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 isofor... See more...

Aliases for VPS28 Gene

Aliases for VPS28 Gene

  • VPS28 Subunit Of ESCRT-I 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 28 Homolog 3 4
  • ESCRT-I Complex Subunit VPS28 3 4
  • VPS28, ESCRT-I Subunit 2 3
  • Vacuolar Protein Sorting 28 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 28-Like Protein 3
  • Yeast Class E Protein Vps28p Homolog 3
  • Vacuolar Protein Sorting 28 (Yeast) 2
  • Vacuolar Protein Sorting 28 Homolog 3
  • H-Vps28 4
  • VPS28 5

External Ids for VPS28 Gene

Previous GeneCards Identifiers for VPS28 Gene

  • GC08M143252
  • GC08M145686
  • GC08M145253
  • GC08M145653
  • GC08M145620
  • GC08M145622
  • GC08M145649
  • GC08M140762

Summaries for VPS28 Gene

Entrez Gene Summary for VPS28 Gene

  • 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]

GeneCards Summary for VPS28 Gene

VPS28 (VPS28 Subunit Of ESCRT-I) is a Protein Coding gene. Diseases associated with VPS28 include Tick Paralysis and Frontotemporal Dementia, Chromosome 3-Linked. Among its related pathways are Budding and maturation of HIV virion and Endocytosis. Gene Ontology (GO) annotations related to this gene include ubiquitin binding.

UniProtKB/Swiss-Prot Summary for VPS28 Gene

  • Component of the ESCRT-I complex, a regulator of vesicular trafficking process.

Gene Wiki entry for VPS28 Gene

Additional gene information for VPS28 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS28 Gene

Genomics for VPS28 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VPS28 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS28 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS28

Top Transcription factor binding sites by QIAGEN in the VPS28 gene promoter:
  • ATF-2
  • c-Ets-1
  • GATA-2
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • NRSF form 1
  • NRSF form 2
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for VPS28 Gene

Genomic Locations for VPS28 Gene
chr8:144,423,601-144,428,563
(GRCh38/hg38)
Size:
4,963 bases
Orientation:
Minus strand
chr8:145,649,000-145,653,931
(GRCh37/hg19)
Size:
4,932 bases
Orientation:
Minus strand

Genomic View for VPS28 Gene

Genes around VPS28 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS28 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS28 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS28 Gene

Proteins for VPS28 Gene

  • Protein details for VPS28 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UK41-VPS28_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 28 homolog
    Protein Accession:
    Q9UK41
    Secondary Accessions:
    • Q86VK0

    Protein attributes for VPS28 Gene

    Size:
    221 amino acids
    Molecular mass:
    25425 Da
    Quaternary structure:
    • Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, a VPS37 protein (VPS37A to -D) and MVB12A or MVB12B in a 1:1:1:1 stoichiometry (PubMed:14505570, PubMed:18005716). Interacts with TSG101, VPS37B, VPS37C, MVB12A and MVB12B (PubMed:14505570, PubMed:15218037, PubMed:18005716). Component of an ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, VPS37A and UBAP1 in a 1:1:1:1 stoichiometry (PubMed:14505570, PubMed:21757351, PubMed:30929741). Interacts WITH VPS36; the interaction mediates the association with the ESCRT-II complex. Interacts with SNF8 and VPS25 (PubMed:18539118). Interacts with CEP55 (PubMed:17853893).

    Alternative splice isoforms for VPS28 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS28 Gene

Post-translational modifications for VPS28 Gene

  • Ubiquitination at Lys58
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS28 Gene

Domains & Families for VPS28 Gene

Gene Families for VPS28 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VPS28 Gene

InterPro:
Blocks:
  • Vacuolar protein sorting-associated, VPS28
ProtoNet:

Suggested Antigen Peptide Sequences for VPS28 Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar protein sorting 28 (Yeast), isoform CRA_d (D3DWM2_HUMAN)
  • Vacuolar sorting protein 28 (Q548N1_HUMAN)
  • Vacuolar protein sorting 28 homolog (S. cerevisiae) (Q86VK0_HUMAN)
  • ESCRT-I complex subunit VPS28 (VPS28_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UK41

UniProtKB/Swiss-Prot:

VPS28_HUMAN :
  • Belongs to the VPS28 family.
Family:
  • Belongs to the VPS28 family.
genes like me logo Genes that share domains with VPS28: view

Function for VPS28 Gene

Molecular function for VPS28 Gene

UniProtKB/Swiss-Prot Function:
Component of the ESCRT-I complex, a regulator of vesicular trafficking process.

Phenotypes From GWAS Catalog for VPS28 Gene

Gene Ontology (GO) - Molecular Function for VPS28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11134028
GO:0043130 ubiquitin binding IDA 11916981
GO:0044877 protein-containing complex binding IBA 21873635
genes like me logo Genes that share ontologies with VPS28: view
genes like me logo Genes that share phenotypes with VPS28: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS28

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS28 Gene

Localization for VPS28 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS28 Gene

Cell membrane. Late endosome membrane. Peripheral 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 VPS28 gene
Compartment Confidence
plasma membrane 5
endosome 5
cytosol 5
extracellular 4
cytoskeleton 3
nucleus 3
golgi apparatus 3
lysosome 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for VPS28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000813 ESCRT I complex IBA,TAS 20588296
GO:0005737 cytoplasm IDA 18077552
GO:0005768 endosome IEA,IDA 11134028
GO:0005769 early endosome IDA 11916981
GO:0005829 cytosol IDA 11134028
genes like me logo Genes that share ontologies with VPS28: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VPS28 Gene

Pathways & Interactions for VPS28 Gene

genes like me logo Genes that share pathways with VPS28: view

Pathways by source for VPS28 Gene

Gene Ontology (GO) - Biological Process for VPS28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016197 endosomal transport TAS --
GO:0016236 macroautophagy TAS 20588296
GO:0019058 viral life cycle TAS --
GO:0031397 negative regulation of protein ubiquitination IDA 18077552
genes like me logo Genes that share ontologies with VPS28: view

No data available for SIGNOR curated interactions for VPS28 Gene

Drugs & Compounds for VPS28 Gene

No Compound Related Data Available

Transcripts for VPS28 Gene

mRNA/cDNA for VPS28 Gene

2 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS28

Alternative Splicing Database (ASD) splice patterns (SP) for VPS28 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b · 8c ·
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - - - - -
SP5:
SP6: - -
SP7: - - - - -
SP8: - - - - - - - - - - -
SP9: - - - - - -
SP10: - - - - - - -
SP11: - - - -
SP12: - - -
SP13: - - - - - -
SP14: -
SP15: - - - -
SP16: - - - - -
SP17: - - - - - - - - -
SP18: - - - - -
SP19: - - - - -
SP20:
SP21:
SP22: -
SP23:
SP24:

ExUns: 8d ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20: -
SP21:
SP22:
SP23:
SP24:

Relevant External Links for VPS28 Gene

GeneLoc Exon Structure for
VPS28

Expression for VPS28 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS28 Gene

Protein differential expression in normal tissues from HIPED for VPS28 Gene

This gene is overexpressed in Bone (12.1) and Peripheral blood mononuclear cells (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS28 Gene



Protein tissue co-expression partners for VPS28 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS28

SOURCE GeneReport for Unigene cluster for VPS28 Gene:

Hs.418175

Evidence on tissue expression from TISSUES for VPS28 Gene

  • Lung(4.6)
  • Nervous system(4)
  • Skin(2.8)
  • Kidney(2.7)
  • Spleen(2.4)
  • Lymph node(2.4)
  • Liver(2.4)
  • Muscle(2.3)
  • Heart(2.3)
  • Blood(2.2)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with VPS28: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS28 Gene

Orthologs for VPS28 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS28 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia VPS28 30 31
  • 97.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VPS28 30 31
  • 92.76 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VPS28 30 31
  • 90.2 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Vps28 30
  • 88.84 (n)
Mouse
(Mus musculus)
Mammalia Vps28 30 17 31
  • 88.08 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia VPS28 31
  • 87 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia VPS28 31
  • 93 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vps28 30
  • 79.94 (n)
African clawed frog
(Xenopus laevis)
Amphibia vps28-prov 30
Zebrafish
(Danio rerio)
Actinopterygii vps28 30 31
  • 79.39 (n)
OneToOne
zgc66078 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005344 30
  • 68.45 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Vps28 30 31 32
  • 68.3 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea vps-28 30 31
  • 52.26 (n)
OneToOne
Y87G2A.10 32
  • 46 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS28 31 33
  • 24 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons VPS28-2 30
  • 50 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0781000 30
  • 54.8 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5272 31
  • 49 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3194 30
Species where no ortholog for VPS28 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • 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 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for VPS28 Gene

ENSEMBL:
Gene Tree for VPS28 (if available)
TreeFam:
Gene Tree for VPS28 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS28: view image

Paralogs for VPS28 Gene

(1) SIMAP similar genes for VPS28 Gene using alignment to 9 proteins:

  • VPS28_HUMAN
  • D3DWM2_HUMAN
  • E9PI55_HUMAN
  • E9PJY2_HUMAN
  • E9PLM9_HUMAN
  • E9PM90_HUMAN
  • E9PQR7_HUMAN
  • E9PR04_HUMAN
  • Q548N1_HUMAN
genes like me logo Genes that share paralogs with VPS28: view

No data available for Paralogs for VPS28 Gene

Variants for VPS28 Gene

Additional dbSNP identifiers (rs#s) for VPS28 Gene

Structural Variations from Database of Genomic Variants (DGV) for VPS28 Gene

Variant ID Type Subtype PubMed ID
dgv12434n54 CNV loss 21841781
dgv12437n54 CNV loss 21841781
dgv907n27 CNV loss 19166990
esv2759652 CNV gain+loss 17122850
nsv1117859 CNV deletion 24896259
nsv428208 CNV gain 18775914
nsv466020 CNV loss 19166990
nsv470249 CNV loss 18288195
nsv482124 CNV gain 20164927
nsv515809 CNV gain+loss 19592680
nsv612935 CNV loss 21841781
nsv612936 CNV loss 21841781
nsv612937 CNV loss 21841781
nsv831489 CNV loss 17160897

Variation tolerance for VPS28 Gene

Residual Variation Intolerance Score: 37.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.65; 13.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS28 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS28

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS28 Gene

Disorders for VPS28 Gene

MalaCards: The human disease database

(3) MalaCards diseases for VPS28 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
tick paralysis
frontotemporal dementia, chromosome 3-linked
  • ftd3
hereditary spastic paraplegia
  • spastic paraplegia 3, autosomal dominant
- elite association - COSMIC cancer census association via MalaCards
Search VPS28 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with VPS28: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS28 Gene

Publications for VPS28 Gene

  1. Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding. (PMID: 18005716) Morita E … Sundquist WI (Cell host & microbe 2007) 3 4 23
  2. The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding. (PMID: 15218037) Stuchell MD … Sundquist WI (The Journal of biological chemistry 2004) 3 4 23
  3. UBAP1 is a component of an endosome-specific ESCRT-I complex that is essential for MVB sorting. (PMID: 21757351) Stefani F … Woodman P (Current biology : CB 2011) 3 4
  4. Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex. (PMID: 18539118) Im YJ … Hurley JH (Developmental cell 2008) 3 4
  5. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. (PMID: 17853893) Morita E … Sundquist WI (The EMBO journal 2007) 3 4

Products for VPS28 Gene

  • Signalway Proteins for VPS28

Sources for VPS28 Gene