Atg13 autophagy related 13 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Atg13provided by MGI
Official Full Name: autophagy related 13provided by MGI
Primary source: MGI:MGI:1196429
See related: Ensembl:ENSMUSG00000027244 AllianceGenome:MGI:1196429
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: Harbi1; D2Ertd391e; 1110053A20Rik
Summary: Predicted to enable protein kinase binding activity and protein serine/threonine kinase activator activity. Involved in several processes, including macroautophagy; regulation of protein lipidation; and response to mitochondrial depolarisation. Located in cytosol and phagophore assembly site. Part of Atg1/ULK1 kinase complex. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and respiratory system. Orthologous to human ATG13 (autophagy related 13). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in cerebellum adult (RPKM 21.0), adrenal adult (RPKM 19.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 E1; 2 50.63 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (91504957..91540947, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (91674612..91710597, complement)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data 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?

Beclin1- and Atg13-dependent autophagy activation and morroniside have synergistic effect on osteoblastogenesis.
Title: Beclin1- and Atg13-dependent autophagy activation and morroniside have synergistic effect on osteoblastogenesis.
acting through histamine 1 receptor, histamine increased miR-206 and miR-216b, which worked in concert to target to Atg13, resulting in the reduction of autophagy activation under hypoxia and acute myocardial infarction condition.
Title: Histamine deficiency aggravates cardiac injury through miR-206/216b-Atg13 axis-mediated autophagic-dependant apoptosis.
these data establish the interaction between ATG13 and ATG101 as a promising target in disease-settings where the inhibition of autophagy is desired.
Title: Systematic analysis of ATG13 domain requirements for autophagy induction.
ATG7, but not ATG13 or ULK1 has a role in functional autophagy in glioblastoma development
Title: Suppression of autophagy impedes glioblastoma development and induces senescence.
ATG13 phosphorylation plays a crucial role in autophagy regulation.
Title: Nutrient-regulated Phosphorylation of ATG13 Inhibits Starvation-induced Autophagy.
autophagy can be executed by mechanisms that are dependent or independent of the ULK1/2-ATG13 interaction.
Title: Expression of a ULK1/2 binding-deficient ATG13 variant can partially restore autophagic activity in ATG13-deficient cells.
Atg13-deficient embryos show growth retardation and myocardial growth defects.
Title: Atg13 Is Essential for Autophagy and Cardiac Development in Mice.

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Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH125946 (e-PCR)
- UniSTS:162658

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

RH127124 (e-PCR)
- UniSTS:167316

D1S3697 (e-PCR)
- UniSTS:474275

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein kinase regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activator activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in autophagosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in autophagosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in piecemeal microautophagy of the nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in protein localization to phagophore assembly site	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein lipidation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein lipidation	ISO Inferred from Sequence Orthology more info
involved_in response to mitochondrial depolarisation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Atg1/ULK1 kinase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Atg1/ULK1 kinase complex	IDA Inferred from Direct Assay more info	PubMed
part_of Atg1/ULK1 kinase complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Atg1/ULK1 kinase complex	ISO Inferred from Sequence Orthology more info
is_active_in autophagosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
is_active_in phagophore assembly site	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site	IDA Inferred from Direct Assay more info	PubMed
located_in phagophore assembly site	ISO Inferred from Sequence Orthology more info
located_in phagophore assembly site membrane	IEA Inferred from Electronic Annotation more info
is_active_in phagophore assembly site membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: autophagy-related protein 13

Names: ATG13 autophagy related 13 homolog

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_001355416.1 → NP_001342345.1 autophagy-related protein 13 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL714023

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_001355417.1 → NP_001342346.1 autophagy-related protein 13 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL714023

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_001355418.1 → NP_001342347.1 autophagy-related protein 13 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' end compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL714023

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_001355419.1 → NP_001342348.1 autophagy-related protein 13 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL714023

Consensus CDS

CCDS89517.1

UniProtKB/Swiss-Prot

A2AH18, Q80TU9, Q91YI1

Related

ENSMUSP00000028678.9, ENSMUST00000028678.9

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_001355420.1 → NP_001342349.1 autophagy-related protein 13 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL714023

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_001355421.1 → NP_001342350.1 autophagy-related protein 13 isoform 6

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL714023

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13
NM_145528.3 → NP_663503.1 autophagy-related protein 13 isoform 7

See identical proteins and their annotated locations for NP_663503.1

Status: VALIDATED

Description

Transcript Variant: This variant (7) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AI574380, AK149672, AK171440, AL714023

Consensus CDS

CCDS16438.1

UniProtKB/Swiss-Prot

Q91YI1

Related

ENSMUSP00000076081.6, ENSMUST00000076803.12

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

91504957..91540947 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499892.3 → XP_006499955.1 autophagy-related protein 13 isoform X1

Conserved Domains (1) summary

pfam10033
Location:19 → 195

ATG13; Autophagy-related protein 13