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    CPNE5 copine 5 [ Homo sapiens (human) ]

    Gene ID: 57699, updated on 14-Nov-2024

    Summary

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    Official Symbol
    CPNE5provided by HGNC
    Official Full Name
    copine 5provided by HGNC
    Primary source
    HGNC:HGNC:2318
    See related
    Ensembl:ENSG00000124772 MIM:604209; AllianceGenome:HGNC:2318
    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
    CPN5; COPN5
    Summary
    Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. More variants may exist, but their full-length natures could not be determined. [provided by RefSeq, Sep 2015]
    Expression
    Biased expression in brain (RPKM 15.7), lymph node (RPKM 8.6) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CPNE5 in Genome Data Viewer
    Location:
    6p21.2
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (36740775..36839998, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (36561362..36660596, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36708552..36807774, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36684729-36685230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24441 Neighboring gene RAB44, member RAS oncogene family Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36703037-36703538 Neighboring gene MPRA-validated peak5789 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:36723139-36724338 Neighboring gene G protein-coupled receptor 166, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36727049-36728017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36733508-36734405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36736445-36736976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36739695-36740194 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:36744935-36745643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36761234-36761900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36761901-36762565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36773485-36773986 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36778800-36778968 Neighboring gene Sharpr-MPRA regulatory region 12831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36808578-36809128 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91463 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:36827605-36828106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36835405-36835904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24445 Neighboring gene peptidylprolyl isomerase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17122 Neighboring gene chromosome 6 open reading frame 89 Neighboring gene Sharpr-MPRA regulatory region 12138 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36907574-36908164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926417-36926918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926919-36927418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36930796-36931421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36931422-36932046 Neighboring gene peptidase inhibitor 16

    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. Genetic variants in the CPNE5 gene are associated with alcohol dependence and obesity in Caucasian populations. Wang KS, et al. J Psychiatr Res, 2015 Dec. PMID 26522866
    2. Copine 5 expression predicts prognosis following curative resection of esophageal squamous cell carcinoma. Umeda S, et al. Oncol Rep, 2018 Dec. PMID 30272363
    3. High expression of CPNE5 and CPNE9 predicts positive prognosis in multiple myeloma. Zhu P, et al. Cancer Biomark, 2021. PMID 33780365
    4. Physical map of human 6p21.2-6p21.3: region flanking the centromeric end of the major histocompatibility complex. Tripodis N, et al. Genome Res, 1998 Jun. PMID 9647638, Free PMC Article
    5. The copines, a novel class of C2 domain-containing, calcium-dependent, phospholipid-binding proteins conserved from Paramecium to humans. Creutz CE, et al. J Biol Chem, 1998 Jan 16. PMID 9430674

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. High expression of CPNE5 and CPNE9 predicts positive prognosis in multiple myeloma.
      Title: High expression of CPNE5 and CPNE9 predicts positive prognosis in multiple myeloma.
    2. Data revealed that CPNE5 mRNA expression was significantly lower in ESCC tissues and cell lines and correlated with significantly shorter overall survival. Multivariable analysis identified low CPNE5 expression to be an independent prognostic factor of OS. Analysis of recurrence patterns revealed that significantly more patients with local recurrence expressed lower levels of CPNE5 mRNA.
      Title: Copine 5 expression predicts prognosis following curative resection of esophageal squamous cell carcinoma.
    3. Results provide the first evidence of genetic variants in the CPNE5 gene influencing both alcohol dependence and obesity
      Title: Genetic variants in the CPNE5 gene are associated with alcohol dependence and obesity in Caucasian populations.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog
    Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42228, KIAA1599, DKFZp666C234

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium-dependent phospholipid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    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
    		  

    General protein information

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    Preferred Names
    copine-5
    Names
    copine V

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001314017.1 → NP_001300946.1  copine-5 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks several 3' exons and contains an alternate 3' terminal exon compared to variant 1. This results in a novel 3' coding region and 3' UTR compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AA912142, AI951562, DA265730
      Conserved Domains (1) summary
      cd04048
      Location:23 → 135
      C2A_Copine; C2 domain first repeat in Copine

    2. NM_001314018.2 → NP_001300947.1  copine-5 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several 5' exons and contains an alternate 5' terminal exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 7 both encode the same isoform (c).
      Source sequence(s)
      BC036840, BC053872, Z85996
      Consensus CDS
      CCDS83078.1
      UniProtKB/Swiss-Prot
      Q9HCH3
      Related
      ENSP00000376885.2, ENST00000393189.2
      Conserved Domains (1) summary
      cd01459
      Location:2 → 262
      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_001314019.2 → NP_001300948.1  copine-5 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several 5' exons and contains an alternate 5' terminal exon and internal exon compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4, 5, and 6 all encode the same isoform (d).
      Source sequence(s)
      BC036840, BC053872, Z85996
      UniProtKB/Swiss-Prot
      Q9HCH3
      Related
      ENST00000459703.5
      Conserved Domains (1) summary
      pfam07002
      Location:1 → 213
      Copine

    4. NM_001314020.2 → NP_001300949.1  copine-5 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several 5' exons and an internal exon and contains an alternate 5' terminal exon compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4, 5, and 6 all encode the same isoform (d).
      Source sequence(s)
      BC012765, BC053872, Z85996
      UniProtKB/Swiss-Prot
      Q9HCH3
      Conserved Domains (1) summary
      pfam07002
      Location:1 → 213
      Copine

    5. NM_001376888.1 → NP_001363817.1  copine-5 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variants 4 and 5, encodes isoform d.
      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      pfam07002
      Location:1 → 213
      Copine

    6. NM_001376889.1 → NP_001363818.1  copine-5 isoform e

      Status: REVIEWED

      Source sequence(s)
      KF510949, Z85996
      Conserved Domains (3) summary
      cd04047
      Location:194 → 305
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:23 → 137
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:315 → 538
      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. ...

    7. NM_001376890.1 → NP_001363819.1  copine-5 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 3, encodes isoform c.
      Source sequence(s)
      Z85996
      Consensus CDS
      CCDS83078.1
      Conserved Domains (1) summary
      cd01459
      Location:2 → 262
      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. ...

    8. NM_001376891.1 → NP_001363820.1  copine-5 isoform f

      Status: REVIEWED

      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      cd01459
      Location:2 → 229
      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. ...

    9. NM_001376892.1 → NP_001363821.1  copine-5 isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10), as well as variant 11, encodes isoform g.
      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      pfam07002
      Location:1 → 191
      Copine

    10. NM_001376893.1 → NP_001363822.1  copine-5 isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11), as well as variant 10, encodes isoform g.
      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      pfam07002
      Location:1 → 191
      Copine

    11. NM_001376894.1 → NP_001363823.1  copine-5 isoform i

      Status: REVIEWED

      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      cd01459
      Location:2 → 204
      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. ...

    12. NM_001376895.1 → NP_001363824.1  copine-5 isoform h

      Status: REVIEWED

      Source sequence(s)
      Z85996
      Conserved Domains (1) summary
      cd01459
      Location:2 → 229
      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. ...

    13. NM_001410887.1 → NP_001397816.1  copine-5 isoform j

      Status: REVIEWED

      Source sequence(s)
      KF510949, Z85996
      Consensus CDS
      CCDS93904.1
      UniProtKB/TrEMBL
      A0A0J9YWA1
      Related
      ENSP00000487872.2, ENST00000633136.2

    14. NM_020939.2 → NP_065990.1  copine-5 isoform a

      See identical proteins and their annotated locations for NP_065990.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AI989513, BC036840, BC053872, DA265730, DB320492, Z85996
      Consensus CDS
      CCDS4825.1
      UniProtKB/Swiss-Prot
      Q7Z6C8, Q9HCH3
      Related
      ENSP00000244751.2, ENST00000244751.7
      Conserved Domains (3) summary
      cd04047
      Location:177 → 288
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:23 → 137
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:298 → 554
      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_164866.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      KF510949, Z85996

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      36740775..36839998 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419191.1 → XP_047275147.1  copine-5 isoform X6

      Conserved Domains (2) summary
      cd04047
      Location:46 → 157
      C2B_Copine; C2 domain second repeat in Copine
      cd01459
      Location:167 → 423
      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. XM_011514769.2 → XP_011513071.1  copine-5 isoform X2

      Conserved Domains (3) summary
      cd04047
      Location:177 → 288
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:23 → 137
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:298 → 521
      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. XM_011514768.2 → XP_011513070.1  copine-5 isoform X1

      Conserved Domains (3) summary
      cd04047
      Location:194 → 305
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:23 → 137
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:315 → 538
      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. XM_011514770.2 → XP_011513072.1  copine-5 isoform X3

      See identical proteins and their annotated locations for XP_011513072.1

      Conserved Domains (3) summary
      cd04047
      Location:156 → 267
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:2 → 99
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:277 → 500
      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. XM_047419190.1 → XP_047275146.1  copine-5 isoform X3

    6. XM_011514771.3 → XP_011513073.1  copine-5 isoform X3

      See identical proteins and their annotated locations for XP_011513073.1

      Conserved Domains (3) summary
      cd04047
      Location:156 → 267
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:2 → 99
      C2A_Copine; C2 domain first repeat in Copine
      cd01459
      Location:277 → 500
      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. ...

    7. XM_017011139.3 → XP_016866628.1  copine-5 isoform X7

    8. XM_011514773.3 → XP_011513075.1  copine-5 isoform X5

      Conserved Domains (2) summary
      cd04047
      Location:1 → 108
      C2B_Copine; C2 domain second repeat in Copine
      cd01459
      Location:118 → 341
      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. ...

    9. XM_011514772.1 → XP_011513074.1  copine-5 isoform X4

      Conserved Domains (3) summary
      cd04047
      Location:194 → 305
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:23 → 137
      C2A_Copine; C2 domain first repeat in Copine
      cl00057
      Location:315 → 495
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    10. XM_047419192.1 → XP_047275148.1  copine-5 isoform X8

    11. XM_047419193.1 → XP_047275149.1  copine-5 isoform X9

    RNA

    1. XR_007059285.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      36561362..36660596 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356120.1 → XP_054212095.1  copine-5 isoform X6

    2. XM_054356114.1 → XP_054212089.1  copine-5 isoform X2

    3. XM_054356113.1 → XP_054212088.1  copine-5 isoform X1

    4. XM_054356115.1 → XP_054212090.1  copine-5 isoform X3

    5. XM_054356116.1 → XP_054212091.1  copine-5 isoform X3

    6. XM_054356118.1 → XP_054212093.1  copine-5 isoform X3

    7. XM_054356121.1 → XP_054212096.1  copine-5 isoform X7

    8. XM_054356119.1 → XP_054212094.1  copine-5 isoform X5

    9. XM_054356117.1 → XP_054212092.1  copine-5 isoform X4

    10. XM_054356122.1 → XP_054212097.1  copine-5 isoform X8

    11. XM_054356123.1 → XP_054212098.1  copine-5 isoform X9

    RNA

    1. XR_008487368.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCH3.2 GenPept UniProtKB/Swiss-Prot:Q9HCH3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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