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TPTEP1 Gene

pseudogene   GIFtS: 24
GCID: GC22P017085

Transmembrane Phosphatase With Tensin Homology Pseudogene...

  Search for TPTEP1
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(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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Aliases
Transmembrane Phosphatase With Tensin Homology Pseudogene 11 2
psiTPTE222

External Ids:    HGNC: 436481   Entrez Gene: 3875902   Ensembl: ENSG000001001817   

Export aliases for TPTEP1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TPTEP1 Gene:
TPTEP1 (transmembrane phosphatase with tensin homology pseudogene 1) is a pseudogene.


(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:
NC_000022.11  NC_018933.2  NT_187355.1  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TPTEP1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TPTEP1


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

Entrez Gene cytogenetic band: 22q11.1   Ensembl cytogenetic band:  22q11.1   HGNC cytogenetic band: 22q11.1

TPTEP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TPTEP1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P017085:  view genomic region     (about GC identifiers)

Start:
17,082,777 bp from pter      End:
17,179,632 bp from pter
Size:
96,856 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TPTEP1

(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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(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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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 TPTEP1
Interactions:

    Search GeneGlobe Interaction Network for TPTEP1

(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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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for TPTEP1



(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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Unigene Cluster for TPTEP1:

Transmembrane phosphatase with tensin homology pseudogene 1
Hs.474116  [show with all ESTs]
Unigene Representative Sequence: AK226145
12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000558085(lincRNA)(uc002zls.1) ENST00000592918(lincRNA) ENST00000400593(lincRNA)(uc010gqq.3 uc002zlq.4 uc002zlr.3)
ENST00000592107(lincRNA) ENST00000426585(lincRNA) ENST00000591299(lincRNA) ENST00000588548(lincRNA) ENST00000383140(lincRNA)(uc002zlt.3)
ENST00000585784(lincRNA) ENST00000588424(lincRNA) ENST00000415121(lincRNA) ENST00000545818(lincRNA)
miRNA
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Additional mRNA sequence: 

AK094889.1 AK095032.1 AK097082.1 AK226145.1 AY219889.1 BC017420.1 BC031001.1 BC107743.1 
EU541207.1 EU541208.1 EU541209.1 NR_001591.1 

11 DOTS entries:

DT.100008511  DT.100020732  DT.91906778  DT.101958699  DT.120643821  DT.120643847  DT.95134895  DT.120653465 
DT.75100643  DT.91687867  DT.91925641 

Selected AceView cDNA sequences (see all 62):

BX281888 AI216041 BG494066 R78133 BX101975 R78134 AK095032 BX106546 
AI554312 BX099128 AA307645 BQ220199 AK097082 NR_001591 AK001299 BC031001 
CB853117 AA427417 BC012110 AY219889 AW572313 BC017420 BQ019789 BP428452 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for TPTEP1 (see all 11)    About this scheme

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

ExUns: 19a · 19b · 19c ^ 20a · 20b ^ 21 ^ 22
SP1:                                          
SP2:                                          
SP3:                                          
SP4:                                          
SP5:                                          


ECgene alternative splicing isoforms for TPTEP1

(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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TPTEP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGTCTTTCCT
TPTEP1 Expression
About this image

TPTEP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.474116
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In Situ
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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 TPTEP1 (if available)
TreeFam Gene Tree for TPTEP1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 TPTEP1 (see all 1250)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1488889601,2
--17080830(+) GCATGA/TGAAAC 1 -- us2k10--------
rs72884051,2
C--17081040(+) GTAATC/TGCCAG 1 -- us2k13Minor allele frequency- T:0.18NA EA 242
rs1846365301,2
--17081267(+) CCAAGA/TAGAAG 1 -- us2k10--------
rs1116000051,2
C,F--17081329(+) CGCTGC/GAAAAG 1 -- us2k13Minor allele frequency- G:0.05CSA WA 122
rs1428597011,2
--17081569(+) TCATCA/GTCCAA 1 -- us2k10--------
rs1882532501,2
C--17081636(+) AGAAAG/TTGCAT 1 -- us2k10--------
rs1912616441,2
--17081706(+) GGCTTA/GGAAAT 1 -- us2k10--------
rs1126744741,2
C--17081763(+) AAGTGG/ATTGGG 1 -- us2k11Minor allele frequency- A:0.50NA 2
rs1850392951,2
--17082533(+) GAGAGC/TGAGCG 1 -- us2k10--------
rs1896050071,2
--17082713(+) AGACCC/TCGGAG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for TPTEP1 (17082777 - 17179632 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TPTEP1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing TPTEP1
DNA2.0 Custom Variant and Variant Library Synthesis for TPTEP1

(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.)
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(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 TPTEP1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TPTEP1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The TPTE gene family: cellular expression, subcellular localization and alternative splicing. (PubMed id 14659893)1, 3 Tapparel C.... Antonarakis S.E. (Gene 2003)
  2. The novel human endogenous retrovirus-related gene, psiTPTE22-HERV, is silenced by DNA methylation in cancers. (PubMed id 20112338)1 Liang Q....Zheng S. (Int. J. Cancer 2010)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. 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)
  5. Members of the RTVL-H family of human endogenous retrovirus-like elements are expressed in placenta. (PubMed id 2551777)1 Johansen T.... Bjorklid E. (Gene 1989)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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, Kegg, and/or H-InvDB)
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Entrez Gene: 387590 HGNC: 43648 AceView: psiTPTE22 Ensembl:ENSG00000100181 euGenes: HUgn387590
ECgene: TPTEP1 H-InvDB: TPTEP1

(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 TPTEP1 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 TPTEP1 gene:
Search GeneIP for patents involving TPTEP1

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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