Nefl (neurofilament light) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Nefl (neurofilament light) Rattus norvegicus
Analyze
Symbol: Nefl
Name: neurofilament light
RGD ID: 621458
Description: Exhibits phospholipase binding activity and protein domain specific binding activity. Involved in several processes, including central nervous system development; intermediate filament cytoskeleton organization; and response to corticosterone. Localizes to growth cone and neurofilament. Used to study congenital hypothyroidism. Biomarker of hypothyroidism; mental depression; middle cerebral artery infarction; sciatic neuropathy; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease (multiple); amyotrophic lateral sclerosis; and invasive ductal carcinoma. Orthologous to human NEFL (neurofilament light); PARTICIPATES IN amyotrophic lateral sclerosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,5-hexanedione; 2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 68 kDa neurofilament protein; 68kDa neurofilament; neurofilament light polypeptide; neurofilament triplet L protein; neurofilament, light polypeptide; NF-L; NF68; Nfl
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   MAMTS3_H  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01544,799,378 - 44,803,251 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1544,799,334 - 44,804,574 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01546,793,526 - 46,797,399 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41547,636,303 - 47,640,176 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11547,652,082 - 47,655,956 (+)NCBI
Celera1541,961,053 - 41,964,926 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,5-hexanedione  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
2-methylcholine  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
5-azacytidine  (ISO)
6-Cyano-7-nitroquinoxaline-2,3-dione  (EXP)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldrin  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
aluminium sulfate (anhydrous)  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP,ISO)
atrazine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
bucladesine  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
Calpeptin  (EXP)
calyculin a  (EXP)
carbon disulfide  (EXP)
chloroethene  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
cycloheximide  (EXP)
cyfluthrin  (ISO)
cypermethrin  (ISO)
daidzein 7-O-beta-D-glucoside  (EXP)
dantrolene  (EXP)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorvos  (EXP)
dieldrin  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
fenvalerate  (EXP)
folic acid  (ISO)
furan  (EXP)
glyburide  (EXP)
Heptachlor epoxide  (ISO)
hydrogen sulfide  (ISO)
indometacin  (EXP)
isotretinoin  (ISO)
ketamine  (EXP)
KN-93  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
leupeptin  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
nifedipine  (EXP)
O-methyleugenol  (ISO)
ouabain  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
parathion  (EXP)
PCB138  (EXP,ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
propanal  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
Soman  (EXP)
staurosporine  (EXP)
sunitinib  (ISO)
terbutaline  (EXP)
tetrachloroethene  (EXP)
thioacetamide  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
U-73122  (EXP)
uranium atom  (ISO)
valproic acid  (EXP,ISO)
verapamil  (EXP)
vinclozolin  (EXP)
vorinostat  (ISO)
Z-Val-Phe-H  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Athlan ES and Mushynski WE, J Biol Chem. 1997 Dec 5;272(49):31073-8.
2. Benson DL, etal., J Neurocytol. 1996 Mar;25(3):181-96.
3. Camargo-De-Morais M, etal., Neurochem Res. 1996 May;21(5):595-602.
4. Cereseto M, etal., Eur J Neurosci. 2006 Dec;24(12):3354-64.
5. Chin SS and Liem RK, Eur J Cell Biol 1989 Dec;50(2):475-90.
6. Ching GY and Liem RK, J Cell Sci. 1999 Jul;112 ( Pt 13):2233-40.
7. Ehler J, etal., PLoS One. 2019 Jan 24;14(1):e0211184. doi: 10.1371/journal.pone.0211184. eCollection 2019.
8. El-Fawal HA and O'Callaghan JP, Neurotoxicology. 2008 Jan;29(1):109-15. Epub 2007 Oct 5.
9. Ferrero AJ, etal., Prog Neuropsychopharmacol Biol Psychiatry. 2007 Oct 1;31(7):1419-28. Epub 2007 Jun 26.
10. Ghosh S, etal., Neuroreport. 1999 Aug 2;10(11):2361-5.
11. Goldstein ME, etal., Brain Res. 1988 Jun;427(3):287-91.
12. Haddad LA, etal., J Biol Chem 2002 Nov 15;277(46):44180-6.
13. KEGG
14. Kim SK, etal., Exp Mol Med. 2006 Jun 30;38(3):265-72.
15. Kim SK, etal., J Neurosci Methods. 2007 Apr 15;161(2):199-204. Epub 2006 Dec 8.
16. Kong J and Xu Z, Neurosci Lett. 2000 Mar 3;281(1):72-4.
17. Li J, etal., Brain Behav. 2019 Aug;9(8):e01354. doi: 10.1002/brb3.1354. Epub 2019 Jul 17.
18. Lopez-Picon FR, etal., Hippocampus. 2003;13(7):767-79.
19. Mages B, etal., Front Cell Neurosci. 2018 Jun 18;12:161. doi: 10.3389/fncel.2018.00161. eCollection 2018.
20. Menke RA, etal., Ann Clin Transl Neurol. 2015 Jul;2(7):748-55. doi: 10.1002/acn3.212. Epub 2015 May 25.
21. MGD data from the GO Consortium
22. Nakagawa T, etal., J Cell Biol. 1995 Apr;129(2):411-29.
23. NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. Norgren N, etal., Brain Res Bull. 2005 Oct 30;67(4):264-8.
25. OMIM Disease Annotation Pipeline
26. Paz MM, etal., J Nutr. 1991 Sep;121(9):1349-54. doi: 10.1093/jn/121.9.1349.
27. Pierson CR, etal., J Neuropathol Exp Neurol. 2003 Mar;62(3):260-71.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Quintanar JL and Salinas E, Neurochem Res. 2008 Jun;33(6):1051-6. Epub 2007 Dec 20.
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Schenker M, etal., Brain Res. 2002 Dec 13;957(2):259-70.
34. Schlaepfer WW and Bruce J, J Neurosci Res. 1990 Jan;25(1):39-49.
35. Shen ZX, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2008 Aug;33(8):693-9.
36. Tsuda M, etal., J Neurochem. 2000 Feb;74(2):860-8.
37. Vahidnia A, etal., Chem Biol Interact. 2008 Nov 25;176(2-3):188-95. doi: 10.1016/j.cbi.2008.07.001. Epub 2008 Jul 12.
38. Wang QS, etal., Toxicology. 2008 Feb 28;244(2-3):166-78. Epub 2007 Nov 22.
39. Yaremko ML, etal., Genes Chromosomes Cancer. 1996 Jul;16(3):189-95.
40. Yu S, etal., Neurochem Res. 2006 Oct;31(10):1197-204. Epub 2006 Oct 17.
41. Zamoner A, etal., Neurotoxicology. 2008 Nov;29(6):1092-9. doi: 10.1016/j.neuro.2008.09.004. Epub 2008 Sep 18.
42. Zuchner S, etal., Neuromuscul Disord 2004 Feb;14(2):147-57.
Additional References at PubMed
PMID:2121744   PMID:2493000   PMID:3920075   PMID:3925999   PMID:7745611   PMID:7946341   PMID:8110465   PMID:8344946   PMID:8634266   PMID:8821035   PMID:9398473   PMID:10221457  
PMID:10350642   PMID:10461886   PMID:10884316   PMID:11034913   PMID:11343650   PMID:11487626   PMID:11834298   PMID:12432080   PMID:14561875   PMID:14662745   PMID:15132161   PMID:15193534  
PMID:15242779   PMID:15857389   PMID:15884021   PMID:16920084   PMID:16940710   PMID:17052987   PMID:17634366   PMID:18556119   PMID:19136565   PMID:19646951   PMID:20124353   PMID:22082260  
PMID:22871113   PMID:23106098   PMID:23228886   PMID:25232125   PMID:25869803   PMID:27369073   PMID:29476059   PMID:30987515  


Genomics

Comparative Map Data
Nefl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01544,799,378 - 44,803,251 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1544,799,334 - 44,804,574 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01546,793,526 - 46,797,399 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41547,636,303 - 47,640,176 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11547,652,082 - 47,655,956 (+)NCBI
Celera1541,961,053 - 41,964,926 (+)NCBICelera
Cytogenetic Map15p12NCBI
NEFL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl824,950,955 - 24,957,110 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl824,950,955 - 24,956,721 (-)EnsemblGRCh38hg38GRCh38
GRCh38824,950,955 - 24,956,612 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37824,808,468 - 24,814,383 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36824,864,385 - 24,870,043 (-)NCBINCBI36hg18NCBI36
Build 34824,866,239 - 24,869,946NCBI
Celera823,772,893 - 23,778,556 (-)NCBI
Cytogenetic Map8p21.2NCBI
HuRef823,353,235 - 23,359,150 (-)NCBIHuRef
CHM1_1825,010,797 - 25,016,712 (-)NCBICHM1_1
Nefl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391468,321,312 - 68,326,544 (+)NCBIGRCm39mm39
GRCm381468,083,863 - 68,089,095 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1468,083,863 - 68,089,095 (+)EnsemblGRCm38mm10GRCm38
MGSCv371468,701,941 - 68,705,802 (+)NCBIGRCm37mm9NCBIm37
MGSCv361467,037,214 - 67,041,075 (+)NCBImm8
Celera1465,851,013 - 65,854,872 (+)NCBICelera
Cytogenetic Map14D1NCBI
Nefl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540347,946,353 - 47,952,026 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540347,946,413 - 47,951,734 (-)NCBIChiLan1.0ChiLan1.0
NEFL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1821,134,533 - 21,140,694 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl821,134,533 - 21,140,694 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0824,218,510 - 24,224,627 (-)NCBIMhudiblu_PPA_v0panPan3
NEFL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2532,463,452 - 32,467,224 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12532,463,361 - 32,468,965 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nefl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367571,642,122 - 1,646,499 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEFL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl148,990,750 - 8,997,300 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1148,991,321 - 8,996,900 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21410,087,492 - 10,093,071 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NEFL
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl823,077,086 - 23,083,222 (-)Ensembl
ChlSab1.1823,077,085 - 23,083,213 (-)NCBI
Nefl
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475820,063,109 - 20,068,459 (-)NCBI

Position Markers
PMC15073P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01544,802,100 - 44,802,933NCBIRnor6.0
Rnor_5.01546,793,844 - 46,794,677UniSTSRnor5.0
RGSC_v3.41547,639,025 - 47,639,858UniSTSRGSC3.4
Celera1541,963,775 - 41,964,608UniSTS
Cytogenetic Map15p12UniSTS
Nefl  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01544,802,145 - 44,803,118NCBIRnor6.0
Rnor_5.01546,793,659 - 46,794,632UniSTSRnor5.0
RGSC_v3.41547,639,070 - 47,640,043UniSTSRGSC3.4
Celera1541,963,820 - 41,964,793UniSTS
Cytogenetic Map15p12UniSTS
Nfl  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01546,793,624 - 46,793,811UniSTSRnor5.0
Cytogenetic Map15p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154309747052831189Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:154
Count of miRNA genes:122
Interacting mature miRNAs:132
Transcripts:ENSRNOT00000018599
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 70 15 9
Low 3 18 16 7 1 7 3 3 4 7 24 8 3
Below cutoff 22 28 21 15 21 5 5 10 6 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018599   ⟹   ENSRNOP00000018599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1544,799,334 - 44,804,574 (+)Ensembl
RefSeq Acc Id: NM_031783   ⟹   NP_113971
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01544,799,378 - 44,803,251 (+)NCBI
Rnor_5.01546,793,526 - 46,797,399 (-)NCBI
RGSC_v3.41547,636,303 - 47,640,176 (+)RGD
Celera1541,961,053 - 41,964,926 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113971   ⟸   NM_031783
- UniProtKB: P19527 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018599   ⟸   ENSRNOT00000018599
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13699766
Promoter ID:EPDNEW_R10289
Type:single initiation site
Name:Nefl_1
Description:neurofilament light
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_6.01544,799,343 - 44,799,403EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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 (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
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 47636974 47636975 G T snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621458 AgrOrtholog
Ensembl Genes ENSRNOG00000013658 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018599 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018599 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.5.1160 UniProtKB/Swiss-Prot
InterPro IF_conserved UniProtKB/Swiss-Prot
  IF_rod_dom UniProtKB/Swiss-Prot
  IF_rod_dom_coil1B UniProtKB/Swiss-Prot
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot
  NF-L UniProtKB/Swiss-Prot
KEGG Report rno:83613 UniProtKB/Swiss-Prot
NCBI Gene 83613 ENTREZGENE
PANTHER PTHR45652:SF8 UniProtKB/Swiss-Prot
Pfam Filament UniProtKB/Swiss-Prot
  Filament_head UniProtKB/Swiss-Prot
PhenoGen Nefl PhenoGen
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot
  IF_ROD_2 UniProtKB/Swiss-Prot
SMART Filament UniProtKB/Swiss-Prot
UniGene Rn.18568 ENTREZGENE
UniProt NFL_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63367 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-17 Nefl  neurofilament light  Nefl  neurofilament, light polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Nefl  neurofilament, light polypeptide  Nfl    Symbol updated 1299863 APPROVED
2002-08-07 Nfl  neurofilament, light polypeptide      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization anchored to the actin cytoskeleton 633519
gene_physical_interaction bound specifically by hamartin 633519