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Aliases for COPA Gene

Aliases for COPA Gene

  • Coatomer Protein Complex Subunit Alpha 2 3 5
  • Alpha-COP 3 4
  • Proxenin 2 3
  • HEP-COP 3 4
  • HEPCOP 3 4
  • Xenin 2 3
  • Coatomer Protein Complex, Subunit Alpha 2
  • Coatomer Subunit Alpha 3
  • Alpha Coat Protein 3
  • Alpha-Coat Protein 4
  • AILJK 3

External Ids for COPA Gene

Previous GeneCards Identifiers for COPA Gene

  • GC01M158051
  • GC01M155991
  • GC01M157036
  • GC01M157475
  • GC01M157072
  • GC01M158525
  • GC01M131615

Summaries for COPA Gene

Entrez Gene Summary for COPA Gene

  • In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COPs). Seven coat proteins have been identified, and they represent subunits of a complex known as coatomer. The subunits are designated alpha-COP, beta-COP, beta-prime-COP, gamma-COP, delta-COP, epsilon-COP, and zeta-COP. The alpha-COP, encoded by COPA, shares high sequence similarity with RET1P, the alpha subunit of the coatomer complex in yeast. Also, the N-terminal 25 amino acids of alpha-COP encode the bioactive peptide, xenin, which stimulates exocrine pancreatic secretion and may act as a gastrointestinal hormone. Alternative splicing results in multiple splice forms encoding distinct isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for COPA Gene

COPA (Coatomer Protein Complex Subunit Alpha) is a Protein Coding gene. Diseases associated with COPA include Autoimmune Interstitial Lung, Joint, And Kidney Disease and Pulmonary Hemosiderosis. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include structural molecule activity and hormone activity. An important paralog of this gene is STRN.

UniProtKB/Swiss-Prot for COPA Gene

  • The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity).

  • Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.

Gene Wiki entry for COPA Gene

Additional gene information for COPA Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COPA Gene

Genomics for COPA Gene

GeneHancer (GH) Regulatory Elements for COPA Gene

Promoters and enhancers for COPA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I160341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 558.4 +0.5 524 3.3 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B NCSTN COPA SNHG28 RPSAP18 ENSG00000272668 USP21 DEDD B4GALT3 PPOX LOC100287049
GH01I161096 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 28 -754.1 -754114 2.9 YBX1 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 MCM3 KLHDC9 USP21 DUSP12 PPOX LOC100287049 DEDD NCSTN RPSAP18 LOC148430 DCAF8
GH01I161130 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.9 -788.8 -788817 3.9 FEZF1 DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 DEDD USP21 DUSP12 PPOX LOC100287049 B4GALT3 DCAF8 NCSTN ATF6 LOC148430
GH01I159908 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.5 +426.1 426081 18.5 CLOCK FEZF1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 ZC3H11A TAGLN2 GC01M159919 GC01M159886 LOC100287049 NCSTN SLAMF8 RAD1P2 ENSG00000272668 SNHG28 VSIG8
GH01I161066 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.5 -725.1 -725051 5.1 HDGF PKNOX1 BMI1 ZBTB40 KLF5 IRF4 ZNF207 ZNF143 ATF7 ETV6 ARHGAP30 FCGR2A TSTD1 DUSP12 USP21 PPOX F11R DEDD NECTIN4 ENSG00000232879
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COPA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COPA gene promoter:

Genomic Locations for COPA Gene

Genomic Locations for COPA Gene
chr1:160,288,587-160,343,564
(GRCh38/hg38)
Size:
54,978 bases
Orientation:
Minus strand
chr1:160,258,377-160,313,354
(GRCh37/hg19)

Genomic View for COPA Gene

Genes around COPA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COPA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COPA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COPA Gene

Proteins for COPA Gene

  • Protein details for COPA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P53621-COPA_HUMAN
    Recommended name:
    Coatomer subunit alpha
    Protein Accession:
    P53621
    Secondary Accessions:
    • Q5T201
    • Q8IXZ9

    Protein attributes for COPA Gene

    Size:
    1224 amino acids
    Molecular mass:
    138346 Da
    Quaternary structure:
    • Oligomeric complex that consists of at least the alpha, beta, beta, gamma, delta, epsilon and zeta subunits. Probably interacts with PEX11A. Interacts with SCYL1 (By similarity). Interacts with JAGN1.

    Alternative splice isoforms for COPA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COPA Gene

Post-translational modifications for COPA Gene

  • Ubiquitination at posLast=6161, posLast=8181, Lys238, posLast=337337, Lys350, posLast=362362, Lys411, Lys441, Lys447, Lys480, Lys598, posLast=600600, Lys727, Lys825, and posLast=10281028

Other Protein References for COPA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COPA Gene

Domains & Families for COPA Gene

Gene Families for COPA Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for COPA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COPA: view

No data available for UniProtKB/Swiss-Prot for COPA Gene

Function for COPA Gene

Molecular function for COPA Gene

GENATLAS Biochemistry:
Golgi coatomer complex alpha subunit,component of the coat of the non-clathrin-coated vesicles,expressed in a wide range of fetal and adult tissues,homolog to the alpha subunit of S cerevisiae coatomer protein complex,involved in the transport between the endoplasmic reticulum and Golgi
UniProtKB/Swiss-Prot Function:
The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity).
UniProtKB/Swiss-Prot Function:
Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.

Phenotypes From GWAS Catalog for COPA Gene

Gene Ontology (GO) - Molecular Function for COPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005179 hormone activity IEA --
GO:0005198 structural molecule activity IEA --
genes like me logo Genes that share ontologies with COPA: view
genes like me logo Genes that share phenotypes with COPA: view

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COPA Gene

Localization for COPA Gene

Subcellular locations from UniProtKB/Swiss-Prot for COPA Gene

Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasmic vesicle, COPI-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Note=The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. {ECO:0000250}.
Xenin: Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COPA gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
cytosol 5
golgi apparatus 5
nucleus 3
plasma membrane 2
cytoskeleton 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA 1429581
GO:0005737 cytoplasm IDA 9115636
GO:0005789 endoplasmic reticulum membrane TAS --
genes like me logo Genes that share ontologies with COPA: view

Pathways & Interactions for COPA Gene

genes like me logo Genes that share pathways with COPA: view

Gene Ontology (GO) - Biological Process for COPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IBA --
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER IBA,TAS --
GO:0006891 intra-Golgi vesicle-mediated transport IBA --
genes like me logo Genes that share ontologies with COPA: view

No data available for SIGNOR curated interactions for COPA Gene

Drugs & Compounds for COPA Gene

(3) Drugs for COPA Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with COPA: view

Transcripts for COPA Gene

Alternative Splicing Database (ASD) splice patterns (SP) for COPA Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c ^
SP1: -
SP2:
SP3: -
SP4:
SP5: -
SP6: -
SP7: - - - -
SP8:
SP9: -
SP10:
SP11:
SP12: -

ExUns: 15a · 15b ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23 ^ 24
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for COPA Gene

GeneLoc Exon Structure for
COPA
ECgene alternative splicing isoforms for
COPA

Expression for COPA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COPA Gene

Protein differential expression in normal tissues from HIPED for COPA Gene

This gene is overexpressed in Breast (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COPA Gene



Protein tissue co-expression partners for COPA Gene

NURSA nuclear receptor signaling pathways regulating expression of COPA Gene:

COPA

SOURCE GeneReport for Unigene cluster for COPA Gene:

Hs.162121

mRNA Expression by UniProt/SwissProt for COPA Gene:

P53621-COPA_HUMAN
Tissue specificity: Uniformly expressed in a wide range of adult and fetal tissues. Xenin is found in gastric, duodenal and jejunal mucosa. Circulates in the blood. Seems to be confined to specific endocrine cells.

Evidence on tissue expression from TISSUES for COPA Gene

  • Nervous system(4.8)
  • Liver(4.7)
  • Stomach(4.3)
  • Lung(3.5)
  • Adrenal gland(3.2)
  • Heart(3.2)
  • Pancreas(3.2)
  • Skin(3)
  • Blood(2.8)
  • Eye(2.7)
  • Intestine(2.7)
  • Kidney(2.2)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with COPA: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for COPA Gene

Orthologs for COPA Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for COPA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COPA 33 34
  • 99.78 (n)
oppossum
(Monodelphis domestica)
Mammalia COPA 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COPA 33 34
  • 93.27 (n)
dog
(Canis familiaris)
Mammalia COPA 33 34
  • 91.93 (n)
rat
(Rattus norvegicus)
Mammalia Copa 33
  • 91.23 (n)
mouse
(Mus musculus)
Mammalia Copa 33 16 34
  • 91.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COPA 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves COPA 33 34
  • 82.9 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 97 (a)
OneToMany
-- 34
  • 80 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia copa 33
  • 80.83 (n)
zebrafish
(Danio rerio)
Actinopterygii copa 33 34
  • 75.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta alphaCop 35 33 34
  • 66.01 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010251 33
  • 65.22 (n)
worm
(Caenorhabditis elegans)
Secernentea Y71F9AL.17 35 33
  • 60.18 (n)
copa-1 34
  • 59 (a)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04884g 33
  • 52.22 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes COP1 33 34 36
  • 51.7 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR077C 33
  • 50.88 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G62020 33
  • 60.04 (n)
rice
(Oryza sativa)
Liliopsida Os09g0127800 33
  • 59.47 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.184 34
  • 73 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU10066 33
  • 55.83 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBPJ4664.04 33
  • 52.84 (n)
Species where no ortholog for COPA was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COPA Gene

ENSEMBL:
Gene Tree for COPA (if available)
TreeFam:
Gene Tree for COPA (if available)

Paralogs for COPA Gene

Paralogs for COPA Gene

genes like me logo Genes that share paralogs with COPA: view

Variants for COPA Gene

Sequence variations from dbSNP and Humsavar for COPA Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs116596416 benign, Autoimmune interstitial lung, joint, and kidney disease 160,297,336(-) T/C intron_variant
rs143115096 likely-benign, Autoimmune interstitial lung, joint, and kidney disease 160,294,803(-) C/T coding_sequence_variant, missense_variant
rs374078706 likely-benign, Autoimmune interstitial lung, joint, and kidney disease 160,314,079(-) A/G coding_sequence_variant, synonymous_variant
rs57425682 benign, Autoimmune interstitial lung, joint, and kidney disease 160,332,508(-) T/A/C coding_sequence_variant, missense_variant
rs74125574 benign, Autoimmune interstitial lung, joint, and kidney disease 160,296,094(-) G/A/T coding_sequence_variant, missense_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for COPA Gene

Variant ID Type Subtype PubMed ID
esv3308421 CNV mobile element insertion 20981092
esv3334227 CNV insertion 20981092
esv3361989 CNV insertion 20981092
esv3587712 CNV loss 21293372
nsv3210 CNV deletion 18451855
nsv946454 CNV duplication 23825009

Variation tolerance for COPA Gene

Residual Variation Intolerance Score: 10.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.54; 64.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COPA Gene

Human Gene Mutation Database (HGMD)
COPA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COPA

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COPA Gene

Disorders for COPA Gene

MalaCards: The human disease database

(5) MalaCards diseases for COPA Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autoimmune interstitial lung, joint, and kidney disease
  • ailjk
pulmonary hemosiderosis
  • hemosiderosis, pulmonary, with deficiency of gamma-a globulin
parainfluenza virus type 3
  • human parainfluenza virus type 3
lung disease
  • disorder of lung
lymphocytic choriomeningitis
  • lcm
- elite association - COSMIC cancer census association via MalaCards
Search COPA in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

COPA_HUMAN
  • Autoimmune interstitial lung, joint, and kidney disease (AILJK) [MIM:616414]: An autoimmune disease characterized by inflammatory arthritis, interstitial lung disease, and immune complex-mediated renal disease. {ECO:0000269 PubMed:25894502}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for COPA

genes like me logo Genes that share disorders with COPA: view

No data available for Genatlas for COPA Gene

Publications for COPA Gene

  1. HEP-COP, a novel human gene whose product is highly homologous to the alpha-subunit of the yeast coatomer protein complex. (PMID: 8647451) Chow VT … Quek HH (Gene 1996) 2 3 4 22 58
  2. Xenin--a review. (PMID: 9533652) Feurle GE (Peptides 1998) 3 4 22 58
  3. Alpha coat protein COPA (HEP-COP): presence of an Alu repeat in cDNA and identity of the amino terminus to xenin. (PMID: 9365789) Chow VT … Quek HH (Annals of human genetics 1997) 3 4 22 58
  4. Identification of xenin, a xenopsin-related peptide, in the human gastric mucosa and its effect on exocrine pancreatic secretion. (PMID: 1429581) Feurle GE … Metzger JW (The Journal of biological chemistry 1992) 3 4 22 58
  5. COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis. (PMID: 25894502) Watkin LB … Shum AK (Nature genetics 2015) 3 4 58

Products for COPA Gene

Sources for COPA Gene

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