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    Atg16l1 autophagy related 16-like 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363278, updated on 21-Jul-2018

    Summary

    Official Symbol
    Atg16l1provided by RGD
    Official Full Name
    autophagy related 16-like 1provided by RGD
    Primary source
    RGD:1310631
    See related
    Ensembl:ENSRNOG00000017913
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Wdr30; Apg16l
    Expression
    Biased expression in Thymus (RPKM 129.1), Brain (RPKM 124.5) and 9 other tissues See more
    Orthologs

    Genomic context

    See Atg16l1 in Genome Data Viewer
    Location:
    9q35
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (94879876..94915231)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 9 NC_005108.3 (94599174..94634551)

    Chromosome 9 - NC_005108.4Genomic Context describing neighboring genes Neighboring gene neuraminidase 2 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene uncharacterized LOC102552946 Neighboring gene S-antigen visual arrestin Neighboring gene diacylglycerol kinase, delta

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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)
    • 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...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    GTPase binding IEA
    Inferred from Electronic Annotation
    more info
     
    GTPase binding ISO
    Inferred from Sequence Orthology
    more info
     
    identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    biological_process ND
    No biological Data available
    more info
     
    negative stranded viral RNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative stranded viral RNA replication ISO
    Inferred from Sequence Orthology
    more info
     
    protein lipidation involved in autophagosome assembly IEA
    Inferred from Electronic Annotation
    more info
     
    protein lipidation involved in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
     
    protein localization to phagophore assembly site IEA
    Inferred from Electronic Annotation
    more info
     
    protein localization to phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
     
    xenophagy IEA
    Inferred from Electronic Annotation
    more info
     
    xenophagy ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    autophagosome ISO
    Inferred from Sequence Orthology
    more info
     
    autophagosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome membrane ISO
    Inferred from Sequence Orthology
    more info
     
    axoneme IEA
    Inferred from Electronic Annotation
    more info
     
    axoneme ISO
    Inferred from Sequence Orthology
    more info
     
    cellular_component ND
    No biological Data available
    more info
     

    General protein information

    Preferred Names
    autophagy-related protein 16-1
    Names
    APG16 autophagy 16-like
    WD repeat domain 30

    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_001108809.3NP_001102279.2  autophagy-related protein 16-1

      Status: PROVISIONAL

      Source sequence(s)
      AABR07068279
      UniProtKB/TrEMBL
      D3ZFK6
      Related
      ENSRNOP00000024445.3, ENSRNOT00000024445.3
      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:90190
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    RefSeqs of Annotated Genomes: Rattus norvegicus 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 Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005108.4 Reference Rnor_6.0 Primary Assembly

      Range
      94879876..94915231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006245419.3XP_006245481.1  autophagy-related protein 16-1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K9U6
      Related
      ENSRNOP00000075135.1, ENSRNOT00000080482.1
      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:90190
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    2. XM_006245420.2XP_006245482.1  autophagy-related protein 16-1 isoform X2

      See identical proteins and their annotated locations for XP_006245482.1

      Conserved Domains (6) 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:130296
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
      pfam08614
      Location:31206
      ATG16; Autophagy protein 16 (ATG16)
      pfam15898
      Location:80169
      PRKG1_interact; cGMP-dependent protein kinase interacting domain
      sd00039
      Location:308345
      7WD40; WD40 repeat [structural motif]

    Alternate Rn_Celera

    Genomic

    1. AC_000077.1 Alternate Rn_Celera

      Range
      85830765..85865957
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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