Nprl2 (NPR2-like, GATOR1 complex subunit) - Rat Genome Database

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Gene: Nprl2 (NPR2-like, GATOR1 complex subunit) Rattus norvegicus
Analyze
Symbol: Nprl2
Name: NPR2-like, GATOR1 complex subunit
RGD ID: 1308927
Description: Predicted to contribute to GTPase activator activity. Predicted to be involved in cellular response to amino acid starvation; negative regulation of TORC1 signaling; and positive regulation of autophagy. Predicted to act upstream of or within several processes, including TORC1 signaling; cellular response to methionine; and regulation of translational initiation. Predicted to be part of GATOR1 complex. Predicted to be active in lysosomal membrane. Human ortholog(s) of this gene implicated in familial focal epilepsy with variable foci 2. Orthologous to human NPRL2 (NPR2 like, GATOR1 complex subunit); PARTICIPATES IN mTOR signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GATOR complex protein NPRL2; GATOR1 complex protein NPRL2; LOC363138; MGC114378; nitrogen permease regulator-like 2; nitrogen permease regulator-like 2 (S. cerevisiae); tumor suppressor candidate 4; Tusc4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88117,094,443 - 117,097,639 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,094,441 - 117,097,637 (+)EnsemblGRCr8
mRatBN7.28108,215,823 - 108,218,996 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,215,814 - 108,218,996 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8113,842,858 - 113,846,031 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,042,014 - 112,045,187 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,884,795 - 109,887,968 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,297,950 - 116,301,123 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,297,950 - 116,301,122 (+)Ensemblrn6Rnor6.0
Rnor_5.08115,654,210 - 115,657,383 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48112,789,664 - 112,792,837 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8107,522,243 - 107,525,416 (+)NCBICelera
RGSC_v3.18112,809,139 - 112,812,182 (+)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
GATOR1 complex  (IBA,IEA,ISO)
lysosomal membrane  (IEA,ISO)
vacuolar membrane  (IBA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Regulation of mTORC1 by amino acids. Bar-Peled L and Sabatini DM, Trends Cell Biol. 2014 Jul;24(7):400-6. doi: 10.1016/j.tcb.2014.03.003. Epub 2014 Mar 31.
2. 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.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7667285   PMID:8889548   PMID:12477932   PMID:18616680   PMID:23723238   PMID:28199306  


Genomics

Comparative Map Data
Nprl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88117,094,443 - 117,097,639 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,094,441 - 117,097,637 (+)EnsemblGRCr8
mRatBN7.28108,215,823 - 108,218,996 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,215,814 - 108,218,996 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8113,842,858 - 113,846,031 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,042,014 - 112,045,187 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,884,795 - 109,887,968 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,297,950 - 116,301,123 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,297,950 - 116,301,122 (+)Ensemblrn6Rnor6.0
Rnor_5.08115,654,210 - 115,657,383 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48112,789,664 - 112,792,837 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8107,522,243 - 107,525,416 (+)NCBICelera
RGSC_v3.18112,809,139 - 112,812,182 (+)NCBI
Cytogenetic Map8q32NCBI
NPRL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38350,347,330 - 50,350,775 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl350,347,330 - 50,350,826 (-)Ensemblhg38GRCh38
GRCh37350,384,761 - 50,388,206 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36350,359,923 - 50,363,490 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34350,359,922 - 50,363,490NCBI
Celera350,357,750 - 50,361,317 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef350,440,520 - 50,444,087 (-)NCBIHuRef
CHM1_1350,337,194 - 50,340,761 (-)NCBICHM1_1
T2T-CHM13v2.0350,377,054 - 50,380,498 (-)NCBIT2T-CHM13v2.0
Nprl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,419,405 - 107,422,905 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9107,419,425 - 107,422,905 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm389107,542,177 - 107,545,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9107,542,226 - 107,545,706 (+)Ensemblmm10GRCm38
MGSCv379107,444,540 - 107,448,037 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369107,400,327 - 107,403,796 (+)NCBIMGSCv36mm8
Celera9107,150,974 - 107,154,469 (+)NCBICelera
Cytogenetic Map9F1NCBI
cM Map958.12NCBI
Nprl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555322,148,950 - 2,152,671 (-)Ensembl
ChiLan1.0NW_0049555322,148,950 - 2,152,671 (-)NCBIChiLan1.0ChiLan1.0
NPRL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2250,328,078 - 50,331,299 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1350,332,856 - 50,336,074 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0350,273,611 - 50,277,175 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1351,508,932 - 51,512,791 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl351,508,932 - 51,512,776 (-)EnsemblpanPan2panpan1.1
NPRL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12039,005,699 - 39,009,183 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2039,005,734 - 39,009,189 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2038,926,898 - 38,930,398 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02039,361,892 - 39,365,392 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2039,361,942 - 39,365,376 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12038,729,727 - 38,733,225 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02039,133,286 - 39,136,787 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02039,413,296 - 39,416,796 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nprl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560263,212,875 - 63,216,191 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049395301,769 - 5,100 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049395301,745 - 5,100 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPRL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1332,830,899 - 32,834,183 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11332,830,895 - 32,834,205 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21336,009,112 - 36,012,405 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPRL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12211,735,853 - 11,739,325 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041155,247,444 - 155,250,916 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nprl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247304,196,154 - 4,200,102 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247304,196,154 - 4,200,100 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nprl2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1898,858,335 - 98,861,578 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nprl2
45 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:41
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000051522
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
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)849849908118871671Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8111249511117802327Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
RH132770  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,218,744 - 108,218,960 (+)MAPPERmRatBN7.2
Rnor_6.08116,300,872 - 116,301,087NCBIRnor6.0
Rnor_5.08115,657,132 - 115,657,347UniSTSRnor5.0
RGSC_v3.48112,792,586 - 112,792,801UniSTSRGSC3.4
Celera8107,525,165 - 107,525,380UniSTS
RH 3.4 Map81120.8UniSTS
Cytogenetic Map8q32UniSTS
BF396742  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr88117,094,620 - 117,095,173 (+)Marker Load Pipeline
mRatBN7.28108,215,977 - 108,216,530 (+)MAPPERmRatBN7.2
Rnor_6.08116,298,105 - 116,298,657NCBIRnor6.0
Rnor_5.08115,654,365 - 115,654,917UniSTSRnor5.0
RGSC_v3.48112,789,819 - 112,790,371UniSTSRGSC3.4
Celera8107,522,398 - 107,522,950UniSTS
RH 3.4 Map81118.9UniSTS
Cytogenetic Map8q32UniSTS


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
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000051522   ⟹   ENSRNOP00000046410
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8117,094,441 - 117,097,637 (+)Ensembl
mRatBN7.2 Ensembl8108,215,814 - 108,218,996 (+)Ensembl
Rnor_6.0 Ensembl8116,297,950 - 116,301,122 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120056   ⟹   ENSRNOP00000077098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8117,094,441 - 117,097,637 (+)Ensembl
mRatBN7.2 Ensembl8108,215,844 - 108,218,884 (+)Ensembl
RefSeq Acc Id: NM_001025744   ⟹   NP_001020915
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,094,466 - 117,097,639 (+)NCBI
mRatBN7.28108,215,823 - 108,218,996 (+)NCBI
Rnor_6.08116,297,950 - 116,301,123 (+)NCBI
Rnor_5.08115,654,210 - 115,657,383 (+)NCBI
RGSC_v3.48112,789,664 - 112,792,837 (+)RGD
Celera8107,522,243 - 107,525,416 (+)RGD
Sequence:
RefSeq Acc Id: XR_010053995
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,094,443 - 117,096,616 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001020915 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77251 (Get FASTA)   NCBI Sequence Viewer  
  EDL77252 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046410
  ENSRNOP00000046410.3
  ENSRNOP00000077098.2
RefSeq Acc Id: NP_001020915   ⟸   NM_001025744
- UniProtKB: D3ZPN1 (UniProtKB/TrEMBL),   A6I2X5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000046410   ⟸   ENSRNOT00000051522
Ensembl Acc Id: ENSRNOP00000077098   ⟸   ENSRNOT00000120056

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZPN1-F1-model_v2 AlphaFold D3ZPN1 1-380 view protein structure

Transcriptome

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

Promoters
RGD ID:13696268
Promoter ID:EPDNEW_R6792
Type:multiple initiation site
Name:Nprl2_1
Description:NPR2-like, GATOR1 complex subunit
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_6.08116,297,956 - 116,298,016EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308927 AgrOrtholog
BioCyc Gene G2FUF-29200 BioCyc
Ensembl Genes ENSRNOG00000021660 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051522 ENTREZGENE
  ENSRNOT00000051522.5 UniProtKB/TrEMBL
  ENSRNOT00000120056.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7192224 IMAGE-MGC_LOAD
  IMAGE:7386309 IMAGE-MGC_LOAD
InterPro NPR2 UniProtKB/TrEMBL
KEGG Report rno:363138 UniProtKB/TrEMBL
MGC_CLONE MGC:114378 IMAGE-MGC_LOAD
  MGC:94669 IMAGE-MGC_LOAD
NCBI Gene 363138 ENTREZGENE
PANTHER GATOR COMPLEX PROTEIN NPRL2 UniProtKB/TrEMBL
  PTHR12991 UniProtKB/TrEMBL
Pfam NPR2 UniProtKB/TrEMBL
PhenoGen Nprl2 PhenoGen
RatGTEx ENSRNOG00000021660 RatGTEx
UniProt A0A8I5Y165_RAT UniProtKB/TrEMBL
  A6I2X5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZPN1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Nprl2  NPR2-like, GATOR1 complex subunit  Nprl2  nitrogen permease regulator-like 2 (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-01 Nprl2  nitrogen permease regulator-like 2 (S. cerevisiae)  Tusc4  tumor suppressor candidate 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tusc4  tumor suppressor candidate 4  Tusc4_predicted  tumor suppressor candidate 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tusc4_predicted  tumor suppressor candidate 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED