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    atg5 ATG5 autophagy related 5 homolog (S. cerevisiae) [ Danio rerio (zebrafish) ]

    Gene ID: 494180, updated on 9-Dec-2024

    Summary

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    Official Symbol
    atg5provided by ZNC
    Official Full Name
    ATG5 autophagy related 5 homolog (S. cerevisiae)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040801-149
    See related
    Ensembl:ENSDARG00000023396 AllianceGenome:ZFIN:ZDB-GENE-040801-149
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    apg5l; zgc:100934
    Summary
    Predicted to contribute to Atg8-family ligase activity. Acts upstream of or within several processes, including autophagosome assembly; heart development; and regulation of skeletal muscle tissue regeneration. Predicted to be located in cytoplasm and membrane. Predicted to be part of Atg12-Atg5-Atg16 complex. Predicted to be active in autophagosome; phagophore; and phagophore assembly site membrane. Is expressed in several structures, including heart; liver; male organism; nervous system; and tail bud. 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]
    Orthologs
    human mouse all
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    Genomic context

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    See atg5 in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (7380463..7416536)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (7463117..7499190)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137487874 Neighboring gene mediator of RNA polymerase II transcription, subunit 18 homolog (yeast) Neighboring gene PR domain containing 1a, with ZNF domain Neighboring gene uncharacterized LOC137487875

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Inactivation of 3-hydroxybutyrate dehydrogenase 2 delays zebrafish erythroid maturation by conferring premature mitophagy. Davuluri G, et al. Proc Natl Acad Sci U S A, 2016 Mar 15. PMID 26929344, Free PMC Article
    2. Autophagy is required for zebrafish caudal fin regeneration. Varga M, et al. Cell Death Differ, 2014 Apr. PMID 24317199, Free PMC Article
    3. Dietary and Pharmacological Interventions That Inhibit Mammalian Target of Rapamycin Activity Alter the Brain Expression Levels of Neurogenic and Glial Markers in an Age-and Treatment-Dependent Manner. Celebi-Birand D, et al. Rejuvenation Res, 2020 Dec. PMID 32279604
    4. The tumor suppressor LKB1 regulates starvation-induced autophagy under systemic metabolic stress. Mans LA, et al. Sci Rep, 2017 Aug 4. PMID 28779098, Free PMC Article
    5. A152T tau allele causes neurodegeneration that can be ameliorated in a zebrafish model by autophagy induction. Lopez A, et al. Brain, 2017 Apr 1. PMID 28334843, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    contributes_to Atg8-family ligase activity IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    acts_upstream_of_or_within autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to nitrogen starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within nervous system 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
    		  
    acts_upstream_of_or_within regulation of skeletal muscle tissue regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in phagophore IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in phagophore assembly site membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    autophagy protein 5
    Names
    autophagy 5-like protein

    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_001009914.2 → NP_001009914.2  autophagy protein 5

      See identical proteins and their annotated locations for NP_001009914.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL928573
      UniProtKB/TrEMBL
      A0A8M1N3W4, F1RDC0
      Related
      ENSDARP00000124077.1, ENSDART00000149086.2
      Conserved Domains (1) summary
      pfam04106
      Location:81 → 270
      APG5; Autophagy protein Apg5

    2. NM_205618.2 → NP_991181.2  autophagy protein 5

      See identical proteins and their annotated locations for NP_991181.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL928573
      UniProtKB/TrEMBL
      A0A8M1N3W4, F1RDC0
      Related
      ENSDARP00000030870.5, ENSDART00000029727.7
      Conserved Domains (1) summary
      pfam04106
      Location:81 → 270
      APG5; Autophagy protein Apg5

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007127.7 Reference GRCz11 Primary Assembly

      Range
      7380463..7416536
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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