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 (-)-anisomycin; 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: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81546,535,857 - 46,541,161 (-)NCBIGRCr8
mRatBN7.21542,360,449 - 42,365,753 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1544,225,130 - 44,230,434 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01545,375,350 - 45,380,655 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01543,820,704 - 43,826,010 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
(-)-anisomycin  (EXP)
(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)
4,4'-sulfonyldiphenol  (EXP)
5-iodotubercidin  (ISO)
6-Cyano-7-nitroquinoxaline-2,3-dione  (EXP)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acrylamide  (EXP)
actinomycin D  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-amanitin  (EXP)
ammonium chloride  (EXP)
amphotericin B  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bucladesine  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
calyculin a  (EXP)
camptothecin  (ISO)
cannabidiol  (ISO)
carbon disulfide  (EXP)
chlorpyrifos  (EXP,ISO)
cisplatin  (EXP,ISO)
cocaine  (ISO)
cordycepin  (EXP)
Cuprizon  (EXP)
curcumin  (EXP)
cycloheximide  (EXP)
dantrolene  (EXP)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dieldrin  (EXP)
dioxygen  (ISO)
dizocilpine maleate  (EXP)
dorsomorphin  (ISO)
emetine  (EXP)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
flavonoids  (EXP)
fonofos  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
iron dichloride  (ISO)
ivermectin  (ISO)
KN-93  (EXP)
lead diacetate  (EXP,ISO)
lidocaine  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
Mesaconitine  (EXP)
methamphetamine  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
Muraglitazar  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (EXP)
nicotine  (ISO)
nifedipine  (EXP)
Nutlin-3  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
PCB138  (EXP)
pentanal  (ISO)
phenylmercury acetate  (ISO)
progesterone  (ISO)
propanal  (ISO)
puromycin  (EXP)
quercetin  (ISO)
rac-lactic acid  (ISO)
Riluzole  (EXP)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
staurosporine  (EXP)
terbufos  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
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)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Electrical stimulation accelerates and enhances expression of regeneration-associated genes in regenerating rat femoral motoneurons. Al-Majed AA, etal., Cell Mol Neurobiol. 2004 Jun;24(3):379-402.
2. An NGF-responsive element targets myo-inositol monophosphatase-1 mRNA to sympathetic neuron axons. Andreassi C, etal., Nat Neurosci. 2010 Mar;13(3):291-301. doi: 10.1038/nn.2486. Epub 2010 Jan 31.
3. Heterodimeric associations between neuronal intermediate filament proteins. Athlan ES and Mushynski WE, J Biol Chem. 1997 Dec 5;272(49):31073-8.
4. Effects of brain ischemia on intermediate filaments of rat hippocampus. Camargo-De-Morais M, etal., Neurochem Res. 1996 May;21(5):595-602.
5. Oxidative stress and 17-alpha- and 17-beta-estradiol modulate neurofilaments differently. Chiasson K, etal., J Mol Neurosci. 2006;30(3):297-310.
6. Analysis of the roles of the head domains of type IV rat neuronal intermediate filament proteins in filament assembly using domain-swapped chimeric proteins. Ching GY and Liem RK, J Cell Sci. 1999 Jul;112 ( Pt 13):2233-40.
7. [Heart innervation in rats (an immunohistochemical study)]. Chumasov EI, etal., Morfologiia. 2009;135(2):33-7.
8. Regioselective binding of 2,5-hexanedione to high-molecular-weight rat neurofilament proteins in vitro. DeCaprio AP, etal., Toxicol Appl Pharmacol. 1997 Jul;145(1):211-7.
9. Regulation between O-GlcNAcylation and phosphorylation of neurofilament-M and their dysregulation in Alzheimer disease. Deng Y, etal., FASEB J. 2008 Jan;22(1):138-45. Epub 2007 Aug 8.
10. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Perikaryal accumulation and proteolysis of neurofilament proteins in the post-mortem rat brain. Geddes JW, etal., Neurobiol Aging. 1995 Jul-Aug;16(4):651-60.
12. Regulation of neurofilament gene expression by thyroid hormone in the developing rat brain. Ghosh S, etal., Neuroreport. 1999 Aug 2;10(11):2361-5.
13. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
14. mRNA levels of all three neurofilament proteins decline following nerve transection. Goldstein ME, etal., Brain Res. 1988 Jun;427(3):287-91.
15. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
16. Schwann cells of the myelin-forming phenotype express neurofilament protein NF-M. Kelly BM, etal., J Cell Biol 1992 Jul;118(2):397-410.
17. Neurofilament-M interacts with the D1 dopamine receptor to regulate cell surface expression and desensitization. Kim OJ, etal., J Neurosci. 2002 Jul 15;22(14):5920-30.
18. Differential expression and localization of the phosphorylated and nonphosphorylated neurofilaments during the early postnatal development of rat hippocampus. Lopez-Picon FR, etal., Hippocampus. 2003;13(7):767-79.
19. O-glycosylation of the tail domain of neurofilament protein M in human neurons and in spinal cord tissue of a rat model of amyotrophic lateral sclerosis (ALS). Ludemann N, etal., J Biol Chem. 2005 Sep 9;280(36):31648-58. Epub 2005 Jul 8.
20. Impaired Neurofilament Integrity and Neuronal Morphology in Different Models of Focal Cerebral Ischemia and Human Stroke Tissue. Mages B, etal., Front Cell Neurosci. 2018 Jun 18;12:161. doi: 10.3389/fncel.2018.00161. eCollection 2018.
21. Temporal changes in beta-tubulin and neurofilament mRNA levels after transection of adult rat retinal ganglion cell axons in the optic nerve. McKerracher L, etal., J Neurosci. 1993 Jun;13(6):2617-26.
22. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
23. Two distinct functions of the carboxyl-terminal tail domain of NF-M upon neurofilament assembly: cross-bridge formation and longitudinal elongation of filaments. Nakagawa T, etal., J Cell Biol. 1995 Apr;129(2):411-29.
24. Complete amino acid sequence and in vitro expression of rat NF-M, the middle molecular weight neurofilament protein. Napolitano EW, etal., J Neurosci 1987 Aug;7(8):2590-9.
25. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Malnutrition induces an increase in intermediate filament protein content of rat cerebral cortex. Paz MM, etal., J Nutr. 1991 Sep;121(9):1349-54. doi: 10.1093/jn/121.9.1349.
27. Insulin deficiency rather than hyperglycemia accounts for impaired neurotrophic responses and nerve fiber regeneration in type 1 diabetic neuropathy. Pierson CR, etal., J Neuropathol Exp Neurol. 2003 Mar;62(3):260-71.
28. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
29. The neurofilament middle molecular mass subunit carboxyl-terminal tail domains is essential for the radial growth and cytoskeletal architecture of axons but not for regulating neurofilament transport rate. Rao MV, etal., J Cell Biol 2003 Dec 8;163(5):1021-31.
30. GOA pipeline RGD automated data pipeline
31. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
32. Neurotrophin-3 prevents the proximal accumulation of neurofilament proteins in sensory neurons of streptozocin-induced diabetic rats. Sayers NM, etal., Diabetes. 2003 Sep;52(9):2372-80.
33. Thyroid hormones stimulate expression and modification of cytoskeletal protein during rat sciatic nerve regeneration. Schenker M, etal., Brain Res. 2002 Dec 13;957(2):259-70.
34. Simultaneous up-regulation of neurofilament proteins during the postnatal development of the rat nervous system. Schlaepfer WW and Bruce J, J Neurosci Res. 1990 Jan;25(1):39-49.
35. [Tetramethylpyrazine accelerated spinal cord repair through regulation of caspase-3 and neurofilament protein expression: an acute spinal cord injury model in rats]. Shen ZX, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2008 Aug;33(8):693-9.
36. Selective solubilization of high-molecular-mass neurofilament subunit during nerve regeneration. Tsuda M, etal., J Neurochem. 2000 Feb;74(2):860-8.
37. Mass spectrometric phosphoproteome analysis of HIV-infected brain reveals novel phosphorylation sites and differential phosphorylation patterns. Uzasci L, etal., Proteomics Clin Appl. 2016 Feb;10(2):126-35. doi: 10.1002/prca.201400134. Epub 2015 Aug 12.
38. Acrylamide alters cytoskeletal protein level in rat sciatic nerves. Yu S, etal., Neurochem Res. 2006 Oct;31(10):1197-204. Epub 2006 Oct 17.
39. Congenital hypothyroidism is associated with intermediate filament misregulation, glutamate transporters down-regulation and MAPK activation in developing rat brain. 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
GRCr81546,535,857 - 46,541,161 (-)NCBIGRCr8
mRatBN7.21542,360,449 - 42,365,753 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1542,360,454 - 42,365,755 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1544,225,130 - 44,230,434 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01545,375,350 - 45,380,655 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01543,820,704 - 43,826,010 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38824,913,761 - 24,919,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl824,913,758 - 24,919,098 (+)EnsemblGRCh38hg38GRCh38
GRCh37824,771,274 - 24,776,606 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36824,827,179 - 24,832,511 (+)NCBINCBI36Build 36hg18NCBI36
Build 34824,827,211 - 24,832,511NCBI
Celera823,734,685 - 23,740,017 (+)NCBICelera
Cytogenetic Map8p21.2NCBI
HuRef823,315,978 - 23,321,310 (+)NCBIHuRef
CHM1_1824,973,582 - 24,978,914 (+)NCBICHM1_1
T2T-CHM13v2.0825,188,914 - 25,194,246 (+)NCBIT2T-CHM13v2.0
Nefm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391468,356,994 - 68,362,453 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1468,320,039 - 68,362,295 (-)EnsemblGRCm39 Ensembl
GRCm381468,119,545 - 68,125,004 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1468,082,590 - 68,124,846 (-)EnsemblGRCm38mm10GRCm38
MGSCv371468,737,602 - 68,743,061 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361467,073,367 - 67,078,143 (-)NCBIMGSCv36mm8
Celera1465,887,284 - 65,892,688 (-)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1435.46NCBI
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
NHGRI_mPanPan1-v2743,421,006 - 43,426,459 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1819,155,199 - 19,160,653 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0824,181,335 - 24,186,701 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1821,097,646 - 21,103,263 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl821,098,005 - 21,107,468 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02532,692,550 - 32,697,657 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2532,692,550 - 32,697,640 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12532,647,982 - 32,653,102 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02532,497,397 - 32,502,517 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02532,663,548 - 32,668,651 (-)NCBIUU_Cfam_GSD_1.0
Nefm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494310,410,240 - 10,415,458 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367571,663,399 - 1,668,075 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl823,039,282 - 23,044,667 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605219,128,898 - 19,136,687 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nefm
13 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
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
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
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
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

Markers in Region
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 6 41 113 66 61 37 9 37 6 166 69 93 45 58 24

Sequence


Ensembl Acc Id: ENSRNOT00000018637   ⟹   ENSRNOP00000018637
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: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81546,535,857 - 46,541,161 (-)NCBI
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  
Ensembl Protein ENSRNOP00000018637.7
GenBank Protein P12839 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_058725   ⟸   NM_017029
- Sequence:
Ensembl Acc Id: ENSRNOP00000018637   ⟸   ENSRNOT00000018637
Protein Domains
IF rod

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P12839-F1-model_v2 AlphaFold P12839 1-846 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3160 AgrOrtholog
BioCyc Gene G2FUF-13294 BioCyc
Ensembl Genes ENSRNOG00000013916 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018637.7 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Single helix bin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vasodilator-stimulated phosphoprotein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermediate_filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Keratin_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24588 UniProtKB/Swiss-Prot
NCBI Gene 24588 ENTREZGENE
PANTHER GLIAL FIBRILLARY ACIDIC PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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, UniProtKB/TrEMBL
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013916 RatGTEx
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6K6R2_RAT UniProtKB/TrEMBL
  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