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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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