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Aliases for VPS13D Gene

Aliases for VPS13D Gene

  • Vacuolar Protein Sorting 13 Homolog D (S. Cerevisiae) 2 3
  • Vacuolar Protein Sorting 13D (Yeast) 2
  • KIAA0453 4

External Ids for VPS13D Gene

Summaries for VPS13D Gene

Entrez Gene Summary for VPS13D Gene

  • This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS13D Gene

VPS13D (Vacuolar Protein Sorting 13 Homolog D (S. Cerevisiae)) is a Protein Coding gene. An important paralog of this gene is VPS13B.

Gene Wiki entry for VPS13D Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS13D Gene

Genomics for VPS13D Gene

Genomic Location for VPS13D Gene

Start:
12,230,056 bp from pter
End:
12,512,047 bp from pter
Size:
281,992 bases
Orientation:
Plus strand

Genomic View for VPS13D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VPS13D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS13D Gene

Regulatory Elements for VPS13D Gene

Proteins for VPS13D Gene

  • Protein details for VPS13D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5THJ4-VP13D_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 13D
    Protein Accession:
    Q5THJ4
    Secondary Accessions:
    • J3KP14
    • Q58F10
    • Q6MZK9
    • Q6ZV12
    • Q709C4
    • Q709C5
    • Q86UB4
    • Q9NSJ3
    • Q9UIM0

    Protein attributes for VPS13D Gene

    Size:
    4388 amino acids
    Molecular mass:
    491916 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC86054.1; Type=Frameshift; Positions=3074; Evidence={ECO:0000305}; Sequence=CAE46021.1; Type=Frameshift; Positions=3689; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS13D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS13D Gene

Proteomics data for VPS13D Gene at MOPED

Post-translational modifications for VPS13D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS13D Gene

No data available for DME Specific Peptides for VPS13D Gene

Domains for VPS13D Gene

UniProtKB/Swiss-Prot:

VP13D_HUMAN
Domain:
  • Contains 1 UBA domain.:
    • Q5THJ4
Family:
  • Belongs to the VPS13 family.:
    • Q5THJ4
genes like me logo Genes that share domains with VPS13D: view

No data available for Gene Families for VPS13D Gene

Function for VPS13D Gene

Gene Ontology (GO) - Molecular Function for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with VPS13D: view

Phenotypes for VPS13D Gene

MGI mutant phenotypes for VPS13D:
inferred from 1 alleles
GenomeRNAi human phenotypes for VPS13D:
genes like me logo Genes that share phenotypes with VPS13D: view

No data available for Molecular function , Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for VPS13D Gene

Localization for VPS13D Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS13D Gene COMPARTMENTS Subcellular localization image for VPS13D gene
Compartment Confidence
cytosol 2
plasma membrane 2
endoplasmic reticulum 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IBA --
GO:0019898 extrinsic component of membrane IBA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with VPS13D: view

Pathways for VPS13D Gene

SuperPathways for VPS13D Gene

No Data Available

Interacting Proteins for VPS13D Gene

Selected Interacting proteins: Q5THJ4-VP13D_HUMAN for VPS13D Gene via I2D

Gene Ontology (GO) - Biological Process for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA --
GO:0045053 protein retention in Golgi apparatus IBA --
genes like me logo Genes that share ontologies with VPS13D: view

No data available for Pathways by source for VPS13D Gene

Transcripts for VPS13D Gene

Unigene Clusters for VPS13D Gene

Vacuolar protein sorting 13 homolog D (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VPS13D Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 24a · 24b ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38a · 38b ^ 39 ^ 40 ^ 41a · 41b ^ 42 ^ 43 ^ 44 ^ 45 ^
SP1: - -
SP2: - - -
SP3: - -
SP4: - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 46 ^ 47 ^ 48 ^ 49 ^ 50 ^ 51 ^ 52 ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60 ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67 ^ 68 ^ 69 ^ 70 ^ 71a ·
SP1: - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: -
SP5:
SP6: - - -
SP7:
SP8:
SP9: - -
SP10: -
SP11:
SP12:

ExUns: 71b ^ 72a · 72b · 72c · 72d · 72e ^
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for VPS13D Gene

GeneLoc Exon Structure for
VPS13D
ECgene alternative splicing isoforms for
VPS13D

Expression for VPS13D Gene

mRNA expression in normal human tissues for VPS13D Gene

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for VPS13D Gene

SOURCE GeneReport for Unigene cluster for VPS13D Gene Hs.439381

mRNA Expression by UniProt/SwissProt for VPS13D Gene

Q5THJ4-VP13D_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expressions with VPS13D: view

Orthologs for VPS13D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VPS13D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS13D 36
  • 99.58 (n)
  • 99.66 (a)
VPS13D 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS13D 36
  • 89.77 (n)
  • 94.59 (a)
VPS13D 37
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS13D 36
  • 90.43 (n)
  • 94.57 (a)
VPS13D 37
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps13d 36
  • 87.07 (n)
  • 93.35 (a)
Vps13d 16
Vps13d 37
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS13D 37
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS13D 37
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps13d 36
  • 86.89 (n)
  • 93.14 (a)
chicken
(Gallus gallus)
Aves VPS13D 36
  • 75.67 (n)
  • 82.51 (a)
VPS13D 37
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 70 (a)
OneToMany
-- 37
  • 86 (a)
OneToMany
-- 37
  • 85 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13d 36
  • 70.2 (n)
  • 75.36 (a)
zebrafish
(Danio rerio)
Actinopterygii vps13d 36
  • 65.36 (n)
  • 68.22 (a)
vps13d 37
  • 66 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009780 36
  • 27.49 (n)
  • 8.76 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG32113 36
  • 45.44 (n)
  • 34.82 (a)
CG32113 37
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C25H3.11 37
  • 25 (a)
OneToOne
CELE_C25H3.8 36
  • 42.67 (n)
  • 31.83 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 37
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 32 (a)
OneToOne
Species with no ortholog for VPS13D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS13D Gene

ENSEMBL:
Gene Tree for VPS13D (if available)
TreeFam:
Gene Tree for VPS13D (if available)

Paralogs for VPS13D Gene

Paralogs for VPS13D Gene

genes like me logo Genes that share paralogs with VPS13D: view

Variants for VPS13D Gene

Sequence variations from dbSNP and Humsavar for VPS13D Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs13028 -- 12,510,000(+) GTTTT(C/T)TTTTT utr-variant-3-prime
rs170954 -- 12,267,724(-) CACTT(G/T)ACCTC intron-variant
rs170955 -- 12,249,867(+) aactc(A/G)gtgtc intron-variant
rs170956 -- 12,249,857(+) tccac(A/T)tatca intron-variant
rs170957 -- 12,228,812(-) aaaat(A/G)aaaat upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VPS13D Gene

Variant ID Type Subtype PubMed ID
nsv508891 CNV Insertion 20534489
nsv471622 CNV Gain+Loss 15918152
esv275384 CNV Loss 21479260
nsv517848 CNV Gain 19592680
nsv2743 CNV Loss 18451855
esv2743809 CNV Deletion 23290073
nsv2854 CNV Loss 18451855
esv2667673 CNV Deletion 23128226
nsv528439 CNV Loss 19592680
nsv817617 CNV Loss 17921354

Relevant External Links for VPS13D Gene

HapMap Linkage Disequilibrium report
VPS13D
Human Gene Mutation Database (HGMD)
VPS13D

Disorders for VPS13D Gene

(1) University of Copenhagen DISEASES for VPS13D Gene

Relevant External Links for VPS13D

Genetic Association Database (GAD)
VPS13D
Human Genome Epidemiology (HuGE) Navigator
VPS13D
genes like me logo Genes that share disorders with VPS13D: view

No data available for UniProtKB/Swiss-Prot for VPS13D Gene

Publications for VPS13D Gene

  1. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N. … Ohara O. (DNA Res. 1997) 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. Analysis of the human VPS13 gene family. (PMID: 15498460) Velayos-Baeza A. … Monaco A.P. (Genomics 2004) 3 4
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4

Products for VPS13D Gene

Sources for VPS13D Gene

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