Atg16l1 autophagy related 16-like 1 (S. cerevisiae) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Atg16l1provided by MGI
Official Full Name: autophagy related 16-like 1 (S. cerevisiae)provided by MGI
Primary source: MGI:MGI:1924290
See related: Ensembl:ENSMUSG00000026289 AllianceGenome:MGI:1924290
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: WDR30; Apg16l; Atg16l; 1500009K01Rik
Summary: Enables identical protein binding activity. Involved in positive regulation of autophagy. Acts upstream of or within macroautophagy and negative stranded viral RNA replication. Located in autophagosome membrane and axoneme. Is expressed in central nervous system and retina. Used to study inflammatory bowel disease 10. Human ortholog(s) of this gene implicated in inflammatory bowel disease 10. Orthologous to human ATG16L1 (autophagy related 16 like 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E18 (RPKM 18.9), CNS E14 (RPKM 16.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1; 1 D

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (87683730..87720150)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (87756007..87792428)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Crohn Disease-associated ATG16L1(T300A) polymorphism regulates inflammatory responses by modulating TLR- and NLR-mediated signaling.
Title: The Crohn Disease-associated ATG16L1(T300A) polymorphism regulates inflammatory responses by modulating TLR- and NLR-mediated signaling.
ATG16L1 functions in cell homeostasis beyond autophagy.
Title: ATG16L1 functions in cell homeostasis beyond autophagy.
ATG16L1 regulated IL-22 induced IFN level in Pseudomonas aeruginosa Lung Infection via cGAS signal passage.
Title: ATG16L1 regulated IL-22 induced IFN level in Pseudomonas aeruginosa Lung Infection via cGAS signal passage.
SPATA33 is an autophagy mediator for cargo selectivity in germline mitophagy.
Title: SPATA33 is an autophagy mediator for cargo selectivity in germline mitophagy.
Atg16L1 as a Novel Biomarker and Autophagy Gene for Diabetic Retinopathy.
Title: Atg16L1 as a Novel Biomarker and Autophagy Gene for Diabetic Retinopathy.
Atg16l1 in dendritic cells is required for antibacterial defense and autophagy in murine colitis.
Title: Atg16l1 in dendritic cells is required for antibacterial defense and autophagy in murine colitis.
Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.
Title: Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.
STING induces LC3B lipidation onto single-membrane vesicles via the V-ATPase and ATG16L1-WD40 domain.
Title: STING induces LC3B lipidation onto single-membrane vesicles via the V-ATPase and ATG16L1-WD40 domain.
ATG16L1 autophagy pathway regulates BAX protein levels and programmed cell death.
Title: ATG16L1 autophagy pathway regulates BAX protein levels and programmed cell death.
Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.
Title: Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.

Submit: New GeneRIF Correction See all GeneRIFs (57)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (2) 1 citation
Targeted (16) 1 citation
Endonuclease-mediated (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH135985 (e-PCR)
- UniSTS:209981

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

AI035639 (e-PCR)
- UniSTS:159352

MARC_16423-16424:1018632150:1 (e-PCR)
- UniSTS:268029

Homology

Homologs of the Atg16l1 gene: The Atg16l1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, fruit fly, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 473 organisms have orthologs with human gene Atg16l1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables GTPase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in C-terminal protein lipidation	ISO Inferred from Sequence Orthology more info
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within autophagosome assembly	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within autophagy	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within corpus callosum development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hippocampus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosomal microautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosomal microautophagy	ISO Inferred from Sequence Orthology more info
involved_in macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within negative stranded viral RNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in protein lipidation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein lipidation involved in autophagosome assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein localization to phagophore assembly site	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within xenophagy	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of Atg12-Atg5-Atg16 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Atg12-Atg5-Atg16 complex	ISO Inferred from Sequence Orthology more info
located_in autophagosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in autophagosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in autophagosome membrane	ISO Inferred from Sequence Orthology more info
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in endolysosome membrane	ISO Inferred from Sequence Orthology more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in phagophore assembly site membrane	IDA Inferred from Direct Assay more info	PubMed
located_in sperm midpiece	IDA Inferred from Direct Assay more info	PubMed
located_in vacuole-isolation membrane contact site	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: autophagy-related protein 16-1

Names: APG16-like 1; Atg16L1 gamma; autophagy-related 16-like 1 gamma

NCBI Reference Sequences (RefSeq)

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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)

NM_001205391.1 → NP_001192320.1 autophagy-related protein 16-1 isoform 1

See identical proteins and their annotated locations for NP_001192320.1

Status: VALIDATED

Description

Transcript Variant: This variant (1, also known as Apg16Lgamma) represents the longest transcript and encodes the longest isoform (1, also known as Apg16Lgamma).

Source sequence(s)

AC102630, AC159967, BC049122, BE988512

Consensus CDS

CCDS56637.1

UniProtKB/Swiss-Prot

Q8C0J2

UniProtKB/TrEMBL

A0A8C6N694, G9M4M6

Related

ENSMUSP00000108815.3, ENSMUST00000113190.3

Conserved Domains (5) summary

COG2319
Location:332 → 589

WD40; WD40 repeat [General function prediction only]

cd00200
Location:333 → 621

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:31 → 206

ATG16; Autophagy protein 16 (ATG16)

sd00039
Location:343 → 380

7WD40; WD40 repeat [structural motif]

cl23720
Location:84 → 190

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001205392.1 → NP_001192321.1 autophagy-related protein 16-1 isoform 3

See identical proteins and their annotated locations for NP_001192321.1

Status: VALIDATED

Description

Transcript Variant: This variant (3, also known as Apg16Lalpha) lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3, also known as Apg16Lalpha) is shorter than isoform 1.

Source sequence(s)

AC102630, AC159967

Consensus CDS

CCDS56638.1

UniProtKB/TrEMBL

A0A8C6ILF1, Q3TDQ5

Related

ENSMUSP00000108811.2, ENSMUST00000113186.8

Conserved Domains (5) summary

COG2319
Location:297 → 554

WD40; WD40 repeat [General function prediction only]

cd00200
Location:298 → 586

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:126 → 296

XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)

sd00039
Location:308 → 345

7WD40; WD40 repeat [structural motif]
NM_029846.4 → NP_084122.2 autophagy-related protein 16-1 isoform 2

See identical proteins and their annotated locations for NP_084122.2

Status: VALIDATED

Description

Transcript Variant: This variant (2, also known as Apg16Lbeta) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2, also known as Apg16Lbeta) is shorter than isoform 1.

Source sequence(s)

AC159967, AK030983, BE988512

Consensus CDS

CCDS15136.1

UniProtKB/Swiss-Prot

Q8C0J2, Q9DB63

UniProtKB/TrEMBL

A0A8C6IL93

Related

ENSMUSP00000027512.7, ENSMUST00000027512.13

Conserved Domains (5) summary

COG2319
Location:316 → 573

WD40; WD40 repeat [General function prediction only]

cd00200
Location:317 → 605

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:31 → 206

ATG16; Autophagy protein 16 (ATG16)

sd00039
Location:327 → 364

7WD40; WD40 repeat [structural motif]

cl23720
Location:84 → 190

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

87683730..87720150

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036154331.1 → XP_036010224.1 autophagy-related protein 16-1 isoform X1

Conserved Domains (1) summary

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)