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Aliases for VPS51 Gene

Aliases for VPS51 Gene

  • VPS51, GARP Complex Subunit 2 3 5
  • Another New Gene 2 Protein 3 4
  • Protein Fat-Free Homolog 3 4
  • C11orf3 3 4
  • C11orf2 3 4
  • ANG2 3 4
  • FFR 3 4
  • Vacuolar Protein Sorting-Associated Protein 51 Homolog 3
  • Vacuolar Protein Sorting 51 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 51 Homolog 3
  • Chromosome 11 Open Reading Frame 3 2
  • Chromosome 11 Open Reading Frame 2 2
  • Fat-Free Homolog (Zebrafish) 2
  • ANG3 3

External Ids for VPS51 Gene

Previous HGNC Symbols for VPS51 Gene

  • C11orf3
  • C11orf2

Previous GeneCards Identifiers for VPS51 Gene

  • GC11P064864

Summaries for VPS51 Gene

Entrez Gene Summary for VPS51 Gene

  • This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the early and late endosomes to the trans-Golgi network. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

GeneCards Summary for VPS51 Gene

VPS51 (VPS51, GARP Complex Subunit) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Retrograde transport at the Trans-Golgi-Network.

UniProtKB/Swiss-Prot for VPS51 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 protein retrieval from endosomes to the TGN, acid hydrolase sorting, lysosome function, endosomal cholesterol traffic and autophagy. VPS51 participates in retrograde transport of acid hydrolase receptors, likely by promoting tethering and SNARE-dependent fusion of endosome-derived carriers to the TGN (PubMed:20685960). 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 CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS51 Gene

Genomics for VPS51 Gene

Regulatory Elements for VPS51 Gene

Enhancers for VPS51 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
GH11G065470 2.7 VISTA FANTOM5 Ensembl ENCODE dbSUPER 10 +400.8 400760 40.0 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 LOC105369352 ZFPL1 KAT5 ENSG00000254461 EIF1AD NEAT1 FRMD8 EHBP1L1 POLA2 LOC101927789
GH11G065650 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10 +563.4 563388 5.4 CREB3L1 MLX AGO1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF263 EIF1AD MAP3K11 ZFPL1 SIPA1 RNASEH2C LOC105369352 MRPL11 RBM14 KAT5 PCNX3
GH11G064354 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.9 -731.4 -731350 6.6 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A ZBTB7B YY1 ZNF207 PLCB3 LOC102723878 ZFPL1 ENSG00000257086 POLA2 VPS51 ATG2A CDC42BPG MRPL49 SNX15
GH11G065288 2 FANTOM5 Ensembl ENCODE dbSUPER 10.1 +206.5 206474 14.5 HDGF PKNOX1 FOXA2 SIN3A ARID4B DMAP1 YY1 SLC30A9 ZNF766 FOS POLA2 EHD1 LOC728975 SLC25A45 DPF2 FRMD8 ENSG00000255478 SPDYC PGAM1P8 CAPN1
GH11G066078 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10 +992.5 992486 7.5 HDGF PKNOX1 FOXA2 AGO1 SIN3A YBX1 FEZF1 ZNF121 GATA2 CBX5 EIF1AD ENSG00000255320 SF3B2 SIPA1 RBM14 PACS1 ENSG00000258297 ZFPL1 PCNX3 KAT5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS51 on UCSC Golden Path with GeneCards custom track

Promoters for VPS51 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040776 385 1001 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21

Genomic Location for VPS51 Gene

Chromosome:
11
Start:
65,089,324 bp from pter
End:
65,111,860 bp from pter
Size:
22,537 bases
Orientation:
Plus strand

Genomic View for VPS51 Gene

Genes around VPS51 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS51 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS51 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS51 Gene

Proteins for VPS51 Gene

  • Protein details for VPS51 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UID3-VPS51_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 51 homolog
    Protein Accession:
    Q9UID3
    Secondary Accessions:
    • Q6PJV5
    • Q7L8A6
    • Q8WZ35
    • Q96DF4
    • Q96GR3

    Protein attributes for VPS51 Gene

    Size:
    782 amino acids
    Molecular mass:
    86042 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:20685960). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061). Interacts with STX6 (PubMed:20685960).

    Three dimensional structures from OCA and Proteopedia for VPS51 Gene

    Alternative splice isoforms for VPS51 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS51 Gene

Post-translational modifications for VPS51 Gene

  • Ubiquitination at posLast=114114, Lys166, posLast=176176, and Lys189
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS51 Gene

Domains & Families for VPS51 Gene

Protein Domains for VPS51 Gene

Suggested Antigen Peptide Sequences for VPS51 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UID3

UniProtKB/Swiss-Prot:

VPS51_HUMAN :
  • Belongs to the VPS51 family.
Family:
  • Belongs to the VPS51 family.
genes like me logo Genes that share domains with VPS51: view

Function for VPS51 Gene

Molecular function for VPS51 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 protein retrieval from endosomes to the TGN, acid hydrolase sorting, lysosome function, endosomal cholesterol traffic and autophagy. VPS51 participates in retrograde transport of acid hydrolase receptors, likely by promoting tethering and SNARE-dependent fusion of endosome-derived carriers to the TGN (PubMed:20685960). 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).

Gene Ontology (GO) - Molecular Function for VPS51 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 20685960
genes like me logo Genes that share ontologies with VPS51: view
genes like me logo Genes that share phenotypes with VPS51: view

Animal Models for VPS51 Gene

MGI Knock Outs for VPS51:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS51 Gene

Localization for VPS51 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS51 Gene

Golgi apparatus, trans-Golgi network. 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}.

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 VPS51 gene
Compartment Confidence
nucleus 5
golgi apparatus 5
endosome 5
cytosol 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS51 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 20685960
GO:0005730 nucleolus IDA --
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IDA,IEA 20685960
GO:0005802 trans-Golgi network IEA,IBA --
genes like me logo Genes that share ontologies with VPS51: view

Pathways & Interactions for VPS51 Gene

genes like me logo Genes that share pathways with VPS51: view

Gene Ontology (GO) - Biological Process for VPS51 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006869 lipid transport IEA --
GO:0006914 autophagy IMP 20685960
GO:0007030 Golgi organization IBA --
GO:0007041 lysosomal transport IMP 25799061
genes like me logo Genes that share ontologies with VPS51: view

No data available for SIGNOR curated interactions for VPS51 Gene

Drugs & Compounds for VPS51 Gene

No Compound Related Data Available

Transcripts for VPS51 Gene

Unigene Clusters for VPS51 Gene

Vacuolar protein sorting 51 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS51 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11a ·
SP1: - - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - - -
SP5: - -
SP6:
SP7:
SP8: - - - - - -
SP9: - -
SP10: - - - - -
SP11:
SP12: -

ExUns: 11b ^ 12a · 12b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for VPS51 Gene

GeneLoc Exon Structure for
VPS51
ECgene alternative splicing isoforms for
VPS51

Expression for VPS51 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS51 Gene

Protein differential expression in normal tissues from HIPED for VPS51 Gene

This gene is overexpressed in Heart (23.2) and Bone (11.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VPS51 Gene



Protein tissue co-expression partners for VPS51 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS51 Gene:

VPS51

SOURCE GeneReport for Unigene cluster for VPS51 Gene:

Hs.277517

Evidence on tissue expression from TISSUES for VPS51 Gene

  • Muscle(4.6)
  • Lung(4.5)
  • Eye(4.3)
  • Nervous system(3.9)
  • Heart(2.8)
  • Skin(2.4)
  • Blood(2.3)
genes like me logo Genes that share expression patterns with VPS51: 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 VPS51 Gene

Orthologs for VPS51 Gene

This gene was present in the common ancestor of animals.

Orthologs for VPS51 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS51 34 35
  • 99.62 (n)
cow
(Bos Taurus)
Mammalia VPS51 34 35
  • 91.35 (n)
dog
(Canis familiaris)
Mammalia VPS51 34 35
  • 89.7 (n)
rat
(Rattus norvegicus)
Mammalia Vps51 34
  • 88.73 (n)
mouse
(Mus musculus)
Mammalia Vps51 34 16 35
  • 88.51 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS51 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS51 35
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS51 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps51 34
  • 66.8 (n)
zebrafish
(Danio rerio)
Actinopterygii vps51 34 35
  • 68.03 (n)
wufi30b05 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5315 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005584 34
  • 56.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG15087 35 34
  • 52.66 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-51 34 35
  • 39.53 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 53 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13318 34
Species where no ortholog for VPS51 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS51 Gene

ENSEMBL:
Gene Tree for VPS51 (if available)
TreeFam:
Gene Tree for VPS51 (if available)

Paralogs for VPS51 Gene

No data available for Paralogs for VPS51 Gene

Variants for VPS51 Gene

Sequence variations from dbSNP and Humsavar for VPS51 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000178121 -- 65,110,168(+) CTTCT(C/T)AGCCC intron-variant, upstream-variant-2KB
rs1000295040 -- 65,106,581(+) TCCAT(C/G)TCTAC intron-variant
rs1000323438 -- 65,099,145(+) GTTTC(A/G)AGACA intron-variant
rs1000517283 -- 65,098,027(+) AAATA(A/C)AAAAA intron-variant
rs1000562482 -- 65,104,707(+) GTATA(G/T)GTGAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS51 Gene

Variant ID Type Subtype PubMed ID
nsv526181 CNV gain 19592680

Variation tolerance for VPS51 Gene

Residual Variation Intolerance Score: 17.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.62; 31.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS51 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS51

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS51 Gene

Disorders for VPS51 Gene

Relevant External Links for VPS51

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS51

No disorders were found for VPS51 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS51 Gene

Publications for VPS51 Gene

  1. 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) 2 3 4 64
  2. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 2015) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Identification and molecular characterization of TM7SF2 in the FAUNA gene cluster on human chromosome 11q13. (PMID: 9615229) Lemmens I.H. … Van de Ven W.J.M. (Genomics 1998) 3 4 64
  5. Construction of a 1.2-Mb sequence-ready contig of chromosome 11q13 encompassing the multiple endocrine neoplasia type 1 (MEN1) gene. The European Consortium on MEN1. (PMID: 9286704) Lemmens I. … Thakker R.V. (Genomics 1997) 2 3 64

Products for VPS51 Gene

Sources for VPS51 Gene

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