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

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: 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, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 166.6), duodenum adult (RPKM 40.8) and 26 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
HSF4 Transcriptionally Activates Autophagy by Regulating ATG9a During Lens Terminal Differentiation.
Title: HSF4 Transcriptionally Activates Autophagy by Regulating ATG9a During Lens Terminal Differentiation.
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.
ATG9A prevents TNF cytotoxicity by an unconventional lysosomal targeting pathway.
Title: ATG9A prevents TNF cytotoxicity by an unconventional lysosomal targeting pathway.
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.
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.
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.
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.
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

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (4)
Targeted (2) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D10Bir8 (e-PCR), detects polymorphism
- UniSTS:141487

RH136427 (e-PCR)
- UniSTS:210415

D9Mco65 (e-PCR)
- UniSTS:518642

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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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

Status: VALIDATED

Source sequence(s)

AC166150

UniProtKB/Swiss-Prot

Q3ZAQ4, Q68FE2
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
NM_001408229.1 → NP_001395158.1 autophagy-related protein 9A isoform c

Status: VALIDATED

Source sequence(s)

AC166150
NM_001408230.1 → NP_001395159.1 autophagy-related protein 9A isoform c

Status: VALIDATED

Source sequence(s)

AC166150
NM_001408231.1 → NP_001395160.1 autophagy-related protein 9A isoform c

Status: VALIDATED

Source sequence(s)

AC166150

RNA

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
NR_176609.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC166150

Related

ENSMUST00000189665.7
NR_176610.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC166150
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

NC_000067.7 Reference GRCm39 C57BL/6J

Range

75157509..75168654 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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