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    COPE COPI coat complex subunit epsilon [ Homo sapiens (human) ]

    Gene ID: 11316, updated on 2-Nov-2024

    Summary

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    Official Symbol
    COPEprovided by HGNC
    Official Full Name
    COPI coat complex subunit epsilonprovided by HGNC
    Primary source
    HGNC:HGNC:2234
    See related
    Ensembl:ENSG00000105669 MIM:606942; AllianceGenome:HGNC:2234
    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
    epsilon-COP
    Summary
    The product of this gene is an epsilon subunit of coatomer protein complex. Coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles. It is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. Coatomer complex consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 53.6), bone marrow (RPKM 48.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COPE in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18899514..18919387, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19035138..19055145, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19010323..19030196, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10421 Neighboring gene NANOG hESC enhancer GRCh37_chr19:18944963-18945515 Neighboring gene UPF1 RNA helicase and ATPase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14333 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18960435-18960659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10422 Neighboring gene ceramide synthase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10423 Neighboring gene growth differentiation factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18994867-18995367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19028406-19029296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14334 Neighboring gene DEAD-box helicase 49 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042288-19042799 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042800-19043310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19043997-19044615 Neighboring gene homer scaffold protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10426 Neighboring gene HOMER3 antisense RNA 1

    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 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. Segregation of COPI-rich and anterograde-cargo-rich domains in endoplasmic-reticulum-to-Golgi transport complexes. Shima DT, et al. Curr Biol, 1999 Jul 29-Aug 12. PMID 10469566
    2. The cytoplasmic coatomer protein COPI. A potential translational regulator. de La Vega LA, et al. J Biol Chem, 1999 Oct 29. PMID 10531302
    3. Ubiquitylation of epsilon-COP by PIRH2 and regulation of the secretion of PSA. Maruyama S, et al. Mol Cell Biochem, 2008 Jan. PMID 17721809
    4. Intracellular phospholipase A1gamma (iPLA1gamma) is a novel factor involved in coat protein complex I- and Rab6-independent retrograde transport between the endoplasmic reticulum and the Golgi complex. Morikawa RK, et al. J Biol Chem, 2009 Sep 25. PMID 19632984, Free PMC Article
    5. Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Travis SM, et al. Proc Natl Acad Sci U S A, 2019 Nov 26. PMID 31712447, Free PMC Article

    See all (144) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    2. Data show that iPLA(1)gamma is a novel membrane transport factor that contributes to a specific Golgi-to-ER retrograde pathway distinct from presently characterized COPI- and Rab6-dependent pathways.
      Title: Intracellular phospholipase A1gamma (iPLA1gamma) is a novel factor involved in coat protein complex I- and Rab6-independent retrograde transport between the endoplasmic reticulum and the Golgi complex.
    3. Ubiquitylation of epsilon-COP by PIRH2; overexpression of the wild type of PIRH2 in prostate cancer cells causes downregulation of the secretion of prostate-specific antigen.
      Title: Ubiquitylation of epsilon-COP by PIRH2 and regulation of the secretion of PSA.
    Submit: New GeneRIF Correction

    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

    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

    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

    Homology

    Clone Names

    • FLJ13241

    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 protein localization to axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum 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
    		  
    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 nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    coatomer subunit epsilon
    Names
    coatomer epsilon subunit
    coatomer protein complex subunit epsilon
    epsilon coat protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001330469.2 → NP_001317398.1  coatomer subunit epsilon isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate exon in the central coding region compared to isoform a. The encoded isoform (d) is longer than isoform a.
      Source sequence(s)
      AC002985, AC005197
      Consensus CDS
      CCDS82321.1
      UniProtKB/TrEMBL
      M0QXB4, Q53HJ6
      Related
      ENSP00000469035.1, ENST00000600932.5
      Conserved Domains (2) summary
      pfam04733
      Location:17 → 328
      Coatomer_E; Coatomer epsilon subunit
      sd00006
      Location:238 → 268
      TPR; TPR repeat [structural motif]

    2. NM_007263.4 → NP_009194.2  coatomer subunit epsilon isoform a

      See identical proteins and their annotated locations for NP_009194.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AI680336, BI520280
      Consensus CDS
      CCDS12387.1
      UniProtKB/Swiss-Prot
      A6NE29, A6NKA3, O14579, O76097, Q6IBB8, Q9UGP6
      UniProtKB/TrEMBL
      Q53HJ6
      Related
      ENSP00000262812.3, ENST00000262812.9
      Conserved Domains (2) summary
      pfam04733
      Location:17 → 305
      Coatomer_E; Coatomer epsilon subunit
      sd00006
      Location:215 → 245
      TPR; TPR repeat [structural motif]

    3. NM_199442.2 → NP_955474.1  coatomer subunit epsilon isoform b

      See identical proteins and their annotated locations for NP_955474.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (b), that is missing an internal segment compared to isoform a.
      Source sequence(s)
      AI680336, BI520280
      Consensus CDS
      CCDS12388.1
      UniProtKB/TrEMBL
      Q53HJ6
      Related
      ENSP00000345674.3, ENST00000351079.8
      Conserved Domains (2) summary
      sd00006
      Location:164 → 194
      TPR; TPR repeat [structural motif]
      pfam04733
      Location:17 → 254
      Coatomer_E; Coatomer epsilon subunit

    4. NM_199444.2 → NP_955476.1  coatomer subunit epsilon isoform c

      See identical proteins and their annotated locations for NP_955476.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (c), that is missing an internal segment compared to isoform a.
      Source sequence(s)
      AI680336, BI520280
      Consensus CDS
      CCDS12389.1
      UniProtKB/TrEMBL
      Q53HJ6
      Related
      ENSP00000343134.3, ENST00000349893.8
      Conserved Domains (1) summary
      pfam04733
      Location:17 → 253
      Coatomer_E; Coatomer epsilon subunit

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      18899514..18919387 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438119.1 → XP_047294075.1  coatomer subunit epsilon isoform X2

    2. XM_011527656.2 → XP_011525958.1  coatomer subunit epsilon isoform X1

      UniProtKB/TrEMBL
      Q53HJ6
      Conserved Domains (1) summary
      pfam04733
      Location:17 → 276
      Coatomer_E; Coatomer epsilon subunit

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      19035138..19055145 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319693.1 → XP_054175668.1  coatomer subunit epsilon isoform X2

    2. XM_054319692.1 → XP_054175667.1  coatomer subunit epsilon isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_025088.1: Suppressed sequence

      Description
      NM_025088.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14579.3 GenPept UniProtKB/Swiss-Prot:O14579

    Gene LinkOut

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

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