Nrde2 (NRDE-2, necessary for RNA interference, domain containing) - Rat Genome Database

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Gene: Nrde2 (NRDE-2, necessary for RNA interference, domain containing) Rattus norvegicus
Analyze
Symbol: Nrde2
Name: NRDE-2, necessary for RNA interference, domain containing
RGD ID: 1565082
Description: Predicted to be involved in several processes, including RNA splicing; positive regulation of RNA export from nucleus; and regulation of gene expression. Predicted to be located in nuclear speck and nucleolus. Orthologous to human NRDE2 (NRDE-2, necessary for RNA interference, domain containing); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC314381; nuclear exosome regulator NRDE2; RGD1565082; similar to Protein C14orf102 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86125,137,121 - 125,177,689 (-)NCBIGRCr8
mRatBN7.26119,405,103 - 119,446,861 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6119,404,334 - 119,448,915 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06124,136,949 - 124,177,426 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6124,142,395 - 124,177,404 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06133,365,208 - 133,404,549 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46124,395,552 - 124,435,239 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6116,936,527 - 116,975,660 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nuclear speck  (ISO)
nucleolus  (ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:30842217  


Genomics

Comparative Map Data
Nrde2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86125,137,121 - 125,177,689 (-)NCBIGRCr8
mRatBN7.26119,405,103 - 119,446,861 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6119,404,334 - 119,448,915 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06124,136,949 - 124,177,426 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6124,142,395 - 124,177,404 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06133,365,208 - 133,404,549 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46124,395,552 - 124,435,239 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6116,936,527 - 116,975,660 (-)NCBICelera
Cytogenetic Map6q32NCBI
NRDE2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381490,267,860 - 90,331,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1490,267,860 - 90,331,969 (-)EnsemblGRCh38hg38GRCh38
GRCh371490,734,204 - 90,798,285 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361489,814,151 - 89,868,032 (-)NCBINCBI36Build 36hg18NCBI36
Build 341489,814,150 - 89,868,032NCBI
Celera1470,791,551 - 70,845,432 (-)NCBICelera
Cytogenetic Map14q32.11NCBI
HuRef1470,918,804 - 70,973,367 (-)NCBIHuRef
CHM1_11490,682,581 - 90,736,658 (-)NCBICHM1_1
T2T-CHM13v2.01484,492,112 - 84,556,677 (-)NCBIT2T-CHM13v2.0
Nrde2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912100,091,709 - 100,126,981 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12100,091,711 - 100,125,912 (-)EnsemblGRCm39 Ensembl
GRCm3812100,125,450 - 100,160,414 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12100,125,452 - 100,159,653 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712101,363,662 - 101,397,863 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612100,526,502 - 100,560,703 (-)NCBIMGSCv36mm8
Celera12101,352,084 - 101,386,229 (-)NCBICelera
Cytogenetic Map12ENCBI
Nrde2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543812,726,357 - 12,780,379 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543812,726,206 - 12,780,364 (-)NCBIChiLan1.0ChiLan1.0
NRDE2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21591,422,268 - 91,476,888 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11490,638,774 - 90,693,397 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01470,895,376 - 70,949,969 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11490,247,035 - 90,300,705 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1490,247,035 - 90,300,705 (-)Ensemblpanpan1.1panPan2
NRDE2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1861,285,998 - 61,332,518 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl861,286,950 - 61,332,431 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha860,864,508 - 60,914,288 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0861,557,124 - 61,607,143 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl861,557,797 - 61,607,072 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1861,238,742 - 61,288,372 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0861,287,701 - 61,337,424 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0861,615,765 - 61,665,804 (-)NCBIUU_Cfam_GSD_1.0
Nrde2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864014,549,748 - 14,595,181 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648817,473,607 - 17,519,536 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648817,473,787 - 17,519,278 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NRDE2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7112,038,234 - 112,090,510 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17112,039,949 - 112,090,632 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27118,608,305 - 118,707,486 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NRDE2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12467,999,010 - 68,055,164 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2467,999,268 - 68,055,093 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605355,284,869 - 55,338,270 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nrde2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473412,098,361 - 12,148,760 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473412,098,386 - 12,151,635 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nrde2
261 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:51
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000005369
Prediction methods:Miranda, Rnahybrid
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6116506292130245370Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1300076Glom8Glomerulus QTL 879e-09kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat

Markers in Region
D6Hmgc18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26119,430,713 - 119,430,856 (+)MAPPERmRatBN7.2
Rnor_6.06124,161,126 - 124,161,268NCBIRnor6.0
Rnor_5.06133,388,421 - 133,388,563UniSTSRnor5.0
Celera6116,960,583 - 116,960,725UniSTS
Cytogenetic Map6q32UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000005369   ⟹   ENSRNOP00000005369
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6119,404,334 - 119,446,670 (-)Ensembl
Rnor_6.0 Ensembl6124,142,395 - 124,177,404 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098050   ⟹   ENSRNOP00000092173
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6119,404,334 - 119,448,915 (-)Ensembl
RefSeq Acc Id: NM_001427742   ⟹   NP_001414671
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86125,137,121 - 125,176,299 (-)NCBI
RefSeq Acc Id: XR_593161
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86125,137,825 - 125,177,689 (-)NCBI
mRatBN7.26119,408,199 - 119,446,861 (-)NCBI
Rnor_6.06124,138,611 - 124,177,425 (-)NCBI
Sequence:
RefSeq Acc Id: XR_593162
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86125,140,705 - 125,177,689 (-)NCBI
mRatBN7.26119,411,082 - 119,446,861 (-)NCBI
Rnor_6.06124,141,544 - 124,177,425 (-)NCBI
Sequence:
RefSeq Acc Id: XR_593163
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86125,140,705 - 125,177,689 (-)NCBI
mRatBN7.26119,411,079 - 119,446,861 (-)NCBI
Rnor_6.06124,141,541 - 124,177,425 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001414671 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL81713 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005369.6
  ENSRNOP00000092173.1
Ensembl Acc Id: ENSRNOP00000005369   ⟸   ENSRNOT00000005369
Ensembl Acc Id: ENSRNOP00000092173   ⟸   ENSRNOT00000098050
RefSeq Acc Id: NP_001414671   ⟸   NM_001427742

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDR9-F1-model_v2 AlphaFold D3ZDR9 1-1054 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565082 AgrOrtholog
BioCyc Gene G2FUF-36498 BioCyc
Ensembl Genes ENSRNOG00000004004 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005369.8 UniProtKB/TrEMBL
  ENSRNOT00000098050.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro DUF1740 UniProtKB/TrEMBL
  HAT UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
NCBI Gene 314381 ENTREZGENE
PANTHER NUCLEAR EXOSOME REGULATOR NRDE2 UniProtKB/TrEMBL
  PTHR13471 UniProtKB/TrEMBL
Pfam DUF1740 UniProtKB/TrEMBL
PhenoGen Nrde2 PhenoGen
RatGTEx ENSRNOG00000004004 RatGTEx
SMART HAT UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A8I6AG13_RAT UniProtKB/TrEMBL
  D3ZDR9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-12 Nrde2  NRDE-2, necessary for RNA interference, domain containing  RGD1565082  similar to Protein C14orf102 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565082  similar to Protein C14orf102 homolog   RGD1565082_predicted  similar to Protein C14orf102 homolog (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565082_predicted  similar to Protein C14orf102 homolog (predicted)  LOC314381  similar to Protein C14orf102 homolog  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC314381  similar to Protein C14orf102 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL