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

TPTEP1 Gene

pseudogene   GIFtS: 26
GCID: GC22P017085

Transmembrane Phosphatase With Tensin Homology Pseudogene...

  Search for TPTEP1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 8

Aliases
Transmembrane Phosphatase With Tensin Homology Pseudogene 11 2
psiTPTE222

External Ids:    HGNC: 436481   Entrez Gene: 3875902   Ensembl: ENSG000001001817   
ORGUL members:         
NONCODE14:n384068 n346264 n342261 n384071 n377323 see all 7      

Export aliases for TPTEP1 gene to outside databases


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

GeneCards Summary for TPTEP1 Gene: 
TPTEP1 (transmembrane phosphatase with tensin homology pseudogene 1) is a pseudogene, and is affiliated with the lncRNA class.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.2  NT_011519.10  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for TPTEP1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TPTEP1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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:
17,179,521 bp from pter
Size:
96,745 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TPTEP1

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


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

(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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TPTEP1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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
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Browse Tocris compounds for TPTEP1

Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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 

24/62 AceView cDNA sequences (see all 62):

AK095032 R78133 AI554312 AI216041 BX106546 R78134 BX101975 BX281888 
BG494066 AW572313 BF000009 AA633529 BG527679 BG333521 NR_001591 BU596236 
AI492518 BQ183004 BC012110 AK128443 BF195570 BX956068 R67329 BQ019789 

GeneLoc Exon Structure

5/11 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™, 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

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


Genevestigator expression for TPTEP1

SOURCE GeneReport for Unigene cluster: Hs.474116
    SABiosciences Custom PCR Arrays for TPTEP1
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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)
About This Section
  --

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)
About This Section
  --

(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) 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

10/1250 SNPs in TPTEP1 are shown (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 - 17179521 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TPTEP1: --
SABiosciences Cancer Mutation PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
  --

(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 TPTEP1 gene integrated from 9 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. (2003)
  2. The novel human endogenous retrovirus-related gene, p siTPTE22-HERV, is silenced by DNA methylation in cancers. (PubMed id 20112338)1 Liang Q....Zheng S. (2010)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (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. (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. (1989)

(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, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 387590 HGNC: 43648 AceView: psiTPTE22 Ensembl:ENSG00000100181 euGenes: HUgn387590
ECgene: TPTEP1 H-InvDB: TPTEP1

(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 TPTEP1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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