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RIOX1 Gene(Protein Coding)

Ribosomal Oxygenase 1

GCID:
GC14P073492
GIFtS:
26
Genes Participants
UDN Logo

Aliases for RIOX1 Gene

Aliases for RIOX1 Gene

  • Ribosomal Oxygenase 1 2 3 3 5
  • Nucleolar Protein 66 2 3 4
  • Bifunctional Lysine-Specific Demethylase And Histidyl-Hydroxylase NO66 3 4
  • 60S Ribosomal Protein L8 Histidine Hydroxylase 3 4
  • Myc-Associated Protein With JmjC Domain 2 4
  • Histone Lysine Demethylase NO66 3 4
  • Ribosomal Oxygenase NO66 3 4
  • C14orf169 3 4
  • HsNO66 3 4
  • MAPJD 3 4
  • NO66 3 4
  • ROX 3 4
  • MYC-Associated Protein With JmjC Domain 3
  • Chromosome 14 Open Reading Frame 169 2
  • Lysine-Specific Demethylase NO66 3
  • Up-Regulated In Lung Cancer 2 3
  • EC 1.14.11.27 4
  • EC 1.14.11.- 4
  • JMJD9 3
  • URLC2 3

External Ids for RIOX1 Gene

Previous HGNC Symbols for RIOX1 Gene

  • C14orf169

Summaries for RIOX1 Gene

GeneCards Summary for RIOX1 Gene

RIOX1 (Ribosomal Oxygenase 1) is a Protein Coding gene. Among its related pathways are Chromatin Regulation / Acetylation. An important paralog of this gene is RIOX2.

UniProtKB/Swiss-Prot for RIOX1 Gene

  • Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates Lys-4 (H3K4me) and Lys-36 (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 Lys-4 (H3K4me3) and monomethylated H3 Lys-4 (H3K4me1) residues, while it has weaker activity for dimethylated H3 Lys-36 (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on His-216. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC-induced transcriptional activation.

Additional gene information for RIOX1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RIOX1 Gene

Genomics for RIOX1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for RIOX1 Gene

Promoters and enhancers for RIOX1 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
GH14J073490 Promoter/Enhancer 1.5 Ensembl ENCODE 650.7 +0.5 467 2.5 PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ACOT1 PIR46009 RIOX1 GC14P073495 LOC100420966 ELMSAN1 ZNF410 RBM25 DCAF4 ENSG00000258695
GH14J073489 Enhancer 0.4 ENCODE 650.7 -1.0 -963 0.2 GATA3 PRDM10 PIR46009 RIOX1 GC14P073495 ENSG00000284930 HEATR4
GH14J073748 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4 +266.7 266692 17.4 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 ELMSAN1 MIR4505 GC14P073756 ZNF410 RBM25 PNMA1 ENSG00000258559 LOC100506476 ABCD4 ENSG00000258891
GH14J073767 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 3.1 +280.6 280605 7.9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A ENSG00000258559 YLPM1 RBM25 NT5CP1 PTGR2 LOC100506476 ABCD4 PNMA1 ENSG00000223300 ELMSAN1
GH14J073226 Enhancer 1.1 FANTOM5 Ensembl ENCODE 1.4 -263.1 -263123 3.3 FOXA2 JUN SIN3A ZIC2 GLIS2 PATZ1 FOS FOSL2 ZBTB20 ZEB2 PIR53719 GC14P073229 PSEN1 LOC101928123 NUMB DPF3 ZFYVE1 RIOX1 GC14P073223
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RIOX1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RIOX1 Gene

Genomic Locations for RIOX1 Gene
chr14:73,490,934-73,493,401
(GRCh38/hg38)
Size:
2,468 bases
Orientation:
Plus strand
chr14:73,957,644-73,960,105
(GRCh37/hg19)
Size:
2,462 bases
Orientation:
Plus strand

Genomic View for RIOX1 Gene

Genes around RIOX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIOX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIOX1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RIOX1 Gene

Proteins for RIOX1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for RIOX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6W3-RIOX1_HUMAN
    Recommended name:
    Ribosomal oxygenase 1
    Protein Accession:
    Q9H6W3
    Secondary Accessions:
    • B4DT02

    Protein attributes for RIOX1 Gene

    Size:
    641 amino acids
    Molecular mass:
    71086 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with SP7/OSX; the interaction is direct (By similarity). Interacts with MYC. Interacts with PHF19; leading to its recruitment to H3K36me3 sites.

    Three dimensional structures from OCA and Proteopedia for RIOX1 Gene

    Alternative splice isoforms for RIOX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RIOX1 Gene

Post-translational modifications for RIOX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RIOX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RIOX1 Gene

Domains & Families for RIOX1 Gene

Gene Families for RIOX1 Gene

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

Protein Domains for RIOX1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RIOX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H6W3

UniProtKB/Swiss-Prot:

RIOX1_HUMAN :
  • Belongs to the ROX family. NO66 subfamily.
Family:
  • Belongs to the ROX family. NO66 subfamily.
genes like me logo Genes that share domains with RIOX1: view

Function for RIOX1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for RIOX1 Gene

UniProtKB/Swiss-Prot Function:
Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates Lys-4 (H3K4me) and Lys-36 (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 Lys-4 (H3K4me3) and monomethylated H3 Lys-4 (H3K4me1) residues, while it has weaker activity for dimethylated H3 Lys-36 (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on His-216. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC-induced transcriptional activation.
UniProtKB/Swiss-Prot CatalyticActivity:
Protein N(6),N(6)-dimethyl-L-lysine + 2 2-oxoglutarate + 2 O(2) = protein L-lysine + 2 succinate + 2 formaldehyde + 2 CO(2).
UniProtKB/Swiss-Prot CatalyticActivity:
L-histidine-[60S ribosomal protein L8] + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-histidine-[60S ribosomal protein L8] + succinate + CO(2).

Enzyme Numbers (IUBMB) for RIOX1 Gene

Phenotypes From GWAS Catalog for RIOX1 Gene

Gene Ontology (GO) - Molecular Function for RIOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding ISS --
GO:0005515 protein binding IPI 19927124
GO:0016491 oxidoreductase activity IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA,ISS --
GO:0032453 histone demethylase activity (H3-K4 specific) IEA,ISS --
genes like me logo Genes that share ontologies with RIOX1: view
genes like me logo Genes that share phenotypes with RIOX1: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RIOX1 Gene

Localization for RIOX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIOX1 Gene

Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Granular part of nucleoli. Nucleoplasm, nucleoplasmic foci, some of them associated with nucleoli.

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RIOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IBA --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IEA,IDA --
genes like me logo Genes that share ontologies with RIOX1: view

No data available for Subcellular locations from COMPARTMENTS for RIOX1 Gene

Pathways & Interactions for RIOX1 Gene

genes like me logo Genes that share pathways with RIOX1: view

Pathways by source for RIOX1 Gene

1 Cell Signaling Technology pathway for RIOX1 Gene

Interacting Proteins for RIOX1 Gene

Selected Interacting proteins: Q9H6W3-RIOX1_HUMAN for RIOX1 Gene via UniProtKB IID

GPS-Prot Interaction Network for RIOX1

Gene Ontology (GO) - Biological Process for RIOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0030961 peptidyl-arginine hydroxylation IBA --
genes like me logo Genes that share ontologies with RIOX1: view

No data available for SIGNOR curated interactions for RIOX1 Gene

Drugs & Compounds for RIOX1 Gene

Products:

  1. Drug

(4) Drugs for RIOX1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Formaldehyde Approved, Vet_approved Pharma 102
Oxygen Approved, Vet_approved Pharma 0
Succinic acid Approved Nutra Full agonist, Agonist 0
Oxogluric acid Experimental, Investigational Nutra 0
genes like me logo Genes that share compounds with RIOX1: view

Transcripts for RIOX1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RIOX1 Gene

(1) REFSEQ mRNAs :
(57) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RIOX1 Gene

No ASD Table

Relevant External Links for RIOX1 Gene

GeneLoc Exon Structure for
RIOX1
ECgene alternative splicing isoforms for
RIOX1

Expression for RIOX1 Gene

Products:

  1. Primer

NURSA nuclear receptor signaling pathways regulating expression of RIOX1 Gene:

RIOX1

mRNA Expression by UniProt/SwissProt for RIOX1 Gene:

Q9H6W3-RIOX1_HUMAN
Tissue specificity: Widely expressed. Overexpressed in lung carcinomas.

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIOX1 Gene

Orthologs for RIOX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RIOX1 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia C8H14orf169 33
  • 89.83 (n)
cow
(Bos Taurus)
 Mammalia NO66 33
  • 87.47 (n)
rat
(Rattus norvegicus)
 Mammalia RGD1307704 33
  • 82.94 (n)
mouse
(Mus musculus)
 Mammalia 2410016O06Rik 33
  • 81.91 (n)
Riox1 16
chicken
(Gallus gallus)
 Aves C5H14ORF169 33
  • 64.03 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100488246 33
  • 59.12 (n)
zebrafish
(Danio rerio)
 Actinopterygii zgc:162967 33
  • 56.92 (n)
Dr.4334 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP001938 33
  • 54.17 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG2982 33
  • 51.89 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea Cin.4160 33
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4160 33
Species where no ortholog for RIOX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RIOX1 Gene

ENSEMBL:
Gene Tree for RIOX1 (if available)
TreeFam:
Gene Tree for RIOX1 (if available)

Paralogs for RIOX1 Gene

Paralogs for RIOX1 Gene

genes like me logo Genes that share paralogs with RIOX1: view

Variants for RIOX1 Gene

Sequence variations from dbSNP and Humsavar for RIOX1 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000414511 -- 73,491,297(+) C/A coding_sequence_variant, synonymous_variant
rs1000468253 -- 73,491,491(+) C/G coding_sequence_variant, synonymous_variant
rs1000764213 -- 73,490,900(+) C/G upstream_transcript_variant
rs1000801752 -- 73,493,195(+) C/T 3_prime_UTR_variant
rs1002535409 -- 73,489,108(+) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RIOX1 Gene

Variant ID Type Subtype PubMed ID
esv3892561 CNV gain 25118596
nsv1035460 CNV gain 25217958
nsv510643 CNV deletion 20534489

Additional Variant Information for RIOX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIOX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for RIOX1 Gene

Disorders for RIOX1 Gene

Additional Disease Information for RIOX1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RIOX1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RIOX1 Gene

Publications for RIOX1 Gene

  1. Identification of Myc-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer. (PMID: 17308053) Suzuki C … Daigo Y (Molecular cancer therapeutics 2007) 2 3 4 58
  2. Structure-function relationships of human JmjC oxygenases-demethylases versus hydroxylases. (PMID: 27309310) Markolovic S … Schofield CJ (Current opinion in structural biology 2016) 2 3 58
  3. Purification, crystallization and preliminary crystallographic analysis of histone lysine demethylase NO66 from Homo sapiens. (PMID: 22750859) Zhou X … Zang J (Acta crystallographica. Section F, Structural biology and crystallization communications 2012) 2 3 58
  4. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. (PMID: 23160351) Brien GL … Bracken AP (Nature structural & molecular biology 2012) 3 4 58
  5. Regulation of the osteoblast-specific transcription factor Osterix by NO66, a Jumonji family histone demethylase. (PMID: 19927124) Sinha KM … de Crombrugghe B (The EMBO journal 2010) 2 3 58

Products for RIOX1 Gene

Sources for RIOX1 Gene

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