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Atg4b autophagy related 4B, cysteine peptidase [ Mus musculus (house mouse) ]

Gene ID: 66615, updated on 27-Nov-2024

Summary

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Official Symbol
Atg4bprovided by MGI
Official Full Name
autophagy related 4B, cysteine peptidaseprovided by MGI
Primary source
MGI:MGI:1913865
See related
Ensembl:ENSMUSG00000026280 AllianceGenome:MGI:1913865
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
Apg4b; Autl1; Atg4bl; MmAPG4B; 2510009N07Rik
Summary
Enables cysteine-type peptidase activity. Involved in several processes, including autophagosome assembly; otolith mineralization completed early in development; and protein delipidation. Located in cytoplasm. Is expressed in central nervous system; genitourinary system; gut; lymph node; and sensory organ. Orthologous to human ATG4B (autophagy related 4B cysteine peptidase). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E14 (RPKM 14.9), whole brain E14.5 (RPKM 14.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Atg4b in Genome Data Viewer
Location:
1 D; 1 47.32 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (93682627..93717328)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (93754905..93789606)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene BCL2-related ovarian killer Neighboring gene THAP domain containing 4 Neighboring gene STARR-seq mESC enhancer starr_01735 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:95698432-95698719 Neighboring gene STARR-positive B cell enhancer ABC_E4338 Neighboring gene deoxythymidylate kinase Neighboring gene predicted gene, 22089 Neighboring gene inhibitor of growth family, member 5

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. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Fujita N, et al. Mol Biol Cell, 2008 Nov. PMID 18768752, Free PMC Article
  2. Histopathological and neurological features of Atg4b knockout mice. Read R, et al. Vet Pathol, 2011 Mar. PMID 20634410
  3. Essential role for the ATG4B protease and autophagy in bleomycin-induced pulmonary fibrosis. Cabrera S, et al. Autophagy, 2015 Apr 3. PMID 25906080, Free PMC Article
  4. Involvement of acetylation of ATG4B in controlling autophagy induction. Xiong H, et al. Autophagy, 2023 Mar. PMID 36056541, Free PMC Article
  5. Impairment of autophagy decreases ventilator-induced lung injury by blockade of the NF-κB pathway. López-Alonso I, et al. Am J Physiol Lung Cell Mol Physiol, 2013 Jun 15. PMID 23585228

See all (63) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
    Title: TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
  2. Circ-0000953 deficiency exacerbates podocyte injury and autophagy disorder by targeting Mir665-3p-Atg4b in diabetic nephropathy.
    Title: Circ-0000953 deficiency exacerbates podocyte injury and autophagy disorder by targeting Mir665-3p-Atg4b in diabetic nephropathy.
  3. FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
    Title: FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
  4. ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
    Title: ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
  5. Involvement of acetylation of ATG4B in controlling autophagy induction.
    Title: Involvement of acetylation of ATG4B in controlling autophagy induction.
  6. Targeting the MicroRNA-490-3p-ATG4B-Autophagy Axis Relieves Myocardial Injury in Ischemia Reperfusion.
    Title: Targeting the MicroRNA-490-3p-ATG4B-Autophagy Axis Relieves Myocardial Injury in Ischemia Reperfusion.
  7. miR-665-3p regulates autophagy by targeting ATG4B expression to relieve inflammation and apoptosis in intestinal ischemia/reperfusion.
    Title: Targeting the miR-665-3p-ATG4B-autophagy axis relieves inflammation and apoptosis in intestinal ischemia/reperfusion.
  8. At the microtubule-actin crossover junction, ATG4B detaches LC3B from melanosomal membranes by enzymatic delipidation.
    Title: Classical autophagy proteins LC3B and ATG4B facilitate melanosome movement on cytoskeletal tracks.
  9. ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8
    Title: ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.
  10. miR-34a might regulate the autophagic activity and can cause injury in ischemia reperfusion injured renal tubular epithelial cells (RTEC) via targeting Atg4B. Atg4B knockdown inhibited autophagy in RTECs.
    Title: MicroRNA-34a Suppresses Autophagy in Tubular Epithelial Cells in Acute Kidney Injury.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Gene trapped (2) 
  • Targeted (3) 

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 cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type endopeptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables cysteine-type peptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables cysteine-type peptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables cysteine-type peptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables endopeptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables peptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-phosphatidylethanolamide deconjugating activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-phosphatidylethanolamide deconjugating activity IEA
Inferred from Electronic Annotation
more info
  
enables protein-phosphatidylethanolamide deconjugating activity ISO
Inferred from Sequence Orthology
more info
  
enables scaffold protein binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in aggrephagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in autophagosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in autophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in autophagy ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to starvation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in microautophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in microautophagy ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mitophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in mitophagy ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in otolith mineralization completed early in development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in piecemeal microautophagy of the nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in protein delipidation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein delipidation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to phagophore assembly site ISO
Inferred from Sequence Orthology
more info
  
involved_in protein processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in autophagosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in autophagosome membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cysteine protease ATG4B
Names
APG4 (ATG4) autophagy-related homolog B
AUT-like 1, cysteine endopeptidase
autophagin 1
autophagy-related 4B
autophagy-related cysteine endopeptidase 1
autophagy-related protein 4 homolog B
cysteine protease involved in autophagy APG4-B
NP_001355195.1
NP_777363.1
XP_006529856.1
XP_036008779.1
XP_036008782.1

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_001368266.1 → NP_001355195.1  cysteine protease ATG4B isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC162891, CJ155817
    UniProtKB/Swiss-Prot
    Q6ZQ22, Q8BGE6, Q8R098

  2. NM_174874.4 → NP_777363.1  cysteine protease ATG4B isoform 1

    See identical proteins and their annotated locations for NP_777363.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC162891, AK031570
    Consensus CDS
    CCDS15195.1
    UniProtKB/Swiss-Prot
    Q6ZQ22, Q8BGE6, Q8R098
    UniProtKB/TrEMBL
    A0A0R4J065
    Related
    ENSMUSP00000027502.9, ENSMUST00000027502.16
    Conserved Domains (1) summary
    pfam03416
    Location:40 → 335
    Peptidase_C54; Peptidase family C54

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_000067.7 Reference GRCm39 C57BL/6J

    Range
    93682627..93717328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036152886.1 → XP_036008779.1  cysteine protease ATG4B isoform X2

    Conserved Domains (1) summary
    pfam03416
    Location:1 → 166
    Peptidase_C54; Peptidase family C54

  2. XM_036152889.1 → XP_036008782.1  cysteine protease ATG4B isoform X2

    Conserved Domains (1) summary
    pfam03416
    Location:1 → 166
    Peptidase_C54; Peptidase family C54

  3. XM_006529793.4 → XP_006529856.1  cysteine protease ATG4B isoform X1

    UniProtKB/Swiss-Prot
    Q6ZQ22, Q8BGE6, Q8R098
    Conserved Domains (1) summary
    pfam03416
    Location:1 → 261
    Peptidase_C54; Peptidase family C54

RNA

  1. XR_004934055.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BGE6.2 GenPept UniProtKB/Swiss-Prot:Q8BGE6

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