Nop58 (NOP58 ribonucleoprotein) - Rat Genome Database
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Gene: Nop58 (NOP58 ribonucleoprotein) Rattus norvegicus
Analyze
Symbol: Nop58
Name: NOP58 ribonucleoprotein
RGD ID: 620484
Description: Predicted to have ATPase binding activity; TFIID-class transcription factor complex binding activity; and snoRNA binding activity. Predicted to be involved in snoRNA localization. Localizes to nucleus. Orthologous to human NOP58 (NOP58 ribonucleoprotein); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC105440; Nap65; Nol5; NOP58 ribonucleoprotein homolog; NOP58 ribonucleoprotein homolog (yeast); Nopp140 associated protein; nopp140-associated protein of 65 kDa; nucleolar protein 5; nucleolar protein 58; nucleolar protein NOP58
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2961,120,939 - 61,144,810 (+)NCBI
Rnor_6.0 Ensembl966,495,832 - 66,519,788 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0966,495,881 - 66,520,521 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0966,300,036 - 66,323,766 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4958,255,685 - 58,279,522 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1958,402,666 - 58,426,502 (+)NCBI
Celera958,555,582 - 58,579,638 (+)NCBICelera
Cytogenetic Map9q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chloropicrin  (ISO)
chloroprene  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
indole-3-methanol  (EXP)
menadione  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
Monobutylphthalate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
p-anisidine  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (EXP)
phorone  (EXP)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10925205   PMID:12477932   PMID:16687569   PMID:17636026   PMID:19946888   PMID:22082260   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Nop58
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2961,120,939 - 61,144,810 (+)NCBI
Rnor_6.0 Ensembl966,495,832 - 66,519,788 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0966,495,881 - 66,520,521 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0966,300,036 - 66,323,766 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4958,255,685 - 58,279,522 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1958,402,666 - 58,426,502 (+)NCBI
Celera958,555,582 - 58,579,638 (+)NCBICelera
Cytogenetic Map9q31NCBI
NOP58
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2202,265,736 - 202,303,661 (+)EnsemblGRCh38hg38GRCh38
GRCh382202,265,763 - 202,303,661 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372203,130,486 - 203,168,384 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362202,838,760 - 202,876,629 (+)NCBINCBI36hg18NCBI36
Build 342202,956,020 - 202,993,888NCBI
Celera2196,882,417 - 196,920,291 (+)NCBI
Cytogenetic Map2q33.1NCBI
HuRef2194,979,023 - 195,015,805 (+)NCBIHuRef
CHM1_12203,136,911 - 203,174,808 (+)NCBICHM1_1
Nop58
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39159,724,134 - 59,750,669 (+)NCBIGRCm39mm39
GRCm39 Ensembl159,724,130 - 59,758,203 (+)Ensembl
GRCm38159,684,961 - 59,711,510 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl159,684,971 - 59,719,044 (+)EnsemblGRCm38mm10GRCm38
MGSCv37159,741,850 - 59,768,354 (+)NCBIGRCm37mm9NCBIm37
MGSCv36159,629,645 - 59,656,054 (+)NCBImm8
Celera160,199,706 - 60,226,206 (+)NCBICelera
Cytogenetic Map1C2NCBI
Nop58
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545712,479,965 - 12,511,678 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545712,481,467 - 12,511,678 (-)NCBIChiLan1.0ChiLan1.0
NOP58
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B207,674,433 - 207,707,763 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B207,674,654 - 207,707,763 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B89,520,961 - 89,558,794 (+)NCBIMhudiblu_PPA_v0panPan3
NOP58
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3711,255,589 - 11,287,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13711,255,562 - 11,287,325 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nop58
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367261,457,038 - 1,487,374 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOP58
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15105,850,294 - 105,930,459 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115105,893,589 - 105,930,458 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215117,351,116 - 117,380,896 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NOP58
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11087,989,687 - 88,026,774 (+)NCBI
ChlSab1.1 Ensembl1087,989,699 - 88,026,904 (+)Ensembl
Nop58
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476514,139,815 - 14,172,413 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)95488504176677636Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:19
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000022676
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.


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 37 56 40 19 40 5 7 74 35 41 11 5
Low 6 1 1 1 3 4 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022676   ⟹   ENSRNOP00000022676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl966,495,832 - 66,519,769 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091283   ⟹   ENSRNOP00000073311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl966,495,840 - 66,519,788 (+)Ensembl
RefSeq Acc Id: NM_021754   ⟹   NP_068522
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2961,120,970 - 61,144,810 (+)NCBI
Rnor_6.0966,495,881 - 66,519,790 (+)NCBI
Rnor_5.0966,300,036 - 66,323,766 (+)NCBI
RGSC_v3.4958,255,685 - 58,279,522 (+)RGD
Celera958,555,582 - 58,579,638 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245013   ⟹   XP_006245075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0966,501,502 - 66,520,521 (+)NCBI
Rnor_5.0966,300,036 - 66,323,766 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039084153   ⟹   XP_038940081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2961,120,939 - 61,144,804 (+)NCBI
RefSeq Acc Id: XM_039084154   ⟹   XP_038940082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2961,120,944 - 61,144,658 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_068522   ⟸   NM_021754
- UniProtKB: Q9QZ86 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245075   ⟸   XM_006245013
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073311   ⟸   ENSRNOT00000091283
RefSeq Acc Id: ENSRNOP00000022676   ⟸   ENSRNOT00000022676
RefSeq Acc Id: XP_038940081   ⟸   XM_039084153
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940082   ⟸   XM_039084154
- Peptide Label: isoform X1
Protein Domains
Nop

Transcriptome

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

Promoters
RGD ID:13696709
Promoter ID:EPDNEW_R7228
Type:initiation region
Name:Nop58_1
Description:NOP58 ribonucleoprotein
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_6.0966,495,853 - 66,495,913EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 66510772 66510773 C G snv LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620484 AgrOrtholog
Ensembl Genes ENSRNOG00000016486 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022676 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073311 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022676 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091283 UniProtKB/TrEMBL
Gene3D-CATH 1.10.246.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.10.287.660 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7309062 IMAGE-MGC_LOAD
InterPro Helix_hairpin_bin_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NOP5_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nop_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nop_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nop_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NOSIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60373 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105440 IMAGE-MGC_LOAD
NCBI Gene 60373 ENTREZGENE
Pfam Nop UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NOP5NT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nop58 PhenoGen
PROSITE NOP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART NOSIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF89124 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NOP58_RAT UniProtKB/Swiss-Prot
  Q5PPK6_RAT UniProtKB/TrEMBL
  Q9QZ86 ENTREZGENE
UniProt Secondary O88525 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-12-18 Nop58  NOP58 ribonucleoprotein  Nop58  NOP58 ribonucleoprotein homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-05-03 Nop58  NOP58 ribonucleoprotein homolog (yeast)  Nop58  nucleolar protein NOP58  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Nop58  nucleolar protein NOP58  Nol5  nucleolar protein 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Nol5  nucleolar protein 5  Nap65  Nopp140 associated protein  Symbol and Name updated 1299863 APPROVED
2002-08-07 Nap65  Nopp140 associated protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology has homology with yeast Nop5/58p 633515
gene_physical_interaction interacts with Nopp140 633515