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Aliases for VPS28 Gene

Aliases for VPS28 Gene

  • VPS28, ESCRT-I Subunit 2 3 5
  • Vacuolar Protein Sorting 28 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 28 (Yeast) 2
  • ESCRT-I Complex Subunit VPS28 4
  • 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 Budding and maturation of HIV virion. GO annotations related to this gene include protein complex binding and 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS28 Gene

Genomics for VPS28 Gene

Regulatory Elements for VPS28 Gene

Enhancers for VPS28 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08G144455 1.4 Ensembl ENCODE 44.3 -27.9 -27884 1.6 HNRNPUL1 HDGF PKNOX1 FOXA2 CREB3L1 ARNT AGO1 ZFP64 SIN3A ZNF2 ZNF251 ZNF623 ZNF250 ZNF34 LRRC14 ZNF517 GPAA1 VPS28 TMED10P1 ENSG00000255164
GH08G144425 1.7 FANTOM5 ENCODE dbSUPER 27.8 -0.4 -376 6.8 HNRNPUL1 PKNOX1 MLX CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 VPS28 SLC39A4 TONSL ZNF517 CPSF1 TONSL-AS1
GH08G144412 1.3 ENCODE dbSUPER 29.9 +12.3 12332 7.3 HDGF PKNOX1 MLX CREB3L1 AGO1 ARID4B SIN3A DMAP1 YY1 SLC30A9 VPS28 SLC39A4 CPSF1 TONSL C8orf82 LOC105375803 HGH1 ZNF252P ENSG00000272115
GH08G144506 1.4 ENCODE dbSUPER 23.4 -80.4 -80407 4.0 HNRNPUL1 HDGF PKNOX1 ARNT CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 ZNF251 LRRC14 ZNF250 VPS28 PPP1R16A ZNF623 LOC105375803 ENSG00000254533 ZNF517 TMED10P1
GH08G144353 1.3 Ensembl ENCODE 24 +72.1 72051 6.7 PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 KLF13 CPSF1 VPS28 TONSL TMEM249 FBXL6 ENSG00000271698
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS28 on UCSC Golden Path with GeneCards custom track

Promoters for VPS28 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000232247 63 2201 HNRNPUL1 PKNOX1 MLX AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B

Genomic Location for VPS28 Gene

Chromosome:
8
Start:
144,423,601 bp from pter
End:
144,428,563 bp from pter
Size:
4,963 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 stoechiometry. 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 stoechiometry. 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 isoforms=258
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS28 Gene

Domains & Families for VPS28 Gene

Gene Families for VPS28 Gene

Protein Domains for VPS28 Gene

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.

Gene Ontology (GO) - Molecular Function for VPS28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11134028
GO:0032403 protein complex binding IBA --
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

CRISPR Products

Inhibitory RNA 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

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:0006810 transport IEA --
GO:0015031 protein transport IEA --
GO:0016197 endosomal transport TAS --
GO:0016236 macroautophagy TAS 20588296
GO:0019058 viral life cycle TAS --
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:

CRISPR Products

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 35
  • 97.35 (n)
cow
(Bos Taurus)
Mammalia VPS28 34 35
  • 92.76 (n)
dog
(Canis familiaris)
Mammalia VPS28 34 35
  • 90.2 (n)
rat
(Rattus norvegicus)
Mammalia Vps28 34
  • 88.84 (n)
mouse
(Mus musculus)
Mammalia Vps28 34 16 35
  • 88.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS28 35
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia VPS28 35
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps28 34
  • 79.94 (n)
African clawed frog
(Xenopus laevis)
Amphibia vps28-prov 34
zebrafish
(Danio rerio)
Actinopterygii vps28 34 35
  • 79.39 (n)
zgc66078 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005344 34
  • 68.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vps28 36 34 35
  • 68.3 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-28 34 35
  • 52.26 (n)
Y87G2A.10 36
  • 46 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS28 35 37
  • 24 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS28-2 34
  • 50 (n)
rice
(Oryza sativa)
Liliopsida Os01g0781000 34
  • 54.8 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5272 35
  • 49 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3194 34
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)

Paralogs for VPS28 Gene

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

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 Sequence Context AA Info Type
rs1000448460 -- 144,428,995(+) CATGT(C/T)AGCCA upstream-variant-2KB, utr-variant-3-prime
rs1000648759 -- 144,424,871(+) CAGGT(A/G)GCCAG intron-variant
rs1000801214 -- 144,429,246(+) CAGCG(C/T)AGAGG upstream-variant-2KB, reference, missense
rs1001644098 -- 144,427,156(+) TAGCC(A/G)GACGT intron-variant
rs1003007101 -- 144,427,920(+) AGGAG(C/G)AGCGG 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)

Relevant External Links for VPS28 Gene

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

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 and GeneCards

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

Relevant External Links for VPS28

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 W.I. (Cell Host Microbe 2007) 3 4 22 64
  2. The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding. (PMID: 15218037) Stuchell M.D. … Sundquist W.I. (J. Biol. Chem. 2004) 3 4 22 64
  3. UBAP1 is a component of an endosome-specific ESCRT-I complex that is essential for MVB sorting. (PMID: 21757351) Stefani F. … Woodman P. (Curr. Biol. 2011) 3 4 64
  4. Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex. (PMID: 18539118) Im Y.J. … Hurley J.H. (Dev. Cell 2008) 3 4 64
  5. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. (PMID: 17853893) Morita E. … Sundquist W.I. (EMBO J. 2007) 3 4 64

Products for VPS28 Gene

  • Addgene plasmids for VPS28

Sources for VPS28 Gene

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