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

Gene ID: 245860, updated on 6-Jun-2024

Summary

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
Acts upstream of or within several processes, including autophagosome assembly; negative regulation of interferon-beta production; and protein localization to Golgi apparatus. Located in autophagosome. Is expressed in several structures, including cochlea; heart; liver; lung; and telencephalon. Orthologous to human ATG9A (autophagy related 9A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 166.6), duodenum adult (RPKM 40.8) and 26 other tissues See more
Orthologs
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Genomic context

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

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 Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC105176

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables phospholipid scramblase activity ISO
Inferred from Sequence Orthology
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 
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 autophagy of mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
 
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_or_within lipid transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of macrophage cytokine production IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 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 cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
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 membrane IEA
Inferred from Electronic Annotation
more info
 
located_in mitochondrion ISO
Inferred from Sequence Orthology
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 recycling endosome ISO
Inferred from Sequence Orthology
more info
 
located_in recycling endosome membrane ISO
Inferred from Sequence Orthology
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 

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)

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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_001003917.5NP_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:37525
    APG9; Autophagy protein Apg9
  2. NM_001288612.2NP_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:37525
    APG9; Autophagy protein Apg9
  3. NM_001408225.1NP_001395154.1  autophagy-related protein 9A isoform a

    Status: VALIDATED

    Source sequence(s)
    AC166150
    UniProtKB/Swiss-Prot
    Q3ZAQ4, Q68FE2
    UniProtKB/TrEMBL
    A0A087WP33
  4. NM_001408227.1NP_001395156.1  autophagy-related protein 9A isoform a

    Status: VALIDATED

    Source sequence(s)
    AC166150
    UniProtKB/Swiss-Prot
    Q3ZAQ4, Q68FE2
    UniProtKB/TrEMBL
    A0A087WP33
    Related
    ENSMUSP00000139641.2, ENSMUST00000189702.7
  5. NM_001408229.1NP_001395158.1  autophagy-related protein 9A isoform c

    Status: VALIDATED

    Source sequence(s)
    AC166150
  6. NM_001408230.1NP_001395159.1  autophagy-related protein 9A isoform c

    Status: VALIDATED

    Source sequence(s)
    AC166150
  7. NM_001408231.1NP_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_011238690.4XP_011236992.1  autophagy-related protein 9A isoform X3

    UniProtKB/TrEMBL
    A0A087WP33
    Conserved Domains (1) summary
    pfam04109
    Location:37525
    APG9; Autophagy protein Apg9