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H3C6 H3 clustered histone 6 [ Homo sapiens (human) ]

Gene ID: 8353, updated on 28-Oct-2024

Summary

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Official Symbol
H3C6provided by HGNC
Official Full Name
H3 clustered histone 6provided by HGNC
Primary source
HGNC:HGNC:4769
See related
Ensembl:ENSG00000274750 MIM:602813; AllianceGenome:HGNC:4769
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
H3.1; H3/d; H3C1; H3C2; H3C3; H3C4; H3C7; H3C8; H3FD; H3C10; H3C11; H3C12; HIST1H3E
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]
Orthologs
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Genomic context

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See H3C6 in Genome Data Viewer
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 (26224178..26227473)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (26092650..26095946)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26224406..26227701)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:26216641-26217292 and GRCh37_chr6:26217293-26217944 Neighboring gene H2A clustered histone 8 Neighboring gene H3 clustered histone 5, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:26225373-26225989 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:26225990-26226605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:26234741-26235728 Neighboring gene H2A clustered histone 9, pseudogene Neighboring gene H1.3 linker histone, cluster member

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-wide analysis of histone H3 lysine 4 trimethylation in peripheral blood mononuclear cells of minimal change nephrotic syndrome patients. Zhang L, et al. Am J Nephrol, 2009. PMID 19797895
  2. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Zhang Y, et al. Nucleic Acids Res, 2010 Jul. PMID 20223770, Free PMC Article
  3. Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases. Lu C, et al. J Am Soc Mass Spectrom, 2021 Jun 2. PMID 33818074, Free PMC Article
  4. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Motallebipour M, et al. Genome Biol, 2009. PMID 19919681, Free PMC Article
  5. New histone incorporation marks sites of UV repair in human cells. Polo SE, et al. Cell, 2006 Nov 3. PMID 17081972

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases.
    Title: Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases.
  2. analysis of the binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells
    Title: Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
  3. there are significant alterations of H3K4me3 in minimal change nephrotic syndrome patients
    Title: Genome-wide analysis of histone H3 lysine 4 trimethylation in peripheral blood mononuclear cells of minimal change nephrotic syndrome patients.
  4. This protein has been found differentially expressed in the temporal lobe from patients with schizophrenia.
    Title: Alterations in oligodendrocyte proteins, calcium homeostasis and new potential markers in schizophrenia anterior temporal lobe are revealed by shotgun proteome analysis.
  5. analysis of histone posttranslational modifications on H3.1 and H3.3
    Title: PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables cadherin binding HDA 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 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in membrane HDA 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 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 D
histone 1, H3e
histone H3/d
histone cluster 1 H3 family member e
histone cluster 1, H3e

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)

  1. NM_001381999.1 → NP_001368928.1  histone H3.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AL031777
    Consensus CDS
    CCDS4596.1
    UniProtKB/Swiss-Prot
    A0PJT7, A5PLR1, P02295, P02296, P16106, P68431, Q6ISV8, Q6NWP8, Q6NWP9, Q6NXU4, Q71DJ3, Q93081
    UniProtKB/TrEMBL
    A8K4Y7, B2R6Y1
    Related
    ENSP00000489282.1, ENST00000634733.1
    Conserved Domains (1) summary
    PTZ00018
    Location:1 → 136
    PTZ00018; histone H3; Provisional

  2. NM_003532.3 → NP_003523.1  histone H3.1

    See identical proteins and their annotated locations for NP_003523.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) and variant 1 encode the same protein.
    Source sequence(s)
    AL031777
    Consensus CDS
    CCDS4596.1
    UniProtKB/Swiss-Prot
    A0PJT7, A5PLR1, P02295, P02296, P16106, P68431, Q6ISV8, Q6NWP8, Q6NWP9, Q6NXU4, Q71DJ3, Q93081
    UniProtKB/TrEMBL
    A8K4Y7, B2R6Y1
    Related
    ENSP00000482271.1, ENST00000614911.3
    Conserved Domains (1) summary
    PTZ00018
    Location:1 → 136
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    26224178..26227473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    26092650..26095946
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P68431.2 GenPept UniProtKB/Swiss-Prot:P68431

Gene LinkOut

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