Nefm (neurofilament medium chain) - Rat Genome Database

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Gene: Nefm (neurofilament medium chain) Rattus norvegicus
Analyze
Symbol: Nefm
Name: neurofilament medium chain
RGD ID: 3160
Description: Enables signaling receptor binding activity and toxic substance binding activity. Involved in several processes, including cellular response to estradiol stimulus; intermediate filament cytoskeleton organization; and nervous system development. Located in axon; neurofilament; and perikaryon. Used to study amyotrophic lateral sclerosis and congenital hypothyroidism. Biomarker of hypothyroidism; sciatic neuropathy; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Alzheimer's disease and human immunodeficiency virus infectious disease. Orthologous to human NEFM (neurofilament medium chain); PARTICIPATES IN amyotrophic lateral sclerosis pathway; INTERACTS WITH 2,5-hexanedione; 2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 160 kDa neurofilament protein; Nef3; neurofilament 3, medium; neurofilament medium; neurofilament medium polypeptide; neurofilament protein middle polypeptide; neurofilament protein, middle polypeptide; neurofilament triplet M protein; neurofilament, medium polypeptide; NF-M; Nfm
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21542,360,449 - 42,365,753 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)Ensembl
Rnor_6.01544,855,307 - 44,860,604 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1544,855,310 - 44,860,604 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01546,736,787 - 46,741,632 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41547,698,371 - 47,703,350 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11547,714,153 - 47,719,121 (-)NCBI
Celera1542,015,992 - 42,021,311 (-)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (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-hydroxypropanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
5-iodotubercidin  (ISO)
6-Cyano-7-nitroquinoxaline-2,3-dione  (EXP)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
bisphenol A  (EXP)
bucladesine  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
calyculin a  (EXP)
carbon disulfide  (EXP)
chlorpyrifos  (EXP,ISO)
cisplatin  (EXP,ISO)
cocaine  (ISO)
Cuprizon  (EXP)
curcumin  (EXP)
dantrolene  (EXP)
dexamethasone  (EXP)
diazinon  (EXP)
dieldrin  (EXP)
dioxygen  (ISO)
dizocilpine maleate  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
flavonoids  (EXP)
fonofos  (ISO)
ivermectin  (ISO)
KN-93  (EXP)
lead diacetate  (EXP,ISO)
lidocaine  (ISO)
lipopolysaccharide  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (EXP)
nicotine  (ISO)
nifedipine  (EXP)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
parathion  (ISO)
PCB138  (EXP)
pentanal  (ISO)
phenylmercury acetate  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
Riluzole  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
staurosporine  (EXP)
terbufos  (ISO)
thioacetamide  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
U-73122  (EXP)
undecane  (EXP)
valproic acid  (ISO)
verapamil  (EXP)
vorinostat  (ISO)
zinc sulfate  (ISO)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Al-Majed AA, etal., Cell Mol Neurobiol. 2004 Jun;24(3):379-402.
2. Andreassi C, etal., Nat Neurosci. 2010 Mar;13(3):291-301. doi: 10.1038/nn.2486. Epub 2010 Jan 31.
3. Athlan ES and Mushynski WE, J Biol Chem. 1997 Dec 5;272(49):31073-8.
4. Camargo-De-Morais M, etal., Neurochem Res. 1996 May;21(5):595-602.
5. Chiasson K, etal., J Mol Neurosci. 2006;30(3):297-310.
6. Ching GY and Liem RK, J Cell Sci. 1999 Jul;112 ( Pt 13):2233-40.
7. Chumasov EI, etal., Morfologiia. 2009;135(2):33-7.
8. DeCaprio AP, etal., Toxicol Appl Pharmacol. 1997 Jul;145(1):211-7.
9. Deng Y, etal., FASEB J. 2008 Jan;22(1):138-45. Epub 2007 Aug 8.
10. Geddes JW, etal., Neurobiol Aging. 1995 Jul-Aug;16(4):651-60.
11. Ghosh S, etal., Neuroreport. 1999 Aug 2;10(11):2361-5.
12. GOA data from the GO Consortium
13. Goldstein ME, etal., Brain Res. 1988 Jun;427(3):287-91.
14. KEGG
15. Kelly BM, etal., J Cell Biol 1992 Jul;118(2):397-410.
16. Kim OJ, etal., J Neurosci. 2002 Jul 15;22(14):5920-30.
17. Lopez-Picon FR, etal., Hippocampus. 2003;13(7):767-79.
18. Ludemann N, etal., J Biol Chem. 2005 Sep 9;280(36):31648-58. Epub 2005 Jul 8.
19. Mages B, etal., Front Cell Neurosci. 2018 Jun 18;12:161. doi: 10.3389/fncel.2018.00161. eCollection 2018.
20. McKerracher L, etal., J Neurosci. 1993 Jun;13(6):2617-26.
21. MGD data from the GO Consortium
22. Nakagawa T, etal., J Cell Biol. 1995 Apr;129(2):411-29.
23. Napolitano EW, etal., J Neurosci 1987 Aug;7(8):2590-9.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Paz MM, etal., J Nutr. 1991 Sep;121(9):1349-54. doi: 10.1093/jn/121.9.1349.
26. Pierson CR, etal., J Neuropathol Exp Neurol. 2003 Mar;62(3):260-71.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. Rao MV, etal., J Cell Biol 2003 Dec 8;163(5):1021-31.
29. RGD automated data pipeline
30. RGD automated import pipeline for gene-chemical interactions
31. Sayers NM, etal., Diabetes. 2003 Sep;52(9):2372-80.
32. Schenker M, etal., Brain Res. 2002 Dec 13;957(2):259-70.
33. Schlaepfer WW and Bruce J, J Neurosci Res. 1990 Jan;25(1):39-49.
34. Shen ZX, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2008 Aug;33(8):693-9.
35. Tsuda M, etal., J Neurochem. 2000 Feb;74(2):860-8.
36. Uzasci L, etal., Proteomics Clin Appl. 2016 Feb;10(2):126-35. doi: 10.1002/prca.201400134. Epub 2015 Aug 12.
37. Yu S, etal., Neurochem Res. 2006 Oct;31(10):1197-204. Epub 2006 Oct 17.
38. Zamoner A, etal., Neurotoxicology. 2008 Nov;29(6):1092-9. doi: 10.1016/j.neuro.2008.09.004. Epub 2008 Sep 18.
Additional References at PubMed
PMID:1537832   PMID:8110465   PMID:8344946   PMID:9566972   PMID:10221457   PMID:10461886   PMID:10482234   PMID:10712642   PMID:12477932   PMID:12659941   PMID:12695506   PMID:12839489  
PMID:12971893   PMID:14561875   PMID:14702039   PMID:15248193   PMID:15322118   PMID:15489334   PMID:15713258   PMID:16012337   PMID:16344560   PMID:17114649   PMID:17634366   PMID:19389377  
PMID:20124353   PMID:20826656   PMID:21219885   PMID:21828286   PMID:21884692   PMID:22871113   PMID:23106098   PMID:23861879   PMID:25869803   PMID:29476059   PMID:32357304  


Genomics

Comparative Map Data
Nefm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21542,360,449 - 42,365,753 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)Ensembl
Rnor_6.01544,855,307 - 44,860,604 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1544,855,310 - 44,860,604 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01546,736,787 - 46,741,632 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41547,698,371 - 47,703,350 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11547,714,153 - 47,719,121 (-)NCBI
Celera1542,015,992 - 42,021,311 (-)NCBICelera
Cytogenetic Map15p12NCBI
NEFM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl824,913,758 - 24,919,098 (+)EnsemblGRCh38hg38GRCh38
GRCh38824,913,761 - 24,919,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37824,771,274 - 24,776,606 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36824,827,179 - 24,832,511 (+)NCBINCBI36hg18NCBI36
Build 34824,827,211 - 24,832,511NCBI
Celera823,734,685 - 23,740,017 (+)NCBI
Cytogenetic Map8p21.2NCBI
HuRef823,315,978 - 23,321,310 (+)NCBIHuRef
CHM1_1824,973,582 - 24,978,914 (+)NCBICHM1_1
Nefm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391468,356,994 - 68,362,453 (-)NCBIGRCm39mm39
GRCm39 Ensembl1468,320,039 - 68,362,295 (-)Ensembl
GRCm381468,119,545 - 68,125,004 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1468,082,590 - 68,124,846 (-)EnsemblGRCm38mm10GRCm38
MGSCv371468,737,602 - 68,743,061 (-)NCBIGRCm37mm9NCBIm37
MGSCv361467,073,367 - 67,078,143 (-)NCBImm8
Celera1465,887,284 - 65,892,688 (-)NCBICelera
Cytogenetic Map14D1NCBI
Nefm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540347,920,408 - 47,926,922 (+)NCBIChiLan1.0ChiLan1.0
NEFM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1821,097,646 - 21,103,263 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl821,098,005 - 21,107,468 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0824,181,335 - 24,186,701 (+)NCBIMhudiblu_PPA_v0panPan3
NEFM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12532,493,517 - 32,498,615 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2532,493,675 - 32,498,570 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2533,076,970 - 33,082,075 (-)NCBI
ROS_Cfam_1.02532,692,550 - 32,697,657 (-)NCBI
UMICH_Zoey_3.12532,647,982 - 32,653,102 (-)NCBI
UNSW_CanFamBas_1.02532,497,397 - 32,502,517 (-)NCBI
UU_Cfam_GSD_1.02532,663,548 - 32,668,651 (-)NCBI
Nefm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBI
SpeTri2.0NW_0049367571,662,905 - 1,668,707 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEFM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1148,955,346 - 8,967,211 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21410,117,172 - 10,122,612 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NEFM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1823,039,187 - 23,044,668 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl823,039,282 - 23,044,667 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605219,128,898 - 19,136,687 (-)NCBIVero_WHO_p1.0
Nefm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475820,030,450 - 20,036,105 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC125376P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21542,360,457 - 42,360,679 (+)MAPPERmRatBN7.2
Rnor_6.01544,855,316 - 44,855,537NCBIRnor6.0
Rnor_5.01546,741,402 - 46,741,623UniSTSRnor5.0
RGSC_v3.41547,698,380 - 47,698,601UniSTSRGSC3.4
Celera1542,016,001 - 42,016,222UniSTS
Cytogenetic Map15p12UniSTS
Nfm  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21542,360,807 - 42,361,028 (+)MAPPERmRatBN7.2
Rnor_6.01544,855,666 - 44,855,886NCBIRnor6.0
Rnor_5.01546,741,053 - 46,741,273UniSTSRnor5.0
RGSC_v3.41547,698,730 - 47,698,950UniSTSRGSC3.4
Celera1542,016,351 - 42,016,571UniSTS
Cytogenetic Map15p12UniSTS
RH131013  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21542,367,268 - 42,367,481 (+)MAPPERmRatBN7.2
Rnor_6.01544,862,120 - 44,862,332NCBIRnor6.0
Rnor_5.01546,735,059 - 46,735,271UniSTSRnor5.0
RGSC_v3.41547,704,866 - 47,705,078UniSTSRGSC3.4
Celera1542,022,827 - 42,023,039UniSTS
Cytogenetic Map15p12UniSTS
UniSTS:465485  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21542,360,804 - 42,361,139 (+)MAPPERmRatBN7.2
Rnor_6.01544,855,663 - 44,855,997NCBIRnor6.0
Rnor_5.01546,740,942 - 46,741,276UniSTSRnor5.0
RGSC_v3.41547,698,727 - 47,699,061UniSTSRGSC3.4
Celera1542,016,348 - 42,016,682UniSTS
Cytogenetic Map15p12UniSTS
D8S1927  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01546,741,260 - 46,741,599UniSTSRnor5.0
Cytogenetic Map15p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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:164
Count of miRNA genes:100
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000018637, ENSRNOT00000071069
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 74 23 12
Low 3 6 17 10 10 10 17 1
Below cutoff 31 20 14 6 14 6 6 2 10 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018637   ⟹   ENSRNOP00000018637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)Ensembl
Rnor_6.0 Ensembl1544,855,310 - 44,860,604 (-)Ensembl
RefSeq Acc Id: NM_017029   ⟹   NP_058725
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21542,360,449 - 42,365,753 (-)NCBI
Rnor_6.01544,855,307 - 44,860,604 (-)NCBI
Rnor_5.01546,736,787 - 46,741,632 (+)NCBI
RGSC_v3.41547,698,371 - 47,703,350 (-)RGD
Celera1542,015,992 - 42,021,311 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058725 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41696 (Get FASTA)   NCBI Sequence Viewer  
  CAA78136 (Get FASTA)   NCBI Sequence Viewer  
  EDL85422 (Get FASTA)   NCBI Sequence Viewer  
  P12839 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058725   ⟸   NM_017029
- UniProtKB: P12839 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018637   ⟸   ENSRNOT00000018637
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13699768
Promoter ID:EPDNEW_R10290
Type:single initiation site
Name:Nefm_1
Description:neurofilament medium
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_6.01544,860,602 - 44,860,662EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
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)
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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
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/DuCrl (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
F344/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
F344/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
F344/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
F344/NRrrc (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
F344/Stm (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
FHH/EurMcwi (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
FHH/EurMcwi (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)
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)
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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)
FHL/EurMcwi (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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
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)
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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
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)
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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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3160 AgrOrtholog
Ensembl Genes ENSRNOG00000013916 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018637 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018637 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.1160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/Swiss-Prot
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom_coil1B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Keratin_I UniProtKB/Swiss-Prot
  NF-M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24588 UniProtKB/Swiss-Prot
NCBI Gene 24588 ENTREZGENE
PANTHER PTHR45652:SF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Filament_head UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB NEFM RGD
PhenoGen Nefm PhenoGen
PRINTS TYPE1KERATIN UniProtKB/Swiss-Prot
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V7S2_RAT UniProtKB/TrEMBL
  NFM_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63370 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-04-12 Nefm  neurofilament medium chain  Nefm  neurofilament medium  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-01-17 Nefm  neurofilament medium  Nefm  neurofilament, medium polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Nefm  neurofilament, medium polypeptide  Nef3  neurofilament 3, medium  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Nef3  neurofilament 3, medium  Nefm  Neurofilament protein, middle polypeptide  Symbol and Name updated 629477 APPROVED
2002-06-10 Nefm  Neurofilament protein, middle polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in Schwann cells 727531