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    Vps13d vacuolar protein sorting 13 homolog D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313825, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Vps13dprovided by RGD
    Official Full Name
    vacuolar protein sorting 13 homolog Dprovided by RGD
    Primary source
    RGD:1308403
    See related
    EnsemblRapid:ENSRNOG00000016443 AllianceGenome:RGD:1308403
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in mitochondrion organization; positive regulation of mitophagy; and protein localization to organelle. Predicted to be located in mitochondrion. 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
    Biased expression in Heart (RPKM 223.1), Adrenal (RPKM 201.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps13d in Genome Data Viewer
    Location:
    5q36
    Exon count:
    71
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (162113732..162339121, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (156830509..157055895, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (162891451..163119239, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene 60S ribosomal protein L9 pseudogene Neighboring gene uncharacterized LOC102550246 Neighboring gene dehydrogenase/reductase 3 Neighboring gene ribosomal protein L36, pseudogene Neighboring gene TNF receptor superfamily member 1B Neighboring gene TNF receptor superfamily member 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. Seong E, et al. Ann Neurol, 2018 Jun. PMID 29604224, Free PMC Article
    2. Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the Regulation of Mitochondrial Size and Clearance. Anding AL, et al. Curr Biol, 2018 Jan 22. PMID 29307555, Free PMC Article
    3. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Morgenstern M, et al. Cell Metab, 2021 Dec 7. PMID 34800366, Free PMC Article
    4. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in 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 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
    		  
    Component Evidence Code Pubs
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 

    General protein information

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

    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_001395589.2 → NP_001382518.1  intermembrane lipid transfer protein VPS13D

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I6GHP9, A6IU14, D3ZKC6
      Related
      ENSRNOP00000089845.1, ENSRNOT00000096625.2
      Conserved Domains (4) summary
      COG5043
      Location:1 → 1271
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd14306
      Location:2643 → 2678
      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 → 349
      VPS13; Vacuolar sorting-associated protein 13, N-terminal

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      162113732..162339121 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006239351.5 → XP_006239413.1  intermembrane lipid transfer protein VPS13D isoform X2

      UniProtKB/TrEMBL
      A6IU14, D3ZKC6
      Conserved Domains (6) summary
      cd14306
      Location:2642 → 2677
      UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
      pfam06650
      Location:3276 → 3559
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:3 → 111
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:140 → 357
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:3985 → 4130
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:615 → 894
      VPS13_mid_rpt; Repeating coiled region of VPS13

    2. XM_006239353.5 → XP_006239415.1  intermembrane lipid transfer protein VPS13D isoform X4

      UniProtKB/TrEMBL
      A6IU14, D3ZKC6
      Conserved Domains (6) summary
      cd14306
      Location:2643 → 2678
      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
      pfam12624
      Location:3 → 111
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:140 → 357
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:3960 → 4105
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:615 → 895
      VPS13_mid_rpt; Repeating coiled region of VPS13

    3. XM_063287848.1 → XP_063143918.1  intermembrane lipid transfer protein VPS13D isoform X3

      UniProtKB/TrEMBL
      A0A0G2JYD4, A6IU14, D3ZKC6
      Related
      ENSRNOP00000070610.1, ENSRNOT00000085291.3

    4. XM_063287847.1 → XP_063143917.1  intermembrane lipid transfer protein VPS13D isoform X1

      UniProtKB/TrEMBL
      A6IU14, D3ZKC6

    5. XM_017593444.3 → XP_017448933.1  intermembrane lipid transfer protein VPS13D isoform X5

      UniProtKB/TrEMBL
      A6IU14, D3ZKC6

    6. XM_039110137.2 → XP_038966065.1  intermembrane lipid transfer protein VPS13D isoform X6

      Conserved Domains (3) summary
      COG5043
      Location:1 → 1271
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd14306
      Location:2643 → 2678
      UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
      pfam16908
      Location:140 → 349
      VPS13; Vacuolar sorting-associated protein 13, N-terminal

    7. XM_039110138.2 → XP_038966066.1  intermembrane lipid transfer protein VPS13D isoform X7

      Conserved Domains (3) summary
      COG5043
      Location:1 → 1271
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam16908
      Location:140 → 349
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      cl21463
      Location:2643 → 2665
      UBA_like_SF; UBA domain-like superfamily

    RNA

    1. XR_005504466.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108006.1: Suppressed sequence

      Description
      NM_001108006.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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