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    Atg9a autophagy related 9A [ Mus musculus (house mouse) ]

    Gene ID: 245860, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Atg9aprovided by MGI
    Official Full Name
    autophagy related 9Aprovided by MGI
    Primary source
    MGI:MGI:2138446
    See related
    Ensembl:ENSMUSG00000033124 AllianceGenome:MGI:2138446
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Atg9; Apg9l1; Atg9l1
    Summary
    Predicted to enable phospholipid scramblase activity. Involved in autophagy; bone morphogenesis; and programmed necrotic cell death. Acts upstream of or within several processes, including autophagosome assembly; negative regulation of cytokine production; and protein localization to Golgi apparatus. Located in Golgi membrane; autophagosome; and endoplasmic reticulum membrane. Is active in synaptic membrane. Is expressed in brain; cochlea; heart; liver; and lung. Orthologous to human ATG9A (autophagy related 9A). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 166.6), duodenum adult (RPKM 40.8) and 26 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Atg9a in Genome Data Viewer
    Location:
    1 C4; 1 38.62 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (75157509..75168654, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (75180861..75192010, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1550 Neighboring gene zinc finger, AN1 type domain 2B Neighboring gene ATP-binding cassette, sub-family B member 6 Neighboring gene STARR-positive B cell enhancer ABC_E8982 Neighboring gene STARR-positive B cell enhancer ABC_E321 Neighboring gene ankyrin repeat and zinc finger domain containing 1 Neighboring gene galactosidase, beta 1-like Neighboring gene serine/threonine kinase 16 Neighboring gene tubulin, alpha 4A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Atg9A protein, an autophagy-related membrane protein, is localized in the neurons of mouse brains. Tamura H, et al. J Histochem Cytochem, 2010 May. PMID 20124090, Free PMC Article
    2. S100a9 inhibits Atg9a transcription and participates in suppression of autophagy in cardiomyocytes induced by β(1)-adrenoceptor autoantibodies. Zhi X, et al. Cell Mol Biol Lett, 2023 Sep 18. PMID 37723445, Free PMC Article
    3. The LC3 recruitment mechanism is separate from Atg9L1-dependent membrane formation in the autophagic response against Salmonella. Kageyama S, et al. Mol Biol Cell, 2011 Jul 1. PMID 21525242, Free PMC Article
    4. Altered distribution of ATG9A and accumulation of axonal aggregates in neurons from a mouse model of AP-4 deficiency syndrome. De Pace R, et al. PLoS Genet, 2018 Apr. PMID 29698489, Free PMC Article
    5. MicroRNA-34a mediates ethanol-induced impairment of neural differentiation of neural crest cells by targeting autophagy-related gene 9a. Fan H, et al. Exp Neurol, 2019 Oct. PMID 31247197, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IL-4 activates ULK1/Atg9a/Rab9 in asthma, NLRP3 inflammasomes, and Golgi fragmentation by increasing autophagy flux and mitochondrial oxidative stress.
      Title: IL-4 activates ULK1/Atg9a/Rab9 in asthma, NLRP3 inflammasomes, and Golgi fragmentation by increasing autophagy flux and mitochondrial oxidative stress.
    2. S100a9 inhibits Atg9a transcription and participates in suppression of autophagy in cardiomyocytes induced by beta1-adrenoceptor autoantibodies.
      Title: S100a9 inhibits Atg9a transcription and participates in suppression of autophagy in cardiomyocytes induced by β(1)-adrenoceptor autoantibodies.
    3. HSF4 Transcriptionally Activates Autophagy by Regulating ATG9a During Lens Terminal Differentiation.
      Title: HSF4 Transcriptionally Activates Autophagy by Regulating ATG9a During Lens Terminal Differentiation.
    4. A neuroprotective role of Ufmylation through Atg9 in the aging brain of Drosophila.
      Title: A neuroprotective role of Ufmylation through Atg9 in the aging brain of Drosophila.
    5. ATG9A prevents TNF cytotoxicity by an unconventional lysosomal targeting pathway.
      Title: ATG9A prevents TNF cytotoxicity by an unconventional lysosomal targeting pathway.
    6. NMMHC IIA triggers neuronal autophagic cell death by promoting F-actin-dependent ATG9A trafficking in cerebral ischemia/reperfusion.
      Title: NMMHC IIA triggers neuronal autophagic cell death by promoting F-actin-dependent ATG9A trafficking in cerebral ischemia/reperfusion.
    7. Axonal autophagosome maturation defect through failure of ATG9A sorting underpins pathology in AP-4 deficiency syndrome.
      Title: Axonal autophagosome maturation defect through failure of ATG9A sorting underpins pathology in AP-4 deficiency syndrome.
    8. These results demonstrate that ethanol-induced inhibition of neural differentiation of neural crest cells is mediated by the miR-34a through targeting Atg9a.
      Title: MicroRNA-34a mediates ethanol-induced impairment of neural differentiation of neural crest cells by targeting autophagy-related gene 9a.
    9. High ATG9A expression is associated with liver fibrosis.
      Title: The lncRNA NEAT1/miR-29b/Atg9a axis regulates IGFBPrP1-induced autophagy and activation of mouse hepatic stellate cells.
    10. Atg9a deficiency causes progressive degeneration in the axons and their terminals, but not in neuronal cell bodies.
      Title: Atg9a deficiency causes axon-specific lesions including neuronal circuit dysgenesis.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Targeted (2)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC105176

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables phospholipid scramblase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phospholipid scramblase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in bone morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of interferon-beta production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of macrophage cytokine production 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 negative regulation of interferon-beta production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of macrophage cytokine production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in plasma membrane phospholipid scrambling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in programmed necrotic cell death IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein localization to Golgi apparatus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in reticulophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT located_in autophagosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in phagophore assembly site membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in synaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synaptic membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    autophagy-related protein 9A
    Names
    APG9 autophagy 9-like 1
    APG9-like 1
    autophagy protein 9
    autophagy-related 9-like 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_001003917.5 → NP_001003917.2  autophagy-related protein 9A isoform a

      See identical proteins and their annotated locations for NP_001003917.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 5, and 6 all encode the same isoform (a).
      Source sequence(s)
      AC166150
      Consensus CDS
      CCDS35622.1
      UniProtKB/Swiss-Prot
      Q3ZAQ4, Q68FE2
      UniProtKB/TrEMBL
      A0A087WP33
      Related
      ENSMUSP00000047449.9, ENSMUST00000040689.15
      Conserved Domains (1) summary
      pfam04109
      Location:37 → 525
      APG9; Autophagy protein Apg9

    2. NM_001288612.2 → NP_001275541.1  autophagy-related protein 9A isoform a

      See identical proteins and their annotated locations for NP_001275541.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1, 2, 5, and 6 all encode the same isoform (a).
      Source sequence(s)
      AC166150
      Consensus CDS
      CCDS35622.1
      UniProtKB/Swiss-Prot
      Q3ZAQ4, Q68FE2
      UniProtKB/TrEMBL
      A0A087WP33
      Related
      ENSMUSP00000139731.2, ENSMUST00000188347.7
      Conserved Domains (1) summary
      pfam04109
      Location:37 → 525
      APG9; Autophagy protein Apg9

    3. NM_001408225.1 → NP_001395154.1  autophagy-related protein 9A isoform a

      Status: VALIDATED

      Source sequence(s)
      AC166150
      UniProtKB/Swiss-Prot
      Q3ZAQ4, Q68FE2

    4. NM_001408227.1 → NP_001395156.1  autophagy-related protein 9A isoform a

      Status: VALIDATED

      Source sequence(s)
      AC166150
      UniProtKB/Swiss-Prot
      Q3ZAQ4, Q68FE2
      Related
      ENSMUSP00000139641.2, ENSMUST00000189702.7

    5. NM_001408229.1 → NP_001395158.1  autophagy-related protein 9A isoform c

      Status: VALIDATED

      Source sequence(s)
      AC166150

    6. NM_001408230.1 → NP_001395159.1  autophagy-related protein 9A isoform c

      Status: VALIDATED

      Source sequence(s)
      AC166150

    7. NM_001408231.1 → NP_001395160.1  autophagy-related protein 9A isoform c

      Status: VALIDATED

      Source sequence(s)
      AC166150

    RNA

    1. NR_109938.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate splice junction at the 3' end of an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC166150
      Related
      ENSMUST00000239085.2

    2. NR_176609.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC166150
      Related
      ENSMUST00000189665.7

    3. NR_176610.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC166150

    4. NR_176611.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC166150

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000067.7 Reference GRCm39 C57BL/6J

      Range
      75157509..75168654 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238690.4 → XP_011236992.1  autophagy-related protein 9A isoform X3

      UniProtKB/TrEMBL
      A0A087WP33
      Conserved Domains (1) summary
      pfam04109
      Location:37 → 525
      APG9; Autophagy protein Apg9
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68FE2.2 GenPept UniProtKB/Swiss-Prot:Q68FE2

    Gene LinkOut

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

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