Human Gene RIOK1 (uc003mxn.3)
  Description: Homo sapiens RIO kinase 1 (RIOK1), transcript variant 1, mRNA.
RefSeq Summary (NM_031480): 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].
Transcript (Including UTRs)
   Position: hg19 chr6:7,390,062-7,418,270 Size: 28,209 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr6:7,390,236-7,417,674 Size: 27,439 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:7,390,062-7,418,270)mRNA (may differ from genome)Protein (568 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RIOK1_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein kinase RIO1; EC=2.7.11.1; AltName: Full=RIO kinase 1;
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SIMILARITY: Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.
SIMILARITY: Contains 1 protein kinase domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RIOK1
CDC HuGE Published Literature: RIOK1
Positive Disease Associations: Pancreatic Neoplasms
Related Studies:
  1. Pancreatic Neoplasms
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 20.59 RPKM in Testis
Total median expression: 430.44 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.12174-0.420 Picture PostScript Text
3' UTR -147.00596-0.247 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011009 - Kinase-like_dom
IPR018934 - RIO-like_kinase
IPR000687 - RIO_kinase
IPR018935 - RIO_kinase_CS
IPR017407 - Ser/Thr_kinase_Rio1

Pfam Domains:
PF01163 - RIO1 family

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q9BRS2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:2000234 positive regulation of rRNA processing

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030688 preribosome, small subunit precursor
GO:0034708 methyltransferase complex


-  Descriptions from all associated GenBank mRNAs
  AY094356 - Homo sapiens truncated hypothetical protein AD034 mRNA, complete cds.
AK314467 - Homo sapiens cDNA, FLJ95270, Homo sapiens RIO kinase 1 (yeast) (RIOK1), transcript variant 1,mRNA.
BC006104 - Homo sapiens RIO kinase 1 (yeast), mRNA (cDNA clone MGC:12903 IMAGE:3537086), complete cds.
AK054568 - Homo sapiens cDNA FLJ30006 fis, clone 3NB691000173.
JD407306 - Sequence 388330 from Patent EP1572962.
JD417169 - Sequence 398193 from Patent EP1572962.
KJ899717 - Synthetic construct Homo sapiens clone ccsbBroadEn_09111 RIOK1 gene, encodes complete protein.
KJ905565 - Synthetic construct Homo sapiens clone ccsbBroadEn_15181 RIOK1 gene, encodes complete protein.
AL834277 - Homo sapiens mRNA; cDNA DKFZp547L2113 (from clone DKFZp547L2113).
AF258661 - Homo sapiens AD034 mRNA, complete cds.
BC000811 - Homo sapiens RIO kinase 1 (yeast), mRNA (cDNA clone IMAGE:3453045), partial cds.
JD501852 - Sequence 482876 from Patent EP1572962.
JD094903 - Sequence 75927 from Patent EP1572962.
JD093701 - Sequence 74725 from Patent EP1572962.
JD550178 - Sequence 531202 from Patent EP1572962.
JD501325 - Sequence 482349 from Patent EP1572962.
JD292217 - Sequence 273241 from Patent EP1572962.
JD268625 - Sequence 249649 from Patent EP1572962.
JD296984 - Sequence 278008 from Patent EP1572962.
JD185224 - Sequence 166248 from Patent EP1572962.
JD494647 - Sequence 475671 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BRS2 (Reactome details) participates in the following event(s):

R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2RB28, NM_031480, NP_694550, Q8NDC8, Q96NV9, Q9BRS2, RIOK1_HUMAN
UCSC ID: uc003mxn.3
RefSeq Accession: NM_031480
Protein: Q9BRS2 (aka RIOK1_HUMAN)
CCDS: CCDS4500.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_031480.2
exon count: 17CDS single in 3' UTR: no RNA size: 2495
ORF size: 1707CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3513.00frame shift in genome: no % Coverage: 99.28
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.