U.S. flag

An official website of the United States government

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    General gene information

    Clone Names

    • MGC112887

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity  
    enables cysteine-type endopeptidase activity  
    enables cysteine-type endopeptidase activity  
    enables cysteine-type peptidase activity  
    enables cysteine-type peptidase activity  
    enables endopeptidase activity  
    enables peptidase activity  
    enables protein-phosphatidylethanolamide deconjugating activity  
    enables protein-phosphatidylethanolamide deconjugating activity  
    enables protein-phosphatidylethanolamide deconjugating activity  
    enables scaffold protein binding  
    enables scaffold protein binding  
    Process Evidence Code Pubs
    involved_in aggrephagy  
    involved_in autophagosome assembly  
    involved_in autophagosome assembly  
    involved_in autophagy  
    involved_in autophagy  
    involved_in cellular response to starvation  
    involved_in microautophagy  
    involved_in microautophagy  
    involved_in mitophagy  
    involved_in mitophagy  
    involved_in mitophagy  
    involved_in otolith mineralization completed early in development  
    involved_in piecemeal microautophagy of the nucleus  
    involved_in positive regulation of protein catabolic process PubMed 
    involved_in protein delipidation  
    involved_in protein localization to phagophore assembly site  
    involved_in protein localization to phagophore assembly site  
    involved_in protein processing  
    involved_in protein transport  
    involved_in proteolysis  
    involved_in proteolysis  
    Component Evidence Code Pubs
    located_in autophagosome  
    located_in autophagosome membrane  
    is_active_in autophagosome membrane  
    is_active_in cytoplasm  
    located_in cytoplasm  
    located_in cytoplasmic vesicle  
    located_in cytosol  
    located_in endoplasmic reticulum  
    located_in mitochondrion  

    General protein information

    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)

    NEW Try the new Transcript table

    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_001399197.1NP_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:39335
      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_006245534.5XP_006245596.1  cysteine protease ATG4B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQY4, A0A8I6GGT0
      Related
      ENSRNOP00000079449.1, ENSRNOT00000116331.2
      Conserved Domains (1) summary
      pfam03416
      Location:40302
      Peptidase_C54; Peptidase family C54
    2. XM_063267328.1XP_063123398.1  cysteine protease ATG4B isoform X2

      UniProtKB/TrEMBL
      A0A8I6GGT0
    3. XM_039083775.1XP_038939703.1  cysteine protease ATG4B isoform X3

      Conserved Domains (1) summary
      pfam03416
      Location:1166
      Peptidase_C54; Peptidase family C54
    4. XM_039083774.2XP_038939702.1  cysteine protease ATG4B isoform X3

      Conserved Domains (1) summary
      pfam03416
      Location:1166
      Peptidase_C54; Peptidase family C54

    External link. Please review our privacy policy.