Vps13c vacuolar protein sorting 13C [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps13cprovided by MGI
Official Full Name: vacuolar protein sorting 13Cprovided by MGI
Primary source: MGI:MGI:2444207
See related: Ensembl:ENSMUSG00000035284 AllianceGenome:MGI:2444207
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: chorein; C230055H22Rik
Summary: Acts upstream of or within response to insulin. Located in dense core granule membrane. Is expressed in several structures, including central nervous system; genitourinary system; gut; immune system; and skeleton. Human ortholog(s) of this gene implicated in Parkinson's disease 23. Orthologous to human VPS13C (vacuolar protein sorting 13 homolog C). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in cerebellum adult (RPKM 4.4), frontal lobe adult (RPKM 3.4) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9; 9 C

Exon count:: 87

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (67747594..67905026)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (67840316..67997744)

Chromosome 9 - NC_000075.7 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?

Loss of VPS13C elevates lipolysis and promotes oxidative gene expression in brown adipocytes.
Title: Vacuolar protein sorting 13C is a novel lipid droplet protein that inhibits lipolysis in brown adipocytes.
The present data thus provide evidence for a limited role for changes in VPS13C expression in conferring altered type 2 diabetes risk at this locus, particularly in females, and suggest that C2CD4A, but not C2CD4B, may also be involved.
Title: Changes in the expression of the type 2 diabetes-associated gene VPS13C in the β-cell are associated with glucose intolerance in humans and mice.
Our findings provide basic information on chorein in vivo and may contribute to taking the first step toward understanding molecular pathogenesis of ChAc.
Title: In vivo distribution and localization of chorein.
VPS13C cDNA sequences and brain-specific variants of VPS13C were identified.
Title: Brain-specific transcript variants of 5' and 3' ends of mouse VPS13A and VPS13C.

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Variation

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Alleles

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

Targeted (3) 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

AI552542 (e-PCR)
- UniSTS:165645

D9Dcr7 (e-PCR), detects polymorphism
- UniSTS:498961

Homology

Homologs of the Vps13c gene: The Vps13c gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 464 organisms have orthologs with human gene Vps13c
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within lipid transport	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in mitochondrion organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization	ISO Inferred from Sequence Orthology more info
involved_in protein retention in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within response to insulin	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dense core granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endosome	IEA Inferred from Electronic Annotation more info
is_active_in extrinsic component of membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in lipid droplet	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrial outer membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intermembrane lipid transfer protein VPS13C; vacuolar protein sorting-associated protein 13C

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_177184.4 → NP_796158.2 intermembrane lipid transfer protein VPS13C

See identical proteins and their annotated locations for NP_796158.2

Status: VALIDATED

Source sequence(s)

AB281675, AC156799

Consensus CDS

CCDS40676.1

UniProtKB/Swiss-Prot

Q8BQI7, Q8BX70

UniProtKB/TrEMBL

A1ILG8

Related

ENSMUSP00000077040.6, ENSMUST00000077879.7

Conserved Domains (8) summary

COG5043
Location:1237 → 2607

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2759 → 3013

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:3503 → 3577

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:185 → 414

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:3318 → 3495

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:612 → 832

VPS13_mid_rpt; Repeating coiled region of VPS13

cl02729
Location:3111 → 3161

WWE; WWE domain

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_000075.7 Reference GRCm39 C57BL/6J

Range

67747594..67905026

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006511224.3 → XP_006511287.1 vacuolar protein sorting-associated protein 13C isoform X1

Conserved Domains (6) summary

COG5043
Location:3 → 1342

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam02825
Location:3090 → 3139

WWE; WWE domain

pfam06650
Location:2737 → 2991

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16908
Location:163 → 392

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:3296 → 3473

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:1665 → 1857

VPS13_mid_rpt; Repeating coiled region of VPS13
XM_006511225.3 → XP_006511288.1 vacuolar protein sorting-associated protein 13C isoform X2

Conserved Domains (6) summary

COG5043
Location:3 → 1321

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam02825
Location:3069 → 3118

WWE; WWE domain

pfam06650
Location:2716 → 2970

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:3275 → 3452

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:1644 → 1836

VPS13_mid_rpt; Repeating coiled region of VPS13
XM_006511226.3 → XP_006511289.1 vacuolar protein sorting-associated protein 13C isoform X3

UniProtKB/Swiss-Prot

Q8BX70

Conserved Domains (6) summary

COG5043
Location:3 → 1364

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam02825
Location:3112 → 3161

WWE; WWE domain

pfam06650
Location:2759 → 3013

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16908
Location:185 → 414

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:3318 → 3495

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:1687 → 1879

VPS13_mid_rpt; Repeating coiled region of VPS13
XM_006511228.4 → XP_006511291.1 vacuolar protein sorting-associated protein 13C isoform X4

Conserved Domains (5) summary

COG5043
Location:1831 → 2309

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam02825
Location:1764 → 1813

WWE; WWE domain

pfam06650
Location:1411 → 1665

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam16909
Location:1970 → 2147

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:339 → 531

VPS13_mid_rpt; Repeating coiled region of VPS13