Human Gene RIOK2 (uc003kmz.3) Description and Page Index
  Description: Homo sapiens RIO kinase 2 (RIOK2), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:96,496,571-96,519,005 Size: 22,435 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr5:96,498,765-96,518,895 Size: 20,131 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:96,496,571-96,519,005)mRNA (may differ from genome)Protein (552 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: RIOK2_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein kinase RIO2; EC=2.7.11.1; AltName: Full=RIO kinase 2;
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.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RIOK2
CDC HuGE Published Literature: RIOK2
Positive Disease Associations: Cholesterol , Cholesterol, LDL
Related Studies:
  1. Cholesterol
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Cholesterol, LDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.

-  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: 6.86 RPKM in Cells - Transformed fibroblasts
Total median expression: 176.08 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 -47.50110-0.432 Picture PostScript Text
3' UTR -524.212194-0.239 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
IPR015285 - RIO2_kinase_winged_hlx_N
IPR018935 - RIO_kinase_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF01163 - RIO1 family
PF06293 - Lipopolysaccharide kinase (Kdo/WaaP) family
PF09202 - Rio2, N-terminal

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q9BVS4
FrontTopSide
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 BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006468 protein phosphorylation
GO:0007049 cell cycle
GO:0016310 phosphorylation
GO:0030071 regulation of mitotic metaphase/anaphase transition
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0046777 protein autophosphorylation
GO:2000208 positive regulation of ribosomal small subunit export from nucleus
GO:2000234 positive regulation of rRNA processing

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


-  Descriptions from all associated GenBank mRNAs
  LF210706 - JP 2014500723-A/18209: Polycomb-Associated Non-Coding RNAs.
AK001697 - Homo sapiens cDNA FLJ10835 fis, clone NT2RP4001210.
LF210707 - JP 2014500723-A/18210: Polycomb-Associated Non-Coding RNAs.
LF340503 - JP 2014500723-A/148006: Polycomb-Associated Non-Coding RNAs.
LF340502 - JP 2014500723-A/148005: Polycomb-Associated Non-Coding RNAs.
LF340501 - JP 2014500723-A/148004: Polycomb-Associated Non-Coding RNAs.
BC000953 - Homo sapiens RIO kinase 2 (yeast), mRNA (cDNA clone MGC:4923 IMAGE:3449997), complete cds.
AK002021 - Homo sapiens cDNA FLJ11159 fis, clone PLACE1006966.
LF340500 - JP 2014500723-A/148003: Polycomb-Associated Non-Coding RNAs.
KJ899191 - Synthetic construct Homo sapiens clone ccsbBroadEn_08585 RIOK2 gene, encodes complete protein.
LF340499 - JP 2014500723-A/148002: Polycomb-Associated Non-Coding RNAs.
AK225348 - Homo sapiens mRNA for Serine/threonine-protein kinase RIO2 variant, clone: HEP13058.
LF385165 - JP 2014500723-A/192668: Polycomb-Associated Non-Coding RNAs.
LF340498 - JP 2014500723-A/148001: Polycomb-Associated Non-Coding RNAs.
LF340497 - JP 2014500723-A/148000: Polycomb-Associated Non-Coding RNAs.
LF340496 - JP 2014500723-A/147999: Polycomb-Associated Non-Coding RNAs.
LF340495 - JP 2014500723-A/147998: Polycomb-Associated Non-Coding RNAs.
LF340494 - JP 2014500723-A/147997: Polycomb-Associated Non-Coding RNAs.
LF340493 - JP 2014500723-A/147996: Polycomb-Associated Non-Coding RNAs.
LF340492 - JP 2014500723-A/147995: Polycomb-Associated Non-Coding RNAs.
LF340490 - JP 2014500723-A/147993: Polycomb-Associated Non-Coding RNAs.
LF340488 - JP 2014500723-A/147991: Polycomb-Associated Non-Coding RNAs.
LF340487 - JP 2014500723-A/147990: Polycomb-Associated Non-Coding RNAs.
MA620742 - JP 2018138019-A/192668: Polycomb-Associated Non-Coding RNAs.
MA446283 - JP 2018138019-A/18209: Polycomb-Associated Non-Coding RNAs.
MA446284 - JP 2018138019-A/18210: Polycomb-Associated Non-Coding RNAs.
MA576080 - JP 2018138019-A/148006: Polycomb-Associated Non-Coding RNAs.
MA576079 - JP 2018138019-A/148005: Polycomb-Associated Non-Coding RNAs.
MA576078 - JP 2018138019-A/148004: Polycomb-Associated Non-Coding RNAs.
MA576077 - JP 2018138019-A/148003: Polycomb-Associated Non-Coding RNAs.
MA576076 - JP 2018138019-A/148002: Polycomb-Associated Non-Coding RNAs.
MA576075 - JP 2018138019-A/148001: Polycomb-Associated Non-Coding RNAs.
MA576074 - JP 2018138019-A/148000: Polycomb-Associated Non-Coding RNAs.
MA576073 - JP 2018138019-A/147999: Polycomb-Associated Non-Coding RNAs.
MA576072 - JP 2018138019-A/147998: Polycomb-Associated Non-Coding RNAs.
MA576071 - JP 2018138019-A/147997: Polycomb-Associated Non-Coding RNAs.
MA576070 - JP 2018138019-A/147996: Polycomb-Associated Non-Coding RNAs.
MA576069 - JP 2018138019-A/147995: Polycomb-Associated Non-Coding RNAs.
MA576067 - JP 2018138019-A/147993: Polycomb-Associated Non-Coding RNAs.
MA576065 - JP 2018138019-A/147991: Polycomb-Associated Non-Coding RNAs.
MA576064 - JP 2018138019-A/147990: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9BVS4 (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: NM_018343, NP_060813, Q9BVS4, Q9NUT0, RIOK2_HUMAN
UCSC ID: uc003kmz.3
RefSeq Accession: NM_018343
Protein: Q9BVS4 (aka RIOK2_HUMAN)
CCDS: CCDS4089.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018343.2
exon count: 10CDS single in 3' UTR: no RNA size: 3980
ORF size: 1659CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3515.00frame shift in genome: no % Coverage: 99.57
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.