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URB2 Gene

protein-coding   GIFtS: 49
GCID: GC01P229761

URB2 Ribosome Biogenesis 2 Homolog (S. Cerevisiae)

(Previous name: KIAA0133)
(Previous symbol: KIAA0133)
  See URB2-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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Aliases
URB2 Ribosome Biogenesis 2 Homolog (S. Cerevisiae)1 2
KIAA01331 2 3
Nucleolar Preribosomal-Associated Protein 11 2
NET102
NPA22
Unhealthy Ribosome Biogenesis Protein 2 Homolog2

External Ids:    HGNC: 289671   Entrez Gene: 98162   Ensembl: ENSG000001357637   UniProtKB: Q141463   

Export aliases for URB2 gene to outside databases

Previous GC identifers: GC01P227829 GC01P200252


(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 URB2 Gene:
URB2 (URB2 ribosome biogenesis 2 homolog (S. cerevisiae)) is a protein-coding gene. Diseases associated with URB2 include buruli ulcer disease.


(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_000001.10  NT_167186.2  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the URB2 gene promoter:
         AhR   ER-alpha   FOXD1   Olf-1   LCR-F1   POU3F2   RORalpha1   AREB6   POU2F1   POU2F1a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for URB2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat URB2


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

Entrez Gene cytogenetic band: 1q42.13   Ensembl cytogenetic band:  1q42.13   HGNC cytogenetic band: 1q42.13

URB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
URB2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P229761:  view genomic region     (about GC identifiers)

Start:
229,761,981 bp from pter      End:
229,795,946 bp from pter
Size:
33,966 bases      Orientation:
plus strand

(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/Swiss-Prot: URB2_HUMAN, Q14146 (See protein sequence)
Recommended Name: Unhealthy ribosome biogenesis protein 2 homolog  
Size: 1524 amino acids; 170544 Da
Sequence caution: Sequence=BAA09482.3; Type=Erroneous initiation;
Secondary accessions: Q5VYC9

Explore the universe of human proteins at neXtProt for URB2: NX_Q14146

Explore proteomics data for URB2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys255, Lys462, Lys858, Lys1387
  • Modification sites at PhosphoSitePlus

  • See URB2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055592.2  
    ENSEMBL proteins: 
     ENSP00000258243   ENSP00000395107  

    URB2 Human Recombinant Protein Products:

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    antibodies-online peptides for URB2

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    antibodies-online kits for URB2 (2 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR018849 Urb2/Npa2_C

    Graphical View of Domain Structure for InterPro Entry Q14146

    ProtoNet protein and cluster: Q14146


    Find genes that share domains with URB2           About GenesLikeMe


    (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 URB2

    miRNA
    Products:
        
    miRTarBase miRNAs that target URB2:
    hsa-mir-15b-5p (MIRT046400), hsa-mir-423-3p (MIRT042651), hsa-mir-92a-3p (MIRT049621), hsa-mir-98-5p (MIRT027740), hsa-mir-26b-5p (MIRT029987)

    Block miRNA regulation of human, mouse, rat URB2 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate URB2:
    hsa-miR-137
    SwitchGear 3'UTR luciferase reporter plasmidURB2 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for URB2


    (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 UniProtKB/Swiss-Prot
    URB2_HUMAN, Q14146: Nucleus, nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    peroxisome2
    cytosol1
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--
    GO:0016235aggresome IDA--

    Find genes that share ontologies with URB2           About GenesLikeMe


    (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 URB2
    Interactions:

        Search GeneGlobe Interaction Network for URB2

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for URB2 (Q141463 ENSP000002582434) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    LMNAP025453, ENSP000003572834I2D: score=3 STRING: ENSP00000357283
    LMNB1P207003, ENSP000002613664I2D: score=2 STRING: ENSP00000261366
    UBCENSP000003448184STRING: ENSP00000344818
    SIRT7ENSP000003294664STRING: ENSP00000329466
    About this table

    (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 URB2



    (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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    REFSEQ mRNAs for URB2 gene: 
    NM_014777.2  

    Unigene Cluster for URB2:

    URB2 ribosome biogenesis 2 homolog (S. cerevisiae)
    Hs.533628  [show with all ESTs]
    Unigene Representative Sequence: NM_014777
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000258243(uc001hts.1 uc009xfd.1) ENST00000434387
    miRNA
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    Block miRNA regulation of human, mouse, rat URB2 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate URB2:
    hsa-miR-137
    SwitchGear 3'UTR luciferase reporter plasmidURB2 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for URB2
    Predesigned siRNA for gene silencing in human, mouse, rat URB2
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    GenScript: all cDNA clones in your preferred vector: URB2 (NM_014777)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat URB2
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for URB2
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat URB2
      QuantiTect SYBR Green Assays in human, mouse, rat URB2
      QuantiFast Probe-based Assays in human, mouse, rat URB2

    Additional mRNA sequence: 

    AK291013.1 BC059381.1 BC114559.1 BC114963.1 D50923.2 

    5 DOTS entries:

    DT.309708  DT.95362257  DT.100754267  DT.91675413  DT.95318951 

    Selected AceView cDNA sequences (see all 60):

    BC059381 BX281142 BG149303 BX281526 D50923 BM710410 BM470125 CA488495 
    BQ049193 CA438458 AW611528 AI970497 CD556794 AA599694 BM931343 AA219132 
    AI806589 BE890699 AI440196 BQ423151 BG114492 AI362314 BM472031 AI286157 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for URB2    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10
    SP1:                                                  -                     
    SP2:                    -     -                                             
    SP3:                                                                        


    ECgene alternative splicing isoforms for URB2

    (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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    URB2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTCTGAAAGA
    URB2 Expression
    About this image

    URB2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    URB2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.533628
        Custom PCR Arrays for URB2
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for URB2

    (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 chordates.

    Orthologs for URB2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Urb21 , 5 URB2 ribosome biogenesis 2 homolog (S. cerevisiae)1, 5 77.72(n)1
    71.91(a)1
      8 (72.33 cM)5
    3820381  NM_001029876.11  NP_001025047.11 
     1240215085 
    chicken
    (Gallus gallus)
    Aves URB21 URB2 ribosome biogenesis 2 homolog (S. cerevisiae) 60.01(n)
    52.94(a)
      421539  XM_419580.4  XP_419580.2 
    lizard
    (Anolis carolinensis)
    Reptilia URB26
    URB2 ribosome biogenesis 2 homolog (S. cerevisiae)...
    49(a)
    1 ↔ 1
    1(222338190-222366674)
    African clawed frog
    (Xenopus laevis)
    Amphibia BM261840.12   -- 72.7(n)    BM261840.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5702671 uncharacterized LOC570267 49.99(n)
    39.14(a)
      570267  NM_001123301.2  NP_001116773.2 


    ENSEMBL Gene Tree for URB2 (if available)
    TreeFam Gene Tree for URB2 (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 URB2 (see all 795)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs612493831,2
    C,F--229763799(+) TAGACG/CAGACT 1 -- int11Minor allele frequency- C:0.50WA 2
    rs1826356901,2
    --229763848(+) ATATAA/TTATAT 1 -- int10--------
    rs1887769791,2
    --229763881(+) ATATAC/TAATAT 1 -- int10--------
    rs1996992861,2
    --229763883(+) ATATA-/ATATATA 1 -- int10--------
    rs1472213461,2
    --229763918(+) AGTATA/GTATGT 1 -- int10--------
    rs711737531,2
    C--229764016(+) atataTATTATACATATACATA
    TTATATATGTATATA
    /-
    aatta
    1 -- int11Minor allele frequency- -:0.00NA 2
    rs1907812891,2
    --229764146(+) GCCTGA/GGCGAT 1 -- int10--------
    rs761159201,2
    C,F--229764152(+) GCGATA/GGAGCA 1 -- int11Minor allele frequency- G:0.02WA 118
    rs38203601,2
    C,F,H--229764211(+) TTTGTT/GTGGAG 1 -- int118Minor allele frequency- G:0.24NS EA WA NA CSA 2340
    rs753515921,2
    F--229764299(+) CATTGA/CTAGCT 1 -- int11Minor allele frequency- C:0.01EA 120

    HapMap Linkage Disequilibrium report for URB2 (229761981 - 229795946 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for URB2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv508698CNV Loss20534489
    esv22567CNV Loss19812545

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing URB2
    DNA2.0 Custom Variant and Variant Library Synthesis for URB2

    (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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    1 disease for URB2:    
    About MalaCards
    buruli ulcer disease

    1 disease from the University of Copenhagen DISEASES database for URB2:
    Buruli ulcer disease

    Find genes that share disorders with URB2           About GenesLikeMe

    Genetic Association Database (GAD): URB2

    Export disorders for URB2 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 URB2 gene, integrated from 10 sources (see all 21):
    (articles sorted by number of sources associating them with URB2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PubMed id 8590280)1, 2, 3 Nagase T.... Nomura N. (DNA Res. 1995)
    2. Nucleolar proteome dynamics. (PubMed id 15635413)1, 2 Andersen J.S.... Mann M. (Nature 2005)
    3. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. (PubMed id 23824909)1 Chen Y....Ge F. (amp 2013)
    4. Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia. (PubMed id 23620142)1 Reiner A.P....Allayee H. (Hum. Mol. Genet. 2013)
    5. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    6. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C.... Cristea I.M. (Mol. Cell. Proteomics 2012)
    7. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    8. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    9. Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (J. Biol. Chem. 2011)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 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: 9816 HGNC: 28967 AceView: KIAA0133 Ensembl:ENSG00000135763 euGenes: HUgn9816
    ECgene: URB2 H-InvDB: URB2

    (According to HUGE)
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    HUGE: KIAA0133

    (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 URB2 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 URB2 gene:
    Search GeneIP for patents involving URB2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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