Ntf3 (neurotrophin 3) - Rat Genome Database

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Pathways
Gene: Ntf3 (neurotrophin 3) Rattus norvegicus
Analyze
Symbol: Ntf3
Name: neurotrophin 3
RGD ID: 619728
Description: Enables nerve growth factor binding activity. Involved in several processes, including myelination; positive regulation of glial cell differentiation; and response to immobilization stress. Predicted to be located in cytoplasmic vesicle. Predicted to be active in several cellular components, including axon; dendrite; and synaptic vesicle. Biomarker of alcohol use disorder; borna disease; and 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
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84160,601,161 - 160,670,623 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4160,600,770 - 160,676,349 (-)EnsemblGRCr8
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4165,144,795 - 165,214,257 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,927,698 - 160,997,163 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04159,561,745 - 159,631,144 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04158,636,883 - 158,705,886 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)Ensemblrn6Rnor6.0
Rnor_5.04225,638,801 - 225,707,719 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44162,435,781 - 162,506,961 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4147,640,921 - 147,710,546 (-)NCBICelera
RGSC_v3.14162,680,717 - 162,751,897 (-)NCBI
Cytogenetic Map4q42NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-adrenaline  (EXP)
(R)-noradrenaline  (EXP)
17beta-estradiol  (EXP,ISO)
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 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
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 atom  (ISO)
cadmium dichloride  (ISO)
Calcimycin  (EXP)
carbon monoxide  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (EXP)
cimetidine  (EXP)
cisplatin  (ISO)
colforsin daropate hydrochloride  (EXP)
cyclophosphamide  (EXP)
decabromodiphenyl ether  (EXP)
dibutyl phthalate  (EXP)
diethyl maleate  (EXP)
Dimaprit  (EXP)
dimethylarsinic acid  (EXP)
dopamine  (EXP)
endosulfan  (EXP)
famotidine  (EXP)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (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)
methimazole  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Chronic neurotrophin-3 strengthens synaptic connections to motoneurons in the neonatal rat. Arvanian VL, etal., J Neurosci 2003 Sep 24;23(25):8706-12.
2. Neurotrophin-3 is required for proper cerebellar development. Bates B, etal., Nat Neurosci 1999 Feb;2(2):115-7.
3. Muscle spindle-derived neurotrophin 3 regulates synaptic connectivity between muscle sensory and motor neurons. Chen HH, etal., J Neurosci 2002 May 1;22(9):3512-9.
4. Increased neurotrophin production in a Penicillium chrysogenum-induced allergic asthma model in mice. Chung YJ, etal., J Toxicol Environ Health A. 2007 Jun;70(12):1020-6.
5. Neurotrophins and neurotrophin receptors in pulmonary sarcoidosis - granulomas as a source of expression. Dagnell C, etal., Respir Res. 2010 Nov 8;11:156.
6. A local action of neurotrophin-3 prevents the death of proliferating sensory neuron precursor cells. ElShamy WM and Ernfors P, Neuron 1996 May;16(5):963-72.
7. Molecular cloning and neurotrophic activities of a protein with structural similarities to nerve growth factor: developmental and topographical expression in the brain. Ernfors P, etal., Proc Natl Acad Sci U S A 1990 Jul;87(14):5454-8.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. A chemoattractant role for NT-3 in proprioceptive axon guidance. Genc B, etal., PLoS Biol 2004 Dec;2(12):e403. Epub 2004 Nov 23.
10. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
11. Transcriptional down-regulation of neurotrophin-3 in chronic obstructive pulmonary disease. Groneberg DA, etal., Biol Chem. 2005 Jan;386(1):53-9.
12. Elevated nerve growth factor and neurotrophin-3 levels in cerebrospinal fluid of children with hydrocephalus. Hochhaus F, etal., BMC Pediatr 2001;1(1):2. Epub 2001 Aug 24.
13. Mice lacking NT-3, and its receptor TrkC, exhibit profound deficiencies in CNS glial cells. Kahn MA, etal., Glia 1999 Apr;26(2):153-65.
14. Possible association of missense mutation (Gly[-63]Glu) of the neurotrophin-3 gene with Alzheimer's disease in Japanese. Kunugi H, etal., Neurosci Lett 1998 Jan 23;241(1):65-7.
15. Human and rat brain-derived neurotrophic factor and neurotrophin-3: gene structures, distributions, and chromosomal localizations. Maisonpierre PC, etal., Genomics 1991 Jul;10(3):558-68.
16. Neurotrophin-3: a neurotrophic factor related to NGF and BDNF. Maisonpierre PC, etal., Science 1990 Mar 23;247(4949 Pt 1):1446-51.
17. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
18. Chronic exposure to ethanol alters neurotrophin content in the basal forebrain-cortex system in the mature rat: effects on autocrine-paracrine mechanisms. Miller MW and Mooney SM, J Neurobiol. 2004 Sep 15;60(4):490-8. doi: 10.1002/neu.20059.
19. Transplants of fibroblasts expressing BDNF and NT-3 promote recovery of bladder and hindlimb function following spinal contusion injury in rats. Mitsui T, etal., Exp Neurol. 2005 Aug;194(2):410-31.
20. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. The influence of inhalative corticosteroids on circulating Nerve Growth Factor, Brain-Derived Neurotrophic Factor and Neurotrophin-3 in allergic asthmatics. Noga O, etal., Clin Exp Allergy. 2001 Dec;31(12):1906-12.
22. Environmental enrichment alters neurotrophin levels after fetal alcohol exposure in rats. Parks EA, etal., Alcohol Clin Exp Res. 2008 Oct;32(10):1741-51. doi: 10.1111/j.1530-0277.2008.00759.x. Epub 2008 Jul 24.
23. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
24. GOA pipeline RGD automated data pipeline
25. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
27. Neurotrophin system activation in bronchoalveolar lavage fluid immune cells in pulmonary sarcoidosis. Ricci A, etal., Sarcoidosis Vasc Diffuse Lung Dis. 2005 Oct;22(3):186-94.
28. Neurotrophin-3 mRNA a putative target of miR21 following status epilepticus. Risbud RM, etal., Brain Res. 2011 Nov 18;1424:53-9. doi: 10.1016/j.brainres.2011.09.039. Epub 2011 Sep 24.
29. In vitro myelination by oligodendrocyte precursor cells transfected with the neurotrophin-3 gene. Rubio N, etal., Glia 2004 Jul;47(1):78-87.
30. Alcohol-induced cognitive deficits are associated with decreased circulating levels of the neurotrophin BDNF in humans and rats. Silva-Peña D, etal., Addict Biol. 2019 Sep;24(5):1019-1033. doi: 10.1111/adb.12668. Epub 2018 Sep 12.
31. Stress and antidepressants differentially regulate neurotrophin 3 mRNA expression in the locus coeruleus. Smith MA, etal., Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8788-92. doi: 10.1073/pnas.92.19.8788.
32. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
33. Alterations in neurotrophin and neurotrophin receptor gene expression patterns in the rat central nervous system following perinatal Borna disease virus infection. Zocher M, etal., J Neurovirol. 2000 Dec;6(6):462-77.
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: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   PMID:33121345   PMID:33763978   PMID:38211776   PMID:38372112  


Genomics

Comparative Map Data
Ntf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84160,601,161 - 160,670,623 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4160,600,770 - 160,676,349 (-)EnsemblGRCr8
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4165,144,795 - 165,214,257 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,927,698 - 160,997,163 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04159,561,745 - 159,631,144 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04158,636,883 - 158,705,886 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)Ensemblrn6Rnor6.0
Rnor_5.04225,638,801 - 225,707,719 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44162,435,781 - 162,506,961 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4147,640,921 - 147,710,546 (-)NCBICelera
RGSC_v3.14162,680,717 - 162,751,897 (-)NCBI
Cytogenetic Map4q42NCBI
NTF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38125,430,332 - 5,495,299 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl125,432,108 - 5,521,536 (+)Ensemblhg38GRCh38
GRCh37125,541,274 - 5,604,465 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36125,411,541 - 5,474,726 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34125,473,526 - 5,474,725NCBI
Celera127,162,184 - 7,225,194 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef125,455,606 - 5,458,036 (+)NCBIHuRef
CHM1_1125,540,527 - 5,604,287 (+)NCBICHM1_1
T2T-CHM13v2.0125,437,400 - 5,502,089 (+)NCBIT2T-CHM13v2.0
Ntf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396126,078,375 - 126,143,703 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6126,078,375 - 126,143,873 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm386126,101,412 - 126,166,772 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6126,101,412 - 126,166,910 (-)Ensemblmm10GRCm38
MGSCv376126,051,430 - 126,116,762 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv366126,067,031 - 126,130,540 (-)NCBIMGSCv36mm8
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 (+)Ensembl
ChiLan1.0NW_0049554133,207,669 - 3,273,371 (+)NCBIChiLan1.0ChiLan1.0
NTF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21010,982,176 - 11,046,479 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11210,978,933 - 11,043,237 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0125,551,734 - 5,615,981 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1125,470,093 - 5,534,300 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl125,530,508 - 5,533,989 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha277,231,693 - 7,233,370 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02739,739,752 - 39,811,227 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2739,739,747 - 39,811,226 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12739,608,720 - 39,679,940 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02739,650,338 - 39,721,747 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0276,639,885 - 6,711,187 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ntf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945103,495,858 - 103,555,782 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367092,163,334 - 2,223,552 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367092,163,510 - 2,223,429 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NTF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl565,052,519 - 65,123,788 (-)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660632,690,949 - 2,765,784 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ntf3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248602,416,503 - 2,479,225 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248602,416,448 - 2,479,216 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ntf3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1621,733,928 - 21,802,823 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ntf3
278 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)4146370897184426481Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4134095016179095016Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4149763204169799698Rat
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)4146370897184426481Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4131384565176384565Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4123870974168870974Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4117559384162559384Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4140059299181024663Rat
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)4146370897184426481Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4157292416184426481Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494638356168870820Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4106848959168870974Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4127263297172263297Rat
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)4126334185171334185Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4147299608184426481Rat
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)4146370897184426481Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4124700988169700988Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155834926184426481Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264174095838Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)4100752691179366077Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4137447185182447185Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4137430611182430611Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486709649168870974Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4134199006168870974Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4148121375176967367Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
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)4116184844161184844Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4160623982184426481Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
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)4146370897184426481Rat
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)4148834094168870974Rat

Markers in Region
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
GRCr84160,601,146 - 160,601,299 (+)Marker Load Pipeline
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
11 12 67 131 91 90 59 25 59 6 284 125 11 104 81 87 31 5 5

Sequence


Ensembl Acc Id: ENSRNOT00000026685   ⟹   ENSRNOP00000026685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,161 - 160,658,633 (-)Ensembl
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,705,886 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082009   ⟹   ENSRNOP00000069580
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,162 - 160,668,689 (-)Ensembl
mRatBN7.2 Ensembl4158,914,985 - 158,982,737 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,704,170 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000087115   ⟹   ENSRNOP00000070420
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,162 - 160,670,667 (-)Ensembl
mRatBN7.2 Ensembl4158,914,985 - 158,984,452 (-)Ensembl
Rnor_6.0 Ensembl4158,636,884 - 158,705,885 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115703   ⟹   ENSRNOP00000090293
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,161 - 160,667,983 (-)Ensembl
mRatBN7.2 Ensembl4158,914,988 - 158,979,500 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000125625   ⟹   ENSRNOP00000108981
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,171 - 160,604,566 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000129844   ⟹   ENSRNOP00000112115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,161 - 160,667,533 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000140521   ⟹   ENSRNOP00000099372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,081 - 160,667,264 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000142532   ⟹   ENSRNOP00000099772
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,600,770 - 160,623,808 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000149553   ⟹   ENSRNOP00000104157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,600,895 - 160,676,349 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000165141   ⟹   ENSRNOP00000109458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4160,601,448 - 160,669,447 (-)Ensembl
RefSeq Acc Id: NM_001270868   ⟹   NP_001257797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84160,601,161 - 160,668,907 (-)NCBI
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
GRCr84160,601,161 - 160,668,907 (-)NCBI
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
GRCr84160,601,161 - 160,670,623 (-)NCBI
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
GRCr84160,601,161 - 160,670,622 (-)NCBI
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:
RefSeq Acc Id: XM_063286750   ⟹   XP_063142820
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84160,601,161 - 160,668,374 (-)NCBI
RefSeq Acc Id: NP_112335   ⟸   NM_031073
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A0G2JXV7 (UniProtKB/TrEMBL),   A6ILU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257799   ⟸   NM_001270870
- Peptide Label: isoform 3 precursor
- UniProtKB: Q6NS33 (UniProtKB/Swiss-Prot),   P18280 (UniProtKB/Swiss-Prot),   A6ILU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257798   ⟸   NM_001270869
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A0G2JXV7 (UniProtKB/TrEMBL),   A6ILU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257797   ⟸   NM_001270868
- Peptide Label: isoform 2 precursor
- UniProtKB: A0A0G2JVQ7 (UniProtKB/TrEMBL),   A6ILU9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000069580   ⟸   ENSRNOT00000082009
Ensembl Acc Id: ENSRNOP00000026685   ⟸   ENSRNOT00000026685
Ensembl Acc Id: ENSRNOP00000070420   ⟸   ENSRNOT00000087115
Ensembl Acc Id: ENSRNOP00000090293   ⟸   ENSRNOT00000115703
RefSeq Acc Id: XP_063142820   ⟸   XM_063286750
- Peptide Label: isoform X1
- UniProtKB: Q6NS33 (UniProtKB/Swiss-Prot),   P18280 (UniProtKB/Swiss-Prot),   A6ILU9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000109458   ⟸   ENSRNOT00000165141
Ensembl Acc Id: ENSRNOP00000104157   ⟸   ENSRNOT00000149553
Ensembl Acc Id: ENSRNOP00000099772   ⟸   ENSRNOT00000142532
Ensembl Acc Id: ENSRNOP00000099372   ⟸   ENSRNOT00000140521
Ensembl Acc Id: ENSRNOP00000108981   ⟸   ENSRNOT00000125625
Ensembl Acc Id: ENSRNOP00000112115   ⟸   ENSRNOT00000129844
Protein Domains
Nerve growth factor-related

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P18280-F1-model_v2 AlphaFold P18280 1-258 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619728 AgrOrtholog
BioCyc Gene G2FUF-42980 BioCyc
Ensembl Genes ENSRNOG00000019716 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026685.6 UniProtKB/Swiss-Prot
  ENSRNOT00000115703 ENTREZGENE
  ENSRNOT00000115703.1 UniProtKB/Swiss-Prot
  ENSRNOT00000149553 ENTREZGENE
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7097740 IMAGE-MGC_LOAD
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot
  Nerve_growth_factor-like UniProtKB/Swiss-Prot
  Nerve_growth_factor-rel UniProtKB/Swiss-Prot
  Nerve_growth_factor_CS UniProtKB/Swiss-Prot
  Neurotrophin-3 UniProtKB/Swiss-Prot
  NTF3_N UniProtKB/Swiss-Prot
KEGG Report rno:81737 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91650 IMAGE-MGC_LOAD
NCBI Gene 81737 ENTREZGENE
PANTHER PTHR11589 UniProtKB/Swiss-Prot
  PTHR11589:SF4 UniProtKB/Swiss-Prot
Pfam NGF UniProtKB/Swiss-Prot
  NTF3_N UniProtKB/Swiss-Prot
PhenoGen Ntf3 PhenoGen
PIRSF NGF UniProtKB/Swiss-Prot
PRINTS NEUROTROPHN3 UniProtKB/Swiss-Prot
  NGF UniProtKB/Swiss-Prot
PROSITE NGF_1 UniProtKB/Swiss-Prot
  NGF_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000019716 RatGTEx
SMART NGF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot
UniProt A0A0G2JVQ7 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JXV7 ENTREZGENE, UniProtKB/TrEMBL
  A6ILU9 ENTREZGENE, UniProtKB/TrEMBL
  A6ILV0_RAT UniProtKB/TrEMBL
  NTF3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6NS33 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