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

    Gene ID: 1315, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See COPB1 in Genome Data Viewer
    Location:
    11p15.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (14457512..14499811, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (14552800..14595086, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. 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
    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. 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
    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 (238) 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
    		not available

    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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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