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

Gene ID: 494180, updated on 28-Oct-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, Oct 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 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

Gene LinkOut

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