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

    Gene ID: 8351, updated on 27-Nov-2024

    Summary

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    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

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    See H3C4 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 (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_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24199 Neighboring gene H4 clustered histone 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:26196641-26197242 Neighboring gene H1.12 linker histone, cluster member, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:26197243-26197843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24203 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26199013-26200212 Neighboring gene H2A clustered histone 7 Neighboring gene H2B clustered histone 7 Neighboring gene ribosomal protein S10 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Fucoxanthin may inhibit cervical cancer cell proliferation via downregulation of HIST1H3D. Ye G, et al. J Int Med Res, 2020 Oct. PMID 33086884, Free PMC Article
    2. HIST1H3D: A promising therapeutic target for lung cancer. Rui Y, et al. Int J Oncol, 2017 Mar. PMID 28112369
    3. Contrasting expression patterns of histone mRNA and microRNA 760 in patients with gastric cancer. Iwaya T, et al. Clin Cancer Res, 2013 Dec 1. PMID 24097871
    4. Crystal structure of DPF3b in complex with an acetylated histone peptide. Li W, et al. J Struct Biol, 2016 Sep. PMID 27402533
    5. Structural basis for molecular recognition and presentation of histone H3 by WDR5. Schuetz A, et al. EMBO J, 2006 Sep 20. PMID 16946699, Free PMC Article

    See all (92) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    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

    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

    Potential readthrough

    Included gene: H2AC7

    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 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)

    1. 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

    2. 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

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      26065245..26067759 complement
      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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