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Vps13d vacuolar protein sorting 13D [ Mus musculus (house mouse) ]

Gene ID: 230895, updated on 5-Mar-2024

Summary

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Official Symbol
Vps13dprovided by MGI
Official Full Name
vacuolar protein sorting 13Dprovided by MGI
Primary source
MGI:MGI:2448530
See related
Ensembl:ENSMUSG00000020220 AllianceGenome:MGI:2448530
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
Summary
Predicted to be involved in mitochondrion organization; positive regulation of mitophagy; and protein localization to organelle. Predicted to be extrinsic component of membrane. Is expressed in adrenal gland; liver; male reproductive gland or organ; pancreas; and thymus. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 4. Orthologous to human VPS13D (vacuolar protein sorting 13 homolog D). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in genital fat pad adult (RPKM 5.8), thymus adult (RPKM 4.6) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
4 E1; 4 78.17 cM
Exon count:
76
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (144597619..144921598, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (144871045..145195037, complement)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_11990 Neighboring gene STARR-seq mESC enhancer starr_11991 Neighboring gene peroxiredoxin 2, pseudogene 2 Neighboring gene STARR-seq mESC enhancer starr_11992 Neighboring gene predicted gene, 46890 Neighboring gene STARR-seq mESC enhancer starr_11993 Neighboring gene STARR-positive B cell enhancer ABC_E8006 Neighboring gene STARR-positive B cell enhancer ABC_E10275 Neighboring gene dehydrogenase/reductase 3 Neighboring gene predicted gene, 42344 Neighboring gene STARR-positive B cell enhancer ABC_E11264 Neighboring gene STARR-positive B cell enhancer mm9_chr4:144575978-144576279 Neighboring gene predicted gene, 36317 Neighboring gene STARR-seq mESC enhancer starr_11999 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:144609228-144609381 Neighboring gene STARR-seq mESC enhancer starr_12001 Neighboring gene STARR-positive B cell enhancer mm9_chr4:144741051-144741352 Neighboring gene STARR-positive B cell enhancer mm9_chr4:144784820-144785121 Neighboring gene STARR-seq mESC enhancer starr_12004 Neighboring gene tumor necrosis factor receptor superfamily, member 1b Neighboring gene STARR-positive B cell enhancer ABC_E11265 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:144832691-144832800 Neighboring gene STARR-positive B cell enhancer ABC_E8008 Neighboring gene predicted gene, 36233

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2004 Jun 30. PMID 15368895
  2. Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette. Taniwaki T, et al. Dev Growth Differ, 2005 Apr. PMID 15840001
  3. Exchangeable gene trap using the Cre/mutated lox system. Araki K, et al. Cell Mol Biol (Noisy-le-grand), 1999 Jul. PMID 10512203
  4. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Sang L, et al. Cell, 2011 May 13. PMID 21565611, Free PMC Article
  5. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Transgenic (1) 
  • Targeted (4) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10619, KIAA0453

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
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 positive regulation of mitophagy 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
  

General protein information

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Preferred Names
intermembrane lipid transfer protein VPS13D
Names
vacuolar protein sorting 13 D

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_001276465.1 → NP_001263394.1  intermembrane lipid transfer protein VPS13D isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal coding exon, compared to isoform 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AI789476, AK172952, AL606909, AL627087
    UniProtKB/TrEMBL
    B1ART1
    Conserved Domains (4) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:3276 → 3560
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:140 → 349
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

  2. NM_001276502.1 → NP_001263431.1  intermembrane lipid transfer protein VPS13D isoform 1

    See identical proteins and their annotated locations for NP_001263431.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL606909, AL627087
    Consensus CDS
    CCDS71517.1
    UniProtKB/TrEMBL
    B1ART1, B1ART2
    Related
    ENSMUSP00000020441.7, ENSMUST00000020441.13
    Conserved Domains (4) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:3277 → 3560
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:140 → 357
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

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_000070.7 Reference GRCm39 C57BL/6J

    Range
    144597619..144921598 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006538804.3 → XP_006538867.1  intermembrane lipid transfer protein VPS13D isoform X1

    See identical proteins and their annotated locations for XP_006538867.1

    UniProtKB/TrEMBL
    B1ART1, B1ART2
    Related
    ENSMUSP00000043240.8, ENSMUST00000036579.14
    Conserved Domains (4) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:3277 → 3560
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:140 → 357
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

  2. XM_006538805.4 → XP_006538868.1  intermembrane lipid transfer protein VPS13D isoform X3

    UniProtKB/TrEMBL
    B1ART1
    Conserved Domains (4) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:3251 → 3534
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:140 → 357
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

  3. XM_011250235.3 → XP_011248537.1  intermembrane lipid transfer protein VPS13D isoform X2

    UniProtKB/TrEMBL
    B1ART1
    Conserved Domains (4) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:3252 → 3535
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:140 → 357
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

  4. XM_036164086.1 → XP_036019979.1  intermembrane lipid transfer protein VPS13D isoform X4

    UniProtKB/TrEMBL
    V9GX23
    Related
    ENSMUSP00000138946.2, ENSMUST00000185113.2
    Conserved Domains (4) summary
    COG5043
    Location:3099 → 3561
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:1903 → 1938
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam06650
    Location:2538 → 2821
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16910
    Location:60 → 156
    VPS13_mid_rpt; Repeating coiled region of VPS13

  5. XM_006538806.5 → XP_006538869.1  intermembrane lipid transfer protein VPS13D isoform X5

    Conserved Domains (3) summary
    COG5043
    Location:1 → 1270
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd14306
    Location:2642 → 2677
    UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
    pfam16908
    Location:140 → 357
    VPS13; Vacuolar sorting-associated protein 13, N-terminal

RNA

  1. XR_003954929.2 RNA Sequence

  2. XR_003954931.1 RNA Sequence

  3. XR_881424.3 RNA Sequence

  4. XR_003954930.1 RNA Sequence

  5. XR_881423.3 RNA Sequence

  6. XR_390739.5 RNA Sequence

  7. XR_881427.4 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033190.1: Suppressed sequence

    Description
    NM_001033190.1: This RefSeq was permanently suppressed because it is entirely UTR sequence.

  2. NM_001128198.1: Suppressed sequence

    Description
    NM_001128198.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

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