Nop56 (NOP56 ribonucleoprotein) - Rat Genome Database

Name: Nop56
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Nop56 (NOP56 ribonucleoprotein) Rattus norvegicus

Analyze

Symbol:

Nop56

Name:

NOP56 ribonucleoprotein

RGD ID:

1308892

Description:

Predicted to enable histone methyltransferase binding activity and snoRNA binding activity. Predicted to be involved in ribosomal small subunit biogenesis. Predicted to be located in fibrillar center. Predicted to be part of box C/D RNP complex; pre-snoRNP complex; and small-subunit processome. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 36. Orthologous to human NOP56 (NOP56 ribonucleoprotein); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC362214; MGC116301; Nol5a; NOP56 ribonucleoprotein homolog; NOP56 ribonucleoprotein homolog (yeast); nucleolar protein 56; nucleolar protein 5A

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):	NOP56 (NOP56 ribonucleoprotein)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Nop56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Nop56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NOP56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NOP56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nop56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NOP56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NOP56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nop56 (NOP56 ribonucleoprotein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NOP56 (NOP56 ribonucleoprotein)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Nop56 (NOP56 ribonucleoprotein)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nop56 (NOP56 ribonucleoprotein homolog)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	NOP56	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Nop56	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	nol-56	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	nop56	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	117,476,963 - 117,481,847 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	117,477,053 - 117,481,841 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	121,375,109 - 121,379,896 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	129,970,728 - 129,975,515 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	127,631,224 - 127,636,012 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	122,803,726 - 122,808,564 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	122,803,772 - 122,808,558 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	129,303,444 - 129,308,279 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	117,887,822 - 117,892,614 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	117,793,394 - 117,798,187 (+)	NCBI
Celera	3	116,293,358 - 116,298,150 (+)	NCBI		Celera
Cytogenetic Map	3	q36	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)

cerebellar ataxia (ISO)

Disease Progression (ISO)

genetic disease (ISO)

Huntington's disease-like 1 (ISO)

lung adenocarcinoma (ISO)

pantothenate kinase-associated neurodegeneration (ISO)

spinocerebellar ataxia type 36 (ISO)

Spinocerebellar Ataxias (ISO)

Stomach Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-alpha-phellandrene (ISO)

(1->4)-beta-D-glucan (ISO)

1,1-dichloroethene (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3-chloropropane-1,2-diol (EXP)

4-amino-2,6-dinitrotoluene (EXP)

aconitine (EXP)

acrolein (ISO)

acrylamide (ISO)

afimoxifene (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-phellandrene (ISO)

alpha-pinene (ISO)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

Benzo[ghi]perylene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

bleomycin A5 (ISO)

cadmium dichloride (EXP)

caffeine (ISO)

carbon nanotube (ISO)

cefaloridine (EXP)

chromium(6+) (ISO)

copper atom (ISO)

copper(0) (ISO)

coumarin (EXP,ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

deoxynivalenol (ISO)

dibutyl phthalate (ISO)

dioxygen (ISO)

elemental selenium (ISO)

ellagic acid (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

glafenine (EXP)

hexadecanoic acid (ISO)

hydrogen peroxide (ISO)

inulin (ISO)

ivermectin (ISO)

leflunomide (ISO)

melphalan (ISO)

menadione (ISO)

methotrexate (ISO)

methylmercury chloride (ISO)

miconazole (ISO)

N-methyl-4-phenylpyridinium (ISO)

nefazodone (EXP)

nickel atom (ISO)

nickel sulfate (ISO)

nimesulide (EXP)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

pentachlorophenol (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

progesterone (ISO)

resveratrol (ISO)

rotenone (ISO)

selenium atom (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP,ISO)

sodium fluoride (ISO)

Soman (EXP)

temozolomide (ISO)

tetrachloromethane (EXP)

thioacetamide (EXP)

tolcapone (EXP)

trichloroethene (ISO)

triphenyl phosphate (EXP)

Triptolide (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

ribosomal small subunit biogenesis (ISO)

Cellular Component

box C/D RNP complex (IBA)

fibrillar center (IEA,ISO)

nucleoplasm (IEA)

pre-snoRNP complex (ISO)

small-subunit processome (IBA,ISO)

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

Molecular Function

histone methyltransferase binding (ISO)

protein binding (ISO)

RNA binding (ISO)

snoRNA binding (IBA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ribosome biogenesis pathway (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
4.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Comprehensive gene review and curation	RGD comprehensive gene curation
7.	The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA.	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.

Additional References at PubMed

PMID:12477932	PMID:17636026	PMID:19946888	PMID:22658674	PMID:22681889	PMID:24013231	PMID:24174535	PMID:25468996

Genomics

Comparative Map Data

Nop56
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	117,476,963 - 117,481,847 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	117,477,053 - 117,481,841 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	121,375,109 - 121,379,896 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	129,970,728 - 129,975,515 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	127,631,224 - 127,636,012 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	122,803,726 - 122,808,564 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	122,803,772 - 122,808,558 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	129,303,444 - 129,308,279 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	117,887,822 - 117,892,614 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	117,793,394 - 117,798,187 (+)	NCBI
Celera	3	116,293,358 - 116,298,150 (+)	NCBI		Celera
Cytogenetic Map	3	q36	NCBI

NOP56
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	2,652,632 - 2,658,393 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	20	2,652,593 - 2,658,393 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	2,633,278 - 2,639,039 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	2,581,254 - 2,587,039 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	2,581,253 - 2,587,038	NCBI
Celera	20	2,697,715 - 2,703,502 (+)	NCBI		Celera
Cytogenetic Map	20	p13	NCBI
HuRef	20	2,582,394 - 2,588,267 (+)	NCBI		HuRef
CHM1_1	20	2,633,579 - 2,639,446 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	2,683,093 - 2,688,860 (+)	NCBI		T2T-CHM13v2.0

Nop56
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	130,112,904 - 130,121,233 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	130,116,350 - 130,121,233 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	130,274,367 - 130,279,313 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	130,274,430 - 130,279,313 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	130,100,148 - 130,105,049 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	129,965,900 - 129,970,754 (+)	NCBI		MGSCv36	mm8
Celera	2	131,498,819 - 131,503,720 (+)	NCBI		Celera
Cytogenetic Map	2	F1	NCBI

Nop56
(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_004955415	13,637,595 - 13,643,938 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955415	13,637,505 - 13,642,809 (+)	NCBI	ChiLan1.0	ChiLan1.0

NOP56
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	20	3,638,472 - 3,644,300 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	20	2,760,689 - 2,766,596 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	20	2,523,619 - 2,529,509 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	2,523,619 - 2,529,509 (+)	Ensembl	panpan1.1		panPan2

NOP56
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	18,561,407 - 18,566,770 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	18,561,408 - 18,566,719 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	18,390,715 - 18,396,112 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	19,019,189 - 19,024,580 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	24	19,019,190 - 19,024,480 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	24	18,575,424 - 18,580,814 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	18,685,676 - 18,691,066 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	19,014,775 - 19,020,160 (-)	NCBI		UU_Cfam_GSD_1.0

Nop56
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	167,606,726 - 167,612,067 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936485	16,038,182 - 16,043,357 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936485	16,038,090 - 16,043,408 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NOP56
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	32,960,102 - 32,965,370 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	32,960,099 - 32,965,396 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	37,441,096 - 37,446,329 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NOP56
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	53,882,070 - 53,887,867 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	2	53,882,169 - 53,887,565 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666087	299,181 - 305,383 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nop56
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624741	3,803,169 - 3,808,342 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624741	3,803,000 - 3,808,439 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Nop56
17 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	53
Count of miRNA genes:	50
Interacting mature miRNAs:	53
Transcripts:	ENSRNOT00000009564
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	89772419	134772419	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	91797474	136797474	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	94856903	159898684	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	95735366	140735366	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	97084464	142084464	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	97551417	147415807	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	98535386	161695835	Rat
619618	Rf3	Renal disease susceptibility QTL 3	6.5	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate to body weight ratio (CMO:0001270)	3	107693393	152693393	Rat
1331758	Bp207	Blood pressure QTL 207	2.848		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	112287552	135181505	Rat
1578754	Stresp16	Stress response QTL 16	4	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	3	112681431	157681431	Rat
1358204	Insglur1	Insulin/glucose ratio QTL 1	3.8		blood glucose amount (VT:0000188)	serum insulin level (CMO:0000358)	3	115638168	135181505	Rat
1358204	Insglur1	Insulin/glucose ratio QTL 1	3.8		blood glucose amount (VT:0000188)	serum glucose level (CMO:0000543)	3	115638168	135181505	Rat

Markers in Region

RH124665

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	117,480,750 - 117,481,489 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	122,807,470 - 122,808,208	NCBI	Rnor6.0
Rnor_5.0	3	129,307,185 - 129,307,923	UniSTS	Rnor5.0
RGSC_v3.4	3	117,891,520 - 117,892,258	UniSTS	RGSC3.4
Celera	3	116,297,056 - 116,297,794	UniSTS
Cytogenetic Map	3	q36	UniSTS

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	43	57	41	19	41	8	11	74	35	40	11	8
Low											1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025732	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005501936	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_352612	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC086568	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC099149	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224806	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232640	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009564 ⟹ ENSRNOP00000009563

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	117,477,053 - 117,481,841 (+)	Ensembl
Rnor_6.0 Ensembl	3	122,803,772 - 122,808,558 (+)	Ensembl

RefSeq Acc Id:

NM_001025732 ⟹ NP_001020903

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	117,477,053 - 117,481,845 (+)	NCBI
Rnor_6.0	3	122,803,772 - 122,808,564 (+)	NCBI
Rnor_5.0	3	129,303,444 - 129,308,279 (+)	NCBI
RGSC_v3.4	3	117,887,822 - 117,892,614 (+)	RGD
Celera	3	116,293,358 - 116,298,150 (+)	RGD

Sequence:

show sequence

GTTCCGCGCGCCAGAGCGCGCTACCCGCATTGCGAGCTGGGCACGGAGCAGGCGCCATGGTTCT
GCTGCACGTGCTCTTCGAGCATGCGGTCGGCTACGCGCTGTTAGCGCTGAAGGAAGTAGAGGAG
ATCAGCTTGCTGTTGCCGCAGGTGGAGGAGTGTGTGCTTAACCTTGGCAAATTCCACAATGTCG
TTCGTCTGGTGGCCTTTTGCCCCTTTTCTTCATCCCAGGTTGCCTTGGAAAATGCTAATGCTGT
GTCTGAAGGTGTTGTTCATGAGGACCTCCGCCTGCTCCTGGAGACATACCTGCCATCTAAAAAG
AAGAAAGTACTTCTGGGGGTCGGAGACCCCAAGATCGGTGCTGCTATACAGGAAGAGTTGGGGT
ACAACTGCCAGACTGGTGGTGTGATAGCTGAGATCCTTCGAGGGGTTCGTCTGCATTTCCATAA
CCTGGTGAAGGGTCTGACAGATCTTTCTGCTTGTAAAGCCCAGCTAGGGCTGGGACACAGCTAT
TCTCGTGCCAAAGTTAAGTTTAATGTGAACCGGGTGGACAACATGATCATTCAGTCTATAAGCC
TTCTGGACCAACTGGATAAAGATATCAATACCTTCTCCATGCGTGTCAGGGAGTGGTATGGGTA
CCACTTTCCAGAGCTGGTGAAGATTATCAACGACAATGCTACATACTGTCGCCTGGCTCAGTTC
ATCGGGAACCGCAGGGAGCTAAATGAAGAAAAGTTAGAGAAGCTGGAAGAAATTACAATGGATG
GAGCCAAGGCTAAGGCCATTCTGGATGCCTCTCGGTCCTCCATGGGCATGGACATATCTGCTAT
CGACTTGATAAACATCGAGAGCTTCTCCAGTCGTGTGGTGTCTTTGTCAGAGTATCGCCAGAGC
CTACACAATTACCTTCGCTCCAAGATGAGCCAAGTAGCCCCCAGCCTGTCAGCCTTAATTGGGG
AAGCGGTAGGTGCACGTCTCATTGCCCATGCTGGCAGCCTCACCAACCTGGCCAAGTACCCAGC
ATCCACAGTGCAGATCCTTGGGGCTGAAAAGGCCCTGTTCAGAGCCCTGAAGACAAGGGGTAAC
ACACCAAAATACGGACTCATTTTTCATTCCACTTTCATTGGCCGAGCAGCTGCAAAGAACAAAG
GCCGTATCTCCCGATACCTAGCAAACAAATGCAGTATTGCCTCAAGAATTGATTGCTTCTCTGA
GGTCCCCACAAGTGTATTTGGGGAGAAACTCCGGGAACAAGTTGAAGAGCGGCTTTCTTTCTAT
GAGACTGGAGAGATTCCACGGAAGAACCTGGATGTCATGAAAGAAGCTGTGGTACAGGCAGAGG
AAGCGGCTGCTGAAATAACCAGAAAGCTGGAAAAACAGGAGAAGAAACGCTTGAAGAAGGAAAA
GAAGCGACTGGCTGCACTGGCCCTGGCCTCTTCAGAAAACAGTAGTACTCCGGAAGAGTGTGAG
GAGGTAAATGAAAAACCTAAGAAGAAAAAGCTAAAACCCCAGGAAACCCTACAGGAAAATGGAA
TGGAAGACCCACCTGTCTCTTTGCCTAAAACCAAGAAAAAGAAAGCTTTTCCCAAGGAGGAGTT
GGCCAGTGATCTTGAAGAGATGGCTACTAGCAGCATAAGTGTTCCTAAGAAAAAGAAGTCCTTA
CCTAAAGAGGAAGTGGCCAGTGAACCCGAAGAGGCAGCGAGCCCCATCACCCCTAAGAAGAAAA
GGAAATTTTCTGAGGAGCCTGAGGCTGCTGCAAGCTGCACAAAGAGCAGCACAAAGAAAAAGAA
AAAGTCGCAGAAGGCCCGGGAGGAGGATTAGAATGGACCTGCTTGGTGGGAGGGGCATACTTTA
TGGTGGCAGTTCCTCCTGCCCATGATAAACCCCAATAAAAACGCAAAACCAGATAAAAAAAAAA
AAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XR_005501936

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	117,476,963 - 117,481,716 (+)	NCBI

RefSeq Acc Id:

XR_352612

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	117,476,963 - 117,481,847 (+)	NCBI
Rnor_6.0	3	122,803,726 - 122,808,561 (+)	NCBI
Rnor_5.0	3	129,303,444 - 129,308,279 (+)	NCBI

Sequence:

show sequence

AGCCTCTGATTGGTCCAACAGGAGAAGGCGTGGCCTCCGCAGTCTGGTTCCGCGCGCCAGAGCG
CGCTACCCGCATTGCGAGCTGGGCACGGAGCAGGCGCCATGGTTCTGCTGCACGTGCTCTTCGA
GCATGCGGTCGGCTACGCGCTGTTAGCGCTGAAGGAAGTAGAGGAGATCAGCTTGCTGTTGCCG
CAGGTGGAGGAGTGTGTGCTTAACCTTGGCAAATTCCACAATGTCGTTCGTCTGGTGGCCTTTT
GCCCCTTTTCTTCATCCCAGGTTGCCTTGGAAAATGCTAATGCTGTGTCTGAAGGTGTTGTTCA
TGAGGACCTCCGCCTGCTCCTGGAGACATACCTGCCATCTAAAAAGAAGAAAGTACTTCTGGGG
GTCGGAGACCCCAAGATCGGTGCTGCTATACAGGAAGAGTTGGGGTACAACTGCCAGACTGGTG
GTGTGATAGCTGAGATCCTTCGAGGGGTTCGTCTGCATTTCCATAACCTGGTGAAGGGTCTGAC
AGATCTTTCTGCTTGTAAAGCCCAGCTAGGGCTGGGACACAGCTATTCTCGTGCCAAAGTTAAG
TTTAATGTGAACCGGGTGGACAACATGATCATTCAGTCTATAAGCCTTCTGGACCAACTGGATA
AAGATATCAATACCTTCTCCATGCGTGTCAGGGAGTGGTATGGGTACCACTTTCCAGAGCTGGT
GAAGATTATCAACGACAATGCTACATACTGTCGCCTGGCTCAGTTCATCGGGAACCGCAGGGAG
CTAAATGAAGAAAAGTTAGAGAAGCTGGAAGAAATTACAATGGATGGAGCCAAGGCTAAGGCCA
TTCTGGATGCCTCTCGGTCCTCCATGGGCATGGACATATCTGCTATCGACTTGATAAACATCGA
GAGCTTCTCCAGTCGTGTGGTGTCTTTGTCAGAGTATCGCCAGAGCCTACACAATTACCTTCGC
TCCAAGATGAGCCAAGTAGCCCCCAGCCTGTCAGCCTTAATTGGGGAAGCGGTAGGTGCACGTC
TCATTGCCCATGCTGGCAGCCTCACCAACCTGGCCAAGTACCCAGCATCCACAGTGCAGATCCT
TGGGGCTGAAAAGGCCCTGTTCAGAGCCCTGAAGACAAGGGGTAACACACCAAAATACGGACTC
ATTTTTCATTCCACTTTCATTGGCCGAGCAGCTGCAAAGAACAAAGGCCGTATCTCCCGATACC
TAGCAAACAAATGCAGTATTGCCTCAAGAATTGATTGCTTCTCTGAGGTCCCCACAAGTGTATT
TGGGGAGAAACTCCGGGAACAAGTTGAAGAGCGGCTTTCTTTCTATGAGACTGGAGAGATTCCA
CGGAAGAACCTGGATGTCATGAAAGAAGCTGTGGTACAGGCAGAGGAAGCGGCTGCTGAAATAA
CCAGAAAGCTGGAAAAACAGGAGAAGAAACGCTTGAAGAAGGAAAAGAAGCGACTGGCTGCACT
GGCCCTGGCCTCTTCAGAAAACAGTAGTACTCCGGAAGAGTGTGAGGGAGGAGATAGGTGCTGA
GAGAACTTGACAAGAGCCCAGAATGCTGGTTGTAGCACATGGCCCATTCCATGGCCGTGTGCTC
TGTCCTCGGCTGCCTCCCAGGAGTCCTCAACAGGGGAGGTAAATGAAAAACCTAAGAAGAAAAA
GCTAAAACCCCAGGAAACCCTACAGGAAAATGGAATGGAAGACCCACCTGTCTCTTTGCCTAAA
ACCAAGAAAAAGAAAGCTTTTCCCAAGGAGGAGTTGGCCAGTGATCTTGAAGAGATGGCTACTA
GCAGCATAAGTGTTCCTAAGAAAAAGAAGTCCTTACCTAAAGAGGAAGTGGCCAGTGAACCCGA
AGAGGCAGCGAGCCCCATCACCCCTAAGAAGAAAAGGAAATTTTCTGAGGAGCCTGAGGCTGCT
GCAAGCTGCACAAAGAGCAGCACAAAGAAAAAGAAAAAGTCGCAGAAGGCCCGGGAGGAGGATT
AGAATGGACCTGCTTGGTGGGAGGGGCATACTTTATGGTGGCAGTTCCTCCTGCCCATGATAAA
CCCCAATAAAAACGCAAAACCAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001020903	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH86568	(Get FASTA)	NCBI Sequence Viewer
	AAH99149	(Get FASTA)	NCBI Sequence Viewer
	EDL80179	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001020903 ⟸ NM_001025732

- UniProtKB:

Q4KLK7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MVLLHVLFEHAVGYALLALKEVEEISLLLPQVEECVLNLGKFHNVVRLVAFCPFSSSQVALENA
NAVSEGVVHEDLRLLLETYLPSKKKKVLLGVGDPKIGAAIQEELGYNCQTGGVIAEILRGVRLH
FHNLVKGLTDLSACKAQLGLGHSYSRAKVKFNVNRVDNMIIQSISLLDQLDKDINTFSMRVREW
YGYHFPELVKIINDNATYCRLAQFIGNRRELNEEKLEKLEEITMDGAKAKAILDASRSSMGMDI
SAIDLINIESFSSRVVSLSEYRQSLHNYLRSKMSQVAPSLSALIGEAVGARLIAHAGSLTNLAK
YPASTVQILGAEKALFRALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDC
FSEVPTSVFGEKLREQVEERLSFYETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKKRLK
KEKKRLAALALASSENSSTPEECEEVNEKPKKKKLKPQETLQENGMEDPPVSLPKTKKKKAFPK
EELASDLEEMATSSISVPKKKKSLPKEEVASEPEEAASPITPKKKRKFSEEPEAAASCTKSSTK
KKKKSQKAREED

hide sequence

RefSeq Acc Id:

ENSRNOP00000009563 ⟸ ENSRNOT00000009564

Protein Domains

Nop

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q4KLK7-F1-model_v2	AlphaFold	Q4KLK7	1-588	view protein structure

Transcriptome

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

Promoters

RGD ID:

13692428

Promoter ID:

EPDNEW_R2953

Type:

multiple initiation site

Name:

Nop56_1

Description:

NOP56 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	3	122,803,800 - 122,803,860	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308892	AgrOrtholog
BioCyc Gene	G2FUF-47874	BioCyc
Ensembl Genes	ENSRNOG00000007128	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000009563	ENTREZGENE
	ENSRNOP00000009563.4	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000009564	ENTREZGENE
	ENSRNOT00000009564.6	UniProtKB/TrEMBL
Gene3D-CATH	1.10.246.90	UniProtKB/TrEMBL
	1.10.287.4070	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7125493	IMAGE-MGC_LOAD
	IMAGE:7366316	IMAGE-MGC_LOAD
InterPro	Nop56/Nop58	UniProtKB/TrEMBL
	NOP5_N	UniProtKB/TrEMBL
	Nop_C	UniProtKB/TrEMBL
	Nop_dom_sf	UniProtKB/TrEMBL
	NOSIC	UniProtKB/TrEMBL
	SnoRNA-bd_dom	UniProtKB/TrEMBL
KEGG Report	rno:362214	UniProtKB/TrEMBL
MGC_CLONE	MGC:105871	IMAGE-MGC_LOAD
	MGC:116301	IMAGE-MGC_LOAD
NCBI Gene	362214	ENTREZGENE
PANTHER	NUCLEOLAR PROTEIN 56	UniProtKB/TrEMBL
	PTHR10894	UniProtKB/TrEMBL
Pfam	Nop	UniProtKB/TrEMBL
	NOP5NT	UniProtKB/TrEMBL
PhenoGen	Nop56	PhenoGen
PROSITE	NOP	UniProtKB/TrEMBL
SMART	NOSIC	UniProtKB/TrEMBL
Superfamily-SCOP	SSF89124	UniProtKB/TrEMBL
UniProt	Q4KLK7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-12-18	Nop56	NOP56 ribonucleoprotein	Nop56	NOP56 ribonucleoprotein homolog (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2010-04-23	Nop56	NOP56 ribonucleoprotein homolog (yeast)	Nol5a	nucleolar protein 5A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Nol5a	nucleolar protein 5A	Nol5a_predicted	nucleolar protein 5A (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Nol5a_predicted	nucleolar protein 5A (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)