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

Gene ID: 320528, updated on 12-May-2024

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
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Genomic context

Location:
9 C; 9 36.77 cM
Exon count:
87
Annotation release Status Assembly Chr Location
RS_2024_02 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_000075.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA M5C1000I18 gene Neighboring gene C2 calcium-dependent domain containing 4B Neighboring gene STARR-seq mESC enhancer starr_24500 Neighboring gene STARR-seq mESC enhancer starr_24501 Neighboring gene C2 calcium-dependent domain containing 4A Neighboring gene STARR-seq mESC enhancer starr_24502 Neighboring gene predicted gene, 20745 Neighboring gene predicted gene, 22382

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (4)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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
 
involved_in protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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

Preferred Names
intermembrane lipid transfer protein VPS13C
Names
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)

  1. NM_177184.4NP_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
    Q3V3W5, Q6ZPE1, Q8BLB1, Q8BQI7, Q8BX70
    UniProtKB/TrEMBL
    A1ILG8
    Related
    ENSMUSP00000077040.6, ENSMUST00000077879.7
    Conserved Domains (8) summary
    COG5043
    Location:12372607
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27593013
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:35033577
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185414
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:33183495
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:612832
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:31113161
    WWE; WWE domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    67747594..67905026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006511224.3XP_006511287.1  intermembrane lipid transfer protein VPS13C isoform X1

    Conserved Domains (6) summary
    COG5043
    Location:31342
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam02825
    Location:30903139
    WWE; WWE domain
    pfam06650
    Location:27372991
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:163392
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:32963473
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:16651857
    VPS13_mid_rpt; Repeating coiled region of VPS13
  2. XM_006511225.3XP_006511288.1  intermembrane lipid transfer protein VPS13C isoform X2

    Conserved Domains (6) summary
    COG5043
    Location:31321
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam02825
    Location:30693118
    WWE; WWE domain
    pfam06650
    Location:27162970
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:142371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:32753452
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:16441836
    VPS13_mid_rpt; Repeating coiled region of VPS13
  3. XM_006511226.3XP_006511289.1  intermembrane lipid transfer protein VPS13C isoform X3

    UniProtKB/Swiss-Prot
    Q8BX70
    Conserved Domains (6) summary
    COG5043
    Location:31364
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam02825
    Location:31123161
    WWE; WWE domain
    pfam06650
    Location:27593013
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:185414
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:33183495
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:16871879
    VPS13_mid_rpt; Repeating coiled region of VPS13
  4. XM_006511228.4XP_006511291.1  intermembrane lipid transfer protein VPS13C isoform X4

    Conserved Domains (5) summary
    COG5043
    Location:18312309
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam02825
    Location:17641813
    WWE; WWE domain
    pfam06650
    Location:14111665
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16909
    Location:19702147
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:339531
    VPS13_mid_rpt; Repeating coiled region of VPS13

RNA

  1. XR_379424.3 RNA Sequence

  2. XR_001778932.3 RNA Sequence