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    H2BC5 H2B clustered histone 5 [ Homo sapiens (human) ]

    Gene ID: 3017, updated on 3-Apr-2024

    Summary

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    Official Symbol
    H2BC5provided by HGNC
    Official Full Name
    H2B clustered histone 5provided by HGNC
    Primary source
    HGNC:HGNC:4747
    See related
    Ensembl:ENSG00000158373 MIM:602799; AllianceGenome:HGNC:4747
    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/a; H2B/b; H2B/g; H2B/h; H2B/k; H2B/l; H2BFA; H2BFB; H2BFG; H2BFH; H2BFK; H2BFL; H2B.1B; HIRIP2; HIST1H2BC; HIST1H2BD; HIST1H2BE; HIST1H2BF; HIST1H2BG; HIST1H2BI; dJ221C16.6
    Summary
    Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Two transcripts that encode the same protein have been identified for this gene, which is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]
    Expression
    Broad expression in prostate (RPKM 17.6), kidney (RPKM 8.8) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    6p22.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (26158121..26171349)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (26026257..26039486)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26158349..26171577)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes 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 ATAC-STARR-seq lymphoblastoid silent region 17001 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26157790-26158541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24195 Neighboring gene Sharpr-MPRA regulatory region 13869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:26160799-26161550 Neighboring gene H2BC6 antisense RNA 1 Neighboring gene H1.4 linker histone, cluster member Neighboring gene LARP1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:26172075-26172967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24196 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26183023-26183752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24198 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26187941-26188566 Neighboring gene H2B clustered histone 6 Neighboring gene H4 clustered histone 4

    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. Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function. Patankar A, et al. Clin Epigenetics, 2021 May 1. PMID 33933143, Free PMC Article
    2. Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. Valencia-Sánchez MI, et al. Mol Cell, 2019 Jun 6. PMID 30981630, Free PMC Article
    3. Gene-specific characterization of human histone H2B by electron capture dissociation. Siuti N, et al. J Proteome Res, 2006 Feb. PMID 16457587
    4. Core histones and HIRIP3, a novel histone-binding protein, directly interact with WD repeat protein HIRA. Lorain S, et al. Mol Cell Biol, 1998 Sep. PMID 9710638, Free PMC Article
    5. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. Albig W, et al. Genomics, 1991 Aug. PMID 1916825

    See all (77) 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

    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
    Rev rev HIV-1 Rev interacting protein, histone cluster 1, H2bd, 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC90432

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    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
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of nucleosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone H2B type 1-D
    Names
    H2B histone family, member B
    HIRA-interacting protein 2
    Histone H2B type 1-C/E/F/G/I
    Histone H2B.1 A
    Histone H2B.a
    Histone H2B.g
    Histone H2B.h
    Histone H2B.k
    Histone H2B.l
    histone 1, H2bd
    histone H2B.1 B
    histone H2B.b
    histone cluster 1 H2B family member d
    histone cluster 1, H2bd

    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_021063.4 → NP_066407.1  histone H2B type 1-D

      See identical proteins and their annotated locations for NP_066407.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains a palindromic termination sequence instead of a polyA signal and tail. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL353759
      Consensus CDS
      CCDS4587.1
      UniProtKB/Swiss-Prot
      P58876
      UniProtKB/TrEMBL
      A8K9J7
      Related
      ENSP00000367008.4, ENST00000377777.6
      Conserved Domains (1) summary
      smart00427
      Location:28 → 124
      H2B; Histone H2B

    2. NM_138720.2 → NP_619790.1  histone H2B type 1-D

      See identical proteins and their annotated locations for NP_619790.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs from variant 1 in its 3' UTR which contains a polyA signal and site. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      BC002842, BM153714
      Consensus CDS
      CCDS4587.1
      UniProtKB/Swiss-Prot
      P58876
      UniProtKB/TrEMBL
      A8K9J7
      Related
      ENSP00000289316.2, ENST00000289316.2
      Conserved Domains (1) summary
      smart00427
      Location:28 → 124
      H2B; Histone H2B

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      26158121..26171349
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005249039.5 → XP_005249096.2  histone H2B type 1-D isoform X1

      UniProtKB/Swiss-Prot
      P58876

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      26026257..26039486
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P58876.2 GenPept UniProtKB/Swiss-Prot:P58876

    Gene LinkOut

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

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