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VTI1A vesicle transport through interaction with t-SNAREs 1A [ Homo sapiens (human) ]

Gene ID: 143187, updated on 17-Jun-2019

Summary

Official Symbol
VTI1Aprovided by HGNC
Official Full Name
vesicle transport through interaction with t-SNAREs 1Aprovided by HGNC
Primary source
HGNC:HGNC:17792
See related
Ensembl:ENSG00000151532 MIM:614316
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MMDS3; MVti1; VTI1RP2; Vti1-rp2
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 1.6), bone marrow (RPKM 1.4) and 25 other tissues See more
Orthologs

Genomic context

See VTI1A in Genome Data Viewer
Location:
10q25.2
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (112446988..112855368)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (114206756..114578503)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene guanylate cyclase 2G, pseudogene Neighboring gene acyl-CoA synthetase long chain family member 5 Neighboring gene Sharpr-MPRA regulatory region 13267 Neighboring gene zinc finger DHHC-type containing 6 Neighboring gene microRNA 4295 Neighboring gene uncharacterized LOC105378487 Neighboring gene uncharacterized LOC112268058 Neighboring gene uncharacterized LOC103344931 Neighboring gene uncharacterized LOC107984158 Neighboring gene transcription factor 7 like 2 Neighboring gene ribosomal protein S15a pseudogene 30

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study of brain lesion distribution in multiple sclerosis.
NHGRI GWA Catalog
Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia.
NHGRI GWA Catalog
Trans-ethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with vesicle transport through interaction with t-SNAREs homolog 1A (VTI1A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TCF7L2

Homology

Clone Names

  • FLJ23106, FLJ23891, FLJ44519, MGC138209

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SNAP receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNAP receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ER to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ER to Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
Golgi ribbon formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
intra-Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle fusion with Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vesicle fusion with Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
voluntary musculoskeletal movement IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
ER to Golgi transport vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane TAS
Traceable Author Statement
more info
 
SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNARE complex ISS
Inferred from Sequence or Structural Similarity
more info
 
SNARE complex TAS
Traceable Author Statement
more info
PubMed 
autophagosome IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron projection terminus ISS
Inferred from Sequence or Structural Similarity
more info
 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vesicle transport through interaction with t-SNAREs homolog 1A
Names
SNARE Vti1a-beta protein
vesicle transport v-SNARE protein Vti1-like 2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001318203.1NP_001305132.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC022018, AI693064, AK095476, AL158212, BC017052, BQ447044, DA324398
    UniProtKB/Swiss-Prot
    Q96AJ9
    Conserved Domains (2) summary
    cd15891
    Location:129190
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  2. NM_001318205.1NP_001305134.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, and uses an alternate splice site that results in an early stop codon and a difference in the 3' UTR, compared to variant 1. The encoded isoform (c) is shorter at the C-terminus, compared to isoform a.
    Source sequence(s)
    AC022018, AK095476, AK303646, AL158212, BC017052, BI010424, BQ447044, DA324398
    UniProtKB/Swiss-Prot
    Q96AJ9
    Conserved Domains (2) summary
    cd15891
    Location:122183
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  3. NM_001365710.2NP_001352639.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform d

    Status: REVIEWED

    Source sequence(s)
    AL139120, BC017052, BG492365
    Conserved Domains (2) summary
    cd15891
    Location:122183
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  4. NM_001365711.1NP_001352640.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform e

    Status: REVIEWED

    Source sequence(s)
    AC022018, AL139120, AL158212
    Conserved Domains (2) summary
    cd15891
    Location:129190
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  5. NM_001365712.1NP_001352641.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform f

    Status: REVIEWED

    Source sequence(s)
    AC022018, AL139120, AL158212
    Conserved Domains (2) summary
    cd15891
    Location:129190
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  6. NM_001365713.1NP_001352642.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform f

    Status: REVIEWED

    Source sequence(s)
    AC022018, AL139120, AL158212
    Conserved Domains (2) summary
    cd15891
    Location:129190
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  7. NM_001365714.1NP_001352643.1  vesicle transport through interaction with t-SNAREs homolog 1A isoform g

    Status: REVIEWED

    Source sequence(s)
    AC022018, AL133323, AL139120
    Conserved Domains (2) summary
    cd15891
    Location:122183
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus
  8. NM_145206.3NP_660207.2  vesicle transport through interaction with t-SNAREs homolog 1A isoform b

    See identical proteins and their annotated locations for NP_660207.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AC022018, AK095476, AK303646, AL158212, BC017052, BQ447044, DA324398
    Consensus CDS
    CCDS7575.2
    UniProtKB/Swiss-Prot
    Q96AJ9
    Related
    ENSP00000376792.2, ENST00000393077.2
    Conserved Domains (2) summary
    cd15891
    Location:122183
    SNARE_Vti1a; SNARE motif of Vti1b-like
    pfam05008
    Location:1290
    V-SNARE; Vesicle transport v-SNARE protein N-terminus

RNA

  1. NR_134521.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) shares the 5' terminal exon but lacks the remaining exons found in variant 1, and instead contains alternate 3' exon structure. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022018, AK095476, BC064614, DA324398
  2. NR_134522.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) shares the 5' terminal exon but lacks the remaining exons found in variant 1, and instead contains alternate 3' exon structure. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022018, AK095476, BC064614, DA324398, DB105695
    Related
    ENST00000483122.1
  3. NR_134523.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) shares the 5' terminal exon but lacks the remaining exons found in variant 1, and instead contains an alternate 3' terminal exon. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC022018, AK095476, BC064614, DA324398, DA349859

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    112446988..112855368
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_015409.1: Suppressed sequence

    Description
    NR_015409.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
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