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

    Gene ID: 51897, updated on 31-Jan-2019

    Summary

    Official Symbol
    Atg13provided by MGI
    Official Full Name
    autophagy related 13provided by MGI
    Primary source
    MGI:MGI:1196429
    See related
    Ensembl:ENSMUSG00000027244
    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
    Expression
    Ubiquitous expression in cerebellum adult (RPKM 21.0), adrenal adult (RPKM 19.8) and 28 other tissues See more
    Orthologs

    Genomic context

    See Atg13 in Genome Data Viewer
    Location:
    2; 2 E1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (91674612..91710599, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (91514782..91550733, complement)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial pseudogene Neighboring gene zinc finger protein 408 Neighboring gene Rho GTPase activating protein 1 Neighboring gene harbinger transposase derived 1 Neighboring gene dyskeratosis congenita 1, dyskerin homolog pseudogene Neighboring gene autophagy/beclin 1 regulator 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Gene trapped (1) 
    • Targeted (2) 
    • Endonuclease-mediated (1)  1 citation

    Pathways from BioSystems

    • Autophagy - animal, organism-specific biosystem (from KEGG)
      Autophagy - animal, organism-specific biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
    • Autophagy - animal, conserved biosystem (from KEGG)
      Autophagy - animal, conserved biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
    • Autophagy - other, organism-specific biosystem (from KEGG)
      Autophagy - other, organism-specific biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
    • Autophagy - other, conserved biosystem (from KEGG)
      Autophagy - other, conserved biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Longevity regulating pathway, organism-specific biosystem (from KEGG)
      Longevity regulating pathway, organism-specific biosystemRegulation of longevity depends on genetic and environmental factors. Caloric restriction (CR), that is limiting food intake, is recognized in mammals as the best characterized and most reproducible ...
    • Macroautophagy, organism-specific biosystem (from REACTOME)
      Macroautophagy, organism-specific biosystemcomputationally inferred pathway (not manually curated)

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein kinase regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    activation of protein kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
     
    autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    autophagy of mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    macroautophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    mitophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein localization to phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    response to mitochondrial depolarisation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Atg1/ULK1 kinase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Atg1/ULK1 kinase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Atg1/ULK1 kinase complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Atg1/ULK1 kinase complex ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extrinsic component of membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    mitochondrion ISO
    Inferred from Sequence Orthology
    more info
     
    phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    phagophore assembly site IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    autophagy-related protein 13
    Names
    ATG13 autophagy related 13 homolog

    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_001355416.1NP_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:19195
      ATG13; Autophagy-related protein 13
    2. NM_001355417.1NP_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:19195
      ATG13; Autophagy-related protein 13
    3. NM_001355418.1NP_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:19195
      ATG13; Autophagy-related protein 13
    4. NM_001355419.1NP_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
      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    5. NM_001355420.1NP_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:19195
      ATG13; Autophagy-related protein 13
    6. NM_001355421.1NP_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:19195
      ATG13; Autophagy-related protein 13
    7. NM_145528.3NP_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
      ENSMUSP00000076081.5, ENSMUST00000076803.11
      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      91674612..91710599 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006499889.3XP_006499952.1  autophagy-related protein 13 isoform X3

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    2. XM_017319122.1XP_017174611.1  autophagy-related protein 13 isoform X6

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    3. XM_006499892.2XP_006499955.1  autophagy-related protein 13 isoform X7

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    4. XM_006499891.3XP_006499954.1  autophagy-related protein 13 isoform X5

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    5. XM_006499890.3XP_006499953.1  autophagy-related protein 13 isoform X4

      UniProtKB/Swiss-Prot
      Q91YI1
      Related
      ENSMUSP00000028678.8, ENSMUST00000028678.8
      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    6. XM_006499888.2XP_006499951.1  autophagy-related protein 13 isoform X2

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
    7. XM_006499887.2XP_006499950.1  autophagy-related protein 13 isoform X1

      Conserved Domains (1) summary
      pfam10033
      Location:19195
      ATG13; Autophagy-related protein 13
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