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    CPNE1 copine 1 [ Homo sapiens (human) ]

    Gene ID: 8904, updated on 5-May-2024

    Summary

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    Official Symbol
    CPNE1provided by HGNC
    Official Full Name
    copine 1provided by HGNC
    Primary source
    HGNC:HGNC:2314
    See related
    Ensembl:ENSG00000214078 MIM:604205; AllianceGenome:HGNC:2314
    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
    mouse all
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    Genomic context

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    Location:
    20q11.22
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35626044..35664900, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37347020..37385875, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34213966..34252822, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene fer-1 like family member 4 (pseudogene) Neighboring gene uncharacterized LOC124904891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34205257-34206207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34206208-34207157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17789 Neighboring gene sperm associated antigen 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34223677-34224176 Neighboring gene RN7SK pseudogene 271 Neighboring gene RNA, U6 small nuclear 759, pseudogene Neighboring gene RNA binding motif protein 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34251645-34252150 Neighboring gene Sharpr-MPRA regulatory region 3991 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34252655-34253159 Neighboring gene NFS1 cysteine desulfurase Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34286841-34287500 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34287501-34288160 Neighboring gene reactive oxygen species modulator 1

    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
    • 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. Overexpression of Copines-1 is associated with clinicopathological parameters and poor outcome in gastric cancer. Yang J, et al. J Clin Lab Anal, 2022 Nov. PMID 36310511, Free PMC Article
    2. Up-regulation of CPNE1 Appears to Enhance Cancer Progression in HER2-positive and Luminal A Breast Cancer Cells. Choi HY, et al. Anticancer Res, 2022 Jul. PMID 35790271
    3. CPNE1 predicts poor prognosis and promotes tumorigenesis and radioresistance via the AKT singling pathway in triple-negative breast cancer. Shao Z, et al. Mol Carcinog, 2020 May. PMID 32181526, Free PMC Article
    4. High expression of Copine 1 promotes cell growth and metastasis in human lung adenocarcinoma. Liu S, et al. Int J Oncol, 2018 Dec. PMID 30221693, Free PMC Article
    5. CPNE1 silencing inhibits the proliferation, invasion and migration of human osteosarcoma cells. Jiang Z, et al. Oncol Rep, 2018 Feb. PMID 29207139, Free PMC Article

    See all (67) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CPNE1, A Potential Therapeutic Target in Nasopharyngeal Carcinoma, Affects Cell Growth and Radiation Resistance.
      Title: CPNE1, A Potential Therapeutic Target in Nasopharyngeal Carcinoma, Affects Cell Growth and Radiation Resistance.
    2. Silencing of CPNE1-TRAF2 Axis Restrains the Development of Pancreatic Cancer.
      Title: Silencing of CPNE1-TRAF2 Axis Restrains the Development of Pancreatic Cancer.
    3. Overexpression of Copines-1 is associated with clinicopathological parameters and poor outcome in gastric cancer.
      Title: Overexpression of Copines-1 is associated with clinicopathological parameters and poor outcome in gastric cancer.
    4. Up-regulation of CPNE1 Appears to Enhance Cancer Progression in HER2-positive and Luminal A Breast Cancer Cells.
      Title: Up-regulation of CPNE1 Appears to Enhance Cancer Progression in HER2-positive and Luminal A Breast Cancer Cells.
    5. CPNE1 promotes non-small cell lung cancer progression by interacting with RACK1 via the MET signaling pathway.
      Title: CPNE1 promotes non-small cell lung cancer progression by interacting with RACK1 via the MET signaling pathway.
    6. Prognostic Value of Copine 1 in Patients With Renal Cell Carcinoma.
      Title: Prognostic Value of Copine 1 in Patients With Renal Cell Carcinoma.
    7. High CPNE1 expression is associated with tumorigenesis and radioresistance via the AKT singling pathway in triple-negative breast cancer.
      Title: CPNE1 predicts poor prognosis and promotes tumorigenesis and radioresistance via the AKT singling pathway in triple-negative breast cancer.
    8. We observed that knockdown of CPNE1 and increased expression of miR-335-5p inhibits cell proliferation and motility in NSCLC cells, and found that CPNE1 was a target of miR-335-5p.
      Title: CPNE1 is a target of miR-335-5p and plays an important role in the pathogenesis of non-small cell lung cancer.
    9. Study find that CPNE1 expression is upregulated in non-small cell lung cancer (NSCLC) and associated with advanced TNM stage, lymph node and distant metastasis. Furthermore, its knockdown inhibits the cell cycle in NSCLC cells. These data strongly suggest that CPNE1 is an oncogene in NSCLC and serves an important role in tumorigenesis of NSCLC progression.
      Title: High expression of Copine 1 promotes cell growth and metastasis in human lung adenocarcinoma.
    10. Results demonstrated that CPNE1 was highly expressed in the osteosarcoma (OS) tissues and cell lines. Its knockdown significantly inhibited cell proliferation, colony formation, invasion and metastasis in OS cell lines.
      Title: CPNE1 silencing inhibits the proliferation, invasion and migration of human osteosarcoma cells.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    Potential readthrough

    Included gene: NFS1

    Homology

    Clone Names

    • MGC1142

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NF-kappaB binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables calcium ion binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables calcium-dependent phospholipid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phosphatidylserine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to calcium ion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to calcium ion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lipid metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of non-canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron projection extension IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in neuron projection extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of tumor necrosis factor-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of tumor necrosis factor-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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-1
    Names
    chromobindin 17
    copine I

    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_001198863.2 → NP_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, BQ433414
      UniProtKB/TrEMBL
      F2Z2V0
      Related
      ENSP00000415597.1, ENST00000437340.5
      Conserved Domains (3) summary
      cd04047
      Location:138 → 245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6 → 124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251 → 508
      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_003915.6 → NP_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, U83246
      Consensus CDS
      CCDS46595.1
      UniProtKB/TrEMBL
      B0QZ18, F2Z2V0
      Related
      ENSP00000317257.5, ENST00000317677.9
      Conserved Domains (3) summary
      cd04047
      Location:143 → 250
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:11 → 129
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:256 → 514
      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_152925.3 → NP_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)
      BC001142, DB091531
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      E1P5Q4, Q6IBL3, Q99829, Q9H243, Q9NTZ7
      UniProtKB/TrEMBL
      F2Z2V0
      Related
      ENSP00000380585.1, ENST00000397443.7
      Conserved Domains (3) summary
      cd04047
      Location:138 → 245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6 → 124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251 → 509
      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_152926.3 → NP_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, DB091531
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      E1P5Q4, Q6IBL3, Q99829, Q9H243, Q9NTZ7
      UniProtKB/TrEMBL
      F2Z2V0
      Related
      ENSP00000380584.1, ENST00000397442.5
      Conserved Domains (3) summary
      cd04047
      Location:138 → 245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6 → 124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251 → 509
      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_152927.3 → NP_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)
      BC001142, BG701713
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      E1P5Q4, Q6IBL3, Q99829, Q9H243, Q9NTZ7
      UniProtKB/TrEMBL
      F2Z2V0
      Conserved Domains (3) summary
      cd04047
      Location:138 → 245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6 → 124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251 → 509
      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_152928.3 → NP_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)
      BC001142, DA983782
      Consensus CDS
      CCDS13260.1
      UniProtKB/Swiss-Prot
      E1P5Q4, Q6IBL3, Q99829, Q9H243, Q9NTZ7
      UniProtKB/TrEMBL
      F2Z2V0
      Related
      ENSP00000336945.4, ENST00000352393.8
      Conserved Domains (3) summary
      cd04047
      Location:138 → 245
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:6 → 124
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:251 → 509
      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_037188.2 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, DB091531
      Related
      ENST00000401607.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      35626044..35664900 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      37347020..37385875 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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99829.1 GenPept UniProtKB/Swiss-Prot:Q99829

    Gene LinkOut

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