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

Gene ID: 11316, updated on 27-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
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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
  • 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. The cytoplasmic coatomer protein COPI. A potential translational regulator. de La Vega LA, et al. J Biol Chem, 1999 Oct 29. PMID 10531302
  2. 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
  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. 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
  5. 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

See all (145) 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)

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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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 [email protected] for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14579.3 GenPept UniProtKB/Swiss-Prot:O14579

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