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CAPN6 calpain 6 [ Homo sapiens (human) ]

Gene ID: 827, updated on 12-Oct-2019

Summary

Official Symbol
CAPN6provided by HGNC
Official Full Name
calpain 6provided by HGNC
Primary source
HGNC:HGNC:1483
See related
Ensembl:ENSG00000077274 MIM:300146
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CANPX; CAPNX; CalpM; DJ914P14.1
Summary
Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is highly expressed in the placenta. Its C-terminal region lacks any homology to the calmodulin-like domain of other calpains. The protein lacks critical active site residues and thus is suggested to be proteolytically inactive. The protein may play a role in tumor formation by inhibiting apoptosis and promoting angiogenesis. [provided by RefSeq, Nov 2009]
Expression
Biased expression in placenta (RPKM 59.5), endometrium (RPKM 13.7) and 5 other tissues See more
Orthologs

Genomic context

See CAPN6 in Genome Data Viewer
Location:
Xq23
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (111245099..111270483, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (110488327..110513774, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene p21 (RAC1) activated kinase 3 Neighboring gene FCF1 pseudogene 4 Neighboring gene glutamate dehydrogenase 1 pseudogene 9 Neighboring gene doublecortin Neighboring gene RNA, U6 small nuclear 496, pseudogene

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of calpain 6 (CAPN6) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Integrin-mediated Cell Adhesion, organism-specific biosystem (from WikiPathways)
    Integrin-mediated Cell Adhesion, organism-specific biosystemIntegrins are receptors that mediate attachment between a cell and the tissues surrounding it, which may be other cells or the extracellular matrix (ECM). They also play a role in cell signaling and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
microtubule binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
microtubule bundle formation ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
spindle microtubule IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
calpain-6
Names
calpain-like protease X-linked
calpamodulin

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.

Genomic

  1. NG_015962.1 RefSeqGene

    Range
    5001..30448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014289.4NP_055104.2  calpain-6

    See identical proteins and their annotated locations for NP_055104.2

    Status: REVIEWED

    Source sequence(s)
    AL031117
    Consensus CDS
    CCDS14555.1
    UniProtKB/Swiss-Prot
    Q9Y6Q1
    Related
    ENSP00000317214.1, ENST00000324068.2
    Conserved Domains (3) summary
    smart00230
    Location:13351
    CysPc; Calpain-like thiol protease family
    cd04046
    Location:514639
    C2_Calpain; C2 domain present in Calpain proteins
    cd00214
    Location:349497
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    111245099..111270483 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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