CBX4 chromobox 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CBX4provided by HGNC
Official Full Name: chromobox 4provided by HGNC
Primary source: HGNC:HGNC:1554
See related: Ensembl:ENSG00000141582 MIM:603079; AllianceGenome:HGNC:1554
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PC2; NBP16
Summary: Enables SUMO binding activity; SUMO ligase activity; and enzyme binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of PRC1 complex. Implicated in hepatocellular carcinoma. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in bone marrow (RPKM 17.4), spleen (RPKM 5.9) and 24 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 17q25.3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (79833156..79839440, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (80730965..80737249, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (77806955..77813239, complement)

Chromosome 17 - NC_000017.11 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?

CBX4/miR-190 regulatory loop inhibits lung cancer metastasis.
Title: CBX4/miR-190 regulatory loop inhibits lung cancer metastasis.
CBX4 plays a bidirectional role in transcriptional regulation and lung adenocarcinoma progression.
Title: CBX4 plays a bidirectional role in transcriptional regulation and lung adenocarcinoma progression.
METTL3 Promotes Osteosarcoma Metastasis via an m6A-dependent Epigenetic Activity of CBX4.
Title: METTL3 Promotes Osteosarcoma Metastasis via an m6A-dependent Epigenetic Activity of CBX4.
Long Noncoding RNA SNHG5 Induces the NF-kappaB Pathway by Regulating miR-181c-5p/CBX4 Axis to Promote the Progression of Non-Small Cell Lung Cancer.
Title: Long Noncoding RNA SNHG5 Induces the NF-κB Pathway by Regulating miR-181c-5p/CBX4 Axis to Promote the Progression of Non-Small Cell Lung Cancer.
MicroRNA-6838-5p suppresses the self-renewal and metastasis of human liver cancer stem cells through downregulating CBX4 expression and inactivating ERK signaling.
Title: MicroRNA-6838-5p suppresses the self-renewal and metastasis of human liver cancer stem cells through downregulating CBX4 expression and inactivating ERK signaling.
MiR-507 inhibits the progression of gastric carcinoma via targeting CBX4-mediated activation of Wnt/beta-catenin and HIF-1alpha pathways.
Title: MiR-507 inhibits the progression of gastric carcinoma via targeting CBX4-mediated activation of Wnt/β-catenin and HIF-1α pathways.
Chromobox homolog 4 overexpression inhibits TNF-alpha-induced matrix catabolism and senescence by suppressing activation of the NF-kappaB signaling pathway in nucleus pulposus cells.
Title: Chromobox homolog 4 overexpression inhibits TNF-α-induced matrix catabolism and senescence by suppressing activation of the NF-κB signaling pathway in nucleus pulposus cells.
CBX4 Regulates Long-Form Thymic Stromal Lymphopoietin-mediated Airway Inflammation through SUMOylation in House Dust Mite-induced Asthma.
Title: CBX4 Regulates Long-Form Thymic Stromal Lymphopoietin-mediated Airway Inflammation through SUMOylation in House Dust Mite-induced Asthma.
CBX4-dependent regulation of HDAC3 nuclear translocation reduces Bmp2-induced osteoblastic differentiation and calcification in adamantinomatous craniopharyngioma.
Title: CBX4-dependent regulation of HDAC3 nuclear translocation reduces Bmp2-induced osteoblastic differentiation and calcification in adamantinomatous craniopharyngioma.
CBX4 Regulates Replicative Senescence of WI-38 Fibroblasts.
Title: CBX4 Regulates Replicative Senescence of WI-38 Fibroblasts.

Submit: New GeneRIF Correction See all GeneRIFs (46)

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
Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations. 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)

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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SUMO binding	IBA Inferred from Biological aspect of Ancestor more info
enables SUMO binding	IDA Inferred from Direct Assay more info	PubMed
enables SUMO ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables SUMO ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables SUMO transferase activity	EXP Inferred from Experiment more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables phosphoprotein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein sumoylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein sumoylation	IEA Inferred from Electronic Annotation more info
involved_in protein sumoylation	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
part_of PRC1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of PRC1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of PcG protein complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
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

General protein information

Go to the top of the page Help

Preferred Names: E3 SUMO-protein ligase CBX4

Names: NS5ATP1-binding protein 16; Pc class 2 homolog; chromobox homolog 4 (Pc class homolog, Drosophila); chromobox protein homolog 4; chromobox-like protein 4; polycomb 2 homolog

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_003655.3 → NP_003646.2 E3 SUMO-protein ligase CBX4

See identical proteins and their annotated locations for NP_003646.2

Status: VALIDATED

Source sequence(s)

AC100791, AF013956, AI796748, BC014967, BG029608, BQ225831

Consensus CDS

CCDS32758.1

UniProtKB/Swiss-Prot

B1PJR7, O00257, Q6TPI8, Q96C04

UniProtKB/TrEMBL

A0A0S2Z5B2

Related

ENSP00000269397.4, ENST00000269397.9

Conserved Domains (2) summary

smart00298
Location:10 → 62

CHROMO; Chromatin organization modifier domain

pfam17218
Location:538 → 559

CBX7_C; CBX family C-terminal motif

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

79833156..79839440 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011525399.3 → XP_011523701.1 E3 SUMO-protein ligase CBX4 isoform X1

Conserved Domains (1) summary

pfam17218
Location:472 → 493

CBX7_C; CBX family C-terminal motif