U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 20480, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    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 and ATP-dependent protein disaggregase activity. Predicted to be involved in several processes, including RIG-I signaling pathway; antiviral innate immune response; and granulocyte differentiation. 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 type 7a; 3-methylglutaconic aciduria type 7b; and severe congenital neutropenia. Orthologous to human CLPB (ClpB family mitochondrial disaggregase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 96.8), kidney adult (RPKM 10.7) and 11 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Clpb in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Schweppe DK, et al. Proc Natl Acad Sci U S A, 2017 Feb 14. PMID 28130547, Free PMC Article
    4. 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
    5. 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

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

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

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent protein disaggregase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent protein disaggregase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity 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 chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in granulocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in granulocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    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 mitochondrial intermembrane space ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion HDA PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    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_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

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools