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    CPNE6 copine 6 [ Homo sapiens (human) ]

    Gene ID: 9362, updated on 10-Dec-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
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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

    Gene LinkOut

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