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    Clec16a C-type lectin domain containing 16A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287044, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Clec16aprovided by RGD
    Official Full Name
    C-type lectin domain containing 16Aprovided by RGD
    Primary source
    RGD:1305773
    See related
    Ensembl:ENSRNOG00000057378 AllianceGenome:RGD:1305773
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1305773
    Summary
    Predicted to be involved in cellular response to starvation; negative regulation of macroautophagy; and positive regulation of TORC1 signaling. Predicted to act upstream of or within negative regulation of mitophagy; negative regulation of proteasomal ubiquitin-dependent protein catabolic process; and positive regulation of autophagosome maturation. Predicted to be located in Golgi apparatus; cytosol; and endolysosome membrane. Human ortholog(s) of this gene implicated in Addison's disease; multiple sclerosis; rheumatoid arthritis; and type 1 diabetes mellitus. Orthologous to human CLEC16A (C-type lectin domain containing 16A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 103.9), Heart (RPKM 93.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Clec16a in Genome Data Viewer
    Location:
    10q11
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (5434725..5631246, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (4927799..5123749, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (5002196..5196914, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095020 Neighboring gene uncharacterized LOC134480746 Neighboring gene suppressor of cytokine signaling 1 Neighboring gene transition protein 2 Neighboring gene uncharacterized LOC120095021 Neighboring gene uncharacterized LOC134480747 Neighboring gene Dexi homolog Neighboring gene class II, major histocompatibility complex, transactivator

    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. Variation within the CLEC16A gene shows consistent disease association with both multiple sclerosis and type 1 diabetes in Sardinia. Zoledziewska M, et al. Genes Immun, 2009 Jan. PMID 18946483
    2. Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. Zuvich RL, et al. Hum Mol Genet, 2011 Sep 1. PMID 21653641, Free PMC Article
    3. Chromosomal region 16p13: further evidence of increased predisposition to immune diseases. Martínez A, et al. Ann Rheum Dis, 2010 Jan. PMID 19221398
    4. The diabetes susceptibility gene Clec16a regulates mitophagy. Soleimanpour SA, et al. Cell, 2014 Jun 19. PMID 24949970, Free PMC Article
    5. Human CLEC16A regulates autophagy through modulating mTOR activity. Tam RC, et al. Exp Cell Res, 2017 Mar 15. PMID 28223137

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cellular response to starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of mitophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of TORC1 signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of proteasome-mediated ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endolysosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein CLEC16A
    Names
    C-type lectin domain family 16, member A

    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_001398551.1 → NP_001385480.1  protein CLEC16A

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8I5ZW56
      Conserved Domains (1) summary
      pfam09758
      Location:51 → 198
      FPL; Uncharacterized conserved protein

    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_086028.1 Reference GRCr8

      Range
      5434725..5631246 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268510.1 → XP_063124580.1  protein CLEC16A isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZW56

    2. XM_063268511.1 → XP_063124581.1  protein CLEC16A isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZW56

    3. XM_008767506.4 → XP_008765728.1  protein CLEC16A isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZW56, A0A8I5ZW58
      Related
      ENSRNOP00000083500.1
      Conserved Domains (1) summary
      pfam09758
      Location:51 → 198
      FPL; uncharacterized conserved protein

    4. XM_039087046.2 → XP_038942974.1  protein CLEC16A isoform X13

      UniProtKB/TrEMBL
      A6K4J0

    5. XM_063268512.1 → XP_063124582.1  protein CLEC16A isoform X4

      UniProtKB/TrEMBL
      A0A8I6ASQ2

    6. XM_063268515.1 → XP_063124585.1  protein CLEC16A isoform X6

      UniProtKB/TrEMBL
      A0A8I6ASQ2, A0A8I6AX58

    7. XM_063268514.1 → XP_063124584.1  protein CLEC16A isoform X5

      UniProtKB/TrEMBL
      A0A8I6ASQ2

    8. XM_063268517.1 → XP_063124587.1  protein CLEC16A isoform X8

      UniProtKB/TrEMBL
      A0A8I6ASQ2

    9. XM_063268516.1 → XP_063124586.1  protein CLEC16A isoform X7

      UniProtKB/TrEMBL
      A0A8I6ASQ2

    10. XM_063268518.1 → XP_063124588.1  protein CLEC16A isoform X9

      UniProtKB/TrEMBL
      A0A8I6ASQ2

    11. XM_063268521.1 → XP_063124591.1  protein CLEC16A isoform X12

    12. XM_063268520.1 → XP_063124590.1  protein CLEC16A isoform X11

    13. XM_063268519.1 → XP_063124589.1  protein CLEC16A isoform X10

      UniProtKB/TrEMBL
      A0A8I6ASQ2
    Nucleotide Protein Strain
    Heading Accession and Version

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