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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
  • RIO1 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. Among its related pathways are Gene Expression and rRNA processing in the nucleus and cytosol. Gene Ontology (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).

Additional gene information for RIOK1 Gene

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

GeneHancer (GH) Regulatory Elements for RIOK1 Gene

Promoters and enhancers for RIOK1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I007388 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 575.8 +0.4 418 3.1 HDGF PKNOX1 ARNT MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 RIOK1 CAGE1 SSR1 DSP RREB1 ENSG00000225092 ENSG00000238221 GC06P007402
GH06I006745 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 36.2 -639.7 -639651 8.4 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A YBX1 DMAP1 YY1 SLC30A9 RIOK1 SNRNP48 SSR1 ENSG00000238221 RREB1 LY86 ENSG00000224532 LOC105374901 GC06P006721 LOC101928004
GH06I006586 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.9 -799.1 -799137 8.1 HDGF PKNOX1 ATF1 SMAD1 YBX1 IRF4 ZNF766 ZNF207 ZNF143 ATF7 LY86 RIOK1 SNRNP48 GC06M006605 LY86-AS1
GH06I007105 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 17.3 -280.9 -280881 5.5 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF416 RREB1 RIOK1 PIR43361 ENSG00000225092
GH06I006798 Enhancer 1.2 Ensembl ENCODE dbSUPER 28.2 -589.2 -589203 3.6 HDGF ZSCAN4 YBX1 BATF ZNF366 ZNF143 BCLAF1 IKZF2 RUNX3 SMARCA5 GC06M006799 LOC101928004 GC06P006801 RIOK1 ENSG00000226281
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RIOK1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RIOK1 gene promoter:

Genomic Locations for RIOK1 Gene

Genomic Locations for RIOK1 Gene
chr6:7,389,419-7,418,037
(GRCh38/hg38)
Size:
28,619 bases
Orientation:
Plus strand
chr6:7,389,729-7,418,270
(GRCh37/hg19)

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

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

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

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

Phenotypes From GWAS Catalog 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

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
  • Nucleoli (2)
See all subcellular structures

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
ATP Investigational Nutra Agonist 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 33 34
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia RIOK1 33 34
  • 89.44 (n)
cow
(Bos Taurus)
Mammalia RIOK1 33 34
  • 85.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RIOK1 34
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Riok1 33
  • 83.3 (n)
mouse
(Mus musculus)
Mammalia Riok1 33 16 34
  • 82.53 (n)
oppossum
(Monodelphis domestica)
Mammalia RIOK1 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves RIOK1 33 34
  • 75.73 (n)
lizard
(Anolis carolinensis)
Reptilia RIOK1 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia riok1 33
  • 73.81 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16329 33
zebrafish
(Danio rerio)
Actinopterygii riok1 33 34
  • 66.85 (n)
Dr.3368 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012121 33
  • 55.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11660 33 34
  • 53.95 (n)
worm
(Caenorhabditis elegans)
Secernentea riok-1 33 34
  • 58.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RIO1 33 34 36
  • 54.36 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E21121g 33
  • 52.6 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER257W 33
  • 51.76 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G37350 33
  • 55.58 (n)
rice
(Oryza sativa)
Liliopsida Os07g0162300 33
  • 54.25 (n)
Os.17949 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC10F6.10 33
  • 55.33 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU10652 33
  • 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 Variation AA Info Type
rs1000001721 -- 7,393,229(+) G/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000039236 -- 7,394,531(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000110048 -- 7,401,148(+) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000132764 -- 7,399,380(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000194608 -- 7,409,267(+) G/T 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)

Additional Variant Information 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

Additional Disease Information for RIOK1

No disorders were found for RIOK1 Gene.

No data available for MalaCards , 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 research 2014) 3 4 58
  2. The kinase activity of human Rio1 is required for final steps of cytoplasmic maturation of 40S subunits. (PMID: 22072790) Widmann B … Kutay U (Molecular biology of the cell 2012) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Benzimidazole inhibitors of protein kinase CK2 potently inhibit the activity of atypical protein kinase Rio1. (PMID: 27909846) Kubiński K … Orzeszko A (Molecular and cellular biochemistry 2017) 3 58

Products for RIOK1 Gene

Sources for RIOK1 Gene

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