 |
 | Services
| |
 |
Aliases & Descriptions for PNKP
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
|
| | | Descriptions |
|---|
| DNA 5'-kinase/3'-phosphatase 3 | | Homo sapiens polynucleotide kinase 3'-phosphatase (PNKP) 2 | | Polynucleotide kinase-3'-phosphatase 3 | | polynucleotide kinase 3' phosphatase 2 | | polynucleotide kinase 3'-phosphatase 2 | | polynucleotide kinase 3-prime-phosphatase 2 |
|
| | Search outside databases for aliases for PNKP genePrevious GC identifers: GC19M051022 GC19M050732 GC19M055040 |
Summaries for PNKP(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60Function: Catalyzes the phosphorylation of DNA at 5'-hydroxyl termini and can dephosphorylate its 3'-phosphate termini. Plays an important function in DNA repair following ionizing radiation or oxidative damageGene Wiki entry for PNKP |
Genomic Location for PNKP
(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 PNKP gene 
Entrez Gene cytogenetic band: 19q13.3-q13.4 Ensembl cytogenetic band: 19q13.33 HGNC cytogenetic band: 19q13.3-q13.4PNKP 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 19 GeneLoc Exon Structure GeneLoc location for GC19M055056:
(about GC identifiers)
Start:
|
55,056,273 bp from pter |
End:
|
55,062,630 bp from pter |
Size:
|
6,358 bases |
Orientation:
|
minus strand |
RefSeq DNA sequence:- NC_000019.8 NT_011109.15
| Proteins for PNKP
(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: PNKP_HUMAN, Q96T60 (See
protein sequence)Recommended Name: Bifunctional polynucleotide phosphatase/kinase Size: 521 amino acids; 57076 Da
Subcellular location: Nucleus
Sequence caution: Sequence=AAD47379.1; Type=Frameshift; Positions=Several;
PDB structure from and Proteopedia :2BRF (3D)
 2W3O (3D)
 
Secondary accessions: Q9P1V2 Q9UKU8 Q9UNF8 Q9UNI0Post-translational modifications:
Phosphorylated upon DNA damage, probably by ATM or ATR1
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_009185.2
ENSEMBL proteins: ENSP00000323511
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
2 Gene Ontology (GO) cellular component terms (links to tree view): About this table
Antibodies for PNKP: Assays for PNKP: | Protein
Domains/ Families for PNKP(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry Q96T60
ProtoNet protein and cluster: Q96T60 1 Blocks protein family: IPB013954 Polynucleotide kinase 3 phosphatase
UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60Similarity: In the N-terminal section; belongs to the DNA 3' phosphatase family | Gene Function for PNKP
(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
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_007254
Applied Biosystems Silencer® siRNAs for PNKP
Sigma-Aldrich siRNA for PNKP  Sigma-Aldrich shRNA Panels and shRNA for PNKP  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_007254                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_007254                                  untagged cDNA clones in CMV expression vector (see all 2): NM_007254 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_007254
UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60Function: Catalyzes the phosphorylation of DNA at 5'-hydroxyl termini and can dephosphorylate its 3'-phosphate termini. Plays an important function in DNA repair following ionizing radiation or oxidative damageCatalytic activity: A 3'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphateCatalytic activity: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNAGenatlas biochemistry entry for PNKP:polynucleotide kinase-3 phosphatase,facilitating DNA repair of DNA strand breaks caused by oxidative damage5/12 Gene Ontology (GO) molecular function terms (links to tree view) (see all 12
): About this table | Pathways & Interactions for PNKP
(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
|
Gene Network CentralTM Interacting Genes and Proteins Network for PNKP 
5/23 Interacting proteins for PNKP (Q96T601, 2 ENSP000003235113) via UniProtKB, MINT, and/or STRING (see all 23
)| Interactant | Interaction Details |
|---|
| GeneCard | External ID(s) |
|---|
| XRCC1 | P188871, ENSP000002628873 | EBI-1045072, EBI-947466 STRING (score=.999) | | LIG3 | P499161, ENSP000003677873 | EBI-1045072, EBI-1753381 STRING (score=.982) | | XRCC4 | Q134261, 2, ENSP000003420113 | EBI-1045072, EBI-717592 MINT-51171 MINT-51174 MINT-51172 MINT-51173 MINT-51175 EBI-1045072, EBI-717592 MINT-51171 MINT-51174 MINT-51172 MINT-51173 MINT-51175 STRING (score=.968) | | DDX20 | Q9UHI61 | EBI-1045072, EBI-347658 | | HEATR2 | Q86Y561 | EBI-1045072, EBI-719966 | About this table
5/8 Gene Ontology (GO) biological process terms (links to tree view) (see all 8
): About this table
|
Drugs & Compounds for PNKP(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 Tocris compounds for PNKP 4 Novoseek chemical compound relationships for PNKP gene
About this table
|
Transcripts for PNKP(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
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_007254
Sigma-Aldrich siRNA for PNKP  Sigma-Aldrich shRNA Panels and shRNA for PNKP  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_007254 REFSEQ mRNAs for PNKP gene: NM_007254.2
Applied Biosystems TaqMan ® Gene Expression Assays: NM_007254               OriGene GFP tagged cDNA clone in CMV expression vector: NM_007254                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_007254                                  untagged cDNA clones in CMV expression vector (see all 2): NM_007254  Additional cDNA sequence: AF120499.1 AF125807.1 AF126486.1 BC002519.2 BC009339.2 BC013034.2 BC033822.1 CR590331.1 CR594341.1 CR598028.1 CR599191.1 CR600664.1 CR605495.1 CR612354.1 CR615833.1 CR620645.1 CR621711.1 CR623076.1 CR624604.1 17 DOTS entries: DT.211706 DT.100789769 DT.121429426 DT.40275406 DT.100789766 DT.121429538 DT.121429380 DT.100789779 DT.100769341 DT.100789767 DT.100789780 DT.40202941 DT.95219672 DT.95219688 DT.121429373 DT.75102180 DT.95219695 24/205 AceView cDNA sequences (see all 205
):BC002519 CR600664 BC033822 CD671425 BM811617 BM664223 CR621711 BF507485 BC009339 BI761490 CR605495 NM_007254 BQ008966 CR612354 BQ002105 CR620645 AF125807 BM021163 BI820868 BE394572 BF037255 BU619715 BI821496 CR615833
highest scoring ESTs for PNKP:AF120499 AL042657 AL518253 AL525997 AL529487 AL530223 AL531398 AL555192 BC033822 BE260690 Unigene Cluster for PNKP: Polynucleotide kinase 3'-phosphatase Hs.78016 [show with all ESTs]Unigene Representative Sequence: BC013034
GeneLoc Exon Structure
5/9 Alternative Splicing Database (ASD) splice patterns (SP) for PNKP (see all 9
)
| ExUns: | 1 | ^ | 2a | · | 2b | · | 2c | ^ | 3a | · | 3b | ^ | 4a | · | 4b | · | 4c | · | 4d | ^ | 5a | · | 5b | ^ | 6 | ^ | 7 | ^ | 8a | · | 8b | ^ | 9a | · | 9b | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 | ^ | 15a | · | 15b | ^ | 16 | ^ | |
| SP1: | |   | |   | |   | |   | - |   | |   | - |   | - |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP2: | |   | |   | |   | |   | |   | |   | - |   | - |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | - |   | |   | |
| SP3: | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP4: | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP5: | |   | |   | |   | |   | |   | |   | - |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   |
| ExUns: | 17 | ^ | 18 | |
| SP1: | |   | |   | |
| SP2: | |   | |   | |
| SP3: | |   | |   | |
| SP4: | |   | |   | |
| SP5: | |   | |   |
About this scheme
ECgene alternative splicing isoforms for PNKP
1 Ensembl transcript including schematic representation: ENST00000322344
|
Expression for PNKP
(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
| PNKP expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for PNKP
1 / 2 / 3 3 probe-sets matching PNKP gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: TATGGCTACA
SOURCE GeneReport for Unigene cluster: Hs.78016 UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60Tissue specificity: Expressed in many tissues with highest expression in spleen and testis, and lowest expression in small intestine (PubMed:10446192). Expressed in higher amount in pancreas, heart and kidney and at lower levels in brain, lung and liver (PubMed:10446193) |
Orthologs for PNKP
(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 PNKP gene from 5/14 species (see all 14
)
About this table Species with no ortholog for PNKP
ENSEMBL Gene Tree for PNKP | Paralogs for PNKP(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| -- |
SNPs/Variants for PNKP(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for PNKP (up to first 250kb)
|
Disorders & Mutations for PNKP
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
|
OMIM: 605610
Human Genome Epidemiology Navigator: PNKP (1 document)
|
Medical News for PNKP(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for PNKP (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
| 10/48 PubMed articles for PNKP gene (see all 48
):- Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage. (PubMed id 10446192)1, 2, 3, 4 Jilani A....Lasko D.D. (1999)
- Molecular characterization of a human DNA kinase. (PubMed id 10446193)2, 3, 4 Karimi-Busheri F....Weinfeld M. (1999)
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)3, 4 Olsen J.V....Mann M. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)3, 4 Gerhard D.S....Malek J. (2004)
- The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)3, 4 Grimwood J.... Lucas S.M. (2004)
- Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK. (PubMed id 19155274)1, 3 Ali A.A....Oliver A.W. (2009)
- AP endonuclease-independent DNA base excision repair in human cells. (PubMed id 15260972)1, 3 Wiederhold L....Hazra T.K. (2004)
- Polynucleotide kinase 3' phosphatase variant, dietary variables and risk of adenoma recurrence in the Polyp Prevention Trial. (PubMed id 18414202)1, 3 Murphy G....Lanza E. (2008)
- Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV. (PubMed id 15385968)1, 3 Koch C.A....Durocher D. (2004)
- XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. (PubMed id 11163244)1, 3 Whitehouse C.J.... Caldecott K.W. (2001)
|
Search for PNKP
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing PNKP
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing PNKP
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PNKP(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
|
| About This Section
| --
| Services for PNKP(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
| 
 Products for PNKP:

 | |
 | | | | |
|
 |  |  |
| Antibodies & Assays for PNKP  (PNK1) |
| | Recombinant Proteins (PNK) | | Antibodies (PNK) |
| | | Search Tocris compounds for PNKP |
|
 |
 | | | |
GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
|