Nploc4 (NPL4 homolog, ubiquitin recognition factor) - Rat Genome Database

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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 and retrograde protein transport, ER to cytosol. 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 Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810106,152,756 - 106,208,306 (-)NCBIGRCr8
GRCr8 Ensembl10106,153,173 - 106,208,264 (-)EnsemblGRCr8 Ensembl
mRatBN7.210105,654,395 - 105,709,958 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10105,654,812 - 105,709,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10110,759,179 - 110,814,263 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010110,222,198 - 110,277,289 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010105,575,294 - 105,630,381 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010109,553,518 - 109,610,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10109,552,649 - 109,610,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,148,086 - 109,198,162 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410109,809,121 - 109,878,278 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera10104,200,159 - 104,255,207 (-)NCBICelera
RGSC_v3.110109,825,236 - 109,862,213 (-)NCBI
Cytogenetic Map10q32.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
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-bromohexadecanoic acid  (ISO)
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)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
CGP 52608  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyproconazole  (EXP)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (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)
isoniazide  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
leflunomide  (EXP)
mercury dichloride  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
nitrates  (ISO)
NMS-873  (ISO)
ozone  (EXP,ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
prochloraz  (EXP)
rac-lactic acid  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (EXP)
titanium dioxide  (ISO)
tolcapone  (EXP)
valdecoxib  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
cytosol  (IEA)
endoplasmic reticulum  (IEA)
nucleus  (IBA,IEA)
UFD1-NPL4 complex  (IDA,IEA,ISO)
VCP-NPL4-UFD1 AAA ATPase complex  (EXP,IDA,IEA,ISO,NAS)

Molecular Pathway Annotations     Click to see Annotation Detail View
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810106,152,756 - 106,208,306 (-)NCBIGRCr8
GRCr8 Ensembl10106,153,173 - 106,208,264 (-)EnsemblGRCr8 Ensembl
mRatBN7.210105,654,395 - 105,709,958 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10105,654,812 - 105,709,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10110,759,179 - 110,814,263 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010110,222,198 - 110,277,289 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010105,575,294 - 105,630,381 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010109,553,518 - 109,610,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10109,552,649 - 109,610,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,148,086 - 109,198,162 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410109,809,121 - 109,878,278 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera10104,200,159 - 104,255,207 (-)NCBICelera
RGSC_v3.110109,825,236 - 109,862,213 (-)NCBI
Cytogenetic Map10q32.3NCBI
NPLOC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381781,556,885 - 81,637,112 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1781,556,887 - 81,648,465 (-)EnsemblGRCh38hg38GRCh38
GRCh371779,523,911 - 79,604,138 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361777,134,357 - 77,214,543 (-)NCBINCBI36Build 36hg18NCBI36
Build 341777,134,358 - 77,214,493NCBI
Celera1776,168,272 - 76,249,182 (-)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1774,971,514 - 75,050,623 (-)NCBIHuRef
CHM1_11779,610,124 - 79,690,039 (-)NCBICHM1_1
T2T-CHM13v2.01782,474,164 - 82,554,047 (-)NCBIT2T-CHM13v2.0
Nploc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911120,270,624 - 120,328,526 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11120,271,196 - 120,328,534 (-)EnsemblGRCm39 Ensembl
GRCm3811120,379,798 - 120,437,700 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,380,370 - 120,437,708 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711120,241,685 - 120,298,982 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611120,196,461 - 120,253,758 (-)NCBIMGSCv36mm8
Celera11132,115,124 - 132,172,461 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1184.09NCBI
Nploc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555061,451,337 - 1,513,455 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555061,451,337 - 1,513,455 (+)NCBIChiLan1.0ChiLan1.0
NPLOC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21998,143,491 - 98,223,643 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan117103,043,770 - 103,123,943 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01776,012,756 - 76,092,901 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11781,713,582 - 81,785,567 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1781,713,582 - 81,788,714 (-)Ensemblpanpan1.1panPan2
NPLOC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.19538,087 - 604,898 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl9537,840 - 603,480 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha91,142,086 - 1,207,840 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.091,133,445 - 1,199,269 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl91,131,519 - 1,198,105 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.191,158,270 - 1,223,977 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.091,284,872 - 1,349,805 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.091,363,947 - 1,429,700 (+)NCBIUU_Cfam_GSD_1.0
Nploc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056021,158,248 - 1,205,737 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365945,205,659 - 5,251,026 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365945,206,222 - 5,251,042 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPLOC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl121,251,053 - 1,285,666 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1121,251,377 - 1,285,668 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2121,102,565 - 1,128,796 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NPLOC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11673,499,737 - 73,570,753 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1673,502,123 - 73,570,710 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607744,881,353 - 44,976,051 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nploc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480110,533,064 - 10,589,096 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480110,531,107 - 10,589,502 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nploc4
232 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093723381107556066Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1089039175107713808Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1097202388107556066Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087807758107713808Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1091127270107556066Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091727883107713808Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1097202388107556066Rat

Markers in Region
RH136692  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210105,763,147 - 105,763,222 (+)MAPPERmRatBN7.2
mRatBN7.210105,763,147 - 105,763,267 (+)MAPPERmRatBN7.2
Rnor_6.010109,662,770 - 109,662,889NCBIRnor6.0
Rnor_6.010109,662,770 - 109,662,844NCBIRnor6.0
Rnor_5.010109,256,038 - 109,256,157UniSTSRnor5.0
Rnor_5.010109,256,038 - 109,256,112UniSTSRnor5.0
RGSC_v3.410109,874,899 - 109,874,973UniSTSRGSC3.4
RGSC_v3.410109,874,899 - 109,875,018UniSTSRGSC3.4
Celera10104,307,077 - 104,307,151UniSTS
Celera10104,307,077 - 104,307,196UniSTS
Cytogenetic Map10q32.3UniSTS
RH141802  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210105,762,113 - 105,762,315 (+)MAPPERmRatBN7.2
Rnor_6.010109,661,736 - 109,661,937NCBIRnor6.0
Rnor_5.010109,255,004 - 109,255,205UniSTSRnor5.0
RGSC_v3.410109,873,865 - 109,874,066UniSTSRGSC3.4
Celera10104,306,043 - 104,306,244UniSTS
Cytogenetic Map10q32.3UniSTS
UniSTS:236796  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210105,655,698 - 105,655,979 (+)MAPPERmRatBN7.2
Rnor_6.010109,554,405 - 109,554,685NCBIRnor6.0
Rnor_5.010109,148,973 - 109,149,253UniSTSRnor5.0
RGSC_v3.410109,810,008 - 109,810,288UniSTSRGSC3.4
Celera10104,201,036 - 104,201,316UniSTS
Cytogenetic Map10q32.3UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 11 49 113 91 90 59 25 59 6 218 97 11 93 45 60 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000054973   ⟹   ENSRNOP00000051856
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10106,153,173 - 106,204,037 (-)Ensembl
mRatBN7.2 Ensembl10105,654,812 - 105,705,684 (-)Ensembl
Rnor_6.0 Ensembl10109,552,649 - 109,610,030 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000080188   ⟹   ENSRNOP00000068982
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10106,153,173 - 106,208,264 (-)Ensembl
mRatBN7.2 Ensembl10105,654,812 - 105,709,913 (-)Ensembl
Rnor_6.0 Ensembl10109,555,241 - 109,604,899 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114737   ⟹   ENSRNOP00000082441
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10106,153,173 - 106,208,264 (-)Ensembl
mRatBN7.2 Ensembl10105,654,812 - 105,709,913 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000168258   ⟹   ENSRNOP00000100116
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10106,153,173 - 106,208,264 (-)Ensembl
RefSeq Acc Id: NM_080577   ⟹   NP_542144
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810106,153,173 - 106,208,264 (-)NCBI
mRatBN7.210105,654,812 - 105,709,913 (-)NCBI
Rnor_6.010109,553,518 - 109,610,087 (-)NCBI
Rnor_5.010109,148,086 - 109,198,162 (-)NCBI
RGSC_v3.410109,809,121 - 109,878,278 (-)RGD
Celera10104,200,159 - 104,255,207 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085086   ⟹   XP_038941014
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810106,152,756 - 106,208,306 (-)NCBI
mRatBN7.210105,654,395 - 105,709,958 (-)NCBI
RefSeq Acc Id: NP_542144   ⟸   NM_080577
- UniProtKB: Q3T1J3 (UniProtKB/Swiss-Prot),   Q9ES54 (UniProtKB/Swiss-Prot),   A6HLC6 (UniProtKB/TrEMBL),   A0A0G2JU66 (UniProtKB/TrEMBL),   F1LQX9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068982   ⟸   ENSRNOT00000080188
Ensembl Acc Id: ENSRNOP00000051856   ⟸   ENSRNOT00000054973
RefSeq Acc Id: XP_038941014   ⟸   XM_039085086
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JU66 (UniProtKB/TrEMBL),   F1LQX9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000082441   ⟸   ENSRNOT00000114737
Ensembl Acc Id: ENSRNOP00000100116   ⟸   ENSRNOT00000168258
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 AssemblyChrPosition (strand)Source
Rnor_6.010109,610,096 - 109,610,156EPDNEW

Additional Information

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
Ensembl Transcript ENSRNOT00000080188 ENTREZGENE
  ENSRNOT00000080188.2 UniProtKB/Swiss-Prot
  ENSRNOT00000168258 ENTREZGENE
Gene3D-CATH Cytidine Deaminase, domain 2 UniProtKB/Swiss-Prot
  Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1 UniProtKB/Swiss-Prot
  Zn-finger domain of Sec23/24 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7930738 IMAGE-MGC_LOAD
InterPro MPN UniProtKB/Swiss-Prot
  Npl4 UniProtKB/Swiss-Prot
  NPL4_C UniProtKB/Swiss-Prot
  Npl4_Ub-like_dom UniProtKB/Swiss-Prot
  NPL4_Zn-bd_put UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
  Znf_RanBP2 UniProtKB/Swiss-Prot
  Znf_RanBP2_sf UniProtKB/Swiss-Prot
KEGG Report rno:140639 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124575 IMAGE-MGC_LOAD
NCBI Gene 140639 ENTREZGENE
PANTHER NUCLEAR PROTEIN LOCALIZATION PROTEIN 4 HOMOLOG UniProtKB/Swiss-Prot
  PTHR12710 UniProtKB/Swiss-Prot
Pfam NPL4 UniProtKB/Swiss-Prot
  UN_NPL4 UniProtKB/Swiss-Prot
  zf-NPL4 UniProtKB/Swiss-Prot
PhenoGen Nploc4 PhenoGen
PIRSF Polyub_prc_Npl4 UniProtKB/Swiss-Prot
PROSITE MPN UniProtKB/Swiss-Prot
  ZF_RANBP2_1 UniProtKB/Swiss-Prot
  ZF_RANBP2_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000036698 RatGTEx
SMART ZnF_RBZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot
  SSF90209 UniProtKB/Swiss-Prot
UniProt A0A0G2JU66 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZTJ3_RAT UniProtKB/TrEMBL
  A6HLC5_RAT UniProtKB/TrEMBL
  A6HLC6 ENTREZGENE, UniProtKB/TrEMBL
  F1LQX9 ENTREZGENE, UniProtKB/TrEMBL
  NPL4_RAT UniProtKB/Swiss-Prot
  Q3T1J3 ENTREZGENE
  Q9ES54 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