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Aliases for VPS39 Gene

Aliases for VPS39 Gene

  • Vacuolar Protein Sorting 39 Homolog (S. Cerevisiae) 2 3
  • VAM6 3 4 6
  • TLP 3 4 6
  • TRAP1-Like Protein 3 4
  • KIAA0770 4 6
  • HVam6p 3 4
  • Vacuolar Protein Sorting 39 (Yeast) 2
  • Vam6/Vps39-Like Protein 3

External Ids for VPS39 Gene

Previous GeneCards Identifiers for VPS39 Gene

  • GC15M037818
  • GC15M035346
  • GC15M040030
  • GC15M040166
  • GC15M040238
  • GC15M042450
  • GC15M019299

Summaries for VPS39 Gene

Entrez Gene Summary for VPS39 Gene

  • This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

GeneCards Summary for VPS39 Gene

VPS39 (Vacuolar Protein Sorting 39 Homolog (S. Cerevisiae)) is a Protein Coding gene. An important paralog of this gene is TGFBRAP1.

UniProtKB/Swiss-Prot for VPS39 Gene

  • May play a role in clustering and fusion of late endosomes and lysosomes. Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.

Gene Wiki entry for VPS39 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS39 Gene

Genomics for VPS39 Gene

Regulatory Elements for VPS39 Gene

Genomic Location for VPS39 Gene

Start:
42,158,701 bp from pter
End:
42,208,316 bp from pter
Size:
49,616 bases
Orientation:
Minus strand

Genomic View for VPS39 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VPS39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS39 Gene

Proteins for VPS39 Gene

  • Protein details for VPS39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JC1-VPS39_HUMAN
    Recommended name:
    Vam6/Vps39-like protein
    Protein Accession:
    Q96JC1
    Secondary Accessions:
    • O94869
    • Q71SQ6
    • Q7Z3V3
    • Q96B93
    • Q96RM0

    Protein attributes for VPS39 Gene

    Size:
    886 amino acids
    Molecular mass:
    101809 Da
    Quaternary structure:
    • Homooligomer. Interacts with TGFBR2 and, less efficiently, with TGFBR1; interaction with TGFBR2 is independent of the receptor kinase activity and of the presence of TGF-beta. Also interacts with ACVR2B, but not with BMPR2. Interacts with SMAD4, preferentially following TGF-beta treatment. Does not interact with SAMD2 or SMAD3.
    SequenceCaution:
    • Sequence=BAA34490.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS39 Gene

Proteomics data for VPS39 Gene at MOPED

Post-translational modifications for VPS39 Gene

  • Ubiquitination at Lys843
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS39 Gene

No data available for DME Specific Peptides for VPS39 Gene

Domains for VPS39 Gene

Suggested Antigen Peptide Sequences for VPS39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96JC1

UniProtKB/Swiss-Prot:

VPS39_HUMAN :
  • Q96JC1
Domain:
  • Contains 1 CNH domain.
Family:
  • Belongs to the VAM6/VPS39 family.
Similarity:
  • Contains 1 CHCR (clathrin heavy-chain) repeat.
genes like me logo Genes that share domains with VPS39: view

No data available for Gene Families for VPS39 Gene

Function for VPS39 Gene

Molecular function for VPS39 Gene

UniProtKB/Swiss-Prot Function: May play a role in clustering and fusion of late endosomes and lysosomes. Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.

Gene Ontology (GO) - Molecular Function for VPS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with VPS39: view
genes like me logo Genes that share phenotypes with VPS39: view

miRNA for VPS39 Gene

miRTarBase miRNAs that target VPS39

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for VPS39 Gene

Localization for VPS39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS39 Gene

Cytoplasm. Lysosome membrane; Peripheral membrane protein. Late endosome membrane; Peripheral membrane protein. Note=Colocalizes with TGFBR1 and TGFBR2 in cytoplasmic vesicular structures and most prominently in cortical vesicles.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS39 Gene COMPARTMENTS Subcellular localization image for VPS39 gene
Compartment Confidence
endosome 5
lysosome 5
vacuole 5
cytosol 2
nucleus 2
golgi apparatus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IDA 17897319
GO:0005768 endosome --
GO:0030897 HOPS complex IDA 19109425
GO:0031902 late endosome membrane IEA --
genes like me logo Genes that share ontologies with VPS39: view

Pathways for VPS39 Gene

SuperPathways for VPS39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0016192 vesicle-mediated transport IBA --
GO:0050790 regulation of catalytic activity --
genes like me logo Genes that share ontologies with VPS39: view

No data available for Pathways by source for VPS39 Gene

Transcripts for VPS39 Gene

Unigene Clusters for VPS39 Gene

Vacuolar protein sorting 39 homolog (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VPS39 Gene

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

ExUns: 22a · 22b ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for VPS39 Gene

GeneLoc Exon Structure for
VPS39
ECgene alternative splicing isoforms for
VPS39

Expression for VPS39 Gene

mRNA expression in normal human tissues for VPS39 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS39 Gene

SOURCE GeneReport for Unigene cluster for VPS39 Gene Hs.88025

mRNA Expression by UniProt/SwissProt for VPS39 Gene

Q96JC1-VPS39_HUMAN
Tissue specificity: Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen.
genes like me logo Genes that share expressions with VPS39: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for VPS39 Gene

Orthologs for VPS39 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS39 35
  • 99.66 (n)
  • 99.77 (a)
VPS39 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS39 35
  • 92.3 (n)
  • 98.51 (a)
VPS39 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS39 35
  • 92.76 (n)
  • 98.4 (a)
VPS39 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps39 35
  • 91.05 (n)
  • 97.26 (a)
Vps39 16
Vps39 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS39 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS39 36
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps39 35
  • 89.98 (n)
  • 96.8 (a)
chicken
(Gallus gallus)
Aves VPS39 35
  • 82.06 (n)
  • 93.94 (a)
VPS39 36
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS39 36
  • 93 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii Dr.18700 35
vps39 35
  • 75.87 (n)
  • 83.62 (a)
vps39 36
  • 83 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002498 35
  • 53.21 (n)
  • 43.2 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG7146 35
  • 49.48 (n)
  • 38.98 (a)
CG7146 36
  • 34 (a)
OneToMany
CG7146 37
  • 35 (a)
worm
(Caenorhabditis elegans)
Secernentea vps-39 35
  • 43.92 (n)
  • 34 (a)
vps-39 36
  • 30 (a)
OneToMany
T08G5.5 37
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAM6 36
  • 18 (a)
OneToMany
VAM6 38
thale cress
(Arabidopsis thaliana)
eudicotyledons EMB2754 35
  • 44.67 (n)
  • 31.64 (a)
rice
(Oryza sativa)
Liliopsida Os03g0715500 35
  • 44.54 (n)
  • 33.5 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU01539 35
  • 46.09 (n)
  • 32.35 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vam6 35
  • 40.65 (n)
  • 28.73 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.986 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 47 (a)
OneToOne
Species with no ortholog for VPS39:
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for VPS39 Gene

ENSEMBL:
Gene Tree for VPS39 (if available)
TreeFam:
Gene Tree for VPS39 (if available)

Paralogs for VPS39 Gene

Paralogs for VPS39 Gene

genes like me logo Genes that share paralogs with VPS39: view

Variants for VPS39 Gene

Sequence variations from dbSNP and Humsavar for VPS39 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type MAF
rs7086 -- 42,158,910(+) TCAAA(C/G)ACAGT utr-variant-3-prime
rs13647 -- 42,182,249(-) CCAGC(A/C)taaaa intron-variant
rs582629 -- 42,204,688(+) AAAAT(A/T)AAATT intron-variant
rs583541 -- 42,204,873(+) ATATA(C/T)AGACA intron-variant
rs588695 -- 42,162,266(+) TTTCC(A/G)CATTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS39 Gene

Variant ID Type Subtype PubMed ID
nsv471683 CNV Gain+Loss 15918152
nsv832985 CNV Loss 17160897
nsv9245 CNV Gain 18304495
nsv1507 CNV Insertion 18451855

Relevant External Links for VPS39 Gene

HapMap Linkage Disequilibrium report
VPS39
Human Gene Mutation Database (HGMD)
VPS39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS39 Gene

Disorders for VPS39 Gene

(1) University of Copenhagen DISEASES for VPS39 Gene

Relevant External Links for VPS39

Genetic Association Database (GAD)
VPS39
Human Genome Epidemiology (HuGE) Navigator
VPS39
genes like me logo Genes that share disorders with VPS39: view

No data available for UniProtKB/Swiss-Prot for VPS39 Gene

Publications for VPS39 Gene

  1. Human Vam6p promotes lysosome clustering and fusion in vivo. (PMID: 11448994) Caplan S. … Bonifacino J.S. (J. Cell Biol. 2001) 2 3 4 23
  2. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T. … Ohara O. (DNA Res. 1998) 3 4
  3. TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling. (PMID: 12941698) Felici A. … Roberts A.B. (EMBO J. 2003) 3 4
  4. 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
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 48

Products for VPS39 Gene

Sources for VPS39 Gene

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