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Aliases for CPNE3 Gene

Aliases for CPNE3 Gene

  • Copine 3 2 3 5
  • Copine III 2 3 4
  • CPN3 3 4
  • Copine-3 3
  • KIAA0636 4
  • PRO1071 3

External Ids for CPNE3 Gene

Previous GeneCards Identifiers for CPNE3 Gene

  • GC08P086047
  • GC08P087258
  • GC08P087483
  • GC08P087566
  • GC08P087497
  • GC08P082736
  • GC08P086485

Summaries for CPNE3 Gene

Entrez Gene Summary for CPNE3 Gene

  • Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a protein which contains two type II C2 domains in the amino-terminus and an A domain-like sequence in the carboxy-terminus. The A domain mediates interactions between integrins and extracellular ligands. [provided by RefSeq, Aug 2008]

GeneCards Summary for CPNE3 Gene

CPNE3 (Copine 3) is a Protein Coding gene. Among its related pathways are Metabolism and Innate Immune System. Gene Ontology (GO) annotations related to this gene include transporter activity. An important paralog of this gene is CPNE1.

UniProtKB/Swiss-Prot for CPNE3 Gene

  • Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation (PubMed:20010870).

Additional gene information for CPNE3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPNE3 Gene

Genomics for CPNE3 Gene

GeneHancer (GH) Regulatory Elements for CPNE3 Gene

Promoters and enhancers for CPNE3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J086513 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 657.9 +0.3 342 1.8 ARID4B SIN3A DMAP1 ZBTB7B ZNF48 YY1 GLIS2 ELK1 ZNF207 ATF7 RMDN1 CPNE3 MIOXP1
GH08J086515 Promoter/Enhancer 1.2 EPDnew ENCODE 650.7 +1.5 1459 0.2 BACH1 EBF1 BMI1 IRF4 EED ATF7 ETV6 IKZF2 RUNX3 CREM CPNE3 RMDN1 MIOXP1
GH08J086507 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 7.5 -6.1 -6077 2.6 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZBTB7B YY1 POLR2B E2F8 ZNF143 RMDN1 WWP1 NTAN1P2 LOC105375624 CPNE3 SLC2A3P4
GH08J086600 Enhancer 0.5 ENCODE 18.7 +87.4 87421 2.7 GATA3 JUND POLR2A RCOR1 CHD2 NR2F2 CPNE3 RMDN1 MIOXP1 PIR57796 CNGB3
GH08J086522 Enhancer 0.9 Ensembl ENCODE 7.5 +8.7 8675 1.7 PKNOX1 ESRRA EBF1 CTBP1 ZNF316 ATF7 FOSL2 FOS IKZF2 RUNX3 RMDN1 CPNE3 MIOXP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CPNE3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CPNE3 gene promoter:
  • HSF2
  • Lmo2
  • AML1a
  • HFH-3
  • FOXI1
  • HOXA3
  • En-1
  • GATA-1
  • IRF-2
  • FOXD1

Genomic Locations for CPNE3 Gene

Genomic Locations for CPNE3 Gene
47,072 bases
Plus strand
76,668 bases
Plus strand

Genomic View for CPNE3 Gene

Genes around CPNE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPNE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPNE3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPNE3 Gene

Proteins for CPNE3 Gene

  • Protein details for CPNE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A8KA47
    • Q8IYA1

    Protein attributes for CPNE3 Gene

    537 amino acids
    Molecular mass:
    60131 Da
    Quaternary structure:
    • Monomer (PubMed:12949241). Interacts with ERBB2 (preferentially with the tyrosine phosphorylated form); this interaction occurs at the cell membrane and is increased in a growth factor heregulin-dependent manner (PubMed:20010870). Interacts with SHC1; this interaction may mediate the binding of CPNE3 with ERBB2 (PubMed:20010870). Interacts with RACK1 (PubMed:20010870).
    • Sequence=BAA31611.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for CPNE3 Gene

Post-translational modifications for CPNE3 Gene

  • Phosphorylated on serine and threonine residues (PubMed:11041869).
  • Ubiquitination at posLast=184184 and Lys158
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CPNE3 Gene

Domains & Families for CPNE3 Gene

Gene Families for CPNE3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CPNE3 Gene

Suggested Antigen Peptide Sequences for CPNE3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the copine family.
  • Belongs to the copine family.
genes like me logo Genes that share domains with CPNE3: view

Function for CPNE3 Gene

Molecular function for CPNE3 Gene

UniProtKB/Swiss-Prot Function:
Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation (PubMed:20010870).
GENATLAS Biochemistry:
copine 3,calcium-dependent,phospholipid binding protein,potentially involved in regulating membrane trafficking,expressed in brain

Phenotypes From GWAS Catalog for CPNE3 Gene

Gene Ontology (GO) - Molecular Function for CPNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0004674 protein serine/threonine kinase activity IDA 11041869
GO:0005215 transporter activity TAS 9430674
GO:0005515 protein binding IPI 20010870
GO:0005544 calcium-dependent phospholipid binding TAS 11041869
genes like me logo Genes that share ontologies with CPNE3: view
genes like me logo Genes that share phenotypes with CPNE3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CPNE3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPNE3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CPNE3 Gene

Localization for CPNE3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPNE3 Gene

Nucleus. Cytoplasm. Cell membrane. Cell junction. Cell junction, focal adhesion. Note=Associates to the membrane in a calcium-dependent manner (PubMed:20010870). Translocates to the cell membrane and the nucleus in a calcium- or growth factor heregulin-dependent manner (PubMed:21087455, PubMed:20010870). Colocalizes with the tyrosine phosphorylated ERBB2 form at cell membrane and focal adhesions in a calcium- or growth factor heregulin-dependent manner (PubMed:20010870). {ECO:0000269 PubMed:20010870, ECO:0000269 PubMed:21087455}.

Subcellular locations from

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 CPNE3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 5
nucleus 5
cytosol 5
lysosome 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
  • Nucleus (3)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CPNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 20010870
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm NAS 11041869
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA 12949241
genes like me logo Genes that share ontologies with CPNE3: view

Pathways & Interactions for CPNE3 Gene

genes like me logo Genes that share pathways with CPNE3: view

Pathways by source for CPNE3 Gene

Interacting Proteins for CPNE3 Gene

Gene Ontology (GO) - Biological Process for CPNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA --
GO:0006629 lipid metabolic process TAS 9430674
GO:0016192 vesicle-mediated transport TAS 9430674
GO:0030335 positive regulation of cell migration IMP 20010870
GO:0038128 ERBB2 signaling pathway IDA 20010870
genes like me logo Genes that share ontologies with CPNE3: view

No data available for SIGNOR curated interactions for CPNE3 Gene

Drugs & Compounds for CPNE3 Gene

(1) Drugs for CPNE3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with CPNE3: view

Transcripts for CPNE3 Gene

Unigene Clusters for CPNE3 Gene

Copine III:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPNE3

Alternative Splicing Database (ASD) splice patterns (SP) for CPNE3 Gene

No ASD Table

Relevant External Links for CPNE3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CPNE3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CPNE3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CPNE3 Gene

This gene is overexpressed in Lymph node (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CPNE3 Gene

Protein tissue co-expression partners for CPNE3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPNE3 Gene:


SOURCE GeneReport for Unigene cluster for CPNE3 Gene:


mRNA Expression by UniProt/SwissProt for CPNE3 Gene:

Tissue specificity: Expressed in breast and weakly in prostate and ovarian tissues (PubMed:20010870). Expressed in neutrophils (at protein level) (PubMed:12949241). Widely expressed (PubMed:11041869). Expressed in the brain. Expressed in neutrophil precursors from the bone marrow and peripheral blood (PubMed:12949241). Expressed in primary breast tumors and ovarian endometrioid adenocarcinoma (PubMed:20010870).

Evidence on tissue expression from TISSUES for CPNE3 Gene

  • Nervous system(4.7)
  • Liver(4.4)
  • Skin(4.3)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with CPNE3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CPNE3 Gene

Orthologs for CPNE3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CPNE3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CPNE3 34 33
  • 99.44 (n)
(Canis familiaris)
Mammalia CPNE3 34 33
  • 92.87 (n)
(Bos Taurus)
Mammalia CPNE3 34 33
  • 90.99 (n)
(Monodelphis domestica)
Mammalia CPNE3 34
  • 90 (a)
(Mus musculus)
Mammalia Cpne3 16 34 33
  • 89.99 (n)
(Ornithorhynchus anatinus)
Mammalia CPNE3 34
  • 89 (a)
(Rattus norvegicus)
Mammalia Cpne3 33
  • 88.62 (n)
(Gallus gallus)
Aves CPNE3 34 33
  • 79.75 (n)
(Anolis carolinensis)
Reptilia CPNE3 34
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cpne3 33
  • 74.73 (n)
Str.3116 33
(Danio rerio)
Actinopterygii cpne3 34 33
  • 69.19 (n)
zgc55622 33
(Caenorhabditis elegans)
Secernentea T12A7.1 35
  • 43 (a)
Y73F8A.19 35
  • 26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons BON2 33
  • 50.43 (n)
(Oryza sativa)
Liliopsida Os02g0521300 33
  • 49.42 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
CSA.7161 34
  • 53 (a)
-- 34
  • 45 (a)
Cin.5235 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5235 33
Species where no ortholog for CPNE3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 CPNE3 Gene

Gene Tree for CPNE3 (if available)
Gene Tree for CPNE3 (if available)
Evolutionary constrained regions (ECRs) for CPNE3: view image

Paralogs for CPNE3 Gene

Paralogs for CPNE3 Gene

(8) SIMAP similar genes for CPNE3 Gene using alignment to 8 proteins:

  • E5RG68_HUMAN
  • E5RG97_HUMAN
  • E5RJ85_HUMAN
  • H0YB26_HUMAN
  • Q05DL8_HUMAN
genes like me logo Genes that share paralogs with CPNE3: view

Variants for CPNE3 Gene

Sequence variations from dbSNP and Humsavar for CPNE3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000034074 -- 86,545,655(+) T/C intron_variant
rs1000045927 -- 86,524,396(+) G/A intron_variant
rs1000146128 -- 86,530,725(+) C/A intron_variant
rs1000156025 -- 86,549,338(+) C/T intron_variant
rs1000286794 -- 86,512,443(+) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CPNE3 Gene

Variant ID Type Subtype PubMed ID
esv2422239 CNV duplication 17116639
esv3302897 CNV tandem duplication 20981092
esv3617911 CNV loss 21293372
nsv1023510 CNV loss 25217958

Variation tolerance for CPNE3 Gene

Residual Variation Intolerance Score: 81.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.13; 92.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CPNE3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPNE3 Gene

Disorders for CPNE3 Gene

Additional Disease Information for CPNE3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CPNE3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CPNE3 Gene

Publications for CPNE3 Gene

  1. Copines-1, -2, -3, -6 and -7 show different calcium-dependent intracellular membrane translocation and targeting. (PMID: 21087455) Perestenko PV … Jeffrey McIlhinney RA (The FEBS journal 2010) 3 4 58
  2. Copine-III interacts with ErbB2 and promotes tumor cell migration. (PMID: 20010870) Heinrich C … Hynes NE (Oncogene 2010) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Tissue expression of copines and isolation of copines I and III from the cytosol of human neutrophils. (PMID: 12949241) Cowland JB … Lollike K (Journal of leukocyte biology 2003) 3 4 58

Products for CPNE3 Gene

Sources for CPNE3 Gene

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