Human Gene RIOK3 (uc002kui.4) Description and Page Index
  Description: Homo sapiens RIO kinase 3 (RIOK3), mRNA.
RefSeq Summary (NM_003831): 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]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660803.144728.1, SRR1660807.22823.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000339486.8/ ENSP00000341874.3 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr18:21,032,787-21,063,099 Size: 30,313 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr18:21,033,404-21,061,243 Size: 27,840 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:21,032,787-21,063,099)mRNA (may differ from genome)Protein (519 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKB

-  Comments and Description Text from UniProtKB
  ID: RIOK3_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein kinase RIO3; EC=2.7.11.1; AltName: Full=RIO kinase 3; AltName: Full=sudD homolog;
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
INTERACTION: Q92851:CASP10; NbExp=4; IntAct=EBI-1047061, EBI-495095;
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.
SIMILARITY: Contains 1 protein kinase domain.

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 41.43 RPKM in Esophagus - Mucosa
Total median expression: 807.99 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -233.72617-0.379 Picture PostScript Text
3' UTR -511.251856-0.275 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
IPR017406 - Ser/Thr_kinase_Rio3

Pfam Domains:
PF01163 - RIO1 family

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

ModBase Predicted Comparative 3D Structure on O14730
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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 orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  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:0046872 metal ion binding
GO:0089720 caspase binding

Biological Process:
GO:0002376 immune system process
GO:0006468 protein phosphorylation
GO:0007059 chromosome segregation
GO:0016310 phosphorylation
GO:0030490 maturation of SSU-rRNA
GO:0032463 negative regulation of protein homooligomerization
GO:0032728 positive regulation of interferon-beta production
GO:0039534 negative regulation of MDA-5 signaling pathway
GO:0042254 ribosome biogenesis
GO:0043124 negative regulation of I-kappaB kinase/NF-kappaB signaling
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0051607 defense response to virus
GO:0071359 cellular response to dsRNA
GO:0098586 cellular response to virus
GO:1990786 cellular response to dsDNA

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


-  Descriptions from all associated GenBank mRNAs
  AK057292 - Homo sapiens cDNA FLJ32730 fis, clone TESTI2001099, highly similar to Serine/threonine-protein kinase RIO3 (EC 2.7.11.1).
AK303938 - Homo sapiens cDNA FLJ54233 complete cds, highly similar to Serine/threonine-protein kinase RIO3 (EC 2.7.11.1).
BC028360 - Homo sapiens RIO kinase 3 (yeast), mRNA (cDNA clone MGC:26362 IMAGE:4828351), complete cds.
LP895363 - Sequence 227 from Patent EP3253886.
JD396580 - Sequence 377604 from Patent EP1572962.
BC039729 - Homo sapiens RIO kinase 3 (yeast), mRNA (cDNA clone MGC:47736 IMAGE:5745005), complete cds.
JD523179 - Sequence 504203 from Patent EP1572962.
AF013591 - Homo sapiens homolog of the Aspergillus nidulans sudD gene product mRNA, complete cds.
JD195020 - Sequence 176044 from Patent EP1572962.
HM005587 - Homo sapiens clone HTL-S-47 testicular secretory protein Li 47 mRNA, complete cds.
AK024958 - Homo sapiens cDNA: FLJ21305 fis, clone COL02124.
AK304571 - Homo sapiens cDNA FLJ50375 complete cds, highly similar to Serine/threonine-protein kinase RIO3 (EC 2.7.11.1).
AK310783 - Homo sapiens cDNA, FLJ17825.
JD515716 - Sequence 496740 from Patent EP1572962.
BX640929 - Homo sapiens mRNA; cDNA DKFZp779L1370 (from clone DKFZp779L1370).
JD354811 - Sequence 335835 from Patent EP1572962.
JD235476 - Sequence 216500 from Patent EP1572962.
JD308799 - Sequence 289823 from Patent EP1572962.
JD364453 - Sequence 345477 from Patent EP1572962.
JD410883 - Sequence 391907 from Patent EP1572962.
JD468001 - Sequence 449025 from Patent EP1572962.
JD109369 - Sequence 90393 from Patent EP1572962.
JD421353 - Sequence 402377 from Patent EP1572962.
JD181156 - Sequence 162180 from Patent EP1572962.
JD165096 - Sequence 146120 from Patent EP1572962.
JD253368 - Sequence 234392 from Patent EP1572962.
JD463414 - Sequence 444438 from Patent EP1572962.
JD219174 - Sequence 200198 from Patent EP1572962.
JD277223 - Sequence 258247 from Patent EP1572962.
JD305558 - Sequence 286582 from Patent EP1572962.
JD349753 - Sequence 330777 from Patent EP1572962.
JD452242 - Sequence 433266 from Patent EP1572962.
JD100297 - Sequence 81321 from Patent EP1572962.
JD542487 - Sequence 523511 from Patent EP1572962.
JD542488 - Sequence 523512 from Patent EP1572962.
JD542489 - Sequence 523513 from Patent EP1572962.
JD283291 - Sequence 264315 from Patent EP1572962.
JD279033 - Sequence 260057 from Patent EP1572962.
JD326715 - Sequence 307739 from Patent EP1572962.
JD290406 - Sequence 271430 from Patent EP1572962.
JD527412 - Sequence 508436 from Patent EP1572962.
JD531478 - Sequence 512502 from Patent EP1572962.
JD332016 - Sequence 313040 from Patent EP1572962.
JD447679 - Sequence 428703 from Patent EP1572962.
JD085110 - Sequence 66134 from Patent EP1572962.
JD249565 - Sequence 230589 from Patent EP1572962.
JD378011 - Sequence 359035 from Patent EP1572962.
JD354051 - Sequence 335075 from Patent EP1572962.
JD269661 - Sequence 250685 from Patent EP1572962.
JD189799 - Sequence 170823 from Patent EP1572962.
JD130865 - Sequence 111889 from Patent EP1572962.
JD219991 - Sequence 201015 from Patent EP1572962.
JD091258 - Sequence 72282 from Patent EP1572962.
JD356843 - Sequence 337867 from Patent EP1572962.
DQ594791 - Homo sapiens piRNA piR-60903, complete sequence.

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

Protein O14730 (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_003831, NP_003822, O14730, Q8IXN9, RIOK3_HUMAN, SUDD
UCSC ID: uc002kui.4
RefSeq Accession: NM_003831
Protein: O14730 (aka RIOK3_HUMAN)
CCDS: CCDS11877.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003831.3
exon count: 13CDS single in 3' UTR: no RNA size: 4035
ORF size: 1560CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2326.00frame shift in genome: no % Coverage: 99.95
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.