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CPNE4 copine 4 [ Homo sapiens (human) ]

Gene ID: 131034, updated on 3-Apr-2024

Summary

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Official Symbol
CPNE4provided by HGNC
Official Full Name
copine 4provided by HGNC
Primary source
HGNC:HGNC:2317
See related
Ensembl:ENSG00000196353 MIM:604208; AllianceGenome:HGNC:2317
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
CPN4; COPN4
Summary
This gene belongs to the highly conserved copine family. It encodes a calcium-dependent, phospholipid-binding protein, which may be involved in membrane trafficking, mitogenesis and development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression
Biased expression in prostate (RPKM 9.1), brain (RPKM 2.4) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
3q22.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (131533569..132039606, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (134277285..134784042, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (131252413..131758450, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131221451-131222137 Neighboring gene uncharacterized LOC105374114 Neighboring gene mitochondrial ribosomal protein L3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14738 Neighboring gene BCL2 like 12 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:131287110-131287684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20534 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:131515358-131515894 Neighboring gene uncharacterized LOC105374113 Neighboring gene Sharpr-MPRA regulatory region 7150 Neighboring gene NANOG hESC enhancer GRCh37_chr3:131633036-131633560 Neighboring gene NANOG hESC enhancer GRCh37_chr3:131716699-131717322 Neighboring gene uncharacterized LOC124906288 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:131735283-131736482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20536 Neighboring gene microRNA 5704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14739 Neighboring gene uncharacterized LOC105374111 Neighboring gene Sharpr-MPRA regulatory region 15178 Neighboring gene PSMC2 pseudogene 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. Molecular studies into cell biological role of Copine-4 in Retinal Ganglion Cells. Goel M, et al. PLoS One, 2021. PMID 34847148, Free PMC Article
  2. Associations between Genetic Variants and Angiographic Characteristics in Patients with Coronary Artery Disease. Lee JY, et al. J Atheroscler Thromb, 2015. PMID 25328121
  3. Genome-wide scan for copy number variation association with age at onset of Alzheimer's disease. Szigeti K, et al. J Alzheimers Dis, 2013. PMID 23202439, Free PMC Article
  4. Cloning, molecular characterization, and expression analysis of Copine 8. Maitra R, et al. Biochem Biophys Res Commun, 2003 Apr 11. PMID 12670487
  5. Pan-genome isolation of low abundance transcripts using SAGE tag. Kim YC, et al. FEBS Lett, 2006 Dec 11. PMID 17113583, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Molecular studies into cell biological role of Copine-4 in Retinal Ganglion Cells.
    Title: Molecular studies into cell biological role of Copine-4 in Retinal Ganglion Cells.
  2. Single nucleotide polymorphisms in CPEN4 gene is associated with Coronary Artery Disease.
    Title: Associations between Genetic Variants and Angiographic Characteristics in Patients with Coronary Artery Disease.
  3. Cloning, molecular characterization, and expression analysis. May have an important role to play in prostate regulation and development.
    Title: Cloning, molecular characterization, and expression analysis of Copine 8.
  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
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
EBI GWAS Catalog
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
EBI GWAS Catalog

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

Homology

Clone Names

  • MGC15604

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
  
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
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
copine-4
Names
copine 8
copine IV

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_001289112.2 → NP_001276041.1  copine-4 isoform 1

    See identical proteins and their annotated locations for NP_001276041.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AF465771, AK295557, BC028613, BM930746, DC330179
    Consensus CDS
    CCDS75010.1
    UniProtKB/TrEMBL
    B7Z370
    Related
    ENSP00000478878.1, ENST00000617767.5
    Conserved Domains (3) summary
    cd04047
    Location:173 → 285
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:42 → 158
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:344 → 561
    Copine; Copine

  2. NM_001388326.1 → NP_001375255.1  copine-4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC076961, AC107027, AC135002, AC136276
    Conserved Domains (3) summary
    cd04047
    Location:42 → 154
    C2B_Copine; C2 domain second repeat in Copine
    pfam07002
    Location:213 → 430
    Copine
    cl14603
    Location:1 → 27
    C2; C2 domain

  3. NM_001388327.1 → NP_001375256.1  copine-4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC076961, AC107027, AC135002, AC136276
    Conserved Domains (3) summary
    cd04047
    Location:42 → 154
    C2B_Copine; C2 domain second repeat in Copine
    pfam07002
    Location:213 → 430
    Copine
    cl14603
    Location:1 → 27
    C2; C2 domain

  4. NM_130808.3 → NP_570720.1  copine-4 isoform 2

    See identical proteins and their annotated locations for NP_570720.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation from a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    BC014396, BC028613, DA156722, DA194161
    Consensus CDS
    CCDS3072.1
    UniProtKB/Swiss-Prot
    D3DNC5, Q8TEX1, Q96A23
    UniProtKB/TrEMBL
    B7Z370
    Related
    ENSP00000411904.1, ENST00000429747.6
    Conserved Domains (3) summary
    cd04047
    Location:155 → 267
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:24 → 140
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:326 → 543
    Copine

  5. NM_153429.2 → NP_702907.1  copine-4 isoform 1

    See identical proteins and their annotated locations for NP_702907.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AF465771, BC028613, BM930746
    Consensus CDS
    CCDS75010.1
    UniProtKB/TrEMBL
    B7Z370
    Related
    ENSP00000424853.1, ENST00000512332.5
    Conserved Domains (3) summary
    cd04047
    Location:173 → 285
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:42 → 158
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:344 → 561
    Copine; Copine

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    131533569..132039606 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447422.1 → XP_047303378.1  copine-4 isoform X1

  2. XM_024453339.2 → XP_024309107.1  copine-4 isoform X2

    UniProtKB/Swiss-Prot
    D3DNC5, Q8TEX1, Q96A23
    UniProtKB/TrEMBL
    B7Z370
    Conserved Domains (3) summary
    cd04047
    Location:155 → 267
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:24 → 140
    C2A_Copine; C2 domain first repeat in Copine
    pfam07002
    Location:326 → 543
    Copine

  3. XM_011512408.3 → XP_011510710.1  copine-4 isoform X4

    See identical proteins and their annotated locations for XP_011510710.1

    Conserved Domains (3) summary
    cd04047
    Location:42 → 154
    C2B_Copine; C2 domain second repeat in Copine
    pfam07002
    Location:213 → 430
    Copine
    cl14603
    Location:1 → 27
    C2; C2 domain

  4. XM_047447423.1 → XP_047303379.1  copine-4 isoform X5

  5. XM_017005694.3 → XP_016861183.2  copine-4 isoform X3

    Conserved Domains (3) summary
    cd04047
    Location:177 → 289
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:46 → 162
    C2A_Copine; C2 domain first repeat in Copine
    cl00057
    Location:348 → 453
    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 ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    134277285..134784042 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345186.1 → XP_054201161.1  copine-4 isoform X1

  2. XM_054345183.1 → XP_054201158.1  copine-4 isoform X2

    UniProtKB/Swiss-Prot
    D3DNC5, Q8TEX1, Q96A23

  3. XM_054345185.1 → XP_054201160.1  copine-4 isoform X4

  4. XM_054345187.1 → XP_054201162.1  copine-4 isoform X5

  5. XM_054345184.1 → XP_054201159.1  copine-4 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96A23.1 GenPept UniProtKB/Swiss-Prot:Q96A23

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