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Aliases for VTA1 Gene

Aliases for VTA1 Gene

  • Vesicle (Multivesicular Body) Trafficking 1 2 3
  • C6orf55 3 4 6
  • LIP5 3 4 6
  • SBP1 3 4 6
  • Dopamine-Responsive Gene 1 Protein 3 4
  • LYST-Interacting Protein 5 3 4
  • SKD1-Binding Protein 1 3 4
  • DRG-1 3 4
  • DRG1 3 6
  • Vacuolar Protein Sorting-Associated Protein VTA1 Homolog 3
  • Vps20-Associated 1 Homolog (S. Cerevisiae) 2
  • Homolog Of Mouse SKD1-Binding Protein 1 3
  • Chromosome 6 Open Reading Frame 55 2
  • Vps20-Associated 1 Homolog 3
  • HSPC228 3
  • My012 3

External Ids for VTA1 Gene

Previous HGNC Symbols for VTA1 Gene

  • C6orf55

Previous GeneCards Identifiers for VTA1 Gene

  • GC06P142511
  • GC06P140034
  • GC06P142468

Summaries for VTA1 Gene

Entrez Gene Summary for VTA1 Gene

  • C6ORF55 encodes a protein involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes (Ward et al., 2005 [PubMed 15644320]).[supplied by OMIM, Mar 2008]

GeneCards Summary for VTA1 Gene

VTA1 (Vesicle (Multivesicular Body) Trafficking 1) is a Protein Coding gene. Among its related pathways are Disease and Endocytosis.

UniProtKB/Swiss-Prot for VTA1 Gene

  • Involved in the endosomal multivesicular bodies (MVB) pathway. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding.

Gene Wiki entry for VTA1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VTA1 Gene

Genomics for VTA1 Gene

Regulatory Elements for VTA1 Gene

Genomic Location for VTA1 Gene

Start:
142,147,162 bp from pter
End:
142,224,689 bp from pter
Size:
77,528 bases
Orientation:
Plus strand

Genomic View for VTA1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VTA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VTA1 Gene

Proteins for VTA1 Gene

  • Protein details for VTA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NP79-VTA1_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein VTA1 homolog
    Protein Accession:
    Q9NP79
    Secondary Accessions:
    • B4DW55
    • E1P594
    • E7ETQ7
    • Q5TGM1
    • Q6IAE8
    • Q9H0R2
    • Q9H3K9
    • Q9P0Q0

    Protein attributes for VTA1 Gene

    Size:
    307 amino acids
    Molecular mass:
    33879 Da
    Quaternary structure:
    • Interacts with VPS4B. Interacts with CHMP1B. Interacts with CHMP2A; the interaction probably involves the open conformation of (polymerized) CHMP2A. Interacts with CHMP3. Interacts with CHMP5; the interaction involves soluble CHMP5. Interacts with IST1.
    SequenceCaution:
    • Sequence=AAF36148.1; Type=Frameshift; Positions=131, 140; Evidence={ECO:0000305}; Sequence=AAG43125.1; Type=Frameshift; Positions=269; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VTA1 Gene

    Alternative splice isoforms for VTA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VTA1 Gene

Proteomics data for VTA1 Gene at MOPED

Post-translational modifications for VTA1 Gene

  • Ubiquitination at Lys277
  • Modification sites at PhosphoSitePlus

Other Protein References for VTA1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for VTA1 Gene

Domains for VTA1 Gene

Protein Domains for VTA1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VTA1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NP79

UniProtKB/Swiss-Prot:

VTA1_HUMAN :
  • Q9NP79
Family:
  • Belongs to the VTA1 family.
genes like me logo Genes that share domains with VTA1: view

No data available for Gene Families for VTA1 Gene

Function for VTA1 Gene

Molecular function for VTA1 Gene

UniProtKB/Swiss-Prot Function: Involved in the endosomal multivesicular bodies (MVB) pathway. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding.

Gene Ontology (GO) - Molecular Function for VTA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15644320
GO:0008022 protein C-terminus binding IPI 18385515
genes like me logo Genes that share ontologies with VTA1: view

Animal Model Products

CRISPR Products

miRNA for VTA1 Gene

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for VTA1 Gene

Localization for VTA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VTA1 Gene

Cytoplasm. Endosome membrane; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VTA1 Gene COMPARTMENTS Subcellular localization image for VTA1 gene
Compartment Confidence
endosome 5
cytosol 4
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VTA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm --
GO:0005768 endosome --
GO:0005829 cytosol TAS --
GO:0010008 endosome membrane IEA --
GO:0016020 membrane --
genes like me logo Genes that share ontologies with VTA1: view

Pathways for VTA1 Gene

genes like me logo Genes that share pathways with VTA1: view

Pathways by source for VTA1 Gene

1 KEGG pathway for VTA1 Gene

Gene Ontology (GO) - Biological Process for VTA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016032 viral process TAS --
GO:0016197 endosomal transport TAS --
GO:0019058 viral life cycle TAS --
GO:0046755 viral budding IMP 15644320
genes like me logo Genes that share ontologies with VTA1: view

Transcripts for VTA1 Gene

Unigene Clusters for VTA1 Gene

Vps20-associated 1 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VTA1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VTA1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b
SP1:
SP2: -
SP3: -
SP4: -

Relevant External Links for VTA1 Gene

GeneLoc Exon Structure for
VTA1
ECgene alternative splicing isoforms for
VTA1

Expression for VTA1 Gene

mRNA expression in normal human tissues for VTA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VTA1 Gene

SOURCE GeneReport for Unigene cluster for VTA1 Gene Hs.431367

genes like me logo Genes that share expressions with VTA1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VTA1 Gene

Orthologs for VTA1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VTA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VTA1 35
  • 99.67 (n)
  • 100 (a)
VTA1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VTA1 35
  • 90.85 (n)
  • 95.75 (a)
VTA1 36
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VTA1 35
  • 92.63 (n)
  • 95.92 (a)
VTA1 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vta1 35
  • 87.76 (n)
  • 91.84 (a)
Vta1 16
Vta1 36
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VTA1 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VTA1 36
  • 63 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vta1 35
  • 84.28 (n)
  • 89.43 (a)
chicken
(Gallus gallus)
Aves VTA1 35
  • 77.97 (n)
  • 80.68 (a)
VTA1 36
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VTA1 36
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.22640 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.15585 35
vta1 35
  • 75.95 (n)
  • 81.1 (a)
zebrafish
(Danio rerio)
Actinopterygii vta1 35
  • 67.46 (n)
  • 71.09 (a)
vta1 36
  • 70 (a)
OneToOne
wufb08c11 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007542 35
  • 54.93 (n)
  • 52.46 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG7967 35
  • 52.07 (n)
  • 49.66 (a)
CG7967 36
  • 47 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T23G11.7 35
  • 52.87 (n)
  • 41.76 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 41 (a)
OneToOne
Species with no ortholog for VTA1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 VTA1 Gene

ENSEMBL:
Gene Tree for VTA1 (if available)
TreeFam:
Gene Tree for VTA1 (if available)

Paralogs for VTA1 Gene

Pseudogenes.org Pseudogenes for VTA1 Gene

genes like me logo Genes that share paralogs with VTA1: view

No data available for Paralogs for VTA1 Gene

Variants for VTA1 Gene

Sequence variations from dbSNP and Humsavar for VTA1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs1835 -- 142,220,632(+) ATATC(A/T)GGAAA utr-variant-3-prime
rs178783 -- 142,216,791(+) TAATG(C/G)TGTAA intron-variant
rs225622 -- 142,146,250(+) TGGGG(A/G)TGAGA upstream-variant-2KB
rs225623 -- 142,146,437(+) AAGTA(A/T)GGGAT upstream-variant-2KB
rs225624 -- 142,150,203(+) AACAT(C/T)GTAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VTA1 Gene

Variant ID Type Subtype PubMed ID
dgv7003n71 CNV Gain 21882294
dgv7004n71 CNV Loss 21882294
nsv830824 CNV Gain 17160897
nsv886735 CNV Loss 21882294
nsv5510 CNV Insertion 18451855
esv2574651 CNV Deletion 19546169
esv2065068 CNV Deletion 18987734

Relevant External Links for VTA1 Gene

HapMap Linkage Disequilibrium report
VTA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VTA1 Gene

Disorders for VTA1 Gene

Relevant External Links for VTA1

Genetic Association Database (GAD)
VTA1
Human Genome Epidemiology (HuGE) Navigator
VTA1
genes like me logo Genes that share disorders with VTA1: view

No data available for UniProtKB/Swiss-Prot for VTA1 Gene

Publications for VTA1 Gene

  1. The role of LIP5 and CHMP5 in multivesicular body formation and HIV-1 budding in mammalian cells. (PMID: 15644320) Ward D.M. … Kaplan J. (J. Biol. Chem. 2005) 2 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. Targeting of AMSH to endosomes is required for epidermal growth factor receptor degradation. (PMID: 17261583) Ma Y.M. … Kirchhausen T. (J. Biol. Chem. 2007) 3 4
  5. Novel interactions of ESCRT-III with LIP5 and VPS4 and their implications for ESCRT-III disassembly. (PMID: 18385515) Shim S. … Hanson P.I. (Mol. Biol. Cell 2008) 3 4

Products for VTA1 Gene

Sources for VTA1 Gene

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