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CNN3 calponin 3 [ Homo sapiens (human) ]

Gene ID: 1266, updated on 7-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94896957..94927110, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94745314..94775463, complement)
105.20220307 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. Calponin 3 Acts as a Potential Diagnostic and Prognostic Marker and Promotes Glioma Cell Proliferation, Migration, and Invasion. Xie Y, et al. World Neurosurg, 2022 Sep. PMID 35792226
  2. Calponin 3 is associated with poor prognosis and regulates proliferation and metastasis in osteosarcoma. Dai F, et al. Aging (Albany NY), 2020 Jul 14. PMID 32667904, Free PMC Article
  3. Calponin-3 is critical for coordinated contractility of actin stress fibers. Ciuba K, et al. Sci Rep, 2018 Dec 5. PMID 30518778, Free PMC Article
  4. Overexpressed Calponin3 by Subsonic Vibration Induces Neural Differentiation of hUC-MSCs by Regulating the Ionotropic Glutamate Receptor. Kim HJ, et al. Appl Biochem Biotechnol, 2015 Sep. PMID 26175098
  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 (81) 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)

Genotypes

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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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_2023_10

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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