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

Gene ID: 8351, updated on 7-Jun-2020

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
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

Genomic context

See H3C4 in Genome Data Viewer
Location:
6p22.2
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (26196784..26199293, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26196982..26199521, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H4 clustered histone 4 Neighboring gene H1.12 linker histone, cluster member pseudogene Neighboring gene H2A clustered histone 7 Neighboring gene H2B clustered histone 7 Neighboring gene ribosomal protein S10 pseudogene 1

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

Phenotypes

NHGRI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: H2AC7

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
cadherin binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA replication-dependent nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
blood coagulation TAS
Traceable Author Statement
more info
 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
chromatin organization TAS
Traceable Author Statement
more info
 
chromatin silencing at rDNA TAS
Traceable Author Statement
more info
 
interleukin-7-mediated signaling pathway TAS
Traceable Author Statement
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene silencing IDA
Inferred from Direct Assay
more info
PubMed 
regulation of gene silencing by miRNA TAS
Traceable Author Statement
more info
 
regulation of megakaryocyte differentiation TAS
Traceable Author Statement
more info
 
telomere organization TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear nucleosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleus HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001376937.1NP_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
    Related
    ENSP00000366999.1, ENST00000356476.2
  2. NM_003530.4NP_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
    P68431
    Conserved Domains (1) summary
    PTZ00018
    Location:1136
    PTZ00018; histone H3; Provisional

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    26196784..26199293 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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