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    CPNE4 copine 4 [ Homo sapiens (human) ]

    Gene ID: 131034, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See CPNE4 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (131533569..132039606, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (134277285..134784042, complement)
    RS_2024_09 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 uncharacterized LOC105374114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131221451-131222137 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Cloning, molecular characterization, and expression analysis of Copine 8. Maitra R, et al. Biochem Biophys Res Commun, 2003 Apr 11. PMID 12670487
    4. 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
    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)

    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 
    located_in glutamatergic synapse 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-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_2024_08

    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

      UniProtKB/TrEMBL
      B7Z370

    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

      UniProtKB/TrEMBL
      B7Z370

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

      UniProtKB/Swiss-Prot
      D3DNC5, Q8TEX1, Q96A23
      UniProtKB/TrEMBL
      B7Z370

    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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