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Aliases for VPS28 Gene

Aliases for VPS28 Gene

  • VPS28, ESCRT-I Subunit 2 3 5
  • ESCRT-I Complex Subunit VPS28 3 4
  • Vacuolar Protein Sorting-Associated Protein 28 Homolog 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 Homolog 3
  • Vacuolar Protein Sorting 28 (Yeast) 2
  • H-Vps28 4

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, ESCRT-I Subunit) is a Protein Coding gene. Diseases associated with VPS28 include Noonan Syndrome 1. Among its related pathways are HIV Life Cycle and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include ubiquitin binding.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for VPS28 Gene

Genomics for VPS28 Gene

GeneHancer (GH) Regulatory Elements for VPS28 Gene

Promoters and enhancers for VPS28 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J144425 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 690.2 -0.4 -376 6.8 PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B VPS28 TONSL CPSF1 ZNF517 SLC39A4 ZNF7 ZNF623 ZNF250 ZNF251 ZNF34
GH08J144785 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 77.7 -361.2 -361168 9 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 NFYC SSRP1 ZNF610 RPL8 ZNF34 PIR52884 VPS28 ZNF7 ZNF250 CPSF1 ZNF251 COMMD5 LRRC14
GH08J144796 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 60.6 -370.4 -370420 5 ARID4B SIN3A DMAP1 ZBTB7B YY1 POLR2B ZNF207 ZNF143 ZNF263 SP3 ZNF517 ZNF7 VPS28 CPSF1 RPL8 ZNF250 LRRC14 ZNF251 GPAA1 ADCK5
GH08J144899 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 53.9 -473.0 -473028 3.6 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 ZNF250 ZNF7 CPSF1 VPS28 RPL8 SLC52A2 GPAA1 COMMD5 LRRC14 ZNF16
GH08J144471 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 49.5 -47.3 -47291 8 HDGF PKNOX1 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF207 ZNF143 FOXH1 VPS28 ZNF7 CPSF1 ZNF623 LRRC14 PPP1R16A ZNF707 ZNF250 COMMD5
- 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 UCSC Golden Path with GeneCards custom track

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

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. Interacts with TSG101, VPS37B, VPS37C, MVB12A and MVB12B. 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. Interacts WITH VPS36; the interaction mediates the association with the ESCRT-II complex. Interacts with SNF8 and VPS25. Interacts with CEP55.

    Alternative splice isoforms for VPS28 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS28 Gene

Post-translational modifications for VPS28 Gene

  • Ubiquitination at posLast=5858
  • 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

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
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

Clone Products

  • Addgene plasmids 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
extracellular 5
cytosol 5
endosome 5
cytoskeleton 3
nucleus 3
golgi apparatus 3
lysosome 2

Gene Ontology (GO) - Cellular Components for VPS28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000813 ESCRT I complex TAS 20588296
GO:0005737 cytoplasm IDA 18077552
GO:0005768 endosome IDA,IEA 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

Unigene Clusters for VPS28 Gene

Vacuolar protein sorting 28 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

  • Addgene plasmids 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
ECgene alternative splicing isoforms for
VPS28

Expression for VPS28 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of VPS28 Gene:

VPS28

SOURCE GeneReport for Unigene cluster for VPS28 Gene:

Hs.418175

Evidence on tissue expression from TISSUES for VPS28 Gene

  • Lung(4.5)
  • Nervous system(3.6)
  • Kidney(2.2)
  • Muscle(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 34 33
  • 97.35 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS28 34 33
  • 92.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS28 34 33
  • 90.2 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps28 33
  • 88.84 (n)
mouse
(Mus musculus)
Mammalia Vps28 16 34 33
  • 88.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS28 34
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 81 (a)
OneToMany
-- 34
  • 81 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia VPS28 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps28 33
  • 79.94 (n)
African clawed frog
(Xenopus laevis)
Amphibia vps28-prov 33
zebrafish
(Danio rerio)
Actinopterygii vps28 34 33
  • 79.39 (n)
OneToOne
zgc66078 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005344 33
  • 68.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vps28 34 35 33
  • 68.3 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-28 34 33
  • 52.26 (n)
OneToOne
Y87G2A.10 35
  • 46 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS28 36 34
  • 24 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS28-2 33
  • 50 (n)
rice
(Oryza sativa)
Liliopsida Os01g0781000 33
  • 54.8 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5272 34
  • 49 (a)
OneToOne
Cin.3194 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3194 33
Species where no ortholog for VPS28 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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

Sequence variations from dbSNP and Humsavar for VPS28 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000448460 -- 144,428,995(-) T/C upstream_transcript_variant
rs1000648759 -- 144,424,871(-) G/A intron_variant
rs1000801214 -- 144,429,246(-) C/T upstream_transcript_variant
rs1001644098 -- 144,427,156(-) G/A intron_variant
rs1003007101 -- 144,427,920(-) G/C intron_variant

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 for VPS28 Gene

Disorders for VPS28 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS28 Gene - From: DISEASES

Disorder Aliases PubMed IDs
noonan syndrome 1
  • ns1
- elite association - COSMIC cancer census association via MalaCards
Search VPS28 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS28

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 22 58
  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 22 58
  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 58
  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 58
  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 58

Products for VPS28 Gene

Sources for VPS28 Gene

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