Nefh (neurofilament heavy chain) - Rat Genome Database

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Gene: Nefh (neurofilament heavy chain) Rattus norvegicus
Analyze
Symbol: Nefh
Name: neurofilament heavy chain
RGD ID: 3159
Description: Exhibits protein-macromolecule adaptor activity and toxic substance binding activity. A structural constituent of cytoskeleton. Involved in several processes, including cellular response to estradiol stimulus; nervous system development; and ovarian follicle atresia. Localizes to several cellular components, including dendrite; intermediate filament; and perikaryon. Used to study congenital hypothyroidism. Biomarker of glaucoma; hypothyroidism; phenylketonuria; sciatic neuropathy; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease axonal type 2CC; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 1; and monoclonal gammopathy of uncertain significance. Orthologous to human NEFH (neurofilament heavy); PARTICIPATES IN amyotrophic lateral sclerosis pathway; INTERACTS WITH (+)-alpha-tocopherol; (R)-adrenaline; 1,2-dichlorobenzene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 200 kDa neurofilament protein; neurofilament heavy; neurofilament heavy polypeptide; neurofilament triplet H protein; neurofilament, heavy polypeptide; NF-H; Nfh
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21479,830,362 - 79,840,347 (-)NCBI
Rnor_6.0 Ensembl1485,181,572 - 85,191,557 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01485,181,572 - 85,191,557 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01485,859,193 - 85,869,187 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41485,594,789 - 85,604,774 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11485,614,415 - 85,623,919 (-)NCBI
Celera1478,720,827 - 78,730,812 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-tocopherol  (EXP)
(R)-adrenaline  (EXP)
1,2-dichlorobenzene  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,5-hexanedione  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-methyladenine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acetonitrile  (EXP)
aldicarb  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
atropine  (EXP)
benzo[a]pyrene  (ISO)
benzyl benzoate  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
caffeine  (EXP)
carbamazepine  (EXP)
carbaryl  (ISO)
carbon disulfide  (EXP)
carbonyl sulfide  (EXP)
chlorpromazine  (EXP)
chlorpyrifos  (EXP)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (EXP)
cyclosporin A  (EXP,ISO)
cyfluthrin  (ISO)
cypermethrin  (ISO)
daidzein 7-O-beta-D-glucoside  (EXP)
diazepam  (EXP)
diazinon  (EXP,ISO)
dibutyl phthalate  (EXP)
dichlorvos  (EXP)
dieldrin  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dimethyl sulfoxide  (ISO)
diquat  (EXP)
disulfiram  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
ethylene glycol  (EXP)
fenvalerate  (EXP)
fulvestrant  (EXP)
genistein  (EXP)
glufosinate  (EXP)
glycerol  (EXP)
graphite  (EXP)
hydroquinone  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (EXP)
lithium sulfate  (EXP)
malathion  (EXP)
manganese(II) chloride  (ISO)
melatonin  (ISO)
mercury dibromide  (ISO)
methanol  (EXP)
methylmercury chloride  (EXP,ISO)
Mipafox  (ISO)
mitoxantrone  (ISO)
morphine  (EXP)
N,N-dimethylformamide  (EXP)
N-acetyl-L-cysteine  (EXP)
ochratoxin A  (EXP)
octanoic acid  (EXP)
octyl gallate  (EXP)
orphenadrine  (EXP)
paraoxon  (ISO)
paraquat  (EXP)
parathion  (EXP)
PCB138  (EXP,ISO)
pentachlorophenol  (EXP)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium citrate monohydrate  (EXP)
potassium sulfate  (EXP)
progesterone  (ISO)
propan-2-ol  (EXP)
propanal  (ISO)
propranolol  (EXP)
resveratrol  (ISO)
Riluzole  (EXP)
sarin  (EXP)
SB 431542  (ISO)
scopolamine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium hydrogencarbonate  (EXP)
Soman  (EXP)
streptozocin  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tetracycline  (EXP)
thapsigargin  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tributylstannane  (EXP)
Tributyltin oxide  (ISO)
trichlorfon  (ISO)
trichostatin A  (ISO)
trimethyltin  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
tris(2-chloroethyl) phosphate  (EXP)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (EXP)
Tryptanthrine  (ISO)
tunicamycin  (ISO)
urea  (EXP)
valproic acid  (EXP,ISO)
vitamin E  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Al-Chalabi A, etal., Hum Mol Genet 1999 Feb;8(2):157-64.
2. Athlan ES and Mushynski WE, J Biol Chem. 1997 Dec 5;272(49):31073-8.
3. Bordone MP, etal., J Neurochem. 2017 Jul;142(2):323-337. doi: 10.1111/jnc.14070. Epub 2017 Jun 9.
4. Breen KC, etal., FEBS Lett 1988 Dec 5;241(1-2):213-8.
5. Camargo-De-Morais M, etal., Neurochem Res. 1996 May;21(5):595-602.
6. Chen J, etal., J Cell Sci. 2000 Nov;113 Pt 21:3861-9.
7. Chiasson K, etal., J Mol Neurosci. 2006;30(3):297-310.
8. Chin SS and Liem RK, J Neurosci 1990 Nov;10(11):3714-26.
9. Dautigny A, etal., Biochem Biophys Res Commun 1988 Aug 15;154(3):1099-106.
10. DeCaprio AP, etal., Toxicol Appl Pharmacol. 1997 Jul;145(1):211-7.
11. Ehler J, etal., PLoS One. 2019 Jan 24;14(1):e0211184. doi: 10.1371/journal.pone.0211184. eCollection 2019.
12. Elder GA, etal., J Cell Biol 1998 Oct 5;143(1):195-205.
13. Garcia ML, etal., J Cell Biol 2003 Dec 8;163(5):1011-20.
14. Geddes JW, etal., Neurobiol Aging. 1995 Jul-Aug;16(4):651-60.
15. Ghosh S, etal., Neuroreport. 1999 Aug 2;10(11):2361-5.
16. GOA data from the GO Consortium
17. Goldstein ME, etal., Brain Res. 1988 Jun;427(3):287-91.
18. KEGG
19. Klosen P and van den Bosch de Aguilar P, Neurosci Lett. 1992 May 11;139(1):108-13.
20. Kong J and Xu Z, Neurosci Lett. 2000 Mar 3;281(1):72-4.
21. Lees JF, etal., EMBO J 1988 Jul;7(7):1947-55.
22. Li J, etal., Brain Behav. 2019 Aug;9(8):e01354. doi: 10.1002/brb3.1354. Epub 2019 Jul 17.
23. Lieberburg I, etal., Proc Natl Acad Sci U S A 1989 Apr;86(7):2463-7.
24. Liu X, etal., Spine (Phila Pa 1976). 2020 Apr 1;45(7):E364-E372. doi: 10.1097/BRS.0000000000003333.
25. Lochner P, etal., Dis Markers. 2017;2017:5434310. doi: 10.1155/2017/5434310. Epub 2017 Sep 11.
26. Lopez-Picon FR, etal., Hippocampus. 2003;13(7):767-79.
27. Mages B, etal., Front Cell Neurosci. 2018 Jun 18;12:161. doi: 10.3389/fncel.2018.00161. eCollection 2018.
28. Meyer L, etal., Pain. 2011 Jan;152(1):170-81. doi: 10.1016/j.pain.2010.10.015. Epub 2010 Nov 10.
29. MGD data from the GO Consortium
30. Monroy-Gómez J, etal., Viruses. 2018 Mar 6;10(3). pii: v10030112. doi: 10.3390/v10030112.
31. Narayana PA, etal., Psychiatry Res. 2014 Mar 30;221(3):220-30. doi: 10.1016/j.pscychresns.2014.01.005. Epub 2014 Jan 23.
32. NCBI rat LocusLink and RefSeq merged data July 26, 2002
33. OMIM Disease Annotation Pipeline
34. Park MH, etal., Hear Res. 2016 Sep;339:155-60. doi: 10.1016/j.heares.2016.07.010. Epub 2016 Jul 22.
35. Pennypacker K, etal., Exp Neurol. 1991 Jan;111(1):25-35.
36. Petzold A and Plant GT, Mult Scler Int. 2012;2012:217802. doi: 10.1155/2012/217802. Epub 2012 Dec 17.
37. Petzold A, etal., J Neuroimmunol. 2003 May;138(1-2):45-8. doi: 10.1016/s0165-5728(03)00092-4.
38. Petzold A, etal., J Neurol Neurosurg Psychiatry. 2004 Aug;75(8):1178-80. doi: 10.1136/jnnp.2003.017236.
39. Petzold A, etal., Mult Scler. 2004 Jun;10(3):281-3. doi: 10.1191/1352458504ms1021sr.
40. Petzold A, etal., Mult Scler. 2006 Jun;12(3):325-8. doi: 10.1191/135248505ms1277oa.
41. Pipeline to import KEGG annotations from KEGG into RGD
42. Reynolds R, etal., Exp Neurol. 1993 Dec;124(2):357-67.
43. RGD automated data pipeline
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. Sasaki T, etal., J Neurosci Res. 2009 Nov 1;87(14):3088-97. doi: 10.1002/jnr.22148.
47. Sayers NM, etal., Diabetes. 2003 Sep;52(9):2372-80.
48. Schenker M, etal., Brain Res. 2002 Dec 13;957(2):259-70.
49. Schlaepfer WW and Bruce J, J Neurosci Res. 1990 Jan;25(1):39-49.
50. Shen ZX, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2008 Aug;33(8):693-9.
51. Stubbs EB Jr, etal., Acta Neuropathol. 2003 Feb;105(2):109-16. Epub 2002 Sep 13.
52. Takahashi N and Ishizuka B, Endocrinology. 2012 Apr;153(4):1990-8. doi: 10.1210/en.2011-2026. Epub 2012 Feb 7.
53. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
54. Tsuda M, etal., J Neurochem. 2000 Feb;74(2):860-8.
55. Vahidnia A, etal., Chem Biol Interact. 2008 Nov 25;176(2-3):188-95. doi: 10.1016/j.cbi.2008.07.001. Epub 2008 Jul 12.
56. Wang R, etal., Pain. 2014 Mar;155(3):476-84. doi: 10.1016/j.pain.2013.11.007. Epub 2013 Nov 21.
57. Yang J, etal., EMBO J. 2011 Jan 5;30(1):165-80. doi: 10.1038/emboj.2010.286. Epub 2010 Nov 30.
58. Yu S, etal., Neurochem Res. 2006 Oct;31(10):1197-204. Epub 2006 Oct 17.
59. Zamoner A, etal., Neurotoxicology. 2008 Nov;29(6):1092-9. doi: 10.1016/j.neuro.2008.09.004. Epub 2008 Sep 18.
60. Zhang X, etal., Cell Physiol Biochem. 2018;48(3):1088-1098. doi: 10.1159/000491975. Epub 2018 Jul 24.
Additional References at PubMed
PMID:2878828   PMID:7536898   PMID:8110465   PMID:8634266   PMID:9313898   PMID:10221457   PMID:10461886   PMID:12130654   PMID:14561875   PMID:14651853   PMID:15248193   PMID:17114649  
PMID:17626162   PMID:17634366   PMID:18434031   PMID:18498707   PMID:18635547   PMID:18729720   PMID:20176735   PMID:20439489   PMID:20633607   PMID:20805831   PMID:21515322   PMID:21828286  
PMID:22763971   PMID:24327345   PMID:25452168   PMID:25869803   PMID:27040688   PMID:28259758   PMID:29476059  


Genomics

Comparative Map Data
Nefh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21479,830,362 - 79,840,347 (-)NCBI
Rnor_6.0 Ensembl1485,181,572 - 85,191,557 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01485,181,572 - 85,191,557 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01485,859,193 - 85,869,187 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41485,594,789 - 85,604,774 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11485,614,415 - 85,623,919 (-)NCBI
Celera1478,720,827 - 78,730,812 (-)NCBICelera
Cytogenetic Map14q21NCBI
NEFH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2229,480,218 - 29,491,390 (+)EnsemblGRCh38hg38GRCh38
GRCh382229,480,218 - 29,491,390 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372229,876,207 - 29,887,379 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362228,206,219 - 28,217,279 (+)NCBINCBI36hg18NCBI36
Build 342228,200,772 - 28,211,829NCBI
Celera2213,676,024 - 13,687,118 (+)NCBI
Cytogenetic Map22q12.2NCBI
HuRef2212,839,995 - 12,851,105 (+)NCBIHuRef
CHM1_12229,835,584 - 29,846,662 (+)NCBICHM1_1
Nefh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39114,888,754 - 4,898,064 (-)NCBIGRCm39mm39
GRCm39 Ensembl114,888,754 - 4,898,064 (-)Ensembl
GRCm38114,938,754 - 4,948,064 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl114,938,754 - 4,948,064 (-)EnsemblGRCm38mm10GRCm38
MGSCv37114,838,757 - 4,848,067 (-)NCBIGRCm37mm9NCBIm37
MGSCv36114,838,761 - 4,851,268 (-)NCBImm8
Celera115,436,254 - 5,444,974 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.12NCBI
Nefh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554553,735,410 - 3,744,107 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554553,735,330 - 3,744,714 (+)NCBIChiLan1.0ChiLan1.0
NEFH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12228,331,778 - 28,341,874 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02210,525,738 - 10,536,788 (+)NCBIMhudiblu_PPA_v0panPan3
NEFH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12622,726,523 - 22,735,129 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2622,726,526 - 22,735,125 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2622,598,106 - 22,606,671 (+)NCBI
ROS_Cfam_1.02623,100,617 - 23,109,200 (+)NCBI
UMICH_Zoey_3.12622,810,029 - 22,818,553 (+)NCBI
UNSW_CanFamBas_1.02623,073,295 - 23,081,873 (+)NCBI
UU_Cfam_GSD_1.02623,138,184 - 23,146,781 (+)NCBI
Nefh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118112,417,611 - 112,427,289 (-)NCBI
SpeTri2.0NW_0049366573,443,406 - 3,453,096 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEFH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1446,559,860 - 46,569,910 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11446,559,698 - 46,568,686 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21449,572,997 - 49,583,859 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NEFH
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11912,357,982 - 12,375,449 (+)NCBI
Vero_WHO_p1.0NW_023666045113,778,644 - 113,789,304 (-)NCBI
Nefh
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247475,806,576 - 5,816,158 (+)NCBI

Position Markers
RH127468  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21479,830,405 - 79,830,599 (+)MAPPER
Rnor_6.01485,181,616 - 85,181,809NCBIRnor6.0
Rnor_5.01485,859,237 - 85,859,430UniSTSRnor5.0
RGSC_v3.41485,594,833 - 85,595,026UniSTSRGSC3.4
Celera1478,720,871 - 78,721,064UniSTS
RH 3.4 Map14554.1UniSTS
Cytogenetic Map14q21UniSTS
RH94567  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21479,830,370 - 79,830,547 (+)MAPPER
Rnor_6.01485,181,581 - 85,181,757NCBIRnor6.0
Rnor_5.01485,859,202 - 85,859,378UniSTSRnor5.0
RGSC_v3.41485,594,798 - 85,594,974UniSTSRGSC3.4
Celera1478,720,836 - 78,721,012UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:60
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000011604
Prediction methods: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 4 38
Low 2 33 21 9 19 9 4 5 34 11 31 9 4
Below cutoff 1 9 12 12 12 4 5 2 24 10 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011604   ⟹   ENSRNOP00000011604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1485,181,572 - 85,191,557 (-)Ensembl
RefSeq Acc Id: NM_012607   ⟹   NP_036739
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21479,830,362 - 79,840,347 (-)NCBI
Rnor_6.01485,181,572 - 85,191,557 (-)NCBI
Rnor_5.01485,859,193 - 85,869,187 (-)NCBI
RGSC_v3.41485,594,789 - 85,604,774 (-)RGD
Celera1478,720,827 - 78,730,812 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036739   ⟸   NM_012607
- UniProtKB: F1LRZ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011604   ⟸   ENSRNOT00000011604
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13699451
Promoter ID:EPDNEW_R9975
Type:single initiation site
Name:Nefh_1
Description:neurofilament heavy
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_6.01485,191,571 - 85,191,631EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 85183148 85183149 C G snv CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3159 AgrOrtholog
Ensembl Genes ENSRNOG00000008716 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011604 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011604 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.1160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DUF1388 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_conserved UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom_coil1B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NF-H UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24587 UniProtKB/TrEMBL
NCBI Gene 24587 ENTREZGENE
PANTHER PTHR23214 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF1388 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nefh PhenoGen
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204032
UniProt F1LRZ7 ENTREZGENE, UniProtKB/TrEMBL
  NFH_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35482 UniProtKB/Swiss-Prot
  Q540Z7 UniProtKB/Swiss-Prot
  Q63368 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-04-12 Nefh  neurofilament heavy chain  Nefh  neurofilament heavy  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-01-17 Nefh  neurofilament heavy  Nefh  neurofilament, heavy polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Nefh  Neurofilament, heavy polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains 51 Lys-Ser-Pro repeat triplets, which are possible sites of phosphorylation 728968