Human Gene ATG16L1 (ENST00000392017.9) Description and Page Index
  Description: Homo sapiens autophagy related 16 like 1 (ATG16L1), transcript variant 1, mRNA. (from RefSeq NM_030803)
RefSeq Summary (NM_030803): 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].
Gencode Transcript: ENST00000392017.9
Gencode Gene: ENSG00000085978.22
Transcript (Including UTRs)
   Position: hg38 chr2:233,251,673-233,295,669 Size: 43,997 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg38 chr2:233,251,828-233,294,350 Size: 42,523 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:233,251,673-233,295,669)mRNA (may differ from genome)Protein (607 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Autophagy-related protein 16-1; AltName: Full=APG16-like 1;
FUNCTION: Plays an essential role in autophagy (By similarity).
SUBUNIT: Homooligomer. Interacts with ATG5. Part of either the minor and major complexes respectively composed of 4 sets of ATG12-ATG5 and ATG16L1 (400 kDa) or 8 sets of ATG12-ATG5 and ATG16L1 (800 kDa) (By similarity). Interacts with RAB33B (By similarity).
INTERACTION: Q9GZQ8:MAP1LC3B; NbExp=2; IntAct=EBI-535909, EBI-373144; Q9BXW4:MAP1LC3C; NbExp=4; IntAct=EBI-535909, EBI-2603996;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Preautophagosomal structure membrane; Peripheral membrane protein (By similarity). Note=Localized to preautophagosomal structure (PAS) where it is involved in the membrane targeting of ATG5 (By similarity).
DISEASE: Genetic variations in ATG16L1 are associated with susceptibility to inflammatory bowel disease type 10 (IBD10) [MIM:611081]. IBD is characterized by a chronic relapsing intestinal inflammation. IBD is subdivided into Crohn disease (CD) and ulcerative colitis phenotypes. IBD10 individuals show the phenotype characteristic to CD. It may involve any part of the gastrointestinal tract, but most frequently the terminal ileum and colon. CD is commonly classified as autoimmune disease.
SIMILARITY: Belongs to the WD repeat ATG16 family.
SIMILARITY: Contains 7 WD repeats.
SEQUENCE CAUTION: Sequence=BAB15448.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=BAB55412.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: ATG16L1
Diseases sorted by gene-association score: inflammatory bowel disease 10* (879), inflammatory bowel disease (42), crohn's disease (23), ulcerative colitis (13), colitis (11), inflammatory bowel disease 5 (7), intestinal disease (5), gastrointestinal system disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.16 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 489.86 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.30155-0.473 Picture PostScript Text
3' UTR -436.001319-0.331 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013923 - Autophagy-rel_prot_16
IPR020472 - G-protein_beta_WD-40_rep
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF08614 - Autophagy protein 16 (ATG16)
PF00400 - WD domain, G-beta repeat

ModBase Predicted Comparative 3D Structure on Q676U5
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019787 ubiquitin-like protein transferase activity
GO:0042802 identical protein binding
GO:0051020 GTPase binding

Biological Process:
GO:0000045 autophagosome assembly
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0034497 protein localization to pre-autophagosomal structure
GO:0039689 negative stranded viral RNA replication
GO:0051260 protein homooligomerization
GO:0061739 protein lipidation involved in autophagosome assembly
GO:0098792 xenophagy

Cellular Component:
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0005930 axoneme
GO:0016020 membrane
GO:0034045 pre-autophagosomal structure membrane

-  Descriptions from all associated GenBank mRNAs
  AK000897 - Homo sapiens cDNA FLJ10035 fis, clone HEMBA1000919.
AK308400 - Homo sapiens cDNA, FLJ98348.
AK123876 - Homo sapiens cDNA FLJ41882 fis, clone OCBBF2022351, weakly similar to TIPD PROTEIN.
BC006253 - Homo sapiens hypothetical protein FLJ10035, mRNA (cDNA clone IMAGE:3949072), partial cds.
BC013411 - Homo sapiens hypothetical protein FLJ10035, mRNA (cDNA clone IMAGE:3030066), partial cds.
BC000061 - Homo sapiens cDNA clone IMAGE:3505827, containing frame-shift errors.
AY358182 - Homo sapiens clone DNA178573 SSGL9393 (UNQ9393) mRNA, complete cds.
AY398617 - Homo sapiens APG16L beta mRNA, complete cds.
AK024453 - Homo sapiens mRNA for FLJ00045 protein, partial cds.
EF560734 - Homo sapiens clone DKFZp686A1859 ATG16L1 protein (ATG16L1) mRNA, complete cds.
AK001690 - Homo sapiens cDNA FLJ10828 fis, clone NT2RP4001122, weakly similar to TIPD PROTEIN.
AB590490 - Synthetic construct DNA, clone: pFN21AE1263, Homo sapiens ATG16L1 gene for ATG16 autophagy related 16-like 1, without stop codon, in Flexi system.
EF079889 - Homo sapiens clone b2 ATG16 autophagy related 16-like protein 1 (ATG16L1) mRNA, complete cds.
EF079890 - Homo sapiens clone g3 ATG16 autophagy related 16-like protein 1 (ATG16L1) mRNA, complete cds.
JQ924062 - Homo sapiens autophagy-related protein 16-1 isoform 2 (ATG16L1) mRNA, complete cds.
JD421663 - Sequence 402687 from Patent EP1572962.
BC117337 - Homo sapiens ATG16 autophagy related 16-like 1 (S. cerevisiae), mRNA (cDNA clone IMAGE:40125888), partial cds.
BC143900 - Homo sapiens ATG16 autophagy related 16-like 1 (S. cerevisiae), mRNA (cDNA clone IMAGE:9052418), partial cds.
AK027854 - Homo sapiens cDNA FLJ14948 fis, clone PLACE2000164, weakly similar to TIPD PROTEIN.
JD318280 - Sequence 299304 from Patent EP1572962.
JD438612 - Sequence 419636 from Patent EP1572962.
HQ258577 - Synthetic construct Homo sapiens clone IMAGE:100073103 Unknown protein gene, encodes complete protein.
KJ894118 - Synthetic construct Homo sapiens clone ccsbBroadEn_03512 ATG16L1 gene, encodes complete protein.
BC071846 - Homo sapiens ATG16 autophagy related 16-like 1 (S. cerevisiae), mRNA (cDNA clone IMAGE:6651664), partial cds.
AK074434 - Homo sapiens cDNA FLJ23854 fis, clone LNG06315.
AK026330 - Homo sapiens cDNA: FLJ22677 fis, clone HSI10648.
AL834526 - Homo sapiens mRNA; cDNA DKFZp434A1211 (from clone DKFZp434A1211).
JD418237 - Sequence 399261 from Patent EP1572962.
JD422006 - Sequence 403030 from Patent EP1572962.
JD368394 - Sequence 349418 from Patent EP1572962.
JD278170 - Sequence 259194 from Patent EP1572962.
JD283779 - Sequence 264803 from Patent EP1572962.
JD139402 - Sequence 120426 from Patent EP1572962.
JD097877 - Sequence 78901 from Patent EP1572962.
JD223370 - Sequence 204394 from Patent EP1572962.
JD456159 - Sequence 437183 from Patent EP1572962.
JD133022 - Sequence 114046 from Patent EP1572962.
JD213462 - Sequence 194486 from Patent EP1572962.
JD065359 - Sequence 46383 from Patent EP1572962.
JD427162 - Sequence 408186 from Patent EP1572962.
JD545929 - Sequence 526953 from Patent EP1572962.
JD116319 - Sequence 97343 from Patent EP1572962.
JD155109 - Sequence 136133 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q676U5 (Reactome details) participates in the following event(s):

R-HSA-5682012 ATG5:ATG12 binds ATG16L1
R-HSA-5679255 WIPI2 binds ATG12:ATG5:ATG16L
R-HSA-5678490 ATG16L1 complex transfers LC3 from ATG3 to PE
R-HSA-1632852 Macroautophagy
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: A16L1_HUMAN, A3EXK9, A3EXL0, APG16L, B6ZDH0, NM_030803, Q676U5, Q6IPN1, Q6UXW4, Q6ZVZ5, Q8NCY2, Q96JV5, Q9H619, uc002vty.1, uc002vty.2, uc002vty.3, uc002vty.4, UNQ9393/PRO34307
UCSC ID: uc002vty.4
RefSeq Accession: NM_030803
Protein: Q676U5 (aka A16L1_HUMAN)
CCDS: CCDS2502.2, CCDS2503.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.