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

PFDN6 Gene

protein-coding   GIFtS: 53
GCID: GC06P033257

prefoldin subunit 6

(Previous names: HLA class II region expressed gene KE2, prefoldin 6 )
(Previous symbol: HKE2)
 Explore 6 diseases affiliated with
PFDN6 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for PFDN6    

Aliases
for PFDN6 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Prefoldin Subunit 61 2     HLA Class II Region Expressed Gene KE21 2
HKE21 2 3     Prefoldin 61
PFD61 2 3     KE2 Protein2
H2-KE21 2     Protein Ke23
KE-21 2     

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


Summaries
for PFDN6 gene

(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:
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)

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)


Genomic Views
for PFDN6 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  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 plasmid: PFDN6 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+,ALT_REF_LOCI_5 33,342,545-33,343,878      Chr6+,ALT_REF_LOCI_3 33,235,008-33,247,678      Chr6+,ALT_REF_LOCI_2 33,178,689-33,219,509     
Chr6+,ALT_REF_LOCI_6 33,185,925-33,223,138     

Proteins
for PFDN6 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O15212

    • PFDN6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    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: 
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    ProSpec Recombinant Protein for PFDN6
    Uscn 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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    Protein Domains /
    Families
    for PFDN6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PFDN6 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR002777 PFD_beta-like
     IPR009053 Prefoldin

    Graphical View of Domain Structure for InterPro Entry O15212

    ProtoNet protein and cluster: O15212

    1 Blocks protein family: IPB002777 Prefoldin-related KE2 protein

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


    Function
    for PFDN6 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

    miRNA
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    hsa-miR-22 hsa-miR-144 hsa-miR-558 hsa-miR-139-5p
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    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



    Pathways & Interactions
    for PFDN6 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Chaperonin-mediated protein folding
    		Chaperonin-mediated protein folding1.00
    		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 proteins0.15

    Pathway sources
    See GeneCards unified pathways
    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



    Drugs & Compounds
    for PFDN6 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
    Search CenterWatch for drugs/clinical trials and news about PFDN6 / PFD6 

    Transcripts
    for PFDN6 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, 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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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PFDN6
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    Additional cDNA 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):

    BE047705 BM834357 BM705176 NM_014260 BM759317 BX353804 BM792413 BU734446 
    BM710321 AI201243 BE795733 BC059783 BM745352 BM782291 BM818422 CR609151 
    BM794052 BI461421 AI144022 BM686351 BM671744 AI032773 BC039033 AW606562 

    GeneLoc Exon Structure


    Expression
    for PFDN6 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTGGGGGGAG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    PFDN6 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryPrimary FolliclePrimary OocyteFemale Gametocytes, Germ Cells
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

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

    SOURCE GeneReport for Unigene cluster: Hs.446374
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    In Situ
    Assay Products:     
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    Orthologs
    for PFDN6 gene

    (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 7/24 species (see all 24)    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 --
    --
    		 --
    		 77(a)
    77(a)
    		 many → 1
    many → 1
    		 GL343733.1(236350-240581)
    GL344099.1(45445-48429)
    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 
    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
    for PFDN6 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for PFDN6 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PFDN6
    DNA2.0 Custom Variant and Variant Library Synthesis for PFDN6

    Disorders / Diseases
    for PFDN6 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    PFDN6 for disorders           About GeneDecksing

    OMIM gene information: 605660    OMIM disorders: --

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

    Human Genome Epidemiology (HuGE) Navigator: PFDN6 (2 documents)

    Export disorders for PFDN6 gene to outside databases

    Publications
    for PFDN6 gene

    (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 30):
    (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. 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)
    4. Characterization of HKE2: an ancient antigen encoded in the major histocompatibility complex. (PubMed id 17257322)1, 9 Ostrov D.A....Iczkowski K.A. (2007)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. The global gene-expression profiles of U-937 human mac rophages treated with Tat peptide and Tat-FITC conjugate. (PubMed id 22632162)1 Lin C.W....Jan M.S. (2012)
    7. 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)
    8. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)

    External Searches for PFDN6 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing PFDN6 gene

    (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

    Other Databases showing PFDN6 gene

    (According to HUGE)
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    Specialized Databases showing PFDN6 gene

    (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

    Intellectual Property
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    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    		Patent Information for PFDN6 gene:
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