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Clpb ClpB family mitochondrial disaggregase [ Rattus norvegicus (Norway rat) ]

Gene ID: 65041, updated on 2-Nov-2024

Summary

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Official Symbol
Clpbprovided by RGD
Official Full Name
ClpB family mitochondrial disaggregaseprovided by RGD
Primary source
RGD:621328
See related
EnsemblRapid:ENSRNOG00000019693 AllianceGenome:RGD:621328
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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. Predicted to be located in mitochondrial intermembrane space. Predicted to be active in mitochondrion. 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 Testes (RPKM 581.1), Kidney (RPKM 198.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Clpb in Genome Data Viewer
Location:
1q32
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (165440705..165563514)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (156028740..156158183)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (166739372..166866095)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120099897 Neighboring gene ADP-ribosyltransferase 2b Neighboring gene lactate dehydrogenase A, pseudogene 3 Neighboring gene uncharacterized LOC102547177 Neighboring gene paired-like homeobox 2a Neighboring gene inositol polyphosphate phosphatase-like 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Attenuated induction of heat shock gene expression in aging diploid fibroblasts. Liu AY, et al. J Biol Chem, 1989 Jul 15. PMID 2745427
  2. 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
  3. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Morgenstern M, et al. Cell Metab, 2021 Dec 7. PMID 34800366, Free PMC Article
  4. A mitochondrial protein compendium elucidates complex I disease biology. Pagliarini DJ, et al. Cell, 2008 Jul 11. PMID 18614015, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 IEA
Inferred from Electronic Annotation
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 protein disaggregase 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
  
Process Evidence Code Pubs
involved_in RIG-I signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in RIG-I signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in antiviral innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in antiviral innate immune response ISO
Inferred from Sequence Orthology
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in cellular response to heat IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to heat IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to heat ISO
Inferred from Sequence Orthology
more info
  
involved_in granulocyte differentiation 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 IEA
Inferred from Electronic Annotation
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
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
 PubMed 

General protein information

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Preferred Names
mitochondrial disaggregase
Names
ClpB caseinolytic peptidase B homolog
ClpB homolog, mitochondrial AAA ATPase chaperonin
caseinolytic mitochondrial matrix peptidase chaperone subunit B
caseinolytic peptidase B protein homolog
suppressor of K+ transport defect 3
suppressor of potassium transport defect 3
NP_075236.2
XP_008758018.1
XP_038945788.1
XP_038945793.1
XP_063128945.1
XP_063128951.1

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_022947.2 → NP_075236.2  mitochondrial disaggregase

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/Swiss-Prot
    Q9WTT2
    UniProtKB/TrEMBL
    F1M955, Q6IRH7
    Related
    ENSRNOP00000026665.9, ENSRNOT00000026665.9
    Conserved Domains (3) summary
    COG0542
    Location:309 → 625
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:137 → 164
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:138 → 266
    Ank_2; Ankyrin repeats (3 copies)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    165440705..165563514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008759796.3 → XP_008758018.1  mitochondrial disaggregase isoform X1

    UniProtKB/TrEMBL
    A0A0G2K3V9, A0A8J8YEH1
    Related
    ENSRNOP00000072796.1, ENSRNOT00000079846.3
    Conserved Domains (7) summary
    smart01086
    Location:575 → 660
    ClpB_D2-small; C-terminal, D2-small domain, of ClpB protein
    smart00382
    Location:373 → 510
    AAA; ATPases associated with a variety of cellular activities
    cd00204
    Location:137 → 315
    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:376 → 564
    AAA_2; AAA domain (Cdc48 subfamily)
    pfam12796
    Location:138 → 296
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:137 → 164
    ANK; ANK repeat [structural motif]
    cl21455
    Location:339 → 401
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. XM_063272875.1 → XP_063128945.1  mitochondrial disaggregase isoform X2

  3. XM_039089860.2 → XP_038945788.1  mitochondrial disaggregase isoform X2

    Conserved Domains (1) summary
    COG0542
    Location:35 → 351
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]

  4. XM_063272881.1 → XP_063128951.1  mitochondrial disaggregase isoform X2

  5. XM_039089865.2 → XP_038945793.1  mitochondrial disaggregase isoform X3

    Conserved Domains (1) summary
    COG0542
    Location:17 → 333
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]

RNA

  1. XR_005491697.2 RNA Sequence

  2. XR_010057345.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9WTT2.1 GenPept UniProtKB/Swiss-Prot:Q9WTT2

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