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Clpb ClpB caseinolytic peptidase B [ Mus musculus (house mouse) ]

Gene ID: 20480, updated on 3-Apr-2024

Summary

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Official Symbol
Clpbprovided by MGI
Official Full Name
ClpB caseinolytic peptidase Bprovided by MGI
Primary source
MGI:MGI:1100517
See related
Ensembl:ENSMUSG00000001829 AllianceGenome:MGI:1100517
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Skd3
Summary
Predicted to enable ATP hydrolysis activity. Predicted to be involved in RIG-I signaling pathway; antiviral innate immune response; and cellular response to heat. Located in mitochondrion. Is expressed in several structures, including central nervous system; inner cell mass; limb; paravertebral ganglion; and retina. Human ortholog(s) of this gene implicated in 3-methylglutaconic aciduria with cataracts, neurologic involvement and neutropenia. Orthologous to human CLPB (caseinolytic mitochondrial matrix peptidase chaperone subunit B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 96.8), kidney adult (RPKM 10.7) and 11 other tissues See more
Orthologs
human all
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Genomic context

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Location:
7 E2; 7 54.63 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (101312958..101444667)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (101663596..101795460)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L6 pseudogene Neighboring gene predicted gene, 45995 Neighboring gene ADP-ribosyltransferase 2b Neighboring gene STARR-seq mESC enhancer starr_19695 Neighboring gene STARR-positive B cell enhancer ABC_E10456 Neighboring gene STARR-positive B cell enhancer ABC_E4958 Neighboring gene STARR-seq mESC enhancer starr_19696 Neighboring gene paired-like homeobox 2a Neighboring gene inositol polyphosphate phosphatase-like 1 Neighboring gene predicted gene 10602

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Expression of a putative ATPase suppresses the growth defect of a yeast potassium transport mutant: identification of a mammalian member of the Clp/HSP104 family. Périer F, et al. Gene, 1995 Jan 23. PMID 7835694
  2. High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization. Yoshikawa T, et al. Gene Expr Patterns, 2006 Jan. PMID 16325481, Free PMC Article
  3. Hdac4 Interactions in Huntington's Disease Viewed Through the Prism of Multiomics. Federspiel JD, et al. Mol Cell Proteomics, 2019 Aug 9. PMID 31040226, Free PMC Article
  4. Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo. Harrison SM, et al. Development, 1995 Aug. PMID 7671812
  5. An Interaction Landscape of Ubiquitin Signaling. Zhang X, et al. Mol Cell, 2017 Mar 2. PMID 28190767

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

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 MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ATP hydrolysis activity ISO
Inferred from Sequence Orthology
more info
  
enables ATP-dependent protein disaggregase activity ISO
Inferred from Sequence Orthology
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RIG-I signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in antiviral innate immune response ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to heat IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to heat ISO
Inferred from Sequence Orthology
more info
  
involved_in granulocyte differentiation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrial intermembrane space ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion HDA PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
mitochondrial disaggregase
Names
ClpB caseinolytic peptidase B homolog
caseinolytic peptidase B protein homolog
suppressor of K+ transport defect 3
suppressor of potassium transport defect 3
NP_001350920.1
NP_001404197.1
NP_001404198.1
NP_033217.1
XP_006507552.1
XP_011240004.1
XP_030098131.1

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_001363991.1 → NP_001350920.1  mitochondrial disaggregase isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC159005, AK032421, BY234145
    Consensus CDS
    CCDS90284.1
    UniProtKB/TrEMBL
    Q3TXD4, Q3U3U6, Q8CCN6
    Related
    ENSMUSP00000148062.2, ENSMUST00000209579.2
    Conserved Domains (3) summary
    COG0542
    Location:309 → 625
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    cd00204
    Location:137 → 285
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    sd00045
    Location:137 → 164
    ANK; ANK repeat [structural motif]

  2. NM_001417268.1 → NP_001404197.1  mitochondrial disaggregase isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005
    UniProtKB/TrEMBL
    E9PY58
    Related
    ENSMUSP00000102611.2, ENSMUST00000106998.8

  3. NM_001417269.1 → NP_001404198.1  mitochondrial disaggregase isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005

  4. NM_009191.4 → NP_033217.1  mitochondrial disaggregase isoform 1 precursor

    See identical proteins and their annotated locations for NP_033217.1

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005
    Consensus CDS
    CCDS21513.1
    UniProtKB/Swiss-Prot
    Q60649
    UniProtKB/TrEMBL
    Q3TXD4, Q3U3U6, Q3URM1
    Related
    ENSMUSP00000001884.8, ENSMUST00000001884.14
    Conserved Domains (7) summary
    smart01086
    Location:545 → 627
    ClpB_D2-small; C-terminal, D2-small domain, of ClpB protein
    smart00382
    Location:343 → 480
    AAA; ATPases associated with a variety of cellular activities
    cd00204
    Location:137 → 285
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam07724
    Location:346 → 534
    AAA_2; AAA domain (Cdc48 subfamily)
    pfam12796
    Location:138 → 266
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:137 → 164
    ANK; ANK repeat [structural motif]
    cl21455
    Location:309 → 371
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RNA

  1. NR_184441.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005

  2. NR_184442.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    101312958..101444667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030242271.2 → XP_030098131.1  mitochondrial disaggregase isoform X5

    Conserved Domains (3) summary
    COG0542
    Location:114 → 430
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:41 → 71
    ANK; ANK repeat [structural motif]
    pfam00023
    Location:40 → 72
    Ank; Ankyrin repeat

  2. XM_011241702.3 → XP_011240004.1  mitochondrial disaggregase isoform X2

    UniProtKB/TrEMBL
    Q3UGS9
    Conserved Domains (3) summary
    COG0542
    Location:201 → 517
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:28 → 59
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:1 → 158
    Ank_2; Ankyrin repeats (3 copies)

  3. XM_006507489.4 → XP_006507552.1  mitochondrial disaggregase isoform X4

    Conserved Domains (4) summary
    COG0542
    Location:119 → 435
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:46 → 76
    ANK; ANK repeat [structural motif]
    pfam00023
    Location:45 → 77
    Ank; Ankyrin repeat
    cl39094
    Location:25 → 95
    Ank_2; Ankyrin repeats (3 copies)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q60649.1 GenPept UniProtKB/Swiss-Prot:Q60649

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