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

    Gene ID: 230895, updated on 9-Dec-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. 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, Dec 2024]
    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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    See Vps13d in Genome Data Viewer
    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 (24) 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)
    • Targeted (4) 
    • Transgenic (1) 

    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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