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Aliases for VPS25 Gene

Aliases for VPS25 Gene

  • Vacuolar Protein Sorting 25 Homolog 2 3 5
  • Dermal Papilla-Derived Protein 9 3 4
  • ELL-Associated Protein Of 20 KDa 3 4
  • ESCRT-II Complex Subunit VPS25 3 4
  • DERP9 3 4
  • EAP20 3 4
  • Vacuolar Protein Sorting 25 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein-Sorting-Associated Protein 25 3
  • Vacuolar Protein Sorting 25 (Yeast) 2
  • HVps25 4
  • FAP20 3

External Ids for VPS25 Gene

Previous GeneCards Identifiers for VPS25 Gene

  • GC17P038179
  • GC17P040925
  • GC17P036689

Summaries for VPS25 Gene

Entrez Gene Summary for VPS25 Gene

  • This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A pseudogene of this gene is present on chromosome 1. [provided by RefSeq, Jul 2013]

GeneCards Summary for VPS25 Gene

VPS25 (Vacuolar Protein Sorting 25 Homolog) is a Protein Coding gene. Among its related pathways are wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF) and Delta508-CFTR traffic / Sorting endosome formation in CF. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and protein N-terminus binding.

UniProtKB/Swiss-Prot for VPS25 Gene

  • Component of the ESCRT-II complex (endosomal sorting complex required for transport II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation, possibly via its interaction with ELL. The ESCRT-II complex may be involved in facilitating the budding of certain RNA viruses.

Gene Wiki entry for VPS25 Gene

Additional gene information for VPS25 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS25 Gene

Genomics for VPS25 Gene

GeneHancer (GH) Regulatory Elements for VPS25 Gene

Promoters and enhancers for VPS25 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
GH17J042772 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +1.0 978 4 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 VPS25 HMGN1P29 DHX8 ENSG00000267758 LINC00910 HMGN2P15 NBR2 NKIRAS2 CNTNAP1 MEOX1
GH17J042672 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.4 -94.7 -94738 11.4 MLX ZFP64 DMAP1 YBX1 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 CNTNAP1 CCR10 PLEKHH3 ENSG00000267042 DHX8 TUBG2 HMGN1P29 ENSG00000267758 ENSG00000267002 ENSG00000266962
GH17J042419 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.7 -351.5 -351492 5.2 PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 POLR2B CAVIN1 LOC102725238 LINC00910 HMGN1P29 NBR2 CNTD1 RETREG3 ENSG00000267758 ACLY DHX58
GH17J042823 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.5 +50.6 50641 1.7 HDGF MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B PSME3 MIR6781 BECN1 COA3 CNTD1 AOC2 AOC3 VPS25 RAMP2-AS1 RAMP2
GH17J041965 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.2 -806.5 -806538 3.5 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF207 ZNF143 SP3 GC17P041968 GC17P041973 PIR42788 CNP NT5C3B ENSG00000267758 NKIRAS2 DNAJC7 ZNF385C DHX58
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS25 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS25 gene promoter:
  • RSRFC4
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • CUTL1
  • Roaz
  • GATA-3
  • MZF-1

Genomic Locations for VPS25 Gene

Genomic Locations for VPS25 Gene
chr17:42,773,436-42,779,600
(GRCh38/hg38)
Size:
6,165 bases
Orientation:
Plus strand
chr17:40,925,454-40,931,617
(GRCh37/hg19)
Size:
6,164 bases
Orientation:
Plus strand

Genomic View for VPS25 Gene

Genes around VPS25 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS25 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS25 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS25 Gene

Proteins for VPS25 Gene

  • Protein details for VPS25 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BRG1-VPS25_HUMAN
    Recommended name:
    Vacuolar protein-sorting-associated protein 25
    Protein Accession:
    Q9BRG1
    Secondary Accessions:
    • B2R581

    Protein attributes for VPS25 Gene

    Size:
    176 amino acids
    Molecular mass:
    20748 Da
    Quaternary structure:
    • Component of a complex at least composed of ELL, SNF8/EAP30, VPS25/EAP20 and VPS36/EAP45 (By similarity). Component of the endosomal sorting complex required for transport II (ESCRT-II), composed of SNF8, VPS36 and 2 copies of VPS25. Interacts with CFTR; the interaction requires misfolded CFTR. Interacts (via C-terminal half) with the ESCRT-III subunit CHMP6 (via N-terminal half).

    Three dimensional structures from OCA and Proteopedia for VPS25 Gene

neXtProt entry for VPS25 Gene

Post-translational modifications for VPS25 Gene

  • Ubiquitination at isoforms=64
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS25 Gene

No data available for DME Specific Peptides for VPS25 Gene

Domains & Families for VPS25 Gene

Gene Families for VPS25 Gene

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

Protein Domains for VPS25 Gene

Suggested Antigen Peptide Sequences for VPS25 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BRG1

UniProtKB/Swiss-Prot:

VPS25_HUMAN :
  • Belongs to the VPS25 family.
Family:
  • Belongs to the VPS25 family.
genes like me logo Genes that share domains with VPS25: view

Function for VPS25 Gene

Molecular function for VPS25 Gene

UniProtKB/Swiss-Prot Function:
Component of the ESCRT-II complex (endosomal sorting complex required for transport II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation, possibly via its interaction with ELL. The ESCRT-II complex may be involved in facilitating the budding of certain RNA viruses.

Phenotypes From GWAS Catalog for VPS25 Gene

Gene Ontology (GO) - Molecular Function for VPS25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IBA --
GO:0005515 protein binding IPI 14505570
GO:0042803 protein homodimerization activity IPI 14519844
GO:0047485 protein N-terminus binding IPI 16973552
genes like me logo Genes that share ontologies with VPS25: view
genes like me logo Genes that share phenotypes with VPS25: view

Animal Models for VPS25 Gene

MGI Knock Outs for VPS25:
  • Vps25 Vps25<tm1(KOMP)Vlcg>
  • Vps25 Vps25<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for VPS25 Gene

miRTarBase miRNAs that target VPS25

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS25

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS25 Gene

Localization for VPS25 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS25 Gene

Cytoplasm. Endosome membrane. Nucleus, nucleoplasm. Note=Distributes diffusely throughout the cytoplasm and nucleoplasm, but exhibits a punctate distribution on coexpression with CHMP6.

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 VPS25 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
endosome 5
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VPS25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000814 ESCRT II complex TAS 20588296
GO:0005634 nucleus IDA,IEA 16371348
GO:0005654 nucleoplasm IEA --
GO:0005737 cytoplasm IDA,IEA 16973552
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with VPS25: view

Pathways & Interactions for VPS25 Gene

genes like me logo Genes that share pathways with VPS25: view

Pathways by source for VPS25 Gene

Gene Ontology (GO) - Biological Process for VPS25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007175 negative regulation of epidermal growth factor-activated receptor activity IMP 16973552
GO:0015031 protein transport IEA --
GO:0016197 endosomal transport TAS --
genes like me logo Genes that share ontologies with VPS25: view

No data available for SIGNOR curated interactions for VPS25 Gene

Drugs & Compounds for VPS25 Gene

No Compound Related Data Available

Transcripts for VPS25 Gene

mRNA/cDNA for VPS25 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(351) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VPS25 Gene

Vacuolar protein sorting 25 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS25

Alternative Splicing Database (ASD) splice patterns (SP) for VPS25 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5: -
SP6:

Relevant External Links for VPS25 Gene

GeneLoc Exon Structure for
VPS25
ECgene alternative splicing isoforms for
VPS25

Expression for VPS25 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS25 Gene

Protein differential expression in normal tissues from HIPED for VPS25 Gene

This gene is overexpressed in Salivary gland (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS25 Gene



Protein tissue co-expression partners for VPS25 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS25 Gene:

VPS25

SOURCE GeneReport for Unigene cluster for VPS25 Gene:

Hs.500165

mRNA Expression by UniProt/SwissProt for VPS25 Gene:

Q9BRG1-VPS25_HUMAN
Tissue specificity: Expressed at the mRNA level in kidney, liver, pancreas, and placenta. Lower levels of expression are found in heart, skeletal muscle, brain and lung.

Evidence on tissue expression from TISSUES for VPS25 Gene

  • Nervous system(4.7)
  • Skin(4.3)
genes like me logo Genes that share expression patterns with VPS25: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS25 Gene

Orthologs for VPS25 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS25 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS25 34 33
  • 99.43 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS25 33
  • 95.27 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS25 34
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS25 34 33
  • 93.56 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps25 33
  • 93.37 (n)
mouse
(Mus musculus)
Mammalia Vps25 16 34 33
  • 92.61 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS25 34
  • 51 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS25 33
  • 74.14 (n)
lizard
(Anolis carolinensis)
Reptilia VPS25 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps25 33
  • 74.52 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7309 33
zebrafish
(Danio rerio)
Actinopterygii vps25 34 33
  • 72.99 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3769 33
fruit fly
(Drosophila melanogaster)
Insecta Vps25 34 33
  • 53.61 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011497 33
  • 50.62 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-25 34 33
  • 48.85 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS25 36 34
  • 27 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS25 33
  • 47.84 (n)
rice
(Oryza sativa)
Liliopsida Os01g0658500 33
  • 45.56 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03898 33
  • 51.07 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps25 33
  • 48.37 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
OneToOne
Species where no ortholog for VPS25 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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)
  • 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 VPS25 Gene

ENSEMBL:
Gene Tree for VPS25 (if available)
TreeFam:
Gene Tree for VPS25 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS25: view image

Paralogs for VPS25 Gene

Pseudogenes.org Pseudogenes for VPS25 Gene

genes like me logo Genes that share paralogs with VPS25: view

No data available for Paralogs for VPS25 Gene

Variants for VPS25 Gene

Sequence variations from dbSNP and Humsavar for VPS25 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000801135 -- 42,773,602(+) T/A/C intron_variant
rs1001297272 -- 42,771,730(+) G/A upstream_transcript_variant
rs1001488901 -- 42,776,778(+) A/G 3_prime_UTR_variant, intron_variant
rs1001754836 -- 42,777,764(+) G/C downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1002086122 -- 42,777,024(+) G/A 3_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS25 Gene

Variant ID Type Subtype PubMed ID
esv33998 OTHER inversion 15654335
nsv1146669 OTHER inversion 26484159
nsv827998 CNV loss 20364138
nsv833450 CNV loss 17160897

Variation tolerance for VPS25 Gene

Residual Variation Intolerance Score: 41.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS25 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS25

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS25 Gene

Disorders for VPS25 Gene

Additional Disease Information for VPS25

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for VPS25 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS25 Gene

Publications for VPS25 Gene

  1. Human CHMP6, a myristoylated ESCRT-III protein, interacts directly with an ESCRT-II component EAP20 and regulates endosomal cargo sorting. (PMID: 15511219) Yorikawa C … Maki M (The Biochemical journal 2005) 2 3 4 58
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Structure and function of the ESCRT-II-III interface in multivesicular body biogenesis. (PMID: 19686684) Im YJ … Hurley JH (Developmental cell 2009) 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-II complex and its role in human immunodeficiency virus type 1 release. (PMID: 16973552) Langelier C … Sundquist WI (Journal of virology 2006) 3 4 58

Products for VPS25 Gene

Sources for VPS25 Gene

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