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

Gene ID: 20480, updated on 4-Mar-2023

Summary

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
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Genomic context

See Clpb in Genome Data Viewer
Location:
7; 7 E2
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (101312807..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 paired-like homeobox 2a Neighboring gene inositol polyphosphate phosphatase-like 1 Neighboring gene predicted gene 10602 Neighboring gene folate receptor 2 (fetal)

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 

General protein information

Preferred Names
caseinolytic peptidase B protein homolog
Names
ClpB caseinolytic peptidase B homolog
suppressor of K+ transport defect 3
suppressor of potassium transport defect 3
NP_001350920.1
NP_033217.1
XP_006507551.1
XP_006507552.1
XP_011240004.1
XP_030098130.1
XP_030098131.1
XP_030098132.1
XP_036008719.1

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_001363991.1NP_001350920.1  caseinolytic peptidase B protein homolog isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC159005, AK032421, BY234145
    Consensus CDS
    CCDS90284.1
    UniProtKB/TrEMBL
    Q8CCN6
    Related
    ENSMUSP00000148062.2, ENSMUST00000209579.2
    Conserved Domains (3) summary
    COG0542
    Location:309625
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    cd00204
    Location:137285
    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:137164
    ANK; ANK repeat [structural motif]
  2. NM_001417268.1NP_001404197.1  caseinolytic peptidase B protein homolog isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005
  3. NM_001417269.1NP_001404198.1  caseinolytic peptidase B protein homolog isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC127586, AC129609, AC159005
  4. NM_009191.4NP_033217.1  caseinolytic peptidase B protein homolog 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
    A0A8C6I9S6, Q3URM1
    Related
    ENSMUSP00000001884.8, ENSMUST00000001884.14
    Conserved Domains (7) summary
    smart01086
    Location:545627
    ClpB_D2-small; C-terminal, D2-small domain, of ClpB protein
    smart00382
    Location:343480
    AAA; ATPases associated with a variety of cellular activities
    cd00204
    Location:137285
    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:346534
    AAA_2; AAA domain (Cdc48 subfamily)
    pfam12796
    Location:138266
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:137164
    ANK; ANK repeat [structural motif]
    cl21455
    Location:309371
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    101312807..101444667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006507488.5XP_006507551.1  caseinolytic peptidase B protein homolog isoform X1

    UniProtKB/TrEMBL
    A0A8C6N447, E9PY58
    Related
    ENSMUSP00000102611.2, ENSMUST00000106998.8
    Conserved Domains (3) summary
    COG0542
    Location:339655
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:137164
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:138296
    Ank_2; Ankyrin repeats (3 copies)
  2. XM_030242272.2XP_030098132.1  caseinolytic peptidase B protein homolog isoform X7

    Conserved Domains (1) summary
    COG0542
    Location:35351
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
  3. XM_036152826.1XP_036008719.1  caseinolytic peptidase B protein homolog isoform X6

  4. XM_030242271.2XP_030098131.1  caseinolytic peptidase B protein homolog isoform X5

    Conserved Domains (3) summary
    COG0542
    Location:114430
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:4171
    ANK; ANK repeat [structural motif]
    pfam00023
    Location:4072
    Ank; Ankyrin repeat
  5. XM_011241702.3XP_011240004.1  caseinolytic peptidase B protein homolog isoform X2

    Conserved Domains (3) summary
    COG0542
    Location:201517
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:2859
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:1158
    Ank_2; Ankyrin repeats (3 copies)
  6. XM_030242270.2XP_030098130.1  caseinolytic peptidase B protein homolog isoform X3

    Conserved Domains (3) summary
    COG0542
    Location:171487
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:2859
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:1128
    Ank_2; Ankyrin repeats (3 copies)
  7. XM_006507489.4XP_006507552.1  caseinolytic peptidase B protein homolog isoform X4

    Conserved Domains (4) summary
    COG0542
    Location:119435
    ClpA; ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]
    sd00045
    Location:4676
    ANK; ANK repeat [structural motif]
    pfam00023
    Location:4577
    Ank; Ankyrin repeat
    cl39094
    Location:2595
    Ank_2; Ankyrin repeats (3 copies)