Human Gene VPS53 (ENST00000437048.7_12) from GENCODE V47lift37
  Description: VPS53 subunit of GARP complex, transcript variant 1 (from RefSeq NM_001128159.3)
Gencode Transcript: ENST00000437048.7_12
Gencode Gene: ENSG00000141252.21_19
Transcript (Including UTRs)
   Position: hg19 chr17:411,908-618,079 Size: 206,172 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr17:422,368-617,949 Size: 195,582 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:411,908-618,079)mRNA (may differ from genome)Protein (832 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPS53_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 53 homolog;
FUNCTION: May be involved in retrograde transport of early and late endosomes to the late Golgi. 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.
SUBUNIT: Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54.
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein.
SIMILARITY: Belongs to the VPS53 family.
SEQUENCE CAUTION: Sequence=AAL55842.1; Type=Frameshift; Positions=562;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VPS53
Diseases sorted by gene-association score: pontocerebellar hypoplasia, type 2e* (1650), cerebral atrophy (27), leukodystrophy, hypomyelinating, 6 (10)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.61 RPKM in Brain - Cerebellum
Total median expression: 183.41 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -64.20130-0.494 Picture PostScript Text
3' UTR -3631.7010460-0.347 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
IPR007234 - Vps53_N

Pfam Domains:
PF04100 - Vps53-like, N-terminal
PF10475 - Vacuolar-sorting protein 54, of GARP complex

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
90257 - Myosin rod fragments
57997 - Tropomyosin
58104 - Methyl-accepting chemotaxis protein (MCP) signaling domain

ModBase Predicted Comparative 3D Structure on Q5VIR6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

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

Biological Process:
GO:0007041 lysosomal transport
GO:0015031 protein transport
GO:0032456 endocytic recycling
GO:0042147 retrograde transport, endosome to Golgi

Cellular Component:
GO:0000938 GARP complex
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0032588 trans-Golgi network membrane
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome
GO:1990745 EARP complex


-  Descriptions from all associated GenBank mRNAs
  LF384769 - JP 2014500723-A/192272: Polycomb-Associated Non-Coding RNAs.
BC040223 - Homo sapiens vacuolar protein sorting 53 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:5180083), containing frame-shift errors.
AK091388 - Homo sapiens cDNA FLJ34069 fis, clone FCBBF3001924.
AX746953 - Sequence 478 from Patent EP1308459.
AF318335 - Homo sapiens pp13624 mRNA, complete cds.
EU021218 - Homo sapiens Vps53 long isoform mRNA, complete cds, alternatively spliced.
AK092532 - Homo sapiens cDNA FLJ35213 fis, clone PROST1000215, highly similar to Vacuolar protein sorting protein 53.
AX747587 - Sequence 1112 from Patent EP1308459.
AK001841 - Homo sapiens cDNA FLJ10979 fis, clone PLACE1001503.
AK290343 - Homo sapiens cDNA FLJ76086 complete cds.
AY444797 - Homo sapiens vacuolar sorting protein 53 long isoform (VPS53) mRNA, complete cds, alternatively spliced.
BC006116 - Homo sapiens vacuolar protein sorting 53 homolog (S. cerevisiae), mRNA (cDNA clone MGC:12993 IMAGE:3504453), complete cds.
EU434648 - Homo sapiens gastric cancer hepatocellular carcinoma suppressor 1 variant (HCCS1) mRNA, complete cds, alternatively spliced.
EU434649 - Homo sapiens gastric cancer hepatocellular carcinoma suppressor 1 variant (HCCS1) mRNA, complete cds, alternatively spliced.
EU434650 - Homo sapiens gastric cancer hepatocellular carcinoma suppressor 1 variant (HCCS1) mRNA, complete cds, alternatively spliced.
KJ899109 - Synthetic construct Homo sapiens clone ccsbBroadEn_08503 VPS53 gene, encodes complete protein.
AF246287 - Homo sapiens clone C63R unknown mRNA.
MA620346 - JP 2018138019-A/192272: Polycomb-Associated Non-Coding RNAs.
AK299543 - Homo sapiens cDNA FLJ61757 complete cds.
BC039432 - Homo sapiens cDNA clone IMAGE:5303499.
AK123107 - Homo sapiens cDNA FLJ41112 fis, clone BRACE1000239.
DQ579845 - Homo sapiens piRNA piR-47957, complete sequence.
DQ579529 - Homo sapiens piRNA piR-47641, complete sequence.
JD558332 - Sequence 539356 from Patent EP1572962.
JD564410 - Sequence 545434 from Patent EP1572962.
JD317581 - Sequence 298605 from Patent EP1572962.
JD319549 - Sequence 300573 from Patent EP1572962.
AK056323 - Homo sapiens cDNA FLJ31761 fis, clone NT2RI2007751.
JD447145 - Sequence 428169 from Patent EP1572962.
AK057942 - Homo sapiens cDNA FLJ25213 fis, clone REC08168.
JD208640 - Sequence 189664 from Patent EP1572962.
JD275671 - Sequence 256695 from Patent EP1572962.
JD378639 - Sequence 359663 from Patent EP1572962.
JD158814 - Sequence 139838 from Patent EP1572962.
JD105595 - Sequence 86619 from Patent EP1572962.
JD366284 - Sequence 347308 from Patent EP1572962.
JD534755 - Sequence 515779 from Patent EP1572962.
JD366283 - Sequence 347307 from Patent EP1572962.
JD292538 - Sequence 273562 from Patent EP1572962.
JD534754 - Sequence 515778 from Patent EP1572962.
JD155806 - Sequence 136830 from Patent EP1572962.
JD092086 - Sequence 73110 from Patent EP1572962.
JD059714 - Sequence 40738 from Patent EP1572962.
JD517385 - Sequence 498409 from Patent EP1572962.
JD149302 - Sequence 130326 from Patent EP1572962.
JD546631 - Sequence 527655 from Patent EP1572962.
JD232346 - Sequence 213370 from Patent EP1572962.
JD366272 - Sequence 347296 from Patent EP1572962.
JD185292 - Sequence 166316 from Patent EP1572962.
JD156874 - Sequence 137898 from Patent EP1572962.
JD221964 - Sequence 202988 from Patent EP1572962.
JD230017 - Sequence 211041 from Patent EP1572962.
JD260822 - Sequence 241846 from Patent EP1572962.
JD353528 - Sequence 334552 from Patent EP1572962.
JD546344 - Sequence 527368 from Patent EP1572962.
JD406685 - Sequence 387709 from Patent EP1572962.
JD461281 - Sequence 442305 from Patent EP1572962.
JD461282 - Sequence 442306 from Patent EP1572962.
JD523356 - Sequence 504380 from Patent EP1572962.
JD537884 - Sequence 518908 from Patent EP1572962.
JD558953 - Sequence 539977 from Patent EP1572962.
JD057129 - Sequence 38153 from Patent EP1572962.
JD100395 - Sequence 81419 from Patent EP1572962.
JD246671 - Sequence 227695 from Patent EP1572962.
JD084156 - Sequence 65180 from Patent EP1572962.
JD552962 - Sequence 533986 from Patent EP1572962.
JD499447 - Sequence 480471 from Patent EP1572962.
JD542686 - Sequence 523710 from Patent EP1572962.
JD246802 - Sequence 227826 from Patent EP1572962.
JD246804 - Sequence 227828 from Patent EP1572962.
JD144650 - Sequence 125674 from Patent EP1572962.
JD246800 - Sequence 227824 from Patent EP1572962.
AF085927 - Homo sapiens full length insert cDNA clone YR50A02.
DQ571669 - Homo sapiens piRNA piR-31781, complete sequence.
BC029560 - Homo sapiens vacuolar protein sorting 53 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4838620), complete cds.
KJ902801 - Synthetic construct Homo sapiens clone ccsbBroadEn_12195 VPS53 gene, encodes complete protein.
AK128440 - Homo sapiens cDNA FLJ46583 fis, clone THYMU3043482.
CU675257 - Synthetic construct Homo sapiens gateway clone IMAGE:100017766 5' read VPS53 mRNA.
LF209198 - JP 2014500723-A/16701: Polycomb-Associated Non-Coding RNAs.
JD409029 - Sequence 390053 from Patent EP1572962.
DL492189 - Novel nucleic acids.
MA444775 - JP 2018138019-A/16701: Polycomb-Associated Non-Coding RNAs.

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

Protein Q5VIR6 (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: A8K2S8, B3FH42, ENST00000437048.1, ENST00000437048.2, ENST00000437048.3, ENST00000437048.4, ENST00000437048.5, ENST00000437048.6, NM_001128159, PP13624, Q5VIR6, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25, uc320fka.1, uc320fka.2, VPS53_HUMAN
UCSC ID: ENST00000437048.7_12
RefSeq Accession: NM_001128159.3
Protein: Q5VIR6 (aka VPS53_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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