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VPS28 VPS28, ESCRT-I subunit [ Homo sapiens (human) ]

Gene ID: 51160, updated on 9-Dec-2018

Summary

Official Symbol
VPS28provided by HGNC
Official Full Name
VPS28, ESCRT-I subunitprovided by HGNC
Primary source
HGNC:HGNC:18178
See related
Ensembl:ENSG00000160948 MIM:611952
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
Summary
This gene encodes a protein subunit of the ESCRT-I complex (endosomal complexes required for transport), which functions in the transport and sorting of proteins into subcellular vesicles. This complex can also be hijacked to facilitate the budding of enveloped viruses from the cell membrane. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in ovary (RPKM 46.0), duodenum (RPKM 44.3) and 25 other tissues See more
Orthologs

Genomic context

See VPS28 in Genome Data Viewer
Location:
8q24.3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (144423601..144428563, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145648984..145653946, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cleavage and polyadenylation specific factor 1 Neighboring gene microRNA 6849 Neighboring gene solute carrier family 39 member 4 Neighboring gene tonsoku like, DNA repair protein Neighboring gene TONSL antisense RNA 1 Neighboring gene microRNA 6893 Neighboring gene cysteine and histidine rich 1

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
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Tsg 101, VPS 28, and VPS 37B form the human endosomal sorting complex required for transport (ESCRT-I), which is required for HIV-1 Gag budding and virus infectivity PubMed
p6 gag ESCRT-I complexes contain three common subunits (TSG101, VPS28, and VPS37), and a fourth subunit MVB12. Recombinant ESCRT-I complexes bind HIV-1 p6 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Assembly Of The HIV Virion, organism-specific biosystem (from REACTOME)
    Assembly Of The HIV Virion, organism-specific biosystemVirion assembly packages all the components required for infectivity. These steps include two copies of the positive sense genomic viral RNA, cellular tRNALys, the viral envelope (Env) protein, the G...
  • 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 ...
  • ESCRT-I complex, organism-specific biosystem (from KEGG)
    ESCRT-I complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • ESCRT-I complex, conserved biosystem (from KEGG)
    ESCRT-I complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • 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...
  • Membrane binding and targetting of GAG proteins, organism-specific biosystem (from REACTOME)
    Membrane binding and targetting of GAG proteins, organism-specific biosystemOne of the mysteries of Gag protein involvement in HIV virion assembly is how the proteins are targeted to the proper membrane for budding. Infectious retroviruses do not bud from all of the availabl...
  • Synthesis And Processing Of GAG, GAGPOL Polyproteins, organism-specific biosystem (from REACTOME)
    Synthesis And Processing Of GAG, GAGPOL Polyproteins, organism-specific biosystemEvidence suggests that the RNA molecules used for the synthesis of Gag and Gag-Pro-Pol are not the same molecules that are packaged into virions. Gag proteins do not appear to aggregate around and ca...
  • 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

  • MGC60323

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
ESCRT I complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ESCRT I complex IDA
Inferred from Direct Assay
more info
PubMed 
ESCRT I complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 28 homolog
Names
ESCRT-I complex subunit VPS28
vacuolar protein sorting 28 homolog
vacuolar protein sorting 28-like protein
yeast class E protein Vps28p homolog

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.

Genomic

  1. NG_029456.2 RefSeqGene

    Range
    4982..9944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016208.4NP_057292.1  vacuolar protein sorting-associated protein 28 homolog isoform 1

    See identical proteins and their annotated locations for NP_057292.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
    Source sequence(s)
    AK026865, BC050438, BP380505, R72904
    Consensus CDS
    CCDS6425.1
    UniProtKB/Swiss-Prot
    Q9UK41
    UniProtKB/TrEMBL
    Q548N1
    Related
    ENSP00000292510.3, ENST00000292510.5
    Conserved Domains (1) summary
    pfam03997
    Location:39219
    VPS28; VPS28 protein
  2. NM_183057.2NP_898880.1  vacuolar protein sorting-associated protein 28 homolog isoform 2

    See identical proteins and their annotated locations for NP_898880.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate segment in ther 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC050713, BP380505, N31929, R72904
    Consensus CDS
    CCDS34967.1
    UniProtKB/Swiss-Prot
    Q9UK41
    Related
    ENSP00000366565.2, ENST00000377348.6
    Conserved Domains (1) summary
    pfam03997
    Location:39187
    VPS28; VPS28 protein

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.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    144423601..144428563 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005272324.4XP_005272381.1  vacuolar protein sorting-associated protein 28 homolog isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5H5
    Related
    ENSP00000431243.1, ENST00000533806.5
    Conserved Domains (1) summary
    pfam03997
    Location:39202
    VPS28; VPS28 protein
  2. XM_005272323.4XP_005272380.1  vacuolar protein sorting-associated protein 28 homolog isoform X1

    Conserved Domains (1) summary
    pfam03997
    Location:39170
    VPS28; VPS28 protein
  3. XM_005272325.4XP_005272382.1  vacuolar protein sorting-associated protein 28 homolog isoform X3

    See identical proteins and their annotated locations for XP_005272382.1

    Conserved Domains (1) summary
    pfam03997
    Location:1149
    VPS28; VPS28 protein
  4. XM_011517099.1XP_011515401.1  vacuolar protein sorting-associated protein 28 homolog isoform X3

    See identical proteins and their annotated locations for XP_011515401.1

    Conserved Domains (1) summary
    pfam03997
    Location:1149
    VPS28; VPS28 protein

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p12 PATCHES

    Range
    154203..159165 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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