Ntf3 (neurotrophin 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ntf3 (neurotrophin 3) Rattus norvegicus
Analyze
Symbol: Ntf3
Name: neurotrophin 3
RGD ID: 619728
Description: Enables nerve growth factor binding activity. Involved in modulation of chemical synaptic transmission; myelination; and positive regulation of glial cell differentiation. Predicted to be located in cytoplasmic vesicle. Predicted to be active in several cellular components, including axon; dendrite; and synaptic vesicle. Biomarker of status epilepticus. Human ortholog(s) of this gene implicated in Alzheimer's disease and asthma. Orthologous to human NTF3 (neurotrophin 3); PARTICIPATES IN mitogen activated protein kinase signaling pathway; neurotrophic factor signaling pathway; INTERACTS WITH (+)-pilocarpine; (R)-adrenaline; (R)-noradrenaline.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: HDNF; nerve growth factor 2; neurotrophic factor; neurotrophin-3; neurotrophin-3 (HDNF/NT-3); NGF-2; NT-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)Ensembl
Rnor_6.04158,636,883 - 158,705,886 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04225,638,801 - 225,707,719 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44162,435,781 - 162,506,961 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14162,680,717 - 162,751,897 (-)NCBI
Celera4147,640,921 - 147,710,546 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-adrenaline  (EXP)
(R)-noradrenaline  (EXP)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,7-dihydropurine-6-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-aminonicotinamide  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (EXP)
cadmium dichloride  (ISO)
Calcimycin  (EXP)
carbon monoxide  (EXP)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
cimetidine  (EXP)
cisplatin  (ISO)
colforsin daropate hydrochloride  (EXP)
cyclophosphamide  (EXP)
decabromodiphenyl ether  (EXP)
dibutyl phthalate  (EXP)
diethyl maleate  (EXP)
Dimaprit  (EXP)
dopamine  (EXP)
endosulfan  (EXP)
famotidine  (EXP)
formaldehyde  (ISO)
furan  (EXP)
glycidol  (EXP)
histamine  (EXP)
hydrogen peroxide  (ISO)
imetit  (EXP)
indole-3-methanol  (EXP)
isoprenaline  (ISO)
ketamine  (EXP)
lead diacetate  (EXP)
lithium atom  (EXP)
lithium hydride  (EXP)
LY294002  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
menadione  (ISO)
mepyramine  (EXP)
mercaptopurine  (EXP)
mercury dichloride  (EXP)
methapyrilene  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
paracetamol  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (EXP)
potassium atom  (EXP)
potassium dichromate  (ISO)
progesterone  (EXP)
purine-6-thiol  (EXP)
scopolamine  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
staurosporine  (EXP)
streptozocin  (EXP)
tetrachloromethane  (EXP)
tetraphene  (ISO)
thioacetamide  (EXP)
Thioperamide  (EXP)
toluene  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
trimethyltin  (ISO)
triprolidine  (EXP)
triptonide  (ISO)
valproic acid  (EXP,ISO)
wortmannin  (ISO)
XL147  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of GTPase activity  (IEA,ISO)
activation of protein kinase B activity  (IEA,ISO)
axon guidance  (ISO)
brain development  (ISO)
enteric nervous system development  (ISO)
epidermis development  (ISO)
generation of neurons  (ISO)
glial cell fate determination  (ISO)
induction of positive chemotaxis  (IEA,ISO)
mechanoreceptor differentiation  (ISO)
memory  (IBA)
modulation of chemical synaptic transmission  (IBA,IDA)
myelination  (IDA)
negative regulation of neuron apoptotic process  (IBA,ISO)
negative regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
nerve development  (IBA,ISO)
nerve growth factor signaling pathway  (IBA)
nervous system development  (IMP)
neuromuscular synaptic transmission  (ISO)
neuron development  (ISO)
neuron projection morphogenesis  (IBA)
peripheral nervous system development  (IBA,ISO)
positive chemotaxis  (IEA)
positive regulation of actin cytoskeleton reorganization  (IEA,ISO)
positive regulation of cell migration  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of glial cell differentiation  (IDA)
positive regulation of MAP kinase activity  (IEA,ISO)
positive regulation of peptidyl-serine phosphorylation  (IBA,IEA,ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
positive regulation of receptor internalization  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
regulation of apoptotic process  (IEA,ISO)
regulation of neuron apoptotic process  (ISO)
regulation of neuron differentiation  (IBA)
signal transduction  (IEA)
smooth muscle cell differentiation  (ISO)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA,IEA,ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arvanian VL, etal., J Neurosci 2003 Sep 24;23(25):8706-12.
2. Bates B, etal., Nat Neurosci 1999 Feb;2(2):115-7.
3. Chen HH, etal., J Neurosci 2002 May 1;22(9):3512-9.
4. Chung YJ, etal., J Toxicol Environ Health A. 2007 Jun;70(12):1020-6.
5. Dagnell C, etal., Respir Res. 2010 Nov 8;11:156.
6. ElShamy WM and Ernfors P, Neuron 1996 May;16(5):963-72.
7. Ernfors P, etal., Proc Natl Acad Sci U S A 1990 Jul;87(14):5454-8.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Genc B, etal., PLoS Biol 2004 Dec;2(12):e403. Epub 2004 Nov 23.
10. GOA data from the GO Consortium
11. Groneberg DA, etal., Biol Chem. 2005 Jan;386(1):53-9.
12. Hochhaus F, etal., BMC Pediatr 2001;1(1):2. Epub 2001 Aug 24.
13. Kahn MA, etal., Glia 1999 Apr;26(2):153-65.
14. Kunugi H, etal., Neurosci Lett 1998 Jan 23;241(1):65-7.
15. Maisonpierre PC, etal., Genomics 1991 Jul;10(3):558-68.
16. Maisonpierre PC, etal., Science 1990 Mar 23;247(4949 Pt 1):1446-51.
17. MGD data from the GO Consortium
18. Mitsui T, etal., Exp Neurol. 2005 Aug;194(2):410-31.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Noga O, etal., Clin Exp Allergy. 2001 Dec;31(12):1906-12.
21. Pipeline to import KEGG annotations from KEGG into RGD
22. RGD automated data pipeline
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. Ricci A, etal., Sarcoidosis Vasc Diffuse Lung Dis. 2005 Oct;22(3):186-94.
26. Risbud RM, etal., Brain Res. 2011 Nov 18;1424:53-9. doi: 10.1016/j.brainres.2011.09.039. Epub 2011 Sep 24.
27. Rubio N, etal., Glia 2004 Jul;47(1):78-87.
28. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:2025430   PMID:7605630   PMID:8809809   PMID:8861722   PMID:9736028   PMID:10908605   PMID:12376548   PMID:12741988   PMID:12914971   PMID:12941778   PMID:14499950   PMID:14519521  
PMID:14715936   PMID:15376326   PMID:15497153   PMID:15548637   PMID:16142215   PMID:16206279   PMID:16516892   PMID:17072373   PMID:17515814   PMID:17561837   PMID:17628607   PMID:17647101  
PMID:17688944   PMID:17898207   PMID:18032527   PMID:18036576   PMID:18191115   PMID:18304740   PMID:18369383   PMID:18601922   PMID:18652597   PMID:18957307   PMID:19026718   PMID:19100726  
PMID:19203225   PMID:19513915   PMID:19565663   PMID:19854260   PMID:19915564   PMID:20148653   PMID:20308067   PMID:20360537   PMID:21135740   PMID:21221027   PMID:21261755   PMID:21340438  
PMID:21370927   PMID:21473141   PMID:21508350   PMID:21527636   PMID:21613508   PMID:21680256   PMID:21783247   PMID:21868332   PMID:22282251   PMID:22544632   PMID:22552353   PMID:22573254  
PMID:22764246   PMID:22871470   PMID:22960790   PMID:22971496   PMID:23027130   PMID:23074106   PMID:23387385   PMID:23581595   PMID:23954828   PMID:24744011   PMID:25215612   PMID:25301495  
PMID:26009773   PMID:26208387   PMID:26239042   PMID:26316168   PMID:26763079   PMID:27056081   PMID:27597902   PMID:27830679   PMID:28440877   PMID:28614398   PMID:30125729   PMID:30672120  
PMID:30915764   PMID:31896816   PMID:32548984  


Genomics

Comparative Map Data
Ntf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)Ensembl
Rnor_6.04158,636,883 - 158,705,886 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04225,638,801 - 225,707,719 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44162,435,781 - 162,506,961 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14162,680,717 - 162,751,897 (-)NCBI
Celera4147,640,921 - 147,710,546 (-)NCBICelera
Cytogenetic Map4q42NCBI
NTF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl125,432,108 - 5,521,536 (+)EnsemblGRCh38hg38GRCh38
GRCh38125,432,108 - 5,495,299 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37125,541,274 - 5,604,465 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36125,411,541 - 5,474,726 (+)NCBINCBI36hg18NCBI36
Build 34125,473,526 - 5,474,725NCBI
Celera127,162,184 - 7,225,194 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef125,455,606 - 5,458,036 (+)NCBIHuRef
CHM1_1125,540,527 - 5,604,287 (+)NCBICHM1_1
Ntf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396126,078,375 - 126,143,734 (-)NCBIGRCm39mm39
GRCm39 Ensembl6126,078,375 - 126,143,873 (-)Ensembl
GRCm386126,101,412 - 126,166,772 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6126,101,412 - 126,166,910 (-)EnsemblGRCm38mm10GRCm38
MGSCv376126,051,430 - 126,116,762 (-)NCBIGRCm37mm9NCBIm37
MGSCv366126,067,031 - 126,130,540 (-)NCBImm8
Celera6127,765,447 - 127,832,752 (-)NCBICelera
Cytogenetic Map6F3NCBI
cM Map660.45NCBI
Ntf3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554133,207,123 - 3,273,491 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554133,207,669 - 3,273,371 (+)NCBIChiLan1.0ChiLan1.0
NTF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1125,470,093 - 5,534,300 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl125,530,508 - 5,533,989 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0125,551,734 - 5,615,981 (+)NCBIMhudiblu_PPA_v0panPan3
NTF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12739,383,017 - 39,454,613 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2739,383,152 - 39,454,601 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha277,231,693 - 7,233,370 (+)NCBI
ROS_Cfam_1.02739,739,752 - 39,811,227 (-)NCBI
UMICH_Zoey_3.12739,608,720 - 39,679,940 (-)NCBI
UNSW_CanFamBas_1.02739,650,338 - 39,721,747 (-)NCBI
UU_Cfam_GSD_1.0276,639,885 - 6,711,187 (+)NCBI
Ntf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945103,495,858 - 103,555,782 (-)NCBI
SpeTri2.0NW_0049367092,163,510 - 2,223,429 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NTF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl565,052,517 - 65,123,788 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1565,052,608 - 65,122,645 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2567,204,186 - 67,204,959 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NTF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1115,477,208 - 5,542,404 (+)NCBI
Vero_WHO_p1.0NW_0236660632,690,949 - 2,765,784 (-)NCBI
Ntf3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248602,416,448 - 2,479,216 (+)NCBI

Position Markers
AI835689  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,915,061 - 158,915,145 (+)MAPPERmRatBN7.2
Rnor_6.04158,636,961 - 158,637,044NCBIRnor6.0
Rnor_5.04225,638,879 - 225,638,962UniSTSRnor5.0
RGSC_v3.44162,435,859 - 162,435,942UniSTSRGSC3.4
Celera4147,640,999 - 147,641,082UniSTS
Cytogenetic Map4q42UniSTS
AW535926  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,948,817 - 158,948,972 (+)MAPPERmRatBN7.2
Rnor_6.04158,670,699 - 158,670,853NCBIRnor6.0
Rnor_5.04225,672,542 - 225,672,696UniSTSRnor5.0
RGSC_v3.44162,470,547 - 162,470,701UniSTSRGSC3.4
Celera4147,674,847 - 147,675,001UniSTS
RH 3.4 Map41000.8UniSTS
Cytogenetic Map4q42UniSTS
PMC137548P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,915,357 - 158,915,841 (+)MAPPERmRatBN7.2
Rnor_6.04158,637,257 - 158,637,740NCBIRnor6.0
Rnor_5.04225,639,175 - 225,639,658UniSTSRnor5.0
RGSC_v3.44162,436,155 - 162,436,638UniSTSRGSC3.4
Celera4147,641,295 - 147,641,778UniSTS
Cytogenetic Map4q42UniSTS
Ntf3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,915,019 - 158,916,045 (+)MAPPERmRatBN7.2
Rnor_6.04158,636,919 - 158,637,944NCBIRnor6.0
Rnor_5.04225,638,837 - 225,639,862UniSTSRnor5.0
RGSC_v3.44162,435,817 - 162,436,842UniSTSRGSC3.4
Celera4147,640,957 - 147,641,982UniSTS
Cytogenetic Map4q42UniSTS
UniSTS:225313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,914,970 - 158,915,122 (+)MAPPERmRatBN7.2
Rnor_6.04158,636,870 - 158,637,021NCBIRnor6.0
Rnor_5.04225,638,788 - 225,638,939UniSTSRnor5.0
RGSC_v3.44162,435,768 - 162,435,919UniSTSRGSC3.4
Celera4147,640,908 - 147,641,059UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:330
Count of miRNA genes:194
Interacting mature miRNAs:231
Transcripts:ENSRNOT00000026685
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 8 11 3
Low 3 43 51 35 16 35 8 11 66 24 31 11 8
Below cutoff 6 6 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026685   ⟹   ENSRNOP00000026685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082009   ⟹   ENSRNOP00000069580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,914,985 - 158,982,737 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,704,170 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087115   ⟹   ENSRNOP00000070420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,914,985 - 158,984,452 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,705,885 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115703   ⟹   ENSRNOP00000090293
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,914,988 - 158,979,500 (-)Ensembl
RefSeq Acc Id: NM_001270868   ⟹   NP_001257797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24158,914,984 - 158,982,737 (-)NCBI
Rnor_6.04158,636,883 - 158,704,170 (-)NCBI
Rnor_5.04225,638,801 - 225,707,719 (-)NCBI
Celera4147,640,921 - 147,708,830 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270869   ⟹   NP_001257798
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24158,914,984 - 158,982,737 (-)NCBI
Rnor_6.04158,636,883 - 158,704,170 (-)NCBI
Rnor_5.04225,638,801 - 225,707,719 (-)NCBI
Celera4147,640,921 - 147,708,830 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270870   ⟹   NP_001257799
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24158,914,984 - 158,984,453 (-)NCBI
Rnor_6.04158,636,883 - 158,705,886 (-)NCBI
Rnor_5.04225,638,801 - 225,707,719 (-)NCBI
Celera4147,640,921 - 147,710,546 (-)NCBI
Sequence:
RefSeq Acc Id: NM_031073   ⟹   NP_112335
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24158,914,984 - 158,984,452 (-)NCBI
Rnor_6.04158,636,883 - 158,705,885 (-)NCBI
Rnor_5.04225,638,801 - 225,707,719 (-)NCBI
RGSC_v3.44162,435,781 - 162,506,961 (-)RGD
Celera4147,640,921 - 147,710,545 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112335   ⟸   NM_031073
- Peptide Label: isoform 1
- UniProtKB: P18280 (UniProtKB/Swiss-Prot),   A0A0G2JXV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257799   ⟸   NM_001270870
- Peptide Label: isoform 3 precursor
- UniProtKB: P18280 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257798   ⟸   NM_001270869
- Peptide Label: isoform 1
- UniProtKB: P18280 (UniProtKB/Swiss-Prot),   A0A0G2JXV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257797   ⟸   NM_001270868
- Peptide Label: isoform 2
- UniProtKB: P18280 (UniProtKB/Swiss-Prot),   A0A0G2JVQ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069580   ⟸   ENSRNOT00000082009
RefSeq Acc Id: ENSRNOP00000026685   ⟸   ENSRNOT00000026685
RefSeq Acc Id: ENSRNOP00000070420   ⟸   ENSRNOT00000087115
RefSeq Acc Id: ENSRNOP00000090293   ⟸   ENSRNOT00000115703
Protein Domains
NGF

Transcriptome

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

Promoters
RGD ID:13693415
Promoter ID:EPDNEW_R3940
Type:single initiation site
Name:Ntf3_1
Description:neurotrophin 3
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_6.04158,704,180 - 158,704,240EPDNEW

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)
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)
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
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)
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
PVG/Seac (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
SBH/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: 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)
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/OlalpcvMcwi (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
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)
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
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)
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/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/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
WKY/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
WKY/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
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)
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
WN/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
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:619728 AgrOrtholog
Ensembl Genes ENSRNOG00000019716 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026685 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000069580 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070420 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026685 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000082009 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087115 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097740 IMAGE-MGC_LOAD
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nerve_growth_factor-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nerve_growth_factor-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nerve_growth_factor_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotrophin-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81737 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91650 IMAGE-MGC_LOAD
NCBI Gene 81737 ENTREZGENE
PANTHER PTHR11589 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11589:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ntf3 PhenoGen
PIRSF NGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS NEUROTROPHN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NGF_2 UniProtKB/Swiss-Prot
SMART NGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JVQ7 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JXV7 ENTREZGENE, UniProtKB/TrEMBL
  NTF3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6NS33 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ntf3  neurotrophin 3    neurotrophin-3 (HDNF/NT-3)  Name updated 1299863 APPROVED
2002-08-07 Ntf3  neurotrophin-3 (HDNF/NT-3)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction can bind to NGF receptor 729140
gene_process involved in the development and maintenance of the vertebrate nervous system 729140