Nop9 (NOP9 nucleolar protein) - Rat Genome Database

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Gene: Nop9 (NOP9 nucleolar protein) Rattus norvegicus
Analyze
Symbol: Nop9
Name: NOP9 nucleolar protein
RGD ID: 1308396
Description: Predicted to enable RNA binding activity. Predicted to be involved in ribosome biogenesis. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. Predicted to be active in nucleolus. Orthologous to human NOP9 (NOP9 nucleolar protein); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC290235; LOC290235; nucleolar protein 9; RGD1308396; similar to chromosome 14 open reading frame 21; uncharacterized protein LOC290235
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81533,213,786 - 33,222,147 (+)NCBIGRCr8
mRatBN7.21529,243,853 - 29,252,220 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,243,862 - 29,252,220 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1531,089,539 - 31,097,897 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,236,751 - 32,245,109 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,479,099 - 30,487,448 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,431,357 - 34,439,861 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,431,357 - 34,439,861 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,320,522 - 38,328,222 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,908,034 - 33,916,489 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11533,923,804 - 33,931,934 (+)NCBI
Celera1528,819,509 - 28,826,943 (+)NCBICelera
Cytogenetic Map15p13NCBI
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

Cellular Component

Molecular Function
RNA binding  (IBA)

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:22658674   PMID:22681889  


Genomics

Comparative Map Data
Nop9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81533,213,786 - 33,222,147 (+)NCBIGRCr8
mRatBN7.21529,243,853 - 29,252,220 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,243,862 - 29,252,220 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1531,089,539 - 31,097,897 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,236,751 - 32,245,109 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,479,099 - 30,487,448 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,431,357 - 34,439,861 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,431,357 - 34,439,861 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,320,522 - 38,328,222 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,908,034 - 33,916,489 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11533,923,804 - 33,931,934 (+)NCBI
Celera1528,819,509 - 28,826,943 (+)NCBICelera
Cytogenetic Map15p13NCBI
NOP9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,271,203 - 24,309,124 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,299,850 - 24,309,124 (+)EnsemblGRCh38hg38GRCh38
GRCh371424,769,056 - 24,778,330 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,838,938 - 23,844,214 (+)NCBINCBI36Build 36hg18NCBI36
Build 341423,838,937 - 23,844,214NCBI
Celera144,633,722 - 4,639,003 (+)NCBICelera
Cytogenetic Map14q12NCBI
HuRef144,884,260 - 4,889,541 (+)NCBIHuRef
CHM1_11424,767,698 - 24,772,974 (+)NCBICHM1_1
T2T-CHM13v2.01418,498,194 - 18,507,467 (+)NCBIT2T-CHM13v2.0
Nop9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391455,983,150 - 55,993,091 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1455,983,150 - 55,992,957 (+)EnsemblGRCm39 Ensembl
GRCm381455,745,693 - 55,755,634 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,745,693 - 55,755,500 (+)EnsemblGRCm38mm10GRCm38
MGSCv371456,364,530 - 56,374,471 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361454,699,784 - 54,708,135 (+)NCBIMGSCv36mm8
Celera1453,550,741 - 53,560,682 (+)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.19NCBI
Nop9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540935,992,160 - 36,002,459 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540935,996,918 - 36,002,460 (-)NCBIChiLan1.0ChiLan1.0
LOC100979193
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,654,963 - 25,667,203 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11424,871,389 - 24,880,710 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0145,076,270 - 5,085,596 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11423,199,608 - 23,208,877 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1423,199,608 - 23,208,877 (+)Ensemblpanpan1.1panPan2
NOP9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,270,192 - 4,275,722 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,270,243 - 4,275,677 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha84,191,860 - 4,197,386 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.084,381,002 - 4,386,524 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl84,381,048 - 4,386,513 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.184,071,346 - 4,076,867 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.084,133,176 - 4,138,695 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,395,760 - 4,401,279 (+)NCBIUU_Cfam_GSD_1.0
Nop9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,133,040 - 36,139,009 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722249,358 - 256,192 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936722250,001 - 255,908 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOP9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl774,985,753 - 74,992,946 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1774,985,748 - 74,992,108 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,256,688 - 80,263,045 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NOP9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,282,877 - 1,288,265 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,282,873 - 1,288,148 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603612,967,398 - 12,976,701 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nop9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,199,110 - 8,204,612 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248208,199,350 - 8,204,619 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nop9
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:32
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000027604
Prediction methods:Miranda, Rnahybrid, Targetscan
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
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat


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 3 20 33 20 19 20 59 28 41 11
Low 23 24 21 21 8 11 15 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027604   ⟹   ENSRNOP00000027604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1529,243,862 - 29,252,220 (+)Ensembl
Rnor_6.0 Ensembl1534,431,357 - 34,439,861 (+)Ensembl
RefSeq Acc Id: NM_001106040   ⟹   NP_001099510
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,213,789 - 33,222,147 (+)NCBI
mRatBN7.21529,243,862 - 29,252,220 (+)NCBI
Rnor_6.01534,431,357 - 34,439,861 (+)NCBI
Rnor_5.01538,320,522 - 38,328,222 (+)NCBI
RGSC_v3.41533,908,034 - 33,916,489 (+)RGD
Celera1528,819,509 - 28,826,943 (+)RGD
Sequence:
RefSeq Acc Id: XM_063274131   ⟹   XP_063130201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,213,786 - 33,221,079 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001099510 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130201 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM14277 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027604
  ENSRNOP00000027604.2
Reference Protein Sequences
RefSeq Acc Id: NP_001099510   ⟸   NM_001106040
- UniProtKB: D3ZKI9 (UniProtKB/TrEMBL),   A6KH48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000027604   ⟸   ENSRNOT00000027604
RefSeq Acc Id: XP_063130201   ⟸   XM_063274131
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKI9-F1-model_v2 AlphaFold D3ZKI9 1-634 view protein structure

Transcriptome

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

Promoters
RGD ID:13699687
Promoter ID:EPDNEW_R10211
Type:initiation region
Name:Nop9_1
Description:NOP9 nucleolar protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01534,431,381 - 34,431,441EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308396 AgrOrtholog
BioCyc Gene G2FUF-13692 BioCyc
Ensembl Genes ENSRNOG00000020321 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027604 ENTREZGENE
  ENSRNOT00000027604.4 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  NOP9 UniProtKB/TrEMBL
  Pumilio_RNA-bd_rpt UniProtKB/TrEMBL
KEGG Report rno:290235 UniProtKB/TrEMBL
NCBI Gene 290235 ENTREZGENE
PANTHER NUCLEOLAR PROTEIN 9 UniProtKB/TrEMBL
  PTHR13102 UniProtKB/TrEMBL
PhenoGen Nop9 PhenoGen
RatGTEx ENSRNOG00000020321 RatGTEx
SMART Pumilio UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt A6KH48 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKI9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-10 Nop9  NOP9 nucleolar protein  RGD1308396  similar to chromosome 14 open reading frame 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308396  similar to chromosome 14 open reading frame 21   RGD1308396_predicted  similar to chromosome 14 open reading frame 21 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308396_predicted  similar to chromosome 14 open reading frame 21 (predicted)  LOC290235_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290235_predicted  similar to chromosome 14 open reading frame 21 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL