Nhp2 (NHP2 ribonucleoprotein) - Rat Genome Database

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Gene: Nhp2 (NHP2 ribonucleoprotein) Rattus norvegicus
Analyze
Symbol: Nhp2
Name: NHP2 ribonucleoprotein
RGD ID: 1309435
Description: Enables U3 snoRNA binding activity and mRNA 3'-UTR binding activity. Involved in snoRNA guided rRNA pseudouridine synthesis. Part of box H/ACA snoRNP complex. Human ortholog(s) of this gene implicated in autosomal recessive dyskeratosis congenita 2. Orthologous to human NHP2 (NHP2 ribonucleoprotein); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4,6-trinitrotoluene; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: H/ACA ribonucleoprotein complex subunit 2; H/ACA ribonucleoprotein complex subunit 2-like; LOC100910210; LOC103690013; LOC287273; NHP2 ribonucleoprotein homolog; NHP2 ribonucleoprotein homolog (yeast); Nola2; nucleolar protein family A, member 2
RGD Orthologs
Human
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21035,877,015 - 35,880,409 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1035,877,054 - 35,882,545 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx363,415,455 - 63,415,690 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0371,999,106 - 71,999,341 (-)NCBIRnor_SHRSP
Rnor_6.01034,975,701 - 34,979,082 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1037,069,344 - 37,072,733 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1034,975,708 - 34,979,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01036,841,672 - 36,845,050 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41037,137,277 - 37,140,651 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1035,233,774 - 35,237,148 (+)NCBICelera
Cytogenetic Map10q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-alpha-phellandrene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
aflatoxin B1  (ISO)
alpha-phellandrene  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chlormequat chloride  (EXP)
chloropicrin  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
fenthion  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
genistein  (EXP)
glafenine  (EXP)
ivermectin  (ISO)
methidathion  (ISO)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phenobarbital  (ISO)
picoxystrobin  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
sodium dichromate  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
tungsten  (ISO)
valdecoxib  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. Wang C and Meier UT, EMBO J. 2004 Apr 21;23(8):1857-67. Epub 2004 Mar 25.
8. Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140. Wang C, etal., Mol Cell Biol 2002 Dec;22(24):8457-66.
9. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Watkins NJ and Bohnsack MT, Wiley Interdiscip Rev RNA. 2012 May-Jun;3(3):397-414. doi: 10.1002/wrna.117. Epub 2011 Nov 7.
Additional References at PubMed
PMID:12477932   PMID:18082603   PMID:19135898   PMID:20351177   PMID:22527283   PMID:22658674   PMID:25467444   PMID:29695869  


Genomics

Comparative Map Data
Nhp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21035,877,015 - 35,880,409 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1035,877,054 - 35,882,545 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx363,415,455 - 63,415,690 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0371,999,106 - 71,999,341 (-)NCBIRnor_SHRSP
Rnor_6.01034,975,701 - 34,979,082 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1037,069,344 - 37,072,733 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1034,975,708 - 34,979,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01036,841,672 - 36,845,050 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41037,137,277 - 37,140,651 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1035,233,774 - 35,237,148 (+)NCBICelera
Cytogenetic Map10q21NCBI
NHP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385178,149,463 - 178,153,885 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5178,149,463 - 178,153,894 (-)EnsemblGRCh38hg38GRCh38
GRCh375177,576,464 - 177,580,886 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365177,509,070 - 177,513,567 (-)NCBINCBI36Build 36hg18NCBI36
Build 345177,509,073 - 177,513,567NCBI
Celera5173,203,446 - 173,207,943 (-)NCBICelera
Cytogenetic Map5q35.3NCBI
HuRef5172,302,433 - 172,306,930 (-)NCBIHuRef
CHM1_15177,007,842 - 177,012,339 (-)NCBICHM1_1
T2T-CHM13v2.05178,699,722 - 178,704,144 (-)NCBIT2T-CHM13v2.0
Nhp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554082,090,772 - 2,094,453 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554082,090,772 - 2,094,453 (+)NCBIChiLan1.0ChiLan1.0
NHP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15180,566,008 - 180,570,502 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5180,566,008 - 180,570,502 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05173,308,560 - 173,313,046 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NHP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1113,389,549 - 3,393,010 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl113,389,591 - 3,395,313 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha113,532,480 - 3,535,984 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0113,365,217 - 3,368,723 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl113,365,309 - 3,368,720 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1113,335,883 - 3,337,251 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0113,413,347 - 3,416,848 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0113,654,898 - 3,659,015 (+)NCBIUU_Cfam_GSD_1.0
Nhp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213113,517,778 - 113,522,464 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936647520,542 - 525,226 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NHP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1280,223,439 - 80,227,614 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2281,839,915 - 81,844,092 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NHP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12379,842,690 - 79,847,138 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2379,842,948 - 79,846,984 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607511,143,336 - 11,147,779 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nhp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473341,371,897 - 41,375,363 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473341,371,897 - 41,375,360 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
AA851865  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21035,879,618 - 35,880,228 (+)MAPPERmRatBN7.2
Rnor_6.01037,071,978 - 37,072,587NCBIRnor6.0
Rnor_6.01034,978,292 - 34,978,901NCBIRnor6.0
Rnor_5.01036,844,260 - 36,844,869UniSTSRnor5.0
Rnor_5.01034,750,893 - 34,751,502UniSTSRnor5.0
RGSC_v3.41037,139,861 - 37,140,470UniSTSRGSC3.4
Celera1035,236,358 - 35,236,967UniSTS
RH 3.4 Map5931.0UniSTS
Cytogenetic Map10q22UniSTS
RH141376  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21035,880,081 - 35,880,283 (+)MAPPERmRatBN7.2
Rnor_6.01037,072,441 - 37,072,642NCBIRnor6.0
Rnor_6.01034,978,755 - 34,978,956NCBIRnor6.0
Rnor_5.01034,751,356 - 34,751,557UniSTSRnor5.0
Rnor_5.01036,844,723 - 36,844,924UniSTSRnor5.0
RGSC_v3.41037,140,324 - 37,140,525UniSTSRGSC3.4
Celera1035,236,821 - 35,237,022UniSTS
Cytogenetic Map10q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102291826836400810Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:237
Count of miRNA genes:108
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000005688, ENSRNOT00000064984, ENSRNOT00000073317
Prediction methods:Microtar, 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 1
Low 3 43 55 39 18 39 8 11 74 35 41 11 8
Below cutoff 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064984   ⟹   ENSRNOP00000063697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1034,975,708 - 34,979,082 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000073317   ⟹   ENSRNOP00000067439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1035,877,054 - 35,882,545 (+)Ensembl
Rnor_6.0 Ensembl1037,069,344 - 37,072,733 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090404   ⟹   ENSRNOP00000072941
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1037,069,461 - 37,072,535 (+)Ensembl
RefSeq Acc Id: NM_001105779   ⟹   NP_001099249
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21035,877,035 - 35,880,409 (+)NCBI
Rnor_6.01034,975,708 - 34,979,082 (+)NCBI
Rnor_5.01036,841,672 - 36,845,050 (+)NCBI
RGSC_v3.41037,137,277 - 37,140,651 (+)RGD
Celera1035,233,774 - 35,237,148 (+)RGD
Sequence:
RefSeq Acc Id: XM_003750818   ⟹   XP_003750866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21035,877,015 - 35,880,399 (+)NCBI
Rnor_6.01034,975,701 - 34,979,072 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099249 (Get FASTA)   NCBI Sequence Viewer  
  XP_003750866 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI62010 (Get FASTA)   NCBI Sequence Viewer  
  EDM04315 (Get FASTA)   NCBI Sequence Viewer  
  EDM04316 (Get FASTA)   NCBI Sequence Viewer  
  EDM04317 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099249   ⟸   NM_001105779
- UniProtKB: D3ZVC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_003750866   ⟸   XM_003750818
- Peptide Label: isoform X1
- UniProtKB: B1WC56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063697   ⟸   ENSRNOT00000064984
RefSeq Acc Id: ENSRNOP00000072941   ⟸   ENSRNOT00000090404
RefSeq Acc Id: ENSRNOP00000067439   ⟸   ENSRNOT00000073317
Protein Domains
Ribosomal_L7Ae

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WC56-F1-model_v2 AlphaFold B1WC56 1-153 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

Database Acc Id Source(s)
AGR Gene RGD:1309435 AgrOrtholog
BioCyc Gene G2FUF-25197 BioCyc
Ensembl Genes ENSRNOG00000004247 Ensembl
  ENSRNOG00000049622 Ensembl
  ENSRNOG00000063470 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067439 ENTREZGENE
  ENSRNOP00000067439.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073317 ENTREZGENE
  ENSRNOT00000073317.3 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1330.30 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9091322 IMAGE-MGC_LOAD
InterPro H/ACA_rnp_Nhp2_euk UniProtKB/TrEMBL
  L30e-like UniProtKB/TrEMBL
  Ribosomal_L7Ae/L30e/S12e/Gad45 UniProtKB/TrEMBL
  Ribosomal_L7Ae/L8/Nhp2 UniProtKB/TrEMBL
MGC_CLONE MGC:187877 IMAGE-MGC_LOAD
NCBI Gene 287273 ENTREZGENE
Pfam Ribosomal_L7Ae UniProtKB/TrEMBL
PhenoGen Nhp2 PhenoGen
PRINTS L7ARS6FAMILY UniProtKB/TrEMBL
  NUCLEARHMG UniProtKB/TrEMBL
Superfamily-SCOP SSF55315 UniProtKB/TrEMBL
UniProt B1WC56 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVC6 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Nhp2  NHP2 ribonucleoprotein  LOC103690013  H/ACA ribonucleoprotein complex subunit 2  Data Merged 737654 PROVISIONAL
2015-02-26 Nhp2  NHP2 ribonucleoprotein  LOC100910210  H/ACA ribonucleoprotein complex subunit 2-like  Data Merged 737654 APPROVED
2014-08-25 LOC103690013  H/ACA ribonucleoprotein complex subunit 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-12-18 Nhp2  NHP2 ribonucleoprotein  Nhp2  NHP2 ribonucleoprotein homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910210  H/ACA ribonucleoprotein complex subunit 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-10-22 Nhp2  NHP2 ribonucleoprotein homolog (yeast)  Nola2  nucleolar protein family A, member 2   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nola2  nucleolar protein family A, member 2   Nola2_predicted  nucleolar protein family A, member 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nola2_predicted  nucleolar protein family A, member 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED