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CNN3 calponin 3 [ Homo sapiens (human) ]

Gene ID: 1266, updated on 5-Apr-2020

Summary

Official Symbol
CNN3provided by HGNC
Official Full Name
calponin 3provided by HGNC
Primary source
HGNC:HGNC:2157
See related
Ensembl:ENSG00000117519 MIM:602374
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

Genomic context

See CNN3 in Genome Data Viewer
Location:
1p21.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (94896949..94927223, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95362507..95392735, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SLC44A3 antisense RNA 1 Neighboring gene microRNA 378g Neighboring gene solute carrier family 44 member 3 Neighboring gene hCG2028352-like Neighboring gene hCG2028352-like Neighboring gene ALG14 UDP-N-acetylglucosaminyltransferase subunit Neighboring gene uncharacterized LOC105378863

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI 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
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding IEA
Inferred from Electronic Annotation
more info
 
cadherin binding involved in cell-cell adhesion HDA PubMed 
calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
microtubule binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
actomyosin structure organization IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
epithelial cell differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of ATPase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
adherens junction HDA PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
focal adhesion HDA PubMed 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001286055.1NP_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:16182
    SCP1; Calponin [Cytoskeleton]
    cd00014
    Location:2879
    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:118141
    Calponin; Calponin family repeat
  2. NM_001286056.1NP_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, DB030660
    Consensus CDS
    CCDS65592.1
    UniProtKB/Swiss-Prot
    Q15417
    Related
    ENSP00000440081.1, ENST00000545882.5
    Conserved Domains (2) summary
    pfam00307
    Location:684
    CH; Calponin homology (CH) domain
    pfam00402
    Location:123146
    Calponin; Calponin family repeat
  3. NM_001839.5NP_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
    Q15417
    Related
    ENSP00000359225.4, ENST00000370206.9
    Conserved Domains (2) summary
    pfam00402
    Location:243266
    Calponin; Calponin family repeat
    cl27700
    Location:16188
    Calponin; Calponin family repeat

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    94896949..94927223 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000245.2XP_016855734.1  calponin-3 isoform X1

    UniProtKB/Swiss-Prot
    Q15417
    Conserved Domains (2) summary
    pfam00307
    Location:684
    CH; Calponin homology (CH) domain
    pfam00402
    Location:123146
    Calponin; Calponin family repeat
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