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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PFDN6 Gene

protein-coding   GIFtS: 56
GCID: GC06P033257

Prefoldin Subunit 6

(Previous names: HLA class II region expressed gene KE2, prefoldin 6)
(Previous symbol: HKE2)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Prefoldin Subunit 61 2     H2-KE22
HKE21 2 3     KE-22
HLA Class II Region Expressed Gene KE21 2     KE2 Protein2
PFD62 3     Protein Ke23
Prefoldin 61     

External Ids:    HGNC: 49261   Entrez Gene: 104712   Ensembl: ENSG000002042207   OMIM: 6056605   UniProtKB: O152123   

Export aliases for PFDN6 gene to outside databases

Previous GC identifers: GC06P033366 GC06P032999


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PFDN6 Gene:
PFDN6 is a subunit of the heteromeric prefoldin complex that chaperones nascent actin (see MIM 102560) and alpha-
and beta-tubulin (see MIM 602529 and MIM 191130, respectively) chains pending their transfer to the cytosolic
chaperonin containing TCP1 (MIM 186980) (CCT) complex (Hansen et al., 1999 (PubMed 10209023)).(supplied by OMIM,
Jul 2010)

GeneCards Summary for PFDN6 Gene: 
PFDN6 (prefoldin subunit 6) is a protein-coding gene. Diseases associated with PFDN6 include intrahepatic cholangiocarcinoma, and corneal dystrophy, and among its related super-pathways are Chaperonin-mediated protein folding and Formation of tubulin folding intermediates by CCT/TriC. GO annotations related to this gene include unfolded protein binding and chaperone binding.

UniProtKB/Swiss-Prot: PFD6_HUMAN, O15212
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

Gene Wiki entry for PFDN6 (Prefoldin subunit 6) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  NT_113891.2  NT_167245.1  NT_167247.1  NT_167248.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PFDN6 gene promoter:
         Sp1   p53   AP-1   ATF-2   Olf-1   HNF-4alpha2   CUTL1   SREBP-1a   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPFDN6 promoter sequence
   Search SABiosciences Chromatin IP Primers for PFDN6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PFDN6


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.32   HGNC cytogenetic band: 6p21.3

PFDN6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PFDN6 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P033257:  view genomic region     (about GC identifiers)

Start:
33,257,079 bp from pter      End:
33,266,178 bp from pter
Size:
9,100 bases      Orientation:
plus strand

4 alternative locations:
Chr6+,NT_167245 4,538,704-4,540,037      Chr6+,NT_167247 4,731,122-4,732,455      Chr6+,NT_167248 4,489,621-4,490,954     
Chr6+,NT_113891.2 4,701,192-4,702,525     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PFD6_HUMAN, O15212 (See protein sequence)
Recommended Name: Prefoldin subunit 6  
Size: 129 amino acids; 14583 Da
Subunit: Heterohexamer of two PFD-alpha type and four PFD-beta type subunits

Explore the universe of human proteins at neXtProt for PFDN6: NX_O15212

Explore proteomics data for PFDN6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O15212

  • PFDN6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PFDN6 Protein Expression
    REFSEQ proteins (4 alternative transcripts): 
    NP_001172110.1  NP_001252524.1  NP_001252525.1  NP_055075.1  

    ENSEMBL proteins: 
     ENSP00000378563   ENSP00000363734   ENSP00000363738   ENSP00000420135   ENSP00000363735  
    Reactome Protein details: O15212
    Human Recombinant Protein Products for PFDN6: 
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    Cloud-Clone Corp. Proteins for PFDN6 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016272prefoldin complex IDA9630229

    PFDN6 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR002777 PFD_beta-like
     IPR009053 Prefoldin

    Graphical View of Domain Structure for InterPro Entry O15212

    ProtoNet protein and cluster: O15212

    1 Blocks protein domain: IPB002777 Prefoldin-related KE2 protein

    UniProtKB/Swiss-Prot: PFD6_HUMAN, O15212
    Similarity: Belongs to the prefoldin subunit beta family


    PFDN6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PFD6_HUMAN, O15212
    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

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0051082unfolded protein binding NAS9630229
    GO:0051087chaperone binding IDA9630229
         
    PFDN6 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for PFDN6 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Chaperonin-mediated protein folding
    Chaperonin-mediated protein folding0.91
    Protein folding0.91
    2Formation of tubulin folding intermediates by CCT/TriC
    Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding0.74
    Prefoldin mediated transfer of substrate to CCT/TriC0.70
    3Asparagine N-linked glycosylation
    Metabolism of proteins0.35

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    5        Reactome Pathways for PFDN6
        Chaperonin-mediated protein folding
    Prefoldin mediated transfer of substrate to CCT/TriC
    Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
    Metabolism of proteins
    Protein folding



    PFDN6 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PFDN6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

    5/23 Interacting proteins for PFDN6 (O152122, 3 ENSP000003637344) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAP3K3Q997592, 3MINT-48383 I2D: score=2 
    PPP2CBP627143, ENSP000002211384I2D: score=2 STRING: ENSP00000221138
    PRPF4O431723, ENSP000003633134I2D: score=2 STRING: ENSP00000363313
    WRAP73Q9P2S53, ENSP000002707084I2D: score=2 STRING: ENSP00000270708
    RUVBL2Q9Y2303, ENSP000002214134I2D: score=1 STRING: ENSP00000221413
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006457protein folding TAS--
    GO:0044267cellular protein metabolic process TAS--
    GO:0051084'de novo' posttranslational protein folding TAS--
    GO:0051131chaperone-mediated protein complex assembly IDA9630229

    PFDN6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PFDN6 (PFD6)

    Search CenterWatch for drugs/clinical trials and news about PFDN6 / PFD6

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PFDN6 gene (4 alternative transcripts): 
    NM_001185181.2  NM_001265595.1  NM_001265596.1  NM_014260.3  

    Unigene Cluster for PFDN6:

    Prefoldin subunit 6
    Hs.446374  [show with all ESTs]
    Unigene Representative Sequence: BM912978
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000395131 ENST00000374606(uc003odt.1 uc010jup.1 uc021ywk.1)
    ENST00000395134 ENST00000374610 ENST00000491382 ENST00000463584 ENST00000374607

    miRNA
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    hsa-miR-22 hsa-miR-144 hsa-miR-558 hsa-miR-139-5p
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    Additional mRNA sequence: 

    AK312150.1 BC039033.1 BC059783.1 

    15 DOTS entries:

    DT.318123  DT.100780052  DT.100780055  DT.112317  DT.100822238  DT.100780054  DT.100805106  DT.92443803 
    DT.100780053  DT.95274858  DT.95340994  DT.121364794  DT.95376362  DT.100709336  DT.100789254 

    24/104 AceView cDNA sequences (see all 104):

    AI201243 BM818422 BM710321 BE795733 BM745352 NM_014260 BM782291 BM794052 
    BM834357 BE047705 BU734446 BC059783 BM759317 BM705176 BM792413 BX353804 
    CR609151 AI186734 BM013631 AI334094 BC039033 BE794658 BM671744 AI183913 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PFDN6 expression in normal human tissues (normalized intensities)      PFDN6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGGGGGGAG
    PFDN6 Expression
    About this image


    PFDN6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/2 selected tissues (see all 2) fully expand
     
     Ovary (Reproductive System)
             Primary Oocyte Primary Follicle
     
     Gonad
             Primary Oocyte Primary Follicle

    See PFDN6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PFDN6

    SOURCE GeneReport for Unigene cluster: Hs.446374
        SABiosciences Custom PCR Arrays for PFDN6
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PFDN6 gene from 8/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia H2-Ke21 , 5 H2-K region expressed gene 21, 5 90.29(n)1
    100(a)1
      17 (17.98 cM)5
    149761  NM_001185182.11  NP_001172111.11 
     339388215 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    77(a)
    73(a)
    many → 1
    many → 1
    GL344099.1(45445-48429)
    GL343733.1(236350-240581)
    zebrafish
    (Danio rerio)
    Actinopterygii pfdn61 prefoldin subunit 6 68.63(n)
    76.47(a)
      393485  NM_200513.1  NP_956807.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG77701 CG7770 53.16(n)
    48.28(a)
      40176  NM_140902.1  NP_649159.1 
    worm
    (Caenorhabditis elegans)
    Secernentea pfd-61 Protein PFD-6 51.79(n)
    42.15(a)
      172474  NM_059657.3  NP_492058.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YKE2(YLR200W)4 Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin less   --   12(549012-549356) 850897  NP_013301.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PFD61 prefoldin 6 51.52(n)
    45.45(a)
      839878  NM_102739.3  NP_174292.2 
    rice
    (Oryza sativa)
    Liliopsida Os02g02463001 hypothetical protein 50.57(n)
    42.24(a)
      4328867  NM_001052960.2  NP_001046425.2 


    ENSEMBL Gene Tree for PFDN6 (if available)
    TreeFam Gene Tree for PFDN6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PFDN6 gene
    1 SIMAP similar gene for PFDN6 using alignment to 3 protein entries:     PFD6_HUMAN (see all proteins):
    HKE2

    PFDN6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section
    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for PFDN6:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv830634CNV Loss17160897
    nsv830635CNV Loss17160897

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 605660    OMIM disorders: --

    6 diseases for PFDN6:    About MalaCards
    intrahepatic cholangiocarcinoma    corneal dystrophy    cholangiocarcinoma    systemic lupus erythematosus
    lupus erythematosus    gastric cancer


    PFDN6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PFDN6
    Human Genome Epidemiology (HuGE) Navigator: PFDN6 (2 documents)

    Export disorders for PFDN6 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PFDN6 gene, integrated from 9 sources (see all 35):
    (articles sorted by number of sources associating them with PFDN6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. TAPASIN, DAXX, RGL2, HKE2 and four new genes (BING 1, 3 to 5) form a dense cluster at the centromeric end of the MHC. (PubMed id 9545376)1, 2, 3 Herberg J.A.... Trowsdale J. (1998)
    2. Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. (PubMed id 9630229)1, 2, 3 Vainberg I.E....Cowan N.J. (1998)
    3. High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (2009)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Characterization of HKE2: an ancient antigen encoded in the major histocompatibility complex. (PubMed id 17257322)1, 9 Ostrov D.A....Iczkowski K.A. (2007)
    6. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PubMed id 23349634)1 Cloutier P.... Coulombe B. (2013)
    7. The functional interactome landscape of the human hist one deacetylase family. (PubMed id 23752268)1 Joshi P....Cristea I.M. (2013)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    9. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
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    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10471 HGNC: 4926 AceView: HKE2 Ensembl:ENSG00000204220 euGenes: HUgn10471
    ECgene: PFDN6 H-InvDB: PFDN6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PFDN6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PFDN6 gene:
    Search GeneIP for patents involving PFDN6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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