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

TUG1 Gene

RNA gene   GIFtS: 27
GCID: GC22P031365

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)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 10

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

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

Export aliases for TUG1 gene to outside databases

Previous GC identifers: GC22P029692 GC22P014327


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

GeneCards Summary for TUG1 Gene: 
TUG1 (taurine upregulated 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.

(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_011520.12  
Regulatory elements:
   SABiosciences 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

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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
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,
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 TUG1

(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 TUG1

Search CenterWatch for drugs/clinical trials and news about 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,
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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 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(uc003ajf.1) ENST00000566220 ENST00000519077(uc003ajg.3 uc003ajh.3 uc003aji.3 uc003ajj.3)
ENST00000521091 ENST00000569149 ENST00000563812 ENST00000602393 ENST00000602971
ENST00000569384
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Additional mRNA sequence: 

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

24/26 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 

24/707 AceView cDNA sequences (see all 707):

AK000625 AW058130 F00396 AL120860 AW189645 N57809 AI872122 AI190196 
AI682014 BM699745 N42704 W95447 AA554572 AU119025 AA770549 CK903894 
AI124515 AI356083 AI130971 AA166764 AA961989 BE348284 AW015493 BG656091 

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™, 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

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


Genevestigator expression for TUG1

SOURCE GeneReport for Unigene cluster: Hs.554829
    SABiosciences Custom PCR Arrays for TUG1
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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)
About This Section

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)
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

10/222 SNPs in TUG1 are shown (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

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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
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)
About This Section

PubMed articles for TUG1 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with TUG1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Analysis of long non-coding RNA expression profiles in gastric cancer. (PubMed id 23801869)1, 3 Cao W.J....Zhang Z.Y. (2013)
  2. Long intergenic non-coding RNA TUG1 is overexpressed i n urothelial carcinoma of the bladder. (PubMed id 22961206)1, 3 Han Y....Cai Z. (2012)
  3. 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. (2005)
  4. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. (PubMed id 22078878)1 Yang L....Rosenfeld M.G. (2011)
  5. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (2006)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
  7. Human follitropin receptor (FSHR) interacts with the adapter protein 14-3-3tau. (PubMed id 15196694)1 Cohen B.D....Dias J.A. (2004)
  8. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (2004)
  9. 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)
  10. Identification of genes differentially expressed in B16 murine melanoma sublines with different metastatic potentials. (PubMed id 8631027)1 Ishiguro T....Tsuruo T. (1996)

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

(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 TUG1 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 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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