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UTP20 Gene

protein-coding   GIFtS: 48
GCID: GC12P101673

UTP20, Small Subunit (SSU) Processome Component, Homolog...

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(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
UTP20, Small Subunit (SSU) Processome Component, Homolog (Yeast)1 2     Novel Nucleolar Protein 732 3
DRIM2 3 5     NNP732 3
Down Regulated In Metastasis1 2     Small Subunit Processome Component 20 Homolog2
Down-Regulated In Metastasis Protein2 3     Protein Key-1A63

External Ids:    HGNC: 178971   Entrez Gene: 273402   Ensembl: ENSG000001208007   OMIM: 6128225   UniProtKB: O756913   

Export aliases for UTP20 gene to outside databases

Previous GC identifers: GC12P100198 GC12P098734


(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 UTP20 Gene:
UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and
is involved in 18S rRNA processing (Wang et al., 2007 (PubMed 17498821)).(supplied by OMIM, Jun 2009)

GeneCards Summary for UTP20 Gene:
UTP20 (UTP20, small subunit (SSU) processome component, homolog (yeast)) is a protein-coding gene.

UniProtKB/Swiss-Prot: UTP20_HUMAN, O75691
Function: Involved in 18S pre-rRNA processing. Associates with U3 snoRNA

Gene Wiki entry for UTP20 Gene


(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_000012.11  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the UTP20 gene promoter:
         HFH-3   USF1   XBP-1   POU6F1 (c2)   Arnt   Evi-1   FOXI1   AREB6   USF-1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUTP20 promoter sequence
   Search Chromatin IP Primers for UTP20

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UTP20


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

Entrez Gene cytogenetic band: 12q23   Ensembl cytogenetic band:  12q23.2   HGNC cytogenetic band: 12q23

UTP20 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UTP20 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P101673:  view genomic region     (about GC identifiers)

Start:
101,673,887 bp from pter      End:
101,780,397 bp from pter
Size:
106,511 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: UTP20_HUMAN, O75691 (See protein sequence)
Recommended Name: Small subunit processome component 20 homolog  
Size: 2785 amino acids; 318385 Da
Subunit: Interacts with FBL and PPP1R26
Sequence caution: Sequence=AAG35208.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q9H3H4

Explore the universe of human proteins at neXtProt for UTP20: NX_O75691

Explore proteomics data for UTP20 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys1149
  • Modification sites at PhosphoSitePlus

  • See UTP20 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055318.2  
    ENSEMBL proteins: 
     ENSP00000261637  

    UTP20 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR011989 ARM-like
     IPR011430 DRIM
     IPR016024 ARM-type_fold

    Graphical View of Domain Structure for InterPro Entry O75691

    ProtoNet protein and cluster: O75691

    UniProtKB/Swiss-Prot: UTP20_HUMAN, O75691
    Similarity: Belongs to the UTP20 family
    Similarity: Contains 2 HEAT repeats


    Find genes that share domains with UTP20           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: UTP20_HUMAN, O75691
    Function: Involved in 18S pre-rRNA processing. Associates with U3 snoRNA

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005488binding ----
    GO:0005515protein binding IPI16053918
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with UTP20           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for UTP20:
     Increased cell death in HCT116 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for UTP20

    miRNA
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    miRTarBase miRNAs that target UTP20:
    hsa-mir-1276 (MIRT035836), hsa-mir-98-5p (MIRT027738), hsa-mir-16-5p (MIRT031895)

    Block miRNA regulation of human, mouse, rat UTP20 using miScript Target Protectors
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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 UniProtKB/Swiss-Prot
    UTP20_HUMAN, O75691: Nucleus, nucleolus. Note=Colocalizes with NCL in the nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005654nucleoplasm ISS17652137
    GO:0005730nucleolus ISS15590835
    GO:0005737cytoplasm ISS17652137
    GO:003068690S preribosome ISS12150911
    GO:0030688preribosome, small subunit precursor ISS17652137

    Find genes that share ontologies with UTP20           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 UTP20
    Interactions:

        Search GeneGlobe Interaction Network for UTP20

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for UTP20 (O756911, 2, 3 ENSP000002616374) via UniProtKB, MINT, STRING, and/or I2D (see all 252)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4HP628053, ENSP000002893524I2D: score=5 STRING: ENSP00000289352
    HIST1H4FP628053, ENSP000003669744I2D: score=5 STRING: ENSP00000366974
    HIST1H4AP628053I2D: score=5 
    HIST1H4BP628053I2D: score=5 
    HIST1H4CP628053I2D: score=5 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000447endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ISS15590835
    GO:0000472endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ISS17652137
    GO:0000480endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ISS17652137
    GO:0006364rRNA processing IMP17498821
    GO:0008285negative regulation of cell proliferation TAS9673349

    Find genes that share ontologies with UTP20           About GenesLikeMe



    (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 UTP20



    (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 UTP20 gene: 
    NM_014503.2  

    Unigene Cluster for UTP20:

    UTP20, small subunit (SSU) processome component, homolog (yeast)
    Hs.295732  [show with all ESTs]
    Unigene Representative Sequence: NM_014503
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000261637(uc001tia.1) ENST00000551825(uc009ztz.1) ENST00000551998
    ENST00000551345
    miRNA
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    Additional mRNA sequence: 

    AF072718.1 AJ006778.1 AK000333.1 AK297739.1 AK307934.1 

    4 DOTS entries:

    DT.306882  DT.92427436  DT.408548  DT.75121208 

    Selected AceView cDNA sequences (see all 83):

    BM561731 BP346218 CB139198 AW955305 CB163774 AI251481 AA085514 AA708041 
    AL545314 AF072718 BM970338 CR616735 BX485493 CD251476 BM023439 BX502181 
    BX957203 AW389210 BQ068937 BX113621 CK724909 BM793235 BQ938545 BF037836 

    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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    UTP20 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    UTP20 Expression
    About this image

    UTP20 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    UTP20 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.295732

    UniProtKB/Swiss-Prot: UTP20_HUMAN, O75691
    Tissue specificity: Expressed in appendix, brain, colon, fetal liver, heart, ovary, pancreas, placenta, prostate,
    skeletal muscle, small intestine, spleen, testis and thymus

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    In Situ
    Assay Products:
     

     
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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)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for UTP20 gene from Selected species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Utp201 , 5 UTP20, small subunit (SSU) processome component, homolog more1, 5 84.25(n)1
    86.09(a)1
      10 (44.21 cM)5
    706831  NM_175158.31  NP_780367.21 
     887466075 
    chicken
    (Gallus gallus)
    Aves UTP201 UTP20, small subunit (SSU) processome component, homolog more 69.14(n)
    69.67(a)
      417933  XM_004937659.1  XP_004937716.1 
    lizard
    (Anolis carolinensis)
    Reptilia UTP206
    UTP20, small subunit (SSU) processome component, h...
    68(a)
    1 ↔ 1
    5(28223299-28302376)
    African clawed frog
    (Xenopus laevis)
    Amphibia BG413953.12   -- 72.3(n)    BG413953.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb83c082 Transcribed sequence with weak similarity to protein more 74.94(n)    BQ605496.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG45541 CG4554 42.13(n)
    29.11(a)
      37570  NM_137832.1  NP_611676.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tag-1841 tag-184 42.8(n)
    27.1(a)
      174080  NM_062922.3  NP_495323.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes UTP20(YBL004W)4
    UTP201
    Component of the small-subunit (SSU) processome, which more4
    UTP201
    42.3(n)1
    26.98(a)1
      2(227636-235117)4
    8522821, 4  NP_009551.21, 4 


    ENSEMBL Gene Tree for UTP20 (if available)
    TreeFam Gene Tree for UTP20 (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 UTP20 (see all 2422)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0362754
    A breast cancer sample4--see VAR_0362752 I F mis40--------
    VAR_0362744
    A breast cancer sample4--see VAR_0362742 K I mis40--------
    rs1854315731,2
    --101671946(+) TGAAAC/TGTGCA 1 -- us2k10--------
    rs2002911111,2
    --101672036(+) AAGGC-/TTTTAA 1 -- us2k10--------
    rs8243141,2
    C,F,A,H--101672039(+) GCTTTA/TAAAAA 1 -- us2k1 tfbs39Minor allele frequency- T:0.22NA WA EA 370
    rs8507861,2
    C,F,A,H--101672093(+) GGCACG/ATCAAT 1 -- us2k111Minor allele frequency- A:0.29NS EA NA WA CSA 660
    rs1901947311,2
    --101672133(+) ATGGAA/GGCATT 1 -- us2k10--------
    rs1482288861,2
    --101672215(+) GTTATA/GTTCAC 1 -- us2k10--------
    rs1825617951,2
    --101672346(+) ATCCTC/TGAATT 1 -- us2k10--------
    rs1872441011,2
    --101672347(+) TCCTCA/GAATTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for UTP20 (101673887 - 101780397 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for UTP20:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2152079CNV Deletion18987734
    esv2497077CNV Deletion19546169
    esv2746279CNV Deletion23290073
    esv2746278CNV Deletion23290073
    esv2663815CNV Deletion23128226
    nsv53174CNV Loss16902084
    nsv510315CNV Loss20534489
    nsv527505CNV Loss19592680
    nsv527122CNV Loss19592680
    nsv470315CNV Gain18288195

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing UTP20
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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.)
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    OMIM gene information: 612822    OMIM disorders: --


    Find genes that share disorders with UTP20           About GenesLikeMe

    Genetic Association Database (GAD): UTP20

    Export disorders for UTP20 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 UTP20 gene, integrated from 10 sources (see all 38):
    (articles sorted by number of sources associating them with UTP20)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis. (PubMed id 9673349)1, 2, 3 Schwirzke M.... Weidle U.H. (Anticancer Res. 1998)
    2. Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study. (PubMed id 17903303)1, 4 O'Donnell C.J....Demissie S. (BMC Med. Genet. 2007)
    3. Human 1A6/DRIM, the homolog of yeast Utp20, functions in the 18S rRNA processing. (PubMed id 17498821)1, 2 Wang Y....Ke Y. (Biochim. Biophys. Acta 2007)
    4. Mapping nucleolar localization sequences of 1A6/DRIM. (PubMed id 16458307)1, 2 Liu J.... Ke Y. (FEBS Lett. 2006)
    5. KIAA0649, a 1A6/DRIM-interacting protein with the oncogenic potential. (PubMed id 16053918)1, 2 Yang L.... Ke Y. (Biochem. Biophys. Res. Commun. 2005)
    6. The small-subunit processome is a ribosome assembly intermediate. (PubMed id 15590835)1, 3 Bernstein K.A....Baserga S.J. (Eukaryotic Cell 2004)
    7. A panoramic view of yeast noncoding RNA processing. (PubMed id 12837249)1, 3 Peng W.T....Hughes T.R. (Cell 2003)
    8. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (Mol. Biol. Cell 2002)
    9. Directed proteomic analysis of the human nucleolus. (PubMed id 11790298)1, 2 Andersen J.S.... Lamond A.I. (Curr. Biol. 2002)
    10. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 27340 HGNC: 17897 AceView: DRIM Ensembl:ENSG00000120800 euGenes: HUgn27340
    ECgene: UTP20 H-InvDB: UTP20

    (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 UTP20 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 UTP20 gene:
    Search GeneIP for patents involving UTP20

    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
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