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VTA1 vesicle trafficking 1 [ Homo sapiens (human) ]

Gene ID: 51534, updated on 17-Jun-2019

Summary

Official Symbol
VTA1provided by HGNC
Official Full Name
vesicle trafficking 1provided by HGNC
Primary source
HGNC:HGNC:20954
See related
Ensembl:ENSG00000009844 MIM:610902
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DRG1; LIP5; SBP1; DRG-1; My012; C6orf55; HSPC228
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 16.7), colon (RPKM 13.5) and 25 other tissues See more
Orthologs

Genomic context

See VTA1 in Genome Data Viewer
Location:
6q24.1-q24.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (142147162..142224685)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (142468372..142542085)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986654 Neighboring gene neuromedin B receptor Neighboring gene Sharpr-MPRA regulatory region 1984 Neighboring gene gap junction protein epsilon 1 Neighboring gene uncharacterized LOC105378032 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene Sharpr-MPRA regulatory regions 3748 and 6738

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
Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
NHGRI GWA Catalog
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog

Pathways from BioSystems

  • Budding and maturation of HIV virion, organism-specific biosystem (from REACTOME)
    Budding and maturation of HIV virion, organism-specific biosystemWith the virus components precariously assembled on the inner leaflet of the plasma membrane, the host cell machinery is required for viral budding. The virus takes advantage of the host ESCRT pathwa...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystem (from REACTOME)
    Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystemMany plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to th...
  • HIV Infection, organism-specific biosystem (from REACTOME)
    HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
  • HIV Life Cycle, organism-specific biosystem (from REACTOME)
    HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Late Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
    Late Phase of HIV Life Cycle, organism-specific biosystemThe late phase of the HIV-1 life cycle includes the regulated expression of the HIV gene products and the assembly of viral particles. The assembly of viral particles will be covered in a later relea...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ27228

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ESCRT III complex disassembly NAS
Non-traceable Author Statement
more info
PubMed 
endosomal transport TAS
Traceable Author Statement
more info
 
macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
multivesicular body assembly NAS
Non-traceable Author Statement
more info
PubMed 
multivesicular body sorting pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
viral budding IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral life cycle TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
vacuolar protein sorting-associated protein VTA1 homolog
Names
LYST-interacting protein 5
SKD1-binding protein 1
Vps20-associated 1 homolog
dopamine-responsive gene 1 protein
homolog of mouse SKD1-binding protein 1
vesicle (multivesicular body) trafficking 1

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_001286371.1NP_001273300.1  vacuolar protein sorting-associated protein VTA1 homolog isoform b

    See identical proteins and their annotated locations for NP_001273300.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF271994, BM806661, DA299959
    Consensus CDS
    CCDS75531.1
    UniProtKB/Swiss-Prot
    Q9NP79
    UniProtKB/TrEMBL
    A0A087WY55
    Related
    ENSP00000481525.1, ENST00000620996.4
    Conserved Domains (1) summary
    pfam04652
    Location:22152
    Vta1; Vta1 like
  2. NM_001286372.1NP_001273301.1  vacuolar protein sorting-associated protein VTA1 homolog isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region that results in the use of an alternate translational start codon, and it lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AF271994, AK301376, DA299959
    Consensus CDS
    CCDS69214.1
    UniProtKB/Swiss-Prot
    Q9NP79
    Related
    ENSP00000395767.2, ENST00000452973.6
    Conserved Domains (2) summary
    pfam04652
    Location:894
    Vta1; Vta1 like
    cl26000
    Location:177215
    YciM; Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain [Cell wall/membrane/envelope biogenesis]
  3. NM_016485.5NP_057569.2  vacuolar protein sorting-associated protein VTA1 homolog isoform a

    See identical proteins and their annotated locations for NP_057569.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF271994, AL033522, BC022536
    Consensus CDS
    CCDS5197.1
    UniProtKB/Swiss-Prot
    Q9NP79
    Related
    ENSP00000356602.3, ENST00000367630.9
    Conserved Domains (1) summary
    pfam04652
    Location:22152
    Vta1; Vta1 like

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_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    142147162..142224685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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