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    CNN3 calponin 3 [ Homo sapiens (human) ]

    Gene ID: 1266, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CNN3provided by HGNC
    Official Full Name
    calponin 3provided by HGNC
    Primary source
    HGNC:HGNC:2157
    See related
    Ensembl:ENSG00000117519 MIM:602374; AllianceGenome:HGNC:2157
    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
    This gene encodes a protein with a markedly acidic C terminus; the basic N-terminus is highly homologous to the N-terminus of a related gene, CNN1. Members of the CNN gene family all contain similar tandemly repeated motifs. This encoded protein is associated with the cytoskeleton but is not involved in contraction. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 52.9), placenta (RPKM 49.2) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CNN3 in Genome Data Viewer
    Location:
    1p21.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94896957..94927110, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94745314..94775463, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95362513..95392666, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SLC44A3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 2553 Neighboring gene microRNA 378g Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95248718-95249480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1100 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95302044-95303243 Neighboring gene solute carrier family 44 member 3 Neighboring gene NANOG hESC enhancer GRCh37_chr1:95331914-95332415 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9624 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:95349823-95350709 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95376115-95377314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95385599-95386099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95401156-95402010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95402011-95402865 Neighboring gene CNN3 divergent transcript Neighboring gene uncharacterized LOC124904224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1351 Neighboring gene ALG14 UDP-N-acetylglucosaminyltransferase subunit Neighboring gene uncharacterized LOC105378863

    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. Acidic calponin immunoreactivity in postnatal rat brain and cultures: subcellular localization in growth cones, under the plasma membrane and along actin and glial filaments. Plantier M, et al. Eur J Neurosci, 1999 Aug. PMID 10457177
    2. Identification of calponin 3 as a novel Smad-binding modulator of BMP signaling expressed in cartilage. Haag J, et al. Exp Cell Res, 2007 Oct 1. PMID 17825283
    3. Increased expression of calponin-3 in epileptic patients and experimental rats. Han Y, et al. Exp Neurol, 2012 Jan. PMID 22119193
    4. Calponin 3 regulates stress fiber formation in dermal fibroblasts during wound healing. Daimon E, et al. Arch Dermatol Res, 2013 Sep. PMID 23545751
    5. CNN3 regulates trophoblast invasion and is upregulated by hypoxia in BeWo cells. Appel S, et al. PLoS One, 2014. PMID 25050546, Free PMC Article

    See all (92) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Calponin 3 Acts as a Potential Diagnostic and Prognostic Marker and Promotes Glioma Cell Proliferation, Migration, and Invasion.
      Title: Calponin 3 Acts as a Potential Diagnostic and Prognostic Marker and Promotes Glioma Cell Proliferation, Migration, and Invasion.
    2. Calponin 3 is associated with poor prognosis and regulates proliferation and metastasis in osteosarcoma.
      Title: Calponin 3 is associated with poor prognosis and regulates proliferation and metastasis in osteosarcoma.
    3. CNN3 acts as a potential oncogene in cervical cancer by affecting RPLP1 mRNA expression.
      Title: CNN3 acts as a potential oncogene in cervical cancer by affecting RPLP1 mRNA expression.
    4. Cnn3 depletion resulted in increased and uncoordinated contractility of stress fibers that often led to breakage of individual actomyosin bundles within the stress fiber network.
      Title: Calponin-3 is critical for coordinated contractility of actin stress fibers.
    5. These results reveal the importance of the MEKK1-calponin-3 signaling pathway to cell contractility.
      Title: MEKK1-dependent phosphorylation of calponin-3 tunes cell contractility.
    6. overexpressed CNN3 during sonic vibration increases expression of glutamate receptors and promotes functional neural differentiation of human umbilical cords-mesenchymal stem cells.
      Title: Overexpressed Calponin3 by Subsonic Vibration Induces Neural Differentiation of hUC-MSCs by Regulating the Ionotropic Glutamate Receptor.
    7. CNN3 as a new pro-invasive protein in trophoblast cells that is induced under low oxygen conditions.
      Title: CNN3 regulates trophoblast invasion and is upregulated by hypoxia in BeWo cells.
    8. Participates in actin stress fiber remodeling
      Title: Calponin 3 regulates stress fiber formation in dermal fibroblasts during wound healing.
    9. The mRNA and protein level of calponin-3 were increase expression in brain in patiens with epilepsy.
      Title: Increased expression of calponin-3 in epileptic patients and experimental rats.
    10. Results indicate that CNN3 regulates actin cytoskeleton rearrangement which is required for the plasma membranes of trophoblasts to become fusion competent.
      Title: Calponin 3 regulates actin cytoskeleton rearrangement in trophoblastic cell fusion.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cadherin binding involved in cell-cell adhesion HDA PubMed 
    enables calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in actomyosin structure organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epithelial cell differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in adherens junction HDA PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in focal adhesion HDA PubMed 

    General protein information

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    Preferred Names
    calponin-3
    Names
    calponin 3, acidic
    dJ639P13.2.2 (acidic calponin 3)

    NCBI Reference Sequences (RefSeq)

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    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_001286055.2 → NP_001272984.1  calponin-3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC093429, AC105942, AK298145
      Consensus CDS
      CCDS65593.1
      UniProtKB/Swiss-Prot
      Q15417
      Related
      ENSP00000377752.4, ENST00000394202.8
      Conserved Domains (3) summary
      COG5199
      Location:16 → 182
      SCP1; Calponin [Cytoskeleton]
      cd00014
      Location:28 → 79
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      pfam00402
      Location:118 → 141
      Calponin; Calponin family repeat

    2. NM_001286056.2 → NP_001272985.1  calponin-3 isoform 3

      See identical proteins and their annotated locations for NP_001272985.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. These differences cause translation initiation at a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC093429, AK316398
      Consensus CDS
      CCDS65592.1
      UniProtKB/Swiss-Prot
      Q15417
      Related
      ENSP00000440081.1, ENST00000545882.5
      Conserved Domains (2) summary
      pfam00307
      Location:6 → 84
      CH; Calponin homology (CH) domain
      pfam00402
      Location:123 → 146
      Calponin; Calponin family repeat

    3. NM_001839.5 → NP_001830.1  calponin-3 isoform 1

      See identical proteins and their annotated locations for NP_001830.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC093429, AC105942, AK312370
      Consensus CDS
      CCDS30775.1
      UniProtKB/Swiss-Prot
      B4DFK6, B4DP09, F8WA86, Q15417, Q6FHA7
      Related
      ENSP00000359225.4, ENST00000370206.9
      Conserved Domains (2) summary
      pfam00402
      Location:243 → 266
      Calponin; Calponin family repeat
      cl27700
      Location:16 → 188
      Calponin; Calponin family repeat

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      94896957..94927110 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444486.1 → XP_047300442.1  calponin-3 isoform X1

    2. XM_047444480.1 → XP_047300436.1  calponin-3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      94745314..94775463 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334226.1 → XP_054190201.1  calponin-3 isoform X1

    2. XM_054334225.1 → XP_054190200.1  calponin-3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15417.1 GenPept UniProtKB/Swiss-Prot:Q15417

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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