Clec16a C-type lectin domain family 16, member A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clec16aprovided by MGI
Official Full Name: C-type lectin domain family 16, member Aprovided by MGI
Primary source: MGI:MGI:1921624
See related: Ensembl:ENSMUSG00000068663 AllianceGenome:MGI:1921624
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: curt; mKIAA0350; 4932416N17Rik
Summary: Acts upstream of or within negative regulation of mitophagy; negative regulation of proteasomal ubiquitin-dependent protein catabolic process; and positive regulation of autophagosome maturation. Located in endolysosome membrane. Used to study neurodegenerative disease. 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: Ubiquitous expression in cerebellum adult (RPKM 3.2), cortex adult (RPKM 3.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16; 16 A1

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (10363173..10562742)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (10545309..10744878)

Chromosome 16 - NC_000082.7 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
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?

Inducible knockout of Clec16a in mice results in sensory neurodegeneration.
Title: Inducible knockout of Clec16a in mice results in sensory neurodegeneration.
Study found that lncRNA Malat1 expression is distinctly regulated in differentially activated macrophages in that it is upregulated in LPS-treated and downregulated in IL-4-treated cells. Malat1 regulates the expression of Clec16a, which is required for the proinflammatory activation of macrophages. Data demonstrate that Malat1 is involved in pulmonary pathogeneses in association with aberrant macrophage activation.
Title: Long noncoding RNA Malat1 regulates differential activation of macrophages and response to lung injury.
CLEC16A restrains secretory functions including cytokine release and cytotoxicity, and a delicate balance of CLEC16A is needed for NK cell function and homeostasis.
Title: The Autoimmune Disorder Susceptibility Gene CLEC16A Restrains NK Cell Function in YTS NK Cell Line and Clec16a Knockout Mice.
regulates splenocyte and NK cell function in part through MEK signaling
Title: CLEC16A regulates splenocyte and NK cell function in part through MEK signaling.
Study provides evidence that Clec16a plays a key role in the survival of Purkinje cells and in the degradative function or clearance of autolysosomes.
Title: Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival.
CLEC16A associations in common variable immunodeficiency disorder represent the first robust evidence of non-HLA associations in this immunodeficiency condition.
Title: Association of CLEC16A with human common variable immunodeficiency disorder and role in murine B cells.
The novel Pdx1-Clec16a-Nrdp1 pathway this study describes provides a genetic basis for the pathogenesis of mitochondrial dysfunction in multiple forms of diabetes.
Title: Diabetes Susceptibility Genes Pdx1 and Clec16a Function in a Pathway Regulating Mitophagy in β-Cells.
Islets from mice with pancreas-specific deletion of Clec16a have abnormal mitochondria with reduced oxygen consumption and ATP concentration, both of which are required for normal beta cell function, Clec16a controls beta cell function and prevents diabetes by controlling mitophagy.
Title: The diabetes susceptibility gene Clec16a regulates mitophagy.

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Variation

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Alleles

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

Spontaneous (1)
Targeted (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16Mit161 (e-PCR), detects polymorphism
- UniSTS:127793

R75266 (e-PCR)
- UniSTS:125541

32.MMHAP9FRC11.seq (e-PCR)
- UniSTS:124011

D16Bwg1278e (e-PCR), detects polymorphism
- UniSTS:142038

RH125198 (e-PCR)
- UniSTS:162020

Homology

Homologs of the Clec16a gene: The Clec16a gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 485 organisms have orthologs with human gene Clec16a
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within autophagy	IEA Inferred from Electronic Annotation more info
involved_in cellular response to starvation	ISO Inferred from Sequence Orthology more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of autophagosome maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of mitophagy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of TORC1 signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of proteasome-mediated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of autophagosome maturation	IBA Inferred from Biological aspect of Ancestor more info	PubMed

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
is_active_in endolysosome membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in endolysosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IEA Inferred from Electronic Annotation more info
colocalizes_with late endosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein CLEC16A

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_001204229.1 → NP_001191158.1 protein CLEC16A isoform 2

See identical proteins and their annotated locations for NP_001191158.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC122352, AC154430, CT010583

Consensus CDS

CCDS57018.1

UniProtKB/Swiss-Prot

Q80U30

Related

ENSMUSP00000123189.2, ENSMUST00000155633.8

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; uncharacterized conserved protein
NM_177562.5 → NP_808230.2 protein CLEC16A isoform 1

See identical proteins and their annotated locations for NP_808230.2

Status: VALIDATED

Description

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

Source sequence(s)

AC122352, AK122255, BU700909

Consensus CDS

CCDS37253.1

UniProtKB/Swiss-Prot

Q80U30, Q8CEQ8

Related

ENSMUSP00000065423.8, ENSMUST00000066345.15

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; uncharacterized conserved protein

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

10363173..10562742

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006522660.3 → XP_006522723.1 protein CLEC16A isoform X1

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_006522662.3 → XP_006522725.1 protein CLEC16A isoform X3

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_030249311.1 → XP_030105171.1 protein CLEC16A isoform X4

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_006522661.3 → XP_006522724.1 protein CLEC16A isoform X2

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_006522663.3 → XP_006522726.1 protein CLEC16A isoform X5

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_036160163.1 → XP_036016056.1 protein CLEC16A isoform X6

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_036160164.1 → XP_036016057.1 protein CLEC16A isoform X7

Related

ENSMUSP00000111493.2, ENSMUST00000115827.8

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_036160165.1 → XP_036016058.1 protein CLEC16A isoform X9

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_017317148.2 → XP_017172637.1 protein CLEC16A isoform X10

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_006522665.4 → XP_006522728.1 protein CLEC16A isoform X12

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_036160166.1 → XP_036016059.1 protein CLEC16A isoform X14

Related

ENSMUSP00000111494.3, ENSMUST00000115828.9

Conserved Domains (2) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein

pfam12485
Location:373 → 432

SLY; Lymphocyte signaling adaptor protein
XM_030249313.2 → XP_030105173.1 protein CLEC16A isoform X16

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_030249312.2 → XP_030105172.1 protein CLEC16A isoform X13

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_017317149.2 → XP_017172638.1 protein CLEC16A isoform X15

Conserved Domains (1) summary

pfam09758
Location:51 → 198

FPL; Uncharacterized conserved protein
XM_011246027.4 → XP_011244329.1 protein CLEC16A isoform X8

Conserved Domains (1) summary

pfam09758
Location:1 → 60

FPL; Uncharacterized conserved protein
XM_006522664.4 → XP_006522727.1 protein CLEC16A isoform X11