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
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
Primer design for this transcript
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: Parkinson Disease , , .
[PubMed 0 ]
Comparative Toxicogenomics Database (CTD)
Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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
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.
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
Gene Model Information
category:
coding
nonsense-mediated-decay:
no
RNA accession:
NM_015303.3
exon count:
47 CDS single in 3' UTR:
no
RNA size:
5058
ORF size:
4281 CDS single in intron:
no
Alignment % ID:
99.98
txCdsPredict score:
8708.00 frame 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
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Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.