Nop58 (NOP58 ribonucleoprotein) - Rat Genome Database

Name: Nop58
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	NOP58 (NOP58 ribonucleoprotein)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Nop58 (NOP58 ribonucleoprotein)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Nop58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NOP58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NOP58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nop58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NOP58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NOP58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nop58 (NOP58 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NOP58 (NOP58 ribonucleoprotein)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Nop58 (NOP58 ribonucleoprotein)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	nop58 (NOP58 ribonucleoprotein homolog (yeast))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	NOP58	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	nol-58	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	nop5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	61,120,939 - 61,144,810 (+)	NCBI
Rnor_6.0 Ensembl	9	66,495,832 - 66,519,788 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	9	66,495,881 - 66,520,521 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	9	66,300,036 - 66,323,766 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	58,255,685 - 58,279,522 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	9	58,402,666 - 58,426,502 (+)	NCBI
Celera	9	58,555,582 - 58,579,638 (+)	NCBI		Celera
Cytogenetic Map	9	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Disease Models (ISO)

lung adenocarcinoma (ISO)

Neurodevelopmental Disorders (ISO)

Primary Pulmonary Hypertension, 1 (ISO)

Pulmonary Arterial Hypertension (ISO)

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

biological_process (ND)

ribosome biogenesis (IEA)

snoRNA localization (ISO)

Cellular Component

box C/D RNP complex (IBA)

Cajal body (ISO)

cytosol (IEA,ISO)

fibrillar center (IEA,ISO)

nucleolus (IEA,ISO)

nucleoplasm (ISO)

nucleus (IDA)

pre-snoRNP complex (ISO)

small-subunit processome (IBA)

sno(s)RNA-containing ribonucleoprotein complex (ISO)

Molecular Function

ATPase binding (ISO)

protein binding (IPI,ISO)

snoRNA binding (IBA,ISO)

TFIID-class transcription factor complex binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ribosome biogenesis pathway (IEA,ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	RGD automated data pipeline
6.	RGD automated import pipeline for gene-chemical interactions
7.	RGD comprehensive gene curation
8.	Watkins NJ and Bohnsack MT, Wiley Interdiscip Rev RNA. 2012 May-Jun;3(3):397-414. doi: 10.1002/wrna.117. Epub 2011 Nov 7.
9.	Yang Y, etal., Mol Biol Cell 2000 Feb;11(2):567-77.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	61,120,939 - 61,144,810 (+)	NCBI
Rnor_6.0 Ensembl	9	66,495,832 - 66,519,788 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	9	66,495,881 - 66,520,521 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	9	66,300,036 - 66,323,766 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	58,255,685 - 58,279,522 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	9	58,402,666 - 58,426,502 (+)	NCBI
Celera	9	58,555,582 - 58,579,638 (+)	NCBI		Celera
Cytogenetic Map	9	q31	NCBI

NOP58
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	202,265,736 - 202,303,661 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	202,265,763 - 202,303,661 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	203,130,486 - 203,168,384 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	202,838,760 - 202,876,629 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	2	202,956,020 - 202,993,888	NCBI
Celera	2	196,882,417 - 196,920,291 (+)	NCBI
Cytogenetic Map	2	q33.1	NCBI
HuRef	2	194,979,023 - 195,015,805 (+)	NCBI		HuRef
CHM1_1	2	203,136,911 - 203,174,808 (+)	NCBI		CHM1_1

Nop58
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	59,724,134 - 59,750,669 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	1	59,724,130 - 59,758,203 (+)	Ensembl
GRCm38	1	59,684,961 - 59,711,510 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	59,684,971 - 59,719,044 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	59,741,850 - 59,768,354 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	1	59,629,645 - 59,656,054 (+)	NCBI			mm8
Celera	1	60,199,706 - 60,226,206 (+)	NCBI		Celera
Cytogenetic Map	1	C2	NCBI

Nop58
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955457	12,479,965 - 12,511,678 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955457	12,481,467 - 12,511,678 (-)	NCBI	ChiLan1.0	ChiLan1.0

NOP58
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	2B	207,674,433 - 207,707,763 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	207,674,654 - 207,707,763 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2B	89,520,961 - 89,558,794 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

NOP58
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	37	11,255,589 - 11,287,279 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	37	11,255,562 - 11,287,325 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Nop58
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936726	1,457,038 - 1,487,374 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NOP58
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	105,850,294 - 105,930,459 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	105,893,589 - 105,930,458 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	117,351,116 - 117,380,896 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NOP58
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	87,989,687 - 88,026,774 (+)	NCBI
ChlSab1.1 Ensembl	10	87,989,699 - 88,026,904 (+)	Ensembl

Nop58
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624765	14,139,815 - 14,172,413 (-)	NCBI

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70186	Niddm26	Non-insulin dependent diabetes mellitus QTL 26	3.87		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	9	25692342	92741406	Rat
70218	Cm28	Cardiac mass QTL 28	8.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	9	29075079	83686404	Rat
2303170	Bp332	Blood pressure QTL 332	3.73	0.027	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	60810298	82732466	Rat
2303180	Bp333	Blood pressure QTL 333		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	61730923	82890620	Rat
2303180	Bp333	Blood pressure QTL 333		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	9	61730923	82890620	Rat
2303180	Bp333	Blood pressure QTL 333		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	61730923	82890620	Rat
724515	Uae16	Urinary albumin excretion QTL 16	8		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	63270073	107878387	Rat
724544	Uae9	Urinary albumin excretion QTL 9	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	9	29075079	122095297	Rat
731164	Uae25	Urinary albumin excretion QTL 25	3.5	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	29466970	107878528	Rat
631643	Bp120	Blood pressure QTL 120	3	0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	25692373	70692373	Rat
631656	Bp108	Blood pressure QTL 108	5.97	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	54177542	99177542	Rat
631680	Cm11	Cardiac mass QTL 11	3.1	0.00089	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	9	24885099	69885099	Rat
1300180	Bw14	Body weight QTL 14	3.776		body mass (VT:0001259)	body weight (CMO:0000012)	9	27486036	66757620	Rat
1641894	Alcrsp12	Alcohol response QTL 12			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	9	32385133	77385133	Rat
1598834	Memor11	Memory QTL 11	2.5		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	9	41261034	90024806	Rat
1598849	Memor17	Memory QTL 17	2.2		exploratory 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)	9	54885041	76677636	Rat
1578760	Cm53	Cardiac mass QTL 53	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	9	61186278	106186278	Rat
2290450	Scl57	Serum cholesterol level QTL 57	4.15		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	9	41261034	102531865	Rat
61352	Bp34	Blood pressure QTL 34	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	46952427	83686153	Rat
6903941	Pur31	Proteinuria QTL 31		0.036	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	9	46579769	91579769	Rat
7207814	Bmd91	Bone mineral density QTL 91	3.5		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	9	27486155	88333183	Rat
7411656	Foco26	Food consumption QTL 26	9.8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	37642351	82642351	Rat
7411571	Bw138	Body weight QTL 138	14.3	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	9	37642351	82642351	Rat
8662828	Vetf6	Vascular elastic tissue fragility QTL 6	3.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	9	41261034	98606834	Rat
10054125	Srcrt7	Stress Responsive Cort QTL 7	3.33	0.0011	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	9	1055222	93442944	Rat
10058949	Gmadr5	Adrenal mass QTL 5	2	0.014	adrenal gland mass (VT:0010420)	both adrenal glands wet weight to body weight ratio (CMO:0002411)	9	47248965	94124663	Rat
11353949	Bp393	Blood pressure QTL 393			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	46579769	91579769	Rat

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_021754	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084153	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084154	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF194371	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087637	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473965	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225580	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230388	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000214	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000022676 ⟹ ENSRNOP00000022676

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	9	66,495,832 - 66,519,769 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000091283 ⟹ ENSRNOP00000073311

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	9	66,495,840 - 66,519,788 (+)	Ensembl

RefSeq Acc Id:

NM_021754 ⟹ NP_068522

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	61,120,970 - 61,144,810 (+)	NCBI
Rnor_6.0	9	66,495,881 - 66,519,790 (+)	NCBI
Rnor_5.0	9	66,300,036 - 66,323,766 (+)	NCBI
RGSC_v3.4	9	58,255,685 - 58,279,522 (+)	RGD
Celera	9	58,555,582 - 58,579,638 (+)	RGD

Sequence:

show sequence

GGCACGAGGGAACGTCTAGGCAACGTGGTCTCCCCGCCCGCGGGTAGGCAAAGGCGTTTGCGCT
TCCCAGCGTCTGAGGCCTAGGGAGCCTTCAGTAGCCGAAAGTTAGTCTTTTGCAGTGGAGTAAG
GGCTCGCGGTTAGCCGCGTAGCGCCCGGATCTGGCCTCACCATGTTGGTCCTATTTGAAACGTC
CGTTGGCTACGCCATCTTTAAGGTTCTGAATGAGAAGAAACTTCAAGAGGTTGATAGTTTGTGG
AAAGAATTTGAAACTCCAGAGAAAGCAAATAAAATAGTAAAGCTAAAACATTTTGAGAAATTTC
AGGATACAGCAGAAGCATTAGCAGCGTTCACAGCTCTGATGGAAGGCAAGATCAATAAGCAGCT
GAAAAAAGTTTTGAAGAAAATAGTCAAAGAAGCCCATGAACCTCTGGCTGTAGCTGATGCTAAG
CTAGGAGGGGTCATAAAGGAAAAATTGAATCTCAGCTGTATCCATAGTCCTGTTGTTAATGAAC
TTATGAGAGGAATACGATCACAAATGGATGGCTTGATTCCTGGGGTAGAACCACGGGAGATGGC
AGCCATGTGTCTTGGACTAGCCCACAGCCTATCTCGATACAGATTGAAATTCAGTGCTGATAAA
GTAGACACAATGATCGTTCAGGCAATTTCCTTGTTAGATGACTTGGATAAAGAACTAAACAACT
ACATTATGCGGTGTAGGGAATGGTATGGCTGGCATTTTCCTGAGTTAGGGAAAATTATTTCAGA
TAATTTGACATACTGCAAGTGTTTACAGAAAGTTGGAGACAGGAAGAACTATGCATCTGCCACT
CTTTCTGAATTCCTGTCAGAGGAAGTAGAAGCTGAAGTGAAAGCAGCTGCAGAGATCTCTATGG
GAACAGAGGTTTCTGAAGAAGATATTTGCAACATTCTACATCTGTGTACTCAGGTCATTGAAAT
TTCTGAATATAGAACTCAGCTGTATGAATATCTGCAAAACCGAATGATGGCCATTGCACCCAAT
GTTACAGTCATGGTTGGGGAGTTGGTTGGAGCGCGGCTTATTGCTCATGCAGGTTCTCTTTTGA
ATTTGGCCAAGCATGCAGCTTCTACAGTTCAGATTCTGGGAGCAGAAAAGGCACTTTTCAGGGC
CCTCAAATCTAGACGAGACACACCTAAATATGGGCTTATTTATCATGCTTCTCTTGTAGGCCAG
ACGAGTCCCAAACACAAAGGAAAGATTTCACGAATGCTGGCGGCCAAAACTGTGTTGGCTATCA
GATACGACGCCTTTGGTGAAGATTCCAGCTCTGCAATGGGAGCTGAGAACAGAGCCAAATTAGA
GGCCAGATTGAGGATTTTGGAGGACAGAGGGATAAGAAAAATAAGTGGAACGGGAAAGGCATTA
GCAAAAGCAGAAAAGTATGAACACAAAAGTGAAGTGAAGACTTACGATCCCTCTGGTGACTCCA
CACTTCCAACTTGTTCTAAAAAACGCAAAATAGAAGAGGTTGATAAAGAGGATGAAATTACTGA
AAAGAAAGCAAAAAAAGCCAAGATTAAAATTAAAGCTGAAGTAGAGGAGGAGATGGAGGAGGCG
GAGGAAGAACAGGTAGTAGAAGAGGAGCCGACTGTAAAGAAGAAAAAGAAGAAGGATAAAAAGA
AACACATAAAGGAAGAGCCACTTTCCGAGGAGGAGCCATGCACCAGCACAGCAGTTCCTAGTCC
AGAGAAAAAGAAGAAAAAGAAAAAAAAGAAAGATGCTGAAGACTAATGTAAAGGAACCGTAATC
CTGTCACCTGAACACATCATGCTTAAGATTCAGTTGGGAGCATATCAGACGCTCTAACATAATC
AAGGGAGGTTGATTAGCTTTAGCTTTTCAAACCTTTTTGTGTCTTGACATCAACTGTTAACCTT
AGAGTCTTTGATACACAAATAAAAATATTTTCTTTGTATTATAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006245013 ⟹ XP_006245075

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	9	66,501,502 - 66,520,521 (+)	NCBI
Rnor_5.0	9	66,300,036 - 66,323,766 (+)	NCBI

Sequence:

show sequence

AGTAAAGCTAAAACATTTTGAGAAATTTCAGGATACAGCAGAAGCATTAGCAGGGTTGGTTTCC
CCCATGTGATGAGAGATGACAAGTGGTTAAGTTGATCTCCCTGTGGAAACCAATAGCCTAATGC
TGAAGCACAATTCAGTAAAAGCTGTTCTACAAGGGACCAAGCGTTCACAGCTCTGATGGAAGGC
AAGATCAATAAGCAGCTGAAAAAAGTTTTGAAGAAAATAGTCAAAGAAGCCCATGAACCTCTGG
CTGTAGCTGATGCTAAGCTAGGAGGGGTCATAAAGGAAAAATTGAATCTCAGCTGTATCCATAG
TCCTGTTGTTAATGAACTTATGAGAGGAATACGATCACAAATGGATGGCTTGATTCCTGGGGTA
GAACCACGGGAGATGGCAGCCATGTGTCTTGGACTAGCCCACAGCCTATCTCGATACAGATTGA
AATTCAGTGCTGATAAAGTAGACACAATGATCGTTCAGGCAATTTCCTTGTTAGATGACTTGGA
TAAAGAACTAAACAACTACATTATGCGGTGTAGGGAATGGTATGGCTGGCATTTTCCTGAGTTA
GGGAAAATTATTTCAGATAATTTGACATACTGCAAGTGTTTACAGAAAGTTGGAGACAGGAAGA
ACTATGCATCTGCCACTCTTTCTGAATTCCTGTCAGAGGAAGTAGAAGCTGAAGTGAAAGCAGC
TGCAGAGATCTCTATGGGAACAGAGGTTTCTGAAGAAGATATTTGCAACATTCTACATCTGTGT
ACTCAGGTCATTGAAATTTCTGAATATAGAACTCAGCTGTATGAATATCTGCAAAACCGAATGA
TGGCCATTGCACCCAATGTTACAGTCATGGTTGGGGAGTTGGTTGGAGCGCGGCTTATTGCTCA
TGCAGGTTCTCTTTTGAATTTGGCCAAGCATGCAGCTTCTACAGTTCAGATTCTGGGAGCAGAA
AAGGCACTTTTCAGGGCCCTCAAATCTAGACGAGACACCCCTAAATATGGGCTTATTTATCATG
CTTCTCTTGTAGGCCAGACGAGTCCCAAACACAAAGGAAAGATTTCACGAATGCTGGCGGCCAA
AACTGTGTTGGCTATCAGATACGACGCCTTTGGTGAAGATTCCAGCTCTGCAATGGGAGCTGAG
AACAGAGCCAAATTAGAGGCCAGATTGAGGATTTTGGAGGACAGAGGGATAAGAAAAATAAGTG
GAACGGGAAAGGCATTAGCAAAAGCAGAAAAGTATGAACACAAAAGTGAAGTGAAGACTTACGA
TCCCTCTGGTGACTCCACACTTCCAACTTGTTCTAAAAAACGCAAAATAGAAGAGGTAGATAAA
GAGGATGAAATTACTGAAAAGAAAGCAAAAAAAGCCAAGATTAAAATTAAAGCTGAAGTAGAGG
AGGAGATGGAGGAGGCGGAGGAAGAACAGGTAGTAGAAGAGGAGCCGACTGTAAAGAAGAAAAA
GAAGAAGGATAAAAAGAAACACATAAAGGAAGAGCCACTTTCCGAGGAGGAGCCATGCACCAGC
ACAGCAGTTCCTAGTCCAGAGAAAAAGAAGAAAAAGAAAAAAAAGAAAGATGCTGAAGACTAAT
GTAAAGGAACCGTAATCCTGTCACCTGAACACATCATGCTTAAGATTCAGTTGGGAGCATATCA
GACGCTCTAACATAATCAAGGGAGGTTGATTAGCTTTAGCTTTTCAAACCTTTTTGTGTCTTGA
CATCAACTGTTAACCTTAGAGTCTTTGATACACAAATAAAAATATTTTCTTTGTATTATAAGGC
AGTTTTGTGATCTATTTATATTTTAGCAAGAGAATCTTTAACCCCTTCTATGTTTGACTTAGCA
TTAAATAGGTATCATTATTGTTAAAAAATGAGTTGCCAGTGATTAGAAGTTTCAGAGTTTTAAA
TGGCTTTTTGGAAGGCGGTGATTAGACAGACCATTTAAGATCTTATGTGTTACCTTGTCTTCTA
AAGTGTTAAAACTGAGAACATTCTGCTATCTGCTTCAGAAAAGAAGAAAGTGGTTGTAATTTTT
ATCATCCACTACTTTTGATGTGTGATTTTAGTGTAGCCAAGAATAACATTGAATTTCTGATACT
CCTGTTTTCCTCCCTGGTGACAGGATTACAGACTTGTGTCAGTAATTTTATGAGGTGCTGGAGA
GCCGGTCAACAGCTCACTCGTGCTTGACAAGCGCTTTACCAACTAAGCTACATTCCCCAGTCCA
AGTTTTCTATTCTTAAAGATTATGATGAAATGTTTTATAGTTTAGACTGCTATGTTTGTGCTGG
GGATGGAACCCAGAGCCTTACTTCTTAACTTGGGTCCCTGGTAGGGTGTGTCCTGTATGTCTCT
TGTTTTTCTTACATGTTGTATGTGTACACTAATTGCATGCCTTTATCCTGGAGGTCAAAAGAGT
CTGTTGGATAACCTGGAGCTGGAATTATAGGTGGTTGTGAGCCAGTATATCACCCGAGGTCCAC
TGTAATAAAATCAACCAATGCTGA

hide sequence

RefSeq Acc Id:

XM_039084153 ⟹ XP_038940081

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	61,120,939 - 61,144,804 (+)	NCBI

RefSeq Acc Id:

XM_039084154 ⟹ XP_038940082

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	61,120,944 - 61,144,658 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_068522	(Get FASTA)	NCBI Sequence Viewer
	XP_038940081	(Get FASTA)	NCBI Sequence Viewer
	XP_038940082	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF05769	(Get FASTA)	NCBI Sequence Viewer
	AAH87637	(Get FASTA)	NCBI Sequence Viewer
	EDL98947	(Get FASTA)	NCBI Sequence Viewer
	EDL98948	(Get FASTA)	NCBI Sequence Viewer
	Q9QZ86	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_068522 ⟸ NM_021754

- UniProtKB:

Q9QZ86 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MLVLFETSVGYAIFKVLNEKKLQEVDSLWKEFETPEKANKIVKLKHFEKFQDTAEALAAFTALM
EGKINKQLKKVLKKIVKEAHEPLAVADAKLGGVIKEKLNLSCIHSPVVNELMRGIRSQMDGLIP
GVEPREMAAMCLGLAHSLSRYRLKFSADKVDTMIVQAISLLDDLDKELNNYIMRCREWYGWHFP
ELGKIISDNLTYCKCLQKVGDRKNYASATLSEFLSEEVEAEVKAAAEISMGTEVSEEDICNILH
LCTQVIEISEYRTQLYEYLQNRMMAIAPNVTVMVGELVGARLIAHAGSLLNLAKHAASTVQILG
AEKALFRALKSRRDTPKYGLIYHASLVGQTSPKHKGKISRMLAAKTVLAIRYDAFGEDSSSAMG
AENRAKLEARLRILEDRGIRKISGTGKALAKAEKYEHKSEVKTYDPSGDSTLPTCSKKRKIEEV
DKEDEITEKKAKKAKIKIKAEVEEEMEEAEEEQVVEEEPTVKKKKKKDKKKHIKEEPLSEEEPC
TSTAVPSPEKKKKKKKKKDAED

hide sequence

RefSeq Acc Id:

XP_006245075 ⟸ XM_006245013

- Peptide Label:

isoform X1

- Sequence:

show sequence

MEGKINKQLKKVLKKIVKEAHEPLAVADAKLGGVIKEKLNLSCIHSPVVNELMRGIRSQMDGLI
PGVEPREMAAMCLGLAHSLSRYRLKFSADKVDTMIVQAISLLDDLDKELNNYIMRCREWYGWHF
PELGKIISDNLTYCKCLQKVGDRKNYASATLSEFLSEEVEAEVKAAAEISMGTEVSEEDICNIL
HLCTQVIEISEYRTQLYEYLQNRMMAIAPNVTVMVGELVGARLIAHAGSLLNLAKHAASTVQIL
GAEKALFRALKSRRDTPKYGLIYHASLVGQTSPKHKGKISRMLAAKTVLAIRYDAFGEDSSSAM
GAENRAKLEARLRILEDRGIRKISGTGKALAKAEKYEHKSEVKTYDPSGDSTLPTCSKKRKIEE
VDKEDEITEKKAKKAKIKIKAEVEEEMEEAEEEQVVEEEPTVKKKKKKDKKKHIKEEPLSEEEP
CTSTAVPSPEKKKKKKKKKDAED

hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	9	66,495,853 - 66,495,913	EPDNEW

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)

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

LN/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

M520/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

MHS/Gib (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

MNS/Gib (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

MR/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

SBH/Ygl (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:	SBH/Ygl sequenced by MCW

SBH/Ygl (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

SBN/Ygl (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:	SBN/Ygl sequenced by MCW

SBN/Ygl (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

SHR/NHsd (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

SHRSP/Gcrc (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

SR/JrHsd (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:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (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

SS/Jr (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

SS/JrHsdMcwi (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)

SS/JrHsdMcwi (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

WAG/Rij (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

WKY/Gcrc (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

WKY/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

WKY/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

WKY/NHsd (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

WN/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

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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - KEGG (archival)