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RNASEK Gene

protein-coding   GIFtS: 43
GCID: GC17P006915

Ribonuclease, RNase K

  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)
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Aliases
Ribonuclease, RNase K1 2
RNase Kappa2 3
Ribonuclease Kappa2
EC 3.1.-.-3
RNase K3

External Ids:    HGNC: 339111   Entrez Gene: 4404002   Ensembl: ENSG000002192007   UniProtKB: Q6P5S73   

Export aliases for RNASEK gene to outside databases

Previous GC identifers: GC17P006862 GC17P006863


(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 RNASEK Gene:
RNASEK (ribonuclease, RNase K) is a protein-coding gene. Diseases associated with RNASEK include intrahepatic cholangiocarcinoma, and cholangiocarcinoma. GO annotations related to this gene include endoribonuclease activity.

UniProtKB/Swiss-Prot: RNK_HUMAN, Q6P5S7
Function: Endoribonuclease which preferentially cleaves ApU and ApG phosphodiester bonds. Hydrolyzes UpU bonds at
a lower rate




(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:
NC_000017.11  NC_018928.2  NT_010718.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the RNASEK gene promoter:
         E2F-4   E2F-3a   E2F-5   Spz1   Nkx2-5   E2F-2   POU3F2   E2F   E2F-1   Sox9   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRNASEK promoter sequence
   Search Chromatin IP Primers for RNASEK

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


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

Entrez Gene cytogenetic band: 17p13.1   Ensembl cytogenetic band:  17p13.1   HGNC cytogenetic band: 17p13.1

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

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P006915:  view genomic region     (about GC identifiers)

Start:
6,915,736 bp from pter      End:
6,917,852 bp from pter
Size:
2,117 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNASEK

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RNK_HUMAN, Q6P5S7 (See protein sequence)
Recommended Name: Ribonuclease kappa  
Size: 137 amino acids; 15420 Da
Caution: It is uncertain whether Met-1 or Met-40 is the initiator. Orthologous sequences cannot be extended
Sequence caution: Sequence=AAH51802.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAH62705.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAF82619.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAN89245.1; Type=Erroneous
initiation; Note=Translation N-terminally extended;
Secondary accessions: G3V1Z9 Q502Z2
Alternative splicing: 2 isoforms:  Q6P5S7-1   Q6P5S7-2   

Explore the universe of human proteins at neXtProt for RNASEK: NX_Q6P5S7

Post-translational modifications: 

  • Ubiquitination2 at Lys132
  • Modification sites at PhosphoSitePlus
  • REFSEQ proteins: NP_001004333.2  
    ENSEMBL proteins: 
     ENSP00000449500   ENSP00000447072   ENSP00000459471   ENSP00000447359   ENSP00000449670  
     ENSP00000450174   ENSP00000450182   ENSP00000385440  

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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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    1 InterPro protein domain:
     IPR026770 RNase_K

    Graphical View of Domain Structure for InterPro Entry Q6P5S7

    ProtoNet protein and cluster: Q6P5S7

    UniProtKB/Swiss-Prot: RNK_HUMAN, Q6P5S7
    Similarity: Belongs to the RNase K family


    RNASEK 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RNK_HUMAN, Q6P5S7
    Function: Endoribonuclease which preferentially cleaves ApU and ApG phosphodiester bonds. Hydrolyzes UpU bonds at
    a lower rate

         Enzyme Number (IUBMB): EC 3.1.-.-1

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004521endoribonuclease activity IDA17881363
         
    RNASEK for ontologies           About GeneDecksing


    Animal Models:
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    hsa-mir-744-5p (MIRT037392), hsa-mir-92b-5p (MIRT037802), hsa-mir-877-5p (MIRT037346), hsa-mir-769-3p (MIRT039109)

    Block miRNA regulation of human, mouse, rat RNASEK using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate RNASEK:
    hsa-miR-2278 hsa-miR-3121-3p
    SwitchGear 3'UTR luciferase reporter plasmidRNASEK 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat RNASEK

    Gene Editing
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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
    RNK_HUMAN, Q6P5S7: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular1
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0016021integral component of membrane IEA--

    RNASEK for ontologies           About GeneDecksing


    (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 RNASEK
    Interactions:

        Search GeneGlobe Interaction Network for RNASEK

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009303rRNA transcription IDA17881363
    GO:0090502RNA phosphodiester bond hydrolysis, endonucleolytic IDA17881363

    RNASEK for ontologies           About GeneDecksing



    (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 RNASEK (RNK)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RNASEK gene: 
    NM_001004333.4  

    Unigene Cluster for RNASEK:

    Ribonuclease, RNase K
    Hs.632232  [show with all ESTs]
    Unigene Representative Sequence: BF213270
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000548577 ENST00000546395 ENST00000570898 ENST00000552039 ENST00000552842
    ENST00000552176(uc021tow.1) ENST00000575822 ENST00000549393 ENST00000552321
    ENST00000402093
    miRNA
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    Block miRNA regulation of human, mouse, rat RNASEK using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate RNASEK:
    hsa-miR-2278 hsa-miR-3121-3p
    SwitchGear 3'UTR luciferase reporter plasmidRNASEK 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for RNASEK
    Predesigned siRNA for gene silencing in human, mouse, rat RNASEK
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    GenScript: all cDNA clones in your preferred vector: RNASEK (NM_001004333)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RNASEK
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RNASEK
    Primer
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    OriGene qPCR primer pairs and template standards for RNASEK
    OriGene qSTAR qPCR primer pairs in human, mouse for RNASEK
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RNASEK
      QuantiTect SYBR Green Assays in human, mouse, rat RNASEK
      QuantiFast Probe-based Assays in human, mouse, rat RNASEK

    Additional mRNA sequence: 

    AK289930.1 AM746459.1 BC032510.2 BC051802.1 BC062705.1 BC070349.1 BC095436.1 NR_037715.1 
    NR_037716.1 

    13 DOTS entries:

    DT.100038061  DT.448584  DT.91683782  DT.100887873  DT.120994270  DT.95220070  DT.95244137  DT.95333750 
    DT.100887889  DT.95094098  DT.95178537  DT.100763830  DT.95276523 

    Selected AceView cDNA sequences (see all 545):

    AI460079 BQ950145 BM694510 AA436860 AA588021 AW025818 R66527 AI829899 
    AA633512 H22336 AK055800 BM991218 AA282509 AA651826 AJ713634 AI867829 
    AA976549 AA342936 AA974927 BU626017 AJ706225 CR607998 AA953158 AA055293 

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

    RNASEK Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.632232

    UniProtKB/Swiss-Prot: RNK_HUMAN, Q6P5S7
    Tissue specificity: Widely expressed

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNASEK

    (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.

    Orthologs for RNASEK gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rnasek1 , 5 ribonuclease, RNase K1, 5 94.56(n)1
    100(a)1
      11 (42.99 cM)5
    528981  NM_173742.31  NP_776103.11 
     702381245 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004931341 ribonuclease kappa-B-like 78.57(n)
    84.69(a)
      100493134  XM_002940054.2  XP_002940100.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1005347691 ribonuclease kappa-B-like 69.76(n)
    74.23(a)
      100534769  XM_003199340.2  XP_003199388.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG401276
    --
    38(a)
    1 ↔ 1
    2R(74991-75661)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RNASEK gene
    1 SIMAP similar gene for RNASEK using alignment to 6 protein entries:     RNK_HUMAN (see all proteins):
    RNASEK-C17orf49

    RNASEK for paralogs           About GeneDecksing



    (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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    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RNASEK:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422288CNV Deletion17116639
    nsv457659CNV Loss19166990
    nsv907634CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for RNASEK

    (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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    2 diseases for RNASEK:    
    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma


    RNASEK for disorders           About GeneDecksing

    Genetic Association Database (GAD): RNASEK
    Human Genome Epidemiology (HuGE) Navigator: RNASEK (3 documents)

    Export disorders for RNASEK 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 RNASEK gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with RNASEK)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of the human RNase kappa, an ortholog of Cc RNase. (PubMed id 17881363)1, 2, 3 Economopoulou M.-A.... Sideris D.C. (Nucleic Acids Res. 2007)
    2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    3. Essential cysteine residues for human RNase I_ catalytic activity. (PubMed id 22324914)1 Kiritsi M.N....Sideris D.C. (FEBS J. 2012)
    4. 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)
    5. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    6. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (Biochem. Biophys. Res. Commun. 2006)
    7. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)
    8. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (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: 440400 HGNC: 33911 AceView: MGC49942andMGC71993 Ensembl:ENSG00000219200 euGenes: HUgn440400
    ECgene: RNASEK H-InvDB: RNASEK

    (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 RNASEK 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 RNASEK gene:
    Search GeneIP for patents involving RNASEK

    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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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 inGenious Targeting Laboratory, genOway)
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