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Aliases for CPNE9 Gene

Aliases for CPNE9 Gene

  • Copine Family Member 9 2 3 5
  • Copine Family Member IX 2 3
  • Copine IX 3 4
  • Copine-Like Protein 3
  • Copine-9 3

External Ids for CPNE9 Gene

Previous GeneCards Identifiers for CPNE9 Gene

  • GC03P009724
  • GC03P009681
  • GC03P009745

Summaries for CPNE9 Gene

GeneCards Summary for CPNE9 Gene

CPNE9 (Copine Family Member 9) is a Protein Coding gene. An important paralog of this gene is CPNE5.

UniProtKB/Swiss-Prot for CPNE9 Gene

  • Probable calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPNE9 Gene

Genomics for CPNE9 Gene

Regulatory Elements for CPNE9 Gene

Enhancers for CPNE9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F009680 0.6 ENCODE 12.1 -22.0 -22004 1.6 ZFP3 POLR2A SMAD4 ZNF24 TEAD3 CPNE9 MTMR14 BRPF1 ARPC4 ARPC4-TTLL3 TADA3
GH03F009679 0.4 FANTOM5 12.1 -24.0 -23957 0.1 MCM3 CPNE9 BRPF1 CIDEC IL17RC MTMR14
GH03F009705 0.7 ENCODE 0.8 +1.4 1365 0.2 DRAP1 TEAD4 ZFHX2 POLR2A SCRT2 PRDM10 EGR2 SRF SCRT1 SP3 CPNE9 GC03M009670
GH03F009648 1.1 ENCODE 0.2 -54.0 -54017 2.2 HDGF PKNOX1 CREB3L1 MLX ARID4B SIN3A ZNF2 ZNF143 ZNF207 FOS RNU6-882P EMC3-AS1 PRRT3 CIDECP MTMR14 CPNE9
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CPNE9 on UCSC Golden Path with GeneCards custom track

Promoters for CPNE9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001844958 1293 601 DRAP1 KLF1 TEAD4 SIN3A ZFHX2 POLR2A SCRT2 SMC3 ZNF600 PRDM10

Genomic Location for CPNE9 Gene

9,703,807 bp from pter
9,729,908 bp from pter
26,102 bases
Plus strand

Genomic View for CPNE9 Gene

Genes around CPNE9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPNE9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPNE9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPNE9 Gene

Proteins for CPNE9 Gene

  • Protein details for CPNE9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A1L430
    • A6NDX6
    • A8MSP8

    Protein attributes for CPNE9 Gene

    553 amino acids
    Molecular mass:
    61864 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CPNE9 Gene


neXtProt entry for CPNE9 Gene

Post-translational modifications for CPNE9 Gene

  • Glycosylation at Asn 95
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CPNE9 Gene

Domains & Families for CPNE9 Gene

Gene Families for CPNE9 Gene

Protein Domains for CPNE9 Gene


Suggested Antigen Peptide Sequences for CPNE9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 2 C2 domains.
  • Belongs to the copine family.
  • Contains 2 C2 domains.
  • Contains 1 VWFA domain.
  • Belongs to the copine family.
genes like me logo Genes that share domains with CPNE9: view

Function for CPNE9 Gene

Molecular function for CPNE9 Gene

UniProtKB/Swiss-Prot Function:
Probable calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003).
genes like me logo Genes that share phenotypes with CPNE9: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CPNE9 Gene

Localization for CPNE9 Gene

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 CPNE9 gene
Compartment Confidence
extracellular 5
cytosol 3
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CPNE9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 23580065
GO:0070062 extracellular exosome IDA 23533145
genes like me logo Genes that share ontologies with CPNE9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CPNE9 Gene

Pathways & Interactions for CPNE9 Gene

SuperPathways for CPNE9 Gene

No Data Available

Interacting Proteins for CPNE9 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: ENSP00000373343 for CPNE9 Gene via STRING

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for CPNE9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030154 cell differentiation IEA --
GO:1903861 positive regulation of dendrite extension IDA 23999003
genes like me logo Genes that share ontologies with CPNE9: view

No data available for Pathways by source and SIGNOR curated interactions for CPNE9 Gene

Drugs & Compounds for CPNE9 Gene

(1) Drugs for CPNE9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with CPNE9: view

Transcripts for CPNE9 Gene

Unigene Clusters for CPNE9 Gene

Copine family member IX:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPNE9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21
SP1: -
SP2: -
SP3: -

Relevant External Links for CPNE9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CPNE9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CPNE9 Gene

mRNA differential expression in normal tissues according to GTEx for CPNE9 Gene

This gene is overexpressed in Brain - Cerebellum (x9.8), Brain - Cerebellar Hemisphere (x9.2), Brain - Cortex (x9.0), Brain - Frontal Cortex (BA9) (x6.7), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for CPNE9 Gene

This gene is overexpressed in Brain (51.5) and Heart (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CPNE9 Gene

Protein tissue co-expression partners for CPNE9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPNE9 Gene:


SOURCE GeneReport for Unigene cluster for CPNE9 Gene:


mRNA Expression by UniProt/SwissProt for CPNE9 Gene:

Tissue specificity: Expressed in melanocytes (PubMed:23999003).
genes like me logo Genes that share expression patterns with CPNE9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for CPNE9 Gene

Orthologs for CPNE9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CPNE9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CPNE9 34 35
  • 99.88 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 96 (a)
-- 35
  • 88 (a)
(Bos Taurus)
Mammalia CPNE9 34 35
  • 94.86 (n)
(Canis familiaris)
Mammalia CPNE9 34 35
  • 93.84 (n)
(Monodelphis domestica)
Mammalia CPNE9 35
  • 92 (a)
(Rattus norvegicus)
Mammalia Cpne9 34
  • 91.86 (n)
(Mus musculus)
Mammalia Cpne9 34 16 35
  • 91.68 (n)
(Gallus gallus)
Aves CPNE9 35
  • 85 (a)
(Anolis carolinensis)
Reptilia CPNE9 35
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cpne5 34
  • 75.22 (n)
(Caenorhabditis elegans)
Secernentea gem-4 35
  • 39 (a)
nra-1 35
  • 39 (a)
cpna-5 35
  • 23 (a)
cpna-4 35
  • 22 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 54 (a)
Species where no ortholog for CPNE9 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for CPNE9 Gene

Gene Tree for CPNE9 (if available)
Gene Tree for CPNE9 (if available)

Paralogs for CPNE9 Gene

Paralogs for CPNE9 Gene

(9) SIMAP similar genes for CPNE9 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CPNE9: view

Variants for CPNE9 Gene

Sequence variations from dbSNP and Humsavar for CPNE9 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs10049122 -- 9,721,597(+) AGCTG(C/G)GTCTA intron-variant
rs1091917 -- 9,722,064(+) AGGTG(C/T)GCACC intron-variant
rs111336803 -- 9,716,475(+) GAGGA(-/T)TTTTT intron-variant
rs111431147 -- 9,712,460(+) CCCTG(A/G)CCCAC intron-variant
rs111454143 -- 9,714,072(+) GTCTC(-/AATA/AATAAATA)AATAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CPNE9 Gene

Variant ID Type Subtype PubMed ID
esv2673134 CNV deletion 23128226
nsv1008805 CNV gain 25217958
nsv1010768 CNV gain 25217958
nsv1109490 CNV deletion 24896259
nsv1139087 CNV deletion 24896259
nsv475951 CNV novel sequence insertion 20440878
nsv589647 CNV loss 21841781

Variation tolerance for CPNE9 Gene

Residual Variation Intolerance Score: 12.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.26; 25.26% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CPNE9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPNE9 Gene

Disorders for CPNE9 Gene

Relevant External Links for CPNE9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CPNE9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CPNE9 Gene

Publications for CPNE9 Gene

  1. SYT14L, especially its C2 domain, is involved in regulating melanocyte differentiation. (PMID: 23999003) Yoo J.C. … Yoon T.J. (J. Dermatol. Sci. 2013) 3 4 64
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  3. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T. … Smith R.D. (J. Proteome Res. 2005) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The copines, a novel class of C2 domain-containing, calcium- dependent, phospholipid-binding proteins conserved from Paramecium to humans. (PMID: 9430674) Creutz C.E. … Cohen J. (J. Biol. Chem. 1998) 2 3 64

Products for CPNE9 Gene

Sources for CPNE9 Gene

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