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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

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