Atg16l1 autophagy related 16-like 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Atg16l1provided by RGD
Official Full Name: autophagy related 16-like 1provided by RGD
Primary source: RGD:1310631
See related: EnsemblRapid:ENSRNOG00000017913 AllianceGenome:RGD:1310631
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Wdr30; Apg16l
Summary: Predicted to enable GTPase binding activity and identical protein binding activity. Predicted to be involved in autophagosome assembly; negative stranded viral RNA replication; and positive regulation of autophagy. Predicted to act upstream of or within protein lipidation involved in autophagosome assembly; protein localization to phagophore assembly site; and xenophagy. Predicted to be located in autophagosome; axoneme; and vacuole-isolation membrane contact site. Predicted to be active in autophagosome membrane. 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: Biased expression in Thymus (RPKM 129.1), Brain (RPKM 124.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q35

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (95869839..95905354)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (88420737..88457530)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (94879876..94915231)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Plasma-derived extracellular vesicles transfer microRNA-130a-3p to alleviate myocardial ischemia/reperfusion injury by targeting ATG16L1.
Title: Plasma-derived extracellular vesicles transfer microRNA-130a-3p to alleviate myocardial ischemia/reperfusion injury by targeting ATG16L1.
The Atg16l1 gene: characterization of wild type, knock-in, and knock-out phenotypes in rats.
Title: The Atg16l1 gene: characterization of wild type, knock-in, and knock-out phenotypes in rats.
Mutational analyses of novel rat models with targeted modifications in inflammatory bowel disease susceptibility genes.
Title: Mutational analyses of novel rat models with targeted modifications in inflammatory bowel disease susceptibility genes.
These findings define a novel modification of ATG16L1 and highlight the importance of an ATG16L1 phosphorylation-methylation switch in determining the fate of hypoxia/reoxygenation-treated cardiomyocytes.
Title: Crosstalk between lysine methylation and phosphorylation of ATG16L1 dictates the apoptosis of hypoxia/reoxygenation-induced cardiomyocytes.
Overexpression of miR-96 significantly prevents SE rats from brain damage by inhibiting the Atg7 and Atg16L1 expression and consequently, autophagosome formation in the hippocampus.
Title: miR-96 attenuates status epilepticus-induced brain injury by directly targeting Atg7 and Atg16L1.
In experimental oxazolone-induced colitis, there was an increase of total number of ATG16L1-positive lymphocytes in lymphoid structures of the colon, whereas the amount of AhR-positive-lymphocytes has not changed.
Title: Expression of aryl hydrocarbon receptor and ATG16L1 protein in experimental oxazolone-induced colitis in rats.
Atg16L1 regulates not only autophagy in all cell types, but also secretion from dense-core vesicles, presumably by acting as a Rab33A effector, in particular cell types.
Title: Atg16L1, an essential factor for canonical autophagy, participates in hormone secretion from PC12 cells independently of autophagic activity.
Functional characterization of the mouse Atg16l1 (Apg16L) ortholog.
Title: Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate.

Submit: New GeneRIF Correction

General gene information

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Markers

BE120484 (e-PCR)
- UniSTS:247344

RH137932 (e-PCR)
- UniSTS:220019

RH139068 (e-PCR)
- UniSTS:221154

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables GTPase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein-membrane adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-membrane adaptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in C-terminal protein lipidation	IEA Inferred from Electronic Annotation more info
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
involved_in autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in axonal transport	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within corpus callosum development	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hippocampus development	ISO Inferred from Sequence Orthology more info
involved_in macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in microautophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative stranded viral RNA replication	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein lipidation involved in autophagosome assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to phagophore assembly site	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within xenophagy	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Atg12-Atg5-Atg16 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Atg12-Atg5-Atg16 complex	ISO Inferred from Sequence Orthology more info
located_in autophagosome	ISO Inferred from Sequence Orthology more info
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in autophagosome membrane	ISO Inferred from Sequence Orthology more info
located_in autophagosome membrane	ISO Inferred from Sequence Orthology more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in axoneme	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in endolysosome membrane	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in phagophore assembly site membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site membrane	ISO Inferred from Sequence Orthology more info
located_in sperm midpiece	ISO Inferred from Sequence Orthology more info
is_active_in synapse	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 autophagy 16-like; WD repeat domain 30

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_001108809.3 → NP_001102279.2 autophagy-related protein 16-1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

D3ZFK6

Related

ENSRNOP00000024445.3, ENSRNOT00000024445.5

Conserved Domains (3) summary

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 ...

sd00039
Location:327 → 364

7WD40; WD40 repeat [structural motif]

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

95869839..95905354

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006245419.5 → XP_006245481.1 autophagy-related protein 16-1 isoform X1

UniProtKB/TrEMBL

A0A0G2K9U6

Related

ENSRNOP00000075135.1, ENSRNOT00000080482.3

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:90 → 190

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_039083917.2 → XP_038939845.1 autophagy-related protein 16-1 isoform X3

Conserved Domains (3) summary

cd00200
Location:249 → 537

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:259 → 296

7WD40; WD40 repeat [structural motif]

pfam08614
Location:31 → 146

ATG16; Autophagy protein 16 (ATG16)
XM_063267450.1 → XP_063123520.1 autophagy-related protein 16-1 isoform X4
XM_006245420.4 → XP_006245482.1 autophagy-related protein 16-1 isoform X2

See identical proteins and their annotated locations for XP_006245482.1

UniProtKB/TrEMBL

A0A8I6GLZ1

Related

ENSRNOP00000097226.1, ENSRNOT00000114063.2

Conserved Domains (6) 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:130 → 296

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

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)

pfam15898
Location:80 → 169

PRKG1_interact; cGMP-dependent protein kinase interacting domain

sd00039
Location:308 → 345

7WD40; WD40 repeat [structural motif]
XM_063267451.1 → XP_063123521.1 autophagy-related protein 16-1 isoform X5
XM_063267452.1 → XP_063123522.1 autophagy-related protein 16-1 isoform X6