Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 245860, updated on 22-Aug-2021

    Summary

    Official Symbol
    Atg9aprovided by MGI
    Official Full Name
    autophagy related 9Aprovided by MGI
    Primary source
    MGI:MGI:2138446
    See related
    Ensembl:ENSMUSG00000033124
    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
    Apg; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Atg9a in Genome Data Viewer
    Location:
    1; 1 C4
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (75157505..75168654, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 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_000067.7Genomic 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 Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC105176

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 endosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    is_active_in phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 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)

    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)

    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
      ENSMUSP00000047449.9, ENSMUST00000040689.15
      Conserved Domains (1) summary
      pfam04109
      Location:37525
      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
      ENSMUSP00000139731.2, ENSMUST00000188347.7
      Conserved Domains (1) summary
      pfam04109
      Location:37525
      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
      ENSMUST00000239085.2

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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
      75157505..75168654 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238689.4XP_011236991.1  autophagy-related protein 9A isoform X2

      Conserved Domains (2) summary
      PHA03247
      Location:657801
      PHA03247; large tegument protein UL36; Provisional
      pfam04109
      Location:37525
      APG9; Autophagy protein Apg9
    2. XM_011238690.4XP_011236992.1  autophagy-related protein 9A isoform X3

      Conserved Domains (1) summary
      pfam04109
      Location:37525
      APG9; Autophagy protein Apg9
    3. XM_011238687.4XP_011236989.1  autophagy-related protein 9A isoform X1

      See identical proteins and their annotated locations for XP_011236989.1

      UniProtKB/TrEMBL
      Q3ZAQ4
      Related
      ENSMUSP00000139641.2, ENSMUST00000189702.7
      Conserved Domains (1) summary
      pfam04109
      Location:37525
      APG9; Autophagy protein Apg9
    4. XM_011238688.4XP_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:37525
      APG9; Autophagy protein Apg9
    5. XM_030254267.2XP_030110127.1  autophagy-related protein 9A isoform X2

      Conserved Domains (2) summary
      PHA03247
      Location:657801
      PHA03247; large tegument protein UL36; Provisional
      pfam04109
      Location:37525
      APG9; Autophagy protein Apg9
    Support Center