Human Gene PFDN5 (uc001scl.3)
  Description: Homo sapiens prefoldin subunit 5 (PFDN5), transcript variant 1, mRNA.
RefSeq Summary (NM_002624): This gene encodes a member of the prefoldin alpha subunit family. The encoded protein is one of six subunits of prefoldin, a molecular chaperone complex that binds and stabilizes newly synthesized polypeptides, thereby allowing them to fold correctly. The complex, consisting of two alpha and four beta subunits, forms a double beta barrel assembly with six protruding coiled-coils. The encoded protein may also repress the transcriptional activity of the proto-oncogene c-Myc. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:53,689,235-53,693,234 Size: 4,000 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr12:53,689,352-53,693,129 Size: 3,778 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:53,689,235-53,693,234)mRNA (may differ from genome)Protein (154 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PFD5_HUMAN
DESCRIPTION: RecName: Full=Prefoldin subunit 5; AltName: Full=C-Myc-binding protein Mm-1; AltName: Full=Myc modulator 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. Represses the transcriptional activity of MYC.
SUBUNIT: Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Binds to MYC; interacts with its N-terminal domain.
INTERACTION: Q9DUN1:vIRF-3 (xeno); NbExp=8; IntAct=EBI-357275, EBI-1647907;
SUBCELLULAR LOCATION: Isoform 1: Nucleus.
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm.
SUBCELLULAR LOCATION: Isoform 3: Nucleus.
TISSUE SPECIFICITY: Highly expressed in pancreas and skeletal muscle and moderately in other tissues.
SIMILARITY: Belongs to the prefoldin subunit alpha family.
SEQUENCE CAUTION: Sequence=BAA14006.1; 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


-  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: 347.94 RPKM in Ovary
Total median expression: 10780.59 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 -40.20117-0.344 Picture PostScript Text
3' UTR -29.40105-0.280 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
IPR011599 - PFD_alpha
IPR009053 - Prefoldin
IPR004127 - Prefoldin_subunit

Pfam Domains:
PF02996 - Prefoldin subunit
PF12998 - Inhibitor of growth proteins N-terminal histone-binding

SCOP Domains:
46579 - Prefoldin

ModBase Predicted Comparative 3D Structure on Q99471
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0051082 unfolded protein binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006457 protein folding
GO:0045892 negative regulation of transcription, DNA-templated
GO:0060041 retina development in camera-type eye
GO:0090090 negative regulation of canonical Wnt signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0016272 prefoldin complex


-  Descriptions from all associated GenBank mRNAs
  JD331208 - Sequence 312232 from Patent EP1572962.
BC003373 - Homo sapiens prefoldin subunit 5, mRNA (cDNA clone IMAGE:2900793).
JD555669 - Sequence 536693 from Patent EP1572962.
AK292623 - Homo sapiens cDNA FLJ76574 complete cds, highly similar to Homo sapiens prefoldin 5 (PFDN5), transcript variant 1, mRNA.
AK024094 - Homo sapiens cDNA FLJ14032 fis, clone HEMBA1004353, highly similar to C-MYC BINDING PROTEIN MM-1.
AB055803 - Homo sapiens mRNA for MM-1 alpha, complete cds.
AB055804 - Homo sapiens mRNA for MM-1 beta, complete cds.
BC062671 - Homo sapiens prefoldin subunit 5, mRNA (cDNA clone MGC:71907 IMAGE:6458093), complete cds.
AB055805 - Homo sapiens mRNA for MM-1 gamma, complete cds.
D89667 - Homo sapiens mRNA for c-myc binding protein, complete cds.
AB527693 - Synthetic construct DNA, clone: pF1KB6786, Homo sapiens PFDN5 gene for prefoldin subunit 5, without stop codon, in Flexi system.
CU687580 - Synthetic construct Homo sapiens gateway clone IMAGE:100023088 5' read PFDN5 mRNA.
KJ891785 - Synthetic construct Homo sapiens clone ccsbBroadEn_01179 PFDN5 gene, encodes complete protein.
BT007195 - Homo sapiens prefoldin 5 mRNA, complete cds.
JD027316 - Sequence 8340 from Patent EP1572962.
JD028057 - Sequence 9081 from Patent EP1572962.
DQ578846 - Homo sapiens piRNA piR-46958, complete sequence.
DQ582923 - Homo sapiens piRNA piR-50035, complete sequence.
JD426473 - Sequence 407497 from Patent EP1572962.
JD532975 - Sequence 513999 from Patent EP1572962.
JD396472 - Sequence 377496 from Patent EP1572962.
JD187523 - Sequence 168547 from Patent EP1572962.
JD196839 - Sequence 177863 from Patent EP1572962.
JD217780 - Sequence 198804 from Patent EP1572962.

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

Protein Q99471 (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: A8K9A8, MM1, NM_002624, NP_002615, PFD5, PFD5_HUMAN, Q54AA8, Q99471, Q9C083, Q9C084
UCSC ID: uc001scl.3
RefSeq Accession: NM_002624
Protein: Q99471 (aka PFD5_HUMAN)
CCDS: CCDS8853.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002624.3
exon count: 6CDS single in 3' UTR: no RNA size: 743
ORF size: 465CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1130.00frame shift in genome: no % Coverage: 92.46
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.