U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 3020, updated on 6-Oct-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
Try the new Gene table
Try the new Transcript table

Genomic context

See H3-3A in Genome Data Viewer
Location:
1q42.12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (226061831..226072019)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225249743..225259926)
RS_2024_09 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 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_2024_08

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)