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COPB2 coatomer protein complex subunit beta 2 [ Homo sapiens (human) ]

Gene ID: 9276, updated on 14-Oct-2018

Summary

Official Symbol
COPB2provided by HGNC
Official Full Name
coatomer protein complex subunit beta 2provided by HGNC
Primary source
HGNC:HGNC:2232
See related
Ensembl:ENSG00000184432 MIM:606990; Vega:OTTHUMG00000159959
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
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

Genomic context

See COPB2 in Genome Data Viewer
Location:
3q23
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (139355595..139389680, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (139076433..139108522, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene blepharophimosis, epicanthus inversus and ptosis candidate 1 Neighboring gene PISRT1 lncRNA Neighboring gene mitochondrial ribosomal protein S22 Neighboring gene uncharacterized LOC100507291 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
MICROCEPHALY 19, PRIMARY, AUTOSOMAL RECESSIVE
MedGen: C4540488 OMIM: 617800 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Two new susceptibility loci for Kawasaki disease identified through genome-wide association analysis.
NHGRI GWA 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 BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPI-dependent Golgi-to-ER retrograde traffic, organism-specific biosystem (from REACTOME)
    COPI-dependent Golgi-to-ER retrograde traffic, organism-specific biosystemRetrograde traffic from the cis-Golgi to the ERGIC or the ER is mediated in part by microtubule-directed COPI-coated vesicles (Letourneur et al, 1994; Shima et al, 1999; Spang et al, 1998; reviewed i...
  • COPI-mediated anterograde transport, organism-specific biosystem (from REACTOME)
    COPI-mediated anterograde transport, organism-specific biosystemThe ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites (Ben-Tekaya et al, 2...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Golgi-to-ER retrograde transport, organism-specific biosystem (from REACTOME)
    Golgi-to-ER retrograde transport, organism-specific biosystemRetrograde traffic from the cis-Golgi to the ERGIC or the ER occurs through either COPI-coated vesicles or through a less well characterized RAB6-dependent route that makes use of tubular carriers (r...
  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
ER to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ER to Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
 
intra-Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intra-Golgi vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde vesicle-mediated transport, Golgi to ER IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde vesicle-mediated transport, Golgi to ER TAS
Traceable Author Statement
more info
PubMed 
toxin transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
COPI vesicle coat IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
COPI vesicle coat IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane TAS
Traceable Author Statement
more info
 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
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 prime
coatomer protein complex, subunit beta 2 (beta prime)
p102

NCBI Reference Sequences (RefSeq)

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_004766.2NP_004757.1  coatomer subunit beta'

    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)
    BC000326, DC347783, X70476
    Consensus CDS
    CCDS3108.1
    UniProtKB/Swiss-Prot
    P35606
    Related
    ENSP00000329419.4, OTTHUMP00000217144, ENST00000333188.9, OTTHUMT00000358495
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    139355595..139389680 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453831.1XP_024309599.1  coatomer subunit beta' isoform X1

    Conserved Domains (1) summary
    pfam04053
    Location:65509
    Coatomer_WDAD; Coatomer WD associated region
  2. XM_017007513.1XP_016863002.1  coatomer subunit beta' isoform X1

    Conserved Domains (1) summary
    pfam04053
    Location:65509
    Coatomer_WDAD; Coatomer WD associated region
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