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UCA1 Gene

RNA gene   GIFtS: 31
GCID: GC19P015939

Urothelial Cancer Associated 1 (Non-Protein Coding)

  See UCA1-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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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 5

Aliases
Urothelial Cancer Associated 1 (Non-Protein Coding)1 2     UCAT12
Cancer Up-Regulated Drug Resistant1     GCAP25
Long Intergenic Non-Protein Coding RNA 1781     GUCA1B5
CUDR2     GUCA25
LINC001782     RP485
NCRNA001782     

External Ids:    HGNC: 371261   Entrez Gene: 6529952   Ensembl: ENSG000002140497   OMIM: 6022755   UniProtKB: Q2VCE54   
ORGUL members:    fRNAdb10:FR407590 FR006815      
H-InvDB12:HIT000017268    
NCBI13:AK092401 DQ343132    
NONCODE14:n377754 n376250 n376439 n376249 n343049    
RNAdb15:LIT3336    

Export aliases for UCA1 gene to outside databases

Previous GC identifers: GC19U900573 GC19P015511


(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 UCA1 Gene:
This gene represents a long non-coding RNA. It plays a regulatory role in bladder cancer cell proliferation.
Several genes can be regulated by this gene, and the most important one is the CREB (cAMP responsive element
binding protein) gene, which encodes a transcriptional factor and affects the oncogenesis. (provided by RefSeq,
Mar 2012)

GeneCards Summary for UCA1 Gene:
UCA1 (urothelial cancer associated 1 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with UCA1 include retinitis pigmentosa 48.



fRNAdb sequence ontologies for UCA1 - the ORGUL cluster for this gene includes several descriptions:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011295.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for UCA1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUCA1 promoter sequence
   Search Chromatin IP Primers for UCA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UCA1


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

Entrez Gene cytogenetic band: 19p13.12   Ensembl cytogenetic band:  19p13.12   HGNC cytogenetic band: 19p13.12

UCA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UCA1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P015939:  view genomic region     (about GC identifiers)

Start:
15,939,757 bp from pter      End:
15,947,130 bp from pter
Size:
7,374 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for UCA1

(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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/TrEMBL: Q2VCE5 (See protein sequence)
Recommended Name: UCA1 protein  
Size: 60 amino acids; 6544 Da


(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

ProtoNet protein and cluster: Q2VCE5


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:
   genOway: Develop your customized and physiologically relevant rodent model for UCA1

miRNA
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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
cytosol1
nucleus1

(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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1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for UCA1
    Visual Cycle in Retinal Rods


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for UCA1
Interactions:

    Search GeneGlobe Interaction Network for UCA1

(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
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Browse Tocris compounds for UCA1



(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 UCA1:

Urothelial cancer associated 1 (non-protein coding)
Hs.644234  [show with all ESTs]
Unigene Representative Sequence: NR_015379
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000397381(processed_transcript) ENST00000589333(processed_transcript) ENST00000600160(processed_transcript)
miRNA
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Additional mRNA sequence: 

AK024303.1 AK092401.1 BC005351.1 BC017567.1 BC022824.1 BC055082.1 BC070340.1 BC107722.1 
DQ249310.1 DQ343132.1 EU334869.1 GU357550.1 GU799561.1 GU799562.1 GU799563.1 GU799564.1 
GU799565.1 HQ833208.1 HQ833209.1 NR_015379.3 

6 DOTS entries:

DT.92042969  DT.100033619  DT.91689580  DT.100817224  DT.86853179  DT.95289769 

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 UCA1:RNAdb

UCA1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAATGGACAA
UCA1 Expression
About this image

UCA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

UCA1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.644234
    Custom PCR Arrays for UCA1
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UCA1

(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 UCA1 (if available)
TreeFam Gene Tree for UCA1 (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 UCA1 (see all 231)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1496634731,2
--15937993(+) CAGGTA/GCCAGG 1 -- us2k10--------
rs1454773391,2
C--15938261(+) ACACGC/TCATCT 1 -- us2k10--------
rs1859204291,2
--15938678(+) ATATAG/TTCTAT 1 -- us2k10--------
rs1395347221,2
--15938682(+) ATTCTA/GTCTTG 1 -- us2k10--------
rs1450971511,2
--15938770(+) CACACC/TTGTAA 1 -- us2k10--------
rs621060931,2
C--15938819(+) GAGCCC/TGGGAG 1 -- us2k14Minor allele frequency- T:0.05NA WA EA 360
rs1909418671,2
--15938865(+) ACTCTA/GTTATA 1 -- us2k10--------
rs1475917451,2
C--15938900(+) TCAAGC/GTGACA 1 -- us2k10--------
rs774019471,2
F--15938939(+) ATACCG/AGCAAG 1 -- us2k11Minor allele frequency- A:0.03WA 118
rs1840273561,2
--15939051(+) ACTGCA/GTTGTG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for UCA1 (15939757 - 15947130 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for UCA1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2671181CNV Deletion23128226
esv2718244CNV Deletion23290073
nsv833766CNV Loss17160897
nsv911139CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for UCA1

(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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OMIM gene information: 602275   
OMIM disorders: 613827  
1 disease for UCA1:    
About MalaCards
retinitis pigmentosa 48

1 disease from the University of Copenhagen DISEASES database for UCA1:
Urinary bladder cancer

Find genes that share disorders with UCA1           About GenesLikeMe

Human Genome Epidemiology (HuGE) Navigator: UCA1 (1 document)

Export disorders for UCA1 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 UCA1 gene, integrated from 10 sources (see all 13):
(articles sorted by number of sources associating them with UCA1)
    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. (World J. Gastroenterol. 2013)
  2. UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. (PubMed id 18501714)1, 3 Wang F....Chen W. (FEBS Lett. 2008)
  3. Induction of drug resistance and transformation in human cancer cells by the noncoding RNA CUDR. (PubMed id 17416635)1, 3 Tsang W.P....Kwok T.T. (RNA 2007)
  4. Long non-coding RNA UCA1a(CUDR) promotes proliferation and tumorigenesis of bladder cancer. (PubMed id 22576688)1 Wang Y....Li X. (Int. J. Oncol. 2012)
  5. Long non-coding RNA UCA1 regulated cell cycle distribution via CREB through PI3-K dependent pathway in bladder carcinoma cells. (PubMed id 22285928)1 Yang C....Chen W. (Gene 2012)
  6. Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes. (PubMed id 22118674)1 Altun M....Kessler B.M. (amp 2011)
  7. [Cellular localization and tissue expression pattern of UCA1, a non-coding RNA]. (PubMed id 20117985)1 Xie X.J....Chen W. (Nan Fang Yi Ke Da Xue Xue Bao 2010)
  8. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. (PubMed id 16914571)1 Wang X.S....Chen W.F. (Clin. Cancer Res. 2006)
  9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  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
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: 652995 HGNC: 37126 Ensembl:ENSG00000214049 euGenes: HUgn652995 ECgene: UCA1
H-InvDB: UCA1

(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 UCA1 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 UCA1 gene:
Search GeneIP for patents involving UCA1

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 genOway)
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