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

Gene ID: 3017, updated on 21-Dec-2019

Summary

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
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

Genomic context

See H2BC5 in Genome Data Viewer
Location:
6p22.2
Exon count:
3
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (26158008..26171349)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26157419..26171577)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H2A clustered histone 6 Neighboring gene H1.4 linker histone, cluster member Neighboring gene LARP1 pseudogene 1 Neighboring gene H2B clustered histone 6 Neighboring gene H4 clustered histone 4

Genomic regions, transcripts, and products

Expression

  • 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

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC90432

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
nucleosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein ubiquitination TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
extracellular exosome HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleosome IEA
Inferred from Electronic Annotation
more info
 
nucleus HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_021063.4NP_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, P62807
    UniProtKB/TrEMBL
    A0A024QZZ7
    Related
    ENSP00000367008.4, ENST00000377777.5
    Conserved Domains (1) summary
    smart00427
    Location:28124
    H2B; Histone H2B
  2. NM_138720.2NP_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
    A0A024QZZ7
    Related
    ENSP00000289316.2, ENST00000289316.2
    Conserved Domains (1) summary
    smart00427
    Location:28124
    H2B; Histone H2B

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    26158008..26171349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249039.4XP_005249096.1  histone H2B type 1-D isoform X1

    Conserved Domains (2) summary
    pfam00125
    Location:20126
    Histone; Core histone H2A/H2B/H3/H4
    cl23830
    Location:36149
    H2B; Histone H2B
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