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    Atg16l1 autophagy related 16-like 1 (S. cerevisiae) [ Mus musculus (house mouse) ]

    Gene ID: 77040, updated on 4-Jun-2017
    Official Symbol
    Atg16l1provided by MGI
    Official Full Name
    autophagy related 16-like 1 (S. cerevisiae)provided by MGI
    Primary source
    MGI:MGI:1924290
    See related
    Ensembl:ENSMUSG00000026289 Vega:OTTMUSG00000016467
    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
    WDR30; Apg16l; Atg16l; 1500009K01Rik
    Orthologs
    Location:
    1; 1 D
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 1 NC_000067.6 (87756006..87792428)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (89652646..89688997)

    Chromosome 1 - NC_000067.6Genomic Context describing neighboring genes Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene predicted gene, 33470 Neighboring gene predicted gene, 33517 Neighboring gene small Cajal body-specific RNA 6 Neighboring gene S-antigen, retina and pineal gland (arrestin) Neighboring gene predicted gene, 38609 Neighboring gene predicted gene, 19582 Neighboring gene diacylglycerol kinase, delta

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • 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)
    • NOD-like receptor signaling pathway, organism-specific biosystem (from KEGG)
      NOD-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
    • NOD-like receptor signaling pathway, conserved biosystem (from KEGG)
      NOD-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    GTPase binding ISO
    Inferred from Sequence Orthology
    more info
     
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    autophagosome assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    negative stranded viral RNA replication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein lipidation involved in autophagosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein localization to pre-autophagosomal structure IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    transport IEA
    Inferred from Electronic Annotation
    more info
     
    xenophagy IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    autophagosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    axoneme IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    autophagy-related protein 16-1
    Names
    APG16-like 1
    Atg16L1 gamma
    autophagy-related 16-like 1 gamma

    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_001205391.1NP_001192320.1  autophagy-related protein 16-1 isoform 1

      See identical proteins and their annotated locations for NP_001192320.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1, also known as Apg16Lgamma) represents the longest transcript and encodes the longest isoform (1, also known as Apg16Lgamma).
      Source sequence(s)
      AC102630, AC159967, BC049122, BE988512
      Consensus CDS
      CCDS56637.1
      UniProtKB/Swiss-Prot
      Q8C0J2
      UniProtKB/TrEMBL
      G9M4M6
      Related
      ENSMUSP00000108815.2, OTTMUSP00000017709, ENSMUST00000113190.2, OTTMUST00000039678
      Conserved Domains (5) summary
      COG2319
      Location:332589
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:333621
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam08614
      Location:31206
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:343380
      7WD40; WD40 repeat [structural motif]
      cl23720
      Location:84190
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    2. NM_001205392.1NP_001192321.1  autophagy-related protein 16-1 isoform 3

      See identical proteins and their annotated locations for NP_001192321.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3, also known as Apg16Lalpha) lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3, also known as Apg16Lalpha) is shorter than isoform 1.
      Source sequence(s)
      AC102630, AC159967
      Consensus CDS
      CCDS56638.1
      UniProtKB/TrEMBL
      Q3TDQ5
      Related
      ENSMUSP00000108811.1, OTTMUSP00000018916, ENSMUST00000113186.7, OTTMUST00000042059
      Conserved Domains (5) summary
      COG2319
      Location:297554
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:298586
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam06632
      Location:126296
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
      pfam08614
      Location:31206
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:308345
      7WD40; WD40 repeat [structural motif]
    3. NM_029846.4NP_084122.2  autophagy-related protein 16-1 isoform 2

      See identical proteins and their annotated locations for NP_084122.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2, also known as Apg16Lbeta) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2, also known as Apg16Lbeta) is shorter than isoform 1.
      Source sequence(s)
      AC159967, AK030983, BE988512
      Consensus CDS
      CCDS15136.1
      UniProtKB/Swiss-Prot
      Q8C0J2
      Related
      ENSMUSP00000027512.6, OTTMUSP00000017708, ENSMUST00000027512.12, OTTMUST00000039677
      Conserved Domains (5) summary
      COG2319
      Location:316573
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:317605
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam08614
      Location:31206
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:327364
      7WD40; WD40 repeat [structural motif]
      cl23720
      Location:84190
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

    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
      87756006..87792428
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529950.3XP_006530013.1  autophagy-related protein 16-1 isoform X1

      Conserved Domains (1) summary
      pfam08614
      Location:31206
      ATG16; Autophagy protein 16 (ATG16)

    RNA

    1. XR_387198.3 RNA Sequence

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