Ncl (nucleolin) - Rat Genome Database

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Gene: Ncl (nucleolin) Rattus norvegicus
Analyze
Symbol: Ncl
Name: nucleolin
RGD ID: 3153
Description: Enables several functions, including ErbB-4 class receptor binding activity; laminin binding activity; and nucleic acid binding activity. Involved in several processes, including cellular response to lipopolysaccharide; liver regeneration; and positive regulation of cytokine production. Located in cell surface; cytoplasm; and nucleolus. Orthologous to human NCL (nucleolin); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC93572; nucleolin-like protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Ncl-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2986,999,588 - 87,008,112 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl986,998,019 - 87,008,136 (-)Ensembl
Rnor_6.0993,369,119 - 93,377,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl993,368,932 - 93,377,643 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0993,097,881 - 93,106,405 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4985,112,752 - 85,121,276 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1985,296,294 - 85,304,569 (-)NCBI
Celera984,415,242 - 84,423,766 (-)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(Z)-3-butylidenephthalide  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-hexachlorocyclohexane  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amsacrine  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenic trichloride  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
caffeine  (ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibric acid  (EXP)
clozapine  (ISO)
cobalt dichloride  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
dopamine  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
felbamate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
gabapentin  (EXP)
gentamycin  (EXP)
haloperidol  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (EXP,ISO)
methotrexate  (ISO)
methoxychlor  (ISO)
methyl methanesulfonate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP,ISO)
phenytoin  (EXP)
pirinixic acid  (EXP,ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
succimer  (ISO)
tanespimycin  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bourbon HM and Amalric F, Gene 1990 Apr 16;88(2):187-96.
2. Chathoth KT, etal., BMC Mol Biol. 2009 Jul 1;10:64. doi: 10.1186/1471-2199-10-64.
3. Di Segni A, etal., PLoS One. 2008 Jun 4;3(6):e2310. doi: 10.1371/journal.pone.0002310.
4. Durut N and Saez-Vasquez J, Gene. 2014 Sep 16. pii: S0378-1119(14)01049-X. doi: 10.1016/j.gene.2014.09.023.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Gilchrist JS, etal., J Cell Biochem 2002;85(2):268-78.
7. Herrera AH and Olson MO, Biochemistry. 1986 Oct 7;25(20):6258-64.
8. Jiang B, etal., Cardiovasc Res. 2013 Jul 1;99(1):92-101. doi: 10.1093/cvr/cvt085. Epub 2013 Apr 16.
9. Jiang B, etal., FEBS J. 2010 Feb;277(3):642-52. doi: 10.1111/j.1742-4658.2009.07510.x. Epub 2009 Dec 29.
10. Jin J, etal., Mol Cell Proteomics. 2007 May;6(5):845-59. Epub 2006 Jul 18.
11. Kibbey MC, etal., J Neurosci Res. 1995 Oct 15;42(3):314-22.
12. Konishi T, etal., J Biochem. 1995 Jun;117(6):1170-7.
13. MGD data from the GO Consortium
14. Milochau A, etal., FEBS Lett. 2014 Jun 27;588(14):2217-22. doi: 10.1016/j.febslet.2014.05.031. Epub 2014 May 29.
15. Miniard AC, etal., Nucleic Acids Res. 2010 Aug;38(14):4807-20. Epub 2010 Apr 12.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Olson MO, etal., Biochemistry. 1983 Jul 5;22(14):3345-51.
18. Ozawa D, etal., Biol Pharm Bull. 2013;36(10):1587-93. Epub 2013 Aug 3.
19. RGD automated data pipeline
20. RGD automated import pipeline for gene-chemical interactions
21. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
22. Sipos K and Olson MO, Biochem Biophys Res Commun. 1991 Jun 14;177(2):673-8.
23. Spector DL, etal., Chromosoma. 1984;90(2):139-48.
24. Suzuki T, etal., Biochem J. 1993 Jan 1;289 ( Pt 1):109-15.
25. Wang Y, etal., Cell Biol Int. 2011 Jul;35(7):677-85. doi: 10.1042/CBI20100625.
26. Yan S, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2014 Feb;39(2):124-8. doi: 10.11817/j.issn.1672-7347.2014.02.003.
27. Yu D, etal., Biochem Biophys Res Commun. 1998 Jun 9;247(1):186-92.
Additional References at PubMed
PMID:2100262   PMID:2906027   PMID:8321232   PMID:8567649   PMID:8702723   PMID:9102301   PMID:12477932   PMID:12944467   PMID:14729462   PMID:15121898   PMID:15364958   PMID:15607978  
PMID:15925566   PMID:16213212   PMID:16403913   PMID:16641100   PMID:17289661   PMID:17971306   PMID:18809582   PMID:19393617   PMID:19946888   PMID:20439489   PMID:20458337   PMID:21575138  
PMID:22658674   PMID:22681889   PMID:23161541   PMID:23353999   PMID:23376485   PMID:23712942   PMID:24071584   PMID:24077883   PMID:24442868   PMID:24530304   PMID:25002582   PMID:25931508  
PMID:29968904   PMID:30053369   PMID:30256395   PMID:30720050   PMID:31975412  


Genomics

Comparative Map Data
Ncl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2986,999,588 - 87,008,112 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl986,998,019 - 87,008,136 (-)Ensembl
Rnor_6.0993,369,119 - 93,377,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl993,368,932 - 93,377,643 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0993,097,881 - 93,106,405 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4985,112,752 - 85,121,276 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1985,296,294 - 85,304,569 (-)NCBI
Celera984,415,242 - 84,423,766 (-)NCBICelera
Cytogenetic Map9q35NCBI
NCL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2231,453,531 - 231,483,641 (-)EnsemblGRCh38hg38GRCh38
GRCh382231,453,531 - 231,464,484 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372232,318,242 - 232,329,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362232,027,703 - 232,037,449 (-)NCBINCBI36hg18NCBI36
Build 342232,144,964 - 232,154,710NCBI
Celera2226,095,812 - 226,105,543 (-)NCBI
Cytogenetic Map2q37.1NCBI
HuRef2224,160,942 - 224,170,673 (-)NCBIHuRef
CHM1_12232,325,275 - 232,335,021 (-)NCBICHM1_1
Ncl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39186,272,441 - 86,287,177 (-)NCBIGRCm39mm39
GRCm39 Ensembl186,272,441 - 86,287,122 (-)Ensembl
GRCm38186,344,719 - 86,359,455 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl186,344,719 - 86,359,400 (-)EnsemblGRCm38mm10GRCm38
MGSCv37188,241,294 - 88,256,030 (-)NCBIGRCm37mm9NCBIm37
MGSCv36188,175,890 - 88,190,626 (-)NCBImm8
Celera189,309,614 - 89,324,350 (-)NCBICelera
Cytogenetic Map1C5NCBI
cM Map143.94NCBI
Ncl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554534,154,627 - 4,164,253 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554534,154,627 - 4,164,253 (+)NCBIChiLan1.0ChiLan1.0
NCL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B237,490,378 - 237,500,193 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B237,490,378 - 237,500,193 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B118,703,148 - 118,712,893 (-)NCBIMhudiblu_PPA_v0panPan3
NCL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12543,330,524 - 43,384,909 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2543,330,799 - 43,384,258 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2543,889,863 - 43,899,381 (-)NCBI
ROS_Cfam_1.02543,588,384 - 43,598,029 (-)NCBI
UMICH_Zoey_3.12543,516,186 - 43,525,614 (-)NCBI
UNSW_CanFamBas_1.02543,359,026 - 43,368,541 (-)NCBI
UU_Cfam_GSD_1.02543,514,740 - 43,524,256 (-)NCBI
NCL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15132,163,002 - 132,174,220 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115132,163,453 - 132,174,214 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215145,945,304 - 145,949,019 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110117,478,279 - 117,487,810 (-)NCBI
Vero_WHO_p1.0NW_02366604081,960,737 - 81,970,758 (+)NCBI
Ncl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248434,620,501 - 4,630,521 (-)NCBI

Position Markers
D9Arb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,008,635 - 87,008,898 (+)MAPPERmRatBN7.2
Rnor_6.0993,378,167 - 93,378,429NCBIRnor6.0
Rnor_5.0993,106,929 - 93,107,191UniSTSRnor5.0
RGSC_v3.4985,121,799 - 85,122,062RGDRGSC3.4
RGSC_v3.4985,121,800 - 85,122,062UniSTSRGSC3.4
RGSC_v3.1985,305,218 - 85,305,481RGD
Celera984,424,290 - 84,424,552UniSTS
RH 2.0 Map9837.5RGD
SHRSP x BN Map956.8299RGD
Cytogenetic Map9q35UniSTS
PMC312758P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,008,064 - 87,008,147 (+)MAPPERmRatBN7.2
Rnor_6.0993,377,596 - 93,377,678NCBIRnor6.0
Rnor_5.0993,106,358 - 93,106,440UniSTSRnor5.0
RGSC_v3.4985,121,229 - 85,121,311UniSTSRGSC3.4
Celera984,423,719 - 84,423,801UniSTS
Cytogenetic Map9q35UniSTS
PMC55360P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,007,919 - 87,008,113 (+)MAPPERmRatBN7.2
Rnor_6.0993,377,451 - 93,377,644NCBIRnor6.0
Rnor_5.0993,106,213 - 93,106,406UniSTSRnor5.0
RGSC_v3.4985,121,084 - 85,121,277UniSTSRGSC3.4
Celera984,423,574 - 84,423,767UniSTS
Cytogenetic Map9q35UniSTS
PMC133987P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,007,322 - 87,007,765 (+)MAPPERmRatBN7.2
Rnor_6.0993,376,854 - 93,377,296NCBIRnor6.0
Rnor_5.0993,105,616 - 93,106,058UniSTSRnor5.0
RGSC_v3.4985,120,487 - 85,120,929UniSTSRGSC3.4
Celera984,422,977 - 84,423,419UniSTS
Cytogenetic Map9q35UniSTS
RH94572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,004,468 - 87,004,628 (+)MAPPERmRatBN7.2
Rnor_6.0993,374,000 - 93,374,159NCBIRnor6.0
Rnor_5.0993,102,762 - 93,102,921UniSTSRnor5.0
RGSC_v3.4985,117,633 - 85,117,792UniSTSRGSC3.4
Celera984,420,123 - 84,420,282UniSTS
Cytogenetic Map9q35UniSTS
Ncl  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,699,188 - 3,699,761 (+)MAPPERmRatBN7.2
Rnor_6.0154,131,898 - 4,132,470NCBIRnor6.0
Rnor_5.0158,233,441 - 8,234,013UniSTSRnor5.0
RGSC_v3.4153,924,612 - 3,925,184UniSTSRGSC3.4
Celera15894,468 - 895,040UniSTS
Cytogenetic Map15p16UniSTS
Cytogenetic Map9q35UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:68
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000024712
Prediction methods:Microtar, 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.


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 6 6 6 4 2
Medium 3 43 51 35 19 35 8 11 70 35 39 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024712   ⟹   ENSRNOP00000024712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl986,999,297 - 87,008,136 (-)Ensembl
Rnor_6.0 Ensembl993,368,932 - 93,377,643 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100834   ⟹   ENSRNOP00000085305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl986,998,019 - 87,006,205 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108022   ⟹   ENSRNOP00000085040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl986,999,297 - 87,006,313 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118117   ⟹   ENSRNOP00000076825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl986,998,019 - 87,008,136 (-)Ensembl
RefSeq Acc Id: NM_012749   ⟹   NP_036881
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2986,999,588 - 87,008,112 (-)NCBI
Rnor_6.0993,369,119 - 93,377,643 (-)NCBI
Rnor_5.0993,097,881 - 93,106,405 (-)NCBI
RGSC_v3.4985,112,752 - 85,121,276 (-)RGD
Celera984,415,242 - 84,423,766 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036881   ⟸   NM_012749
- UniProtKB: Q5U328 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024712   ⟸   ENSRNOT00000024712
RefSeq Acc Id: ENSRNOP00000085040   ⟸   ENSRNOT00000108022
RefSeq Acc Id: ENSRNOP00000085305   ⟸   ENSRNOT00000100834
RefSeq Acc Id: ENSRNOP00000076825   ⟸   ENSRNOT00000118117
Protein Domains
RRM

Transcriptome

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

Promoters
RGD ID:13696822
Promoter ID:EPDNEW_R7347
Type:multiple initiation site
Name:Ncl_1
Description:nucleolin
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_6.0993,377,658 - 93,377,718EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
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/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
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
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
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/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
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
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
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
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
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
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
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/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
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
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
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/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
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/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
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/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3153 AgrOrtholog
Ensembl Genes ENSRNOG00000018273 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024712 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024712 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109097 IMAGE-MGC_LOAD
InterPro Nucleolin_RRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleolin_RRM2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleolin_RRM3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleolin_RRM4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25135 UniProtKB/TrEMBL
MGC_CLONE MGC:93572 IMAGE-MGC_LOAD
NCBI Gene 25135 ENTREZGENE
Pfam RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ncl PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NUCL_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5U328 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ncl  Nucleolin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process binds calcium 727360