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    CPNE1 copine 1 [ Homo sapiens (human) ]

    Gene ID: 8904, updated on 2-Oct-2018

    Summary

    Official Symbol
    CPNE1provided by HGNC
    Official Full Name
    copine 1provided by HGNC
    Primary source
    HGNC:HGNC:2314
    See related
    Ensembl:ENSG00000214078 MIM:604205; Vega:OTTHUMG00000032356
    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
    CPN1; COPN1
    Summary
    Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a calcium-dependent protein that also contains two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. However, the encoded protein does not contain a predicted signal sequence or transmembrane domains. This protein has a broad tissue distribution and it may function in membrane trafficking. This gene and the gene for RNA binding motif protein 12 overlap at map location 20q11.21. Alternate splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Aug 2008]
    Expression
    Ubiquitous expression in spleen (RPKM 33.6), placenta (RPKM 33.3) and 25 other tissues See more
    Orthologs

    Genomic context

    See CPNE1 in Genome Data Viewer
    Location:
    20q11.22
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (35626031..35664956, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34213953..34252878, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene fer-1 like family member 4, pseudogene Neighboring gene ribosomal protein L37 pseudogene 1 Neighboring gene sperm associated antigen 4 Neighboring gene RNA, 7SK small nuclear pseudogene 271 Neighboring gene RNA, U6 small nuclear 759, pseudogene Neighboring gene RNA binding motif protein 12 Neighboring gene NFS1, cysteine desulfurase Neighboring gene reactive oxygen species modulator 1 Neighboring gene RNA binding motif protein 39

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Glycerophospholipid biosynthesis, organism-specific biosystem (from REACTOME)
      Glycerophospholipid biosynthesis, organism-specific biosystemGlycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
      Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
    • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
      Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
    • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
      Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: NFS1

    Homology

    Clone Names

    • MGC1142

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NF-kappaB binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    calcium ion binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    calcium-dependent phospholipid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    phosphatidylserine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular response to calcium ion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cellular response to calcium ion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glycerophospholipid biosynthetic process TAS
    Traceable Author Statement
    more info
     
    lipid metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of NIK/NF-kappaB signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neuron projection extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron projection extension IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neutrophil degranulation TAS
    Traceable Author Statement
    more info
     
    positive regulation of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of protein kinase B signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of protein kinase B signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of tumor necrosis factor-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of tumor necrosis factor-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of I-kappaB kinase/NF-kappaB signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of I-kappaB kinase/NF-kappaB signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    azurophil granule membrane TAS
    Traceable Author Statement
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    copine-1
    Names
    chromobindin 17
    copine I

    NCBI Reference Sequences (RefSeq)

    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_001198863.1NP_001185792.1  copine-1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) uses a different splice site in the 5' UTR and in the 3' coding region, compared to variant 1. The resulting protein (isoform c) is shorter by one amino acid when it is compared to isoform a.
      Source sequence(s)
      BC021010, BG231745, BM755522, BQ433414
      Related
      ENSP00000415597.1, OTTHUMP00000274444, ENST00000437340.5, OTTHUMT00000473128
      Conserved Domains (3) summary
      cd04047
      Location:138245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251508
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...
    2. NM_003915.5NP_003906.2  copine-1 isoform b

      See identical proteins and their annotated locations for NP_003906.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses a different exon in its 5' UTR and 5' coding region, compared to variant 1. It encodes isoform b, which has a longer and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AW964878, BC001142, BG231745, U83246
      Consensus CDS
      CCDS46595.1
      UniProtKB/Swiss-Prot
      Q99829
      UniProtKB/TrEMBL
      B0QZ18
      Related
      ENSP00000317257.5, OTTHUMP00000030776, ENST00000317677.9, OTTHUMT00000078910
      Conserved Domains (3) summary
      cd04047
      Location:143250
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:11129
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:256514
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...
    3. NM_152925.2NP_690902.1  copine-1 isoform a

      See identical proteins and their annotated locations for NP_690902.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant transcript.
      Source sequence(s)
      AL109827, BC001142, BG231745, DB091531
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      Q99829
      Related
      ENSP00000380585.1, OTTHUMP00000281487, ENST00000397443.6, OTTHUMT00000488473
      Conserved Domains (3) summary
      cd04047
      Location:138245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251509
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...
    4. NM_152926.2NP_690903.1  copine-1 isoform a

      See identical proteins and their annotated locations for NP_690903.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses a different splice site which creates a shorter 5' UTR, compared to variant 1.
      Source sequence(s)
      BC001142, BG231745, BM755522, DB091531
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      Q99829
      Related
      ENSP00000380584.1, OTTHUMP00000196688, ENST00000397442.5, OTTHUMT00000316948
      Conserved Domains (3) summary
      cd04047
      Location:138245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251509
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...
    5. NM_152927.2NP_690904.1  copine-1 isoform a

      See identical proteins and their annotated locations for NP_690904.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an additional exon in its 5' UTR, compared to variant 1.
      Source sequence(s)
      AL109827, BC001142, BG231745, BG701713
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      Q99829
      Conserved Domains (3) summary
      cd04047
      Location:138245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251509
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...
    6. NM_152928.2NP_690905.1  copine-1 isoform a

      See identical proteins and their annotated locations for NP_690905.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an additional exon in its 5' UTR, compared to variant 1.
      Source sequence(s)
      AL109827, BC001142, BG231745, DA983782
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      Q99829
      Related
      ENSP00000336945.4, OTTHUMP00000030775, ENST00000352393.8, OTTHUMT00000078909
      Conserved Domains (3) summary
      cd04047
      Location:138245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251509
      vWA_copine_like; VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. ...

    RNA

    1. NR_037188.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC001142, BG231745, DB091531
      Related
      ENST00000483359.5

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

      Range
      35626031..35664956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152930.1: Suppressed sequence

      Description
      NM_152930.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    2. NM_152931.1: Suppressed sequence

      Description
      NM_152931.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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