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vps-13D Ricin B-type lectin domain-containing protein [ Caenorhabditis elegans ]

Gene ID: 173962, updated on 9-Dec-2024

Summary

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Official Symbol
vps-13D
Official Full Name
Ricin B-type lectin domain-containing protein
Primary source
WormBase:WBGene00016120
Locus tag
CELE_C25H3.11
See related
AllianceGenome:WB:WBGene00016120
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Caenorhabditis elegans (strain: Bristol N2)
Lineage
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary
Predicted to enable metal ion binding activity and transferase activity. Predicted to be involved in mitochondrion organization; protein retention in Golgi apparatus; and protein targeting to vacuole. 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]
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Genomic context

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See vps-13D in Genome Data Viewer
Location:
chromosome: II
Exon count:
22
Sequence:
Chromosome: II; NC_003280.10 (5669771..5689040, complement)

Chromosome II - NC_003280.10Genomic Context describing neighboring genes Neighboring gene Sensor histidine kinase Neighboring gene GST_C_6 domain-containing protein Neighboring gene PET117 cytochrome c oxidase chaperone Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene EASAFGDIIGELKGKGLGGRMRF-amide Neighboring gene pseudo Neighboring gene NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genetic screen identifies non-mitochondrial proteins involved in the maintenance of mitochondrial homeostasis. Rolland S, et al. MicroPubl Biol, 2022. PMID 35622507, Free PMC Article
  2. Rapid and Efficient Identification of Caenorhabditis elegans Legacy Mutations Using Hawaiian SNP-Based Mapping and Whole-Genome Sequencing. Jaramillo-Lambert A, et al. G3 (Bethesda), 2015 Mar 4. PMID 25740937, Free PMC Article
  3. A map of the interactome network of the metazoan C. elegans. Li S, et al. Science, 2004 Jan 23. PMID 14704431, Free PMC Article
  4. OrthoList: a compendium of C. elegans genes with human orthologs. Shaye DD, et al. PLoS One, 2011. PMID 21647448, Free PMC Article
  5. OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. Kim W, et al. Genetics, 2018 Oct. PMID 30120140, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by WormBase

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
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 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
Ricin B-type lectin domain-containing protein
NP_001348703.1
  • Confirmed by transcript evidence
NP_001348705.1
  • Confirmed by transcript evidence
NP_001348706.1
  • Confirmed by transcript evidence
NP_001368683.1
  • Partially confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

  1. NC_003280.10 Reference assembly

    Range
    5669771..5689040 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001361857.4 → NP_001348706.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A2K5ATR9
    Conserved Domains (5) summary
    COG5043
    Location:1 → 2079
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd00161
    Location:2533 → 2637
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam06650
    Location:2204 → 2478
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:145 → 369
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2896 → 3026
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  2. NM_001361860.2 → NP_001348703.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A2K5ATR5
    Conserved Domains (5) summary
    COG5043
    Location:1 → 2091
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd00161
    Location:2545 → 2649
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam06650
    Location:2216 → 2490
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:145 → 369
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2908 → 3038
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  3. NM_001361858.3 → NP_001348705.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A2K5ATQ8
    Conserved Domains (5) summary
    COG5043
    Location:1 → 2081
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd00161
    Location:2535 → 2639
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam06650
    Location:2206 → 2480
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:145 → 369
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2898 → 3028
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  4. NM_001381432.1 → NP_001368683.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A2K5ATQ3
    Conserved Domains (5) summary
    COG5043
    Location:1 → 2089
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    cd00161
    Location:2543 → 2647
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam06650
    Location:2214 → 2488
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:145 → 369
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2919 → 3036
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
Nucleotide Protein
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