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CPNE1 copine 1 [ Homo sapiens (human) ]

Gene ID: 8904, updated on 5-Aug-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 
calcium-dependent phospholipid binding TAS
Traceable Author Statement
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 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
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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