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    H2BC4 H2B clustered histone 4 [ Homo sapiens (human) ]

    Gene ID: 8347, updated on 27-Nov-2024

    Summary

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    Official Symbol
    H2BC4provided by HGNC
    Official Full Name
    H2B clustered histone 4provided by HGNC
    Primary source
    HGNC:HGNC:4757
    See related
    Ensembl:ENSG00000180596 MIM:602847; AllianceGenome:HGNC:4757
    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
    H2B.1; H2B/l; H2BC6; H2BC7; H2BC8; H2BFL; H2BC10; HIST1H2BC; dJ221C16.3
    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. The protein has antibacterial and antifungal antimicrobial activity. The main transcript variant of this gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. This transcript variant lacks a polyA tail but instead contains a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Apr 2020]
    Orthologs
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    Genomic context

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    See H2BC4 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 (26113170..26123926, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25981318..25992074, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26113398..26124154, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:26103833-26104523 Neighboring gene H4 clustered histone 3 Neighboring gene H1.6 linker histone, cluster member Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26121574-26122260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26122261-26122945 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26123079-26124278 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:26124310-26125509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24192 Neighboring gene H2A clustered histone 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26156285-26157036 Neighboring gene H1.4 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. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Lyons SM, et al. Nucleic Acids Res, 2016 Nov 2. PMID 27402160, Free PMC Article
    2. Human spleen histone H2B. Isolation and amino acid sequence. Ohe Y, et al. J Biochem, 1979 Feb. PMID 422550
    3. The structural basis of modified nucleosome recognition by 53BP1. Wilson MD, et al. Nature, 2016 Aug 4. PMID 27462807
    4. Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Falk SJ, et al. Science, 2015 May 8. PMID 25954010, Free PMC Article
    5. Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity. Budziszewski GR, et al. Nucleic Acids Res, 2022 May 6. PMID 35390161, Free PMC Article

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone H2B antimicrobial peptides participate in the colonic defense against bacteria and fungi.
      Title: Antimicrobial peptides in the first line defence of human colon mucosa.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association meta-analysis for total serum bilirubin levels.
    EBI GWAS Catalog

    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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    Replication interactions

    Interaction Pubs
    Knockdown of histone cluster 1, H2bc (HIST1H2BC) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, histone cluster 1, H2bc, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    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

    Clone Names

    • MGC104246

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    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 antibacterial humoral response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to Gram-positive bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in innate immune response in mucosa IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nucleosome assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    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 NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    histone H2B type 1-C/E/F/G/I
    Names
    H2B histone family, member L
    histone 1, H2bc
    histone H2B.1 A
    histone H2B.l
    histone cluster 1 H2B family member c
    histone cluster 1, H2bc

    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_001381989.1 → NP_001368918.1  histone H2B type 1-C/E/F/G/I

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      U91328
      Consensus CDS
      CCDS4584.1
      UniProtKB/Swiss-Prot
      P02278, P62807, Q3B872, Q4VB69, Q93078, Q93080
      UniProtKB/TrEMBL
      B2R4S9, Q0D2M2
      Related
      ENSP00000321744.4, ENST00000314332.5
      Conserved Domains (1) summary
      smart00427
      Location:28 → 124
      H2B; Histone H2B

    2. NM_003526.3 → NP_003517.2  histone H2B type 1-C/E/F/G/I

      See identical proteins and their annotated locations for NP_003517.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      U91328
      Consensus CDS
      CCDS4584.1
      UniProtKB/Swiss-Prot
      P02278, P62807, Q3B872, Q4VB69, Q93078, Q93080
      UniProtKB/TrEMBL
      B2R4S9, Q0D2M2
      Related
      ENSP00000380180.1, ENST00000396984.2
      Conserved Domains (1) summary
      smart00427
      Location:28 → 124
      H2B; Histone H2B

    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
      26113170..26123926 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      25981318..25992074 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P62807.4 GenPept UniProtKB/Swiss-Prot:P62807

    Gene LinkOut

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

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