Nploc4 (NPL4 homolog, ubiquitin recognition factor)

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Gene: Nploc4 (NPL4 homolog, ubiquitin recognition factor) Rattus norvegicus

Analyze

Symbol:

Nploc4

Name:

NPL4 homolog, ubiquitin recognition factor

RGD ID:

620794

Description:

Enables ATPase binding activity; ubiquitin binding activity; and ubiquitin protein ligase binding activity. Contributes to K48-linked polyubiquitin modification-dependent protein binding activity and K63-linked polyubiquitin modification-dependent protein binding activity. Involved in Golgi organization. Located in cytosol and nucleus. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Orthologous to human NPLOC4 (NPL4 homolog, ubiquitin recognition factor); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homolog of yeast nuclear protein localization 4; MGC124575; Npl4; nuclear protein localization 4; nuclear protein localization 4 homolog; nuclear protein localization 4 homolog (S. cerevisiae); nuclear protein localization protein 4 homolog

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):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Nploc4 (NPL4 homolog, ubiquitin recognition factor)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Nploc4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nploc4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nploc4 (NPL4 homolog, ubiquitin recognition factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NPLOC4 (NPL4 homolog, ubiquitin recognition factor)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Nploc4 (NPL4 homolog, ubiquitin recognition factor)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nploc4 (NPL4 homolog, ubiquitin recognition factor)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	NPL4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Npl4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	npl-4.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	npl-4.2	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	10	105,654,395 - 105,709,958 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	105,654,812 - 105,709,913 (-)	Ensembl
Rnor_6.0	10	109,553,518 - 109,610,087 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	109,552,649 - 109,610,030 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	109,148,086 - 109,198,162 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	109,809,121 - 109,878,278 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	109,825,236 - 109,862,213 (-)	NCBI
Celera	10	104,200,159 - 104,255,207 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

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

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

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

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

4,4'-sulfonyldiphenol (ISO)

acetamide (EXP)

acrolein (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

arsenous acid (ISO)

bisphenol A (EXP,ISO)

butan-1-ol (ISO)

CGP 52608 (ISO)

clozapine (ISO)

cobalt dichloride (EXP,ISO)

copper(II) sulfate (ISO)

cyproconazole (EXP)

diarsenic trioxide (ISO)

dibutyl phthalate (ISO)

doxorubicin (ISO)

endosulfan (EXP,ISO)

epoxiconazole (EXP)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

fulvestrant (ISO)

gold atom (ISO)

gold(0) (ISO)

ivermectin (ISO)

lead(0) (ISO)

lead(2+) (ISO)

leflunomide (EXP)

mercury dichloride (EXP)

nefazodone (EXP)

nimesulide (EXP)

ozone (EXP,ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

phorbol 13-acetate 12-myristate (ISO)

prochloraz (EXP)

rac-lactic acid (ISO)

sodium arsenite (ISO)

temozolomide (ISO)

tetrachloromethane (EXP,ISO)

tolcapone (EXP)

valdecoxib (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

Golgi organization (IDA)

membrane fusion (IDA)

negative regulation of RIG-I signaling pathway (IEA,ISO,ISS)

negative regulation of type I interferon production (IEA,ISO,ISS)

retrograde protein transport, ER to cytosol (IC,IEA,ISO,ISS)

ubiquitin-dependent ERAD pathway (IC)

ubiquitin-dependent protein catabolic process (IBA,IEA,ISO,ISS)

Cellular Component

cytosol (IDA)

nucleus (IBA,IDA)

UFD1-NPL4 complex (IDA,IEA,ISO)

VCP-NPL4-UFD1 AAA ATPase complex (IC,IDA,IEA,ISO,NAS)

Molecular Function

ATPase binding (IPI)

K48-linked polyubiquitin modification-dependent protein binding (IDA)

K63-linked polyubiquitin modification-dependent protein binding (IDA)

metal ion binding (IEA)

protein binding (IPI,ISO)

protein-containing complex binding (IPI)

ubiquitin binding (IBA,IDA)

ubiquitin protein ligase binding (IBA,IDA)

Molecular Pathway Annotations Click to see Annotation Detail View

Endoplasmic Reticulum-associated degradation pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover.	Alexandru G, etal., Cell. 2008 Sep 5;134(5):804-16. doi: 10.1016/j.cell.2008.06.048.
2.	Involvement of the p97-Ufd1-Npl4 complex in the regulated endoplasmic reticulum-associated degradation of inositol 1,4,5-trisphosphate receptors.	Alzayady KJ, etal., J Biol Chem. 2005 Oct 14;280(41):34530-7. Epub 2005 Aug 15.
3.	Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy.	Bebeacua C, etal., Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1098-103. doi: 10.1073/pnas.1114341109. Epub 2012 Jan 9.
4.	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.
5.	A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways.	Meyer HH, etal., EMBO J 2000 May 15;19(10):2181-92.
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	Structural insights into the p97-Ufd1-Npl4 complex.	Pye VE, etal., Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):467-72. Epub 2007 Jan 3.
9.	GOA pipeline	RGD automated data pipeline
10.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
11.	Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3.	Wang Q, etal., J Cell Biol. 2006 Sep 25;174(7):963-71.
12.	Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains.	Ye Y, etal., J Cell Biol. 2003 Jul 7;162(1):71-84.

Additional References at PubMed

PMID:11574150	PMID:11740563	PMID:11781570	PMID:12411482	PMID:12477932	PMID:12644454	PMID:14636562	PMID:15029239	PMID:19182904	PMID:21630459	PMID:25660456	PMID:26471729

Genomics

Comparative Map Data

Nploc4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	105,654,395 - 105,709,958 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	105,654,812 - 105,709,913 (-)	Ensembl
Rnor_6.0	10	109,553,518 - 109,610,087 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	109,552,649 - 109,610,030 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	109,148,086 - 109,198,162 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	109,809,121 - 109,878,278 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	109,825,236 - 109,862,213 (-)	NCBI
Celera	10	104,200,159 - 104,255,207 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

NPLOC4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	81,556,885 - 81,637,112 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	17	81,556,887 - 81,648,465 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	79,523,911 - 79,604,138 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	77,134,357 - 77,214,543 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	77,134,358 - 77,214,493	NCBI
Celera	17	76,168,272 - 76,249,182 (-)	NCBI
Cytogenetic Map	17	q25.3	NCBI
HuRef	17	74,971,514 - 75,050,623 (-)	NCBI		HuRef
CHM1_1	17	79,610,124 - 79,690,039 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	82,474,164 - 82,554,047 (-)	NCBI

Nploc4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	120,270,624 - 120,328,526 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	120,271,196 - 120,328,534 (-)	Ensembl
GRCm38	11	120,379,798 - 120,437,700 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	120,380,370 - 120,437,708 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	120,241,685 - 120,298,982 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	120,196,461 - 120,253,758 (-)	NCBI			mm8
Celera	11	132,115,124 - 132,172,461 (-)	NCBI		Celera
Cytogenetic Map	11	E2	NCBI

Nploc4
(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_004955506	1,451,337 - 1,513,455 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955506	1,451,337 - 1,513,455 (+)	NCBI	ChiLan1.0	ChiLan1.0

NPLOC4
(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	17	81,713,582 - 81,785,567 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	81,713,582 - 81,788,714 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	76,012,756 - 76,092,901 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NPLOC4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	538,087 - 604,898 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	537,840 - 603,480 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	1,142,086 - 1,207,840 (+)	NCBI
ROS_Cfam_1.0	9	1,133,445 - 1,199,269 (+)	NCBI
ROS_Cfam_1.0 Ensembl	9	1,131,519 - 1,198,105 (+)	Ensembl
UMICH_Zoey_3.1	9	1,158,270 - 1,223,977 (+)	NCBI
UNSW_CanFamBas_1.0	9	1,284,872 - 1,349,805 (+)	NCBI
UU_Cfam_GSD_1.0	9	1,363,947 - 1,429,700 (+)	NCBI

Nploc4
(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_024405602	1,158,248 - 1,205,737 (+)	NCBI
SpeTri2.0	NW_004936594	5,206,222 - 5,251,042 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NPLOC4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	1,251,053 - 1,285,666 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	1,251,377 - 1,285,668 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	1,102,565 - 1,128,796 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NPLOC4
(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	16	73,499,737 - 73,570,753 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	16	73,502,123 - 73,570,710 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666077	44,881,353 - 44,976,051 (-)	NCBI	Vero_WHO_p1.0

Nploc4
(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_004624801	10,533,064 - 10,589,096 (-)	Ensembl	HetGla_female_1.0		hetGla2
HetGla 1.0	NW_004624801	10,531,107 - 10,589,502 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH136692

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	105,763,147 - 105,763,222 (+)	MAPPER	mRatBN7.2
mRatBN7.2	10	105,763,147 - 105,763,267 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	109,662,770 - 109,662,889	NCBI	Rnor6.0
Rnor_6.0	10	109,662,770 - 109,662,844	NCBI	Rnor6.0
Rnor_5.0	10	109,256,038 - 109,256,157	UniSTS	Rnor5.0
Rnor_5.0	10	109,256,038 - 109,256,112	UniSTS	Rnor5.0
RGSC_v3.4	10	109,874,899 - 109,874,973	UniSTS	RGSC3.4
RGSC_v3.4	10	109,874,899 - 109,875,018	UniSTS	RGSC3.4
Celera	10	104,307,077 - 104,307,151	UniSTS
Celera	10	104,307,077 - 104,307,196	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

RH141802

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	105,762,113 - 105,762,315 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	109,661,736 - 109,661,937	NCBI	Rnor6.0
Rnor_5.0	10	109,255,004 - 109,255,205	UniSTS	Rnor5.0
RGSC_v3.4	10	109,873,865 - 109,874,066	UniSTS	RGSC3.4
Celera	10	104,306,043 - 104,306,244	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

UniSTS:236796

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	105,655,698 - 105,655,979 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	109,554,405 - 109,554,685	NCBI	Rnor6.0
Rnor_5.0	10	109,148,973 - 109,149,253	UniSTS	Rnor5.0
RGSC_v3.4	10	109,810,008 - 109,810,288	UniSTS	RGSC3.4
Celera	10	104,201,036 - 104,201,316	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

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
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	72224939	107211142	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
1579915	Bp280	Blood pressure QTL 280		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	90404397	107211142	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	76452683	107211142	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	69738412	107211142	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	63221094	107211142	Rat
12880385	Cm108	Cardiac mass QTL 108		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)		90404397	107211142	Rat
12880384	Cm107	Cardiac mass QTL 107		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)		90404397	107211142	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	69738412	107211142	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
2303589	Bw87	Body weight QTL 87	2		body mass (VT:0001259)	body weight (CMO:0000012)	10	81285008	107211142	Rat
12880396	Am13	Aortic mass QTL 13		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	90404397	107211142	Rat
61363	Oia3	Oil induced arthritis QTL 3		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	87307617	107211142	Rat
12880395	Cm109	Cardiac mass QTL 109		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	90404397	107211142	Rat
12880398	Kidm67	Kidney mass QTL 67		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	90404397	107211142	Rat
1578672	Bmd16	Bone mineral density QTL 16	6.2		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	96703043	107057807	Rat
634320	Niddm49	Non-insulin dependent diabetes mellitus QTL 49	4.41		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	10	88539139	107211142	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	72224939	107211142	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	76748906	107211142	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	69738412	107211142	Rat
1300137	Bp186	Blood pressure QTL 186	3.57		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	10	90627439	107057807	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	62057807	107057807	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	76246085	107211142	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68420376	107211142	Rat
2292436	Bp310	Blood pressure QTL 310			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	94759759	107211142	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68383129	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	51770177	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	51770177	107211142	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	62057807	107057807	Rat
1558652	Bw57	Body weight QTL 57	4.2	0.0008	body mass (VT:0001259)	body weight (CMO:0000012)	10	90910316	107211142	Rat
724530	Bp149	Blood pressure QTL 149		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	90627439	107211142	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	70199100	107211142	Rat
2317754	Glom25	Glomerulus QTL 25	3.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	82685200	107211142	Rat
631538	Oia5	Oil induced arthritis QTL 5			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	87055121	107211142	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	53797385	107211142	Rat
1578663	Bss18	Bone structure and strength QTL 18	3.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	10	96703043	107057807	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	66978955	107211142	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	66978955	107211142	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	67750049	107211142	Rat
10450493	Bp382	Blood pressure QTL 382		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	94759759	107211142	Rat
1354641	Bvd2	Brain ventricular dilatation QTL 2	6.36	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	10	93223816	107057807	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	199
Count of miRNA genes:	150
Interacting mature miRNAs:	163
Transcripts:	ENSRNOT00000054973
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	35	49	33	19	33	7	10	74	31	41	11	7
Low		8	8	8		8	1	1		4			1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_080577	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039085086	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF234600	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC101887	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000054973 ⟹ ENSRNOP00000051856

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	105,654,812 - 105,705,684 (-)	Ensembl
Rnor_6.0 Ensembl	10	109,552,649 - 109,610,030 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000080188 ⟹ ENSRNOP00000068982

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	105,654,812 - 105,709,913 (-)	Ensembl
Rnor_6.0 Ensembl	10	109,555,241 - 109,604,899 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000114737 ⟹ ENSRNOP00000082441

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	105,654,812 - 105,709,913 (-)	Ensembl

RefSeq Acc Id:

NM_080577 ⟹ NP_542144

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	105,654,812 - 105,709,913 (-)	NCBI
Rnor_6.0	10	109,553,518 - 109,610,087 (-)	NCBI
Rnor_5.0	10	109,148,086 - 109,198,162 (-)	NCBI
RGSC_v3.4	10	109,809,121 - 109,878,278 (-)	RGD
Celera	10	104,200,159 - 104,255,207 (-)	RGD

Sequence:

show sequence

CGCTGGCGGAGCCGGGCGGCGAAGCTGGAGCGGCGGTGGCGGCGGCGGCGGGAGGCCGGGGCCG
GGGCTGAGGCCGAGGCCGGGGCTGCGAGGCCCTTGGGGAGACAGGCGGCGGCAGCCCGGGGCCC
GAGCCCGGAGGCAGGAGCGACCGCCATGGCCGAGAGCATCATAATCCGTGTCCAATCCCCCGAT
GGAGTGAAGAGGATCACAGCAACAAAGAGAGAAACAGCCGCAACATTTCTGAAAAAGGTTGCAA
AGGAGTTTGGCTTCCAAAACAACGGCTTCTCGGTTTACATCAATAGAAACAAGACTGGAGAGAT
AACAGCATCGTCCAGCAAATCCCTGCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTG
TTCCCCTCAAGCCTTGCTGGACCCTCATCTGAAATGGAAACATCGACCTCAGTAGGGTTAAAGG
CCTTTGGTGCTCCTCACGTGGTTGAAGATGAGATTGATCAATACCTCAGCAAGCAGGATGGGAA
GATTTATAGGAGCCGAGACCCACAGTTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGT
GTCCCACTGGAGCCATTTGATGAAGACTATCTGAACCACTTGGAGCCTCCTGTGAAGCACATGT
CCTTCCATGCCTACATCCGGAAGCTGACTGGAGGGGCTGACAAGGGGAAGTTCGTTGCCCTGGA
GAACATCAGCTGCAAGATTAAGTCAGGATGTGAGGGACACCTCCCTTGGCCAAATGGTATCTGT
ACCAAATGCCAGCCTAGTGCCATCACATTGAACAGACAGAAATATAGACATGTGGACAACATTA
TGTTTGAGAATCACACTGTTGCTGACCGTTTCCTTGACTTCTGGAGAAAGACAGGAAACCAACA
TTTCGGGTACTTATATGGACGGTACACAGAGCACAAAGACATTCCCCTTGGCATCAGGGCTGAA
GTGGCTGCAATTTATGAGCCTCCTCAGATTGGTACACAGAACAGCCTGGAGCTTCTGGAAGATC
CAAAAGCTGAGGTGGTTGACGAGATTGCCTCCAAACTTGGCCTGAGGAAGGTTGGATGGATATT
CACGGACCTTGTCTCAGAAGATACCCGAAAGGGTACAGTCCGATACAGTCGGAATAAGGACACC
TATTTCCTGAGTTCAGAAGAATGCATCACTGCAGGAGACTTTCAAAACAAGCACCCCAACATTT
GCCGGCTCTCTCCGGATGGTCATTTTGGATCCAAGTTTGTTACTGCAGTGGCCACAGGTGGTCC
TGATAACCAGGTTCACTTTGAAGGGTACCAGGTATCCAATCAGTGCATGGCACTGGTCCGAGAT
GAGTGTCTTCTACCTTGTAAGGATGCCCCTGAGCTCGGCTATGCCAAGGAGTCCAGCAGTGAAC
AATATGTTCCTGACGTGTTTTACAAGGACATAGACAAGTTTGGCAATGAGATCACCCAGCTGGC
CCGTCCCCTGCCTGTGGAGTATCTCATCATAGATATCACAACCACCTTCCCCAAGGATCCAGTT
TACACTTTTTCTATTTCTCAAAATCCGTTTCCTATTGAAAACCGGGATGTGCTGGGTGAGACAC
AGGACTTCCATAGTTTGGCCACCTACTTGTCCCAGAATACCTCATCTGTGTTCTTGGATACCAT
CTCCGACTTCCATCTCCTGTTGTTTCTGGTCACCAATGAAGTCATGCCACTGCAGGACAGTATC
AGCCTGCTGCTAGAAGCCGTCAGGACCAGAAACGAGGAGCTAGCACAGACATGGAAAAAGTCTG
AACAGTGGGCCACCATTGAGCAGCTGTGCAGCACTGTTGGTGTGCAGCTCCCAGGCCTCCATGA
GTTTGGTGCAGTCGGGGGCTCTGCACGCGCTGCTACCTCTGCCATGTGGGCTTGTCAGCACTGC
ACCTTCATGAACCAGCCTGGCACAGGCCACTGCGAGATGTGCAGCCTTCCCCGGACCTAGGGCT
CTGGACCTCTGCTGTGTAGGACTGGGCCTGTCCAGCCCTCTCTGAAGTCTGGAGTGCCATATGT
TCCCTATAAGGCCTGAAGCCCACAGCCCTGAAACAGTGGGGCCAGCTACCCTGGTATTCCAGAT
ATACTGAAGCGTCTCAGTGCAGATCTTGAAGAGAAAGAACCCCAACTGCTGTGCTGGGGTTGAA
CACAACCTCCCAACTGGAAAGGCAGAGCAGACTTGCCCAAGAGCACCCCACTTGCCTCACTTAG
TCAATAACTCCCCACTGTGTTGGAGGACTGGACACCTCCGACCAACCACCTGAAATCGGGGTGC
ACAGAGAGGGTGCTGCTGTCACCCAGCCATCTTTCCTTCCTCTATGATTTTTGTTTTCTGCCTT
CCCACCTTCTTCCCCAGTGTTTGGATGGATGCTCCTAGTTGTCTCTGTTCCCTTGTTGTGGGGC
TGTGTCCCTCCTTTGGGAGCATGTGTGGCTAGGGTGTGGTAGCCTTGGTCTGACATGCAGTGTA
GTACGTCCCTGCCCTTTACTTGTCTGAAATCAGCAGTTATCAGTAATTCCCACCCAGGAAACTT
TTATTTATTGTTTTTTTTTTGTTGTTGTTTGTTTTGTTTTGTTTTTTAAGATAAAACTGCACAG
ATGGAGTGAGATAGATTTAATTCTACTCTCTTTCCTCCTTTAGTGCAGCCCCTCTTGGGTGGTT
TATTGGGCAGGAGGCCACCATCTTTTCTCCTCTGAAGCAAACCTCAGTGCCTGAGACTTTCCTG
CCTGCCACGCTGCAGACAGTAGAGATTGGTAGCACAGGTGGTTCATCAGAGCAGTAGTGGCTCT
TGCCTCACAGACAGCCCCTTCAAGTCTAGGGCAGCCCTGGAGTTCTGGTCCCTAATGTGTCCCT
ACATTATGGCCTTCTTGCACGGTGCTGTGGCAGTTGAGAAAGCCTAGAAAAGGTGCCCCTGTGA
CCACTGTGAGGCATGTAGAAACAGTTTGAGGGTCCTGTGTGGCTGCGTTATGACAGCCCTTACC
CAGGTAAGATATGGATATCTTGATGCCTCGTTGCCTTAATGAGAGCTAAGTCAGCTGTCCTTCA
CCCTGGGAAAGGCCATGCCAACTGTGGACTGCTGGGAGCCATGCGTGTCACTTGAGTAGAGTGC
ACCCGTGCTTCCTTCCCCATCTTTGGCCCTATGGACAGAGCACTTGTTGCTAGGTTATCGTGTG
GCAGGGCTGGCCAGCACCGTCGGTCTCACCTGACATGAGATCTGAAGCTACAGCCCTGGAGCTG
AGGAGCCACTGTGCTTGGTTTGGTATTGACAGGGTCATCTTGGAGGGTTGGGAGTGGTGGAGAG
CAGGGCAAGCAATCTCTCCAGCTACCTGCCAACAGTATAGAGATAAAGTGCTGAGGGCTGTCTA
ACCTCCCTCCTGGTAGTGTCCCGGCTAGGGCTTCACCTTTCTGTTTTTTTCTGGTCCCTAAGTC
TGGTAGACTGGATGTCCTTGTATTTCTGTGTCTGCAACTAAGCTATGTTTCTGATGCCAATCAT
TCTAGCACTATTACTCACGTTGGGCAGGTGCTGGGCAGCACAGACTCTGGAGACCTGTTTGCTA
CTGCTTATTCCCCCATTCATCTTTGTCTACAAAGTTAATTACGTTCTCGAGTTCTGGCATCCAC
ATAATTCTTGTTTTTCTCTGACTTTTAGCTAAAGAAATTTTTTGTGATTTCTCTGAAAAAAAAA
AAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039085086 ⟹ XP_038941014

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	105,654,395 - 105,709,958 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_542144	(Get FASTA)	NCBI Sequence Viewer
	XP_038941014	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAG27534	(Get FASTA)	NCBI Sequence Viewer
	AAI01888	(Get FASTA)	NCBI Sequence Viewer
	EDM06830	(Get FASTA)	NCBI Sequence Viewer
	EDM06831	(Get FASTA)	NCBI Sequence Viewer
	Q9ES54	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_542144 ⟸ NM_080577

- UniProtKB:

Q9ES54 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSL
HLLKIKHGDLLFLFPSSLAGPSSEMETSTSVGLKAFGAPHVVEDEIDQYLSKQDGKIYRSRDPQ
LCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADKGKFVALENISCKIKS
GCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDFWRKTGNQHFGYLYGRY
TEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIASKLGLRKVGWIFTDLVSEDT
RKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEG
YQVSNQCMALVRDECLLPCKDAPELGYAKESSSEQYVPDVFYKDIDKFGNEITQLARPLPVEYL
IIDITTTFPKDPVYTFSISQNPFPIENRDVLGETQDFHSLATYLSQNTSSVFLDTISDFHLLLF
LVTNEVMPLQDSISLLLEAVRTRNEELAQTWKKSEQWATIEQLCSTVGVQLPGLHEFGAVGGSA
RAATSAMWACQHCTFMNQPGTGHCEMCSLPRT

hide sequence

RefSeq Acc Id:

ENSRNOP00000068982 ⟸ ENSRNOT00000080188

RefSeq Acc Id:

ENSRNOP00000051856 ⟸ ENSRNOT00000054973

RefSeq Acc Id:	XP_038941014 ⟸ XM_039085086
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSRNOP00000082441 ⟸ ENSRNOT00000114737

Protein Domains

MPN RanBP2-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9ES54-F1-model_v2	AlphaFold	Q9ES54	1-608	view protein structure

Transcriptome

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

Promoters

RGD ID:

13697955

Promoter ID:

EPDNEW_R8480

Type:

initiation region

Name:

Nploc4_1

Description:

NPL4 homolog, ubiquitin recognition factor

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	10	109,610,096 - 109,610,156	EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)

ACI/EurMcwi (2019)

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CSV

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

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CSV

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

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CSV

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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CSV

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

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CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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CSV

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620794	AgrOrtholog
BIND	130678
	130682
	130685
BioCyc Gene	G2FUF-22433	BioCyc
Ensembl Genes	ENSRNOG00000036698	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000051856.4	UniProtKB/TrEMBL
	ENSRNOP00000068982	ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOP00000082441.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000054973.4	UniProtKB/TrEMBL
	ENSRNOT00000080188	ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOT00000114737.1	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7930738	IMAGE-MGC_LOAD
InterPro	MPN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Npl4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NPL4_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Npl4_Ub-like_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NPL4_Zn-bd_put	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RanBP2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RanBP2_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:140639	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:124575	IMAGE-MGC_LOAD
NCBI Gene	140639	ENTREZGENE
PANTHER	PTHR12710	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	NPL4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UN_NPL4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	zf-NPL4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Nploc4	PhenoGen
PIRSF	Polyub_prc_Npl4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	MPN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ZF_RANBP2_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ZF_RANBP2_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	ZnF_RBZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF54236	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF90209	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JU66_RAT	UniProtKB/TrEMBL
	A0A8I5ZTJ3_RAT	UniProtKB/TrEMBL
	F1LQX9_RAT	UniProtKB/TrEMBL
	NPL4_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q3T1J3	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-07-09	Nploc4	NPL4 homolog, ubiquitin recognition factor	Nploc4	nuclear protein localization 4 homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Nploc4	nuclear protein localization 4 homolog (S. cerevisiae)	Npl4	nuclear protein localization 4	Symbol and Name updated	1299863	APPROVED
2005-01-20	Npl4	nuclear protein localization 4		homolog of yeast nuclear protein localization 4	Name updated	1299863	APPROVED
2002-08-07	Npl4	homolog of yeast nuclear protein localization 4			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	forms a complex with Ufd1	633500

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)

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Imported Annotations - KEGG (archival)