Ntf3 (neurotrophin 3) - Rat Genome Database

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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
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84160,601,161 - 160,670,623 (-)NCBIGRCr8
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4165,144,795 - 165,214,257 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,927,698 - 160,997,163 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04159,561,745 - 159,631,144 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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,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 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)
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

Biological Process

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 (-)NCBIGRCr8
mRatBN7.24158,914,984 - 158,984,453 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,914,957 - 158,984,596 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4165,144,795 - 165,214,257 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,927,698 - 160,997,163 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04159,561,745 - 159,631,144 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38125,430,332 - 5,495,299 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl125,432,108 - 5,521,536 (+)EnsemblGRCh38hg38GRCh38
GRCh37125,541,274 - 5,604,465 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36125,411,541 - 5,474,726 (+)NCBINCBI36Build 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 Ensembl
GRCm386126,101,412 - 126,166,772 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6126,101,412 - 126,166,910 (-)EnsemblGRCm38mm10GRCm38
MGSCv376126,051,430 - 126,116,762 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)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
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 (+)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02739,739,752 - 39,811,227 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)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 (+)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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248602,416,448 - 2,479,216 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ntf3
497 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)4144639524182687754Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
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
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)426775591168368347Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
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
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
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
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
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
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
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
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
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
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
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
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

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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 56 31

Sequence


Ensembl Acc Id: ENSRNOT00000026685   ⟹   ENSRNOP00000026685
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
Ensembl Acc Id: ENSRNOT00000082009   ⟹   ENSRNOP00000069580
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
Ensembl Acc Id: ENSRNOT00000087115   ⟹   ENSRNOP00000070420
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
Ensembl Acc Id: ENSRNOT00000115703   ⟹   ENSRNOP00000090293
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
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)
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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026685.6 UniProtKB/Swiss-Prot
  ENSRNOT00000082009.2 UniProtKB/TrEMBL
  ENSRNOT00000087115.2 UniProtKB/TrEMBL
  ENSRNOT00000115703 ENTREZGENE
  ENSRNOT00000115703.1 UniProtKB/Swiss-Prot
  ENSRNOT00000149553 ENTREZGENE
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
  NTF3_N 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
  NTF3_N 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, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019716 RatGTEx
SMART NGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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