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    Atg16l2 autophagy related 16-like 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308865, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Atg16l2provided by RGD
    Official Full Name
    autophagy related 16-like 2provided by RGD
    Primary source
    RGD:1311400
    See related
    EnsemblRapid:ENSRNOG00000019413 AllianceGenome:RGD:1311400
    Gene type
    protein coding
    RefSeq status
    INFERRED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1311400
    Summary
    Predicted to be involved in autophagosome assembly. Predicted to act upstream of or within negative stranded viral RNA replication. Predicted to be located in cytosol; nucleoplasm; and phagophore assembly site membrane. Predicted to be part of Atg12-Atg5-Atg16 complex. Orthologous to human ATG16L2 (autophagy related 16 like 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 52.1), Thymus (RPKM 36.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atg16l2 in Genome Data Viewer
    Location:
    1q32
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (165100946..165123307, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (155687386..155703419, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (166401271..166415078, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene FCH and double SH3 domains 2 Neighboring gene uncharacterized LOC120097346 Neighboring gene ribosomal protein L7a, pseudogene 36 Neighboring gene StAR-related lipid transfer domain containing 10 Neighboring gene ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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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    Related articles in PubMed

    1. Mammalian autophagy: core molecular machinery and signaling regulation. Yang Z, et al. Curr Opin Cell Biol, 2010 Apr. PMID 20034776, Free PMC Article
    2. LC3 conjugation system in mammalian autophagy. Tanida I, et al. Int J Biochem Cell Biol, 2004 Dec. PMID 15325588, Free PMC Article
    3. UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs. Pirooz SD, et al. Proc Natl Acad Sci U S A, 2014 Feb 18. PMID 24550300, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    NOT involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative stranded viral RNA replication ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT located_in autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in phagophore assembly site membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein Atg16l2
    Names
    ATG16 autophagy related 16-like 2
    autophagy-related protein 16-2

    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)

    1. NM_001191560.1 → NP_001178489.1  protein Atg16l2

      Status: INFERRED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      D4A9M7
      Related
      ENSRNOP00000026286.5, ENSRNOT00000026286.7
      Conserved Domains (5) summary
      COG2319
      Location:327 → 622
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:335 → 612
      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:20 → 207
      ATG16; Autophagy protein 16 (ATG16)
      pfam16034
      Location:21 → 198
      JAKMIP_CC3; JAKMIP CC3 domain
      sd00039
      Location:345 → 382
      7WD40; WD40 repeat [structural motif]

    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

    1. NC_086019.1 Reference GRCr8

      Range
      165100946..165123307 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006229876.4 → XP_006229938.1  protein Atg16l2 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AAM8, D4A9M7
      Related
      ENSRNOP00000090932.1, ENSRNOT00000104610.2
      Conserved Domains (5) summary
      COG2319
      Location:321 → 616
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:329 → 606
      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:35 → 222
      ATG16; Autophagy protein 16 (ATG16)
      pfam16034
      Location:36 → 213
      JAKMIP_CC3; JAKMIP CC3 domain
      sd00039
      Location:339 → 376
      7WD40; WD40 repeat [structural motif]

    2. XM_039113327.2 → XP_038969255.1  protein Atg16l2 isoform X2

      UniProtKB/TrEMBL
      A6I6T2
      Conserved Domains (4) summary
      COG1196
      Location:4 → 202
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd00200
      Location:225 → 502
      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:235 → 272
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:1 → 97
      ATG16; Autophagy protein 16 (ATG16)

    3. XM_039113328.2 → XP_038969256.1  protein Atg16l2 isoform X2

      UniProtKB/TrEMBL
      A6I6T2
      Conserved Domains (4) summary
      COG1196
      Location:4 → 202
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd00200
      Location:225 → 502
      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:235 → 272
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:1 → 97
      ATG16; Autophagy protein 16 (ATG16)

    4. XM_017589189.3 → XP_017444678.1  protein Atg16l2 isoform X2

      UniProtKB/TrEMBL
      A6I6T2
      Conserved Domains (4) summary
      COG1196
      Location:4 → 202
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd00200
      Location:225 → 502
      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:235 → 272
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:1 → 97
      ATG16; Autophagy protein 16 (ATG16)

    5. XM_039113331.2 → XP_038969259.1  protein Atg16l2 isoform X2

      UniProtKB/TrEMBL
      A6I6T2
      Conserved Domains (4) summary
      COG1196
      Location:4 → 202
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd00200
      Location:225 → 502
      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:235 → 272
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:1 → 97
      ATG16; Autophagy protein 16 (ATG16)

    6. XM_006229877.5 → XP_006229939.1  protein Atg16l2 isoform X2

      UniProtKB/TrEMBL
      A6I6T2
      Conserved Domains (4) summary
      COG1196
      Location:4 → 202
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd00200
      Location:225 → 502
      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:235 → 272
      7WD40; WD40 repeat [structural motif]
      pfam08614
      Location:1 → 97
      ATG16; Autophagy protein 16 (ATG16)

    7. XM_063262819.1 → XP_063118889.1  protein Atg16l2 isoform X3

    RNA

    1. XR_010052892.1 RNA Sequence

    2. XR_010052894.1 RNA Sequence

    3. XR_005506130.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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