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CPNE9 copine family member 9 [ Homo sapiens (human) ]

Gene ID: 151835, updated on 5-Mar-2024

Summary

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Official Symbol
CPNE9provided by HGNC
Official Full Name
copine family member 9provided by HGNC
Primary source
HGNC:HGNC:24336
See related
Ensembl:ENSG00000144550 AllianceGenome:HGNC:24336
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable calcium-dependent phospholipid binding activity. Involved in positive regulation of dendrite extension. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.5), skin (RPKM 0.4) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
3p25.3
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9703833..9729908)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9695788..9721866)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9745517..9771592)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dual specificity phosphatase 5 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9690821-9691716 Neighboring gene myotubularin related protein 14 Neighboring gene uncharacterized LOC124909344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9745156-9746066 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:9757470-9757599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19405 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:9772855-9773414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9773975-9774534 Neighboring gene bromodomain and PHD finger containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19407 Neighboring gene 8-oxoguanine DNA glycosylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14040 Neighboring gene calcium/calmodulin dependent protein kinase I

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. High expression of CPNE5 and CPNE9 predicts positive prognosis in multiple myeloma. Zhu P, et al. Cancer Biomark, 2021. PMID 33780365
  2. Biochemical characterization of copine: a ubiquitous Ca2+-dependent, phospholipid-binding protein. Tomsig JL, et al. Biochemistry, 2000 Dec 26. PMID 11123945
  3. Bridging expressed sequence alignments through targeted cDNA sequencing. Xie H, et al. Genomics, 2004 Apr. PMID 15028280
  4. 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
  5. SYT14L, especially its C2 domain, is involved in regulating melanocyte differentiation. Yoo JC, et al. J Dermatol Sci, 2013 Dec. PMID 23999003

See all (19) 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. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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

  • KIAA4217

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
 PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in extracellular space 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-9
Names
copine IX
copine family member IX
copine-like protein

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_001308388.2 → NP_001295317.1  copine-9 isoform 2

    See identical proteins and their annotated locations for NP_001295317.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate 3' exon and contains an alternate 3' terminal exon, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC035735
    Consensus CDS
    CCDS77695.1
    UniProtKB/Swiss-Prot
    Q8IYJ1
    Related
    ENSP00000373342.3, ENST00000383831.7
    Conserved Domains (3) summary
    cd04047
    Location:148 → 259
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:14 → 135
    C2A_Copine; C2 domain first repeat in Copine
    cl00057
    Location:269 → 492
    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 ...

  2. NM_153635.3 → NP_705899.2  copine-9 isoform 1

    See identical proteins and their annotated locations for NP_705899.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BM545574, BU101942, BX453546, CA307982
    Consensus CDS
    CCDS2574.2
    UniProtKB/Swiss-Prot
    A1L430, A6NDX6, A8MSP8, Q8IYJ1
    Related
    ENSP00000373343.3, ENST00000383832.8
    Conserved Domains (3) summary
    cd04047
    Location:148 → 259
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:14 → 135
    C2A_Copine; C2 domain first repeat in Copine
    cd01459
    Location:269 → 525
    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. ...

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
    9703833..9729908
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533386.3 → XP_011531688.1  copine-9 isoform X1

    Conserved Domains (3) summary
    cd04047
    Location:257 → 368
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:132 → 244
    C2A_Copine; C2 domain first repeat in Copine
    cd01459
    Location:378 → 634
    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_011533388.3 → XP_011531690.1  copine-9 isoform X2

    Conserved Domains (3) summary
    cd04047
    Location:257 → 368
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:132 → 244
    C2A_Copine; C2 domain first repeat in Copine
    cl00057
    Location:378 → 480
    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 ...

  3. XM_011533389.3 → XP_011531691.1  copine-9 isoform X3

    Conserved Domains (3) summary
    cd04047
    Location:257 → 368
    C2B_Copine; C2 domain second repeat in Copine
    cd04048
    Location:132 → 244
    C2A_Copine; C2 domain first repeat in Copine
    cl00057
    Location:378 → 420
    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 ...

  4. XM_047447493.1 → XP_047303449.1  copine-9 isoform X4

  5. XM_047447494.1 → XP_047303450.1  copine-9 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9695788..9721866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345343.1 → XP_054201318.1  copine-9 isoform X1

  2. XM_054345344.1 → XP_054201319.1  copine-9 isoform X2

  3. XM_054345345.1 → XP_054201320.1  copine-9 isoform X3

  4. XM_054345346.1 → XP_054201321.1  copine-9 isoform X4

  5. XM_054345347.1 → XP_054201322.1  copine-9 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033755.1: Suppressed sequence

    Description
    NM_001033755.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IYJ1.3 GenPept UniProtKB/Swiss-Prot:Q8IYJ1

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