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    CPNE4 copine 4 [ Homo sapiens (human) ]

    Gene ID: 131034, updated on 2-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    copine-4
    Names
    copine 8
    copine IV

    NCBI Reference Sequences (RefSeq)

    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_001289112.2NP_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:173285
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:42158
      C2A_Copine; C2 domain first repeat in Copine
      pfam07002
      Location:344561
      Copine; Copine
    2. NM_001388326.1NP_001375255.1  copine-4 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC076961, AC107027, AC135002, AC136276
      Conserved Domains (3) summary
      cd04047
      Location:42154
      C2B_Copine; C2 domain second repeat in Copine
      pfam07002
      Location:213430
      Copine
      cl14603
      Location:127
      C2; C2 domain
    3. NM_001388327.1NP_001375256.1  copine-4 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC076961, AC107027, AC135002, AC136276
      Conserved Domains (3) summary
      cd04047
      Location:42154
      C2B_Copine; C2 domain second repeat in Copine
      pfam07002
      Location:213430
      Copine
      cl14603
      Location:127
      C2; C2 domain
    4. NM_130808.3NP_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:155267
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:24140
      C2A_Copine; C2 domain first repeat in Copine
      pfam07002
      Location:326543
      Copine
    5. NM_153429.2NP_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:173285
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:42158
      C2A_Copine; C2 domain first repeat in Copine
      pfam07002
      Location:344561
      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_047447422.1XP_047303378.1  copine-4 isoform X1

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

      UniProtKB/Swiss-Prot
      D3DNC5, Q8TEX1, Q96A23
      UniProtKB/TrEMBL
      B7Z370
      Conserved Domains (3) summary
      cd04047
      Location:155267
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:24140
      C2A_Copine; C2 domain first repeat in Copine
      pfam07002
      Location:326543
      Copine
    3. XM_011512408.3XP_011510710.1  copine-4 isoform X4

      See identical proteins and their annotated locations for XP_011510710.1

      Conserved Domains (3) summary
      cd04047
      Location:42154
      C2B_Copine; C2 domain second repeat in Copine
      pfam07002
      Location:213430
      Copine
      cl14603
      Location:127
      C2; C2 domain
    4. XM_047447423.1XP_047303379.1  copine-4 isoform X5

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

      Conserved Domains (3) summary
      cd04047
      Location:177289
      C2B_Copine; C2 domain second repeat in Copine
      cd04048
      Location:46162
      C2A_Copine; C2 domain first repeat in Copine
      cl00057
      Location:348453
      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_054345186.1XP_054201161.1  copine-4 isoform X1

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

      UniProtKB/Swiss-Prot
      D3DNC5, Q8TEX1, Q96A23
    3. XM_054345185.1XP_054201160.1  copine-4 isoform X4

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

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