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TUG1 Gene

RNA gene   GIFtS: 27
GCID: GC22P031365

Taurine Up-Regulated 1 (Non-Protein Coding)

(Previous name: taurine upregulated 1 (non-protein coding))
  See related diseases
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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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 5.2

Aliases
Taurine Up-Regulated 1 (Non-Protein Coding)1 2     LINC000802
Long Intergenic Non-Protein Coding RNA 801     NCRNA000802
Non-Protein Coding RNA 801     TI-227H2
Taurine Upregulated 1 (Non-Protein Coding)1     

External Ids:    HGNC: 260661   Entrez Gene: 550002   Ensembl: ENSG000002533527   OMIM: 6149715   
ORGUL members:    fRNAdb10:FR323829 FR144446      
NONCODE14:n343050 n384135 n344466 n380562 n377360 see all 8    
Rfam:RF01891    
RNAdb15:LIT3426 EVF48228    

Export aliases for TUG1 gene to outside databases

Previous GC identifers: GC22P029692 GC22P014327


(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 TUG1 Gene:
TUG1 (taurine up-regulated 1 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with TUG1 include intrahepatic cholangiocarcinoma, and cholangiocarcinoma.

Gene Wiki entry for TUG1 Gene

fRNAdb sequence ontologies for TUG1 - the ORGUL cluster for this gene includes several descriptions:
Taurine upregulated gene 1 conserved region 3 - TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in retina and brain. It was first identified in a screen for genes upregulated by in developing retinal cells in response to taurine. It is required for the normal development of photoreceptors in the retina [1].
Taurine upregulated gene 1 conserved region 3 - TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in retina and brain. It was first identified in a screen for genes upregulated by in developing retinal cells in response to taurine. It is required for the normal development of photoreceptors in the retina [1].
mature_transcript - A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for TUG1

(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_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the TUG1 gene promoter:
         NF-1/L   NF-1   p53   Olf-1   Pax-2   Pax-2a   Nkx2-5   CP2   
         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 TUG1


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

Entrez Gene cytogenetic band: 22q12.2   Ensembl cytogenetic band:  22q12.2   HGNC cytogenetic band: 22q12.2

TUG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TUG1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P031365:  view genomic region     (about GC identifiers)

Start:
31,365,634 bp from pter      End:
31,375,381 bp from pter
Size:
9,748 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TUG1

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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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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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, 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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
nucleus2
cytosol1

(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 TUG1
Interactions:

    Search GeneGlobe Interaction Network for TUG1

(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 TUG1



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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1 fRNAdb Secondary structure:


Unigene Cluster for TUG1:

Taurine upregulated 1 (non-protein coding)
Hs.554829  [show with all ESTs]
Unigene Representative Sequence: NR_002323
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000540687(antisense) ENST00000566220(antisense) ENST00000519077(antisense) ENST00000521091(antisense) ENST00000569149(antisense)
ENST00000563812(antisense) ENST00000602393(antisense) ENST00000602971(antisense) ENST00000569384(antisense)
miRNA
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Additional mRNA sequence: 

AB073661.1 AK000625.1 AK000749.1 AK056480.1 AK057695.1 BC037986.1 CR456447.1 NR_002323.1 

Selected DOTS entries (see all 26):

DT.92055265  DT.100044805  DT.451540  DT.101983227  DT.100825373  DT.95154725  DT.92045755  DT.95129190 
DT.97784528  DT.100825371  DT.75101604  DT.92437763  DT.100825378  DT.95352250  DT.95183217  DT.95352089 
DT.100825376  DT.120656890  DT.100044808  DT.100671803  DT.120656919  DT.120656921  DT.91932775  DT.92056047 

Selected AceView cDNA sequences (see all 707):

BQ576280 AA074726 CR594262 AI989394 CA867396 BM705871 AI619772 BQ343188 
AI127759 AI143162 BM764486 W42709 BM142407 BG656091 AI985169 BQ631820 
BM975213 AI352231 AI384096 AW082208 CA440622 BQ926254 AA349127 BG572349 

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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Expression evidence for TUG1:RNAdb

TUG1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TUG1 Expression
About this image

TUG1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TUG1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.554829
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TUG1

(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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This gene was present in the common ancestor of human and mouse.

Orthologs for TUG1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tug15 taurine upregulated gene 1   --   11 (2.56 cM) 3639785 


ENSEMBL Gene Tree for TUG1 (if available)
TreeFam Gene Tree for TUG1 (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 TUG1 (see all 222)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs773641731,2
C,F--15286479(+) CCAGTG/AGGATA 1 -- us2k12Minor allele frequency- A:0.04NA 122
rs731567421,2
C,F--15286593(+) GAATTT/CGTGTG 1 -- us2k11Minor allele frequency- C:0.01EU 593
rs1897691731,2
--15286638(+) CTGCTA/GTAATT 1 -- us2k10--------
rs1928036141,2
--15286717(+) TGATAG/TCGATT 1 -- us2k10--------
rs1456539231,2
C--15286841(+) AAGTG-/TTTTTT 1 -- us2k10--------
rs1844402131,2
--15286859(+) CTTCTC/TAATGA 1 -- us2k10--------
rs1150631531,2
C,F--15286979(+) TGGTCC/TTGAAG 1 -- us2k11Minor allele frequency- T:0.04WA 118
rs1436776181,2
--15287041(+) CAGCC-/TTTTTT 1 -- us2k10--------
rs1464332181,2
--15287084(+) CAACGC/TGGAAA 1 -- us2k10--------
rs1171926041,2
F--15287203(+) ATGGCG/CCAAGT 1 -- us2k11Minor allele frequency- C:0.01EA 120

HapMap Linkage Disequilibrium report for TUG1 (31365634 - 31375381 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for TUG1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv9896CNV Gain18304495

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for TUG1

(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.)
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OMIM gene information: 614971    OMIM disorders: --

3 diseases for TUG1:    
About MalaCards
intrahepatic cholangiocarcinoma    cholangiocarcinoma    melanoma


TUG1 for disorders           About GeneDecksing

Genetic Association Database (GAD): TUG1

Export disorders for TUG1 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 TUG1 gene, integrated from 10 sources (see all 21):
(articles sorted by number of sources associating them with TUG1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Long intergenic non-coding RNA TUG1 is overexpressed in urothelial carcinoma of the bladder. (PubMed id 22961206)1, 3 Han Y....Cai Z. (J Surg Oncol 2013)
  2. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PubMed id 24381249)1, 3 Sauvageau M....Rinn J.L. (Elife 2013)
  3. Analysis of long non-coding RNA expression profiles in gastric cancer. (PubMed id 23801869)1, 3 Cao W.J....Zhang Z.Y. (World J. Gastroenterol. 2013)
  4. The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. (PubMed id 15797018)1, 3 Young T.L....Cepko C.L. (Curr. Biol. 2005)
  5. Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. (PubMed id 24393600)1 van Heesch S....Simonis M. (Genome Biol. 2014)
  6. Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells. (PubMed id 22487937)1 A9zgA1r E....Gezer U. (Clin. Exp. Med. 2013)
  7. Down-regulation of long non-coding RNA TUG1 inhibits osteosarcoma cell proliferation and promotes apoptosis. (PubMed id 23725133)1 Zhang Q....Yao J. (Asian Pac. J. Cancer Prev. 2013)
  8. WITHDRAWN: Down-regulation of long non-coding RNA TUG1 suppresses melanoma cell proliferation and induces apoptosis via up-regulating microRNA-9. (PubMed id 24055035)1 Liu Y....Zhang X. (Biochem. Biophys. Res. Commun. 2013)
  9. Long non-coding RNAs in Huntington's disease neurodegeneration. (PubMed id 22202438)1 Johnson R. (Neurobiol. Dis. 2012)
  10. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. (PubMed id 22078878)1 Yang L....Rosenfeld M.G. (Cell 2011)

(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: 55000 HGNC: 26066 AceView: FLJ20618 Ensembl:ENSG00000253352 euGenes: HUgn55000
ECgene: TUG1 H-InvDB: TUG1

(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 TUG1 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 TUG1 gene:
Search GeneIP for patents involving TUG1

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



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