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 cadherin binding activity; protein homodimerization activity; and ubiquitin protein ligase binding activity. Involved in several processes, including negative regulation of neuron projection regeneration; nervous system development; and positive regulation of dopamine secretion. Located in several cellular components, including endoplasmic reticulum; myelin sheath; and neuronal cell body. Is integral component of endoplasmic reticulum membrane. Part of protein-containing complex. Is active in glutamatergic synapse. Is integral component of postsynaptic density membrane. Biomarker of visual epilepsy. Orthologous to human RTN4 (reticulon 4); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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
mRatBN7.214103,450,074 - 103,497,687 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (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)
carbamazepine  (ISO)
carbon nanotube  (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)
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)
lead(2+)  (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)
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
aging  (IEP)
angiogenesis  (ISO)
axonal fasciculation  (IDA,IEA,ISO)
blastocyst formation  (IEA,ISO)
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)
cellular sphingolipid homeostasis  (IEA,ISO)
central nervous system vasculogenesis  (ISO,ISS)
cerebral cortex radial glia-guided migration  (IEA,ISO,ISS)
endoplasmic reticulum organization  (ISO)
endoplasmic reticulum tubular network formation  (IEA,ISO,ISS)
endoplasmic reticulum tubular network membrane organization  (IEA,ISO,ISS)
endoplasmic reticulum tubular network organization  (ISO,ISS)
leukocyte migration involved in inflammatory response  (ISO,ISS)
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 dendrite extension  (ISO)
negative regulation of formation of growth cone in injured axon  (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)
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 collateral sprouting of injured axon  (ISO)
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 protein kinase B signaling  (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 sensory perception of pain  (IDA)
response to activity  (IEP)

Molecular Function

References

References - curated
1. Bareyre FM, etal., J Neurosci 2002 Aug 15;22(16):7097-110.
2. Chen MS, etal., Nature 2000 Jan 27;403(6768):434-9.
3. Chytrova G, etal., Eur J Neurosci. 2008 Jan;27(1):1-11. Epub 2007 Dec 15.
4. Craveiro LM, etal., Eur J Neurosci. 2008 Nov;28(9):1808-24.
5. Dodd DA, etal., J Biol Chem. 2005 Apr 1;280(13):12494-502. Epub 2005 Jan 7.
6. Gao Y, etal., Neurosci Lett. 2009 Jul 24;458(3):132-5. Epub 2009 Apr 18.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. GrandPre T, etal., Nature. 2000 Jan 27;403(6768):439-44.
10. Hasegawa Y, etal., J Neurosci. 2004 Jul 28;24(30):6826-32.
11. Hu J, etal., Cell. 2009 Aug 7;138(3):549-61. doi: 10.1016/j.cell.2009.05.025.
12. Jiang W, etal., Transl Res. 2009 Jul;154(1):40-8. Epub 2009 May 19.
13. Kempf A, etal., PLoS Biol. 2014 Jan;12(1):e1001763. doi: 10.1371/journal.pbio.1001763. Epub 2014 Jan 14.
14. Kern F, etal., Biochem J. 2013 Oct 15;455(2):217-27. doi: 10.1042/BJ20130579.
15. Li L, etal., Neurosci Lett. 2007 Sep 13;424(3):145-8. Epub 2007 Aug 1.
16. Liu X, etal., Mol Cell Neurosci. 2009 May;41(1):51-61. Epub 2009 Feb 6.
17. Ma Z, etal., Exp Neurol. 2009 May;217(1):184-96. Epub 2009 Feb 21.
18. MGD data from the GO Consortium
19. Morris NJ, etal., Biochim Biophys Acta 1999 May 6;1450(1):68-76.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Niederost B, etal., J Neurosci 2002 Dec 1;22(23):10368-76.
22. Oertle T, etal., FASEB J 2003 Jul;17(10):1238-47.
23. Oertle T, etal., J Neurosci 2003 Jul 2;23(13):5393-406.
24. Petrinovic MM, etal., Development. 2010 Aug 1;137(15):2539-50. doi: 10.1242/dev.048371. Epub 2010 Jun 23.
25. Pot C, etal., J Cell Biol 2002 Oct 14;159(1):29-35.
26. Reindl M, etal., J Neuroimmunol. 2003 Dec;145(1-2):139-47.
27. RGD automated import pipeline for gene-chemical interactions
28. Richard M, etal., Eur J Neurosci. 2005 Nov;22(9):2145-58.
29. Schweigreiter R, etal., Proteomics. 2007 Dec;7(24):4457-67.
30. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
31. Tagami S, etal., Oncogene. 2000 Nov 23;19(50):5736-46.
32. Takeda Y, etal., Neurol Res. 2007 Mar;29(2):199-203.
33. Taketomi M, etal., Neurosci Lett 2002 Oct 25;332(1):37-40.
34. Trifunovski A, etal., Neuroreport. 2006 Jun 26;17(9):913-6.
35. Venkatesh K, etal., J Neurosci. 2005 Jan 26;25(4):808-22.
36. Voeltz GK, etal., Cell. 2006 Feb 10;124(3):573-86.
37. Xiong NX, etal., Neuro Endocrinol Lett. 2008 Dec;29(6):884-8.
38. Ye J, etal., Zhonghua Yi Xue Za Zhi 2002 Apr 10;82(7):498-500.
39. 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:33495810  


Genomics

Comparative Map Data
Rtn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214103,450,074 - 103,497,687 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl14103,449,930 - 103,497,686 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl254,972,187 - 55,112,621 (-)EnsemblGRCh38hg38GRCh38
GRCh38254,972,189 - 55,137,831 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37255,199,325 - 55,364,967 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,052,829 - 55,131,238 (-)NCBINCBI36hg18NCBI36
Build 34255,110,979 - 55,187,977NCBI
Celera255,039,812 - 55,118,248 (-)NCBI
Cytogenetic Map2p16.1NCBI
HuRef254,934,258 - 55,012,692 (-)NCBIHuRef
CHM1_1255,129,380 - 55,207,793 (-)NCBICHM1_1
Rtn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391129,642,898 - 29,694,414 (+)NCBIGRCm39mm39
GRCm39 Ensembl1129,642,947 - 29,694,331 (+)Ensembl
GRCm381129,692,898 - 29,744,414 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1129,692,947 - 29,744,331 (+)EnsemblGRCm38mm10GRCm38
MGSCv371129,592,898 - 29,644,414 (+)NCBIGRCm37mm9NCBIm37
MGSCv361129,592,947 - 29,642,916 (+)NCBImm8
Celera1132,055,366 - 32,110,540 (+)NCBICelera
Cytogenetic Map11A3.3NCBI
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
PanPan1.12A56,271,214 - 56,348,117 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02A55,129,272 - 55,207,031 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.01056,886,721 - 56,957,194 (-)NCBI
UMICH_Zoey_3.11056,588,329 - 56,658,758 (-)NCBI
UNSW_CanFamBas_1.01056,866,767 - 56,937,240 (-)NCBI
UU_Cfam_GSD_1.01057,157,709 - 57,228,145 (-)NCBI
Rtn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629227,097,303 - 27,163,878 (+)NCBI
SpeTri2.0NW_0049364911,407,414 - 1,474,031 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl386,180,047 - 86,252,122 (+)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 (+)NCBI
Vero_WHO_p1.0NW_02366604559,766,791 - 59,846,774 (-)NCBI
Rtn4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248336,514,409 - 6,584,061 (+)NCBI

Position Markers
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


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


Genetic Models
This gene Rtn4 is modified in the following models/strains
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.


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
  XM_039092504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092505 (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
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006443   ⟹   ENSRNOP00000006443
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,450,160 - 103,497,687 (+)NCBI
Rnor_6.014114,126,948 - 114,174,459 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092504   ⟹   XP_038948432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,450,144 - 103,495,728 (+)NCBI
RefSeq Acc Id: XM_039092505   ⟹   XP_038948433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,450,160 - 103,497,687 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_114019   ⟸   NM_031831
- Sequence:
RefSeq Acc Id: XP_006251670   ⟸   XM_006251608
- Peptide Label: isoform X4
- UniProtKB: Q9JK11 (UniProtKB/Swiss-Prot),   Q6IRL3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251671   ⟸   XM_006251609
- Peptide Label: isoform X5
- UniProtKB: Q9JK11 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017454882   ⟸   XM_017599393
- Peptide Label: isoform X3
- UniProtKB: Q9JK11 (UniProtKB/Swiss-Prot),   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: XP_038948432   ⟸   XM_039092504
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948433   ⟸   XM_039092505
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000094900   ⟸   ENSRNOT00000103934
Protein Domains
Reticulon

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

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620989 AgrOrtholog
Ensembl Genes ENSRNOG00000004621 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006443 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000006957 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000040760 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000042870 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006443 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000006957 UniProtKB/Swiss-Prot
  ENSRNOT00000041638 UniProtKB/Swiss-Prot
  ENSRNOT00000042965 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7189728 IMAGE-MGC_LOAD
InterPro Reticulon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83765 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105388 IMAGE-MGC_LOAD
NCBI Gene 83765 ENTREZGENE
Pfam Reticulon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rtn4 PhenoGen
PROSITE RETICULON UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Transposagen Rtn4 Transposagen
UniProt F1LQN3_RAT UniProtKB/TrEMBL
  Q540J3 ENTREZGENE, UniProtKB/TrEMBL
  Q5U1Z3_RAT UniProtKB/TrEMBL
  Q6IRL3 ENTREZGENE, UniProtKB/TrEMBL
  Q9JK11 ENTREZGENE, 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