COPB2 COPI coat complex subunit beta 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: COPB2provided by HGNC
Official Full Name: COPI coat complex subunit beta 2provided by HGNC
Primary source: HGNC:HGNC:2232
See related: Ensembl:ENSG00000184432 MIM:606990; AllianceGenome:HGNC:2232
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: OPDD; MCPH19; beta'-COP
Summary: The Golgi coatomer complex (see MIM 601924) constitutes the coat of nonclathrin-coated vesicles and is essential for Golgi budding and vesicular trafficking. It consists of 7 protein subunits, including COPB2.[supplied by OMIM, Jul 2002]
Expression: Ubiquitous expression in thyroid (RPKM 30.4), prostate (RPKM 28.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q23

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (139357406..139389680, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (142104959..142137239, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (139076248..139108522, complement)

Chromosome 3 - NC_000003.12 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?

beta-COP Suppresses the Surface Expression of the TREK2.
Title: β-COP Suppresses the Surface Expression of the TREK2.
Comprehensive analysis reveals COPB2 and RYK associated with tumor stages of larynx squamous cell carcinoma.
Title: Comprehensive analysis reveals COPB2 and RYK associated with tumor stages of larynx squamous cell carcinoma.
An Integrative Pan-Cancer Analysis of the Oncogenic Role of COPB2 in Human Tumors.
Title: An Integrative Pan-Cancer Analysis of the Oncogenic Role of COPB2 in Human Tumors.
COPB2: a transport protein with multifaceted roles in cancer development and progression.
Title: COPB2: a transport protein with multifaceted roles in cancer development and progression.
COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay.
Title: COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay.
High expression of COPB2 predicts adverse outcomes: A potential therapeutic target for glioma.
Title: High expression of COPB2 predicts adverse outcomes: A potential therapeutic target for glioma.
COPB2: A Novel Prognostic Biomarker That Affects Progression of HCC.
Title: COPB2: A Novel Prognostic Biomarker That Affects Progression of HCC.
MiR-216a-3p regulates the proliferation, apoptosis, migration, and invasion of lung cancer cells via targeting COPB2.
Title: MiR-216a-3p regulates the proliferation, apoptosis, migration, and invasion of lung cancer cells via targeting COPB2.
COPB2 gene silencing inhibits colorectal cancer cell proliferation and induces apoptosis via the JNK/c-Jun signaling pathway.
Title: COPB2 gene silencing inhibits colorectal cancer cell proliferation and induces apoptosis via the JNK/c-Jun signaling pathway.
Upregulation of the Coatomer Protein Complex Subunit beta 2 (COPB2) Gene Targets microRNA-335-3p in NCI-H1975 Lung Adenocarcinoma Cells to Promote Cell Proliferation and Migration.
Title: Upregulation of the Coatomer Protein Complex Subunit beta 2 (COPB2) Gene Targets microRNA-335-3p in NCI-H1975 Lung Adenocarcinoma Cells to Promote Cell Proliferation and Migration.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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

Associated conditions

Description	Tests
Microcephaly 19, primary, autosomal recessive MedGen: C4540488 OMIM: 617800 GeneReviews: Not available	Compare labs
Osteoporosis, childhood- or juvenile-onset, with developmental delay MedGen: C5676992 OMIM: 619884 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Two new susceptibility loci for Kawasaki disease identified through genome-wide association analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed

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
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with COPB2; predicted interaction to be within the Golgi	PubMed
Nef	nef	HIV-1 Nef weakly and directly interacts with COPB2 (beta-COP) in 293T cells and this interaction is dependent on Nef membrane localization as shown by FACS-Forster resonance energy transfer (FRET)-based and site-directed mutagenesis experiments	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

D3S3336 (e-PCR)
- UniSTS:66314

RH48045 (e-PCR)
- UniSTS:14625

RH93913 (e-PCR)
- UniSTS:89144

D3S2902E (e-PCR)
- UniSTS:52853

COPB2 (e-PCR)
- UniSTS:505253

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intra-Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intra-Golgi vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of COPI vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
part_of COPI vesicle coat	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in transport vesicle	TAS Traceable Author Statement more info

General protein information

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Preferred Names: coatomer subunit beta'

Names: beta'-coat protein; betaprime-COP; coatomer binding complex, beta prime subunit; coatomer protein complex subunit beta 2; coatomer protein complex subunit beta prime; coatomer protein complex, subunit beta 2 (beta prime); p102

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_001410834.1 → NP_001397763.1 coatomer subunit beta' isoform 2

Status: VALIDATED

Source sequence(s)

AC024933

Consensus CDS

CCDS93395.1

UniProtKB/TrEMBL

H0Y938

Related

ENSP00000427185.2, ENST00000512242.6
NM_004766.3 → NP_004757.1 coatomer subunit beta' isoform 1

See identical proteins and their annotated locations for NP_004757.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) uses an alternate splice donor site in the first coding exon and is predicted to encode a protein.

Source sequence(s)

AC024933, BC000326, DC347783, X70476

Consensus CDS

CCDS3108.1

UniProtKB/Swiss-Prot

B4DZI8, P35606

UniProtKB/TrEMBL

H0Y938

Related

ENSP00000329419.4, ENST00000333188.10

Conserved Domains (4) summary

COG2319
Location:24 → 428

WD40; WD40 repeat [General function prediction only]

cd00200
Location:8 → 297

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam04053
Location:320 → 763

Coatomer_WDAD; Coatomer WD associated region

sd00039
Location:103 → 140

7WD40; WD40 repeat [structural motif]

RNA

NR_023350.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice donor site which introduces a stop codon shortly after the initiating AUG site and renders the transcript a candidate for nonsense-mediated decay.

Source sequence(s)

BC000326, DC347783, DC385126