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Aliases for VTA1 Gene

Aliases for VTA1 Gene

  • Vesicle Trafficking 1 2 3
  • Vesicle (Multivesicular Body) Trafficking 1 2 3 5
  • Dopamine-Responsive Gene 1 Protein 3 4
  • LYST-Interacting Protein 5 3 4
  • SKD1-Binding Protein 1 3 4
  • C6orf55 3 4
  • DRG-1 3 4
  • SBP1 3 4
  • LIP5 3 4
  • 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
  • DRG1 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 Trafficking 1) is a Protein Coding gene. Diseases associated with VTA1 include amyotrophic lateral sclerosis type 15 and amyotrophic lateral sclerosis 9. Among its related pathways are Endocytosis and Budding and maturation of HIV virion. GO annotations related to this gene include protein C-terminus binding.

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

Enhancers for VTA1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VTA1 on UCSC Golden Path with GeneCards custom track

Promoters for VTA1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VTA1 on UCSC Golden Path with GeneCards custom track

Genomic Location for VTA1 Gene

Chromosome:
6
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

Genes around VTA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VTA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 Lys 277
  • Modification sites at PhosphoSitePlus

Other Protein References for VTA1 Gene

No data available for DME Specific Peptides for VTA1 Gene

Domains & Families for VTA1 Gene

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

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.
genes like me logo Genes that share phenotypes with VTA1: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
cytosol 5
extracellular 5
endosome 4
mitochondrion 3
nucleus 2
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for VTA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010008 endosome membrane IEA --
genes like me logo Genes that share ontologies with VTA1: view

Pathways & Interactions for VTA1 Gene

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

Pathways by source for VTA1 Gene

Gene Ontology (GO) - Biological Process for VTA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy NAS 20588296
GO:0016197 endosomal transport TAS --
GO:0046755 viral budding IMP 15644320
GO:0061024 membrane organization TAS --
GO:0071985 multivesicular body sorting pathway IMP 15644320
genes like me logo Genes that share ontologies with VTA1: view

No data available for SIGNOR curated interactions for VTA1 Gene

Drugs & Compounds for VTA1 Gene

No Compound Related Data Available

Transcripts for VTA1 Gene

Unigene Clusters for VTA1 Gene

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

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

Protein differential expression in normal tissues from HIPED for VTA1 Gene

This gene is overexpressed in Fetal Brain (8.1), Urine (7.5), and Bone marrow stromal cell (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with VTA1: view

Protein tissue co-expression partners for VTA1 Gene

- Elite partner

Primer Products

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
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
chimpanzee
(Pan troglodytes)
Mammalia VTA1 35
  • 99.67 (n)
  • 100 (a)
VTA1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vta1 35
  • 84.28 (n)
  • 89.43 (a)
oppossum
(Monodelphis domestica)
Mammalia VTA1 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VTA1 36
  • 63 (a)
OneToOne
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
tropical clawed frog
(Silurana tropicalis)
Amphibia vta1 35
  • 75.95 (n)
  • 81.1 (a)
Str.15585 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.22640 35
zebrafish
(Danio rerio)
Actinopterygii vta1 35
  • 67.46 (n)
  • 71.09 (a)
wufb08c11 35
vta1 36
  • 70 (a)
OneToOne
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
rs2232307 - 142,204,004(+) ACTAT(C/G)CAACC intron-variant, reference, missense
rs1064507 -- 142,219,633(-) AGCAG(A/G)CAAAT utr-variant-3-prime
rs1064508 -- 142,219,613(-) CATTT(G/T)TCTTT utr-variant-3-prime
rs1064509 -- 142,219,611(-) TTTGT(C/T)TTTGT utr-variant-3-prime
rs1064510 -- 142,219,607(-) TCTTT(G/T)TAGTA utr-variant-3-prime

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

Variation tolerance for VTA1 Gene

Residual Variation Intolerance Score: 57.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.86; 34.83% of all genes are more intolerant (likely to be disease-causing)

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

MalaCards: The human disease database

(3) MalaCards diseases for VTA1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis type 15
  • amyotrophic lateral sclerosis 15, with or without frontotemporal dementia
amyotrophic lateral sclerosis 9
  • amyotrophic lateral sclerosis type 9
amyotrophic lateral sclerosis type 6
  • amyotrophic lateral sclerosis 6, with or without frontotemporal dementia
- elite association - COSMIC cancer census association via MalaCards
Search VTA1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for VTA1

Genetic Association Database (GAD)
VTA1
Human Genome Epidemiology (HuGE) Navigator
VTA1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VTA1
genes like me logo Genes that share disorders with VTA1: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 67
  2. Characterization of human dopamine responsive protein DRG-1 that binds to p75NTR-associated cell death executor NADE. (PMID: 16777077) Yu Y. … Lu H. (Brain Res. 2006) 3 23
  3. Mammalian class E Vps proteins, SBP1 and mVps2/CHMP2A, interact with and regulate the function of an AAA-ATPase SKD1/Vps4B. (PMID: 15173323) Fujita H. … Himeno M. (J. Cell. Sci. 2004) 3 23
  4. Identification of dopamine responsive mRNAs in glial cells by suppression subtractive hybridization. (PMID: 11489251) Shi J. … Xie Y. (Brain Res. 2001) 2 3
  5. A novel mechanism of regulating the ATPase VPS4 by its cofactor LIP5 and the endosomal sorting complex required for transport (ESCRT)-III protein CHMP5. (PMID: 25637630) Vild C.J. … Xu Z. (J. Biol. Chem. 2015) 3

Products for VTA1 Gene

Sources for VTA1 Gene

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