Nefl (neurofilament light chain) - Rat Genome Database

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Gene: Nefl (neurofilament light chain) Rattus norvegicus
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Symbol: Nefl
Name: neurofilament light chain
RGD ID: 621458
Description: Enables 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. Located in growth cone and neurofilament. Colocalizes with neuron projection. Used to study congenital hypothyroidism. Biomarker of hypothyroidism; mental depression; 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 chain); 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; 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21542,301,920 - 42,305,793 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1542,301,916 - 42,305,793 (+)Ensembl
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


Disease Annotations     Click to see Annotation Detail View
acute disseminated encephalomyelitis  (ISO)
AIDS Dementia Complex  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
Anti-N-Methyl-D-Aspartate Receptor Encephalitis  (ISO)
autosomal dominant distal hereditary motor neuronopathy  (ISO)
Charcot-Marie-Tooth disease  (ISO)
Charcot-Marie-Tooth disease dominant intermediate G  (ISO)
Charcot-Marie-Tooth disease type 1  (ISO)
Charcot-Marie-Tooth disease type 1C  (ISO)
Charcot-Marie-Tooth disease type 1F  (ISO)
Charcot-Marie-Tooth disease type 2E  (ISO)
congenital hypothyroidism  (IDA)
COVID-19  (ISO)
Creutzfeldt-Jakob disease  (ISO)
demyelinating disease  (ISO)
distal hereditary motor neuronopathy type 7B  (ISO)
distal myopathy  (ISO)
Experimental Autoimmune Encephalomyelitis  (IEP)
fatal familial insomnia  (ISO)
frontotemporal dementia  (ISO)
Frontotemporal Lobar Degeneration  (ISO)
genetic disease  (ISO)
HIV Seropositivity  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hypothyroidism  (IEP)
invasive ductal carcinoma  (ISO)
Lewy body dementia  (ISO)
Malnutrition  (IEP)
mental depression  (IEP)
middle cerebral artery infarction  (ISO)
mild cognitive impairment  (ISO)
multiple sclerosis  (ISO)
neuritis  (ISO)
neuromyelitis optica  (ISO)
neuropathy  (ISO)
Neurosyphilis  (ISO)
Parkinson's disease  (ISO)
peripheral nervous system disease  (ISO)
progressive multifocal leukoencephalopathy  (ISO)
relapsing-remitting multiple sclerosis  (ISO)
sciatic neuropathy  (IEP)
Sepsis  (ISO)
Sepsis-Associated Encephalopathy  (ISO)
Sjogren's syndrome  (ISO)
Spinal Cord Injuries  (IDA)
spinal muscular atrophy  (ISO)
Sporadic Creutzfeldt-Jakob Disease  (ISO)
Stroke  (ISO)
syphilis  (ISO)
Talipes Cavus  (ISO)
transient cerebral ischemia  (IEP)
vascular dementia  (ISO)
Wallerian Degeneration  (IEP)

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)
antimycin A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP,ISO)
atrazine  (ISO)
azoxystrobin  (ISO)
BAPTA  (EXP)
belinostat  (ISO)
Benzamil  (EXP)
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)
Cuprizon  (EXP)
cycloheximide  (EXP)
cyfluthrin  (ISO)
cypermethrin  (ISO)
daidzein 7-O-beta-D-glucoside  (EXP)
dantrolene  (EXP)
deguelin  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorvos  (EXP)
dieldrin  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
diuron  (EXP)
dizocilpine maleate  (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)
idebenone  (EXP)
indometacin  (EXP)
isotretinoin  (ISO)
ivermectin  (ISO)
ketamine  (EXP)
KN-93  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
leupeptin  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
memantine  (EXP)
mercury dibromide  (ISO)
methylmercury chloride  (EXP,ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-D-aspartic acid  (EXP)
N-Nitrosopyrrolidine  (ISO)
nicardipine  (EXP)
nifedipine  (EXP)
Nilvadipine  (EXP)
O-methyleugenol  (ISO)
ouabain  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
parathion  (EXP)
PCB138  (EXP,ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
picoxystrobin  (ISO)
propanal  (ISO)
raloxifene  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
Soman  (EXP)
staurosporine  (EXP)
sunitinib  (ISO)
tebufenpyrad  (ISO)
temozolomide  (ISO)
terbutaline  (EXP)
tetrachloroethene  (EXP)
thifluzamide  (ISO)
thioacetamide  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trifluoperazine  (EXP)
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. Aamodt AH, etal., J Neurol. 2021 Mar 20. pii: 10.1007/s00415-021-10517-6. doi: 10.1007/s00415-021-10517-6.
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5. Anderson AM, etal., J Neurovirol. 2017 Feb;23(1):106-112. doi: 10.1007/s13365-016-0466-z. Epub 2016 Jul 11.
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25. KEGG
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27. Kim SK, etal., J Neurosci Methods. 2007 Apr 15;161(2):199-204. Epub 2006 Dec 8.
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34. Menke RA, etal., Ann Clin Transl Neurol. 2015 Jul;2(7):748-55. doi: 10.1002/acn3.212. Epub 2015 May 25.
35. MGD data from the GO Consortium
36. Nakagawa T, etal., J Cell Biol. 1995 Apr;129(2):411-29.
37. NCBI rat LocusLink and RefSeq merged data July 26, 2002
38. Norgren N, etal., Brain Res Bull. 2005 Oct 30;67(4):264-8.
39. OMIM Disease Annotation Pipeline
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42. Pipeline to import KEGG annotations from KEGG into RGD
43. Quintanar JL and Salinas E, Neurochem Res. 2008 Jun;33(6):1051-6. Epub 2007 Dec 20.
44. RGD automated data pipeline
45. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
46. RGD automated import pipeline for gene-chemical interactions
47. Schenker M, etal., Brain Res. 2002 Dec 13;957(2):259-70.
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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   PMID:32357304   PMID:33028339   PMID:33727100  


Genomics

Comparative Map Data
Nefl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21542,301,920 - 42,305,793 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1542,301,916 - 42,305,793 (+)Ensembl
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 - 24,956,721 (-)EnsemblGRCh38hg38GRCh38
GRCh38824,950,955 - 24,956,612 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37824,808,468 - 24,814,126 (-)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
GRCm39 Ensembl1468,321,312 - 68,326,544 (+)Ensembl
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
CanFam3.12532,463,361 - 32,468,965 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2532,463,452 - 32,467,224 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2533,046,764 - 33,052,425 (+)NCBI
ROS_Cfam_1.02532,662,329 - 32,667,982 (+)NCBI
UMICH_Zoey_3.12532,617,778 - 32,623,430 (+)NCBI
UNSW_CanFamBas_1.02532,467,208 - 32,472,860 (+)NCBI
UU_Cfam_GSD_1.02532,633,319 - 32,638,980 (+)NCBI
Nefl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494310,389,433 - 10,393,833 (+)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1823,077,085 - 23,083,213 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl823,077,086 - 23,083,222 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605219,090,237 - 19,096,168 (+)NCBIVero_WHO_p1.0
Nefl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475820,063,109 - 20,068,459 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC15073P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21542,304,641 - 42,305,475 (+)MAPPERmRatBN7.2
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
mRatBN7.21542,304,686 - 42,305,660 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat

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
mRatBN7.2 Ensembl1542,301,916 - 42,305,793 (+)Ensembl
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
mRatBN7.21542,301,920 - 42,305,793 (+)NCBI
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018599 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018599 UniProtKB/Swiss-Prot
InterPro IF_conserved UniProtKB/Swiss-Prot
  IF_rod_dom 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
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
2021-04-12 Nefl  neurofilament light chain  Nefl  neurofilament light  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
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