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

Summary

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

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

STS-Z40910 (e-PCR)
- UniSTS:29447

MARC_6997-6998:996689895:1 (e-PCR)
- UniSTS:269700

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 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	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	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 chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation 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

EC 3.6.1.3

XP_008758018.1

EC 3.6.1.3

XP_038945788.1

EC 3.6.1.3

XP_038945793.1

EC 3.6.1.3

XP_063128945.1

EC 3.6.1.3

XP_063128951.1

EC 3.6.1.3

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)

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

NC_086019.1 Reference GRCr8

Range

165440705..165563514

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_063272875.1 → XP_063128945.1 mitochondrial disaggregase isoform X2
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]
XM_063272881.1 → XP_063128951.1 mitochondrial disaggregase isoform X2
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]