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, H3 histone, family 3B (H3F3B), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    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

    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 3B
    H3 histone, family 3B (H3.3B)

    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.

    mRNA and Protein(s)

    1. NM_005324.5NP_005315.1  histone H3.3

      See identical proteins and their annotated locations for NP_005315.1

      Status: REVIEWED

      Source sequence(s)
      AC087289
      Consensus CDS
      CCDS11729.1
      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1
      Related
      ENSP00000254810.3, ENST00000254810.8
      Conserved Domains (1) summary
      PTZ00018
      Location:1136
      PTZ00018; histone H3; Provisional

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      75776434..75779779 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      76669660..76678707 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315890.1XP_054171865.1  histone H3.3 isoform X1

      UniProtKB/Swiss-Prot
      P06351, P33155, P84243, Q5VV55, Q5VV56, Q66I33, Q9V3W4
      UniProtKB/TrEMBL
      A0A024R3S0, A8K4Y7, B2R4P9, B2R6Y1