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

Gene ID: 9276, updated on 7-Jan-2024

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
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Genomic context

See COPB2 in Genome Data Viewer
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_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909439 Neighboring gene Sharpr-MPRA regulatory region 3993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20611 Neighboring gene mitochondrial ribosomal protein S22 Neighboring gene uncharacterized LOC124906339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:139108213-139108774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:139108775-139109337 Neighboring gene COPB2 divergent transcript Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:139191689-139192888 Neighboring gene retinol binding protein 2 Neighboring gene actin gamma 1 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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

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)

  1. NM_001410834.1NP_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
  2. NM_004766.3NP_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:24428
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:8297
    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:320763
    Coatomer_WDAD; Coatomer WD associated region
    sd00039
    Location:103140
    7WD40; WD40 repeat [structural motif]

RNA

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    139357406..139389680 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449233.1XP_047305189.1  coatomer subunit beta' isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    142104959..142137239 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348439.1XP_054204414.1  coatomer subunit beta' isoform X1