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Aliases for VTI1A Gene

Aliases for VTI1A Gene

  • Vesicle Transport Through Interaction With T-SNAREs 1A 2 3 5
  • Vesicle Transport V-SNARE Protein Vti1-Like 2 3 4
  • Vti1-Rp2 3 4
  • Vesicle Transport Through Interaction With T-SNAREs Homolog 1A (Yeast) 2
  • Vesicle Transport Through Interaction With T-SNAREs Homolog 1A 3
  • SNARE Vti1a-Beta Protein 3
  • VTI1RP2 3
  • MMDS3 3
  • MVti1 3

External Ids for VTI1A Gene

Previous GeneCards Identifiers for VTI1A Gene

  • GC10P113440
  • GC10P114337
  • GC10P113871
  • GC10P114197
  • GC10P107834

Summaries for VTI1A Gene

Entrez Gene Summary for VTI1A Gene

  • The protein encoded by this gene is a member of the family of soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptors (SNAREs) that function in intracellular trafficking. This family member is involved in vesicular transport between endosomes and the trans-Golgi network. It is a vesicle-associated SNARE (v-SNARE) that interacts with target membrane SNAREs (t-SNAREs). Polymorphisms in this gene have been associated with binocular function, and also with susceptibility to colorectal and lung cancers. A recurrent rearrangement has been found between this gene and the transcription factor 7-like 2 (TCF7L2) gene in colorectal cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

GeneCards Summary for VTI1A Gene

VTI1A (Vesicle Transport Through Interaction With T-SNAREs 1A) is a Protein Coding gene. Diseases associated with VTI1A include Megalencephalic Leukoencephalopathy With Subcortical Cysts. Among its related pathways are Vesicle-mediated transport and Intra-Golgi traffic. GO annotations related to this gene include SNARE binding and SNAP receptor activity. An important paralog of this gene is VTI1B.

UniProtKB/Swiss-Prot for VTI1A Gene

  • V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence.

Gene Wiki entry for VTI1A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VTI1A Gene

Genomics for VTI1A Gene

Regulatory Elements for VTI1A Gene

Enhancers for VTI1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10F113090 1.7 FANTOM5 Ensembl ENCODE 21.6 +647.2 647175 6.4 PKNOX1 ATF1 MLX ARID4B FEZF1 GTF3C2 ZNF121 GATA2 FOS SP3 ZDHHC6 VTI1A TCF7L2 LOC105378488 NHLRC2 RPS15AP30 LOC105378489
GH10F113055 1.7 FANTOM5 Ensembl ENCODE 13.1 +612.9 612870 9.2 HDGF PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF143 ZNF207 TCF7L2 ZDHHC6 VTI1A NHLRC2 LOC105378488 HABP2 RPS15AP30 LOC105378489
GH10F112359 1.2 Ensembl ENCODE 12.4 -83.5 -83515 7.5 TBP MLX DMAP1 ZBTB40 RAD21 RARA YY1 GTF3C2 POLR3A CREM ACSL5 ZDHHC6 VTI1A GUCY2GP
GH10F112445 1.1 ENCODE 13 +0.0 45 2.5 PKNOX1 ARNT WRNIP1 ZFP64 ARID4B SIN3A ZNF2 YY1 ZNF143 ZNF207 ZDHHC6 ACSL5 VTI1A
GH10F113018 1.2 Ensembl ENCODE 11.1 +573.4 573403 4.4 MLX ZNF133 ARID4B FEZF1 ZNF2 YY1 FOS TSHZ1 PPARG ZNF264 ZDHHC6 VTI1A NHLRC2 TCF7L2 RPS15AP30 LOC105378489
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VTI1A on UCSC Golden Path with GeneCards custom track

Promoters for VTI1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001427222 202 2801 PKNOX1 ARNT WRNIP1 ZFP64 ARID4B SIN3A ZNF2 YY1 ZNF143 ZNF207

Genomic Location for VTI1A Gene

Chromosome:
10
Start:
112,446,998 bp from pter
End:
112,855,364 bp from pter
Size:
408,367 bases
Orientation:
Plus strand

Genomic View for VTI1A Gene

Genes around VTI1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VTI1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VTI1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VTI1A Gene

Proteins for VTI1A Gene

  • Protein details for VTI1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96AJ9-VTI1A_HUMAN
    Recommended name:
    Vesicle transport through interaction with t-SNAREs homolog 1A
    Protein Accession:
    Q96AJ9
    Secondary Accessions:
    • A2A307
    • B4E137
    • Q5W0D7

    Protein attributes for VTI1A Gene

    Size:
    217 amino acids
    Molecular mass:
    25218 Da
    Quaternary structure:
    • Interacts with distinct SNARE complexes that contain either STX5 or STX6. Interacts with NAPA and, to a lesser extent, with NAPG. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A.

    Alternative splice isoforms for VTI1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VTI1A Gene

Post-translational modifications for VTI1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VTI1A Gene

Domains & Families for VTI1A Gene

Gene Families for VTI1A Gene

Protein Domains for VTI1A Gene

Suggested Antigen Peptide Sequences for VTI1A Gene

Graphical View of Domain Structure for InterPro Entry

Q96AJ9

UniProtKB/Swiss-Prot:

VTI1A_HUMAN :
  • Belongs to the VTI1 family.
Family:
  • Belongs to the VTI1 family.
genes like me logo Genes that share domains with VTI1A: view

Function for VTI1A Gene

Molecular function for VTI1A Gene

UniProtKB/Swiss-Prot Function:
V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence.

Gene Ontology (GO) - Molecular Function for VTI1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA --
GO:0005484 SNAP receptor activity IDA 15215310
GO:0005515 protein binding IPI 24095276
genes like me logo Genes that share ontologies with VTI1A: view
genes like me logo Genes that share phenotypes with VTI1A: view

Animal Models for VTI1A Gene

MGI Knock Outs for VTI1A:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VTI1A Gene

Localization for VTI1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for VTI1A Gene

Cytoplasmic vesicle. Golgi apparatus membrane; Single-pass type IV membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VTI1A gene
Compartment Confidence
golgi apparatus 5
endoplasmic reticulum 4
endosome 4
cytosol 3
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for VTI1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005768 endosome ISS --
GO:0005776 autophagosome IDA 24095276
GO:0005789 endoplasmic reticulum membrane IBA --
GO:0005794 Golgi apparatus IDA 19224922
genes like me logo Genes that share ontologies with VTI1A: view

Pathways & Interactions for VTI1A Gene

genes like me logo Genes that share pathways with VTI1A: view

Pathways by source for VTI1A Gene

1 KEGG pathway for VTI1A Gene
1 GeneGo (Thomson Reuters) pathway for VTI1A Gene

Gene Ontology (GO) - Biological Process for VTI1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA --
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport ISS,IBA --
GO:0006891 intra-Golgi vesicle-mediated transport IBA --
genes like me logo Genes that share ontologies with VTI1A: view

No data available for SIGNOR curated interactions for VTI1A Gene

Transcripts for VTI1A Gene

Unigene Clusters for VTI1A Gene

Vesicle transport through interaction with t-SNAREs 1A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VTI1A Gene

No ASD Table

Relevant External Links for VTI1A Gene

GeneLoc Exon Structure for
VTI1A
ECgene alternative splicing isoforms for
VTI1A

Expression for VTI1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VTI1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VTI1A Gene

This gene is overexpressed in Nasal epithelium (53.9) and Fetal Brain (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VTI1A Gene



Protein tissue co-expression partners for VTI1A Gene

NURSA nuclear receptor signaling pathways regulating expression of VTI1A Gene:

VTI1A

SOURCE GeneReport for Unigene cluster for VTI1A Gene:

Hs.194554
genes like me logo Genes that share expression patterns with VTI1A: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VTI1A Gene

Orthologs for VTI1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VTI1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VTI1A 34 35
  • 100 (n)
dog
(Canis familiaris)
Mammalia VTI1A 34 35
  • 94.47 (n)
cow
(Bos Taurus)
Mammalia VTI1A 34 35
  • 94.15 (n)
rat
(Rattus norvegicus)
Mammalia Vti1a 34
  • 90.63 (n)
oppossum
(Monodelphis domestica)
Mammalia VTI1A 35
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VTI1A 35
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vti1a 34 16 35
  • 89.71 (n)
chicken
(Gallus gallus)
Aves VTI1A 34 35
  • 84.11 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 87 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vti1a 34
  • 78.97 (n)
Str.11914 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.24211 34
zebrafish
(Danio rerio)
Actinopterygii vti1a 34 35
  • 75 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6797 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009322 34
  • 51.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vti1 34 35
  • 48.15 (n)
worm
(Caenorhabditis elegans)
Secernentea vti-1 34 35
  • 51.13 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL168W 34
  • 42.19 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VTI1 35
  • 29 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons SGR4 34
  • 47.76 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vti1 34
  • 44.99 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05959 34
  • 44.66 (n)
Species where no ortholog for VTI1A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)

Evolution for VTI1A Gene

ENSEMBL:
Gene Tree for VTI1A (if available)
TreeFam:
Gene Tree for VTI1A (if available)

Paralogs for VTI1A Gene

Paralogs for VTI1A Gene

(1) SIMAP similar genes for VTI1A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VTI1A: view

Variants for VTI1A Gene

Sequence variations from dbSNP and Humsavar for VTI1A Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs10047299 -- 112,941,651(+) TTAAA(G/T)ttttt intron-variant
rs10082351 -- 112,617,743(+) TAAAA(A/T)CAAAA intron-variant
rs10082356 -- 112,518,422(+) ATGAA(A/G)TAACT intron-variant
rs10082359 -- 112,518,611(+) TATAT(A/G)TGTGT intron-variant
rs10082480 -- 112,518,589(+) TCTCT(A/C)TATAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VTI1A Gene

Variant ID Type Subtype PubMed ID
dgv167e214 CNV loss 21293372
dgv285e212 CNV loss 25503493
esv2761631 CNV loss 21179565
esv3307007 CNV mobile element insertion 20981092
esv3328379 CNV insertion 20981092
esv3411839 CNV insertion 20981092
esv3624587 CNV loss 21293372
nsv1069965 CNV deletion 25765185
nsv1143518 CNV deletion 24896259
nsv474572 CNV novel sequence insertion 20440878
nsv510234 OTHER sequence alteration 20534489
nsv525880 CNV loss 19592680
nsv526766 CNV loss 19592680
nsv7211 OTHER inversion 18451855
nsv831990 CNV loss 17160897
nsv831991 CNV loss 17160897
nsv831992 CNV loss 17160897
nsv948188 CNV duplication 23825009

Variation tolerance for VTI1A Gene

Residual Variation Intolerance Score: 42.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VTI1A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VTI1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VTI1A Gene

Disorders for VTI1A Gene

MalaCards: The human disease database

(1) MalaCards diseases for VTI1A Gene - From: GeneCards

Disorder Aliases PubMed IDs
megalencephalic leukoencephalopathy with subcortical cysts
  • vacuolating megalencephalic leukoencephalopathy with subcortical cysts
- elite association - COSMIC cancer census association via MalaCards
Search VTI1A in MalaCards View complete list of genes associated with diseases

Relevant External Links for VTI1A

Genetic Association Database (GAD)
VTI1A
Human Genome Epidemiology (HuGE) Navigator
VTI1A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VTI1A
genes like me logo Genes that share disorders with VTI1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VTI1A Gene

Publications for VTI1A Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Gene variants associated with ischemic stroke: the cardiovascular health study. (PMID: 19023099) Luke M.M. … Psaty B.M. (Stroke 2009) 3 46 64
  3. A VAMP7/Vti1a SNARE complex distinguishes a non-conventional traffic route to the cell surface used by KChIP1 and Kv4 potassium channels. (PMID: 19138172) Flowerdew S.E. … Burgoyne R.D. (Biochem. J. 2009) 3 4 64
  4. Association of gene variants with incident myocardial infarction in the Cardiovascular Health Study. (PMID: 17975119) Shiffman D. … Psaty B.M. (Arterioscler. Thromb. Vasc. Biol. 2008) 3 46 64
  5. A syntaxin 10-SNARE complex distinguishes two distinct transport routes from endosomes to the trans-Golgi in human cells. (PMID: 18195106) Ganley I.G. … Pfeffer S.R. (J. Cell Biol. 2008) 3 4 64

Products for VTI1A Gene

Sources for VTI1A Gene

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