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

    Gene ID: 8353, updated on 10-Dec-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
    all
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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)

    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

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

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