Human Gene VBP1 (ENST00000286428.7_5) from GENCODE V47lift37
  Description: VHL binding protein 1, transcript variant 1 (from RefSeq NM_003372.7)
Gencode Transcript: ENST00000286428.7_5
Gencode Gene: ENSG00000155959.12_8
Transcript (Including UTRs)
   Position: hg19 chrX:154,444,737-154,468,122 Size: 23,386 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:154,444,760-154,467,123 Size: 22,364 Coding Exon Count: 6 

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 (chrX:154,444,737-154,468,122)mRNA (may differ from genome)Protein (197 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PFD3_HUMAN
DESCRIPTION: RecName: Full=Prefoldin subunit 3; AltName: Full=HIBBJ46; AltName: Full=Von Hippel-Lindau-binding protein 1; Short=VBP-1; Short=VHL-binding protein 1;
FUNCTION: Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.
SUBUNIT: Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Binds to the C-terminal part of VHL.
INTERACTION: Q9Q2G4:ORF (xeno); NbExp=3; IntAct=EBI-357430, EBI-6248094;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=In complex with VHL can translocate to the nucleus.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the prefoldin subunit alpha family.
SEQUENCE CAUTION: Sequence=AAC23907.1; Type=Erroneous initiation;

-  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: VBP1
Diseases sorted by gene-association score: renal cell carcinoma (2)

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

+  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: 27.55 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 731.43 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 -2.2023-0.096 Picture PostScript Text
3' UTR -210.60999-0.211 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
IPR009053 - Prefoldin
IPR016655 - Prefoldin_su-3
IPR004127 - Prefoldin_subunit

Pfam Domains:
PF02996 - Prefoldin subunit

SCOP Domains:
46579 - Prefoldin

ModBase Predicted Comparative 3D Structure on P61758
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 orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0015631 tubulin binding

Biological Process:
GO:0006457 protein folding
GO:0007017 microtubule-based process
GO:0007021 tubulin complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005844 polysome
GO:0016272 prefoldin complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK301646 - Homo sapiens cDNA FLJ59776 complete cds, highly similar to Prefoldin subunit 3.
U96759 - Homo sapiens von Hippel-Lindau binding protein (VBP-1) mRNA, complete cds.
LF385332 - JP 2014500723-A/192835: Polycomb-Associated Non-Coding RNAs.
BC009570 - Homo sapiens cDNA clone IMAGE:4109149, containing frame-shift errors.
AK313420 - Homo sapiens cDNA, FLJ93958, Homo sapiens von Hippel-Lindau binding protein 1 (VBP1), mRNA.
BC046094 - Homo sapiens von Hippel-Lindau binding protein 1, mRNA (cDNA clone MGC:57501 IMAGE:6058145), complete cds.
Y17394 - Homo sapiens mRNA for prefoldin subunit 3.
BC040002 - Homo sapiens von Hippel-Lindau binding protein 1, mRNA (cDNA clone IMAGE:5786380), containing frame-shift errors.
CU692296 - Synthetic construct Homo sapiens gateway clone IMAGE:100021292 5' read VBP1 mRNA.
AB464347 - Synthetic construct DNA, clone: pF1KB7551, Homo sapiens VBP1 gene for von Hippel-Lindau binding protein 1, without stop codon, in Flexi system.
BT019604 - Homo sapiens von Hippel-Lindau binding protein 1 mRNA, complete cds.
KJ892368 - Synthetic construct Homo sapiens clone ccsbBroadEn_01762 VBP1 gene, encodes complete protein.
U56833 - Human VHL binding protein-1 (VBP-1) mRNA, partial cds.
CR541932 - Homo sapiens full open reading frame cDNA clone RZPDo834C0434D for gene VBP1, von Hippel-Lindau binding protein 1; complete cds, incl. stopcodon.
LF380996 - JP 2014500723-A/188499: Polycomb-Associated Non-Coding RNAs.
LF381001 - JP 2014500723-A/188504: Polycomb-Associated Non-Coding RNAs.
LF381002 - JP 2014500723-A/188505: Polycomb-Associated Non-Coding RNAs.
JD168369 - Sequence 149393 from Patent EP1572962.
JD240678 - Sequence 221702 from Patent EP1572962.
JD566661 - Sequence 547685 from Patent EP1572962.
LF381004 - JP 2014500723-A/188507: Polycomb-Associated Non-Coding RNAs.
JD548839 - Sequence 529863 from Patent EP1572962.
LF381005 - JP 2014500723-A/188508: Polycomb-Associated Non-Coding RNAs.
JD323883 - Sequence 304907 from Patent EP1572962.
JD491444 - Sequence 472468 from Patent EP1572962.
MA620909 - JP 2018138019-A/192835: Polycomb-Associated Non-Coding RNAs.
MA616573 - JP 2018138019-A/188499: Polycomb-Associated Non-Coding RNAs.
MA616578 - JP 2018138019-A/188504: Polycomb-Associated Non-Coding RNAs.
MA616579 - JP 2018138019-A/188505: Polycomb-Associated Non-Coding RNAs.
MA616581 - JP 2018138019-A/188507: Polycomb-Associated Non-Coding RNAs.
MA616582 - JP 2018138019-A/188508: Polycomb-Associated Non-Coding RNAs.

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

Protein P61758 (Reactome details) participates in the following event(s):

R-HSA-389980 unfolded actin/tubulin associates with prefoldin
R-HSA-389970 Actin/tubulin:prefoldin complex associates with CCT/TriC
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
R-HSA-390466 Chaperonin-mediated protein folding
R-HSA-391251 Protein folding
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8L5, B4DWR3, ENST00000286428.1, ENST00000286428.2, ENST00000286428.3, ENST00000286428.4, ENST00000286428.5, ENST00000286428.6, F5H2A7, NM_003372, O55228, P61758, PFD3_HUMAN, PFDN3, Q15765, Q5JT81, Q86X96, uc317kka.1, uc317kka.2
UCSC ID: ENST00000286428.7_5
RefSeq Accession: NM_003372.7
Protein: P61758 (aka PFD3_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.