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PRKDC Gene

protein-coding   GIFtS: 72

GC08M048848
protein kinase, DNA-activated, catalytic polypeptide
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: HYRC, HYRC1)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
DNA-PKcs 1, 2, 3
DNAPK 1, 2
DNPK1 1, 2, 3, 5
EC 2.7.11.1 3
HYRC 2, 3
HYRC1 2, 3, 5
XRCC7 1, 2
p350 1, 2
p460 3
Descriptions
DNA-PK catalytic subunit 3
hyper-radiosensitivity of murine scid mutation,
complementing 1 2
protein kinase, DNA-activated, catalytic polypeptide 2
External Ids
HGNC: 94131
Entrez Gene: 55912
UniProtKB: P785273
Ensembl: ENSG000001210317
Search outside databases for aliases for PRKDC gene

Previous GC identifers: GC08P047830 GC08M048689 GC08M048408 GC08M048735

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

EntrezGene summary for PRKDC:
The PRKDC gene encodes the catalytic subunit of a nuclear DNA-dependent serine/threonine protein
kinase (DNA-PK). The second component is the autoimmune antigen Ku (MIM 152690), which is encoded
by the G22P1 gene on chromosome 22q. On its own, the catalytic subunit of DNA-PK is inactive and
relies on the G22P1 component to direct it to the DNA and trigger its kinase activity; PRKDC must
be bound to DNA to express its catalytic properties.[supplied by OMIM]

UniProtKB/Swiss-Prot: PRKDC_HUMAN, P78527
Function: Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage. Involved
in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J
recombination. Must be bound to DNA to express its catalytic properties. Promotes processing of
hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis
(DCLRE1C). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation
step. Required to protect and align broken ends of DNA. May also act as a scaffold protein to aid
the localization of DNA repair proteins to the site of damage. Found at the ends of chromosomes,
suggesting a further role in the maintenance of telomeric stability and the prevention of
chromosomal end fusion. Also involved in modulation of transcription. Recognizes the substrate
consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX, thereby
regulating DNA damage response mechanism. Phosphorylates DCLRE1C, c-Abl/ABL1, histone H1, HSPCA,
c-jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, SRF, XRCC1, XRCC1, XRCC4, XRCC5, XRCC6, WRN, c-myc/MYC
and RFA2. Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of
supercoiled DNA. Ability to phosphorylate TP53/p53 in the presence of supercoiled DNA is dependent
on C1D

Gene Wiki entry for PRKDC

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the PRKDC gene  

Entrez Gene cytogenetic band: 8q11   Ensembl cytogenetic band:  8q11.21   HGNC cytogenetic band: 8q11

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

GeneLoc gene densities for chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M048848:     (about GC identifiers)

Start:
48,848,222 bp from pter
End:
49,035,296 bp from pter
Size:
187,075 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000008.9  NT_008183.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: PRKDC_HUMAN, P78527 (See protein sequence)
Recommended Name: DNA-dependent protein kinase catalytic subunit  
Size: 4128 amino acids; 469089 Da
Subunit: DNA-PK is a heterotrimer of PRKDC and the Ku p70-p86 (XRCC6-XRCC5) dimer. Formation of
this complex may be promoted by interaction with ILF3. Associates with the DNA-bound Ku
heterodimer, but it can also bind to and be activated by free DNA. Interacts with
DNA-PKcs-interacting protein (KIP) with the region upstream the kinase domain. PRKDC alone also
interacts with and phosphorylates DCLRE1C, thereby activating the latent endonuclease activity of
this protein. Interacts with C1D
Subcellular location: Nucleus
Secondary accessions: P78528 Q13327 Q13337 Q14175 Q59H99 Q7Z611 Q96SE6 Q9UME3
Alternative splicing: 2 isoforms:  P78527-1   P78527-2   

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR. Autophosphorylated on Thr-2609, Thr-2638
    and Thr-2647. Thr-2609 is a DNA damage-inducible phosphorylation site (inducible with ionizing
    radiation, IR). Autophosphorylation induces a conformational change that leads to remodeling of
    the DNA-PK complex, requisite for efficient end processing and DNA repair1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001075109.1  NP_008835.5  


    ENSEMBL proteins: 
    ENSP00000313420 ENSP00000345182 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (DNA PKcs)
    Human Recombinant Proteins from Abnova (PRKDC)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    3 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    GO:0005654 nucleoplasm EXP12023295 12065431
    GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex IDA15194694
    About this table

    Antibodies for PRKDC: 
    Invitrogen Antibodies for PRKDC
    Millipore Mono- and Polyclonal Antibodies for the study of PRKDC
    Sigma-Aldrich Antibodies for PRKDC
    R&D Systems Antibodies for PRKDC (DNA-PKcs)
    Cell Signaling Technology (CST) Antibodies for PRKDC  (DNA-PK)
    Antibodies from Abcam (DNA PKcs), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (PRKDC)
    Novus Biologicals Antibodies for PRKDC

    Assays for PRKDC: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    5/7 InterPro domains/families (see all 7 ):
     IPR000357 HEAT
     IPR000403 PI3/4_kinase_cat
     IPR012582 NUC194
     IPR003151 PIK-rel_kinase_FAT
     IPR014009 PIK_FAT


       GeneDecks  PRKDC for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P78527

    ProtoNet protein and cluster: P78527

    4 Blocks protein families:
    IPB000357 HEAT repeat
    IPB000403 Phosphatidylinositol 3- and 4-kinase
    IPB003151 PIK-related kinase
    IPB012582 NUC194


    UniProtKB/Swiss-Prot: PRKDC_HUMAN, P78527
    Similarity: Belongs to the PI3/PI4-kinase family
    Similarity: Contains 1 FAT domain
    Similarity: Contains 1 FATC domain
    Similarity: Contains 2 HEAT repeats
    Similarity: Contains 1 PI3K/PI4K domain
    Similarity: Contains 3 TPR repeats

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (PRKDC)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PRKDC)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_006904

                  Applied Biosystems Silencer® siRNAs for PRKDC

                  Sigma-Aldrich siRNA and siRNA Panels for PRKDC  
                         Sigma-Aldrich shRNA Panels and shRNA for PRKDC  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006904
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006904
                                     untagged cDNA clone in CMV expression vector: NM_006904 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_006904

    UniProtKB/Swiss-Prot: PRKDC_HUMAN, P78527
    Function: Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage. Involved
    in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J
    recombination. Must be bound to DNA to express its catalytic properties. Promotes processing of
    hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis
    (DCLRE1C). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation
    step. Required to protect and align broken ends of DNA. May also act as a scaffold protein to aid
    the localization of DNA repair proteins to the site of damage. Found at the ends of chromosomes,
    suggesting a further role in the maintenance of telomeric stability and the prevention of
    chromosomal end fusion. Also involved in modulation of transcription. Recognizes the substrate
    consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX, thereby
    regulating DNA damage response mechanism. Phosphorylates DCLRE1C, c-Abl/ABL1, histone H1, HSPCA,
    c-jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, SRF, XRCC1, XRCC1, XRCC4, XRCC5, XRCC6, WRN, c-myc/MYC
    and RFA2. Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of
    supercoiled DNA. Ability to phosphorylate TP53/p53 in the presence of supercoiled DNA is dependent
    on C1D
    Catalytic activity: ATP + a protein = ADP + a phosphoprotein
    Enzyme regulation: Inhibited by wortmannin. Activity of the enzyme seems to be attenuated by
    autophosphorylation
    Enzyme Number (IUBMB): EC 2.7.11.1 

    Genatlas biochemistry entry for PRKDC:
    DNA dependent serine/threonine protein kinase catalytic subunit,dimerizing with Ku antigen (see
    KUP70 (CLU),KUP80),involved in DNA double-strand break repair by end joining (non homologous
    recombination) and V(D)J recombination,same as HYRC1

    15/18 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Prkdc) (see all 18 ):

    behavior/neurologicalcellularcraniofacialdigestive/alimentaryendocrine/exocrine gland
    hearing/vestibular/earhematopoietic systemhomeostasis/metabolismimmune systemlife span-post-weaning/aging
    liver/biliary systemnervous systemrenal/urinary systemreproductive systemskeleton

    5 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677 DNA binding IEA--
    GO:0004677 DNA-dependent protein kinase activity IDA15194694
    GO:0005515 protein binding IPI9442054
    GO:0005524 ATP binding IEA--
    GO:0016740 transferase activity IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    3 Invitrogen iPath™ Online BioAtlas - Pathways for PRKDC (Maps provided by GeneGo):
     Cdc25 regulation of cell cycle
     Caspases activation via nuclear import
     ATM-H2AX-NFBD1 DNA damage response

       GeneDecks  PRKDC for the pathways selected above  
    About GeneDecksing

    2 Millipore Pathways for PRKDC
     DNA damage DNA-damage-induced responses
     DNA damage NHEJ mechanisms of DSBs repair

       GeneDecks  PRKDC for the pathways selected above  
    About GeneDecksing

    4 Sigma-Aldrich "Your Favorite Gene" Pathways for  PRKDC  (Your Favorite Gene powered by Ingenuity) 
     p53 Signaling
     Estrogen Receptor Signaling
     Cell Cycle: G2/M DNA Damage Checkpoint Regulation
     Molecular Mechanisms of Cancer

       GeneDecks  PRKDC for the pathways selected above  
    About GeneDecksing

    2 Cell Signaling Technology (CST) Pathways for PRKDC: 
     Cell Cycle Control: G2/M DNA Damage Checkpoint
     Akt/PKB Signaling

       GeneDecks  PRKDC for the pathways selected above  
    About GeneDecksing

    2 Kegg Pathways  (Kegg details for PRKDC):
     hsa03450 Non-homologous end-joining
     hsa04110 Cell cycle

       GeneDecks  PRKDC for the pathways selected above  
    About GeneDecksing
     Gene Network CentralTM Interacting Genes and Proteins Network for  PRKDC 


    5/60 Interacting proteins for PRKDC (ENSP000003134203 P785271, 2) via UniProtKB, MINT, and/or STRING (see all 60 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PARP1P098742STRING (score=.886) MINT-4790124
    XRCC5P130102STRING (score=.999) MINT-4790124
    XRCC6P129562STRING (score=.999) MINT-4790124
    ZIC2O954092STRING (score=.763) MINT-6175887
    HOXB7P096291EBI-352053, EBI-1248457
    About this table

    5/6 Gene Ontology (GO) biological process terms (links to tree view) (see all 6 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006281 DNA repair IEA--
    GO:0006303 double-strand break repair via nonhomologous end joining IEA--
    GO:0006310 DNA recombination IEA--
    GO:0006464 protein modification process TAS7671312
    GO:0006974 response to DNA damage stimulus IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Sigma-Aldrich Small Molecules for PRKDC:
    Inhibitor

    Compounds for PRKDC available from Tocris Bioscience
    CompoundAction CAS number
    DMNBDNA-dependent protein kinase inhibitor[20357-25-9]
    PI 103 hydrochlorideInhibitor of PI 3-kinase, mTOR and DNA-PK[371935-74-9]
    NU 7026Selective DNA-dependent protein kinase inhibitor[154447-35-5]
    Compound 401Selective DNA-PK and mTOR inhibitor[168425-64-7]
    About this table


    5 Novoseek chemical compound relationships for PRKDC gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    p-350 85.90 16 7855601 (4), 7724535 (3), 8538653 (3)
    phosphatidylinositol 58.46 5 10500142 (1), 9808536 (1), 12695618 (1), 19071136 (1) (see all 5)
    threonine 53.37 2 9539023 (1), 17638905 (1)
    pkcs 51.53 3 19029686 (1), 17110150 (1), 16168844 (1)
    nitric oxide 0.00 2 10854324 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (PRKDC)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PRKDC)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_006904

                  Sigma-Aldrich siRNA and siRNA Panels for PRKDC  
                         Sigma-Aldrich shRNA Panels and shRNA for PRKDC  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001081640  NM_006904  

    REFSEQ mRNAs for PRKDC gene (2 alternative transcripts): 

    NM_001081640.1   NM_006904.6   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001081640  NM_006904  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006904
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006904
                                     untagged cDNA clone in CMV expression vector: NM_006904 

    Additional cDNA sequence: 

    AB208860.1 AK022387.1 AK296833.1 BC017494.1 BC024963.1 BC037968.1 CR607506.1 U34994.3 
    U35835.1 U47077.5 

    24 DOTS entries:

    DT.447515  DT.91810315  DT.100798110  DT.100798105  DT.91724527  DT.86840995  DT.207420  DT.118545 
    DT.91986268  DT.95155071  DT.95261648  DT.99952979  DT.120635215  DT.120635274  DT.40194022  DT.91863895 
    DT.91926822  DT.92024383  DT.95073263  DT.95155076  DT.97822103  DT.100662770  DT.121449421  DT.40132575 

    24/489 AceView cDNA sequences (see all 489 ):

    AL521287 CB111630 BP362147 AI435413 BQ072273 AI799494 BM747522 U47077 
    BM756081 CR607506 CB160397 BC024963 BQ223426 AV656425 CB850939 AA846794 
    AI810280 BQ687868 T35292 AW673866 BM665892 AI354543 AU125778 BG403059 

    highest scoring ESTs for PRKDC:

    U34994 U47077 AA936954 AV727617 BX955969 AA037793 AA055286 AA113343 AA258602 AA298049 

    Unigene Cluster for PRKDC:

    Protein kinase, DNA-activated, catalytic polypeptide
    Hs.491682  [show with all ESTs]
    Unigene Representative Sequence: NM_006904


    GeneLoc Exon Structure

    5/16 Alternative Splicing Database (ASD) splice patterns (SP) for PRKDC (see all 16 )

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38 ^ 39a · 39b ^ 40 ^ 41a · 41b ^ 42 ^ 43 ^ 44a · 44b ^
    SP1:                                                                                      -                 -                 -                                 
    SP2:                                                                                      -           -     -                 -                                 
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 45a · 45b
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            

    About this scheme

    ECgene alternative splicing isoforms for PRKDC

    2 Ensembl transcripts including schematic representations:
    ENST00000314191  ENST00000338368  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    PRKDC expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for PRKDC

    1 / 2 / 3

    9 probe-sets matching PRKDC gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    1250_at2, 3 U95-A 1 1.00 1.00 0.94 0.98 U47077 1.00 0.90 0.95 1

    2012_s_at2, 3 U95-A 2 1.00 0.81 0.95 0.86 U34994 1.00 0.90 0.95 1

    40129_at2, 3 U95-A 2 0.88 0.88 0.92 1.17 U47077 1.00 0.90 0.95 1

    208694_at2, 3 U133-A 1 1.00 1.00 -- -- U47077 1.00 0.90 0.95 1

    210543_s_at2, 3 U133-A 2 1.00 0.64 -- -- U34994 1.00 0.90 0.95 1

    215757_at*2, 3 U133-A 1 1.00 1.00 -- -- AK022387 0.40 1.00 0.76 1

    208694_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    210543_s_at2 U133Plus2 2 1.00 0.64 -- -- -- -- -- -- --

    215757_at*2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  PRKDC for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TGCAGTCCCT

    SOURCE GeneReport for Unigene cluster: Hs.491682

    Expression variation in blood from EXPOLDB for PRKDC

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for PRKDC gene from 5/9 species (see all 9 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    PRKDC1   -- protein kinase, DNA-activated, catalytic polypeptide 85.28(n)
    83.28(a)
    474176  NM_001006651.1  NP_001006652.1 
    chimpanzee
    (Pan troglodytes)
    PRKDC1   -- protein kinase, DNA-activated, catalytic polypeptide 99.61(n)
    99.54(a)
    464165  XM_001147162.1  XP_001147162.1 
    cow
    (Bos taurus)
    PRKDC1   -- protein kinase, DNA-activated, catalytic polypeptide 78.89(n)
    78.15(a)
    512740  XM_874222.2  XP_879315.2 
    rat
    (Rattus norvegicus)
    Prkdc1   -- protein kinase, DNA activated, catalytic polypeptide 80.91(n)
    78.49(a)
    360748  XM_341020.3  XP_341021.3 
    mouse
    (Mus musculus)
    Prkdc1, 5 16 (9.20 cM)5
    protein kinase, DNA activated, catalytic polypeptide1, 5 81.23(n)1
    79.37(a)1
    190901  NM_011159.21  NP_035289.21 
     AB0006295  AB0051505  (see all 90)
    About this table        Species with no ortholog for PRKDC

    ENSEMBL Gene Tree for PRKDC
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for PRKDC gene
    ENSG000002055362  ENSG000001807472  ENSG000002056852  ENSG000002055352  SLC7A5P12  ENSG000002051522  ENSG000001573412  LOC5951012  
    ENSG000002055342  ENSG000002056912  SMG12  MTOR2  ENSG000001857102  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/836 NCBI SNPs in PRKDC are shown (see all 836 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 244)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 8 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    --
    rs81780901,2
    C,F,H48965501(-) CTTTGG/TCACTG 2 G/V mis1 ese35Minor allele frequency- T:0.01NS EU EA WA 580
    --
    rs81782711,2
    C,F,H48848652(-) CTTTAT/CTTAGG 2 -- ut318Minor allele frequency- C:0.03NS EU EA WA NA 738
    rs81780701,2
    C,F,H48977739(-) CCCCAA/GTGCTT 2 N/S mis1 ese315Minor allele frequency- G:0.03NS EU EA WA 1678
    rs81780331,2
    C,F,H49005863(-) CCCAAC/GTTCAG 2 T/S mis118Minor allele frequency- G:0.03NS EU EA WA NA 1814
    rs81782161,2
    C,F,H48882397(-) CTCTTC/TCAGAA 2 P/S mis1 ese3 trp39Minor allele frequency- T:0.00NS EU EA WA 1008
    rs78307431,2
    C,F,H48873508(+) AATCAA/GTAACT 2 I/T mis123Minor allele frequency- G:0.18NS EU EA WA NA 1906
    rs81780401,2
    C,F,H49004978(-) AAAATA/GAAATA 2 I/M mis115Minor allele frequency- G:0.01NS EU EA WA 1662
    rs81780171,2
    C,F,H49014778(-) GAAATG/ACATAA 2 I/M mis1 ese315Minor allele frequency- A:0.02NS EU EA WA 1682
    rs42781571,2
    C,F,H48901858(-) TGCTCC/TGCCTG 2 R/C mis114Minor allele frequency- T:0.02NS EU EA WA NA 1400
    --
    rs81782281,2
    C,F,H48873433(-) TTCCAA/GTGAAG 2 N/S mis15Minor allele frequency- G:0.02NS EU EA WA 574
    About this table

    HapMap Linkage Disequilibrium images for PRKDC (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 600899

    7 Novoseek disease relationships for PRKDC gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    ataxia telangiectasia 78.16 19 19029686 (1), 15758953 (1), 18451257 (1), 18483401 (1) (see all 12)
    severe combined immunodeficiency 66.37 5 9205842 (1), 9539023 (1), 12695618 (1), 9380717 (1)
    glioma 30.87 2 19435898 (1), 18202016 (1)
    tumors 21.03 4 12670903 (1), 10629611 (1), 12377759 (1), 11096417 (1)
    cancer 18.87 3 16077955 (1), 17143500 (1), 19281848 (1)
    glioblastoma 18.56 1 10629611 (1)
    melanoma 0.00 2 16000590 (1), 15179184 (1)
    About this table

    1 PharmGKB disease relationship for PRKDC gene
    Disease PharmGKB Relations PubMed IDs for articles supporting these relationships
    Leukemia, Lymphocytic, Acute, L1FA  GN  12086872
    About this table

    Human Gene Mutation Database: PRKDC
    Genetic Association Database: PRKDC
    Human Genome Epidemiology Navigator: PRKDC (14 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

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

    10/303 PubMed articles for PRKDC gene (see all 303 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 5591 HGNC: 9413 AceView: PRKDC Ensembl:ENSG00000121031 euGenes: HUgn5591
    ECgene: PRKDC H-InvDB: PRKDC
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for PRKDC Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/prkdc/
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



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