CBX5 chromobox 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CBX5provided by HGNC
Official Full Name: chromobox 5provided by HGNC
Primary source: HGNC:HGNC:1555
See related: Ensembl:ENSG00000094916 MIM:604478; AllianceGenome:HGNC:1555
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: HP1; HP1A; HEL25; HP1alpha
Summary: This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family. The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The encoded product is involved in the formation of functional kinetochore through interaction with essential kinetochore proteins. The gene has a pseudogene located on chromosome 3. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 15.3), thyroid (RPKM 14.2) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 12q13.13

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54230942..54280122, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (54197516..54246699, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54624726..54673906, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

How to evict HP1 from H3: Using a complex salt bridge.
Title: How to evict HP1 from H3: Using a complex salt bridge.
HP1alpha promotes the progression of prostate cancer.
Title: HP1α promotes the progression of prostate cancer.
Molecular interactions underlying the phase separation of HP1alpha: role of phosphorylation, ligand and nucleic acid binding.
Title: Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding.
Circ_0037866 Contributes to the Tumorigenesis of Renal Cell Carcinoma by Sequestering miR-384 to Elevate Chromobox 5 Expression.
Title: Circ_0037866 Contributes to the Tumorigenesis of Renal Cell Carcinoma by Sequestering miR-384 to Elevate Chromobox 5 Expression.
Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.
Title: Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.
HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
Title: HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
Changes in the properties of membrane tethers in response to HP1alpha depletion in MCF7 cells.
Title: Changes in the properties of membrane tethers in response to HP1α depletion in MCF7 cells.
HP1alpha is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
Title: HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
Structural dynamics of the chromo-shadow domain and chromodomain of HP1 bound to histone H3K9 methylated peptide, as measured by site-directed spin-labeling EPR spectroscopy.
Title: Structural dynamics of the chromo-shadow domain and chromodomain of HP1 bound to histone H3K9 methylated peptide, as measured by site-directed spin-labeling EPR spectroscopy.
Depletion of HP1alpha alters the mechanical properties of MCF7 nuclei.
Title: Depletion of HP1α alters the mechanical properties of MCF7 nuclei.

Submit: New GeneRIF Correction See all GeneRIFs (102)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat is recruited by CTIP2 into a complex with HP1alpha, leading to the relocalization of Tat and inactivation of Tat-mediated transactivation of the HIV-1 LTR promoter	PubMed
Vpr	vpr	HIV-1 Vpr actively recruits p300/HAT to a range of chromatin regions including the centromere, resulting in the displacement of HP1-alpha	PubMed
	vpr	HIV-1 Vpr interferes with the heterochromatin structure by displacing HP1-alpha and HP1-gamma proteins in interphase, which leads to relocalization of the centromere chromatin proteins Mis12, Sgo1, and CPC after prophase	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH93620 (e-PCR)
- UniSTS:84993

D11S2921 (e-PCR)
- UniSTS:152074

RH68193 (e-PCR)
- UniSTS:88855

D10S275 (e-PCR)
- UniSTS:147992

PMC156606P1 (e-PCR)
- UniSTS:271408

RH102227 (e-PCR)
- UniSTS:96561

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

STS-Z40708 (e-PCR)
- UniSTS:80211

RH64861 (e-PCR)
- UniSTS:90198

GDB:314949 (e-PCR)
- UniSTS:156503

L18426 (e-PCR)
- UniSTS:34648

SGC34021 (e-PCR)
- UniSTS:63585

D12S1966 (e-PCR)
- UniSTS:14702

D1S1425 (e-PCR)
- UniSTS:149621

RH36905 (e-PCR)
- UniSTS:87932

WI-12071 (e-PCR)
- UniSTS:64708

D12S110E (e-PCR)
- UniSTS:79567

D12S110E (e-PCR)
- UniSTS:147411

WI-15869 (e-PCR)
- UniSTS:40429

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone deacetylase binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-macromolecule adaptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables ribonucleoprotein complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with PML body	IMP Inferred from Mutant Phenotype more info	PubMed
located_in chromocenter	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	HDA more info	PubMed
part_of heterochromatin	TAS Traceable Author Statement more info	PubMed
part_of histone deacetylase complex	ISS Inferred from Sequence or Structural Similarity more info
part_of histone methyltransferase complex	ISS Inferred from Sequence or Structural Similarity more info
located_in kinetochore	IEA Inferred from Electronic Annotation more info
located_in nuclear envelope	TAS Traceable Author Statement more info	PubMed
located_in nucleolus	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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of pericentric heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
part_of pericentric heterochromatin	NAS Non-traceable Author Statement more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in site of DNA damage	IMP Inferred from Mutant Phenotype more info	PubMed
part_of transcription repressor complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

Go to the top of the page Help

Preferred Names: chromobox protein homolog 5

Names: HP1 alpha homolog; HP1-ALPHA; HP1Hs alpha; antigen p25; chromobox homolog 5 (HP1 alpha homolog, Drosophila); epididymis luminal protein 25; heterochromatin protein 1 homolog alpha; heterochromatin protein 1-alpha

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001127321.1 → NP_001120793.1 chromobox protein homolog 5

See identical proteins and their annotated locations for NP_001120793.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC078778, BC006821, BC030149, BP236173

Consensus CDS

CCDS8875.1

UniProtKB/Swiss-Prot

B2R8T9, P45973

UniProtKB/TrEMBL

Q6I9T7, V9HWG0

Related

ENSP00000401009.2, ENST00000439541.6

Conserved Domains (2) summary

cd18651
Location:19 → 68

CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha

cd18655
Location:116 → 173

CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
NM_001127322.1 → NP_001120794.1 chromobox protein homolog 5

See identical proteins and their annotated locations for NP_001120794.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC078778, AK313506, BC030149, DT217255

Consensus CDS

CCDS8875.1

UniProtKB/Swiss-Prot

B2R8T9, P45973

UniProtKB/TrEMBL

Q6I9T7, V9HWG0

Related

ENSP00000449207.1, ENST00000550411.5

Conserved Domains (2) summary

cd18651
Location:19 → 68

CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha

cd18655
Location:116 → 173

CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
NM_012117.3 → NP_036249.1 chromobox protein homolog 5

See identical proteins and their annotated locations for NP_036249.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC078778, BC030149, BP336150

Consensus CDS

CCDS8875.1

UniProtKB/Swiss-Prot

B2R8T9, P45973

UniProtKB/TrEMBL

Q6I9T7, V9HWG0

Related

ENSP00000209875.4, ENST00000209875.9

Conserved Domains (2) summary

cd18651
Location:19 → 68

CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha

cd18655
Location:116 → 173

CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha