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

    Gene ID: 245860, updated on 9-Sep-2018

    Summary

    Official Symbol
    Atg9aprovided by MGI
    Official Full Name
    autophagy related 9Aprovided by MGI
    Primary source
    MGI:MGI:2138446
    See related
    Ensembl:ENSMUSG00000033124 Vega:OTTMUSG00000048480
    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; AU019532
    Expression
    Ubiquitous expression in testis adult (RPKM 166.6), duodenum adult (RPKM 40.8) and 26 other tissues See more
    Orthologs

    Genomic context

    See Atg9a in Genome Data Viewer
    Location:
    1; 1 C4
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 1 NC_000067.6 (75180861..75192010, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (75177440..75188497, complement)

    Chromosome 1 - NC_000067.6Genomic Context describing neighboring genes Neighboring gene zinc finger, AN1 type domain 2B Neighboring gene ATP-binding cassette, sub-family B (MDR/TAP), member 6 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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    • Autophagy - animal, organism-specific biosystem (from KEGG)
      Autophagy - animal, organism-specific biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
    • Autophagy - animal, conserved biosystem (from KEGG)
      Autophagy - animal, conserved biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
    • Autophagy - other, organism-specific biosystem (from KEGG)
      Autophagy - other, organism-specific biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
    • Autophagy - other, conserved biosystem (from KEGG)
      Autophagy - other, conserved biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Macroautophagy, organism-specific biosystem (from REACTOME)
      Macroautophagy, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Mitophagy - animal, organism-specific biosystem (from KEGG)
      Mitophagy - animal, organism-specific biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...
    • Mitophagy - animal, conserved biosystem (from KEGG)
      Mitophagy - animal, conserved biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...

    General gene information

    Markers

    Homology

    Clone Names

    • MGC105176

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    autophagy of mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    late nucleophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of interferon-beta production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein localization to Golgi apparatus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein localization to phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT autophagosome membrane ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    endosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    late endosome ISO
    Inferred from Sequence Orthology
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
     
    recycling endosome ISO
    Inferred from Sequence Orthology
    more info
     
    synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    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)

    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_001003917.4NP_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 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC166150, AU019532, BC056488, BC079884
      Consensus CDS
      CCDS35622.1
      UniProtKB/Swiss-Prot
      Q68FE2
      UniProtKB/TrEMBL
      Q3ZAQ4
      Related
      ENSMUSP00000047449.8, ENSMUST00000040689.14
      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
    2. NM_001288612.1NP_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 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC166150, AU019532, BC056488, BC079884
      Consensus CDS
      CCDS35622.1
      UniProtKB/Swiss-Prot
      Q68FE2
      UniProtKB/TrEMBL
      Q3ZAQ4
      Related
      ENSMUSP00000139731.1, OTTMUSP00000067643, ENSMUST00000188347.6, OTTMUST00000124249
      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
    3. NM_001288613.1NP_001275542.1  autophagy-related protein 9A isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction at the 5' end of an exon and initiates translation at an alternate start codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC166150, AU019532, BC056488
      Conserved Domains (1) summary
      pfam04109
      Location:1310
      APG9; Autophagy protein Apg9

    RNA

    1. NR_109938.1 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, AU019532, BC079884
      Related
      ENSMUST00000189665.6, OTTMUST00000124248

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000067.6 Reference GRCm38.p4 C57BL/6J

      Range
      75180861..75192010 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238687.2XP_011236989.1  autophagy-related protein 9A isoform X1

      See identical proteins and their annotated locations for XP_011236989.1

      UniProtKB/TrEMBL
      Q3ZAQ4
      Related
      ENSMUSP00000139641.1, OTTMUSP00000067640, ENSMUST00000189702.6, OTTMUST00000124246
      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
    2. XM_011238688.2XP_011236990.1  autophagy-related protein 9A isoform X1

      See identical proteins and their annotated locations for XP_011236990.1

      UniProtKB/TrEMBL
      Q3ZAQ4
      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
    3. XM_011238689.2XP_011236991.1  autophagy-related protein 9A isoform X2

      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
    4. XM_011238690.2XP_011236992.1  autophagy-related protein 9A isoform X3

      Conserved Domains (1) summary
      pfam04109
      Location:179528
      APG9; Autophagy protein Apg9
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