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

Summary

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

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_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
Title: FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
Title: ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
Involvement of acetylation of ATG4B in controlling autophagy induction.
Title: Involvement of acetylation of ATG4B in controlling autophagy induction.
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.
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.
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.
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.
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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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

EC 3.4.22.-

NP_777363.1

EC 3.4.22.-

XP_006529856.1

EC 3.4.22.-

XP_036008779.1

EC 3.4.22.-

XP_036008782.1

EC 3.4.22.-

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_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
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

NC_000067.7 Reference GRCm39 C57BL/6J

Range

93682627..93717328

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam03416
Location:1 → 166

Peptidase_C54; Peptidase family C54
XM_036152889.1 → XP_036008782.1 cysteine protease ATG4B isoform X2

Conserved Domains (1) summary

pfam03416
Location:1 → 166

Peptidase_C54; Peptidase family C54
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