Aliases for VPS52 Gene
Aliases for VPS52 Gene
External Ids for VPS52 Gene
- HGNC: 10518
- Entrez Gene: 6293
- Ensembl: ENSG00000223501
- OMIM: 603443
- UniProtKB: Q8N1B4
Previous HGNC Symbols for VPS52 Gene
- SACM2L
Previous GeneCards Identifiers for VPS52 Gene
- GC06M033210
- GC06M033264
- GC06M033326
- GC06M033218
- GC06M032960
Summaries for VPS52 Gene
-
This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
GeneCards Summary for VPS52 Gene
VPS52 (VPS52, GARP Complex Subunit) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Retrograde transport at the Trans-Golgi-Network. GO annotations related to this gene include syntaxin binding.
UniProtKB/Swiss-Prot for VPS52 Gene
-
Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).
No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS52 Gene
Genomics for VPS52 Gene
Regulatory Elements for VPS52 Gene
Enhancers for VPS52 Gene
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around VPS52 on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the VPS52 gene promoter:
Regulatory Element Products
Genomic Location for VPS52 Gene
- Chromosome:
- 6
- Start:
- 33,250,272 bp from pter
- End:
- 33,272,047 bp from pter
- Size:
- 21,776 bases
- Orientation:
- Minus strand
Genomic View for VPS52 Gene
Genes around VPS52 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 6p21.32 by Ensembl
- 6p21.32 by Entrez Gene
- 6p21.32 by HGNC
VPS52 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for VPS52 Gene
Proteins for VPS52 Gene
-
Protein details for VPS52 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q8N1B4-VPS52_HUMAN
- Recommended name:
- Vacuolar protein sorting-associated protein 52 homolog
- Protein Accession:
- Q8N1B4
- A2BF38
- B0UZZ4
- B4DNI9
- Q53GR4
- Q5JPA0
- Q5SQW1
- Q8IUN6
- Q9NPT5
Protein attributes for VPS52 Gene
- Size:
- 723 amino acids
- Molecular mass:
- 82221 Da
- Quaternary structure:
-
- Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54 (PubMed:15878329, PubMed:20685960). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061). Interacts with RAB6A and STX10 (PubMed:15878329, PubMed:20685960).
- SequenceCaution:
-
- Sequence=CAI95619.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Protein Expression for VPS52 Gene
Post-translational modifications for VPS52 Gene
Other Protein References for VPS52 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
-
Custom Antibody ServicesOriGene Antibodies for VPS52
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- Invitrogen Antibodies for VPS52
- antibodies-online Antibodies for VPS52: See all 28
- GeneTex VPS52 antibody for VPS52
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for VPS52
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- antibodies-online Proteins for VPS52: See all 7
- Search antibodies-online for peptides
- Search GeneTex for Proteins for VPS52
Assay Products
No data available for DME Specific Peptides for VPS52 Gene
Domains & Families for VPS52 Gene
Suggested Antigen Peptide Sequences for VPS52 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q8N1B4- Family:
-
- Belongs to the VPS52 family.
No data available for Gene Families for VPS52 Gene
Function for VPS52 Gene
Molecular function for VPS52 Gene
- UniProtKB/Swiss-Prot Function:
- Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005515 | protein binding | IPI | 15878329 |
| GO:0017137 | Rab GTPase binding | IBA | -- |
| GO:0019905 | syntaxin binding | IPI | 15878329 |
Phenotypes for VPS52 Gene
- MGI mutant phenotypes for VPS52:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for VPS52:
Animal Models for VPS52 Gene
- MGI Knock Outs for VPS52:
-
- Vps52 tm1.2Kab
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
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-
-
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-
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CRISPR Products
-
OriGene CRISPR knockouts for VPS52
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miRNA for VPS52 Gene
- miRTarBase miRNAs that target VPS52
-
- hsa-mir-4728-5p (MIRT491942)
- hsa-mir-607 (MIRT491943)
- hsa-mir-3591-5p (MIRT491944)
- hsa-mir-628-5p (MIRT491945)
- hsa-mir-3671 (MIRT491946)
- hsa-mir-6807-5p (MIRT491947)
- hsa-mir-124-5p (MIRT491948)
- hsa-mir-3175 (MIRT491949)
- hsa-mir-6731-5p (MIRT491950)
- hsa-mir-8085 (MIRT491951)
- hsa-mir-8077 (MIRT491952)
- hsa-mir-7160-5p (MIRT491953)
- hsa-mir-655-5p (MIRT491954)
- hsa-mir-4663 (MIRT491955)
- hsa-mir-665 (MIRT491956)
- hsa-mir-4459 (MIRT491957)
- hsa-mir-4779 (MIRT491958)
- hsa-mir-4255 (MIRT491959)
- hsa-mir-7161-3p (MIRT491960)
- hsa-mir-302f (MIRT491961)
- hsa-mir-142-3p (MIRT491962)
- hsa-mir-513b-5p (MIRT651663)
- hsa-mir-6829-3p (MIRT651664)
- hsa-mir-6791-3p (MIRT651665)
- hsa-mir-4252 (MIRT651666)
- hsa-mir-205-5p (MIRT651667)
- hsa-mir-4719 (MIRT651668)
- hsa-mir-7853-5p (MIRT651669)
- hsa-mir-105-5p (MIRT651670)
- hsa-mir-330-3p (MIRT651671)
- hsa-mir-7109-3p (MIRT651672)
- hsa-mir-6771-3p (MIRT651673)
miRNA Products
- Search ViGene Biosciences for VPS52
Clone Products
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- Sino Biological Human cDNA Clone for VPS52
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- VectorBuilder custom plasmid, inducible vectors for VPS52
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-
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- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Cell Line Products
-
Horizon Cell Lines for VPS52
-
ViGene Biosciences adenoviral particle packaged cDNA for VPS52 gene
-
ViGene Biosciences lentiviral particle packaged cDNA for VPS52 gene
-
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Flow Cytometry Products
No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS52 Gene
Localization for VPS52 Gene
Subcellular locations from UniProtKB/Swiss-Prot for VPS52 Gene
- Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Recycling endosome. Note=Localizes to the trans-Golgi network as part of the GARP complex, while it localizes to recycling endosomes as part of the EARP complex (PubMed:25799061). {ECO:0000269 PubMed:25799061}.
| Compartment | Confidence |
|---|---|
| golgi apparatus | 5 |
| endosome | 5 |
| cytosol | 3 |
| nucleus | 2 |
| plasma membrane | 1 |
| mitochondrion | 1 |
| peroxisome | 1 |
| endoplasmic reticulum | 1 |
| lysosome | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000938 | GARP complex | IDA | 25799061 |
| GO:0005768 | endosome | IEA | -- |
| GO:0005794 | Golgi apparatus | IEA,IDA | 15878329 |
| GO:0005829 | cytosol | IEA | -- |
| GO:0010008 | endosome membrane | IEA | -- |
Pathways & Interactions for VPS52 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Vesicle-mediated transport | ||
| 2 | Golgi-to-ER retrograde transport | ||
| 3 | Retrograde transport at the Trans-Golgi-Network | ||
Pathways by source for VPS52 Gene
4 Reactome pathways for VPS52 Gene
Interacting Proteins for VPS52 Gene
Selected Interacting proteins:
ENSP00000409952
Q8N1B4-VPS52_HUMAN
for VPS52 Gene via
STRING
MINT
UniProtKB
IID
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006810 | transport | IEA | -- |
| GO:0006896 | Golgi to vacuole transport | IBA | -- |
| GO:0007041 | lysosomal transport | IDA | 25799061 |
| GO:0010668 | ectodermal cell differentiation | IEA | -- |
| GO:0015031 | protein transport | IEA | -- |
No data available for SIGNOR curated interactions for VPS52 Gene
Transcripts for VPS52 Gene
mRNA/cDNA for VPS52 Gene
- (10) REFSEQ mRNAs :
- (12) Additional mRNA sequences :
- (325) Selected AceView cDNA sequences:
- (11) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for VPS52 Gene
CRISPR Products
-
OriGene CRISPR knockouts for VPS52
- GenScript: Design CRISPR guide RNA sequences for VPS52
miRNA Products
- Search ViGene Biosciences for VPS52
Clone Products
-
GenScript: Next-day shipping cDNA clones in your preferred vector
- NM_001289176
- NM_001289175
- NM_001289174
- NM_022553
- XM_011548459
- XM_011548458
- XM_011548457
- XM_011548456
- XM_011548264
- XM_011548263
- XM_011548262
- XM_011548261
- XM_011548075
- XM_011548074
- XM_011548073
- XM_011548072
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- XM_011547673
- XM_011547273
- XM_011547272
- XM_011547271
- XM_011547270
- XM_011514800
- XM_011514799
- XM_011514798
- XM_011514797
- Sino Biological Human cDNA Clone for VPS52
- Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat
- VectorBuilder custom plasmid, inducible vectors for VPS52
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for VPS52
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Flow Cytometry Products
Expression for VPS52 Gene
This gene is overexpressed in Peripheral blood mononuclear cells (12.7) and Bone (9.5).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VPS52 Gene
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of VPS52 Gene:
VPS52SOURCE GeneReport for Unigene cluster for VPS52 Gene:
Hs.480356Primer Products
-
OriGene qPCR primer pairs and template standards for VPS52
-
OriGene qPCR primer pairs for VPS52
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VPS52 Gene
Orthologs for VPS52 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | VPS52 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | VPS52 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | VPS52 34 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | -- 35 |
|
OneToMany | |
| -- 35 |
|
OneToMany | |||
| mouse (Mus musculus) |
Mammalia | Vps52 34 16 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Vps52 34 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | VPS52 35 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | vps52 34 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.11507 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | vps52 34 35 |
|
||
| fruit fly (Drosophila melanogaster) |
Insecta | CG7371 34 35 |
|
||
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP009739 34 |
|
||
| worm (Caenorhabditis elegans) |
Secernentea | vps-52 34 35 |
|
||
| baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | VPS52 35 |
|
OneToOne | |
| thale cress (Arabidopsis thaliana) |
eudicotyledons | POK 34 |
|
||
| rice (Oryza sativa) |
Liliopsida | Os03g0417900 34 |
|
||
| sea squirt (Ciona savignyi) |
Ascidiacea | CSA.6752 35 |
|
OneToOne | |
| sea squirt (Ciona intestinalis) |
Ascidiacea | Cin.7505 34 |
|
- Species where no ortholog for VPS52 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)
- platypus (Ornithorhynchus anatinus)
- 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)
Paralogs for VPS52 Gene
No data available for Paralogs for VPS52 Gene
Variants for VPS52 Gene
| SNP ID | Clin | Chr 06 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1002011 | -- | 33,250,460(+) | GCTGA(A/G)GAGGC | intron-variant, utr-variant-3-prime | |
| rs10080745 | -- | 33,271,935(+) | AAGGC(A/G)CACCG | upstream-variant-2KB, utr-variant-5-prime | |
| rs10456072 | -- | 33,258,109(+) | AAggc(A/G/T)ggacg | intron-variant | |
| rs10539952 | -- | 33,273,960(+) | TCATG(-/TTTA)TTTAT | intron-variant, upstream-variant-2KB | |
| rs10630652 | -- | 33,273,898(+) | TAATT(-/AATA)AATAA | intron-variant, upstream-variant-2KB |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv10609n54 | CNV | loss | 21841781 |
| nsv1073969 | CNV | deletion | 25765185 |
| nsv1112900 | CNV | deletion | 24896259 |
| nsv1119076 | CNV | deletion | 24896259 |
| nsv5249 | CNV | deletion | 18451855 |
| nsv830634 | CNV | loss | 17160897 |
| nsv830635 | CNV | loss | 17160897 |
Residual Variation Intolerance Score:
19.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
1.64;
31.49% of all genes are more intolerant (likely to be disease-causing)
Relevant External Links for VPS52 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- VPS52
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS52 Gene
Disorders for VPS52 Gene
Relevant External Links for VPS52
No disorders were found for VPS52 Gene.
No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS52 Gene
Publications for VPS52 Gene
- Characterization of the human GARP (Golgi associated retrograde protein) complex. (PMID: 15878329) Liewen H. … Stenner-Liewen F. (Exp. Cell Res. 2005) 2 3 4 64
- Identification of a novel highly conserved gene in the centromeric part of the major histocompatibility complex. (PMID: 9790748) Walter L. … Guenther E. (Genomics 1998) 2 3 22 64
- EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 2015) 3 4 64
- Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex. (PMID: 20685960) Perez-Victoria F.J. … Bonifacino J.S. (Mol. Biol. Cell 2010) 3 4 64
- High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos L.F. … Criswell L.A. (PLoS Genet. 2009) 3 46 64
Products for VPS52 Gene
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- antibodies-online Antibodies for VPS52: See all 28
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- antibodies-online Proteins for VPS52: See all 7
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- GeneTex VPS52 antibody for VPS52
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- ViGene Biosciences adenoviral particle packaged cDNA for VPS52 gene
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- Search ViGene Biosciences for VPS52
- Horizon Cell Lines for VPS52
- Cyagen custom Knockout/knockin (KOKI) mouse models for VPS52
- VectorBuilder custom plasmid, inducible vectors for VPS52
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for VPS52
- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for VPS52 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
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