Npm1 (nucleophosmin 1) - Rat Genome Database

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Gene: Npm1 (nucleophosmin 1) Rattus norvegicus
Analyze
Symbol: Npm1
Name: nucleophosmin 1
RGD ID: 3192
Description: Enables several functions, including anion binding activity; p53 binding activity; and protein kinase B binding activity. Involved in several processes, including RNA metabolic process; negative regulation of apoptotic process; and regulation of DNA replication. Located in cytoplasm and nuclear lumen. Human ortholog(s) of this gene implicated in acute myeloid leukemia. Orthologous to human NPM1 (nucleophosmin 1); PARTICIPATES IN hypoxia inducible factor pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: B23NP; MGC108517; NPM; nucleolar phosphoprotein B23; nucleolar protein B23.1; nucleolar protein NO38; nucleophosmin; nucleophosmin (nucleolar phosphoprotein B23, numatrin); Nucleoplasmin-related protein (Nuclear protein B23; numatrin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC108352500  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21017,741,512 - 17,751,626 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1017,739,941 - 17,751,645 (-)Ensembl
Rnor_6.01018,080,949 - 18,091,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,080,950 - 18,090,950 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,965,977 - 17,975,978 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41018,051,990 - 18,062,714 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11018,053,038 - 18,063,763 (-)NCBI
Celera1017,382,029 - 17,392,033 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-nitrofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
9-cis-retinoic acid  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
bortezomib  (ISO)
bromobenzene  (EXP)
busulfan  (ISO)
butyric acid  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
Deguelin  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
diethylstilbestrol  (EXP)
dihydroartemisinin  (ISO)
doxorubicin  (ISO)
elemental selenium  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
flavonoids  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gemcitabine  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glafenine  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
idarubicin  (ISO)
indometacin  (ISO)
isoflavones  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
melatonin  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
Monobutylphthalate  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nocodazole  (ISO)
ochratoxin A  (EXP,ISO)
oxaliplatin  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
pemetrexed  (ISO)
perfluorooctanoic acid  (EXP)
PhIP  (EXP)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
quercetin  (ISO)
raloxifene  (ISO)
selenium atom  (EXP)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
sunitinib  (ISO)
T-2 toxin  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
tributylstannane  (ISO)
Tributyltin oxide  (EXP,ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triphenylstannane  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vinorelbine  (ISO)
vitamin E  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cardiac muscle hypertrophy  (IEP)
cell aging  (ISO,ISS)
cell volume homeostasis  (ISO)
cellular response to hypoxia  (IEP)
cellular response to testosterone stimulus  (IEP)
cellular response to UV  (ISO)
centrosome cycle  (ISO,ISS)
chromatin remodeling  (IBA)
cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)  (IDA)
DNA repair  (ISO,ISS)
liver regeneration  (IEP)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of cardiac muscle cell apoptotic process  (IMP)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of centrosome duplication  (ISO)
negative regulation of epithelial cell proliferation  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of mRNA splicing, via spliceosome  (ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of protein kinase activity by regulation of protein phosphorylation  (ISO,ISS)
nucleocytoplasmic transport  (ISO)
nucleosome assembly  (ISO)
positive regulation of catalytic activity  (IDA)
positive regulation of cell cycle G2/M phase transition  (ISO,ISS)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of cellular biosynthetic process  (ISO)
positive regulation of centrosome duplication  (ISO)
positive regulation of DNA metabolic process  (IDA)
positive regulation of DNA replication  (IDA)
positive regulation of DNA-directed DNA polymerase activity  (IDA)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein localization to nucleolus  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of translation  (ISO,ISS)
posttranscriptional regulation of gene expression  (ISO)
protein destabilization  (ISO)
protein localization  (ISO)
protein stabilization  (ISO)
regulation of cell cycle  (ISO)
regulation of cell growth  (ISO)
regulation of centriole replication  (ISO,ISS)
regulation of centrosome duplication  (IBA,ISO)
regulation of DNA damage response, signal transduction by p53 class mediator  (ISO)
regulation of eIF2 alpha phosphorylation by dsRNA  (ISO,ISS)
regulation of endodeoxyribonuclease activity  (ISO,ISS)
regulation of endoribonuclease activity  (ISO,ISS)
regulation of mRNA stability involved in cellular response to UV  (ISO)
regulation of neuron apoptotic process  (IMP)
regulation of protein stability  (ISO)
ribosomal large subunit biogenesis  (IBA,ISO)
ribosomal large subunit export from nucleus  (IBA,ISO)
ribosomal small subunit biogenesis  (IBA,ISO)
ribosomal small subunit export from nucleus  (IBA,ISO)
rRNA export from nucleus  (IBA,ISO)
rRNA transcription  (IMP)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ahn JY, etal., Mol Cell. 2005 May 13;18(4):435-45.
2. Avitabile D, etal., Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6145-50. doi: 10.1073/pnas.1017935108. Epub 2011 Mar 28.
3. Chang JH and Olson MO, J Biol Chem 1989 Jul 15;264(20):11732-7.
4. Chang JH and Olson MO, J Biol Chem 1990 Oct 25;265(30):18227-33.
5. Chang JH, etal., J Biol Chem 1988 Sep 15;263(26):12824-7.
6. Choi JW, etal., BMB Rep. 2008 Dec 31;41(12):840-5.
7. Chou SH, etal., PLoS One. 2012;7(11):e49769. doi: 10.1371/journal.pone.0049769. Epub 2012 Nov 30.
8. Falini B, etal., N Engl J Med. 2005 Jan 20;352(3):254-66.
9. Gale RE, etal., Blood. 2008 Mar 1;111(5):2776-84. Epub 2007 Oct 23.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Grisendi S and Pandolfi PP, N Engl J Med. 2005 Jan 20;352(3):291-2.
13. Herrera JE, etal., Biochemistry. 1996 Feb 27;35(8):2668-73.
14. Kuzelova K, etal., PLoS One. 2015 May 20;10(5):e0127637. doi: 10.1371/journal.pone.0127637. eCollection 2015.
15. Lee SB, etal., Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16584-9. doi: 10.1073/pnas.0807668105. Epub 2008 Oct 17.
16. MGD data from the GO Consortium
17. Milochau A, etal., FEBS Lett. 2014 Jun 27;588(14):2217-22. doi: 10.1016/j.febslet.2014.05.031. Epub 2014 May 29.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Nishimura Y, etal., Biosci Biotechnol Biochem. 2002 Oct;66(10):2239-42.
20. OMIM Disease Annotation Pipeline
21. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. Rau R, etal., Exp Hematol. 2014 Feb;42(2):101-13.e5. doi: 10.1016/j.exphem.2013.10.005. Epub 2013 Oct 29.
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Savkur RS and Olson MO, Nucleic Acids Res. 1998 Oct 1;26(19):4508-15.
26. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
27. Takemura M, etal., Biochem Biophys Res Commun. 1994 Feb 28;199(1):46-51.
28. Takemura M, etal., J Biochem. 1999 May;125(5):904-9.
29. Tawfic S, etal., Cell Mol Biol Res. 1993;39(1):43-51.
30. Umekawa H, etal., J Biochem (Tokyo). 2001 Aug;130(2):199-205.
31. Vassiliou GS, etal., Nat Genet. 2011 May;43(5):470-5. doi: 10.1038/ng.796. Epub 2011 Mar 27.
32. Wang G, etal., Biochemistry. 2010 May 11;49(18):3842-52. doi: 10.1021/bi9021928.
33. Yun JP, etal., J Cell Biochem. 2003 Dec 15;90(6):1140-8.
34. Zou T, etal., Am J Physiol Cell Physiol. 2005 Sep;289(3):C686-96. Epub 2005 May 4.
Additional References at PubMed
PMID:2100262   PMID:9094689   PMID:9121481   PMID:10211837   PMID:10716735   PMID:11051553   PMID:11420665   PMID:11602260   PMID:12058066   PMID:12080348   PMID:12374805   PMID:12511551  
PMID:12882984   PMID:15087454   PMID:15485902   PMID:15489334   PMID:15596447   PMID:15607978   PMID:15615785   PMID:15989966   PMID:16007073   PMID:16027046   PMID:16041368   PMID:16099430  
PMID:16129783   PMID:16199867   PMID:16297385   PMID:16376875   PMID:16641100   PMID:16648475   PMID:16690610   PMID:16854843   PMID:16855206   PMID:17015463   PMID:17475909   PMID:17951246  
PMID:18023416   PMID:18420587   PMID:18625840   PMID:18809582   PMID:19160485   PMID:19188445   PMID:19208757   PMID:19581374   PMID:19946888   PMID:20352051   PMID:21423176   PMID:21630459  
PMID:22166220   PMID:22528486   PMID:22658674   PMID:22681889   PMID:22720776   PMID:23027902   PMID:24616519   PMID:24625528   PMID:25931508   PMID:25956029   PMID:27510036   PMID:31904090  


Genomics

Comparative Map Data
Npm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21017,741,512 - 17,751,626 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1017,739,941 - 17,751,645 (-)Ensembl
Rnor_6.01018,080,949 - 18,091,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,080,950 - 18,090,950 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,965,977 - 17,975,978 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41018,051,990 - 18,062,714 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11018,053,038 - 18,063,763 (-)NCBI
Celera1017,382,029 - 17,392,033 (-)NCBICelera
Cytogenetic Map10q12NCBI
NPM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5171,387,116 - 171,411,810 (+)EnsemblGRCh38hg38GRCh38
GRCh385171,387,116 - 171,410,900 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375170,814,120 - 170,837,904 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365170,747,403 - 170,770,493 (+)NCBINCBI36hg18NCBI36
Build 345170,747,461 - 170,770,492NCBI
Celera5166,847,258 - 166,870,233 (+)NCBI
Cytogenetic Map5q35.1NCBI
HuRef5165,912,826 - 165,935,666 (+)NCBIHuRef
CHM1_15170,247,232 - 170,270,413 (+)NCBICHM1_1
Npm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391133,102,498 - 33,114,143 (-)NCBIGRCm39mm39
GRCm39 Ensembl1133,102,287 - 33,113,206 (-)Ensembl
GRCm381133,152,498 - 33,164,142 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,152,287 - 33,163,206 (-)EnsemblGRCm38mm10GRCm38
MGSCv371133,052,511 - 33,063,056 (-)NCBIGRCm37mm9NCBIm37
MGSCv361133,052,511 - 33,063,056 (-)NCBImm8
Celera1135,564,831 - 35,575,324 (-)NCBICelera
Cytogenetic Map11A4NCBI
Npm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540824,151,070 - 24,218,783 (+)NCBIChiLan1.0ChiLan1.0
NPM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15173,490,197 - 173,510,657 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5173,490,197 - 173,510,656 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05166,735,904 - 166,756,321 (+)NCBIMhudiblu_PPA_v0panPan3
NPM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1440,756,464 - 40,770,174 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl440,756,465 - 40,770,175 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha440,705,264 - 40,718,971 (-)NCBI
ROS_Cfam_1.0441,134,159 - 41,147,850 (-)NCBI
UMICH_Zoey_3.1440,949,115 - 40,962,816 (-)NCBI
UNSW_CanFamBas_1.0441,139,397 - 41,153,096 (-)NCBI
UU_Cfam_GSD_1.0441,649,467 - 41,663,173 (-)NCBI
Npm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721394,989,965 - 95,002,964 (-)NCBI
SpeTri2.0NW_0049366093,712,628 - 3,725,635 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1652,765,296 - 52,781,740 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11652,767,263 - 52,781,862 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21656,963,998 - 56,978,524 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12373,555,020 - 73,575,910 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2373,555,260 - 73,575,925 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660345,065,310 - 5,086,261 (-)NCBIVero_WHO_p1.0
Npm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473318,645,269 - 18,655,073 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
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
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
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
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101724551319388279Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:48
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000006591, ENSRNOT00000064744
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 4 12 12 12 16 12 19
Medium 3 39 45 29 19 29 8 11 58 23 22 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC060579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC088088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J03969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006591   ⟹   ENSRNOP00000006591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,739,941 - 17,751,645 (-)Ensembl
Rnor_6.0 Ensembl1018,080,950 - 18,090,950 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000064744   ⟹   ENSRNOP00000062356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,743,494 - 17,751,519 (-)Ensembl
Rnor_6.0 Ensembl1018,082,932 - 18,090,932 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118471   ⟹   ENSRNOP00000092710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,739,941 - 17,751,514 (-)Ensembl
RefSeq Acc Id: NM_012992   ⟹   NP_037124
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21017,741,512 - 17,751,514 (-)NCBI
Rnor_6.01018,080,949 - 18,090,950 (-)NCBI
Rnor_5.01017,965,977 - 17,975,978 (-)NCBI
RGSC_v3.41018,051,990 - 18,062,714 (-)RGD
Celera1017,382,029 - 17,392,033 (-)RGD
Sequence:
RefSeq Acc Id: XR_005489693
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21017,741,512 - 17,751,626 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037124   ⟸   NM_012992
- UniProtKB: P13084 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006591   ⟸   ENSRNOT00000006591
RefSeq Acc Id: ENSRNOP00000062356   ⟸   ENSRNOT00000064744
RefSeq Acc Id: ENSRNOP00000092710   ⟸   ENSRNOT00000118471

Transcriptome

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

Promoters
RGD ID:13697094
Promoter ID:EPDNEW_R7619
Type:multiple initiation site
Name:Npm1_1
Description:nucleophosmin 1
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_6.01018,090,953 - 18,091,013EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
ACI/EurMcwi (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)
ACI/EurMcwi (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
ACI/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
F344/NCrl (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
F344/NRrrc (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
F344/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
FHH/EurMcwi (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/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
FXLE18/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
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/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
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)
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: 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)
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
MHS/Gib (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
MNS/Gib (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
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)
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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
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)
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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
SBN/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: SBN/Ygl sequenced by MCW
SBN/Ygl (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/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)
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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
SHRSP/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
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)
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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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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/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)
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
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:3192 AgrOrtholog
Ensembl Genes ENSRNOG00000004616 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000006591 UniProtKB/Swiss-Prot
  ENSRNOP00000062356 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006591 UniProtKB/Swiss-Prot
  ENSRNOT00000064744 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.2100 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6888417 IMAGE-MGC_LOAD
  IMAGE:7382200 IMAGE-MGC_LOAD
InterPro NPM1_C UniProtKB/Swiss-Prot
  NPM1_C_sf UniProtKB/Swiss-Prot
  Nucleoplasmin UniProtKB/Swiss-Prot
  Nucleoplasmin_core_dom UniProtKB/Swiss-Prot
  Nucleoplasmin_core_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:25498 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108517 IMAGE-MGC_LOAD
  MGC:72897 IMAGE-MGC_LOAD
NCBI Gene 25498 ENTREZGENE
PANTHER PTHR22747 UniProtKB/Swiss-Prot
Pfam NPM1-C UniProtKB/Swiss-Prot
  Nucleoplasmin UniProtKB/Swiss-Prot
PhenoGen Npm1 PhenoGen
Superfamily-SCOP SSF69203 UniProtKB/Swiss-Prot
UniProt NPM_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63698 UniProtKB/Swiss-Prot
  Q64269 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Npm1  nucleophosmin 1  Npm1  nucleophosmin (nucleolar phosphoprotein B23, numatrin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-10 Npm1  nucleophosmin (nucleolar phosphoprotein B23, numatrin)  Npm1  nucleophosmin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Npm1  nucleophosmin 1    Nucleoplasmin-related protein (Nuclear protein B23  Name updated 625702 APPROVED
2002-06-10 Npm1  Nucleoplasmin-related protein (Nuclear protein B23      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction has a high affinity for silver ions 729271
gene_transcript has two alternative splice forms 728939