Riox1 (ribosomal oxygenase 1) - Rat Genome Database

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Gene: Riox1 (ribosomal oxygenase 1) Rattus norvegicus
Analyze
Symbol: Riox1
Name: ribosomal oxygenase 1
RGD ID: 1307704
Description: Predicted to enable 2-oxoglutarate-dependent dioxygenase activity and iron ion binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of osteoblast differentiation. Predicted to be located in nucleus. Predicted to be active in nucleolus. Orthologous to human RIOX1 (ribosomal oxygenase 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66; histone lysine demethylase NO66; hypothetical protein LOC314300; LOC314300; lysine-specific demethylase NO66; myc-associated protein with JmjC domain; No66; nucleolar protein 66; RGD1307704; similar to RIKEN cDNA 2410016O06; uncharacterized protein LOC314300
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86109,310,748 - 109,313,365 (+)NCBIGRCr8
mRatBN7.26103,579,642 - 103,582,260 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6103,579,642 - 103,582,250 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6103,741,389 - 103,744,008 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,040,602 - 104,043,221 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06103,410,068 - 103,412,687 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06107,428,508 - 107,431,126 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6107,428,508 - 107,431,116 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06118,113,014 - 118,115,632 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46107,985,351 - 107,987,969 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16107,989,236 - 107,991,030 (+)NCBI
Celera6101,409,543 - 101,412,161 (+)NCBICelera
Cytogenetic Map6q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IBA,ISO)
nucleoplasm  (IEA)
nucleus  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14742713   PMID:19927124  


Genomics

Comparative Map Data
Riox1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86109,310,748 - 109,313,365 (+)NCBIGRCr8
mRatBN7.26103,579,642 - 103,582,260 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6103,579,642 - 103,582,250 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6103,741,389 - 103,744,008 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,040,602 - 104,043,221 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06103,410,068 - 103,412,687 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06107,428,508 - 107,431,126 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6107,428,508 - 107,431,116 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06118,113,014 - 118,115,632 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46107,985,351 - 107,987,969 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16107,989,236 - 107,991,030 (+)NCBI
Celera6101,409,543 - 101,412,161 (+)NCBICelera
Cytogenetic Map6q31NCBI
RIOX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381473,490,933 - 73,493,394 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1473,490,933 - 73,493,394 (+)EnsemblGRCh38hg38GRCh38
GRCh371473,957,638 - 73,960,098 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361473,027,397 - 73,029,858 (+)NCBINCBI36Build 36hg18NCBI36
Build 341473,027,421 - 73,029,850NCBI
Celera1454,021,934 - 54,024,395 (+)NCBICelera
Cytogenetic Map14q24.3NCBI
HuRef1454,124,500 - 54,126,962 (+)NCBIHuRef
CHM1_11473,897,062 - 73,899,526 (+)NCBICHM1_1
T2T-CHM13v2.01467,698,891 - 67,701,354 (+)NCBIT2T-CHM13v2.0
Riox1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391283,997,382 - 83,999,727 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1283,997,382 - 83,999,725 (+)EnsemblGRCm39 Ensembl
GRCm381283,950,608 - 83,952,953 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1283,950,608 - 83,952,951 (+)EnsemblGRCm38mm10GRCm38
MGSCv371285,291,558 - 85,293,903 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361284,840,418 - 84,842,694 (+)NCBIMGSCv36mm8
Celera1285,397,188 - 85,399,533 (+)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1238.97NCBI
Riox1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555231,908,024 - 1,909,944 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555231,907,570 - 1,910,038 (-)NCBIChiLan1.0ChiLan1.0
RIOX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21574,608,141 - 74,637,133 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11473,824,655 - 73,853,647 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01454,078,798 - 54,110,366 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11472,937,767 - 72,940,614 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1472,937,119 - 72,939,242 (+)Ensemblpanpan1.1panPan2
RIOX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1846,815,064 - 46,849,992 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl846,815,125 - 46,849,991 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha846,499,197 - 46,501,632 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0847,043,793 - 47,046,228 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1846,711,521 - 46,713,956 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0846,729,654 - 46,731,930 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0847,119,648 - 47,121,925 (+)NCBIUU_Cfam_GSD_1.0
Riox1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864029,300,071 - 29,302,595 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364882,766,451 - 2,768,408 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364882,766,406 - 2,768,551 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIOX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl796,823,130 - 96,827,719 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1796,823,073 - 96,831,582 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27102,609,718 - 102,613,921 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RIOX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12450,744,200 - 50,746,925 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605338,929,635 - 38,940,359 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Riox1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473427,958,942 - 27,961,917 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Riox1
10 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:90
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000013431
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)683190345106747639Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 6 13 12 2 12 53 16 28 2
Low 3 37 44 29 17 29 8 11 21 19 13 9 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000013431   ⟹   ENSRNOP00000013431
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6103,579,642 - 103,582,250 (+)Ensembl
Rnor_6.0 Ensembl6107,428,508 - 107,431,116 (+)Ensembl
RefSeq Acc Id: NM_001108040   ⟹   NP_001101510
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86109,310,748 - 109,313,365 (+)NCBI
mRatBN7.26103,579,642 - 103,582,260 (+)NCBI
Rnor_6.06107,428,508 - 107,431,126 (+)NCBI
Rnor_5.06118,113,014 - 118,115,632 (-)NCBI
RGSC_v3.46107,985,351 - 107,987,969 (+)RGD
Celera6101,409,543 - 101,412,161 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101510 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZU57 (Get FASTA)   NCBI Sequence Viewer  
  EDL81467 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013431
  ENSRNOP00000013431.2
  ENSRNOP00055039136
  ENSRNOP00060036730
  ENSRNOP00065039673
RefSeq Acc Id: NP_001101510   ⟸   NM_001108040
- UniProtKB: D3ZU57 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013431   ⟸   ENSRNOT00000013431
Protein Domains
JmjC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZU57-F1-model_v2 AlphaFold D3ZU57 1-597 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307704 AgrOrtholog
BioCyc Gene G2FUF-36848 BioCyc
Ensembl Genes ENSRNOG00000010126 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055027474 UniProtKB/Swiss-Prot
  ENSRNOG00060025608 UniProtKB/Swiss-Prot
  ENSRNOG00065028064 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013431 ENTREZGENE
  ENSRNOT00000013431.6 UniProtKB/Swiss-Prot
  ENSRNOT00055047559 UniProtKB/Swiss-Prot
  ENSRNOT00060044297 UniProtKB/Swiss-Prot
  ENSRNOT00065048355 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.930.40 UniProtKB/Swiss-Prot
  Cupin UniProtKB/Swiss-Prot
  JmjC domain-containing ribosomal oxygenase (ROX), dimer domain UniProtKB/Swiss-Prot
InterPro JmjC_dom UniProtKB/Swiss-Prot
  JmjC_protein UniProtKB/Swiss-Prot
  RIOX1/NO66-like_C_WH UniProtKB/Swiss-Prot
KEGG Report rno:314300 UniProtKB/Swiss-Prot
NCBI Gene 314300 ENTREZGENE
PANTHER PTHR13096 UniProtKB/Swiss-Prot
  RIBOSOMAL OXYGENASE 1-RELATED UniProtKB/Swiss-Prot
Pfam Cupin_4 UniProtKB/Swiss-Prot
  RIOX1_C_WH UniProtKB/Swiss-Prot
PhenoGen Riox1 PhenoGen
PROSITE JMJC UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000010126 RatGTEx
  ENSRNOG00055027474 RatGTEx
  ENSRNOG00060025608 RatGTEx
  ENSRNOG00065028064 RatGTEx
SMART JmjC UniProtKB/Swiss-Prot
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot
UniProt D3ZU57 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Riox1  ribosomal oxygenase 1  RGD1307704  similar to RIKEN cDNA 2410016O06  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1307704  similar to RIKEN cDNA 2410016O06   RGD1307704_predicted  similar to RIKEN cDNA 2410016O06 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1307704_predicted  similar to RIKEN cDNA 2410016O06 (predicted)  LOC314300_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314300_predicted  similar to RIKEN cDNA 2410016O06 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL