H2BC12 H2B clustered histone 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: H2BC12provided by HGNC
Official Full Name: H2B clustered histone 12provided by HGNC
Primary source: HGNC:HGNC:13954
See related: Ensembl:ENSG00000197903 MIM:615045; AllianceGenome:HGNC:13954
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: H2BK; H2B/S; H2BFT; H2BFAiii; HIST1H2BK
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. This gene encodes a replication-dependent histone that is a member of the histone H2B family. The protein encoded is an antimicrobial protein with antibacterial and antifungal activity. Two transcripts that encode the same protein have been identified for this gene, which is found in the histone microcluster on chromosome 6p21.33. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in prostate (RPKM 42.3), testis (RPKM 29.8) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 6p22.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (27138293..27146858, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (27007108..27015674, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (27106072..27114637, complement)

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
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?

The physical interaction between lipin1 and eEF1A1 was further affirmed in 293T cells transfected with 6-His tagged lipin1 and hepatocyte SMMC7721 cells by protein immunoprecipitation and immunofluorescence microscopy. Lipin1 also interacted with HIST1H2BK, which was confirmed in SMMC7721 cells by protein immunoprecipitation.
Title: Mass spectrometry-based proteomic analysis reveals the interacting partners of lipin1.
Histone H2B antimicrobial peptides exhibit antibacterial activity and contribute to the formation of the antimicrobial barrier of the colonic epithelium
Title: Antimicrobial polypeptides of the human colonic epithelium.

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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
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

RH79884 (e-PCR)
- UniSTS:87081

WI-11733 (e-PCR)
- UniSTS:7041

NoName (e-PCR)
- UniSTS:482788

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

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-negative bacterium	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 killing of cells of another organism	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
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	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-K

Names: H2B K; H2B histone family, member T; HIRA-interacting protein 1; histone 1, H2bk; histone cluster 1 H2B family member k; histone cluster 1, H2bk; histone family member

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_001312653.2 → NP_001299582.1 histone H2B type 1-K

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)

AL021807

Consensus CDS

CCDS4621.1

UniProtKB/Swiss-Prot

A8K7P7, O60814, Q2VPI7

UniProtKB/TrEMBL

Q0D2M2

Related

ENSP00000349430.2, ENST00000356950.2

Conserved Domains (1) summary

smart00427
Location:28 → 124

H2B; Histone H2B
NM_080593.2 → NP_542160.1 histone H2B type 1-K

See identical proteins and their annotated locations for NP_542160.1

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)

BC000893, DA873786

Consensus CDS

CCDS4621.1

UniProtKB/Swiss-Prot

A8K7P7, O60814, Q2VPI7

UniProtKB/TrEMBL

Q0D2M2

Related

ENSP00000520531.1, ENST00000715895.1

Conserved Domains (1) summary

smart00427
Location:28 → 124

H2B; Histone H2B