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    Atg5 autophagy related 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 365601, updated on 9-Dec-2024

    Summary

    Official Symbol
    Atg5provided by RGD
    Official Full Name
    autophagy related 5provided by RGD
    Primary source
    RGD:1359580
    See related
    EnsemblRapid:ENSRNOG00000000322 AllianceGenome:RGD:1359580
    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
    Summary
    Predicted to contribute to Atg8-family ligase activity. Involved in several processes, including chaperone-mediated autophagy; positive regulation of stress granule assembly; and response to iron(II) ion. Located in axon. Part of protein-containing complex. Is active in glutamatergic synapse. Biomarker of ischemia. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 25. Orthologous to human ATG5 (autophagy related 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 103.7), Liver (RPKM 79.4) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Atg5 in Genome Data Viewer
    Location:
    20q13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (49380835..49471826)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (47798217..47889216)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (49301783..49393147)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene heat shock cognate 71 kDa protein-like Neighboring gene uncharacterized LOC102554815 Neighboring gene PR/SET domain 1 Neighboring gene uncharacterized LOC120098943

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to Atg8-family ligase activity  
    enables Atg8-family ligase activity  
    enables Atg8-family ligase activity  
    enables protein binding PubMed 
    Items 1 - 25 of 99
    Process Evidence Code Pubs
    involved_in aggrephagy  
    involved_in aggrephagy  
    involved_in aggrephagy  
    involved_in antigen processing and presentation of endogenous antigen  
    acts_upstream_of_or_within antigen processing and presentation of endogenous antigen  
    acts_upstream_of apoptotic process  
    involved_in autophagosome assembly  
    involved_in autophagosome assembly  
    involved_in autophagosome assembly PubMed 
    acts_upstream_of_or_within autophagosome assembly  
    involved_in autophagosome assembly  
    involved_in autophagy PubMed 
    involved_in autophagy  
    involved_in autophagy  
    involved_in axonal transport  
    involved_in axonal transport  
    involved_in blood vessel remodeling  
    acts_upstream_of_or_within blood vessel remodeling  
    involved_in cardiac muscle cell apoptotic process  
    acts_upstream_of cardiac muscle cell apoptotic process  
    involved_in cellular response to nitrogen starvation  
    involved_in cellular response to nitrosative stress  
    involved_in cellular response to nitrosative stress  
    involved_in cellular response to starvation  
    acts_upstream_of_or_within cellular response to starvation  
    involved_in chaperone-mediated autophagy PubMed 
    involved_in chromatin organization  
    acts_upstream_of_positive_effect chromatin organization  
    involved_in defense response to virus  
    acts_upstream_of_or_within defense response to virus  
    acts_upstream_of establishment of localization in cell  
    involved_in heart contraction  
    acts_upstream_of_or_within heart contraction  
    involved_in innate immune response  
    acts_upstream_of_or_within innate immune response  
    involved_in macroautophagy  
    acts_upstream_of_or_within macroautophagy  
    involved_in macroautophagy  
    involved_in mitophagy  
    involved_in mitophagy  
    involved_in mucus secretion  
    acts_upstream_of mucus secretion  
    involved_in negative regulation of apoptotic process PubMed 
    involved_in negative regulation of autophagic cell death  
    acts_upstream_of_or_within negative regulation of autophagic cell death  
    involved_in negative regulation of cardiac muscle cell apoptotic process  
    acts_upstream_of_or_within negative regulation of cardiac muscle cell apoptotic process  
    involved_in negative regulation of defense response to virus  
    involved_in negative regulation of defense response to virus  
    involved_in negative regulation of innate immune response  
    involved_in negative regulation of innate immune response  
    involved_in negative regulation of phagocytosis  
    acts_upstream_of_or_within negative regulation of phagocytosis  
    involved_in negative regulation of protein ubiquitination  
    acts_upstream_of_or_within negative regulation of protein ubiquitination  
    involved_in negative regulation of reactive oxygen species metabolic process  
    involved_in negative regulation of type I interferon production  
    involved_in negative regulation of type I interferon production  
    involved_in negative stranded viral RNA replication  
    acts_upstream_of_or_within negative stranded viral RNA replication  
    involved_in negative thymic T cell selection  
    acts_upstream_of_or_within negative thymic T cell selection  
    involved_in otolith development  
    acts_upstream_of_or_within otolith development  
    involved_in piecemeal microautophagy of the nucleus  
    involved_in positive regulation of autophagy PubMed 
    involved_in positive regulation of mucus secretion  
    acts_upstream_of_or_within positive regulation of mucus secretion  
    involved_in positive regulation of stress granule assembly PubMed 
    involved_in positive regulation of viral translation  
    involved_in positive regulation of viral translation  
    involved_in post-translational protein modification  
    involved_in postsynaptic modulation of chemical synaptic transmission  
    involved_in postsynaptic modulation of chemical synaptic transmission  
    acts_upstream_of_or_within protein lipidation involved in autophagosome assembly  
    involved_in protein ubiquitination  
    acts_upstream_of protein ubiquitination  
    involved_in regulation of autophagosome maturation  
    involved_in regulation of autophagosome maturation  
    involved_in regulation of cilium assembly  
    involved_in regulation of cilium assembly  
    involved_in regulation of cilium assembly  
    involved_in regulation of cytokine production involved in immune response  
    acts_upstream_of_or_within regulation of cytokine production involved in immune response  
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels  
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels  
    acts_upstream_of_or_within regulation of reactive oxygen species metabolic process  
    involved_in regulation of release of sequestered calcium ion into cytosol  
    acts_upstream_of_or_within regulation of release of sequestered calcium ion into cytosol  
    involved_in response to fluoride PubMed 
    involved_in response to fungus  
    acts_upstream_of_or_within response to fungus  
    involved_in response to iron(II) ion PubMed 
    involved_in response to xenobiotic stimulus  
    acts_upstream_of_or_within response to xenobiotic stimulus  
    involved_in vasodilation  
    acts_upstream_of_or_within vasodilation  
    involved_in ventricular cardiac muscle cell development  
    acts_upstream_of_or_within ventricular cardiac muscle cell development  
    Items 1 - 25 of 99
    Items 1 - 20 of 29
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex  
    part_of Atg12-Atg5-Atg16 complex  
    part_of Atg12-Atg5-Atg16 complex  
    located_in Schaffer collateral - CA1 synapse  
    is_active_in Schaffer collateral - CA1 synapse  
    is_active_in autophagosome  
    located_in autophagosome  
    located_in autophagosome  
    located_in axon PubMed 
    located_in axon  
    located_in axoneme  
    located_in axoneme  
    located_in axoneme  
    located_in cytoplasm  
    located_in cytoplasm  
    is_active_in glutamatergic synapse PubMed 
    located_in glutamatergic synapse  
    is_active_in glutamatergic synapse  
    located_in membrane  
    located_in mitochondria-associated endoplasmic reticulum membrane contact site  
    located_in mitochondria-associated endoplasmic reticulum membrane contact site  
    is_active_in phagophore  
    is_active_in phagophore assembly site membrane  
    located_in phagophore assembly site membrane  
    located_in phagophore assembly site membrane  
    located_in postsynapse  
    part_of protein-containing complex PubMed 
    is_active_in synapse PubMed 
    part_of transferase complex  
    Items 1 - 20 of 29

    General protein information

    Preferred Names
    autophagy protein 5
    Names
    ATG5 autophagy related 5 homolog

    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_001014250.2NP_001014272.1  autophagy protein 5 isoform 1

      See identical proteins and their annotated locations for NP_001014272.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      Q5XIS0
      Related
      ENSRNOP00000086278.1, ENSRNOT00000101057.2
      Conserved Domains (1) summary
      pfam04106
      Location:79164
      APG5; Autophagy protein Apg5
    2. NM_001399019.1NP_001385948.1  autophagy protein 5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      Related
      ENSRNOP00000107876.1, ENSRNOT00000133750.1
      Conserved Domains (1) summary
      pfam04106
      Location:2166
      APG5; Autophagy protein Apg5
    3. NM_001399020.1NP_001385949.1  autophagy protein 5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      Q3MQ06
      UniProtKB/TrEMBL
      A0A0G2KAB9, A6K6V9
      Conserved Domains (1) summary
      pfam04106
      Location:79270
      APG5; Autophagy protein Apg5
    4. NM_001399021.1NP_001385950.1  autophagy protein 5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      Q3MQ06
      UniProtKB/TrEMBL
      A0A0G2KAB9, A6K6V9
      Related
      ENSRNOP00000075339.2, ENSRNOT00000080283.3
      Conserved Domains (1) summary
      pfam04106
      Location:79270
      APG5; Autophagy protein Apg5

    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_086038.1 Reference GRCr8

      Range
      49380835..49471826
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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