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CPNE6 copine 6 [ Homo sapiens (human) ]

Gene ID: 9362, updated on 28-Oct-2024

Summary

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Official Symbol
CPNE6provided by HGNC
Official Full Name
copine 6provided by HGNC
Primary source
HGNC:HGNC:2319
See related
Ensembl:ENSG00000100884 MIM:605688; AllianceGenome:HGNC:2319
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
copine-6
Summary
This gene encodes a member of the copine family. Members of this family are calcium-dependent, phospholipid-binding proteins with C2 domains, two calcium- and phospholipid-binding domains. Through their domain structure and lipid binding capabilities, these proteins may play a role in membrane trafficking. This protein is thought to be brain-specific and has a domain structure of two N-terminal C2 domains and one von Willebrand factor A domain. It may have a role in synaptic plasticity. [provided by RefSeq, Jul 2013]
Expression
Biased expression in brain (RPKM 23.5), small intestine (RPKM 2.5) and 3 other tissues See more
Orthologs
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Genomic context

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See CPNE6 in Genome Data Viewer
Location:
14q11.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (24070949..24078087)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (18269265..18276403)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (24540158..24547296)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene dehydrogenase/reductase 4 like 1 (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24521876-24522575 Neighboring gene capping protein regulator and myosin 1 linker 3 Neighboring gene uncharacterized LOC105370412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8184 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:24544925-24546124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24551461-24552375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24558209-24558708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8186 Neighboring gene neural retina leucine zipper Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5622 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:24563543-24564192 Neighboring gene phosphoenolpyruvate carboxykinase 2, mitochondrial Neighboring gene Sharpr-MPRA regulatory region 2696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:24583239-24583954 Neighboring gene DDB1 and CUL4 associated factor 11

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. Copines: a ubiquitous family of Ca(2+)-dependent phospholipid-binding proteins. Tomsig JL, et al. Cell Mol Life Sci, 2002 Sep. PMID 12440769, Free PMC Article
  2. Increased expression of copine VI in patients with refractory epilepsy and a rat model. Zhu B, et al. J Neurol Sci, 2016 Jan 15. PMID 26723968
  3. N-copine: a novel two C2-domain-containing protein with neuronal activity-regulated expression. Nakayama T, et al. FEBS Lett, 1998 May 22. PMID 9645480
  4. Characterization of human copine III as a phosphoprotein with associated kinase activity. Caudell EG, et al. Biochemistry, 2000 Oct 24. PMID 11041869
  5. Copine-6 Binds to SNAREs and Selectively Suppresses Spontaneous Neurotransmission. Liu P, et al. J Neurosci, 2018 Jun 27. PMID 29802203, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. we identify copine-6 as a specific regulator of spontaneous neurotransmission
    Title: Copine-6 Binds to SNAREs and Selectively Suppresses Spontaneous Neurotransmission.
  2. expression of CPNE6 increased remarkably in brains of epileptic patients and in experimental epileptic rats. Expression is mainly in neurons.
    Title: Increased expression of copine VI in patients with refractory epilepsy and a rat model.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding TAS
Traceable Author Statement
more info
 PubMed 
enables calcium-dependent phospholipid binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylserine binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to calcium ion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of dendrite extension IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in postsynaptic actin cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in clathrin-coated endocytic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
copine-6
Names
N-copine
copine VI (neuronal)

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_001280558.2 → NP_001267487.1  copine-6 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS61413.1
    UniProtKB/Swiss-Prot
    O95741
    Related
    ENSP00000440077.1, ENST00000537691.5
    Conserved Domains (3) summary
    cd04047
    Location:207 → 321
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:75 → 192
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:380 → 596
    Copine; Copine

  2. NM_001385056.1 → NP_001371985.1  copine-6 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 2. Variants 2-5 all encode the same isoform (2).
    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS9607.1
    UniProtKB/Swiss-Prot
    B2RAG6, B7Z1M3, D3DS55, F5GXN1, O95741, Q53HA6, Q8WVG1
    Conserved Domains (3) summary
    cd04047
    Location:152 → 266
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:20 → 137
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:325 → 541
    Copine

  3. NM_001385057.1 → NP_001371986.1  copine-6 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 2. Variants 2-5 all encode the same isoform (2).
    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS9607.1
    UniProtKB/Swiss-Prot
    B2RAG6, B7Z1M3, D3DS55, F5GXN1, O95741, Q53HA6, Q8WVG1
    Conserved Domains (3) summary
    cd04047
    Location:152 → 266
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:20 → 137
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:325 → 541
    Copine

  4. NM_001385058.1 → NP_001371987.1  copine-6 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 2. Variants 2-5 all encode the same isoform (2).
    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS9607.1
    UniProtKB/Swiss-Prot
    B2RAG6, B7Z1M3, D3DS55, F5GXN1, O95741, Q53HA6, Q8WVG1
    Related
    ENSP00000380211.2, ENST00000397016.6
    Conserved Domains (3) summary
    cd04047
    Location:152 → 266
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:20 → 137
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:325 → 541
    Copine

  5. NM_006032.4 → NP_006023.1  copine-6 isoform 2

    See identical proteins and their annotated locations for NP_006023.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region and initiates translation at a downstream start codon,, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AB009288, AL136295, BX118572
    Consensus CDS
    CCDS9607.1
    UniProtKB/Swiss-Prot
    B2RAG6, B7Z1M3, D3DS55, F5GXN1, O95741, Q53HA6, Q8WVG1
    Related
    ENSP00000510387.1, ENST00000689861.1
    Conserved Domains (3) summary
    cd04047
    Location:152 → 266
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:20 → 137
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:325 → 541
    Copine

RNA

  1. NR_169564.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL136295

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    24070949..24078087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654722.1 Reference GRCh38.p14 PATCHES

    Range
    371927..379065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    18269265..18276403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95741.3 GenPept UniProtKB/Swiss-Prot:O95741

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