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Aliases for RIOK1 Gene

Aliases for RIOK1 Gene

  • RIO Kinase 1 2 3 4 5
  • Serine/Threonine-Protein Kinase RIO1 3
  • RIO Kinase 1 (Yeast) 2
  • EC 2.7.11.1 4
  • EC 3.6.3.- 4
  • BA288G3.1 3
  • AD034 3
  • RRP10 3

External Ids for RIOK1 Gene

Previous GeneCards Identifiers for RIOK1 Gene

  • GC06P007380
  • GC06P007335
  • GC06P007267

Summaries for RIOK1 Gene

Entrez Gene Summary for RIOK1 Gene

  • The protein encoded by this gene competes with pICln for inclusion in the protein arginine methyltransferase 5 complex. This complex targets substrates for dimethylation. The encoded protein is essential for the last steps in the maturation of 40S subunits. [provided by RefSeq, Jan 2017]

GeneCards Summary for RIOK1 Gene

RIOK1 (RIO Kinase 1) is a Protein Coding gene. Diseases associated with RIOK1 include Giant Axonal Neuropathy. Among its related pathways are rRNA processing in the nucleus and cytosol and Ribosome biogenesis in eukaryotes. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein serine/threonine kinase activity. An important paralog of this gene is RIOK3.

UniProtKB/Swiss-Prot for RIOK1 Gene

  • Involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in processing of 18S-E pre-rRNA to the mature 18S rRNA. Required for the recycling of NOB1 and PNO1 from the late 40S precursor (PubMed:22072790). The association with the very late 40S subunit intermediate may involve a translation-like checkpoint point cycle preceeding the binding to the 60S ribosomal subunit (By similarity). Despite the protein kinase domain is proposed to act predominantly as an ATPase (By similarity). The catalytic activity regulates its dynamic association with the 40S subunit (By similarity).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RIOK1 Gene

Genomics for RIOK1 Gene

Regulatory Elements for RIOK1 Gene

Enhancers for RIOK1 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
GH06G006878 2 FANTOM5 Ensembl ENCODE dbSUPER 32.8 -506.0 -505956 9.4 HDGF PKNOX1 CREB3L1 ARNT YY1 ZNF766 CBX5 KLF13 DEK CEBPZ RIOK1 ENSG00000238221 RREB1 LY86 LOC105374902 GC06P006872
GH06G007388 1.2 ENCODE 40.6 +0.4 418 3.1 CREB3L1 MLX DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC SSRP1 RIOK1 SSR1 DSP ENSG00000225092 ENSG00000238221 CAGE1 GC06P007402
GH06G006889 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.4 -497.2 -497240 5.7 HDGF HDAC1 CREB3L1 ARNT ZNF76 ETS1 ZNF335 GATA2 ZNF143 CREM RIOK1 LY86 RREB1 LOC105374903 GC06M006897
GH06G006809 1.9 FANTOM5 Ensembl ENCODE dbSUPER 15.8 -578.0 -578015 3.1 PKNOX1 FOXA2 BRCA1 YY1 GLIS2 GATA2 FOS DEK SP3 SMARCB1 RIOK1 RREB1 LY86 GC06P006814 GC06P006801
GH06G007056 1.9 FANTOM5 Ensembl ENCODE dbSUPER 15.8 -330.1 -330051 5.0 HDGF FOXA2 PKNOX1 ARID4B DMAP1 YY1 ZNF766 CBX5 FOS DEK RIOK1 RREB1 DSP GC06M007056 GC06P007051
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RIOK1 on UCSC Golden Path with GeneCards custom track

Promoters for RIOK1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000192782 481 1801 CREB3L1 MLX DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 SSRP1 ZNF610

Genomic Location for RIOK1 Gene

Chromosome:
6
Start:
7,389,419 bp from pter
End:
7,418,037 bp from pter
Size:
28,619 bases
Orientation:
Plus strand

Genomic View for RIOK1 Gene

Genes around RIOK1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIOK1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIOK1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RIOK1 Gene

Proteins for RIOK1 Gene

  • Protein details for RIOK1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BRS2-RIOK1_HUMAN
    Recommended name:
    Serine/threonine-protein kinase RIO1
    Protein Accession:
    Q9BRS2
    Secondary Accessions:
    • B2RB28
    • Q8NDC8
    • Q96NV9

    Protein attributes for RIOK1 Gene

    Size:
    568 amino acids
    Molecular mass:
    65583 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Associates with the precursor of the 40S ribosome subunit. Interacts with PRMT5 and WDR77.

    Three dimensional structures from OCA and Proteopedia for RIOK1 Gene

neXtProt entry for RIOK1 Gene

Post-translational modifications for RIOK1 Gene

  • Ubiquitination at Lys81
  • Modification sites at PhosphoSitePlus

Other Protein References for RIOK1 Gene

No data available for DME Specific Peptides for RIOK1 Gene

Domains & Families for RIOK1 Gene

Gene Families for RIOK1 Gene

Suggested Antigen Peptide Sequences for RIOK1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BRS2

UniProtKB/Swiss-Prot:

RIOK1_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 RIOK1: view

Function for RIOK1 Gene

Molecular function for RIOK1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot Function:
Involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in processing of 18S-E pre-rRNA to the mature 18S rRNA. Required for the recycling of NOB1 and PNO1 from the late 40S precursor (PubMed:22072790). The association with the very late 40S subunit intermediate may involve a translation-like checkpoint point cycle preceeding the binding to the 60S ribosomal subunit (By similarity). Despite the protein kinase domain is proposed to act predominantly as an ATPase (By similarity). The catalytic activity regulates its dynamic association with the 40S subunit (By similarity).

Enzyme Numbers (IUBMB) for RIOK1 Gene

Gene Ontology (GO) - Molecular Function for RIOK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004674 protein serine/threonine kinase activity IEA --
GO:0005515 protein binding IPI 25852190
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with RIOK1: view
genes like me logo Genes that share phenotypes with RIOK1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for RIOK1

CRISPR Products

miRNA for RIOK1 Gene

miRTarBase miRNAs that target RIOK1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RIOK1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RIOK1 Gene

Localization for RIOK1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIOK1 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 RIOK1 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for RIOK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0030688 preribosome, small subunit precursor IDA 22072790
genes like me logo Genes that share ontologies with RIOK1: view

Pathways & Interactions for RIOK1 Gene

genes like me logo Genes that share pathways with RIOK1: view

Gene Ontology (GO) - Biological Process for RIOK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
GO:0006468 protein phosphorylation IEA --
GO:0016310 phosphorylation IEA --
GO:0030490 maturation of SSU-rRNA IMP 22072790
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with RIOK1: view

No data available for SIGNOR curated interactions for RIOK1 Gene

Drugs & Compounds for RIOK1 Gene

(1) Drugs for RIOK1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for RIOK1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with RIOK1: view

Transcripts for RIOK1 Gene

Unigene Clusters for RIOK1 Gene

RIO kinase 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RIOK1

Alternative Splicing Database (ASD) splice patterns (SP) for RIOK1 Gene

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

Relevant External Links for RIOK1 Gene

GeneLoc Exon Structure for
RIOK1
ECgene alternative splicing isoforms for
RIOK1

Expression for RIOK1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RIOK1 Gene

Protein differential expression in normal tissues from HIPED for RIOK1 Gene

This gene is overexpressed in Monocytes (14.8), Testis (13.8), Liver, secretome (11.8), Lung (9.7), and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RIOK1 Gene



Protein tissue co-expression partners for RIOK1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RIOK1 Gene:

RIOK1

SOURCE GeneReport for Unigene cluster for RIOK1 Gene:

Hs.437474

Evidence on tissue expression from TISSUES for RIOK1 Gene

  • Lung(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with RIOK1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIOK1 Gene

Orthologs for RIOK1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RIOK1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RIOK1 34 35
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia RIOK1 34 35
  • 89.44 (n)
cow
(Bos Taurus)
Mammalia RIOK1 34 35
  • 85.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RIOK1 35
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Riok1 34
  • 83.3 (n)
mouse
(Mus musculus)
Mammalia Riok1 34 16 35
  • 82.53 (n)
oppossum
(Monodelphis domestica)
Mammalia RIOK1 35
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves RIOK1 34 35
  • 75.73 (n)
lizard
(Anolis carolinensis)
Reptilia RIOK1 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia riok1 34
  • 73.81 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16329 34
zebrafish
(Danio rerio)
Actinopterygii riok1 34 35
  • 66.85 (n)
Dr.3368 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012121 34
  • 55.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11660 34 35
  • 53.95 (n)
worm
(Caenorhabditis elegans)
Secernentea riok-1 34 35
  • 58.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RIO1 34 35 37
  • 54.36 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E21121g 34
  • 52.6 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER257W 34
  • 51.76 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G37350 34
  • 55.58 (n)
rice
(Oryza sativa)
Liliopsida Os07g0162300 34
  • 54.25 (n)
Os.17949 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC10F6.10 34
  • 55.33 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU10652 34
  • 52.1 (n)
Species where no ortholog for RIOK1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RIOK1 Gene

ENSEMBL:
Gene Tree for RIOK1 (if available)
TreeFam:
Gene Tree for RIOK1 (if available)

Paralogs for RIOK1 Gene

Paralogs for RIOK1 Gene

(1) SIMAP similar genes for RIOK1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RIOK1: view

Variants for RIOK1 Gene

Sequence variations from dbSNP and Humsavar for RIOK1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000001721 -- 7,393,229(+) ATGAT(A/G)ATGAC reference, missense, utr-variant-5-prime
rs1000039236 -- 7,394,531(+) TTTAT(A/G)TCGTC intron-variant
rs1000110048 -- 7,401,148(+) GAAAG(A/G)AAAAC intron-variant, upstream-variant-2KB
rs1000132764 -- 7,399,380(+) AGCCG(A/G)GTCTG intron-variant
rs1000194608 -- 7,409,267(+) TGTGT(G/T)TGTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RIOK1 Gene

Variant ID Type Subtype PubMed ID
esv3890787 CNV loss 25118596
nsv1032371 CNV gain 25217958
nsv1133014 OTHER inversion 24896259
nsv1151332 OTHER inversion 26484159
nsv462623 CNV gain 19166990
nsv470797 CNV gain 18288195
nsv600890 CNV gain 21841781
nsv981350 CNV duplication 23825009

Variation tolerance for RIOK1 Gene

Residual Variation Intolerance Score: 70.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.71; 46.42% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RIOK1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIOK1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIOK1 Gene

Disorders for RIOK1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RIOK1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
giant axonal neuropathy
  • gan
- elite association - COSMIC cancer census association via MalaCards
Search RIOK1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RIOK1

Genetic Association Database (GAD)
RIOK1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RIOK1
genes like me logo Genes that share disorders with RIOK1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RIOK1 Gene

Publications for RIOK1 Gene

  1. Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes. (PMID: 24948609) Ferreira-Cerca S. … Hurt E. (Nucleic Acids Res. 2014) 3 4 64
  2. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Benzimidazole inhibitors of protein kinase CK2 potently inhibit the activity of atypical protein kinase Rio1. (PMID: 27909846) KubiA8ski K. … Orzeszko A. (Mol. Cell. Biochem. 2017) 3 64

Products for RIOK1 Gene

  • Addgene plasmids for RIOK1

Sources for RIOK1 Gene

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