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    ATG16L2 autophagy related 16 like 2 [ Homo sapiens (human) ]

    Gene ID: 89849, updated on 8-Dec-2022

    Summary

    Official Symbol
    ATG16L2provided by HGNC
    Official Full Name
    autophagy related 16 like 2provided by HGNC
    Primary source
    HGNC:HGNC:25464
    See related
    Ensembl:ENSG00000168010 MIM:618716; AllianceGenome:HGNC:25464
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    WDR80; ATG16B
    Summary
    Predicted to be involved in autophagosome assembly and negative stranded viral RNA replication. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in spleen (RPKM 22.5), skin (RPKM 19.9) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ATG16L2 in Genome Data Viewer
    Location:
    11q13.4
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (72814411..72843740)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (72742639..72757867)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (72525456..72540680)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene StAR related lipid transfer domain containing 10 Neighboring gene uncharacterized LOC107984421 Neighboring gene microRNA 4692 Neighboring gene FCH and double SH3 domains 2 Neighboring gene RNA, U6 small nuclear 672, pseudogene Neighboring gene ribosomal protein L15 pseudogene 16

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
    EBI GWAS Catalog
    Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    EBI GWAS Catalog

    HIV-1 interactions

    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
    Knockdown of ATG16 autophagy related 16-like 2 (ATG16L2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ00012

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
     
    NOT involved_in autophagosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative stranded viral RNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein lipidation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT located_in autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in autophagosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in phagophore assembly site membrane ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    protein Atg16l2
    Names
    APG16-like 2
    ATG16 autophagy related 16-like 2
    WD repeat-containing protein 80
    autophagy-related protein 16-2

    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_001318766.2NP_001305695.1  protein Atg16l2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK090597, AL832974, AP002381, BC137489
      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225513
      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 ...
      pfam14971
      Location:1898
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235272
      7WD40; WD40 repeat [structural motif]
    2. NM_033388.2NP_203746.1  protein Atg16l2 isoform 1

      See identical proteins and their annotated locations for NP_203746.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK024423, AK090597, AL832974, BC036713, BC069189, BQ929430
      Consensus CDS
      CCDS31634.1
      UniProtKB/Swiss-Prot
      Q8NAA4, Q8NBG0
      UniProtKB/TrEMBL
      Q9H7Q5
      Related
      ENSP00000326340.5, ENST00000321297.10
      Conserved Domains (5) summary
      COG2319
      Location:324619
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:331619
      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 ...
      pfam02050
      Location:86190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:341378
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      72814411..72843740
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005274376.6XP_005274433.1  protein Atg16l2 isoform X1

      Conserved Domains (5) summary
      COG2319
      Location:324586
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:331588
      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 ...
      pfam02050
      Location:86190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:341378
      7WD40; WD40 repeat [structural motif]
    2. XM_047427840.1XP_047283796.1  protein Atg16l2 isoform X4

    3. XM_006718732.3XP_006718795.1  protein Atg16l2 isoform X2

      Conserved Domains (5) summary
      COG2319
      Location:303598
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:310598
      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 ...
      pfam02050
      Location:86190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:320357
      7WD40; WD40 repeat [structural motif]
    4. XM_011545332.2XP_011543634.1  protein Atg16l2 isoform X3

      Conserved Domains (5) summary
      COG2319
      Location:286581
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:293581
      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 ...
      pfam02050
      Location:86190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:303340
      7WD40; WD40 repeat [structural motif]
    5. XM_047427841.1XP_047283797.1  protein Atg16l2 isoform X6

    6. XM_006718733.4XP_006718796.1  protein Atg16l2 isoform X7

      Conserved Domains (1) summary
      pfam08614
      Location:17203
      ATG16; Autophagy protein 16 (ATG16)
    7. XM_011545334.2XP_011543636.1  protein Atg16l2 isoform X5

      See identical proteins and their annotated locations for XP_011543636.1

      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225513
      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 ...
      pfam14971
      Location:1898
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235272
      7WD40; WD40 repeat [structural motif]
    8. XM_011545333.2XP_011543635.1  protein Atg16l2 isoform X5

      See identical proteins and their annotated locations for XP_011543635.1

      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225513
      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 ...
      pfam14971
      Location:1898
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235272
      7WD40; WD40 repeat [structural motif]
    9. XM_047427842.1XP_047283798.1  protein Atg16l2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      72742639..72757867
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)