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

PFDN1 Gene

protein-coding   GIFtS: 56
GCID: GC05M139604

prefoldin subunit 1

(Previous name: prefoldin 1 )
 Explore 6 diseases affiliated with
PFDN1 via our new
 Human Malady Compendium 
Biological research products
for PFDN1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Prefoldin Subunit 11 2
PFD11 2 3
Prefoldin 11 2
PDF2

External Ids:    HGNC: 88661   Entrez Gene: 52012   Ensembl: ENSG000001130687   OMIM: 6048975   UniProtKB: O609253   

Export aliases for PFDN1 gene to outside databases

Previous GC identifers: GC05M139447 GC05M140207 GC05M139607 GC05M139653 GC05M134769


(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 PFDN1:
This gene encodes a member of the prefoldin beta 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. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PFD1_HUMAN, O60925
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 PFDN1


(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_000005.9  NC_018916.1  NT_029289.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PFDN1 gene promoter:
         ATF-2   LCR-F1   Evi-1   CREB   POU2F1   FOXO4   FOXJ2 (long isoform)   POU2F1a   deltaCREB   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPFDN1 promoter sequence
   Search SABiosciences Chromatin IP Primers for PFDN1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PFDN1


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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PFDN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PFDN1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M139604:  view genomic region     (about GC identifiers)

Start:
139,624,624 bp from pter      End:
139,682,706 bp from pter
Size:
58,083 bases      Orientation:
minus strand

(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: PFD1_HUMAN, O60925 (See protein sequence)
Recommended Name: Prefoldin subunit 1  
Size: 122 amino acids; 14210 Da
Subunit: Heterohexamer of two PFD-alpha type and four PFD-beta type subunits
Secondary accessions: B2RD02 Q53F95 Q96EX6

Explore the universe of human proteins at neXtProt for PFDN1: NX_O60925

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O60925

  • PFDN1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_002613.2  
    ENSEMBL proteins: 
     ENSP00000261813   ENSP00000426383   ENSP00000428707  
    Reactome Protein details: O60925
    Human Recombinant Protein Products: 
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    ProSpec Recombinant Protein for PFDN1
    Uscn Proteins for PFDN1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016272prefoldin complex IEA--


    PFDN1 for ontologies           About GeneDecksing



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

    PFDN1 for domains           About GeneDecksing

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

    Graphical View of Domain Structure for InterPro Entry O60925

    ProtoNet protein and cluster: O60925

    1 Blocks protein family: IPB002777 Prefoldin-related KE2 protein

    UniProtKB/Swiss-Prot: PFD1_HUMAN, O60925
    Similarity: Belongs to the prefoldin subunit beta family


    (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: PFD1_HUMAN, O60925
    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

         Genatlas biochemistry entry for PFDN1:
    prefoldin subunit 1,keratin homologous

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    hsa-miR-3065-5p
    SwitchGear 3'UTR luciferase reporter plasmidPFDN1 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity TAS8744932
    GO:0051082unfolded protein binding IEA--


    PFDN1 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for PFDN1:
     Decreased nuclei size in G2M  Increased cell death in breast  Synthetic lethal with Ras 

    Animal Models:
         8 MGI mutant phenotypes (inferred from 1 allele(MGI details for Pfdn1):
     behavior/neurological  cellular  growth/size  hematopoietic system  immune system 
     mortality/aging  nervous system  respiratory system 

    PFDN1 for phenotypes           About GeneDecksing


    (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 PFDN1
        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



    PFDN1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PFDN1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/90 Interacting proteins for PFDN1 (O609252, 3 ENSP000002618134) via UniProtKB, MINT, STRING, and/or I2D (see all 90)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GIT1Q9Y2X72, 3MINT-63198 MINT-8265853 I2D: score=5 
    IMMTQ168912, 3MINT-63192 MINT-8265897 I2D: score=5 
    RPLP1P053862, 3, ENSP000003460374MINT-63189 I2D: score=5 STRING: ENSP00000346037
    EIF3CQ996132, 3MINT-8265783 I2D: score=2 
    EIF3CLQ996132, 3MINT-8265783 I2D: score=2 
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-dependent TAS8744932
    GO:0006457protein folding TAS--
    GO:0007049cell cycle TAS8744932
    GO:0021537telencephalon development IEA--
    GO:0021549cerebellum development IEA--


    PFDN1 for ontologies           About GeneDecksing



    (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 PFDN1
    Search CenterWatch for drugs/clinical trials and news about PFDN1 / PFD1 

    (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 PFDN1 gene: 
    NM_002622.4  

    Unigene Cluster for PFDN1:

    Prefoldin subunit 1
    Hs.483564  [show with all ESTs]
    Unigene Representative Sequence: AK093558
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000261813(uc003lff.1) ENST00000514611 ENST00000510217 ENST00000512707
    ENST00000524074 ENST00000512925 ENST00000507185

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    hsa-miR-3065-5p
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    Inhib. RNA
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    Additional cDNA sequence: 

    AK093558.1 AK223394.1 AK315353.1 BC003620.1 BC006202.1 BC011869.2 Y17392.1 

    20 DOTS entries:

    DT.101974730  DT.100880577  DT.319565  DT.100880562  DT.92470190  DT.120860634  DT.120860658  DT.100880575 
    DT.95082069  DT.120867829  DT.100880580  DT.95334063  DT.100880581  DT.40129481  DT.92470195  DT.100880579 
    DT.120860629  DT.92470179  DT.95112501  DT.92004836 

    24/538 AceView cDNA sequences (see all 538):

    BM453017 CD369109 BQ440995 CR597655 BM759781 BM968723 BQ670938 AA310202 
    BQ045317 AW160381 AI262235 BP430122 BM768510 R17413 BQ646780 AW162003 
    AI016676 CR603344 BE393751 BU161515 BQ018957 AI021998 AI246208 BM856055 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PFDN1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b
    SP1:                          -               
    SP2:              -           -               
    SP3:                                          


    ECgene alternative splicing isoforms for PFDN1

    (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

    PFDN1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAGTAGACAG

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

    About this image
    See PFDN1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PFDN1

    SOURCE GeneReport for Unigene cluster: Hs.483564
        SABiosciences Expression via Pathway-Focused PCR Array including PFDN1: 
              Heat Shock Proteins & Chaperones in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PFDN1

    (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 PFDN1 gene from 9/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pfdn11 , 5 prefoldin 11, 5 91.26(n)1
    97.54(a)1
      18 (19.46 cM)5
    671991  NM_026027.31  NP_080303.11 
     364036795 
    chicken
    (Gallus gallus)
    Aves PFDN11 prefoldin subunit 1 80.87(n)
    93.44(a)
      416142  XM_414472.3  XP_414472.3 
    lizard
    (Anolis carolinensis)
    Reptilia PFDN16
    --
    93(a)
    1 ↔ 1
    4(78192468-78234847)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.114722 Xenopus laevis transcribed sequence with moderate similarity more 78.44(n)    BX844357.1 
    zebrafish
    (Danio rerio)
    Actinopterygii pfdn11 prefoldin subunit 1 73.5(n)
    77.87(a)
      503766  NM_001013344.1  NP_001013362.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG139936
    --
    34(a)
    1 ↔ 1
    2L(6069079-6069838)
    worm
    (Caenorhabditis elegans)
    Secernentea pfd-16
    Probable prefoldin subunit 1
    32(a)
    1 ↔ 1
    IV(11149833-11150911)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PFD16
    prefoldin 1
    31(a)
    1 ↔ 1
    2(3045559-3046744)
    rice
    (Oryza sativa)
    Liliopsida --
    prefoldin subunit, putative, expressed
    34(a)
    1 ↔ 1
    2(15518249-15522294)


    ENSEMBL Gene Tree for PFDN1 (if available)
    TreeFam Gene Tree for PFDN1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PFDN1 gene

    PFDN1 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for PFDN1
    PGOHUM00000237941 PGOHUM00000245856


    (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

    10/857 NCBI SNPs in PFDN1 are shown (see all 857    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1421571841,2
    --139624188(+) CCCCAC/GCTCGT 1 -- ds50010--------
    rs790270061,2
    F,--139624258(+) AGTCCG/AATTTT 1 -- ds50011Minor allele frequency- A:0.06WA 118
    rs1167483931,2
    C,--139624378(+) TTTACC/TGGTGC 1 -- ds50010--------
    rs2001979601,2
    --139624387(+) CTCTC-/TTTTAA 1 -- ds50010--------
    rs68989381,2
    H--139624439(+) tatttC/Ttgatg 1 -- ds50014Minor allele frequency- T:0.00NS EA 418
    rs49127071,2
    C,F,H,--139624461(+) ATTTCT/CGTGGT 1 -- ds500121Minor allele frequency- C:0.26NS EA NA WA CSA 2236
    rs1122908231,2
    C,--139624471(+) TGTACG/ATGTTC 1 -- ds50012Minor allele frequency- A:0.05WA 120
    rs1397179771,2
    --139624526(+) GACTGA/GAGCTG 1 -- ds50010--------
    rs1453021501,2
    --139624615(+) TCAGTG/TCACAG 1 -- ds50010--------
    rs1476521311,2
    --139624625(+) GATAGA/CGCACA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for PFDN1 (139624624 - 139682706 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for PFDN1: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PFDN1
    DNA2.0 Custom Variant and Variant Library Synthesis for PFDN1

    (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

    PFDN1 for disorders           About GeneDecksing

    OMIM gene information: 604897    OMIM disorders: --

    6 diseases for PFDN1:    About MalaCards
    limb-girdle muscular dystrophy    muscular dystrophy    acute myeloid leukemia    myeloid leukemia
    hermaphroditism    leukemia


    Export disorders for PFDN1 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 PFDN1 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with PFDN1)
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    1. Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. (PubMed id 9630229)1, 2, 3 Vainberg I.E....Cowan N.J. (1998)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Expression, cellular distribution and protein binding of the glioma amplified sequence (GAS41), a highly conserved putative transcription factor. (PubMed id 11521196)1, 9 Munnia A.... Meese E. (2001)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. 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)
    7. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5201 HGNC: 8866 AceView: PFDN1 Ensembl:ENSG00000113068 euGenes: HUgn5201
    ECgene: PFDN1 H-InvDB: PFDN1

    (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 PFDN1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PFDN1 gene:
    Search GeneIP for patents involving PFDN1

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