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COPB1 COPI coat complex subunit beta 1 [ Homo sapiens (human) ]

Gene ID: 1315, updated on 5-Mar-2024

Summary

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Official Symbol
COPB1provided by HGNC
Official Full Name
COPI coat complex subunit beta 1provided by HGNC
Primary source
HGNC:HGNC:2231
See related
Ensembl:ENSG00000129083 MIM:600959; AllianceGenome:HGNC:2231
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
COPB; BARMACS
Summary
This gene encodes a protein subunit of the coatomer complex associated with non-clathrin coated vesicles. The coatomer complex, also known as the coat protein complex 1, forms in the cytoplasm and is recruited to the Golgi by activated guanosine triphosphatases. Once at the Golgi membrane, the coatomer complex may assist in the movement of protein and lipid components back to the endoplasmic reticulum. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]
Expression
Ubiquitous expression in thyroid (RPKM 49.1), prostate (RPKM 35.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11p15.2
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (14457512..14499811, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (14552800..14595086, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (14479058..14521357, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4471 Neighboring gene RAS related 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:14362237-14362911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14373862-14374748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14374749-14375635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3172 Neighboring gene NANOG hESC enhancer GRCh37_chr11:14385715-14386272 Neighboring gene Sharpr-MPRA regulatory region 2156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:14428638-14429316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14443710-14444362 Neighboring gene 60S ribosomal protein L13a-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4474 Neighboring gene RNA, U7 small nuclear 49 pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:14541725-14542339 Neighboring gene proteasome 20S subunit alpha 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14654809-14655398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3173 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14683201-14683380 Neighboring gene mortality factor 4 like 1 pseudogene 3 Neighboring gene phosphodiesterase 3B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. An integrative pan-cancer analysis of COPB1 based on data mining. Chen H, et al. Cancer Biomark, 2021. PMID 32986658
  2. Structural integrity of the Golgi stack is essential for normal secretory functions of rat parotid acinar cells: effects of brefeldin A and okadaic acid. Tamaki H, et al. J Histochem Cytochem, 2002 Dec. PMID 12486083
  3. An endosomal beta COP is involved in the pH-dependent formation of transport vesicles destined for late endosomes. Aniento F, et al. J Cell Biol, 1996 Apr. PMID 8601610, Free PMC Article
  4. The oculocerebrorenal syndrome gene product is a 105-kD protein localized to the Golgi complex. Olivos-Glander IM, et al. Am J Hum Genet, 1995 Oct. PMID 7573041, Free PMC Article
  5. Surface expression of TTYH2 is attenuated by direct interaction with β-COP. Ryu J, et al. BMB Rep, 2019 Jul. PMID 30670146, Free PMC Article

See all (210) citations in PubMed

GeneRIFs: Gene References Into Functions

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
Baralle-Macken syndrome
MedGen: C5543241 OMIM: 619255 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef utilizes beta-COP in CD28 downregulation PubMed
nef beta-COP as a cellular cofactor is required for HIV-1 Nef-mediated HLA-A2, CD4, and CD8 downregulation PubMed
nef MHC-I is found in the Rab7(+) vesicles and targeted for degradation via the activity of the Nef-interacting protein, beta-COP PubMed
nef Binding of HIV-1 Nef to Beta-COP has been demonstrated by yeast two-hybrid and coimmunoprecipitation experiments and may be involved in the downregulation of CD4 by Nef PubMed
nef Co-localization of HIV-1 Nef, ARF1, and Beta-COP in early endosomes depends on Nef residues at E154 and E155; this co-localization is required for the downregulation and transport of CD4 to acidic late-endosomal compartments PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: PSMA1

Homology

Clone Names

  • FLJ10341, FLJ46444, FLJ57957, DKFZp761K102

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 ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in intracellular protein transport 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 ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in Golgi-associated vesicle TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment IEA
Inferred from Electronic Annotation
more info
  
located_in ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in membrane HDA PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in secretory granule membrane TAS
Traceable Author Statement
more info
  
located_in tertiary granule 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
beta-cop
coatomer protein complex subunit beta 1

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_001144061.2 → NP_001137533.1  coatomer subunit beta

    See identical proteins and their annotated locations for NP_001137533.1

    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)
    AA443270, AL136593, DA725605
    Consensus CDS
    CCDS7815.1
    UniProtKB/Swiss-Prot
    D3DQX0, P53618, Q6GTT7, Q9NTK2, Q9UNW7
    Related
    ENSP00000397873.2, ENST00000439561.7
    Conserved Domains (4) summary
    pfam01602
    Location:18 → 550
    Adaptin_N; Adaptin N terminal region
    pfam07718
    Location:667 → 807
    Coatamer_beta_C; Coatomer beta C-terminal region
    pfam14806
    Location:816 → 944
    Coatomer_b_Cpla; Coatomer beta subunit appendage platform
    sd00044
    Location:137 → 161
    HEAT; HEAT repeat [structural motif]

  2. NM_001144062.2 → NP_001137534.1  coatomer subunit beta

    See identical proteins and their annotated locations for NP_001137534.1

    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)
    AA443270, AF111807, DA725605
    Consensus CDS
    CCDS7815.1
    UniProtKB/Swiss-Prot
    D3DQX0, P53618, Q6GTT7, Q9NTK2, Q9UNW7
    Conserved Domains (4) summary
    pfam01602
    Location:18 → 550
    Adaptin_N; Adaptin N terminal region
    pfam07718
    Location:667 → 807
    Coatamer_beta_C; Coatomer beta C-terminal region
    pfam14806
    Location:816 → 944
    Coatomer_b_Cpla; Coatomer beta subunit appendage platform
    sd00044
    Location:137 → 161
    HEAT; HEAT repeat [structural motif]

  3. NM_016451.5 → NP_057535.1  coatomer subunit beta

    See identical proteins and their annotated locations for NP_057535.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC037280, DA725605
    Consensus CDS
    CCDS7815.1
    UniProtKB/Swiss-Prot
    D3DQX0, P53618, Q6GTT7, Q9NTK2, Q9UNW7
    Related
    ENSP00000249923.3, ENST00000249923.7
    Conserved Domains (4) summary
    pfam01602
    Location:18 → 550
    Adaptin_N; Adaptin N terminal region
    pfam07718
    Location:667 → 807
    Coatamer_beta_C; Coatomer beta C-terminal region
    pfam14806
    Location:816 → 944
    Coatomer_b_Cpla; Coatomer beta subunit appendage platform
    sd00044
    Location:137 → 161
    HEAT; HEAT repeat [structural motif]

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    14457512..14499811 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    14552800..14595086 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P53618.3 GenPept UniProtKB/Swiss-Prot:P53618

Gene LinkOut

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