Nrtn (neurturin) - Rat Genome Database

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Gene: Nrtn (neurturin) Rattus norvegicus
Analyze
Symbol: Nrtn
Name: neurturin
RGD ID: 621494
Description: Enables growth factor activity. Predicted to act upstream of or within nervous system development; neural crest cell migration; and transmembrane receptor protein tyrosine kinase signaling pathway. Located in axon. Human ortholog(s) of this gene implicated in Hirschsprung's disease. Orthologous to human NRTN (neurturin); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
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
GRCr891,669,099 - 1,674,957 (-)NCBIGRCr8
mRatBN7.291,581,860 - 1,587,835 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,581,975 - 1,583,102 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,016,109 - 2,017,236 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,365,227 - 7,366,354 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,321,307 - 6,322,434 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,299,881 - 10,306,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,305,470 - 10,306,597 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,297,308 - 9,303,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,933,647 - 6,934,774 (+)NCBICelera
Cytogenetic Map9q11NCBI
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  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetaldehyde  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP)
amitrole  (EXP)
arachidonic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
carbamazepine  (ISO)
carmustine  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
coumarin  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
maneb  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenethyl caffeate  (EXP)
phenethyl isothiocyanate  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triacsin C  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
zearalenone  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IDA)
extracellular space  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Patterns of developmental mRNA expression of neurturin and GFRalpha2 in the rat striatum and substantia nigra do not suggest a role in the regulation of natural cell death in dopamine neurons. Cho J, etal., Brain Res Dev Brain Res. 2004 Jan 31;148(1):143-9.
2. Mutation of the RET ligand, neurturin, supports multigenic inheritance in Hirschsprung disease. Doray B, etal., Hum Mol Genet. 1998 Sep;7(9):1449-52.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Developmental expression of glial cell-line derived neurotrophic factor, neurturin, and their receptor mRNA in the rat urinary bladder. Kawakami T, etal., Neurourol Urodyn 2003;22(1):83-8.
6. Immunohistochemical expression of two members of the GDNF family of growth factors and their receptors in the olfactory system. Maroldt H, etal., J Neurocytol. 2005 Sep;34(3-5):241-55. Epub 2006 Jul 13.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. Neurturin-deficient mice develop dry eye and keratoconjunctivitis sicca. Song XJ, etal., Invest Ophthalmol Vis Sci. 2003 Oct;44(10):4223-9.
14. Expression of the GDNF family members and their receptors in the mature rat cochlea. Stover T, etal., Brain Res Mol Brain Res 2000 Mar 10;76(1):25-35.
Additional References at PubMed
PMID:9576965   PMID:10069332   PMID:12176170   PMID:14596863   PMID:15019945   PMID:15242795   PMID:15896320   PMID:16325003   PMID:17336076   PMID:21723942   PMID:29712778   PMID:38219812  


Genomics

Comparative Map Data
Nrtn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,669,099 - 1,674,957 (-)NCBIGRCr8
mRatBN7.291,581,860 - 1,587,835 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,581,975 - 1,583,102 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,016,109 - 2,017,236 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,365,227 - 7,366,354 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,321,307 - 6,322,434 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,299,881 - 10,306,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,305,470 - 10,306,597 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,297,308 - 9,303,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,933,647 - 6,934,774 (+)NCBICelera
Cytogenetic Map9q11NCBI
NRTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38195,805,067 - 5,828,324 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl195,805,067 - 5,828,324 (+)EnsemblGRCh38hg38GRCh38
GRCh37195,805,078 - 5,828,335 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36195,774,818 - 5,779,335 (+)NCBINCBI36Build 36hg18NCBI36
Build 34195,774,817 - 5,779,335NCBI
Celera195,762,840 - 5,767,355 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef195,583,694 - 5,588,209 (+)NCBIHuRef
CHM1_1195,823,836 - 5,828,353 (+)NCBICHM1_1
T2T-CHM13v2.0195,792,545 - 5,815,815 (+)NCBIT2T-CHM13v2.0
Nrtn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,058,323 - 57,064,548 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,058,325 - 57,064,530 (-)EnsemblGRCm39 Ensembl
GRCm381756,751,323 - 56,757,548 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,751,325 - 56,757,530 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,890,748 - 56,896,953 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,436,449 - 56,442,654 (-)NCBIMGSCv36mm8
Celera1761,095,466 - 61,101,671 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.49NCBI
NRTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22010,200,428 - 10,223,717 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1199,426,648 - 9,449,959 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0194,821,307 - 4,844,295 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NRTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,228,431 - 54,242,338 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,211,973 - 54,242,398 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2053,955,933 - 53,970,110 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02054,865,117 - 54,884,199 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2054,864,768 - 54,895,465 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12053,931,479 - 53,950,528 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,380,552 - 54,399,676 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,609,064 - 54,628,256 (-)NCBIUU_Cfam_GSD_1.0
Nrtn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,478,325 - 214,482,413 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365883,352,789 - 3,356,461 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365883,352,440 - 3,356,457 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NRTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,173,926 - 73,188,129 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1273,174,285 - 73,188,382 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,638,786 - 73,639,375 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NRTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,444,514 - 5,458,769 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl65,444,878 - 5,458,617 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660812,577,380 - 2,600,530 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nrtn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,400,392 - 4,412,972 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,400,392 - 4,412,990 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nrtn
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:64
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000072592
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat

Markers in Region
Nrtn  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,582,100 - 1,582,201 (-)MAPPERmRatBN7.2
Rnor_6.0910,306,371 - 10,306,471NCBIRnor6.0
Rnor_5.099,303,451 - 9,303,551UniSTSRnor5.0
Celera96,934,548 - 6,934,648UniSTS
Cytogenetic Map9q11UniSTS


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 13 12 12 12 6
Low 3 30 45 29 19 29 8 11 70 35 35 11 8
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072592   ⟹   ENSRNOP00000066997
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,581,975 - 1,583,102 (-)Ensembl
Rnor_6.0 Ensembl910,305,470 - 10,306,597 (+)Ensembl
RefSeq Acc Id: NM_053399   ⟹   NP_445851
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,669,101 - 1,670,228 (-)NCBI
mRatBN7.291,581,975 - 1,583,102 (-)NCBI
Rnor_6.0910,305,470 - 10,306,597 (+)NCBI
Rnor_5.099,297,308 - 9,303,679 (+)NCBI
Celera96,933,647 - 6,934,774 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244347   ⟹   XP_006244409
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,669,099 - 1,674,957 (-)NCBI
mRatBN7.291,581,860 - 1,587,835 (-)NCBI
Rnor_6.0910,299,881 - 10,306,599 (+)NCBI
Rnor_5.099,297,308 - 9,303,679 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_445851 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244409 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF01244 (Get FASTA)   NCBI Sequence Viewer  
  AAO27768 (Get FASTA)   NCBI Sequence Viewer  
  BAA92851 (Get FASTA)   NCBI Sequence Viewer  
  EDL83608 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000066997
  ENSRNOP00000066997.1
Reference Protein Sequences
RefSeq Acc Id: NP_445851   ⟸   NM_053399
- Peptide Label: precursor
- UniProtKB: Q811Q5 (UniProtKB/TrEMBL),   M0RBQ2 (UniProtKB/TrEMBL),   Q9QZG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244409   ⟸   XM_006244347
- Peptide Label: isoform X1
- UniProtKB: Q811Q5 (UniProtKB/TrEMBL),   M0RBQ2 (UniProtKB/TrEMBL),   Q9QZG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066997   ⟸   ENSRNOT00000072592
Protein Domains
TGF-beta family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q811Q5-F1-model_v2 AlphaFold Q811Q5 1-195 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:621494 AgrOrtholog
BioCyc Gene G2FUF-28514 BioCyc
Ensembl Genes ENSRNOG00000048651 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072592 ENTREZGENE
  ENSRNOT00000072592.2 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/TrEMBL
  GDNF_fam UniProtKB/TrEMBL
  TGFb UniProtKB/TrEMBL
KEGG Report rno:84423 UniProtKB/TrEMBL
NCBI Gene 84423 ENTREZGENE
PANTHER NEURTURIN UniProtKB/TrEMBL
  PTHR12173 UniProtKB/TrEMBL
Pfam TGF_beta UniProtKB/TrEMBL
PhenoGen Nrtn PhenoGen
PROSITE TGF_BETA_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000048651 RatGTEx
Superfamily-SCOP SSF57501 UniProtKB/TrEMBL
UniProt M0RBQ2 ENTREZGENE, UniProtKB/TrEMBL
  Q811Q5 ENTREZGENE, UniProtKB/TrEMBL
  Q9QZG0 ENTREZGENE, UniProtKB/TrEMBL


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

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the cochlea and substantia nigra 631959
gene_product member of the glial cell line-derived neurotrophic factor (GDNF)family which is a a subgroup of the TGF-beta superfamily of growth factors 631959