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

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; 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

Location:: 6p22.2

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (26158121..26171349)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (26026257..26039486)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (26158349..26171577)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function.
Title: Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function.
We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 A and 4.9 A, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub.
Title: Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination.

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
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

STS-N33927 (e-PCR)
- UniSTS:9799

RH47386 (e-PCR)
- UniSTS:39754

D6S2372 (e-PCR)
- UniSTS:57679

NoName (e-PCR)
- UniSTS:482908

RH69154 (e-PCR)
- UniSTS:52890

D12S1124 (e-PCR)
- UniSTS:150204

RH80280 (e-PCR)
- UniSTS:91615

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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 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	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	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)

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
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