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    ATG16L1 autophagy related 16 like 1 [ Homo sapiens (human) ]

    Gene ID: 55054, updated on 23-May-2018
    Official Symbol
    ATG16L1provided by HGNC
    Official Full Name
    autophagy related 16 like 1provided by HGNC
    Primary source
    HGNC:HGNC:21498
    See related
    Ensembl:ENSG00000085978 MIM:610767
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IBD10; WDR30; APG16L; ATG16A; ATG16L
    Summary
    The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in bone marrow (RPKM 12.7), testis (RPKM 12.0) and 25 other tissues See more
    Orthologs
    See ATG16L1 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (233251571..233295674)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (234160217..234204320)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuraminidase 2 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene Neighboring gene small Cajal body-specific RNA 5 Neighboring gene small Cajal body-specific RNA 6 Neighboring gene S-antigen visual arrestin Neighboring gene diacylglycerol kinase delta

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Inflammatory bowel disease 10
    MedGen: C1970207 OMIM: 611081 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
    NHGRI GWA Catalog
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    NHGRI GWA Catalog
    Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
    NHGRI GWA Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    NHGRI GWA Catalog
    Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis.
    NHGRI GWA Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    NHGRI GWA Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    NHGRI GWA Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    NHGRI GWA Catalog

    Replication interactions

    Interaction Pubs
    High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed
    Pol gag-pol High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed
    reverse transcriptase gag-pol High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed

    Go to the HIV-1, Human Interaction Database

    • 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 biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • Macroautophagy, organism-specific biosystem (from REACTOME)
      Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
    • 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...
    • Nanoparticle triggered autophagic cell death, organism-specific biosystem (from WikiPathways)
      Nanoparticle triggered autophagic cell death, organism-specific biosystemProgrammed cell death: autophagic cell death. Autophagy (self-eating) is a survival mechanism deployed by cells to cope with conditions of nutrient deprivation. However, unrestrained autophagy can re...
    • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
      Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ00045, FLJ10035, FLJ10828, FLJ22677

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    ubiquitin-like protein transferase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    macroautophagy TAS
    Traceable Author Statement
    more info
     
    negative stranded viral RNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein homooligomerization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein lipidation involved in autophagosome assembly IEA
    Inferred from Electronic Annotation
    more info
     
    protein localization to phagophore assembly site IEA
    Inferred from Electronic Annotation
    more info
     
    protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    xenophagy IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    autophagosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    axoneme ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    phagophore assembly site membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    autophagy-related protein 16-1
    Names
    APG16L beta
    ATG16 autophagy related 16-like 1
    WD repeat domain 30

    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.

    Genomic

    1. NG_023038.1 RefSeqGene

      Range
      5001..49104
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190266.1NP_001177195.1  autophagy-related protein 16-1 isoform 4

      See identical proteins and their annotated locations for NP_001177195.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AA809053, AC013726, BC000061, BC071846, DB084962
      UniProtKB/Swiss-Prot
      Q676U5
      UniProtKB/TrEMBL
      Q53SV2
      Conserved Domains (3) summary
      cd00200
      Location:231521
      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 ...
      sd00039
      Location:243280
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:2122
      ATG16; Autophagy protein 16 (ATG16)
    2. NM_001190267.1NP_001177196.1  autophagy-related protein 16-1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (5) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AA809053, AC013726, BC000061, BC006253, BC071846, DB084962
      UniProtKB/Swiss-Prot
      Q676U5
      Conserved Domains (4) summary
      COG2319
      Location:199457
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:199489
      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 ...
      sd00039
      Location:211248
      7WD40; WD40 repeat [structural motif]
      cl23720
      Location:1110
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    3. NM_017974.3NP_060444.3  autophagy-related protein 16-1 isoform 2

      See identical proteins and their annotated locations for NP_060444.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA809053, AC013726, AK001690, BC117337, DB084962, DB474638
      Consensus CDS
      CCDS2502.2
      UniProtKB/Swiss-Prot
      Q676U5
      UniProtKB/TrEMBL
      A0A024R494, Q17RG0
      Related
      ENSP00000375875.4, ENST00000392020.8
      Conserved Domains (5) summary
      COG2319
      Location:296554
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:296586
      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:308345
      7WD40; WD40 repeat [structural motif]
      cl23720
      Location:117222
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    4. NM_030803.6NP_110430.5  autophagy-related protein 16-1 isoform 1

      See identical proteins and their annotated locations for NP_110430.5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA809053, AC013726, AY398617, BC117337, DB084962
      Consensus CDS
      CCDS2503.2
      UniProtKB/Swiss-Prot
      Q676U5
      UniProtKB/TrEMBL
      Q17RG0
      Related
      ENSP00000375872.4, ENST00000392017.8
      Conserved Domains (5) summary
      COG2319
      Location:315573
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:315605
      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:117222
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    5. NM_198890.2NP_942593.2  autophagy-related protein 16-1 isoform 3

      See identical proteins and their annotated locations for NP_942593.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame segment and an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA809053, AC013726, BC071846, DB084962, EF079890
      Consensus CDS
      CCDS54438.1
      UniProtKB/Swiss-Prot
      Q676U5
      Related
      ENSP00000318259.6, ENST00000347464.9
      Conserved Domains (3) summary
      COG2319
      Location:152410
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:152442
      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 ...
      sd00039
      Location:164201
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

      Range
      233251571..233295674
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005246082.3XP_005246139.1  autophagy-related protein 16-1 isoform X1

      See identical proteins and their annotated locations for XP_005246139.1

      UniProtKB/TrEMBL
      E7EVC7
      Related
      ENSP00000375873.1, ENST00000392018.1
      Conserved Domains (5) summary
      COG2319
      Location:332590
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:332622
      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:344381
      7WD40; WD40 repeat [structural motif]
      cl23720
      Location:117222
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    2. XM_006712608.3XP_006712671.1  autophagy-related protein 16-1 isoform X2

      See identical proteins and their annotated locations for XP_006712671.1

      Conserved Domains (4) summary
      COG2319
      Location:248506
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:248538
      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 ...
      pfam13874
      Location:83140
      Nup54; Nucleoporin complex subunit 54
      sd00039
      Location:260297
      7WD40; WD40 repeat [structural motif]
    3. XM_005246084.2XP_005246141.1  autophagy-related protein 16-1 isoform X3

      See identical proteins and their annotated locations for XP_005246141.1

      Conserved Domains (3) summary
      COG2319
      Location:188446
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:188478
      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 ...
      sd00039
      Location:200237
      7WD40; WD40 repeat [structural motif]
    4. XM_005246086.2XP_005246143.1  autophagy-related protein 16-1 isoform X4

      See identical proteins and their annotated locations for XP_005246143.1

      UniProtKB/TrEMBL
      A0A024R4B6
      Related
      ENSP00000362625.5, ENST00000373525.9
      Conserved Domains (3) summary
      COG2319
      Location:171429
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:171461
      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 ...
      sd00039
      Location:183220
      7WD40; WD40 repeat [structural motif]

    RNA

    1. XR_241242.3 RNA Sequence

    2. XR_001738801.2 RNA Sequence

      Related
      ENST00000392021.7

    Reference GRCh38.p12 PATCHES

    Genomic

    1. NW_011332690.1 Reference GRCh38.p12 PATCHES

      Range
      196909..241012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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