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Human Gene VPS51 (ENST00000279281.8) from GENCODE V38
  Description: Homo sapiens VPS51 subunit of GARP complex (VPS51), transcript variant 2, non-coding RNA. (from RefSeq NR_073519)
RefSeq Summary (NM_013265): 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].
Gencode Transcript: ENST00000279281.8
Gencode Gene: ENSG00000149823.9
Transcript (Including UTRs)
   Position: hg38 chr11:65,096,214-65,111,862 Size: 15,649 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr11:65,096,251-65,111,587 Size: 15,337 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:65,096,214-65,111,862)mRNA (may differ from genome)Protein (782 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
ReactomeUniProtKB

-  Comments and Description Text from UniProtKB
  ID: VPS51_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 51 homolog; AltName: Full=Another new gene 2 protein; AltName: Full=Protein fat-free homolog;
FUNCTION: Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi networkl (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.
SUBUNIT: Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. Interacts with STX6.
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network.
SIMILARITY: Belongs to the VPS51 family.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 63.14 RPKM in Ovary
Total median expression: 1600.49 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.4037-0.362 Picture PostScript Text
3' UTR -131.10275-0.477 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016159 - Cullin_repeat-like_dom
IPR014812 - Vps51

Pfam Domains:
PF08700 - Vps51/Vps67

ModBase Predicted Comparative 3D Structure on Q9UID3
FrontTopSide
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005515 protein binding

Biological Process:
GO:0006869 lipid transport
GO:0006914 autophagy
GO:0007030 Golgi organization
GO:0007041 lysosomal transport
GO:0015031 protein transport
GO:0032456 endocytic recycling
GO:0042147 retrograde transport, endosome to Golgi
GO:0048193 Golgi vesicle transport

Cellular Component:
GO:0000938 GARP complex
GO:0005730 nucleolus
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032588 trans-Golgi network membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0055037 recycling endosome
GO:1990745 EARP complex


-  Descriptions from all associated GenBank mRNAs
  LF211187 - JP 2014500723-A/18690: Polycomb-Associated Non-Coding RNAs.
MA446764 - JP 2018138019-A/18690: Polycomb-Associated Non-Coding RNAs.
JD023327 - Sequence 4351 from Patent EP1572962.
JD556140 - Sequence 537164 from Patent EP1572962.
AF024631 - Homo sapiens ANG2 (ANG2) mRNA, complete cds.
JD517214 - Sequence 498238 from Patent EP1572962.
JD030308 - Sequence 11332 from Patent EP1572962.
BC010540 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone MGC:17523 IMAGE:3458443), complete cds.
BC010872 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone IMAGE:3878765).
BC007198 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone MGC:12548 IMAGE:2961456), complete cds.
BC017438 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone MGC:12952 IMAGE:2960352), complete cds.
BC006555 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone IMAGE:2821394), partial cds.
AL833818 - Homo sapiens mRNA; cDNA DKFZp434P194 (from clone DKFZp434P194).
AF289557 - Homo sapiens clone pp5382 unknown mRNA.
JD022075 - Sequence 3099 from Patent EP1572962.
JD029490 - Sequence 10514 from Patent EP1572962.
BC009285 - Homo sapiens chromosome 11 open reading frame2, mRNA (cDNA clone IMAGE:4299190), partial cds.
JD119612 - Sequence 100636 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UID3 (Reactome details) participates in the following event(s):

R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6814674 Tethering of late endosome-derived vesicles by GARP, STX10:ST16:VTI1A and Golgins
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ANG2, C11orf2, C11orf3, ENST00000279281.1, ENST00000279281.2, ENST00000279281.3, ENST00000279281.4, ENST00000279281.5, ENST00000279281.6, ENST00000279281.7, FFR, NR_073519, PP5382, Q6PJV5, Q7L8A6, Q8WZ35, Q96DF4, Q96GR3, Q9UID3, uc001ocr.1, uc001ocr.2, uc001ocr.3, uc001ocr.4, VPS51_HUMAN
UCSC ID: ENST00000279281.8
RefSeq Accession: NM_013265
Protein: Q9UID3 (aka VPS51_HUMAN)
CCDS: CCDS8093.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.