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

UPK3B Gene

protein-coding   GIFtS: 45
GCID: GC07P076139

Uroplakin 3B

  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

Aliases
Uroplakin 3B1 2     uroplakin-3b2
Uroplakin IIIb1 2 3     UP3b3
P352 5     UPIIIb3
UPIIIB2 5     p353
UP3B2     

External Ids:    HGNC: 214441   Entrez Gene: 807612   Ensembl: ENSG000002435667   OMIM: 6118875   UniProtKB: Q9BT763   

Export aliases for UPK3B gene to outside databases

Previous GC identifers: GC07P074676 GC07P075738 GC07P075751 GC07P075784 GC07P075977 GC07P071187


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

Entrez Gene summary for UPK3B Gene:
UPK3B is a minor component of the apical plaques of mammalian urothelium that binds and dimerizes with
uroplakin-1b (UPK1B; MIM 602380), one of the major conserved urothelium membrane proteins. The other major
conserved integral membrane proteins of urothelial plaques are UPK1A (MIM 611557), UPK2 (MIM 611558), and UPK3A
(MIM 611559) (Deng et al., 2002 (PubMed 12446744)).(supplied by OMIM, Mar 2008)

GeneCards Summary for UPK3B Gene: 
UPK3B (uroplakin 3B) is a protein-coding gene. Diseases associated with UPK3B include williams-beuren syndrome, and retinitis pigmentosa. An important paralog of this gene is UPK3BL.

UniProtKB/Swiss-Prot: UPK3B_HUMAN, Q9BT76
Function: Component of the asymmetric unit membrane (AUM); a highly specialized biomembrane elaborated by
terminally differentiated urothelial cells. May play an important role in AUM-cytoskeleton interaction in
terminally differentiated urothelial cells. It also contributes to the formation of urothelial glycocalyx which
may play an important role in preventing bacterial adherence (By similarity)




(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_000007.13  NT_007933.15  NC_018918.2  NT_079595.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the UPK3B gene promoter:
         MZF-1   Spz1   AML1a   NRF-2   CP2   ARP-1   Pax-4a   LCR-F1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUPK3B promoter sequence
   Search SABiosciences Chromatin IP Primers for UPK3B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UPK3B


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

Entrez Gene cytogenetic band: 7q11.2   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11.2

UPK3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UPK3B gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P076139:  view genomic region     (about GC identifiers)

Start:
76,139,745 bp from pter      End:
76,648,340 bp from pter
Size:
508,596 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 75,472,809-75,490,263     

(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/Swiss-Prot: UPK3B_HUMAN, Q9BT76 (See protein sequence)
Recommended Name: Uroplakin-3b precursor  
Size: 320 amino acids; 33882 Da
Subunit: Heterodimer with uroplakin-1B (UPK1B)
Subcellular location: Cell membrane; Single-pass type I membrane protein (Potential). Note=Heterodimer formation
with UPK1B is a prerequisite to exit out of the endoplasmic reticulum (ER)
Sequence caution: Sequence=AAO89507.1; Type=Frameshift; Positions=210; Sequence=AAS07526.1; Type=Erroneous gene
model prediction;
Secondary accessions: A8K231 A8MZA8 B3KPU5 Q75MM5 Q86W06
Alternative splicing: 2 isoforms:  Q9BT76-1   Q9BT76-2   

Explore the universe of human proteins at neXtProt for UPK3B: NX_Q9BT76

Explore proteomics data for UPK3B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BT76

  • UPK3B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    UPK3B Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_085047.1  NP_872624.1  NP_872625.1  

    ENSEMBL proteins: 
     ENSP00000334938   ENSP00000257632   ENSP00000378319   ENSP00000441602   ENSP00000441284  
     ENSP00000444585  

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    Cloud-Clone Corp. Proteins for UPK3B 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--

    UPK3B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR024828 Uroplakin-3b
     IPR024831 Uroplakin-3

    Graphical View of Domain Structure for InterPro Entry Q9BT76

    ProtoNet protein and cluster: Q9BT76

    UniProtKB/Swiss-Prot: UPK3B_HUMAN, Q9BT76
    Similarity: Belongs to the uroplakin-3 family


    UPK3B for domains           About GeneDecksing


    (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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: UPK3B_HUMAN, Q9BT76
    Function: Component of the asymmetric unit membrane (AUM); a highly specialized biomembrane elaborated by
    terminally differentiated urothelial cells. May play an important role in AUM-cytoskeleton interaction in
    terminally differentiated urothelial cells. It also contributes to the formation of urothelial glycocalyx which
    may play an important role in preventing bacterial adherence (By similarity)

    Phenotypes:
         1 GenomeRNAi human phenotype for UPK3B:

     Decreased nuclei size in G2M 

    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 UPK3B

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for UPK3B (Q9BT763 ENSP000002576324) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UPK1BO758413, ENSP000002642344I2D: score=1 STRING: ENSP00000264234
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0010629negative regulation of gene expression IMP18776082

    UPK3B for ontologies           About GeneDecksing



    (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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for UPK3B

    Search CenterWatch for drugs/clinical trials and news about UPK3B

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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

    REFSEQ mRNAs for UPK3B gene (3 alternative transcripts): 
    NM_030570.2  NM_182683.1  NM_182684.1  

    Unigene Cluster for UPK3B:

    Uroplakin 3B
    Hs.488861  [show with all ESTs]
    Unigene Representative Sequence: NM_030570
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000334348(uc010ldk.1) ENST00000257632 ENST00000394849 ENST00000490360
    ENST00000469114 ENST00000419923 ENST00000448265(uc003ufo.3 uc003ufq.3)
    ENST00000443097
    miRNA
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    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat UPK3B
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat UPK3B

    Additional mRNA sequence: 

    AK056760.1 AK290096.1 AY233462.1 BC004304.1 BC128439.1 

    4 DOTS entries:

    DT.95269765  DT.100739485  DT.87015106  DT.210789 

    24/59 AceView cDNA sequences (see all 59):

    BI489725 BQ695124 BE378901 BU150542 BE735871 BE378075 BE388690 BE563033 
    NM_030570 BE615406 BQ067150 BE515303 BE395788 BE614826 BE378584 NM_182683 
    BE392047 NM_182684 BE615872 BE378500 BI767901 BP352210 BE394632 BP381559 

    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

    UPK3B expression in normal human tissues (normalized intensities)      UPK3B embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    UPK3B Expression
    About this image


    UPK3B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/5 selected tissues (see all 5) fully expand
     
     Adipose (Muscoskeletal System)    fully expand to see all 2 entries
             Thoracic Perivascular Adipose
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             Renal Collecting Duct System
     
     Heart (Cardiovascular System)
             Atrioventricular Canal Cells Atrioventricular Canal
     
     Lung (Respiratory System)
     
     Uterus (Reproductive System)

    See UPK3B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for UPK3B

    SOURCE GeneReport for Unigene cluster: Hs.488861
        SABiosciences Custom PCR Arrays for UPK3B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UPK3B

    (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 chordates.

    Orthologs for UPK3B gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Upk3b1 , 5 uroplakin 3B1, 5 78.89(n)1
    80(a)1
      5 (75.70 cM)5
    1006471  NM_175309.41  NP_780518.11 
     1360384965 
    chicken
    (Gallus gallus)
    Aves UPK3B6
    uroplakin 3B
    33(a)
    1 ↔ 1
    19(4178760-4181450)
    zebrafish
    (Danio rerio)
    Actinopterygii upk3l6
    uroplakin 3l
    15(a)
    1 → many
    5(60950865-60962871)


    ENSEMBL Gene Tree for UPK3B (if available)
    TreeFam Gene Tree for UPK3B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for UPK3B gene
    UPK3BL2  ENSG000002052362  
    3 SIMAP similar genes for UPK3B using alignment to 2 protein entries:     UPK3B_HUMAN (see all proteins):
    PMS2P11    POLR2J3    UPK3BL

    UPK3B for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for UPK3B
    PGOHUM00000250954


    (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

    2 SNPs in UPK3B are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0478054
    ----see VAR_0478052 W R mis40--------
    VAR_0345614
    ----see VAR_0345612 Q R mis40--------

    HapMap Linkage Disequilibrium report for UPK3B (76139745 - 76389745 bp, first 250kb of UPK3B)

    Structural Variations
         Database of Genomic Variants (DGV) 10/48 variations for UPK3B (see all 48):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2666635CNV Deletion23128226
    dgv120n16CNV Deletion17901297
    esv2734687CNV Deletion23290073
    dgv1218e199CNV Deletion23128226
    nsv821067CNV Deletion20802225
    esv2422494CNV Duplication17116639
    dgv22n31CNV Duplication19718026
    nsv509211CNV Insertion20534489
    dgv121n16CNV Insertion17901297
    dgv1118n67CNV Loss20364138

    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
    OMIM gene information: 611887    OMIM disorders: --

    4 diseases for UPK3B:    About MalaCards
    williams-beuren syndrome    retinitis pigmentosa    retinitis    breast cancer

    1 disease from the University of Copenhagen DISEASES database for UPK3B:
    Williams-Beuren syndrome

    UPK3B for disorders           About GeneDecksing


    Export disorders for UPK3B 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 UPK3B gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with UPK3B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Uroplakin IIIb, a urothelial differentiation marker, dimerizes with uroplakin Ib as an early step of urothelial plaque assembly. (PubMed id 12446744)1, 2, 3, 9 Deng F.-M.... Sun T.-T. (2002)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    5. LRRN4 and UPK3B are markers of primary mesothelial ce lls. (PubMed id 21984916)1 Kanamori-Katayama M....Hayashizaki Y. (2011)
    6. Regulation of the divalent metal ion transporter DMT1 and iron homeostasis by a ubiquitin-dependent mechanism involving Ndfips and WWP2. (PubMed id 18776082)1 Foot N.J....Kumar S. (2008)
    7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    9. Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and function. (PubMed id 16814572)1 Garcia-Espana A....Desalle R. (2006)
    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. (2002)

    (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: 80761 HGNC: 21444 AceView: UPK3B Ensembl:ENSG00000243566 euGenes: HUgn80761
    ECgene: UPK3B H-InvDB: UPK3B

    (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 UPK3B 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 UPK3B gene:
    Search GeneIP for patents involving UPK3B

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



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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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