Rtn4 (reticulon 4) - Rat Genome Database

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Gene: Rtn4 (reticulon 4) Rattus norvegicus
Analyze
Symbol: Rtn4
Name: reticulon 4
RGD ID: 620989
Description: Predicted to enable several functions, including cadherin binding activity; protein homodimerization activity; and ubiquitin protein ligase binding activity. Involved in several processes, including negative regulation of neuron projection development; nervous system development; and positive regulation of dopamine secretion. Located in endoplasmic reticulum membrane and neuronal cell body. Part of protein-containing complex. Is active in glutamatergic synapse and postsynaptic density membrane. Biomarker of visual epilepsy. Orthologous to human RTN4 (reticulon 4); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: foocen; glut4 vesicle 20 kDa protein; GLUT4 vesicle 20kDa protein; MGC116054; neurite outgrowth inhibitor; NI-220/250; NI-250; Nogo; Nogo-A; r; rat N; rat NogoA; reticulon-4; Vp20
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Rtn4Tn(sb-T2/Bart3)2.316Mcwi  
Genetic Models: F344-Rtn4Tn(sb-T2/Bart3)2.316Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814107,651,001 - 107,698,610 (+)NCBIGRCr8
mRatBN7.214103,450,074 - 103,497,687 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14107,788,449 - 107,835,806 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014109,022,006 - 109,069,463 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014105,494,428 - 105,541,884 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014114,126,931 - 114,174,459 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14114,126,943 - 114,174,458 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014113,792,257 - 113,839,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,725,089 - 110,772,578 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114110,751,435 - 110,798,925 (+)NCBI
Celera14102,325,054 - 102,372,199 (+)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
caffeine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
dieldrin  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP)
genistein  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
haloperidol  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
manganese(II) chloride  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nickel dichloride  (EXP)
nickel subsulfide  (EXP)
nitrofen  (EXP)
olanzapine  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phencyclidine  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
propiconazole  (ISO)
pyrogallol  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (EXP,ISO)
testosterone  (ISO)
testosterone undecanoate  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axonal fasciculation  (IDA,IEA,ISO)
blastocyst formation  (IEA,ISO)
brain development  (IBA,IEA)
cardiac epithelial to mesenchymal transition  (IEA,ISO)
cell adhesion involved in sprouting angiogenesis  (ISO,ISS)
cell migration involved in vasculogenesis  (ISO,ISS)
cellular response to hypoxia  (ISO,ISS)
central nervous system vasculogenesis  (ISO,ISS)
cerebral cortex radial glia-guided migration  (IEA,ISO,ISS)
endoplasmic reticulum organization  (ISO)
endoplasmic reticulum tubular network formation  (IBA,IEA,ISO,ISS)
endoplasmic reticulum tubular network membrane organization  (IEA,ISO,ISS)
endoplasmic reticulum tubular network organization  (ISO,ISS)
intracellular sphingolipid homeostasis  (IEA,ISO)
leukocyte migration involved in inflammatory response  (ISO,ISS)
modulation of chemical synaptic transmission  (IEA,ISO)
negative regulation of amyloid-beta formation  (IEA,ISO,ISS)
negative regulation of axon extension  (IDA,IEA,ISO,ISS)
negative regulation of axonogenesis  (IDA,IMP)
negative regulation of cell growth  (ISO)
negative regulation of neuron differentiation  (IDA)
negative regulation of neuron projection development  (IDA)
negative regulation of neuron projection regeneration  (IMP)
negative regulation of vasculogenesis  (ISO,ISS)
nervous system development  (ISO)
neuron differentiation  (IBA,IEA)
nuclear pore complex assembly  (IEA,ISO,ISS)
olfactory nerve development  (IEP)
oligodendrocyte differentiation  (IEP)
positive regulation of angiogenesis  (ISO,ISS)
positive regulation of artery morphogenesis  (ISO,ISS)
positive regulation of dopamine secretion  (IMP)
positive regulation of epithelial cell migration  (IEA,ISO)
positive regulation of ERBB3 signaling pathway  (IEA,ISO)
positive regulation of glial cell differentiation  (IDA)
positive regulation of hepatocyte proliferation  (ISO,ISS)
positive regulation of macrophage cytokine production  (ISO,ISS)
positive regulation of macrophage migration  (ISO,ISS)
positive regulation of mammary gland epithelial cell proliferation  (IEA,ISO)
positive regulation of neutrophil migration  (ISO,ISS)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (IEA,ISO)
positive regulation of protein localization to endoplasmic reticulum  (IEA,ISO)
positive regulation of Rac protein signal transduction  (ISO,ISS)
positive regulation of toll-like receptor 9 signaling pathway  (IEA,ISO,ISS)
protein localization to lysosome  (IEA,ISO,ISS)
protein stabilization  (IEA,ISO)
regulation of branching morphogenesis of a nerve  (IDA,IEA,ISO)
regulation of cell migration  (ISO)
regulation of nervous system development  (ISO)
regulation of postsynapse assembly  (ISO)
response to activity  (IEP)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Long-lasting sprouting and gene expression changes induced by the monoclonal antibody IN-1 in the adult spinal cord. Bareyre FM, etal., J Neurosci 2002 Aug 15;22(16):7097-110.
2. Nogo-A is a myelin-associated neurite outgrowth inhibitor and an antigen for monoclonal antibody IN-1. Chen MS, etal., Nature 2000 Jan 27;403(6768):434-9.
3. Exercise normalizes levels of MAG and Nogo-A growth inhibitors after brain trauma. Chytrova G, etal., Eur J Neurosci. 2008 Jan;27(1):1-11. Epub 2007 Dec 15.
4. Neutralization of the membrane protein Nogo-A enhances growth and reactive sprouting in established organotypic hippocampal slice cultures. Craveiro LM, etal., Eur J Neurosci. 2008 Nov;28(9):1808-24.
5. Nogo-A, -B, and -C are found on the cell surface and interact together in many different cell types. Dodd DA, etal., J Biol Chem. 2005 Apr 1;280(13):12494-502. Epub 2005 Jan 7.
6. Effect of different regions of Nogo-A on the differentiation of neural progenitors. Gao Y, etal., Neurosci Lett. 2009 Jul 24;458(3):132-5. Epub 2009 Apr 18.
7. 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.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Identification of the Nogo inhibitor of axon regeneration as a Reticulon protein. GrandPre T, etal., Nature. 2000 Jan 27;403(6768):439-44.
10. Promotion of axon regeneration by myelin-associated glycoprotein and Nogo through divergent signals downstream of Gi/G. Hasegawa Y, etal., J Neurosci. 2004 Jul 28;24(30):6826-32.
11. A class of dynamin-like GTPases involved in the generation of the tubular ER network. Hu J, etal., Cell. 2009 Aug 7;138(3):549-61. doi: 10.1016/j.cell.2009.05.025.
12. Patterns of Nogo-A, NgR, and RhoA expression in the brain tissues of rats with focal cerebral infarction. Jiang W, etal., Transl Res. 2009 Jul;154(1):40-8. Epub 2009 May 19.
13. The sphingolipid receptor S1PR2 is a receptor for Nogo-a repressing synaptic plasticity. Kempf A, etal., PLoS Biol. 2014 Jan;12(1):e1001763. doi: 10.1371/journal.pbio.1001763. Epub 2014 Jan 14.
14. Nogo-A couples with Apg-1 through interaction and co-ordinate expression under hypoxic and oxidative stress. Kern F, etal., Biochem J. 2013 Oct 15;455(2):217-27. doi: 10.1042/BJ20130579.
15. Local Nogo-66 administration reduces neuropathic pain after sciatic nerve transection in rat. Li L, etal., Neurosci Lett. 2007 Sep 13;424(3):145-8. Epub 2007 Aug 1.
16. Nogo-A inhibits necdin-accelerated neurite outgrowth by retaining necdin in the cytoplasm. Liu X, etal., Mol Cell Neurosci. 2009 May;41(1):51-61. Epub 2009 Feb 6.
17. Electron microscopic localization of Nogo-A at the postsynaptic active zone of the rat. Liu YY, etal., Neurosci Lett. 2003 Aug 7;346(3):153-6. doi: 10.1016/s0304-3940(03)00508-1.
18. Oligodendrocyte precursor cells differentially expressing Nogo-A but not MAG are more permissive to neurite outgrowth than mature oligodendrocytes. Ma Z, etal., Exp Neurol. 2009 May;217(1):184-96. Epub 2009 Feb 21.
19. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
20. Cloning and characterization of a 22 kDa protein from rat adipocytes: a new member of the reticulon family. Morris NJ, etal., Biochim Biophys Acta 1999 May 6;1450(1):68-76.
21. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Nogo-A and myelin-associated glycoprotein mediate neurite growth inhibition by antagonistic regulation of RhoA and Rac1. Niederost B, etal., J Neurosci 2002 Dec 1;22(23):10368-76.
23. A reticular rhapsody: phylogenic evolution and nomenclature of the RTN/Nogo gene family. Oertle T, etal., FASEB J 2003 Jul;17(10):1238-47.
24. Nogo-A inhibits neurite outgrowth and cell spreading with three discrete regions. Oertle T, etal., J Neurosci 2003 Jul 2;23(13):5393-406.
25. Neuronal Nogo-A regulates neurite fasciculation, branching and extension in the developing nervous system. Petrinovic MM, etal., Development. 2010 Aug 1;137(15):2539-50. doi: 10.1242/dev.048371. Epub 2010 Jun 23.
26. Nogo-A expressed in Schwann cells impairs axonal regeneration after peripheral nerve injury. Pot C, etal., J Cell Biol 2002 Oct 14;159(1):29-35.
27. Serum and cerebrospinal fluid antibodies to Nogo-A in patients with multiple sclerosis and acute neurological disorders. Reindl M, etal., J Neuroimmunol. 2003 Dec;145(1-2):139-47.
28. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
29. Neuronal expression of Nogo-A mRNA and protein during neurite outgrowth in the developing rat olfactory system. Richard M, etal., Eur J Neurosci. 2005 Nov;22(9):2145-58.
30. Phosphorylation-regulated cleavage of the reticulon protein Nogo-B by caspase-7 at a noncanonical recognition site. Schweigreiter R, etal., Proteomics. 2007 Dec;7(24):4457-67.
31. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
32. A novel protein, RTN-XS, interacts with both Bcl-XL and Bcl-2 on endoplasmic reticulum and reduces their anti-apoptotic activity. Tagami S, etal., Oncogene. 2000 Nov 23;19(50):5736-46.
33. Hippocampal Nogo-A and neo-Timm's staining in amygdala kindling rats. Takeda Y, etal., Neurol Res. 2007 Mar;29(2):199-203.
34. Nogo-A expression in mature oligodendrocytes of rat spinal cord in association with specific molecules. Taketomi M, etal., Neurosci Lett 2002 Oct 25;332(1):37-40.
35. Selective decline of Nogo mRNA in the aging brain. Trifunovski A, etal., Neuroreport. 2006 Jun 26;17(9):913-6.
36. The Nogo-66 receptor homolog NgR2 is a sialic acid-dependent receptor selective for myelin-associated glycoprotein. Venkatesh K, etal., J Neurosci. 2005 Jan 26;25(4):808-22.
37. A class of membrane proteins shaping the tubular endoplasmic reticulum. Voeltz GK, etal., Cell. 2006 Feb 10;124(3):573-86.
38. Effect of Nogo-A gene inhibition on dopamine release in PC12 cells. Xiong NX, etal., Neuro Endocrinol Lett. 2008 Dec;29(6):884-8.
39. [Expression and localization of Nogo-A mRNA in rat nerve tissue] Ye J, etal., Zhonghua Yi Xue Za Zhi 2002 Apr 10;82(7):498-500.
40. Neutralization of Nogo-A enhances synaptic plasticity in the rodent motor cortex and improves motor learning in vivo. Zemmar A, etal., J Neurosci. 2014 Jun 25;34(26):8685-98. doi: 10.1523/JNEUROSCI.3817-13.2014.
Additional References at PubMed
PMID:12037567   PMID:12225863   PMID:12577319   PMID:12718855   PMID:12837628   PMID:14592966   PMID:14697671   PMID:15034570   PMID:15121177   PMID:15306002   PMID:15661372   PMID:16260091  
PMID:16321384   PMID:16641100   PMID:16697217   PMID:16791210   PMID:17022955   PMID:17114649   PMID:17382469   PMID:17428512   PMID:17630211   PMID:17963852   PMID:18095590   PMID:18467652  
PMID:18779370   PMID:19125329   PMID:19156209   PMID:19805174   PMID:19901030   PMID:20083601   PMID:20093372   PMID:20374087   PMID:20463223   PMID:20473744   PMID:20844138   PMID:21183689  
PMID:21418929   PMID:21420413   PMID:21624429   PMID:21636572   PMID:21643729   PMID:21700703   PMID:21862940   PMID:21985178   PMID:22261619   PMID:22658674   PMID:23299899   PMID:23376485  
PMID:23454728   PMID:23576723   PMID:23625008   PMID:24129566   PMID:24211256   PMID:24262037   PMID:24355710   PMID:24533107   PMID:24567055   PMID:25331889   PMID:25468996   PMID:25554426  
PMID:25612671   PMID:25612921   PMID:25917084   PMID:26301690   PMID:26348872   PMID:26472924   PMID:26583134   PMID:26648565   PMID:26718118   PMID:26728376   PMID:26748478   PMID:26906412  
PMID:26987715   PMID:27035338   PMID:27056081   PMID:27353365   PMID:27619977   PMID:27763637   PMID:27786289   PMID:27869233   PMID:29325876   PMID:29476059   PMID:30024789   PMID:31006538  
PMID:31948754   PMID:32446356   PMID:32589081   PMID:33450132   PMID:33495810   PMID:33555537   PMID:34638704   PMID:35263212   PMID:35352799   PMID:37685993  


Genomics

Comparative Map Data
Rtn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814107,651,001 - 107,698,610 (+)NCBIGRCr8
mRatBN7.214103,450,074 - 103,497,687 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14107,788,449 - 107,835,806 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014109,022,006 - 109,069,463 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014105,494,428 - 105,541,884 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014114,126,931 - 114,174,459 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14114,126,943 - 114,174,458 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014113,792,257 - 113,839,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,725,089 - 110,772,578 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114110,751,435 - 110,798,925 (+)NCBI
Celera14102,325,054 - 102,372,199 (+)NCBICelera
Cytogenetic Map14q22NCBI
RTN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38254,972,189 - 55,137,831 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl254,972,187 - 55,112,621 (-)EnsemblGRCh38hg38GRCh38
GRCh37255,199,325 - 55,364,967 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,052,829 - 55,131,238 (-)NCBINCBI36Build 36hg18NCBI36
Build 34255,110,979 - 55,187,977NCBI
Celera255,039,812 - 55,118,248 (-)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef254,934,258 - 55,012,692 (-)NCBIHuRef
CHM1_1255,129,380 - 55,207,793 (-)NCBICHM1_1
T2T-CHM13v2.0254,969,379 - 55,135,031 (-)NCBIT2T-CHM13v2.0
Rtn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391129,642,898 - 29,694,414 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1129,642,947 - 29,694,331 (+)EnsemblGRCm39 Ensembl
GRCm381129,692,898 - 29,744,414 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1129,692,947 - 29,744,331 (+)EnsemblGRCm38mm10GRCm38
MGSCv371129,592,898 - 29,644,414 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361129,592,947 - 29,642,916 (+)NCBIMGSCv36mm8
Celera1132,055,366 - 32,110,540 (+)NCBICelera
Cytogenetic Map11A3.3NCBI
cM Map1116.79NCBI
Rtn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542428,061,346 - 28,125,838 (+)NCBIChiLan1.0ChiLan1.0
RTN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21271,272,917 - 71,354,172 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A71,277,237 - 71,358,124 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A55,129,272 - 55,207,031 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A56,271,214 - 56,348,117 (-)NCBIpanpan1.1PanPan1.1panPan2
RTN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11055,884,452 - 55,954,476 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1055,885,125 - 55,936,574 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1055,839,508 - 55,910,109 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01056,886,721 - 56,957,194 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1056,886,724 - 56,957,662 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11056,588,329 - 56,658,758 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01056,866,767 - 56,937,240 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01057,157,709 - 57,228,145 (-)NCBIUU_Cfam_GSD_1.0
Rtn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629227,097,303 - 27,163,878 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364911,407,414 - 1,474,360 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364911,407,414 - 1,474,031 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl386,180,022 - 86,252,126 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1386,180,022 - 86,252,126 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2391,013,117 - 91,202,777 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTN4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11451,876,697 - 51,955,788 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604559,766,791 - 59,846,774 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtn4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248336,514,409 - 6,584,061 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtn4
185 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1024
Count of miRNA genes:224
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000006443, ENSRNOT00000006957, ENSRNOT00000041638, ENSRNOT00000042965
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
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat

Markers in Region
RH143221  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,473,541 - 103,473,644 (+)MAPPERmRatBN7.2
Rnor_6.014114,150,316 - 114,150,418NCBIRnor6.0
Rnor_5.014113,815,793 - 113,815,895UniSTSRnor5.0
RGSC_v3.414110,748,439 - 110,748,541UniSTSRGSC3.4
Celera14102,348,085 - 102,348,187UniSTS
Cytogenetic Map14q22UniSTS
RH140746  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,464,183 - 103,464,358 (+)MAPPERmRatBN7.2
Rnor_6.014114,140,960 - 114,141,134NCBIRnor6.0
Rnor_5.014113,806,437 - 113,806,611UniSTSRnor5.0
RGSC_v3.414110,739,083 - 110,739,257UniSTSRGSC3.4
Celera14102,338,811 - 102,338,985UniSTS
Cytogenetic Map14q22UniSTS


Genetic Models
This gene Rtn4 is modified in the following models/strains:
F344-Rtn4Tn(sb-T2/Bart3)2.316Mcwi    


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 3 43 47 31 19 31 8 11 74 35 41 11 8
Low 10 10 10
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF051335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF132045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF132046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ242961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ242962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ242963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY164740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY164741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC070879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CQ829507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS061814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HI649240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006443   ⟹   ENSRNOP00000006443
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)Ensembl
Rnor_6.0 Ensembl14114,126,966 - 114,174,458 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000006957   ⟹   ENSRNOP00000006957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)Ensembl
Rnor_6.0 Ensembl14114,127,025 - 114,173,670 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000041638   ⟹   ENSRNOP00000042870
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)Ensembl
Rnor_6.0 Ensembl14114,126,943 - 114,174,458 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042965   ⟹   ENSRNOP00000040760
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,475,637 - 103,497,617 (+)Ensembl
Rnor_6.0 Ensembl14114,152,472 - 114,173,643 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103934   ⟹   ENSRNOP00000094900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,450,186 - 103,496,470 (+)Ensembl
RefSeq Acc Id: NM_031831   ⟹   NP_114019
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,651,117 - 107,698,606 (+)NCBI
mRatBN7.214103,450,190 - 103,497,683 (+)NCBI
Rnor_6.014114,126,966 - 114,174,455 (+)NCBI
Rnor_5.014113,792,257 - 113,839,936 (+)NCBI
RGSC_v3.414110,725,089 - 110,772,578 (+)RGD
Celera14102,325,054 - 102,372,199 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251608   ⟹   XP_006251670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,651,001 - 107,698,610 (+)NCBI
mRatBN7.214103,450,074 - 103,497,687 (+)NCBI
Rnor_6.014114,126,950 - 114,174,459 (+)NCBI
Rnor_5.014113,792,257 - 113,839,936 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251609   ⟹   XP_006251671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,676,572 - 107,698,610 (+)NCBI
mRatBN7.214103,475,553 - 103,497,687 (+)NCBI
Rnor_6.014114,151,915 - 114,174,459 (+)NCBI
Rnor_5.014113,792,257 - 113,839,936 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599393   ⟹   XP_017454882
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,651,080 - 107,698,610 (+)NCBI
mRatBN7.214103,450,160 - 103,497,687 (+)NCBI
Rnor_6.014114,126,948 - 114,174,459 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_114019   ⟸   NM_031831
- UniProtKB: Q9WUF0 (UniProtKB/Swiss-Prot),   Q9WUE9 (UniProtKB/Swiss-Prot),   Q9R0D9 (UniProtKB/Swiss-Prot),   Q9JK11 (UniProtKB/Swiss-Prot),   Q9JK10 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251670   ⟸   XM_006251608
- Peptide Label: isoform X2
- UniProtKB: Q6IRL3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251671   ⟸   XM_006251609
- Peptide Label: isoform X3
- UniProtKB: A6JQC2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454882   ⟸   XM_017599393
- Peptide Label: isoform X1
- UniProtKB: Q540J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006443   ⟸   ENSRNOT00000006443
RefSeq Acc Id: ENSRNOP00000042870   ⟸   ENSRNOT00000041638
RefSeq Acc Id: ENSRNOP00000006957   ⟸   ENSRNOT00000006957
RefSeq Acc Id: ENSRNOP00000040760   ⟸   ENSRNOT00000042965
RefSeq Acc Id: ENSRNOP00000094900   ⟸   ENSRNOT00000103934
Protein Domains
Reticulon

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JK11-F1-model_v2 AlphaFold Q9JK11 1-1163 view protein structure

Transcriptome

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

Promoters
RGD ID:13699539
Promoter ID:EPDNEW_R10061
Type:initiation region
Name:Rtn4_1
Description:reticulon 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10062  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,126,966 - 114,127,026EPDNEW
RGD ID:13699542
Promoter ID:EPDNEW_R10062
Type:initiation region
Name:Rtn4_2
Description:reticulon 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10061  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,152,392 - 114,152,452EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620989 AgrOrtholog
BioCyc Gene G2FUF-14646 BioCyc
Ensembl Genes ENSRNOG00000004621 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006443 ENTREZGENE
  ENSRNOT00000006443.8 UniProtKB/TrEMBL
  ENSRNOT00000006957.7 UniProtKB/TrEMBL
  ENSRNOT00000041638.7 UniProtKB/TrEMBL
  ENSRNOT00000042965.4 UniProtKB/Swiss-Prot
  ENSRNOT00000103934.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.2480 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7189728 IMAGE-MGC_LOAD
InterPro Reticulon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RTN1-4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83765 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105388 IMAGE-MGC_LOAD
NCBI Gene 83765 ENTREZGENE
PANTHER RETICULON-4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RETICULON-LIKE PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Reticulon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rtn4 PhenoGen
PROSITE RETICULON UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004621 RatGTEx
UniProt A0A8I6GLD1_RAT UniProtKB/TrEMBL
  A0A8L2QL56_RAT UniProtKB/TrEMBL
  A0A8L2UHV9_RAT UniProtKB/TrEMBL
  A6JQC1_RAT UniProtKB/TrEMBL
  A6JQC2 ENTREZGENE, UniProtKB/TrEMBL
  A6JQC3_RAT UniProtKB/TrEMBL
  F1LQN3_RAT UniProtKB/TrEMBL
  Q540J3 ENTREZGENE, UniProtKB/TrEMBL
  Q5U1Z3_RAT UniProtKB/TrEMBL
  Q6IRL3 ENTREZGENE, UniProtKB/TrEMBL
  Q9JK10 ENTREZGENE
  Q9JK11 ENTREZGENE
  Q9R0D9 ENTREZGENE
  Q9WUE9 ENTREZGENE
  Q9WUF0 ENTREZGENE
  RTN4_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q9JK10 UniProtKB/Swiss-Prot
  Q9R0D9 UniProtKB/Swiss-Prot
  Q9WUE9 UniProtKB/Swiss-Prot
  Q9WUF0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Rtn4  reticulon 4    Nogo-A  Name updated 625702 APPROVED
2002-08-07 Rtn4  Nogo-A      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization integral membrane protein 628411
gene_domains contains active NiG and Nogo-66 domains 628411
gene_expression expressed in brain, spinal cord, optic nerve, and not in sciatic nerve 633937
gene_expression predominantly expressed in oligodendrocytes 628411
gene_function glia derived inhibitory factor  
gene_process may have a role in inhibition of CNS myelin mediated neurite growth 628411
gene_process glia derived inhibitory factor 628411
gene_process affects neurite outgrowth and cell spreading 628411
gene_process inhibits neurite outgrowth in CNS myelin 628316
gene_process may be involved in neurite outgrowth inhibitory activity 628417
gene_protein 3 forms of protein exist- Noga A,B and C 628411
gene_regulation inhibition of function with monoclonal Ab against protein induces regeneration of adult lesioned corticospinal tract and optic nerve fibers and also greatly increases compensatory sprouting in the adult and CST sprouts grew from the unlesioned to the cont 628411