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Aliases for RIOK3 Gene

Aliases for RIOK3 Gene

  • RIO Kinase 3 2 3 4 5
  • SudD (Suppressor Of BimD6, Aspergillus Nidulans) Homolog 2 3
  • SudD Homolog 3 4
  • SUDD 3 4
  • Homolog Of The Aspergillus Nidulans SudD Gene Product 3
  • SudD Suppressor Of Aspergillus Nidulans BimD6 Homolog 3
  • Serine/Threonine-Protein Kinase RIO3 3
  • Testicular Secretory Protein Li 47 3
  • SudD Suppressor Of BimD6 Homolog 3
  • RIO Kinase 3 (Yeast) 2
  • EC 2.7.11.1 4

External Ids for RIOK3 Gene

Previous HGNC Symbols for RIOK3 Gene

  • SUDD

Previous GeneCards Identifiers for RIOK3 Gene

  • GC18P020920
  • GC18P019285
  • GC18P019287
  • GC18P021032
  • GC18P017887

Summaries for RIOK3 Gene

Entrez Gene Summary for RIOK3 Gene

  • This gene was first identified by the similarity of its product to the Aspergillus nidulans SUDD protein. This gene is now recognized as a member of the right open reading frame (RIO) kinase gene family. This gene encodes a serine/threonine kinase that localizes to the cytoplasm and plays a role in the processing of the pre-40 S ribosomal subunit. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2017]

GeneCards Summary for RIOK3 Gene

RIOK3 (RIO Kinase 3) is a Protein Coding gene. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and phosphotransferase activity, alcohol group as acceptor. An important paralog of this gene is RIOK1.

UniProtKB/Swiss-Prot for RIOK3 Gene

  • Involved in regulation of type I interferon (IFN)-dependent immune response which plays a critical role in the innate immune response against DNA and RNA viruses. May act as an adapter protein essential for the recruitment of TBK1 to IRF3 (PubMed:24807708). Phosphorylates IFIH1 on Ser-828 interfering with IFIH1 filament assembly on long dsRNA and resulting in attenuated IFIH1-signaling (PubMed:25865883). Can inhibit CASP10 isoform 7-mediated activation of the NF-kappaB signaling pathway (PubMed:19557502). May play a role in the biogenesis of the 40S ribosomal subunit. Involved in the processing of 21S pre-rRNA to the mature 18S rRNA (PubMed:22418843).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RIOK3 Gene

Genomics for RIOK3 Gene

Regulatory Elements for RIOK3 Gene

Enhancers for RIOK3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G023420 1.6 FANTOM5 Ensembl ENCODE 12 -30.3 -30316 3.3 HDGF PKNOX1 FOXA2 ATF1 ARNT SIN3A TCF12 ZNF766 ZNF207 FOS NPC1 C18orf8 RIOK3 CABLES1 RBBP8 TMEM241 ENSG00000266495
GH18G023279 1.1 Ensembl ENCODE 10.7 -170.3 -170280 6.6 HDGF PKNOX1 BMI1 RARA KAT2B GATA2 ELK1 RELB FOS IKZF2 RIOK3 NPC1 ENSG00000266495 TMEM241
GH18G023478 0.9 ENCODE dbSUPER 12.4 +27.4 27394 2.7 GATA3 ZSCAN4 IKZF1 ZSCAN29 MLLT1 RELB DPF2 IKZF2 SPI1 C18orf8 RIOK3 TMEM241 PIR55902 GC18P023472
GH18G023484 0.7 ENCODE dbSUPER 11.6 +31.5 31453 0.3 ZNF121 POLR2A SUPT5H RIOK3 TMEM241 NPC1 ENSG00000283084 PIR55902
GH18G023482 0.6 dbSUPER 11.6 +30.3 30331 1.6 ZNF121 ZFHX2 POLR2A SP7 SUPT5H EGR2 TMEM241 RIOK3 ENSG00000283084 PIR55902
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RIOK3 on UCSC Golden Path with GeneCards custom track

Promoters for RIOK3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000101436 877 2201 HDGF PKNOX1 FOXA2 CREB3L1 AGO1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for RIOK3 Gene

Chromosome:
18
Start:
23,452,823 bp from pter
End:
23,486,603 bp from pter
Size:
33,781 bases
Orientation:
Plus strand

Genomic View for RIOK3 Gene

Genes around RIOK3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIOK3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIOK3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RIOK3 Gene

Proteins for RIOK3 Gene

  • Protein details for RIOK3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14730-RIOK3_HUMAN
    Recommended name:
    Serine/threonine-protein kinase RIO3
    Protein Accession:
    O14730
    Secondary Accessions:
    • Q8IXN9

    Protein attributes for RIOK3 Gene

    Size:
    519 amino acids
    Molecular mass:
    59093 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with CASP10 (PubMed:19557502). Interacts with IRF3; RIOK3 probybly mediates the interaction of TBK1 with IRF3 (PubMed:24807708). Associated with 40S pre-ribosomal particles.

    Alternative splice isoforms for RIOK3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RIOK3 Gene

Post-translational modifications for RIOK3 Gene

  • Autophosphorylated (in vitro).
  • Ubiquitination at isoforms=2108, isoforms=2160, isoforms=2207, Lys290, Lys300, and isoforms=452
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RIOK3 Gene

Domains & Families for RIOK3 Gene

Gene Families for RIOK3 Gene

Graphical View of Domain Structure for InterPro Entry

O14730

UniProtKB/Swiss-Prot:

RIOK3_HUMAN :
  • Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.
Family:
  • Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.
genes like me logo Genes that share domains with RIOK3: view

Function for RIOK3 Gene

Molecular function for RIOK3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot Function:
Involved in regulation of type I interferon (IFN)-dependent immune response which plays a critical role in the innate immune response against DNA and RNA viruses. May act as an adapter protein essential for the recruitment of TBK1 to IRF3 (PubMed:24807708). Phosphorylates IFIH1 on Ser-828 interfering with IFIH1 filament assembly on long dsRNA and resulting in attenuated IFIH1-signaling (PubMed:25865883). Can inhibit CASP10 isoform 7-mediated activation of the NF-kappaB signaling pathway (PubMed:19557502). May play a role in the biogenesis of the 40S ribosomal subunit. Involved in the processing of 21S pre-rRNA to the mature 18S rRNA (PubMed:22418843).

Enzyme Numbers (IUBMB) for RIOK3 Gene

Gene Ontology (GO) - Molecular Function for RIOK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004674 protein serine/threonine kinase activity IEA,IDA 25865883
GO:0005515 protein binding IPI 19557502
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with RIOK3: view
genes like me logo Genes that share phenotypes with RIOK3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for RIOK3

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RIOK3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RIOK3 Gene

Localization for RIOK3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIOK3 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RIOK3 gene
Compartment Confidence
cytosol 5
plasma membrane 2
cytoskeleton 2
nucleus 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for RIOK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0030688 preribosome, small subunit precursor IDA 22072790
genes like me logo Genes that share ontologies with RIOK3: view

Pathways & Interactions for RIOK3 Gene

genes like me logo Genes that share pathways with RIOK3: view

Gene Ontology (GO) - Biological Process for RIOK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
GO:0006468 protein phosphorylation IEA --
GO:0007059 chromosome segregation TAS 9602165
GO:0016310 phosphorylation IEA --
GO:0030490 maturation of SSU-rRNA IMP 22418843
genes like me logo Genes that share ontologies with RIOK3: view

No data available for SIGNOR curated interactions for RIOK3 Gene

Drugs & Compounds for RIOK3 Gene

No Compound Related Data Available

Transcripts for RIOK3 Gene

Unigene Clusters for RIOK3 Gene

RIO kinase 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RIOK3

Alternative Splicing Database (ASD) splice patterns (SP) for RIOK3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b
SP1: - - -
SP2: - - - -
SP3: - -
SP4:
SP5:
SP6: -
SP7: - -
SP8:

Relevant External Links for RIOK3 Gene

GeneLoc Exon Structure for
RIOK3
ECgene alternative splicing isoforms for
RIOK3

Expression for RIOK3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RIOK3 Gene

Protein differential expression in normal tissues from HIPED for RIOK3 Gene

This gene is overexpressed in Breast (35.1) and Cervix (27.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RIOK3 Gene



Protein tissue co-expression partners for RIOK3 Gene

NURSA nuclear receptor signaling pathways regulating expression of RIOK3 Gene:

RIOK3

SOURCE GeneReport for Unigene cluster for RIOK3 Gene:

Hs.728452

mRNA Expression by UniProt/SwissProt for RIOK3 Gene:

O14730-RIOK3_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for RIOK3 Gene

  • Nervous system(4.7)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with RIOK3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIOK3 Gene

Orthologs for RIOK3 Gene

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

Orthologs for RIOK3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RIOK3 34 35
  • 99.81 (n)
cow
(Bos Taurus)
Mammalia RIOK3 34 35
  • 94.8 (n)
dog
(Canis familiaris)
Mammalia RIOK3 34 35
  • 94.61 (n)
oppossum
(Monodelphis domestica)
Mammalia RIOK3 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Riok3 34 16 35
  • 90.12 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RIOK3 35
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Riok3 34
  • 88.82 (n)
chicken
(Gallus gallus)
Aves RIOK3 34 35
  • 80.18 (n)
lizard
(Anolis carolinensis)
Reptilia RIOK3 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia riok3 34
  • 72.45 (n)
Str.17119 34
African clawed frog
(Xenopus laevis)
Amphibia MGC68555 34
zebrafish
(Danio rerio)
Actinopterygii riok3 34 35
  • 70.66 (n)
wufb10c11 34
fruit fly
(Drosophila melanogaster)
Insecta CG3008 34 35
  • 51.73 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009993 34
  • 49.85 (n)
worm
(Caenorhabditis elegans)
Secernentea riok-3 34 35
  • 48.44 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RIO1 35
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8977 34
Species where no ortholog for RIOK3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RIOK3 Gene

ENSEMBL:
Gene Tree for RIOK3 (if available)
TreeFam:
Gene Tree for RIOK3 (if available)

Paralogs for RIOK3 Gene

Paralogs for RIOK3 Gene

(1) SIMAP similar genes for RIOK3 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for RIOK3 Gene

genes like me logo Genes that share paralogs with RIOK3: view

Variants for RIOK3 Gene

Sequence variations from dbSNP and Humsavar for RIOK3 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1000133621 -- 23,482,032(+) CTACA(C/T)TTATC utr-variant-3-prime
rs1000138880 -- 23,469,019(+) CAACT(C/T)CTTGA intron-variant
rs1000187522 -- 23,480,567(+) CACAC(A/G)CACAC intron-variant
rs1000237685 -- 23,462,106(+) AGAAA(A/T)AAAAT intron-variant
rs1000418817 -- 23,472,791(+) AGCCA(A/G)GTCTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RIOK3 Gene

Variant ID Type Subtype PubMed ID
esv2716859 CNV deletion 23290073
esv2716860 CNV deletion 23290073
esv3337127 CNV duplication 20981092
esv34149 CNV loss 18971310

Variation tolerance for RIOK3 Gene

Residual Variation Intolerance Score: 26% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.76; 33.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RIOK3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIOK3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIOK3 Gene

Disorders for RIOK3 Gene

Relevant External Links for RIOK3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RIOK3

No disorders were found for RIOK3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RIOK3 Gene

Publications for RIOK3 Gene

  1. Isolation of the Aspergillus nidulans sudD gene and its human homologue. (PMID: 9602165) Anaya P. … May G.S. (Gene 1998) 2 3 4 22 64
  2. RIOK3-mediated phosphorylation of MDA5 interferes with its assembly and attenuates the innate immune response. (PMID: 25865883) Takashima K. … Seya T. (Cell Rep 2015) 3 4 64
  3. RIOK3 is an adaptor protein required for IRF3-mediated antiviral type I interferon production. (PMID: 24807708) Feng J. … Sun R. (J. Virol. 2014) 3 4 64
  4. Human RioK3 is a novel component of cytoplasmic pre-40S pre-ribosomal particles. (PMID: 22418843) Baumas K. … Mougin A. (RNA Biol 2012) 3 4 64
  5. The kinase activity of human Rio1 is required for final steps of cytoplasmic maturation of 40S subunits. (PMID: 22072790) Widmann B. … Kutay U. (Mol. Biol. Cell 2012) 3 4 64

Products for RIOK3 Gene

  • Addgene plasmids for RIOK3

Sources for RIOK3 Gene

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