Rtn4r (reticulon 4 receptor) - Rat Genome Database

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Gene: Rtn4r (reticulon 4 receptor) Rattus norvegicus
Analyze
Symbol: Rtn4r
Name: reticulon 4 receptor
RGD ID: 620810
Description: Enables signaling receptor activity. Involved in cell surface receptor signaling pathway and negative regulation of neuron projection development. Located in cell surface and membrane raft. Is active in glutamatergic synapse and presynapse. Human ortholog(s) of this gene implicated in schizophrenia. Orthologous to human RTN4R (reticulon 4 receptor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: NgR; NgR1; nogo receptor; nogo-66 receptor; Nogo66 receptor; Nogor; reticulon-4 receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21182,844,585 - 82,869,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,844,309 - 82,869,466 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,572,958 - 91,597,436 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01184,234,074 - 84,258,552 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,287,699 - 83,312,175 (-)NCBIRnor_WKY
Rnor_6.01186,992,665 - 87,017,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1186,992,399 - 87,017,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,085,449 - 90,109,875 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,839,082 - 84,863,508 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,879,678 - 84,904,105 (-)NCBI
Celera1181,620,565 - 81,644,966 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. AMIGO3 is an NgR1/p75 co-receptor signalling axon growth inhibition in the acute phase of adult central nervous system injury. Ahmed Z, etal., PLoS One. 2013 Apr 16;8(4):e61878. doi: 10.1371/journal.pone.0061878. Print 2013.
2. 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.
3. Nogo-66 receptor antagonist peptide promotes axonal regeneration. GrandPre T, etal., Nature 2002 May 30;417(6888):547-51.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. LINGO-1 is a component of the Nogo-66 receptor/p75 signaling complex. Mi S, etal., Nat Neurosci. 2004 Mar;7(3):221-8. doi: 10.1038/nn1188. Epub 2004 Feb 15.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. Nogo-A inhibits neurite outgrowth and cell spreading with three discrete regions. Oertle T, etal., J Neurosci 2003 Jul 2;23(13):5393-406.
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Molecular basis of the interactions of the Nogo-66 receptor and its homolog NgR2 with myelin-associated glycoprotein: development of NgROMNI-Fc, a novel antagonist of CNS myelin inhibition. Robak LA, etal., J Neurosci. 2009 May 6;29(18):5768-83. doi: 10.1523/JNEUROSCI.4935-08.2009.
12. 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.
13. The nogo receptor family restricts synapse number in the developing hippocampus. Wills ZP, etal., Neuron. 2012 Feb 9;73(3):466-81. doi: 10.1016/j.neuron.2011.11.029.
14. 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:11201742   PMID:11891768   PMID:15297463   PMID:15504325   PMID:15548200   PMID:15548666   PMID:15694322   PMID:15737741   PMID:16088223   PMID:16321384   PMID:16603920   PMID:16712417  
PMID:17294731   PMID:17329206   PMID:17428512   PMID:17640868   PMID:18182498   PMID:18337405   PMID:18365011   PMID:18411262   PMID:18625710   PMID:19063867   PMID:19524873   PMID:19575706  
PMID:19901030   PMID:20075346   PMID:20337950   PMID:20463223   PMID:20473744   PMID:20828545   PMID:20844138   PMID:21418929   PMID:21817055   PMID:22139298   PMID:22406547   PMID:22923615  
PMID:23158614   PMID:23533145   PMID:23829864   PMID:24244357   PMID:26472924   PMID:26945033   PMID:26987715   PMID:27033267   PMID:27288754   PMID:27339102   PMID:28489665   PMID:31948754  
PMID:32598099   PMID:33495810   PMID:35263202  


Genomics

Comparative Map Data
Rtn4r
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21182,844,585 - 82,869,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,844,309 - 82,869,466 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,572,958 - 91,597,436 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01184,234,074 - 84,258,552 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,287,699 - 83,312,175 (-)NCBIRnor_WKY
Rnor_6.01186,992,665 - 87,017,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1186,992,399 - 87,017,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,085,449 - 90,109,875 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,839,082 - 84,863,508 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,879,678 - 84,904,105 (-)NCBI
Celera1181,620,565 - 81,644,966 (-)NCBICelera
Cytogenetic Map11q23NCBI
RTN4R
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382220,241,415 - 20,268,318 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2220,241,415 - 20,283,246 (-)EnsemblGRCh38hg38GRCh38
GRCh372220,228,938 - 20,255,841 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362218,608,938 - 18,635,816 (-)NCBINCBI36Build 36hg18NCBI36
Celera224,079,624 - 4,107,575 (-)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef223,848,286 - 3,849,983 (-)NCBIHuRef
CHM1_12220,228,468 - 20,255,665 (-)NCBICHM1_1
T2T-CHM13v2.02220,621,207 - 20,649,434 (-)NCBIT2T-CHM13v2.0
Rtn4r
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,945,506 - 17,970,272 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,945,506 - 17,970,272 (+)EnsemblGRCm39 Ensembl
GRCm381618,127,642 - 18,152,408 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1618,127,642 - 18,152,408 (+)EnsemblGRCm38mm10GRCm38
MGSCv371618,127,799 - 18,152,501 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361618,041,269 - 18,065,971 (+)NCBIMGSCv36mm8
Celera1618,700,292 - 18,725,154 (+)NCBICelera
Cytogenetic Map16A3NCBI
Rtn4r
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544217,866,398 - 17,891,820 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544217,866,508 - 17,891,803 (+)NCBIChiLan1.0ChiLan1.0
RTN4R
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12218,673,548 - 18,675,537 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2218,673,548 - 18,680,017 (-)Ensemblpanpan1.1panPan2
RTN4R
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12629,109,991 - 29,117,319 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2629,113,428 - 29,115,918 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2629,049,600 - 29,074,655 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02630,493,710 - 30,518,771 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2630,493,543 - 30,518,786 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12628,542,789 - 28,567,865 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02628,168,179 - 28,193,248 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02629,252,843 - 29,277,947 (+)NCBIUU_Cfam_GSD_1.0
Rtn4r
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118138,598,174 - 138,623,308 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366194,130,748 - 4,155,894 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366194,130,757 - 4,155,885 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTN4R
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1451,579,046 - 51,602,968 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11451,579,043 - 51,603,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21455,216,090 - 55,240,021 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTN4R
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1195,469,854 - 5,497,858 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660851,437,876 - 1,466,276 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtn4r
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624747829,850 - 855,991 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624747829,947 - 855,942 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtn4r
70 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:86
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000051037
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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)117695713183051965Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat

Markers in Region
D11Rat50  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21182,846,466 - 82,846,715 (+)MAPPERmRatBN7.2
Rnor_6.01186,994,547 - 86,994,795NCBIRnor6.0
Rnor_5.01190,087,331 - 90,087,579UniSTSRnor5.0
RGSC_v3.41184,840,963 - 84,841,212RGDRGSC3.4
RGSC_v3.41184,840,964 - 84,841,212UniSTSRGSC3.4
RGSC_v3.11184,881,561 - 84,881,809RGD
Celera1181,622,447 - 81,622,695UniSTS
RH 3.4 Map11699.5UniSTS
RH 3.4 Map11699.5RGD
SHRSP x BN Map1139.3498UniSTS
SHRSP x BN Map1139.3498RGD
Cytogenetic Map11q23UniSTS


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 64 17
Low 3 36 23 10 13 10 1 10 35 22 10
Below cutoff 7 29 26 6 26 7 9 2 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051037   ⟹   ENSRNOP00000041517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,844,309 - 82,869,466 (-)Ensembl
Rnor_6.0 Ensembl1186,992,399 - 87,017,115 (-)Ensembl
RefSeq Acc Id: NM_053613   ⟹   NP_446065
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21182,844,585 - 82,869,012 (-)NCBI
Rnor_6.01186,992,665 - 87,017,091 (-)NCBI
Rnor_5.01190,085,449 - 90,109,875 (-)NCBI
RGSC_v3.41184,839,082 - 84,863,508 (-)RGD
Celera1181,620,565 - 81,644,966 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446065 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK20166 (Get FASTA)   NCBI Sequence Viewer  
  AAM46772 (Get FASTA)   NCBI Sequence Viewer  
  EDL77921 (Get FASTA)   NCBI Sequence Viewer  
  Q99M75 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446065   ⟸   NM_053613
- Peptide Label: precursor
- UniProtKB: Q99M75 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000041517   ⟸   ENSRNOT00000051037
Protein Domains
LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99M75-F1-model_v2 AlphaFold Q99M75 1-473 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620810 AgrOrtholog
BioCyc Gene G2FUF-20635 BioCyc
Ensembl Genes ENSRNOG00000030920 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000041517 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000051037 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot
  LRR_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:113912 UniProtKB/Swiss-Prot
NCBI Gene 113912 ENTREZGENE
Pfam LRR_8 UniProtKB/Swiss-Prot
PhenoGen Rtn4r PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot
SMART LRR_TYP UniProtKB/Swiss-Prot
  LRRCT UniProtKB/Swiss-Prot
UniProt Q99M75 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Rtn4r  reticulon 4 receptor      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Rtn4r        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease inhibition of receptor activity by antagonist NEP1-40 may improve axonal regeneration after CNS injury 727379