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UCA1 Gene

RNA gene GIFtS: 31
GCID: GC19P015939

Urothelial Cancer Associated 1 (Non-Protein Coding)

See UCA1-related disease
at

MalaCards

(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 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)
About This Section

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)
About This Section

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

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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, antibodies-online, and/or GeneTex,
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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 GenesLikeMe)
About This Section

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, Sets of similar genes according to GenesLikeMe)
About This Section

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
extracellular	2
cytosol	1
nucleus	1

About this image

(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 GenesLikeMe, 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, Sets of similar genes according to GenesLikeMe)
About This Section

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for UCA1

Visual Cycle in Retinal Rods

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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, Sets of similar genes according to GenesLikeMe)
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(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,
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About This Section

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)

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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 GenesLikeMe, 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)
About This Section

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

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

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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 UCA1 (if available)
TreeFam Gene Tree for UCA1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
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), 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)
About This Section

SNP ID	Valid	Clinical significance	Chr 19 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs149663473^1,2		--	15937993(+)	`CAGGTA/GCCAGG`	1	--	us2k¹		0	--	--	--	--
rs145477339^1,2	C	--	15938261(+)	`ACACGC/TCATCT`	1	--	us2k¹		0	--	--	--	--
rs185920429^1,2		--	15938678(+)	`ATATAG/TTCTAT`	1	--	us2k¹		0	--	--	--	--
rs139534722^1,2		--	15938682(+)	`ATTCTA/GTCTTG`	1	--	us2k¹		0	--	--	--	--
rs145097151^1,2		--	15938770(+)	`CACACC/TTGTAA`	1	--	us2k¹		0	--	--	--	--
rs62106093^1,2	C	--	15938819(+)	`GAGCCC/TGGGAG`	1	--	us2k¹		4		NA WA EA	360
rs190941867^1,2		--	15938865(+)	`ACTCTA/GTTATA`	1	--	us2k¹		0	--	--	--	--
rs147591745^1,2	C	--	15938900(+)	`TCAAGC/GTGACA`	1	--	us2k¹		0	--	--	--	--
rs77401947^1,2	F	--	15938939(+)	`ATACCG/AGCAAG`	1	--	us2k¹		1		WA	118
rs184027356^1,2		--	15939051(+)	`ACTGCA/GTTGTG`	1	--	us2k¹		0	--	--	--	--

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

Structural Variations
Database of Genomic Variants (DGV) 4 variations for UCA1: About this table

Variant ID	Type	Subtype	PubMed ID
esv2671181	CNV	Deletion	23128226
esv2718244	CNV	Deletion	23290073
nsv833766	CNV	Loss	17160897
nsv911139	CNV	Gain	21882294

Site Specific Mutation Identification with PCR Assays

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(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, Sets of similar genes according to GenesLikeMe)
About This Section

OMIM gene information: 602275
OMIM disorders: 613827
1 disease for UCA1:
About MalaCards

retinitis pigmentosa 48

1 inferred disease relationship 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)
About This Section

PubMed articles for UCA1 gene, integrated from 10 sources (see all 13):
(articles sorted by number of sources associating them with UCA1)

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)
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)
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)
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)
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)
Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes. (PubMed id 22118674)¹ Altun M....Kessler B.M. (amp 2011)
[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)
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)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)¹ Ota T.... Sugano S. (Nat. Genet. 2004)
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)
About This Section

		AND	OR
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: 652995	HGNC: 37126	Ensembl:ENSG00000214049	euGenes: HUgn652995	ECgene: UCA1
H-InvDB: UCA1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for UCA1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for UCA1 gene
(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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UCA1 Gene

Urothelial Cancer Associated 1 (Non-Protein Coding)

Aliases
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UCA1 Gene

Urothelial Cancer Associated 1 (Non-Protein Coding)

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Specialized Databases showing UCA1 gene

Intellectual Propertyfor UCA1 gene

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Aliases
for UCA1 gene

Summaries
for UCA1 gene

Genomic Views
for UCA1 gene

Proteins
for UCA1 gene

Domains /
Families
for UCA1 gene

Function
for UCA1 gene

Localization
for UCA1 gene

Pathways & Interactions
for UCA1 gene

Drugs & Compounds
for UCA1 gene

Transcripts
for UCA1 gene

Expression
for UCA1 gene

Orthologs
for UCA1 gene

Paralogs
for UCA1 gene

Genomic Variants
for UCA1 gene

Disorders / Diseases
for UCA1 gene

Publications
for UCA1 gene

Intellectual Property
for UCA1 gene

Products
for UCA1 gene