Human Gene VPS18 (ENST00000220509.10_4) from GENCODE V47lift37
  Description: VPS18 core subunit of CORVET and HOPS complexes (from RefSeq NM_020857.3)
Gencode Transcript: ENST00000220509.10_4
Gencode Gene: ENSG00000104142.11_7
Transcript (Including UTRs)
   Position: hg19 chr15:41,186,648-41,196,173 Size: 9,526 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr15:41,186,967-41,195,539 Size: 8,573 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:41,186,648-41,196,173)mRNA (may differ from genome)Protein (973 aa)
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-  Comments and Description Text from UniProtKB
  ID: VPS18_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 18 homolog; Short=hVPS18;
FUNCTION: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes.
SUBUNIT: Interacts with HOOK1 (By similarity). Part of a large heterooligomeric complex together with VPS11, VPS16 and VPS33A. Interacts with STX7.
INTERACTION: Q7L1V2:MON1B; NbExp=2; IntAct=EBI-1053363, EBI-2655311;
SUBCELLULAR LOCATION: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Note=Cytoplasmic, peripheral membrane protein associated with late endosomes/lysosomes.
TISSUE SPECIFICITY: Ubiquitous. Expression was highest in heart and low in lung.
SIMILARITY: Belongs to the VPS18 family.
SIMILARITY: Contains 1 clathrin repeat.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH01513.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Aberrant splice sites; Sequence=BAA95999.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  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: 10.85 RPKM in Spleen
Total median expression: 362.81 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -136.90319-0.429 Picture PostScript Text
3' UTR -236.40634-0.373 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
IPR000547 - Clathrin_H-chain/VPS_repeat
IPR007810 - Pep3_Vps18

Pfam Domains:
PF00637 - Region in Clathrin and VPS
PF05131 - Pep3/Vps18/deep orange family

SCOP Domains:
48371 - ARM repeat
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
69322 - Tricorn protease domain 2
57850 - RING/U-box
57889 - Cysteine-rich domain

ModBase Predicted Comparative 3D Structure on Q9P253
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
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 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein binding
GO:0019905 syntaxin binding
GO:0030674 protein binding, bridging
GO:0046872 metal ion binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006904 vesicle docking involved in exocytosis
GO:0006914 autophagy
GO:0007032 endosome organization
GO:0007040 lysosome organization
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0035542 regulation of SNARE complex assembly
GO:0046718 viral entry into host cell

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005776 autophagosome
GO:0005884 actin filament
GO:0016020 membrane
GO:0030123 AP-3 adaptor complex
GO:0030136 clathrin-coated vesicle
GO:0030897 HOPS complex
GO:0031410 cytoplasmic vesicle
GO:0031902 late endosome membrane
GO:0033263 CORVET complex


-  Descriptions from all associated GenBank mRNAs
  AL713725 - Homo sapiens mRNA; cDNA DKFZp762G147 (from clone DKFZp762G147).
AB040908 - Homo sapiens KIAA1475 mRNA for KIAA1475 protein.
AF308802 - Homo sapiens vacuolar protein sorting protein 18 (VPS18) mRNA, complete cds.
JD110035 - Sequence 91059 from Patent EP1572962.
BC001513 - Homo sapiens vacuolar protein sorting 18 homolog (S. cerevisiae), mRNA (cDNA clone MGC:2738 IMAGE:2822780), complete cds.
JD238512 - Sequence 219536 from Patent EP1572962.
JD253096 - Sequence 234120 from Patent EP1572962.
JD172537 - Sequence 153561 from Patent EP1572962.
DQ895998 - Synthetic construct Homo sapiens clone IMAGE:100010458; FLH189362.01L; RZPDo839E0564D vacuolar protein sorting protein 18 (VPS18) gene, encodes complete protein.
DQ892752 - Synthetic construct clone IMAGE:100005382; FLH189366.01X; RZPDo839E0574D vacuolar protein sorting protein 18 (VPS18) gene, encodes complete protein.
AB463338 - Synthetic construct DNA, clone: pF1KA1475, Homo sapiens VPS18 gene for vacuolar protein sorting 18 homolog, without stop codon, in Flexi system.
JD310448 - Sequence 291472 from Patent EP1572962.
JD440603 - Sequence 421627 from Patent EP1572962.
JD474794 - Sequence 455818 from Patent EP1572962.
JD474795 - Sequence 455819 from Patent EP1572962.
JD495710 - Sequence 476734 from Patent EP1572962.
JD478782 - Sequence 459806 from Patent EP1572962.
JD218217 - Sequence 199241 from Patent EP1572962.
JD479513 - Sequence 460537 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000220509.1, ENST00000220509.2, ENST00000220509.3, ENST00000220509.4, ENST00000220509.5, ENST00000220509.6, ENST00000220509.7, ENST00000220509.8, ENST00000220509.9, KIAA1475, NM_020857, Q8TCG0, Q96DI3, Q9H268, Q9P253, uc317cza.1, uc317cza.2, VPS18 , VPS18_HUMAN
UCSC ID: ENST00000220509.10_4
RefSeq Accession: NM_020857.3
Protein: Q9P253 (aka VPS18_HUMAN or VP18_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.