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PTENP1 Gene

pseudogene   GIFtS: 38
GCID: GC09M033665

Phosphatase And Tensin Homolog Pseudogene 1 (Functional)

(Previous name: phosphatase and tensin homolog pseudogene 1)
  See PTENP1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3.2

Aliases
Phosphatase And Tensin Homolog Pseudogene 1 (Functional)1 2     PTEN22
PTH22 4     PTENpg12
Phosphatase And Tensin Homolog Pseudogene 11     psiPTEN2
PTEN-rs2     

External Ids:    HGNC: 95891   Entrez Gene: 111912   Ensembl: ENSG000002379847   OMIM: 6135315   UniProtKB: O434604   
ORGUL members:    fRNAdb10:FR272101 FR299930 FR279969      
RNAdb15:EVF30331 EVF30326 EVF30328    

Export aliases for PTENP1 gene to outside databases

Previous GC identifers: GC09M033987 GC09M033844


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PTENP1 Gene:
The phosphatase and tensin homolog (PTEN) gene encodes a tumor suppressor that functions by negatively regulating
the AKT/PKB signaling pathway. A highly homologous processed pseudogene of PTEN is found on chromosome 9 and
regulates PTEN by both sense and antisense RNAs (Gene ID: 101243555). This long-noncoding RNA (lncRNA) acts as a
decoy for PTEN targeting microRNAs and also exerts a tumor suppressive activity. (provided by RefSeq, Apr 2013)

GeneCards Summary for PTENP1 Gene:
PTENP1 (phosphatase and tensin homolog pseudogene 1 (functional)) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with PTENP1 include cowden disease.

Gene Wiki entry for PTENP1 Gene

fRNAdb sequence ontology for PTENP1:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for PTENP1

(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008413.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the PTENP1 gene promoter:
         ISGF-3   Pbx1a   AP-1   FOXO3   Ik-3   Evi-1   FOXO3b   POU2F1   POU2F1a   FOXO3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPTENP1 promoter sequence
   Search Chromatin IP Primers for PTENP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PTENP1


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

Entrez Gene cytogenetic band: 9p21   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p13.3

PTENP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PTENP1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M033665:  view genomic region     (about GC identifiers)

Start:
33,673,502 bp from pter      End:
33,677,497 bp from pter
Size:
3,996 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for PTENP1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/TrEMBL: O43460 (See protein sequence)
Recommended Name: Phosphatase and tensin homolog 2  
Size: 403 amino acids; 47163 Da


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Selected InterPro protein domains (see all 6):
 IPR014019 Phosphatase_tensin-typ
 IPR016130 Tyr_Pase_AS
 IPR017361 Bifunc_PIno_P3_Pase/Pase_PTEN
 IPR000340 Dual-sp_phosphatase_cat-dom
 IPR014020 Tensin_phosphatase_C2-dom

Graphical View of Domain Structure for InterPro Entry O43460

ProtoNet protein and cluster: O43460

1 Blocks protein domain: IPB000340 Dual specificity protein phosphatase


Find genes that share domains with PTENP1           About GenesLikeMe


(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:
     Genatlas biochemistry entry for PTENP1:
phosphatase and tensin homolog 2,pseudogene 1,playing a role in small cell lung cancer tumorigenesis (see TSG9A)

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PTENP1
Interactions:

    Search GeneGlobe Interaction Network for PTENP1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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3 fRNAdb Secondary structures:


Unigene Cluster for PTENP1:

Phosphatase and tensin homolog pseudogene 1
Hs.493716  [show with all ESTs]
Unigene Representative Sequence: NR_023917
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000532280(uc003zth.4) ENST00000447117 ENST00000451527
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Additional mRNA sequence: 

AF017999.1 AF019083.1 AF023139.1 BC038293.2 NR_023917.1 

6 DOTS entries:

DT.418393  DT.91643032  DT.99934702  DT.97863861  DT.100768844  DT.91647834 

Selected AceView cDNA sequences (see all 41):

AF023139 CR593710 BM665711 AF017999 BM129589 BG204429 BG192634 AA009520 
BE157176 AV681754 BM711908 BI462416 BE157177 BX372630 BX374997 AF019083 
BC038293 BE552297 BE842255 BG196242 AW235340 BG186407 AI880365 BF055297 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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PTENP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TATCTGATAA
PTENP1 Expression
About this image


PTENP1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Blood (Hematopoietic System)
         Granulocytes Peripheral Blood
PTENP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.493716
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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)
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ENSEMBL Gene Tree for PTENP1 (if available)
TreeFam Gene Tree for PTENP1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for PTENP1 gene
4 SIMAP similar genes for PTENP1 using alignment to 1 protein entry:     O43460_HUMAN:
PTEN2    PTEN    TPTE2    TPTE

Find genes that share paralogs with PTENP1           About GenesLikeMe



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for PTENP1 (see all 126)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs8554641,2
C,A,H--33673025(+) gcacaC/Tgtatg 1 -- int11Minor allele frequency- T:0.50NA 2
rs1481928391,2
--33673036(+) TTTATC/TGTGGC 1 -- int10--------
rs78704641,2
C,F,A,H--33673108(+) aagaaG/Aatgtg 1 -- int13Minor allele frequency- A:0.40NA CSA 5
rs1908276911,2
--33673301(+) CGGGGA/GACATT 1 -- int10--------
rs1829801791,2
--33673312(+) GCACAA/CCGGGG 1 -- int10--------
rs70434961,2
C,F,H--33673319(+) ggggcC/Ttgtca 1 -- int12Minor allele frequency- T:0.16NA WA 120
rs1475324351,2
C--33673380(+) AATGAC/TGAGTT 1 -- int10--------
rs132934451,2
F--33673439(+) ctgcaT/Cgttgt 1 -- int12Minor allele frequency- C:0.25NA 4
rs132924791,2
F--33673440(+) tgcatG/Attgtg 1 -- int12Minor allele frequency- A:0.25NA 4
rs1830405251,2
--33673503(+) TAAATA/CTTTGT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for PTENP1 (33673502 - 33677497 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for PTENP1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv518977CNV Gain19592680
nsv893027CNV Gain21882294
nsv893026CNV Gain21882294
nsv471653CNV Gain15918152

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 613531OMIM information: 601728    
1 disease for PTENP1:    
About MalaCards
cowden disease


Find genes that share disorders with PTENP1           About GenesLikeMe

1 Novoseek inferred disease relationship for PTENP1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
tumors 30.1 2 9467947 (1), 10855797 (1)

Human Genome Epidemiology (HuGE) Navigator: PTENP1 (1 document)

Export disorders for PTENP1 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)
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PubMed articles for PTENP1 gene, integrated from 10 sources (see all 22):
(articles sorted by number of sources associating them with PTENP1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A highly conserved processed PTEN pseudogene is located on chromosome band 9p21. (PubMed id 9620558)1, 3, 9 Dahia P.L....Eng C. (Oncogene 1998)
  2. MMAC1/PTEN mutations in primary tumor specimens and tumor cell lines. (PubMed id 9393738)1, 3 Teng D.H....Steck P.A. (Cancer Res. 1997)
  3. Alterations of PTEN/MMAC1, a candidate tumor suppressor gene, and its homologue, PTH2, in small cell lung cancer cell lines. (PubMed id 9467947)1, 9 Kim S.K.... Mao L. (Oncogene 1998)
  4. Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. (PubMed id 10208437)1, 9 Fujii G.H....Bolen J.B. (Oncogene 1999)
  5. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. (PubMed id 23435381)1 Johnsson P....Morris K.V. (amp 2013)
  6. Phosphatase and tensin homolog (PTEN) pseudogene expression in endometrial cancer: a conserved regulatory mechanism important in tumorigenesis? (PubMed id 22005521)1 Ioffe Y.J....Goodfellow P.J. (Gynecol. Oncol. 2012)
  7. Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph. (PubMed id 21048031)1 Casabonne D....de Sanjose S. (Haematologica 2011)
  8. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. (PubMed id 20577206)1 Poliseno L....Pandolfi P.P. (Nature 2010)
  9. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. (PubMed id 16368877)1 Choy K.W....Pang C.P. (Physiol. Genomics 2006)
  10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
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, Kegg, and/or H-InvDB)
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Entrez Gene: 11191 HGNC: 9589 AceView: PTENP1 Ensembl:ENSG00000237984 euGenes: HUgn11191
ECgene: PTENP1 H-InvDB: PTENP1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for PTENP1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for PTENP1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for PTENP1 gene:
Search GeneIP for patents involving PTENP1

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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 Addgene plasmids for PTENP1
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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