Human Gene VPS8 (uc003fpb.1)
  Description: Homo sapiens vacuolar protein sorting 8 homolog (S. cerevisiae) (VPS8), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:184,529,931-184,770,402 Size: 240,472 Total Exon Count: 47 Strand: +
Coding Region
   Position: hg19 chr3:184,542,421-184,769,813 Size: 227,393 Coding Exon Count: 46 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:184,529,931-184,770,402)mRNA (may differ from genome)Protein (1426 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VPS8
CDC HuGE Published Literature: VPS8
Positive Disease Associations: Parkinson Disease
Related Studies:
  1. Parkinson Disease
    , , . [PubMed 0]

-  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: 10.10 RPKM in Pituitary
Total median expression: 290.25 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 -52.50171-0.307 Picture PostScript Text
3' UTR -196.72589-0.334 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
  Pfam Domains:
PF12816 - Golgi CORVET complex core vacuolar protein 8

SCOP Domains:
48371 - ARM repeat
63829 - Calcium-dependent phosphotriesterase
101898 - NHL repeat
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50978 - WD40 repeat-like
69322 - Tricorn protease domain 2
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q8N3P4-3
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
   Gene DetailsGene Details 
   Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  AK056661 - Homo sapiens cDNA FLJ32099 fis, clone OCBBF2001140, weakly similar to VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS8.
AK292423 - Homo sapiens cDNA FLJ78757 complete cds.
BX647915 - Homo sapiens mRNA; cDNA DKFZp686M17141 (from clone DKFZp686M17141).
BC140768 - Homo sapiens vacuolar protein sorting 8 homolog (S. cerevisiae), mRNA (cDNA clone MGC:176445 IMAGE:9021636), complete cds.
BC036005 - Homo sapiens cDNA clone IMAGE:4733107, partial cds.
AB384529 - Synthetic construct DNA, clone: pF1KA0804, Homo sapiens VPS8 gene for vacuolar protein sorting-associated protein 8 homolog, complete cds, without stop codon, in Flexi system.
AL833838 - Homo sapiens mRNA; cDNA DKFZp761L03121 (from clone DKFZp761L03121).
AB018347 - Homo sapiens mRNA for KIAA0804 protein, partial cds.
AK309244 - Homo sapiens cDNA, FLJ99285.
AK022945 - Homo sapiens cDNA FLJ12883 fis, clone NT2RP2003981, weakly similar to VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS8.
AK308728 - Homo sapiens cDNA, FLJ98769.
EF491783 - Homo sapiens clone VPS8 mRNA, partial sequence; alternatively spliced.
EF491808 - Homo sapiens clone VPS8 mRNA, partial sequence; alternatively spliced.
JD026029 - Sequence 7053 from Patent EP1572962.
BC001001 - Homo sapiens vacuolar protein sorting 8 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3048733), partial cds.
JD035086 - Sequence 16110 from Patent EP1572962.
JD159218 - Sequence 140242 from Patent EP1572962.
JD074811 - Sequence 55835 from Patent EP1572962.
JD201716 - Sequence 182740 from Patent EP1572962.
JD432337 - Sequence 413361 from Patent EP1572962.
JD387040 - Sequence 368064 from Patent EP1572962.
JD507222 - Sequence 488246 from Patent EP1572962.
JD435284 - Sequence 416308 from Patent EP1572962.
JD214358 - Sequence 195382 from Patent EP1572962.
JD347358 - Sequence 328382 from Patent EP1572962.
JD333886 - Sequence 314910 from Patent EP1572962.
JD537643 - Sequence 518667 from Patent EP1572962.
JD455550 - Sequence 436574 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0804, NM_015303, NP_056118, Q8N3P4-3
UCSC ID: uc003fpb.1
RefSeq Accession: NM_015303
Protein: Q8N3P4-3, splice isoform of Q8N3P4 CCDS: CCDS46971.1, CCDS46972.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015303.3
exon count: 47CDS single in 3' UTR: no RNA size: 5058
ORF size: 4281CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 8708.00frame shift in genome: no % Coverage: 99.66
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.