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

UTP6 Gene

protein-coding   GIFtS: 53
GCID: GC17M030187

UTP6, small subunit (SSU) processome component, homolog...

(Previous name: chromosome 17 open reading frame 40 )
(Previous symbol: C17orf40)
 Explore 4 diseases affiliated with
UTP6 via our new
 Human Malady Compendium 
Biological research products
for UTP6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
UTP6, Small Subunit (SSU) Processome Component, Homolog (Yeast)1 2     Chromosome 17 Open Reading Frame 401
C17orf401 2 3     Hepatocellular Carcinoma Associated Antigen 662
HCA661 2 3     U3 Small Nucleolar RNA-Associated Protein 6 Homolog2
Hepatocellular Carcinoma-Associated Antigen 662 3     MHAT3
Multiple Hat Domains Protein2 3     

External Ids:    HGNC: 182791   Entrez Gene: 558132   Ensembl: ENSG000001086517   UniProtKB: Q9NYH93   

Export aliases for UTP6 gene to outside databases

Previous GC identifers: GC17M027216 GC17M026401


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

UniProtKB/Swiss-Prot: UTP6_HUMAN, Q9NYH9
Function: Involved in nucleolar processing of pre-18S ribosomal RNA (By similarity)

Gene Wiki entry for UTP6


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010799.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the UTP6 gene promoter:
         NF-1   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUTP6 promoter sequence
   Search SABiosciences Chromatin IP Primers for UTP6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UTP6


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

Entrez Gene cytogenetic band: 17q11.2   Ensembl cytogenetic band:  17q11.2   HGNC cytogenetic band: 17q11.2

UTP6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UTP6 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M030187:  view genomic region     (about GC identifiers)

Start:
30,187,923 bp from pter      End:
30,228,784 bp from pter
Size:
40,862 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: UTP6_HUMAN, Q9NYH9 (See protein sequence)
Recommended Name: U3 small nucleolar RNA-associated protein 6 homolog  
Size: 597 amino acids; 70194 Da
Subcellular location: Nucleus, nucleolus
Secondary accessions: Q8IX96 Q96BL2 Q9NQ91

Explore the universe of human proteins at neXtProt for UTP6: NX_Q9NYH9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NYH9

  • UTP6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060898.2  
    ENSEMBL proteins: 
     ENSP00000261708   ENSP00000462135   ENSP00000464599  

    Human Recombinant Protein Products: 
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    Novus Biologicals UTP6 Protein
    Novus Biologicals UTP6 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for UTP6

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005730nucleolus IDA--


    UTP6 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for UTP6


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    UTP6 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR003107 HAT
     IPR011990 TPR-like_helical
     IPR013949 U3_snoRNA_assoc-6

    Graphical View of Domain Structure for InterPro Entry Q9NYH9

    ProtoNet protein and cluster: Q9NYH9

    2 Blocks protein families:
    IPB003107 RNA-processing protein
    IPB013949 U3 small nucleolar RNA-associated protein 6


    UniProtKB/Swiss-Prot: UTP6_HUMAN, Q9NYH9
    Similarity: Belongs to the UTP6 family
    Similarity: Contains 5 HAT repeats


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: UTP6_HUMAN, Q9NYH9
    Function: Involved in nucleolar processing of pre-18S ribosomal RNA (By similarity)

    miRNA
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    hsa-miR-616* hsa-miR-373*
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    Inhib. RNA
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UTP6

    5 GenomeRNAi human phenotypes for UTP6:
     Decreased nuclei size in G2M  Decreased viability of wild-ty  Increased G2M DNA content  Increased gamma-H2AX phosphory 
     Nucleolar pre-40S maturation d 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for UTP6):
        Ribosome biogenesis in eukaryotes


    UTP6 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for UTP6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/8 Interacting proteins for UTP6 (Q9NYH92, 3 ENSP000002617084) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCDC85BQ158342, 3, ENSP000003116954MINT-68353 I2D: score=5 STRING: ENSP00000311695
    RHOXF2Q9BQY42, 3, ENSP000003604414MINT-68193 I2D: score=5 STRING: ENSP00000360441
    KXD1Q9BQD32, 3, ENSP000002223074MINT-67466 I2D: score=4 STRING: ENSP00000222307
    BCL6P411823, ENSP000002320144I2D: score=2 STRING: ENSP00000232014
    NECAB2Q7Z6G33I2D: score=1 
    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:0006364rRNA processing IEA--


    UTP6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 UTP6
    Search CenterWatch for drugs/clinical trials and news about UTP6 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for UTP6 gene: 
    NM_018428.2  

    Unigene Cluster for UTP6:

    UTP6, small subunit (SSU) processome component, homolog (yeast)
    Hs.589862  [show with all ESTs]
    Unigene Representative Sequence: AK126564
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000261708(uc002hgr.3) ENST00000581012 ENST00000579459 ENST00000477128(uc002hgq.3)
    ENST00000484661 ENST00000477860 ENST00000583408(uc010wbw.1) ENST00000490218
    ENST00000579878

    miRNA
    Products:
         
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    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat UTP6
    2 QIAGEN miScript miRNA Assays for microRNAs that regulate UTP6:
    hsa-miR-616* hsa-miR-373*
    SwitchGear 3'UTR luciferase reporter plasmidUTP6 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for UTP6 (see all 4)
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    OriGene siRNA: UTP6
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat UTP6
    Clone
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    Additional cDNA sequence: 

    AF116631.1 AF244135.1 AF334386.1 AJ272197.1 AK057202.1 AK126564.1 AK225448.1 AK299806.1 
    AK315929.1 BC015454.1 BC035325.1 

    12 DOTS entries:

    DT.207560  DT.101981307  DT.91746371  DT.100824134  DT.100824141  DT.120953784  DT.97817416  DT.120953780 
    DT.70103540  DT.91942184  DT.95140773  DT.99985401 

    24/138 AceView cDNA sequences (see all 138):

    AK057202 F24299 BE675092 NM_018428 CR625726 BM478186 AI862739 AL535002 
    AW613268 AJ272197 AI805121 CD721821 AW196869 BM905762 AI924993 AA100219 
    BQ938611 BC035325 AI784001 AL565738 AI949382 BM550227 BE876142 BC015454 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for UTP6 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b ^ 17 ^ 18 ^
    SP1:                                                  -                 -                                               -     -                 -               
    SP2:                                                                                                                    -     -                 -               
    SP3:                                      -     -     -     -           -                                                                                       
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                            -               

    ExUns: 19a · 19b
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for UTP6

    (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

    UTP6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTATGCATCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See UTP6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for UTP6

    SOURCE GeneReport for Unigene cluster: Hs.589862
        SABiosciences Custom PCR Arrays for UTP6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UTP6

    (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 eukaryotes.

    Orthologs for UTP6 gene from 8/28 species (see all 28)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Utp61 , 5 UTP6, small subunit (SSU) processome component, homolog more1, 5 85.35(n)1
    86.24(a)1
      11 (47.29 cM)5
    2169871  NM_144826.31  NP_659075.11 
     799323215 
    chicken
    (Gallus gallus)
    Aves UTP61 UTP6, small subunit (SSU) processome component, homolog more 69.29(n)
    66.19(a)
      417405  NM_001006207.1  NP_001006207.1 
    lizard
    (Anolis carolinensis)
    Reptilia UTP66
    --
    64(a)
    1 ↔ 1
    GL343198.1(1407723-1430714)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC539632 hypothetical protein MGC53963 72.97(n)    BC048226.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc556482 similar to DSCAM-interacting protein 1 73.84(n)   393107  BC044444.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG72461 CG7246 40.95(n)
    28.62(a)
      31833  NM_132292.3  NP_572520.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G282001 hypothetical protein 43.37(n)
    29.77(a)
      828935  NM_118960.2  NP_194549.1 
    rice
    (Oryza sativa)
    Liliopsida Os02g01039001 hypothetical protein 43.29(n)
    31.98(a)
      4328001  NM_001052144.1  NP_001045609.1 


    ENSEMBL Gene Tree for UTP6 (if available)
    TreeFam Gene Tree for UTP6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for UTP6 gene

    UTP6 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for UTP6
    PGOHUM00000246784 PGOHUM00000233117


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/672 NCBI SNPs in UTP6 are shown (see all 672    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs590477241,2
    F,--30189871(+) ACAGGC/AGTTGA 1 -- ds50011Minor allele frequency- A:0.13WA 118
    rs7397991,2
    C,F,H,--30189950(+) CTTGAC/TCTGGG 1 -- ds500111Minor allele frequency- T:0.01NA MN NS EA 1140
    rs1836175911,2
    --30189964(+) ATTTTA/TAAAAA 1 -- ds50010--------
    rs1887153181,2
    --30189990(+) ATCCAC/TGTATT 1 -- ds50010--------
    rs7398001,2
    C,F,O,A,H,--30190083(+) CAAACA/TGAGCA 1 -- ds500123Minor allele frequency- T:0.20MN NS EA NA WA CSA 1183
    rs563669141,2
    C,--30190090(+) AGCAGT/AGTCAT 1 -- ds50011Minor allele frequency- A:0.50WA 2
    rs1463538221,2
    --30190211(+) TTTTTA/CATTTT 1 -- ut310--------
    rs169670281,2
    C,F,H,--30190348(+) ATACTA/GTTTCA 1 -- ut3118Minor allele frequency- G:0.08NA NS EA WA EU 3681
    rs1996559911,2
    --30190458(+) CGCTCA/GCCAGT 2 R * stg10--------
    rs2017625671,2
    --30190475(+) GTCCAC/TAGTTC 2 Y C mis10--------

    HapMap Linkage Disequilibrium report for UTP6 (30187923 - 30228784 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for UTP6
         1 CNV: 4030

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing UTP6
    DNA2.0 Custom Variant and Variant Library Synthesis for UTP6

    (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.)
    About This Section

    UTP6 for disorders           About GeneDecksing

    4 diseases for UTP6:    About MalaCards
    hepatocellular carcinoma    carcinoma    congenital heart defect    neurofibromatosis


    Export disorders for UTP6 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 UTP6 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with UTP6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A common set of at least 11 functional genes is lost in the majority of NF1 patients with gross deletions. (PubMed id 10843809)1, 2, 3 Jenne D.E.... Thiel G. (2000)
    2. Evidence by expression analysis of candidate genes fo r congenital heart defects in the NF1 microdeletion interval. (PubMed id 16138909)1, 3 Venturin M....Riva P. (2005)
    3. 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)
    4. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    5. Large scale identification of human hepatocellular carcinoma- associated antigens by autoantibodies. (PubMed id 12097419)1, 2 Wang Y....Chen W.-F. (2002)
    6. Positive regulation of apoptosis by HCA66, a new Apaf-1 interacting protein, and its putative role in the physiopathology of NF1 microdeletion syndrome patients. (PubMed id 17380155)1, 9 Piddubnyak V....Poyet J.L. (2007)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55813 HGNC: 18279 AceView: HCA66 Ensembl:ENSG00000108651 euGenes: HUgn55813
    ECgene: UTP6 Kegg: 55813 H-InvDB: UTP6

    (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 UTP6 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 UTP6 gene:
    Search GeneIP for patents involving UTP6

    GeneCards and IP:
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