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

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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies.
Title: Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies.
Histone variant H3.3 promotes metastasis in alveolar rhabdomyosarcoma.
Title: Histone variant H3.3 promotes metastasis in alveolar rhabdomyosarcoma.
The clinicopathological features and prognosis of multifocal high-grade gliomas in adults with H3F3A mutation.
Title: The clinicopathological features and prognosis of multifocal high-grade gliomas in adults with H3F3A mutation.
Brain Abnormalities in Patients with Germline Variants in H3F3: Novel Imaging Findings and Neurologic Symptoms Beyond Somatic Variants and Brain Tumors.
Title: Brain Abnormalities in Patients with Germline Variants in H3F3: Novel Imaging Findings and Neurologic Symptoms Beyond Somatic Variants and Brain Tumors.
The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential.
Title: The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential.
Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.
Title: Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.
Reliability and Role of Mutation-specific H3F3A (Histone 3-3) G34W Immunohistochemistry to Differentiate Giant Cell Tumor of Bone From its Clinicoradiologic and Histologic Mimics: An Institutional Study.
Title: Reliability and Role of Mutation-specific H3F3A (Histone 3-3) G34W Immunohistochemistry to Differentiate Giant Cell Tumor of Bone From its Clinicoradiologic and Histologic Mimics: An Institutional Study.
Diagnostic Utility of Genetic and Immunohistochemical H3-3A Mutation Analysis in Giant Cell Tumour of Bone.
Title: Diagnostic Utility of Genetic and Immunohistochemical H3-3A Mutation Analysis in Giant Cell Tumour of Bone.
Gene of the month: H3F3A and H3F3B.
Title: Gene of the month: H3F3A and H3F3B.
The histone variant H3.3 regulates the transcription of the hepatitis B virus.
Title: The histone variant H3.3 regulates the transcription of the hepatitis B virus.

Submit: New GeneRIF Correction See all GeneRIFs (67)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Bryant-Li-Bhoj neurodevelopmental syndrome 1 MedGen: C5676905 OMIM: 619720 GeneReviews: Bryant-Li-Bhoj Neurodevelopmental Syndrome	Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

H3f3a (e-PCR), detects polymorphism
- UniSTS:525689

WI-6046 (e-PCR)
- UniSTS:73465

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleosomal DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables structural constituent of chromatin	IDA Inferred from Direct Assay more info	PubMed

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 more info	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 more info	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

Go to the top of the page Help

Preferred Names: histone H3.3

Names: H3 histone family member 3A; H3 histone, family 3A

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.