H3C4 H3 clustered histone 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: H3C4provided by HGNC
Official Full Name: H3 clustered histone 4provided by HGNC
Primary source: HGNC:HGNC:4767
See related: Ensembl:ENSG00000197409 MIM:602811; AllianceGenome:HGNC:4767
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/b; H3C1; H3C2; H3C3; H3C6; H3C7; H3C8; H3FB; H3C10; H3C11; H3C12; HIST1H3D
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 is intronless and encodes a replication-dependent histone that is a member of the histone H3 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]
Expression: Broad expression in bone marrow (RPKM 2.8), prostate (RPKM 1.5) and 14 other tissues See more
Orthologs: all
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Genomic context

Location:: 6p22.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (26196784..26199293, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (26065245..26067759, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (26197012..26199521, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Fucoxanthin may inhibit cervical cancer cell proliferation via downregulation of HIST1H3D.
Title: Fucoxanthin may inhibit cervical cancer cell proliferation via downregulation of HIST1H3D.
HIST1H3D is highly expressed in lung cancer cell lines and tissues, and may be important in cell proliferation, apoptosis and cell cycle progression, and is implicated as a potential therapeutic target for lung cancer.
Title: HIST1H3D: A promising therapeutic target for lung cancer.
HIST1H3D expression in the bone marrow, peripheral blood, and primary tumor of stage IV patients is higher than that in stage I patients.
Title: Contrasting expression patterns of histone mRNA and microRNA 760 in patients with gastric cancer.

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Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH77901 (e-PCR)
- UniSTS:56863

SGC33007 (e-PCR)
- UniSTS:41302

RH66549 (e-PCR)
- UniSTS:39368

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables cadherin binding	HDA more info	PubMed
enables protein 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	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	NAS Non-traceable Author Statement more info	PubMed
involved_in epigenetic regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_positive_effect gene expression	IDA Inferred from Direct Assay more info	PubMed
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 telomere organization	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
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
part_of nucleosome	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone H3.1

Names: H3 histone family, member B; histone 1, H3d; histone H3/b; histone cluster 1 H3 family member d; histone cluster 1, H3d

NCBI Reference Sequences (RefSeq)

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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)

NM_001376937.1 → NP_001363866.1 histone H3.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AL031777

Consensus CDS

CCDS4590.1

UniProtKB/Swiss-Prot

A0PJT7, A5PLR1, P02295, P02296, P16106, P68431, Q6ISV8, Q6NWP8, Q6NWP9, Q6NXU4, Q71DJ3, Q93081

UniProtKB/TrEMBL

A8K4Y7, B2R6Y1

Related

ENSP00000366999.2, ENST00000356476.3

Conserved Domains (1) summary

PTZ00018
Location:1 → 136

PTZ00018; histone H3; Provisional
NM_003530.4 → NP_003521.2 histone H3.1

See identical proteins and their annotated locations for NP_003521.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the longer transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

BC031333, DB242999

Consensus CDS

CCDS4590.1

UniProtKB/Swiss-Prot

A0PJT7, A5PLR1, P02295, P02296, P16106, P68431, Q6ISV8, Q6NWP8, Q6NWP9, Q6NXU4, Q71DJ3, Q93081

UniProtKB/TrEMBL

A8K4Y7, B2R6Y1

Conserved Domains (1) summary

PTZ00018
Location:1 → 136

PTZ00018; histone H3; Provisional