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

    Gene ID: 151835, updated on 10-Dec-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, Dec 2024]
    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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    See CPNE9 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9703833..9729908)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9695788..9721866)
    RS_2024_09 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: 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. 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)

    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_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
      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 [email protected] 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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