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

Gene ID: 89849, updated on 5-Jul-2020

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
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
Expression
Broad expression in spleen (RPKM 22.5), skin (RPKM 19.9) and 24 other tissues See more
Orthologs

Genomic context

See ATG16L2 in Genome Data Viewer
Location:
11q13.4
Exon count:
20
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (72814407..72845132)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (72525451..72553793)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene StAR related lipid transfer domain containing 10 Neighboring gene uncharacterized LOC105369380 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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
NHGRI GWA 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.
NHGRI GWA 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

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
autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative stranded viral RNA replication IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
autophagosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

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

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_001318766.2NP_001305695.1  autophagy-related protein 16-2 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  autophagy-related protein 16-2 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
    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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    72814407..72845132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274376.5XP_005274433.1  autophagy-related protein 16-2 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_006718732.2XP_006718795.1  autophagy-related protein 16-2 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]
  3. XM_011545332.1XP_011543634.1  autophagy-related protein 16-2 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]
  4. XM_006718733.3XP_006718796.1  autophagy-related protein 16-2 isoform X5

    Conserved Domains (1) summary
    pfam08614
    Location:17203
    ATG16; Autophagy protein 16 (ATG16)
  5. XM_011545333.1XP_011543635.1  autophagy-related protein 16-2 isoform X4

    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]
  6. XM_011545334.1XP_011543636.1  autophagy-related protein 16-2 isoform X4

    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]
  7. XM_006718734.2XP_006718797.1  autophagy-related protein 16-2 isoform X6

    Conserved Domains (3) summary
    COG2319
    Location:64334
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:64334
    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:4693
    7WD40; WD40 repeat [structural motif]

RNA

  1. XR_001748024.2 RNA Sequence

  2. XR_950094.1 RNA Sequence

    Related
    ENST00000435507.6
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