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    Atg4b autophagy related 4B, cysteine peptidase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 316640, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Atg4bprovided by RGD
    Official Full Name
    autophagy related 4B, cysteine peptidaseprovided by RGD
    Primary source
    RGD:1309664
    See related
    EnsemblRapid:ENSRNOG00000018403 AllianceGenome:RGD:1309664
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Apg4b
    Summary
    Predicted to enable cysteine-type endopeptidase activity; protein-phosphatidylethanolamide deconjugating activity; and scaffold protein binding activity. Involved in positive regulation of protein catabolic process. Predicted to be located in several cellular components, including autophagosome; endoplasmic reticulum; and mitochondrion. Predicted to be active in autophagosome membrane. Orthologous to human ATG4B (autophagy related 4B cysteine peptidase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 105.0), Thymus (RPKM 95.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atg4b in Genome Data Viewer
    Location:
    9q36
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (101729772..101761456)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (94282417..94314109)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (100888457..100920123)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene BCL2 family apoptosis regulator BOK Neighboring gene THAP domain containing 4 Neighboring gene deoxythymidylate kinase 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: 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. Effects of RNA interference of Atg4B on the limited proteolysis of LC3 in PC12 cells and expression of Atg4B in various rat tissues. Yoshimura K, et al. Autophagy, 2006 Jul-Sep. PMID 16874114
    2. A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. Hemelaar J, et al. J Biol Chem, 2003 Dec 19. PMID 14530254
    3. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. Li M, et al. J Biol Chem, 2011 Mar 4. PMID 21177865, Free PMC Article
    4. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. Kabeya Y, et al. J Cell Sci, 2004 Jun 1. PMID 15169837
    5. LC3 conjugation system in mammalian autophagy. Tanida I, et al. Int J Biochem Cell Biol, 2004 Dec. PMID 15325588, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC112887

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type peptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables peptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in microautophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in microautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in otolith mineralization completed early in development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein delipidation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to phagophore assembly site IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in autophagosome membrane 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    ATG4 autophagy related 4 homolog B
    autophagy related 4 homolog B
    autophagy-related 4B
    autophagy-related protein 4 homolog B
    NP_001386126.1
    XP_006245596.1
    XP_038939702.1
    XP_038939703.1
    XP_063123398.1

    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_001399197.1 → NP_001386126.1  cysteine protease ATG4B

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      A0A0G2QC33, F1LRG2, Q4KM36
      UniProtKB/TrEMBL
      A0A8I6GGT0
      Related
      ENSRNOP00000025529.6, ENSRNOT00000025529.9
      Conserved Domains (1) summary
      pfam03416
      Location:39 → 335
      Peptidase_C54; Peptidase family C54

    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_086027.1 Reference GRCr8

      Range
      101729772..101761456
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006245534.5 → XP_006245596.1  cysteine protease ATG4B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQY4, A0A8I6GGT0
      Related
      ENSRNOP00000079449.1, ENSRNOT00000116331.2
      Conserved Domains (1) summary
      pfam03416
      Location:40 → 302
      Peptidase_C54; Peptidase family C54

    2. XM_063267328.1 → XP_063123398.1  cysteine protease ATG4B isoform X2

      UniProtKB/TrEMBL
      A0A8I6GGT0

    3. XM_039083775.1 → XP_038939703.1  cysteine protease ATG4B isoform X3

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

    4. XM_039083774.2 → XP_038939702.1  cysteine protease ATG4B isoform X3

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

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001025711.1: Suppressed sequence

      Description
      NM_001025711.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0A0G2QC33.1 GenPept UniProtKB/Swiss-Prot:A0A0G2QC33

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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