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

Gene ID: 308865, updated on 27-Nov-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, Nov 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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